post future everything commit

1) Live/interactive version of one or two of the algorithms. I'd vote
for IResponse, RelaxRate and ColorMulti as the ones to do live on the
laptop.  David is looking at this...

2) The frame skipping issue remains.  I looked at this while travelling
today, but couldn't figure it out.  We're still saving out meshes at
about half the rate of them being created.

3) The following three analyses do exactly the same thing currently,
and it would be good if they had something approaching a real analysis
happening.  Right now it's just a simple z-map in black and white with
some noise on top and lighting... kind of pretty but bit boring
currently:
	ShapeFromShadingAnalysis
	CamNoiseAnalysis
	ShadowScapesAnalysis

.gitignore

@@ -1,2 +1,8 @@
 
 src/.DS_Store
+.DS_Store
+Project.xcconfig
+bin/
+openFrameworks-Info.plist
+opencvExample.xcodeproj/
+config.refindx

config.refindx

@@ -1,115 +0,0 @@
-<!-- THIS FILE NEEDS TO GO IN THE APPLICATION /data/ folder -->
-
-<config>
-    <mode>analysing</mode>
-	<camera>
-		<id>1</id>
-		<width>640</width>
-		<height>480</height>
-	</camera>
-	<display>
-		<fps>30</fps>
-    </display>
-	<locale>
-		<name>FUTURE</name>
-	</locale>
-
-    <analysis_NUM_RUN>
-        <NUM_RUN_shadowscapes>          1      </NUM_RUN_shadowscapes>
-        <NUM_RUN_relaxrate>             1      </NUM_RUN_relaxrate>
-        <NUM_RUN_iresponse>             1      </NUM_RUN_iresponse>
-        <NUM_RUN_shapefromshading>      1      </NUM_RUN_shapefromshading>
-        <NUM_RUN_strobe>                1      </NUM_RUN_strobe>
-        <NUM_RUN_camnoise>              1      </NUM_RUN_camnoise>
-        <NUM_RUN_colorsingle>           1      </NUM_RUN_colorsingle>
-        <NUM_RUN_colormulti>            1      </NUM_RUN_colormulti>
-        <NUM_RUN_diffnoise>             1      </NUM_RUN_diffnoise>
-    </analysis_NUM_RUN>
-
-    <analysis_time>
-        <acquiretime_shadowscapes>      5      </acquiretime_shadowscapes>
-        <acquiretime_relaxrate>         5      </acquiretime_relaxrate>
-        <acquiretime_iresponse>         5      </acquiretime_iresponse>
-        <acquiretime_shapefromshading>  5      </acquiretime_shapefromshading>
-        <acquiretime_strobe>            5      </acquiretime_strobe>
-        <acquiretime_camnoise>          5      </acquiretime_camnoise>
-        <acquiretime_colorsingle>       5      </acquiretime_colorsingle>
-        <acquiretime_colormulti>        5      </acquiretime_colormulti>
-        <acquiretime_diffnoise>         5      </acquiretime_diffnoise>
-    </analysis_time>
-    
-    <viewport>
-        <tx>0</tx>
-        <ty>-20</ty>
-        <tz>-400</tz>
-        <rx>-10</rx>
-        <ry>0</ry>
-        <rz>0</rz>        
-    </viewport>
-    
-    <algorithms>
-        <vertices_per_frame>1000</vertices_per_frame>
-        <pixel_per_vertex>4</pixel_per_vertex>
-        <colormulti>
-            <algo>2</algo>
-            <scale>1</scale>
-            <draw_style>2</draw_style>
-            <line_width>0.5</line_width>
-        </colormulti>
-        <colorsingle>
-            <algo>2</algo>
-            <scale>1</scale>
-            <draw_style>2</draw_style>
-            <line_width>0.5</line_width>
-        </colorsingle>        
-        <relaxrate>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </relaxrate>
-        <diffnoise>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </diffnoise>        
-        <shapeshade>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </shapeshade>        
-        <strobe>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </strobe>                
-        <camnoise>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </camnoise>                        
-        <shadowscapes>
-            <algo>4</algo>
-            <scale>500</scale>        
-            <draw_style>2</draw_style>
-            <line_width>2</line_width>
-        </shadowscapes>   
-        <iresponse>
-            <algo>1</algo>
-            <scale>500</scale>
-            <draw_style>1</draw_style>
-            <line_width>2</line_width>
-            <point_size>2</point_size>            
-        </iresponse>             
-    </algorithms>
-    
-</config>

dviid/hessian.cl

@@ -1,372 +0,0 @@
-/*
- ~ copyright (c) 2011 dviid
- ~ contact: dviid@labs.ciid.dk 
- 
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
- 
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- */
-
-const sampler_t smp = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;
-
-const sampler_t smp_adrs = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP | CLK_FILTER_NEAREST;
-
-
-float box_integral(read_only image2d_t src, int width, int height, int row, int col, int nbrrows, int nbrcols)
-{
-    float A = 0.0f;
-    float B = 0.0f;
-    float C = 0.0f;
-    float D = 0.0f;
-    
-    int r0 = min(row, height) - 1;
-    int c0 = min(col, width) - 1;
-    int r1 = min(row + nbrrows, height) - 1;
-    int c1 = min(col + nbrcols, width) - 1;
-    
-    A = read_imagef(src, smp, (int2)(c0, r0)).x;
-    B = read_imagef(src, smp, (int2)(c1, r0)).x;
-    C = read_imagef(src, smp, (int2)(c0, r1)).x;
-    D = read_imagef(src, smp, (int2)(c1, r1)).x;
-    
-    return max(0.0f, A - B - C + D);
-    
-}
-
-
-__kernel void hessian_det(
-                          read_only image2d_t src,
-                          int width,
-                          int height,
-                          write_only image2d_t determinant,
-                          write_only image2d_t laplacians,
-                          int layer_width,
-                          int layer_height,
-                          int step,
-                          int filter)
-{
-    int l, w, b;
-    float Dxx, Dxy, Dyy, inverse;
-    
-    int idx = get_global_id(0);
-    int idy = get_global_id(1);
-    
-    w = filter;
-    l = w / 3;
-    b = (w - 1) / 2 + 1
-    inverse = 1.0f / (w * w);
-    
-    int c = idx * step;
-    int r = idy * step;
-    
-    if(r >= height || c >= width) return;
-    
-    Dxx = box_integral(src, width, height, r - l + 1, c - b, 2 * l - 1, w) -
-          box_integral(src, width, height, r - l + 1, c - l / 2, 2 * l - 1, l) * 3;
-    
-    Dxy = box_integral(src, width, height, r - l, c + 1, l, l) +
-          box_integral(src, width, height, r + 1, c - l, l, l) -
-          box_integral(src, width, height, r - 1, c - l, l, l) -
-          box_integral(src, widht, height, r + 1, c + 1, l, l);
-    
-    DYY = box_integral(src, width, height, r - b, c - l + 1, w, 2 * l - 1) -
-          box_integral(src, width, height, r - l / 2, c - l + 1, l, 2 * l -1) * 3;
-    
-    Dxx += inverse; 
-    Dxy += inverse; 
-    Dyy += inverse; 
-    
-    float4 det = {0.0f, 0.0f, 0.0f, 0.0f};
-    det.x = (Dxx * Dyy - 0.81f * Dxy * Dxy);
-    
-    int4 lap = {0, 0, 0, 0};
-    lap.x = (Dxx + Dyy >= 0 ? 1 : 0);
-    
-    write_imagef(determinant, (int2)(idx, idy), det);
-    write_imagef(laplacians, (int2)(idx, idy), lap);
-    
-}
-
-int pop_laplacian(read_only image2d_t layer, int c, int r, int width)
-{
-    int lap;
-    lap = read_imagei(layer, smp_adrs, (int2)(c,r)).x;
-    return lap;
-}
-
-float pop_response(read_only image2d_t layer, int c, int r, int width, int scale)
-{
-    float resp;
-    resp = read_imagef(layer, smp_adrs, (int2)(c*scale, r*scale)).x;
-    return resp;
-}
-
-bool interpolate_extremum(
-                          int r,
-                          int c,
-                __global int* pts_cnt;
-                      float2* pos,
-                       float* det_scale
-                         int* laplacian,
-          read_only image2d_t t,
-                          int t_width,
-                          int t_height,
-                          int t_step,
-          read_only image2d_t m,
-          read_only image2d_t mlaplacian,
-                          int m_width,
-                          int m_height,
-                          int m_filter,
-          read_only image2d_t b,
-                          int b_width,
-                          int b_height,
-                          int b_filter
-                          )
-{
-    
-    // 3D derivatives
-    
-    int mscale = (m_width / m_height);
-    int bscale = (b_width / b_height);
-    
-    float Dx, Dy, Dz;
-    
-    Dx = (pop_response(m, c+1, r,   m_width, mscale) -
-          pop_response(m, c-1, r,   m_width, mscale)) / 2.0f;
-    Dy = (pop_response(m, c,   r+1, m_width, mscale) -
-          pop_response(m, c,   r-1, m_width, mscale)) / 2.0f;
-    
-    Dz = (pop_response(t, c, r, t_width, 1) - 
-          pop_response(b, c, r, b_width, bscale)) / 2.0f;
-          
-    // inverse hessian
-    
-    float v, Dxx, Dyy, Dzz, Dxy, Dxz, Dyz;
-    
-    v = pop_response(m, r, c, m_width, mscale);
-    
-    Dxx = pop_response(m, c+1, r,   m_width, mscale) + 
-          pop_response(m, c-1, r,   m_width, mscale) - 2.0f * v;
-    
-    Dyy = pop_response(m, c,   r+1, m_width, mscale) +
-          pop_response(m, c,   r-1, m_width, mscale) - 2.0f * v;
-        
-    Dxy = (pop_response(m, c+1, r+1, m_width, mscale) -
-           pop_response(m, c-1, r+1, m_width, mscale) -
-           pop_response(m, c+1, r-1, m_width, mscale) +
-           pop_response(m, c-1, r-1, m_width, mscale)) / 4.0f;
-    
-    Dzz = pop_response(t, c, r, t_width, 1) - 
-          pop_response(b, c, r, b_width, bscale) - 2.0f * v;
-    
-    Dxz = (pop_response(t, c+1, r, t_width, 1) -
-           pop_response(t, c-1, r, t_width, 1) -
-           pop_response(b, c+1, r, b_width, bscale) +
-           pop_response(b, c-1, r, b_width, bscale)) / 4.0f;
-    
-    Dyz = (pop_response(t, c, r+1, t_width, 1) -
-           pop_response(t, c, r-1, t_width, 1) -
-           pop_response(b, c, r+1, b_width, bscale) +
-           pop_response(b, c, r-1, b_width, bscale)) / 4.0f;
-    
-    float det = Dxx * (Dyy*Dzz - Dyz*Dyz) -
-                Dxy * (Dxy*Dzz - Dyz*Dxz) +
-                Dxz * (Dxy*Dyz - Dyy*Dxz);
-
-    float invdet = 1.0f / det;
-    
-    float invDxx =  (Dyy*Dzz-Dyz*Dyz) * invdet;
-    float invDxy = -(Dxy*Dzz-Dyz*Dxz) * invdet;
-    float invDxz =  (Dxy*Dyz-Dyy*Dxz) * invdet;
-    float invDyx = -(Dxy*Dzz-Dxz*Dyz) * invdet;
-    float invDyy =  (Dxx*Dzz-Dxz*Dxz) * invdet;
-    float invDyz = -(Dxx*Dyz-Dxy*Dxz) * invdet;
-    float invDzx =  (Dxy*Dyz-Dxz*Dyy) * invdet;
-    float invDzy = -(Dxx*Dyz-Dxz*Dxy) * invdet;
-    float invDzz =  (Dxx*Dyy-Dxy*Dxy) * invdet;
-    
-    // derivative * hessian
-    
-    float xi = 0.0f, xr = 0.0f, xc = 0.0f;
-    
-    xc -= invDxx * Dx;
-    xc -= invDxy * Dy;
-    xc -= invDxz * Dz;
-    
-    xr -= invDyx * Dx;
-    xr -= invDyy * Dy;
-    xr -= invDyz * Dz;
-    
-    xc -= invDzx * Dx;
-    xc -= invDzy * Dy;
-    xc -= invDzz * Dz;
-    
-    // extremum??
-    if(fabs(xi) < 0.5f && fabs(xr) < 0.5f && fabs(xc) < 0.5f) {
-        
-        int fstep = m_filter - b_filter;
-        
-        (*pos).x = (float)((c + xc) * fstep);
-        (*pos).y = (float)((c + xr) * fstep);
-        *det_scale = (float)(0.1333f) * (m_filter + (xi * fstep));
-        
-        int s = m_width / t_width;
-        *laplacian = pop_laplacian(mlaplacian, c * s, r * s, m_width);
-        
-        return true;
-    }
-    
-    return false;
-        
-}
-
-bool is_extremum(
-                 int r,
-                 int c,
-                 read_only image2d_t t,
-                 int t_width,
-                 int t_height,
-                 int t_step,
-                 int t_filter,
-                 read_only image2d_t m,
-                 int m_width,
-                 int m_height,
-                 read_only image2d_t b,
-                 int b_width,
-                 int b_height,
-                 float tresh
-                 )
-{
-    int border = (t_filter + 1) / (2 * t_step);
-    
-    if(r <= border || r >= t_height - border || c <= border || c >= t_width - border) {
-        return false;
-    }
- 
-    int mscale = m_width / t_width;
-    
-    float candidate = pop_response(m, c, r, m_width, mscale);
-    if(candidate < tresh) {
-        return false;
-    }
-    
-    // If any response in 3x3x3 is greater candidate not maximum
-    float localMax =          getResponse(t, c-1, r-1, t_width, 1);
-    localMax = fmax(localMax, getResponse(t, c,   r-1, t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c+1, r-1, t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c-1, r,   t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c,   r,   t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c+1, r,   t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c-1, r+1, t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c,   r+1, t_width, 1));
-    localMax = fmax(localMax, getResponse(t, c+1, r+1, t_width, 1));
-    
-    int bScale = b_width/t_width;
-    
-    localMax = fmax(localMax, getResponse(b, c-1, r-1, b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c,   r-1, b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c+1, r-1, b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c-1, r,   b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c,   r,   b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c+1, r,   b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c-1, r+1, b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c,   r+1, b_width, bScale));
-    localMax = fmax(localMax, getResponse(b, c+1, r+1, b_width, bScale));
-    
-    //int mScale = m_width/t_width;
-    
-    localMax = fmax(localMax, getResponse(m, c-1, r-1, m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c,   r-1, m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c+1, r-1, m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c-1, r,   m_width, mScale));
-    // This is the candidate pixel
-    localMax = fmax(localMax, getResponse(m, c+1, r,   m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c-1, r+1, m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c,   r+1, m_width, mScale));
-    localMax = fmax(localMax, getResponse(m, c+1, r+1, m_width, mScale));
-    
-    // If localMax > candidate, candidate is not the local maxima
-    if(localMax > candidate) {
-        return false;
-    }
-    
-    return true;   
-    
-}
-
-__kernel void suppress_non_max(                               
-               read_only image2d_t tResponse,
-                               int t_width,
-                               int t_height,
-                               int t_filter,
-                               int t_step,
-               read_only image2d_t mResponse,                
-               read_only image2d_t mLaplacian,
-                               int m_width,
-                               int m_height,
-                               int m_filter,
-               read_only image2d_t bResponse,           
-                               int b_width;
-                               int b_height,
-                               int b_filter,
-                      __global int* pts_cnt,
-                   __global float2* pix_pos,
-                    __global float* scale,
-                      __global int* laplacian,
-                               int max_pts,
-                             float tresh                               
-                               )
-{
-    int r = get_global_id(0);
-    int c = get_global_id(1);
-    
-    float2 pixpos;
-    float s;
-    int lap;
-    
-    
-    if(is_extremum(r, c, tResponse, t_width, t_height, t_step, t_filter, mResponse, m_width, m_height, bResponse, b_width, b_height, tresh)) {
-        
-        if(interpolate_extremum(r, c, pts_cnt, &pixpos, &s, &lap, tResponse, t_width, t_height, t_step, mResponse, mLaplacian, m_width, m_height, m_filter, bResponse, b_width, b_height, b_filter)) {
-            
-            int indx = atom_add(&pts_cnt[0],1);
-            if(indx < max_pts) {
-                pix_pos[indx] = pix_pos;
-                scale[indx] = s;
-                laplacian[indx] = lap;
-            }
-            
-        }
-        
-    }
-}
-                               
-                               
-                          
-                          
-                          
-
-
-
-

dviid/imgproc.cl

@@ -1,148 +0,0 @@
-/*
- ~ copyright (c) 2011 dviid
- ~ contact: dviid@labs.ciid.dk 
- 
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
- 
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- */
-
-const sampler_t smp = CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;
-
-__kernel void sobel(read_only image2d_t src, write_only image2d_t dst)
-{
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    int2 dx = (int2)(1,0);
-    int2 dy = (int2)(0,1);
-    float Gx, Gy, G, theta, p;
-    
-    if(coords.x > get_image_width(dst) || coords.y > get_image_height(dst))
-        return;
-    
-    p = read_imagef(src, smp, coords - dx + dy).s0;
-    Gx = p;
-    Gy = p;
-    
-    p = read_imagef(src, smp, coords + dy).s0;
-    Gy += 2 * p;
-
-    p = read_imagef(src, smp, coords + dx + dy).s0;
-    Gx -= p;
-    Gy += p;
-    
-    p = read_imagef(src, smp, coords - dx).s0;
-    Gx += 2 * p;
-    
-    p = read_imagef(src, smp, coords + dx).s0;
-    Gx -= 2 * p;
-
-    p = read_imagef(src, smp, coords - dx - dy).s0;
-    Gx += p;
-    Gy -= p;
-    
-    p = read_imagef(src, smp, coords - dy).s0;
-    Gy -= 2 * p;
-    
-    p = read_imagef(src, smp, coords + dx - dy).s0;
-    Gx -= p;
-    Gy -= p;
-    
-    G = sqrt(Gx * Gx + Gy * Gy);
-    theta = atan(Gx / Gy);
-    
-    write_imagef(dst, coords, G);                
-    
-}
-
-__kernel void hgauss(read_only image2d_t src, write_only image2d_t dst, 
-                     global read_only float* weights, global float* offsets, const int nbr_weights)
-{
-    int2    coords = (int2) (get_global_id(0), get_global_id(1));
-    float2  src_coords = (float2) (get_global_id(0), get_global_id(1));
-    float4  pix = (float4)(0,0,0,0);
-
-    int i;
-    for(i = 0; i < nbr_weights; i++) {
-        pix += read_imagef(src, smp, src_coords + (float2) (offsets[i], 0.0f)) * weights[i];
-    }
-    
-    write_imagef(dst, coords, clamp(pix, 0.0f, 1.0f));
-}
-
-__kernel void vgauss(read_only image2d_t src, write_only image2d_t dst, 
-                     global read_only float* weights, global float* offsets, const int nbr_weights)
-{
-    int2    coords = (int2) (get_global_id(0), get_global_id(1));
-    float2  src_coords = (float2) (get_global_id(0), get_global_id(1));
-    float4  pix = (float4)(0,0,0,0);
-    
-    int i;
-    for(i = 0; i < nbr_weights; i++) {
-        pix += read_imagef(src, smp, src_coords + (float2) (0.0f, offsets[i])) * weights[i];
-    }
-    
-    write_imagef(dst, coords, clamp(pix, 0.0f, 1.0f));
-}
-
-
-
-__kernel void grey(read_only image2d_t src, write_only image2d_t dst)
-{
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    float4 color = read_imagef(src, smp, coords);
-	float luminance = 0.3f * color.x + 0.59 * color.y + 0.11 * color.z;
-	color = (float4)(luminance, luminance, luminance, 1.0f);
-	write_imagef(dst, coords, color);
-}
-
-__kernel void brightness(read_only image2d_t src, write_only image2d_t dst)
-{
-    float max = 0;
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    float4 color = read_imagef(src, smp, coords);
-
-    max = color.x;
-    if(color.y > max) { max = color.y; }
-    if(color.z > max) { max = color.z; }    
-    
-	write_imagef(dst, coords, max);
-}
-
-__kernel void lightness(read_only image2d_t src, write_only image2d_t dst)
-{
-    float l = 0;
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    float4 color = read_imagef(src, smp, coords);
-    
-    l = (color.x + color.y + color.z) / 3.0f;
-    
-	write_imagef(dst, coords, l);
-}
-
-
-
-__kernel void hist()
-{
-    
-}

dviid/intimg.cl

@@ -1,130 +0,0 @@
-/*
- ~ copyright (c) 2011 dviid
- ~ contact: dviid@labs.ciid.dk 
- 
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
- 
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- */
-
-#define WORK_G_SIZE         64
-#define HALF_WORK_G_SIZE    (WORK_G_SIZE / 2)
-
-const sampler_t smp = CLK_NORMALIZED_COORDS_FALSE | CLK_ADDRESS_CLAMP_TO_EDGE | CLK_FILTER_NEAREST;
-
-__kernel void scan(read_only image2d_t src, write_only image2d_t dst, int rows, int cols)
-{
-    __local float data0[WORK_G_SIZE + HALF_WORK_G_SIZE];
-    __local float data1[WORK_G_SIZE + HALF_WORK_G_SIZE];
-    
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    int X = coords.x;
-    int Y = coords.x;
-    
-    if(coords.x < HALF_WORK_G_SIZE) {
-        data0[coords.x] = 0.0f;
-        data1[coords.x] = 0.0f;
-    }
-    
-    X += HALF_WORK_G_SIZE;    
-    float max_val = 0.0f;    
-    
-    int it = cols / WORK_G_SIZE;    
-    if(cols % WORK_G_SIZE != 0) {
-        it++;
-    }
-    
-    for(int i = 0; i < it; i++) {
-        
-        int col_offset = i * WORK_G_SIZE + coords.x;
-        
-        data0[X] = read_imagef(src, smp, (int2)(col_offset, Y)).x;        
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 1
-        data1[X] = data0[X] + data0[X-1];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 2
-        data0[X] = data1[X] + data1[X-2];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 4
-        data1[X] = data0[X] + data0[X-4];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 8
-        data0[X] = data1[X] + data1[X-8];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 16
-        data1[X] = data0[X] + data0[X-16];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        // 32
-        data0[X] = data1[X] + data1[X-32];
-        barrier(CLK_LOCAL_MEM_FENCE);
-        
-        if(col_offset < cols) {
-            write_imagef(dst, (int2)(col_offset, Y), (float4)(data0[X] + max_val, 0.0f, 0.0f, 0.0f));
-        }
-        
-        max_val += data0[WORK_G_SIZE + HALF_WORK_G_SIZE - 1];
-    }
-    
-}
-
-__kernel void transpose(read_only image2d_t src, write_only image2d_t dst, int rows, int cols)
-{
-    
-    __local float buff[256];
-    
-    int2 coords = (int2) (get_global_id(0), get_global_id(1));
-    
-    int inX = coords.x;
-    int inY = coords.y;
-    
-    int lX = coords.x;
-    int lY = coords.y;
-    
-    int ginX = coords.x * 16 + lX;
-    int ginY = coords.y * 16 + lY;
-    
-    buff[lY * 16 + lX] = read_imagef(src, smp, (int2)(ginX, ginY)).x;
-    barrier(CLK_LOCAL_MEM_FENCE);
-    
-    int outRows = rows;
-    int outCols = cols;
-    
-    int outX = inX;
-    int outY = inY;
-    
-    int goutX = coords.x * 16 + lX;
-    int goutY = coords.y * 16 + lY;
-    
-    if(goutX >= 0 && goutX < outCols && goutY >=0 && goutY < outRows) {
-        write_imagef(dst, (int2)(goutX, goutY), (float4)(buff[lX * 16 + lY], 0.0f, 0.0f, 0.0f));
-    }
-}
-

dviid/rfi.frag.glsl

@@ -1,18 +0,0 @@
-#version 120
-
-uniform int           algo;
-uniform sampler2DRect tex0;
-
-void main() {
-
-    if(algo == 4) {
-        vec4 color = texture2DRect(tex0, gl_TexCoord[0].st);
-        float luminance = 0.3f * color.x + 0.59 * color.y + 0.11 * color.z;
-        //gl_FragColor = vec4(luminance, luminance, luminance, 1.0f);
-        gl_FragColor = vec4(1.0f, 1.0f, 1.0f, 0.5f);   
-        return;     
-    }
-
-    gl_FragColor = texture2DRect(tex0, gl_TexCoord[0].st);
-
-}

dviid/rfi.geom.glsl

@@ -1,127 +0,0 @@
-#version 120
-#extension GL_EXT_geometry_shader4 : enable
-
-#define ALGO_1  1
-#define ALGO_2  2
-#define ALGO_3  3
-#define ALGO_4  4
-
-uniform int             algo;
-uniform float           scale;
-uniform sampler2DRect   tex0;
-
-float max_color(vec3 rgb)
-{
-    float max = rgb.r;
-    if(rgb.g > max) { max = rgb.g; }
-    if(rgb.b > max) { max = rgb.b; }  
-    return max;
-} 
-
-float min_color(vec3 rgb)
-{
-    float min = rgb.r;
-    if(rgb.g < min) { min = rgb.g; }
-    if(rgb.b < min) { min = rgb.b; }  
-    return min;
-} 
-
-void hue(in vec4 color, out float h)
-{
-	float max = max_color(color.rgb);	
-	float min = min_color(color.rgb);
-    if(max == min) { h = 0.f; }
-    
-	float hueSixth;
-	if(color.r == max) {
-		hueSixth = (color.g - color.b) / (max - min);
-		if(hueSixth < 0.f)
-			hueSixth += 6.f;
-	} else if (color.g == max) {
-		hueSixth = 2.f + (color.b - color.r) / (max - min);
-	} else {
-		hueSixth = 4.f + (color.r - color.g) / (max - min);
-	}
-    
-	h = 255.f * hueSixth / 6.f;    
-}
-
-void saturation(in vec4 color, out float s)
-{
-	float max = max_color(color.rgb);	
-	float min = min_color(color.rgb);
-    if(max == min) { s = 0.f; }
-    
-    s = 255.f * (max - min) / max;
-}
-
-void brightness(in vec4 color, out float b)
-{
-    b = max_color(color.rgb);
-}
-
-void toHSB(in vec3 rgb, out vec3 hsb) 
-{
-	float max = max_color(rgb);	
-	float min = min_color(rgb);
-	
-	if(max == min) {
-		hsb.x = 0.f;
-		hsb.y = 0.f;
-		hsb.z = 255.f * max;
-		return;
-	}
-	
-	float hueSixth;
-	if(rgb.r == max) {
-		hueSixth = (rgb.g - rgb.b) / (max - min);
-		if(hueSixth < 0.f)
-			hueSixth += 6.f;
-	} else if (rgb.g == max) {
-		hueSixth = 2.f + (rgb.b - rgb.r) / (max - min);
-	} else {
-		hueSixth = 4.f + (rgb.r - rgb.g) / (max - min);
-	}
-	hsb.x = 255.f * hueSixth / 6.f;
-	hsb.y = 255.f * (max - min) / max;
-	hsb.z = max;
-}
-
-void main()
-{
-
-    if(algo == ALGO_4 && mod(gl_PositionIn[0].y, 2.f) != 0) return;
-
-	for (int i = 0; i < gl_VerticesIn; i++)
-	{
- 
-		gl_Position = gl_PositionIn[i];
-        
-        vec4 color0 = texture2DRect(tex0, gl_TexCoordIn[i][0].st);
-        
-        float depth = 0.f;
-        
-        if(algo == ALGO_1) {
-            brightness(color0, depth);
-        } 
-        else if(algo == ALGO_2) {
-            hue(color0, depth);
-        }
-        else if(algo == ALGO_3) {
-            saturation(color0, depth);
-        }
-        else if(algo == ALGO_4) {
-            brightness(color0, depth);
-        }
-        else {
-            brightness(color0, depth);
-        }                
-                
-        gl_Position = gl_ModelViewProjectionMatrix * vec4(gl_Position.x, gl_Position.y, depth * scale, 1.0);
-        gl_TexCoord[0] = gl_TexCoordIn[i][0];
-                
-		EmitVertex();        
-	}    
-    
-    
-}

dviid/rfi.vert.glsl

@@ -1,11 +0,0 @@
-#version 120
-
-void main()
-{
-
-	gl_FrontColor =  gl_Color;
-	gl_TexCoord[0] = gl_MultiTexCoord0;
-	gl_Position = gl_Vertex;
-    
-    
-}

example/RefractiveIndex.cpp

@@ -15,16 +15,11 @@
 
 #include "ofxXmlSettings.h"
 
-#include "ofxArcBall.h"
-
-#include <stdio.h>
-#include <stdlib.h>
-
 #define CAMERA_ID           0
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
-#define LOCATION            "MIDDLESBOROUGH"
+#define LOCATION            "MANCHESTER"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -32,22 +27,6 @@
 #define ISTATE_TRANSITION   0xCCCC
 #define ISTATE_END          0xDDDD
 
-static const int subdiv_pixels = 4;
-
-static const int VID_W = 640, VID_H = 480;
-static const int VERTICES_X = VID_W / subdiv_pixels, VERTICES_Y = VID_W / subdiv_pixels;
-static const int TRI_W = 1000;
-
-int draw_style = FACE;
-
-#define ALGO_1  1
-#define ALGO_2  2
-#define ALGO_3  3
-#define ALGO_4  4
-
-int             algo = ALGO_2;
-float           scale = 1.f;
-
 
 int _state = ISTATE_UNDEF;
 
@@ -61,64 +40,12 @@ string           RefractiveIndex::_location;
 
 ofxXmlSettings   RefractiveIndex::XML;
 
-ofShader        RefractiveIndex::_shader;
-ofVboMesh       RefractiveIndex::_mesh_vbo;
-
-ofxArcBall      RefractiveIndex::cam;
-
-string          msg;
-
-void RefractiveIndex::setup_shader_vbo()
-{
-    
-    int vertices_per_frame = XML.getValue("config:algorithms:vertices_per_frame", TRI_W);
-    int pixel_per_vertex = XML.getValue("config:algorithms:pixel_per_vertex", subdiv_pixels);
-    
-    int vertices_X = _vid_w / pixel_per_vertex, vertices_Y = _vid_h / pixel_per_vertex;
-    
-    // VBO        
-    for(int i = 0; i < vertices_X; i++){
-        for(int j = 0; j < vertices_Y; j++) {
-            _verts.push_back(ofVec3f((i / (float)vertices_X) * vertices_per_frame, (j / (float) vertices_Y) * vertices_per_frame, 0.0f));
-            _tex.push_back(ofVec2f(i / (float)vertices_X * _vid_w, j / (float) vertices_Y * _vid_h));
-			if( ( i + 1 < vertices_X ) && ( j + 1 < vertices_Y ) ) {                
-                //triangle #1
-                _ind.push_back( (i+0) * vertices_Y + (j+0) );
-                _ind.push_back( (i+1) * vertices_Y + (j+0) );
-                _ind.push_back( (i+1) * vertices_Y + (j+1) );
-                
-                //triangle #2
-                _ind.push_back( (i+1) * vertices_Y + (j+1) );
-                _ind.push_back( (i+0) * vertices_Y + (j+1) );
-                _ind.push_back( (i+0) * vertices_Y + (j+0) );
-			}
-        }
-    }
-    
-    //ofEnableNormalizedTexCoords();
-    
-    _mesh_vbo.addVertices(_verts);
-    _mesh_vbo.addTexCoords(_tex);
-    _mesh_vbo.addIndices(_ind);
-    
-    _mesh_vbo.setMode(OF_PRIMITIVE_TRIANGLES);
-        
-    // geometry shader
-    
-	_shader.setGeometryInputType(GL_TRIANGLES);
-	_shader.setGeometryOutputType(GL_TRIANGLES);
-	_shader.setGeometryOutputCount(3);
-    _shader.load("dviid/rfi.vert.glsl", "dviid/rfi.frag.glsl", "dviid/rfi.geom.glsl"); 	
-	printf("Maximum number of output vertices support is: %i\n", _shader.getGeometryMaxOutputCount());    
-}
-
-
 void RefractiveIndex::setup()
 {
-    ofSetLogLevel(OF_LOG_VERBOSE);
+    camDist=1000;
-    
-    ofHideCursor();
     
+    ofBackground(0, 0, 0);
+    ofSetBackgroundAuto(false);
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -174,38 +101,45 @@ void RefractiveIndex::setup()
 
     _analysisAdapator = NULL;
 
-    _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR_ALPHA); 
+    //getting a warning from the OFlog that the pixels aren't allocated
-    
+    //void ofPixels::allocate(int w, int h, ofImageType type)    
-    
+    _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR); 
-    setup_shader_vbo();
-    
     
     //TODO:  whichever one of these is first - it always runs twice ?
     
     _analysisVector.push_back(new ShadowScapesAnalysis(V));  //1
     _analysisVector.push_back(new ShadowScapesAnalysis(H));  //2
     _analysisVector.push_back(new ShadowScapesAnalysis(D));  //3
+	    
     _analysisVector.push_back(new RelaxRateAnalysis());   //4
+	
     _analysisVector.push_back(new IResponseAnalysis());   //5
+    
     _analysisVector.push_back(new ShapeFromShadingAnalysis());   //6
+    
     _analysisVector.push_back(new StrobeAnalysis());   //7
+    
     _analysisVector.push_back(new CamNoiseAnalysis());    //8
+    
     _analysisVector.push_back(new ColorSingleAnalysis());    //9
-    _analysisVector.push_back(new ColorMultiAnalysis());    //10
+    
-    _analysisVector.push_back(new DiffNoiseAnalysis());	    //11
+    _analysisVector.push_back(new ColorMultiAnalysis());    //0
+    
+    _analysisVector.push_back(new DiffNoiseAnalysis());	  //Q
+    
+    //_currentAnalysisIndx = 0;
+    //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
+    //_state = ISTATE_START;
     
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
   
-    // disbale <ESC> ?
-    //ofSetEscapeQuitsApp(false);
     
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
 {
     assert(analysis == _currentAnalysis->_name);
-    
     _state = ISTATE_STOP;    
 }
 
@@ -215,6 +149,17 @@ void RefractiveIndex::start_analysis()
     _analysisAdapator = new AnalysisAdaptor(_currentAnalysis);
     _currentAnalysis->setup(_vid_w, _vid_h);
     _analysisAdapator->start();    
+    
+    //allocate fbo for HD
+    fbo.allocate(1920,1080);
+
+    //    fbo.allocate( _currentAnalysis->_mesh_size_multiplier *_vid_w,_currentAnalysis->_mesh_size_multiplier * _vid_h);
+    //camera.setPosition((fbo.getWidth()/2), fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
+    camera.setPosition(0, (fbo.getHeight()/2)+150,  _currentAnalysis->_mesh_size_multiplier*500);
+    camera.setFov(65.0);
+    camera.setOrientation(ofVec3f(-2,0,0));
+    _meshRotation=0;
+
 }
 
 void RefractiveIndex::stop_analysis()
@@ -240,6 +185,7 @@ void RefractiveIndex::state_analysis()
                 _currentAnalysisIndx = 0;
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;                
+                //_state = ISTATE_END;
             } else {
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;
@@ -271,11 +217,58 @@ void RefractiveIndex::update()
 
 void RefractiveIndex::draw()
 {
+    // refractive mauve - this doesn't work... looks weird in various places.
+    //ofBackground(113, 110, 136);
+    
     // black
     ofBackground(0, 0, 0);
    
-    if(_currentAnalysis)
+    if(_currentAnalysis){
+        
         _currentAnalysis->draw();
+       
+        if(_currentAnalysis->meshIsComplete){
+            
+            fbo.begin();
+            ofClear(0,0,0);
+
+            glShadeModel(GL_SMOOTH);  
+            
+            
+            camera.begin();
+            
+                //this is a hack, I don't know how to colour the fbo with black pixels so I'm drawing a massive black rectangle in the  background
+                /*
+                ofPushMatrix();
+                    ofTranslate(0, 0,-500);
+                    ofSetColor(0, 0, 0);
+                    ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);                
+                    ofPopMatrix();
+                ofSetColor(255);
+                */
+                //float xDiff= (fbo.getWidth()- 1.55*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
+                float xDiff= (fbo.getWidth()- 1.33333*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
+                float yDiff= (fbo.getHeight()-(_currentAnalysis->_mesh_size_multiplier * _vid_h))/2;
+                
+                ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
+                    //ofScale(1.33333,1.0,1.0);
+                    //_currentAnalysis->aMesh.drawVertices();     // TODO: tom - why do you have the vertices drawing here? 
+                    _currentAnalysis->aMesh.drawFaces();
+                    _currentAnalysis->aMesh.draw();
+                
+            camera.end();
+            fbo.end();
+
+            ofPixels pixels;
+            fbo.readToPixels(pixels);
+          
+            ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
+            //saving jpgs doesn't work - pngs only!
+            // PNG is fine - better for Final Cut anyway! 
+
+            ofDisableBlendMode() ;  
+        }
+    }
 }
 
 void RefractiveIndex::setup_camera()
@@ -309,10 +302,15 @@ void RefractiveIndex::stop_camera()
 
 void RefractiveIndex::keyPressed  (int key)
 {
-    
     if( key =='f')
         ofToggleFullscreen();
     
+    /*  TODO:  complete the below... would be good to trigger the Analysis from keypresses if needed... */
+    // currently this doesn't work... the save_cb's in the individual 
+    // tried to add a  stop_analysis(); call but it blocks the whole programme
+    
+    // i.e.: ask david how to shut off the prior Analysis if it's not finished running from here? 
+    
     if(key == 'x')
     {
         if(_currentAnalysis)
@@ -420,6 +418,48 @@ void RefractiveIndex::keyPressed  (int key)
             _state = ISTATE_TRANSITION;            
     }
     
+    /*
+     TO DO:  add a file dialog so we can save images to another hard drive...
+     e.g.: http://dev.openframeworks.cc/pipermail/of-dev-openframeworks.cc/2011-April/003125.html
+     
+>> 		case 's':
+>> 			doSave ^= true;
+>> 			doLoad = false;
+>> 			if(doSave) {
+>> 				ofFileDialogResult r = ofSystemLoadDialog("Select path to save to", true);
+>> 				if(r.bSuccess) {
+>> 					saveCounter = 0;
+>> 					savePath = r.getPath();
+>> 					ofDirectory::createDirectory(savePath + "/color/");
+>> 					ofDirectory::createDirectory(savePath + "/depth/");
+>> 					printf("SAVE %s %s\n", r.getPath().c_str(), r.getName().c_str());
+>> 				} else {
+>> 					doSave = false;
+>> 				}
+>> 				
+>> 			}
+>> 			break;
+>> 			
+>> 		case 'l':
+>> 			doLoad ^= true;
+>> 			doSave = false;
+>> 			if(doLoad) {
+>> 				ofFileDialogResult r = ofSystemLoadDialog("Select path to load from", true);
+>> 				if(r.bSuccess) {
+>> 					loadCounter = 0;
+>> 					loadPath = r.getPath();
+>> 					ofDirectory dir;
+>> 					loadMaxFiles = MAX(dir.listDir(loadPath + "/color"), dir.listDir(loadPath + "/depth"));
+>> 					printf("LOAD %i %s %s\n", loadMaxFiles, r.getPath().c_str(), r.getName().c_str());
+>> 				} else {
+>> 					doLoad = false;
+>> 				}
+>> 				
+>> 			}
+>> 			break;
+    */
+    
+    
 }
 
 void RefractiveIndex::exit()

example/RefractiveIndex.h

@@ -10,16 +10,12 @@
 
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
 
-#include "ofxArcBall.h"
 
 #define MODE_DRAWING        0xEEFF
 #define MODE_ANALYSING      0xFFEE
 
-#define VERTS   1
-#define WIRE    2
-#define FACE    3
-
 class RefractiveIndex : public ofBaseApp
 {
 public:
@@ -38,8 +34,6 @@ public:
     void stop_analysis();
     void state_analysis();
     
-    void setup_shader_vbo();
-    
     // ofx
     void keyPressed  (int key);
     void keyReleased(int key){;}
@@ -62,6 +56,9 @@ protected:
     AnalysisAdaptor*            _analysisAdapator;
     vector<AbstractAnalysis*>   _analysisVector;    
     
+    float                         _meshRotation;
+    float                           camDist;
+    ofEasyCam                     cam;
 public:    
     // acquisition
     static ofPixels         _pixels;    
@@ -76,17 +73,8 @@ public:
     // this should be in xml
     static string           _location;
     static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
-    
+    ofCamera    camera;
-    
+    ofPixels    keepOnScreen;
-    static ofVboMesh       _mesh_vbo;
+    ofFbo fbo;
-    
-    vector<ofVec3f> _verts;
-    vector<ofVec2f> _tex;
-    vector<unsigned int> _ind;
-    
-    static ofxArcBall cam;
-    
-    static ofShader        _shader;
-    
    
 };

example/main.cpp

@@ -1,8 +1,8 @@
 #include "ofAppGlutWindow.h"
 #include "RefractiveIndex.h"
 
-#define SCREEN_WIDTH        800
+#define SCREEN_WIDTH        1280
-#define SCREEN_HEIGHT       600
+#define SCREEN_HEIGHT       800
 
 int main() {
     
@@ -10,8 +10,8 @@ int main() {
    
     bool fullscreen;
     
-    fullscreen = true; 
+    //fullscreen = true; 
-    //fullscreen = false;
+    fullscreen = false;
     
     cout << "> display configuration" << endl;
     cout << "* fullscreen: " << (fullscreen ? "yes" : "no") << endl;

src/AbstractAnalysis.cpp

@@ -7,8 +7,10 @@
 
 void AbstractAnalysis::setup(int camWidth, int camHeight) {
     
-    _cam_w = camWidth; _cam_h = camHeight;
+    meshIsComplete=false;
+    imageForContourAvailable=false;
     
+    _cam_w = camWidth; _cam_h = camHeight;
     if(RefractiveIndex::_mode == MODE_DRAWING) {
         ofFileDialogResult r = ofSystemLoadDialog("choooose da folda", true);
         if(!r.bSuccess) {
@@ -20,16 +22,6 @@ void AbstractAnalysis::setup(int camWidth, int camHeight) {
         _whole_file_path_synthesis = r.filePath + "/darwings";        
     }
 
-    // viewport
-    
-    tx = RefractiveIndex::XML.getValue("config:viewport:tx", 200.0);
-    ty = RefractiveIndex::XML.getValue("config:viewport:ty", 50.0);
-    tz = RefractiveIndex::XML.getValue("config:viewport:tz", -500.0);
-    
-    rx = RefractiveIndex::XML.getValue("config:viewport:rx", 0.0);
-    ry = RefractiveIndex::XML.getValue("config:viewport:ry", 0.0);
-    rz = RefractiveIndex::XML.getValue("config:viewport:rz", 0.0);
-    
 }
 
 // this is the main threaded loop for a given analysis
@@ -54,13 +46,14 @@ void AbstractAnalysis::do_synthesize() {
                 if(_state == STATE_STOP) goto exit;
                 _state = STATE_DISPLAY_RESULTS;
                 displayresults();
+                cleanup();
             }                    
-            
-            break;
         }
             
         case MODE_DRAWING:
         {            
+
+
             ofxFileHelper fileHelperDrawing;
             if(!fileHelperDrawing.doesDirectoryExist(_whole_file_path_synthesis)){
                 fileHelperDrawing.makeDirectory(_whole_file_path_synthesis);
@@ -72,14 +65,12 @@ void AbstractAnalysis::do_synthesize() {
             if(_state == STATE_STOP) goto exit;
             _state = STATE_DISPLAY_RESULTS;
             displayresults();
-            
+            cleanup();            
-            break;
         }
     }
     
 exit:    
     cleanup();
-    ofxFileHelper::deleteFolder(_whole_file_path_analysis);
     ofNotifyEvent(_synthesize_cb, _name);    
     
 }
@@ -131,7 +122,6 @@ void AbstractAnalysis::create_dir_allocate_images()
         
     }
     
-    
     _whole_file_path_synthesis = SYNTHESIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime;
     
     if(!fileHelperSynthesis.doesDirectoryExist(_whole_file_path_synthesis)){
@@ -149,7 +139,6 @@ void AbstractAnalysis::create_dir_allocate_images()
         fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
         
     }
-    
     //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////  
     
     
@@ -168,6 +157,7 @@ void AbstractAnalysis::create_dir_allocate_images()
     myGrayImage1.setUseTexture(false);
     myGrayImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_GRAYSCALE);
     
+
     //////////////////////////////END ALLOCATE IMAGES //////////////////////////////////////////////////  
 
 }
@@ -192,6 +182,9 @@ void AbstractAnalysis::read_dir_create_list(string folder_path)
         for(int i = 0; i < list.size(); i++) {
             string filepath = folder_path + "/" + list[i]; 
             _saved_filenames_analysis.push_back(filepath);
+                        
+            cout << list[i] << endl; 
+            
         }                
     }
 }
@@ -204,7 +197,6 @@ void AbstractAnalysis::saveImageAnalysis(string filename)
     if (RefractiveIndex::_vidGrabber.isFrameNew())
     {
         RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-        
     } else {
         return;
     }
@@ -236,7 +228,6 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
     
 #ifdef TARGET_OSX   
 
-
     ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
     
 #elif defined(TARGET_WIN32)    
@@ -264,4 +255,3 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
             
     
 }
-

src/AbstractAnalysis.h

@@ -61,6 +61,23 @@ public:
     
     // event
     ofEvent<string> _synthesize_cb;    
+    bool    meshIsComplete;
+    bool    imageForContourAvailable;
+    ofMesh  aMesh;
+    ofLight light;
+    ofLight lightStatic; 
+    
+    string  meshFileName;
+    //difference between our image size and the size of the fbo
+    float   widthScaleFactor;
+    float   heightScaleFactor;
+    ofImage  contourImage;
+    ofPixels meshPix;
+    ofPixels publicColorImage;
+    float    zPlaneAverage;
+    
+    //added Tom 1/5/12 defines the stretch we make to the mesh to make it fit HD proportions
+    float           _mesh_size_multiplier;
     
 protected:    
     int             _cam_w, _cam_h;          
@@ -81,9 +98,5 @@ protected:
     int             NUM_RUN;
     int             NUM_SAVE_PER_RUN;    
     
-    //viewport
-    
-    float tx, ty, tz, rx, ry, rz;    
-    
     friend class AnalysisAdaptor;
 };

src/CamNoiseAnalysis.cpp

@@ -13,13 +13,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
-
-
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -28,6 +21,62 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
 
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 1;
+    chooseColour            = 6;
+    multiplier              = 4.0;
+    
+    ofSetLineWidth(5.0f);
+    glPointSize(5.0f);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+   // meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    meshMode = OF_PRIMITIVE_POINTS;
+    
+    ///setup light    
+    ofEnableLighting();    
+    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
+    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
+    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
+    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+    
+    glEnable(GL_LIGHT0);  
+    
+    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
+    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
+    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
+    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+    
+    glEnable(GL_LIGHT1);     
+    glPointSize(9.0f);
+    glEnable(GL_POINT_SMOOTH);
+    glCullFace(GL_BACK);
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;
@@ -54,26 +103,49 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
 
-    
     image1.clear();
     image2.clear();
+    image3.clear();
+    image4.clear();
+    image5.clear();
 
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
 
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage"
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
 
 
-    ////---------
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    algo = RefractiveIndex::XML.getValue("config:algorithms:camnoise:algo", algo_default);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    scale = RefractiveIndex::XML.getValue("config:algorithms:camnoise:scale", scale_default);
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:camnoise:draw_style", draw_style_default);
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:camnoise:line_width", line_width_default);        
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:camnoise:point_size", point_size_default);
 
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
 
@@ -107,27 +179,160 @@ void CamNoiseAnalysis::acquire()
 
 void CamNoiseAnalysis::synthesise()
 {
-    // we don't need to synthesise
+    //cout << "CamNoiseAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    _returnAveragePixelValues();
+    vector<vector<float> > averagePixelBrightnessesForEachLevel = averagePixelValuesForAllLevels;
+    float lightLevel=0;
+    float pLightLevel=0;
+    cout<<_listOfLightLevels.size()<<" "<<averagePixelBrightnessesForEachLevel.size()<<" these should be the same";
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
+        
+        lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
+        //cout << "CamNoiseAnalysis::synthesis FOR LOOP...\n";
+        
+        //find which list of average pixel values is for THIS light level
+        int _averagePixelVectorIndex;
+        for (int j=0; j<_listOfLightLevels.size(); j+=3) {
+            if(lightLevel==_listOfLightLevels[j]){
+                _averagePixelVectorIndex=j;
+            }
+        }
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+
+        if(_state == STATE_STOP) return;
+
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        }
+
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //    cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+             /*   cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                //cvGrayDiff1.erode();
+                
+                cvGrayImage1.dilate();
+                cvGrayImage1.blur(5);
+                cvGrayImage1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef());  
+                */
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */ 
+                
+                //DIFFERENCING THE BACKGROUND
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-backgroundPixels[i]>0){
+                 imagePixels1[i]-=backgroundPixels[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, averagePixelBrightnessesForEachLevel[_averagePixelVectorIndex], _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+                
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+
+    }
 
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-     */
-    
-
 }
 
 void CamNoiseAnalysis::displayresults()
 {
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
 
         if(_state == STATE_STOP) return;
 
@@ -138,15 +343,13 @@ void CamNoiseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
 
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         }
 
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -308,6 +511,8 @@ void CamNoiseAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
 
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -316,47 +521,21 @@ void CamNoiseAnalysis::draw()
 
             _frame_cnt++;
 
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {
+                //cout << "_show_image...\n" << endl;
 
-            image2.bind();        
+                ofEnableAlphaBlending();
 
-            RefractiveIndex::_shader.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
 
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
+                ofDisableAlphaBlending();
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
 
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
+            _RUN_DONE = true;
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             break;
 
         }
@@ -377,3 +556,533 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 
     saveImageAnalysis(file_name);
 }
+
+
+
+void CamNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //to do 
+    
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    if(chooseColour==6){
+        
+        for(int i=0;i<sPixels.size();i++){
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x++;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y++;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+
+}
+
+
+vector<float> CamNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    int inc=0;
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            
+            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
+            
+            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
+            
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            if(i<100){
+                
+              //  cout<<" average: "<<averageDepths[inc]<<" actual: "<<imageColor1.getBrightness()<<" ";
+            }
+           // int thisDiff=imageColor1.getBrightness();
+            
+            int thisDiff=-(imageColor1.getBrightness() - averageDepths[inc] );
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+            inc++;
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+
+
+void CamNoiseAnalysis:: _returnAveragePixelValues(){
+    
+    
+    //second number in 15_204.00_2.jpg is the light level
+    
+    float lightLevel=0;
+    float pLightLevel=0;
+    float numberOfImagesActuallyLoaded=0;
+    vector<float> averagePixelValuesForOneLevel;
+
+    for (int j=0; j<RefractiveIndex::_vid_w*RefractiveIndex::_vid_h; j++) {
+        averagePixelValuesForOneLevel.push_back(0.0);
+    }
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        }
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+
+            //split file name by under score
+            vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
+            
+            lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
+           // cout<<" lightLevel "<<lightLevel;
+
+            ofPixels image1Pixels=image1.getPixelsRef();
+            
+            int x=0;
+            int y=0;
+            int inc=0;
+            for (int j=0; j<image1Pixels.size(); j+=3) {
+                ofColor color=image1Pixels.getColor(x, y);
+                averagePixelValuesForOneLevel[inc]+= color.getBrightness();
+                x++;
+                inc++;
+                if(x>=image1Pixels.getWidth()){ 
+                    x=0;
+                    y++;
+                }
+            }
+           // _listOfLightLevels}
+            numberOfImagesActuallyLoaded++;
+            
+            //if this is a new light level advance
+            if (lightLevel!=pLightLevel) {
+                
+                ///check that this light level is not already in our list
+                
+                
+             _listOfLightLevels.push_back(lightLevel);
+                
+                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
+                    averagePixelValuesForOneLevel[j]/=numberOfImagesActuallyLoaded;
+                    //cout<<" "<<averagePixelValuesForOneLevel[j]<<" ";
+                }
+                averagePixelValuesForAllLevels.push_back(averagePixelValuesForOneLevel);
+                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
+                    averagePixelValuesForOneLevel[j]=0;
+                }
+
+                pLightLevel=lightLevel;
+                numberOfImagesActuallyLoaded=0;
+
+            }
+
+        }
+    }
+    
+    for(int j=0;j<_listOfLightLevels.size();j++){
+        //cout<<_listOfLightLevels[j]<<" lightlevel ";
+    }
+    
+}

src/CamNoiseAnalysis.h

@@ -37,13 +37,53 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+   
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImage);
+    
+    //returns a vector of floats for each distinct light level
+   void _returnAveragePixelValues();
+    //this vector of vectors will be returned
+    vector<vector<float> > averagePixelValuesForAllLevels;
+    
+    vector<float> _listOfLightLevels;
+    
+    int vertexSubsampling;
+    
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
     
-    int algo;
-    int scale;
-    int draw_style;   
-    float line_width;
-    float point_size;    
 };

src/ColorMultiAnalysis.cpp

@@ -12,11 +12,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const float line_width_default = 0.5f;
-
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -25,6 +20,14 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=8;
+    vertexSubsampling = 1;
+    chooseColour=1;
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
@@ -51,21 +54,50 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    ////---------
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:colormulti:algo", algo_default);
+    cvColorImage2.clear();
-    scale = RefractiveIndex::XML.getValue("config:algorithms:colormulti:scale", scale_default);
+	cvGrayImage2.clear();
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:colormulti:draw_style", draw_style_default);
+    cvGrayDiff2.clear();
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:colormulti:line_width", line_width_default);
+    
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -101,25 +133,124 @@ void ColorMultiAnalysis::acquire()
 void ColorMultiAnalysis::synthesise()
 {
     
-    // we don't need to synthesise
+    //cout << "ColorMultiAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorMultiAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+            //cvColorImage1.blur(1);
+            //cvColorImage1.erode();
+            
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+
+            cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 15, 15);
+            cvXorS( cvColorImage1.getCvImage(), cvScalarAll(2), cvColorImage1.getCvImage(), 0 );
+            
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+            // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            //ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-backgroundPixels[i]>0){
+                    imagePixels1[i]-=backgroundPixels[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+            
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            // }
+        }
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+        _RUN_DONE = true;
+    */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-     */
 }
 
 void ColorMultiAnalysis::displayresults()
 {
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -130,15 +261,13 @@ void ColorMultiAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -150,6 +279,27 @@ void ColorMultiAnalysis::displayresults()
 void ColorMultiAnalysis::draw()
 {
     
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();     
+    light.enable();
+	
+    light.setPosition(200,200,-150);
+    lightStatic.enable();
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(2.0f);
+    //glPointSize(4.0f);
+    
+    ofEnableBlendMode ( OF_BLENDMODE_ADD );
+    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
+    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
+    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
+    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
+
+    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -280,9 +430,8 @@ void ColorMultiAnalysis::draw()
                 _anim_cnt++;
                 
             } else {
-                //_state = STATE_DISPLAY_RESULTS;
+                _state = STATE_DISPLAY_RESULTS;
                 _anim_cnt=0;
-                _RUN_DONE = true;
             }
             ofPopMatrix();
             ofSetRectMode(OF_RECTMODE_CORNER);
@@ -296,6 +445,7 @@ void ColorMultiAnalysis::draw()
             
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -304,46 +454,20 @@ void ColorMultiAnalysis::draw()
             
             _frame_cnt++;
             
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
                 
                 ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);              
                 
-                RefractiveIndex::cam.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-                ofTranslate(tx, ty, tz);
+                ofDisableAlphaBlending();
-                ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-                glScalef(1.5, 1, 1);
-                
-                if (_show_image)
-                    image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
-                                
-                image2.bind();        
-                
-                RefractiveIndex::_shader.begin();
-                
-                RefractiveIndex::_shader.setUniform1i("algo", algo);
-                RefractiveIndex::_shader.setUniform1f("scale", scale);
-                RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                                
-                switch (draw_style) {
-                    case VERTS:
-                        RefractiveIndex::_mesh_vbo.drawVertices();
-                        break;
-                    case WIRE:
-                        RefractiveIndex::_mesh_vbo.drawWireframe();
-                        break;
-                    case FACE:
-                        RefractiveIndex::_mesh_vbo.drawFaces();
-                        break;            
             }
             
-                RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-                
-                image2.unbind();
-                
-                RefractiveIndex::cam.end();    
-                
             _RUN_DONE = true;
             break;
             
@@ -361,8 +485,156 @@ void ColorMultiAnalysis::draw()
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-            
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-
     saveImageAnalysis(file_name);    
 }
+
+
+void ColorMultiAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //mesh.setMode(OF_PRIMITIVE_LINES);
+    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    //mesh.setMode(OF_PRIMITIVE_POINTS);
+    
+    /*
+     OF_PRIMITIVE_TRIANGLES,
+     OF_PRIMITIVE_TRIANGLE_STRIP,
+     OF_PRIMITIVE_TRIANGLE_FAN,
+     OF_PRIMITIVE_LINES,
+     OF_PRIMITIVE_LINE_STRIP,
+     OF_PRIMITIVE_LINE_LOOP,
+     OF_PRIMITIVE_POINTS
+     
+     */
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+   
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+}
+
+
+
+vector<float> ColorMultiAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        //float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            //float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getLightness());
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            float multiplier=15.0*((thisDiff)/255.0);
+            
+            differences.push_back(multiplier* thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}

src/ColorMultiAnalysis.h

@@ -31,14 +31,45 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
 
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    int algo;
+    ofxCvColorImage         cvColorImage1;
-    int scale;
+    ofxCvColorImage         cvColorImage2;
-    int draw_style;
+    ofxCvColorImage         cvColorImage3;
-    float line_width;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
 
 };

src/ColorSingleAnalysis.cpp

@@ -1,9 +1,11 @@
 #include "ColorSingleAnalysis.h"
 #include "ofMain.h"
-
 #include "Poco/Timer.h"
 #include "Poco/Thread.h"
 
+#include <string>
+#include <iostream>
+
 #include "RefractiveIndex.h"
 
 using Poco::Timer;
@@ -13,11 +15,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const float line_width_default = 0.5f;
-
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -26,10 +23,18 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier=8;
+    vertexSubsampling = 1;
+    chooseColour=1;
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
 
+    
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 1*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
@@ -52,34 +57,62 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     b = 0;
     
     fileNameTag = "";
+    fileNameColor = "";
     
     _show_image = false;
     _image_shown = false;
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    ////---------
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:algo", algo_default);
+    cvColorImage2.clear();
-    scale = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:scale", scale_default);
+	cvGrayImage2.clear();
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:draw_style", draw_style_default);
+    cvGrayDiff2.clear();
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:line_width", line_width_default);
     
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);    
 }
 
 
 void ColorSingleAnalysis::acquire()
 {
-
     Timer* save_timer;
 
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
@@ -102,33 +135,156 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
-  
-    // }
 }
 
 void ColorSingleAnalysis::synthesise()
 {
     
-    // we don't need to synthesise
+    //cout << "ColorSingleAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorSingleAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+                //cout << "LOADED image1!!!" << endl;
+                //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+
+            
+                cout << "_saved_filenames_analysis[i].find(RED): " << _saved_filenames_analysis[i].find("RED") << endl;                
+            
+                if(_saved_filenames_analysis[i].find("RED")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "RED";
+                    cout<<"FOUND RED"<<endl;
+                } else if (_saved_filenames_analysis[i].find("GREEN")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "GREEN";
+                    cout<<"FOUND GREEN"<<endl;
+                } else if(_saved_filenames_analysis[i].find("BLUE")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "BLUE";
+                    cout<<"FOUND BLUE"<<endl;
+                } else if(_saved_filenames_analysis[i].find("FADING")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "FADING";
+                    cout<<"FOUND FADING"<<endl;
+                }
+                          
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.blur(1);
+            
+                //cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 9, 9 );
+                
+                cvColorImage1.erode();
+                
+                cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 3, 3 );
+            
+                //cvColorImage1.erode();
+            
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+            
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+            
+                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(255), cvColorImage1.getCvImage(), 0 );
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+            
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+        
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+            
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+            
+           // }
+        }
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-     */
     
 }
 
 void ColorSingleAnalysis::displayresults()
 {
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -139,15 +295,13 @@ void ColorSingleAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -159,12 +313,31 @@ void ColorSingleAnalysis::displayresults()
 
 void ColorSingleAnalysis::draw()
 {
+    ofEnableSmoothing();
+
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();     
+    light.enable();
+	
+    light.setPosition(200,200,-150);
+    lightStatic.enable();
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(1.0f);
+    
+    ofEnableBlendMode ( OF_BLENDMODE_ADD );
+    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
+    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
+    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
+    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
+    
     
     switch (_state) {
         case STATE_ACQUIRING:
         {
 
-            
             if (_frame_cnt < _frame_cnt_max)
             {
                     
@@ -312,6 +485,7 @@ void ColorSingleAnalysis::draw()
             
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -320,46 +494,20 @@ void ColorSingleAnalysis::draw()
             
             _frame_cnt++;
             
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
                 
                 ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);              
                 
-            RefractiveIndex::cam.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-            ofTranslate(tx, ty, tz);
+                ofDisableAlphaBlending();
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
-            if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
-            
-            image2.bind();        
-            
-            RefractiveIndex::_shader.begin();
-            
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             _RUN_DONE = true;
             break;
 
@@ -381,3 +529,278 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
+
+
+
+void ColorSingleAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+   
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //mesh.setMode(OF_PRIMITIVE_LINES);
+    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    mesh.setMode(OF_PRIMITIVE_POINTS);
+  
+    /*
+     OF_PRIMITIVE_TRIANGLES,
+     OF_PRIMITIVE_TRIANGLE_STRIP,
+     OF_PRIMITIVE_TRIANGLE_FAN,
+     OF_PRIMITIVE_LINES,
+     OF_PRIMITIVE_LINE_STRIP,
+     OF_PRIMITIVE_LINE_LOOP,
+     OF_PRIMITIVE_POINTS
+     
+     */
+    
+    ofColor meshColour=ofColor(255,255,255, 255);
+    
+      //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+                
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+             
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+      
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        ofColor currentSecondImageColor;
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            if(fileNameColor=="RED")
+            {
+                currentSecondImageColor.r=255;
+                currentSecondImageColor.g=0;
+                currentSecondImageColor.b=0;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="GREEN")
+            {
+                currentSecondImageColor.r=0;
+                currentSecondImageColor.g=255;
+                currentSecondImageColor.b=0;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="BLUE")
+            {
+                currentSecondImageColor.r=0;
+                currentSecondImageColor.g=0;
+                currentSecondImageColor.b=255;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="FADING")
+            {
+                currentSecondImageColor.r= 255;
+                currentSecondImageColor.g= 255;
+                currentSecondImageColor.b= 255;
+                currentSecondImageColor.a= 255;
+            }
+                       
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+           
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor( currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            //x++;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //y++;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+}
+
+
+vector<float> ColorSingleAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+        
+            int thisDiff;
+            
+            if(fileNameColor=="RED")
+            {   
+                //thisDiff=abs(imageColor1.r);
+
+                thisDiff=abs(255-imageColor1.r);
+            } else if(fileNameColor=="GREEN")
+            {
+                //thisDiff=abs(imageColor1.g);                
+
+                thisDiff=abs(255-imageColor1.g);  
+                
+            } else if(fileNameColor=="BLUE")
+            {
+                //thisDiff=abs(imageColor1.b);
+
+                thisDiff=abs(255-imageColor1.b);
+            
+            } else if(fileNameColor=="FADING") {
+            
+                //thisDiff=imageColor1.getBrightness();
+                thisDiff=255-imageColor1.getBrightness();
+
+            }
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            float multiplier=8.0;
+            
+            differences.push_back(multiplier* thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-/*
+    /*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -32,19 +32,53 @@ protected:
 
     bool    _RUN_DONE;
     string  fileNameTag;
+    string  fileNameColor;
     float   r,g,b;
     
     int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
     bool _show_image, _image_shown;
-
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    int algo;
+    ofxCvColorImage         cvColorImage1;
-    int scale;
+    ofxCvColorImage         cvColorImage2;
-    int draw_style;
+    ofxCvColorImage         cvColorImage3;
-    float line_width;    
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvFloatImage       	cvFloatImage1;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
 };

src/DiffNoiseAnalysis.cpp

@@ -13,20 +13,37 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
-
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
     
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
+ 
     cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 10;
+    vertexSubsampling       = 1;
+    chooseColour            = 5;
+    multiplier              = 4.0;
+
+    blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+        
+    meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    //meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
@@ -53,23 +70,50 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    ////---------
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:algo", algo_default);
+    cvColorImage2.clear();
-    scale = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:scale", scale_default);
+	cvGrayImage2.clear();
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:draw_style", draw_style_default);
+    cvGrayDiff2.clear();
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:line_width", line_width_default);        
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:point_size", point_size_default);
     
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
 
@@ -104,27 +148,167 @@ void DiffNoiseAnalysis::acquire()
 void DiffNoiseAnalysis::synthesise()
 {   
     
-    // we don't need to synthesise
+    //cout << "DiffNoiseAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "DiffNoiseAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+        
+            //cvColorImage1.erode();
+            //cvColorImage1.dilate();
+                     
+            //cvColorImage1.blur(5);
+            //cvColorImage2.blur(5);
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            //cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+            //cvGrayImage1.convertToRange(0.0, 255.0);
+            //cvGrayImage2.convertToRange(0.0, 255.0);
+                
+            //cvGrayImage1.adaptiveThreshold( 200, 0);
+            //cvGrayImage2.adaptiveThreshold( 200, 0);
+                
+            //cvGrayImage1.contrastStretch();
+            //cvGrayImage2.contrastStretch();
+            
+            //cvGrayImage1.brightnessContrast(1.0,0.5);
+            //cvGrayImage2.brightnessContrast(1.0,0.5);
+               
+            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+            cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+            
+            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+                
+             // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            //image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+                
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            //ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+                //DIFFERENCING SUBSEQUENT IMAGES
+                 /*
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-imagePixels2[i]>0){
+                    imagePixels1[i]-=imagePixels2[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+                 
+                */ 
+                    //DIFFERENCING THE BACKGROUND
+                /*
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-backgroundPixels[i]>0){
+                    imagePixels1[i]-=backgroundPixels[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+              */                
+             
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            //}
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+    _RUN_DONE = true;
+    */
+    
+     meshIsComplete=false;
+    _synth_save_cnt=0;
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-     */
     
 }
 
 void DiffNoiseAnalysis::displayresults()
 {
     
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -135,27 +319,46 @@ void DiffNoiseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
     }    
     
+    
 }
 
 
 // this runs at frame rate = 33 ms for 30 FPS
 void DiffNoiseAnalysis::draw()
 {    
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+
+    light.enable();	
+    lightStatic.enable();
+
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(5.0f);
+    
+    ofEnableBlendMode(blendMode);
+
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -202,7 +405,6 @@ void DiffNoiseAnalysis::draw()
                     }        
                 }
                 
-                
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
@@ -319,6 +521,9 @@ void DiffNoiseAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -327,47 +532,22 @@ void DiffNoiseAnalysis::draw()
             
             _frame_cnt++;
             
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {  
+                //cout << "_show_image...\n" << endl;
                 
-            image2.bind();        
+                ofEnableAlphaBlending();
                 
-            RefractiveIndex::_shader.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                //image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
+                ofDisableAlphaBlending();
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
+            _RUN_DONE = true;
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             break;
             
         }
@@ -385,3 +565,408 @@ void DiffNoiseAnalysis::save_cb(Timer& timer)
 
     saveImageAnalysis(file_name);
 }
+
+
+void DiffNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+        
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+        
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+        
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+        
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> DiffNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}

src/DiffNoiseAnalysis.h

@@ -36,14 +36,47 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    int algo;
+    ofxCvColorImage         cvColorImage1;
-    int scale;
+    ofxCvColorImage         cvColorImage2;
-    int draw_style;   
+    ofxCvColorImage         cvColorImage3;
-    float line_width;
+    ofxCvColorImage         cvColorImage4;
-    float point_size;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
 };

src/IResponseAnalysis.cpp

@@ -13,13 +13,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
-
-
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -28,10 +21,21 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
 
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=4;
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME IResponseAnalysis " << acq_run_time << endl;
 
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=8;
     
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
@@ -54,28 +58,50 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    ////---------
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:iresponse:algo", algo_default);
+    cvColorImage2.clear();
-    scale = RefractiveIndex::XML.getValue("config:algorithms:iresponse:scale", scale_default);
+	cvGrayImage2.clear();
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:iresponse:draw_style", draw_style_default);
+    cvGrayDiff2.clear();
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:iresponse:line_width", line_width_default);        
+     
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:iresponse:point_size", point_size_default);    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
-
 void IResponseAnalysis::acquire()
 {
-
     Timer* save_timer;
     TimerCallback<IResponseAnalysis> save_callback(*this, &IResponseAnalysis::save_cb);
 
@@ -103,28 +129,92 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
-    
+    cout<<"SYNTHESISING IRESPONSE";
-    // we don't need to synthesise
-    return;
-    
-    /*
  
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "IResponseAnalysis::synthesis FOR LOOP...\n";
+    
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+             //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                //ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+
+                //background subtraction// 
+                /*
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+               */
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                 //meshPix=make3DZmap(image1, image5, _background);
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        //}
+    }
+
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-     */    
-    
 }
 
 
 void IResponseAnalysis::displayresults()
 {
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -135,15 +225,13 @@ void IResponseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            cout << "didn't load image" << endl;
+            // cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -284,6 +372,8 @@ void IResponseAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -292,47 +382,21 @@ void IResponseAnalysis::draw()
             
             _frame_cnt++;
             
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {  
+                //cout << "_show_image...\n" << endl;
                 
-            image2.bind();        
+                ofEnableAlphaBlending();
                 
-            RefractiveIndex::_shader.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
             
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
+                ofDisableAlphaBlending();
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
+            _RUN_DONE = true;
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             break;
             
         }
@@ -352,3 +416,125 @@ void IResponseAnalysis::save_cb(Timer& timer)
         
     saveImageAnalysis(file_name);
 }
+
+void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    
+    ofColor meshColour=ofColor(255,0,0);
+    
+    int chooseColour=1  ;
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+         
+    if(chooseColour==1){
+        
+            for(int i=0;i<sPixels.size();i++){
+                mesh.addColor(  currentSecondImage.getColor(x, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+
+                x++;
+                if(x>=currentSecondImage.getWidth()-1){
+                    x=0;
+                    y++;
+                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                    if(y>=currentSecondImage.getHeight()-1){
+                        break;
+                    }
+                }
+            }
+    }
+}
+
+vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+        for(int i=0;i<imagePixels1.size();i++){
+            thesePixels[i]=0;
+        }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+           
+            //float _presumedBrightness=255;
+            
+            int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            float multiplier=4.0;
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+
+

src/IResponseAnalysis.h

@@ -35,14 +35,35 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
   
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    int algo;
+    ofxCvColorImage         cvColorImage1;
-    int scale;
+    ofxCvColorImage         cvColorImage2;
-    int draw_style;   
+    ofxCvColorImage         cvColorImage3;
-    float line_width;
+    ofxCvColorImage         cvColorImage4;
-    float point_size;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
     
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    //returns ofPixels but these pixels actually hold depth data.
+    //ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    bool _gotFirstImage;
+    ofImage _background;
 };

src/RelaxRateAnalysis.cpp

@@ -12,12 +12,8 @@ using Poco::Thread;
 
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
-
+#define TRESHOLD        80
-const int algo_default = 1;
+#define MAXBLOBS        15
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
 
 void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
@@ -27,10 +23,41 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling_x       = 1; //must be at least '1'
+    vertexSubsampling_y       = 5; //must be at least '1'
+    chooseColour            = 2;
+    multiplier              = 4.0;
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    //meshMode = OF_PRIMITIVE_LINES;
+    meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_relaxrate", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
     
+    _treshold = RefractiveIndex::XML.getValue("config:relaxrate:treshold", TRESHOLD);
+    cout << "TRESHOLD RelaxRateAnalysis " << _treshold << endl;
+    
+    _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
+    cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
+
+    
+    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    
     DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
     // or 10 times per second = every 100 ms
     
@@ -53,22 +80,45 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
     
     
-    ////---------
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:algo", algo_default);
-    scale = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:scale", scale_default);
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:draw_style", draw_style_default);
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:line_width", line_width_default);        
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:point_size", point_size_default);
         
 }
 
@@ -102,47 +152,189 @@ void RelaxRateAnalysis::acquire()
 
 void RelaxRateAnalysis::synthesise()
 {
-    // we don't need to synthesise
+    // cout << "RelaxRate::saving synthesis...\n";
-    return;
-    
-    /*
-    
-    //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-    _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
-    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+        //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
-    while(!_RUN_DONE && _state != STATE_STOP)
+        
-        Thread::sleep(3);
+        //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            //        cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                //cvColorImage1.erode();
+                //cvColorImage1.erode();
+                //cvColorImage1.dilate();
+                
+                cvColorImage1.blur(1);
+                cvColorImage2.blur(1);
+                
+                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayImage1.convertToRange(0.0, 255.0);
+                //cvGrayImage2.convertToRange(0.0, 255.0);
+                
+                //cvGrayImage1.adaptiveThreshold( 200, 0);
+                //cvGrayImage2.adaptiveThreshold( 200, 0);
+                
+                //cvGrayImage1.contrastStretch();
+                //cvGrayImage2.contrastStretch();
+                
+                cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
+                
+                //cvGrayDiff1.brightnessContrast(1.0,0.5);
+                
+                //cvGrayImage1.brightnessContrast(1.0,0.5);
+                //cvGrayImage2.brightnessContrast(1.0,0.5);
+                
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
                  */ 
                 
+                //DIFFERENCING THE BACKGROUND
+                
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+                
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(10);
     
 }
-
 void RelaxRateAnalysis::displayresults()
 {
         
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
-        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        //    cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
         while(!_image_shown){
             Thread::sleep(2);
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            cout << "didn't load image" << endl;
+            //      cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -156,6 +348,24 @@ void RelaxRateAnalysis::displayresults()
 void RelaxRateAnalysis::draw()
 {
 
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+    
+    light.enable();	
+    lightStatic.enable();
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(2.0f);
+    glPointSize(1.0f);
+    
+    ofEnableBlendMode(blendMode);
+        
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -289,47 +499,16 @@ void RelaxRateAnalysis::draw()
             
             _frame_cnt++;
             
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {  
-            
+                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
-            image2.bind();        
+                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
-            
-            RefractiveIndex::_shader.begin();
-            
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
                 }
 
-            RefractiveIndex::_shader.end();                
+            }
-            
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
             
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
         
         }
@@ -348,5 +527,438 @@ void RelaxRateAnalysis::save_cb(Timer& timer)
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
     saveImageAnalysis(file_name);
+    
+    
+}
+
+void RelaxRateAnalysis::cleanup()
+{
+}
+
+
+void RelaxRateAnalysis::clearcfindervect()
+{
+    for(int i = 0; i < cvContourFinderVect.size(); i++) {
+        rfiCvContourFinder* f = cvContourFinderVect[i];
+
+        // maybe it's erase here?  http://forum.openframeworks.cc/index.php/topic,3016.0.html
+        // cvContourFinderVect.erase(i);
+        
+        delete f;        
+    }
+    cvContourFinderVect.clear();
+    
+}
+
+void RelaxRateAnalysis::clearcfindervectdisplay()
+{
+    cvContourFinderVectDisplay.clear();
+}
+
+
+
+
+void RelaxRateAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> RelaxRateAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
 }
 

src/RelaxRateAnalysis.h

@@ -23,6 +23,7 @@ public:
     void acquire();
     void synthesise(); 
     void displayresults();
+    void cleanup();
 
     void draw();
     
@@ -30,6 +31,8 @@ public:
     
 protected:
     
+    void clearcfindervect();
+    void clearcfindervectdisplay();
     
     bool    _RUN_DONE;
     float     _flip, _level;
@@ -43,11 +46,45 @@ protected:
     
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    
+    vector<rfiCvContourFinder*>      cvContourFinderVect;
+    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling_x;
+    int vertexSubsampling_y;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
     
-    int algo;
-    int scale;
-    int draw_style;   
-    float line_width;
-    float point_size;
 
 };

src/ShadowScapesAnalysis.cpp

@@ -17,11 +17,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const double line_width_default = 0.5;
-
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -30,6 +25,57 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 1;
+    chooseColour            = 5;
+    multiplier              = 4.0;
+    
+    ofSetLineWidth(5.0f);
+    glPointSize(5.0f);
+    glEnable(GL_DEPTH_TEST);
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    ///setup light    
+    ofEnableLighting();    
+    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
+    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
+    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
+    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+    
+    glEnable(GL_LIGHT0);  
+    
+    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
+    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
+    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
+    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+    
+    glEnable(GL_LIGHT1);     
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
@@ -47,7 +93,7 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     DELTA_T_SAVE = 3*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 100 files
                                             // or 5 times per second = every 200 ms
     
-    _scanLineWidth = 300.0;
+    _scanLineWidth = 100.0;
     _run_cnt = 0;
     _save_cnt = 0;
     _synth_save_cnt = 0;
@@ -60,21 +106,48 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
         
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+        
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
        
     
-    ////---------
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:shadowscapes:algo", algo_default);
-    scale = RefractiveIndex::XML.getValue("config:algorithms:shadowscapes:scale", scale_default);
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:shadowscapes:draw_style", draw_style_default);
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:shadowscapes:line_width", line_width_default);
     
 }
 
@@ -102,50 +175,167 @@ void ShadowScapesAnalysis::acquire()
 
 void ShadowScapesAnalysis::synthesise()
 {
-    // we don't need to synthesise
+    //cout << "ShadowScapesAnalysis::saving synthesis...\n";
-    return;
     
-    /*
+    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
+      //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
-     if(_state == STATE_STOP) return;
         
-     _RUN_DONE = false;
+        // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
-     
-     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-     while(!_RUN_DONE && _state != STATE_STOP)
-     Thread::sleep(3);
-     */
-}
-
-
-void ShadowScapesAnalysis::displayresults()
-{
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
                 
-        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
-        
-        while(!_image_shown){
-            Thread::sleep(2);
-            //cout << "!_image_shown" << endl;
-        }
-        
-        _show_image = false;
-        
-        
         if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
+            //    cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                //cvGrayDiff1.erode();
+                
+                cvGrayImage1.dilate();
+                cvGrayImage1.blur(5);
+                cvGrayImage1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef());  
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */ 
+                
+                //DIFFERENCING THE BACKGROUND
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-backgroundPixels[i]>0){
+                 imagePixels1[i]-=backgroundPixels[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+        
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShadowScapeAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+                
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+    }
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+     while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+}
+
+
+void ShadowScapesAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+       // cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
     }
+
 }
 
 
@@ -333,47 +523,27 @@ void ShadowScapesAnalysis::draw()
             
             _frame_cnt++;
             
+            if (_show_image)
+            {  
+              //  cout << "_show_image...\n" << endl;
                 
                 ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
                 
-            RefractiveIndex::cam.begin();
+                    ofSetColor(255, 255, 255);
                 
-            ofTranslate(tx, ty, tz);
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
+                    image2.draw(0,0, ofGetWidth(), ofGetHeight());
-            glScalef(1.5, 1, 1);
                 
-            if (_show_image)
+                ofDisableAlphaBlending();
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
                 
-            image2.bind();        
                 
-            RefractiveIndex::_shader.begin();
-            
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             _RUN_DONE = true;
+            
+            // clear allocated memory...? 
+            
             break;
         }
             
@@ -406,3 +576,413 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     saveImageAnalysis(file_name);
         
 }
+
+
+
+
+void ShadowScapesAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> ShadowScapesAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            
+            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
+            
+            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
+            
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/ShadowScapesAnalysis.h

@@ -42,13 +42,44 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
     bool _show_image, _image_shown;
-        
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
-    int algo;
-    int scale;
-    int draw_style;    
-    double line_width;
 
 };

src/ShapeFromShadingAnalysis.cpp

@@ -13,13 +13,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
-
-
 void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 {       
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -28,6 +21,56 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 1;
+    chooseColour            = 5;
+    multiplier              = 3.0;
+    
+    ofSetLineWidth(5.0f);
+    glPointSize(5.0f);
+
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    ///setup light    
+    ofEnableLighting();    
+    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
+    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
+    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
+    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+    
+    glEnable(GL_LIGHT0);  
+    
+    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
+    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
+    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
+    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+    
+    glEnable(GL_LIGHT1);  
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;
@@ -54,21 +97,50 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
     
-    image1.setUseTexture(false);  
+    //  images use for drawing the synthesized files to the screen ///
-    image2.setUseTexture(true);  
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
     
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
-    ////---------
+   // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+   // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:algo", algo_default);
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    scale = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:scale", scale_default);
+    // that we're getting in OSX/Windows and is maybe crashing Windows
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:draw_style", draw_style_default);
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:line_width", line_width_default);        
+    cvColorImage1.clear();
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:point_size", point_size_default);
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
     
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -124,46 +196,207 @@ void ShapeFromShadingAnalysis::acquire()
 
 void ShapeFromShadingAnalysis::synthesise()
 {
-    // we don't need to synthesise
+   // cout << "ShapeFromShadingAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
-     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    //    cout << "ShapeFromShadingAnalysis::synthesis FOR LOOP...\n";
-     while(!_RUN_DONE && _state != STATE_STOP)
-     Thread::sleep(3);
-     */
         
-    
+     //   cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
-}
-
-void ShapeFromShadingAnalysis::displayresults()
-{
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
-        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
-        
-        while(!_image_shown){
-            Thread::sleep(2);
-            //cout << "!_image_shown" << endl;
-        }
-        
-        _show_image = false;
-        
-        
         if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
+        //    cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                if(_saved_filenames_analysis[i].find("QUAD1")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameQuad = "QUAD1";
+                    cout<<"FOUND QUAD1"<<endl;
+                } else if (_saved_filenames_analysis[i].find("QUAD2")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameQuad = "QUAD2";
+                    cout<<"FOUND QUAD2"<<endl;
+                } else if(_saved_filenames_analysis[i].find("QUAD3")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameQuad = "QUAD3";
+                    cout<<"FOUND QUAD3"<<endl;
+                } else if(_saved_filenames_analysis[i].find("QUAD4")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameQuad = "QUAD4";
+                    cout<<"FOUND QUAD4"<<endl;
+                }
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                //cvGrayDiff1.erode();
+                
+                cvGrayImage1.dilate();
+                cvGrayImage1.blur(5);
+                cvGrayImage1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef());  
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */ 
+                
+                //DIFFERENCING THE BACKGROUND
+                /*
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+                */
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                if(fileNameQuad=="QUAD1")
+                {       
+                    
+                    //with jpgs this was refusing to save out
+                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
+                    _saved_filenames_synthesis.push_back(meshFileName);
+                    
+                    
+                } else if(fileNameQuad=="QUAD2")
+                {
+                    
+                    //with jpgs this was refusing to save out
+                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
+                    _saved_filenames_synthesis.push_back(meshFileName);
+                    
+                } else if(fileNameQuad=="QUAD3")
+                {
+                    
+                    //with jpgs this was refusing to save out
+                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
+                    _saved_filenames_synthesis.push_back(meshFileName);
+                
+                } else if(fileNameQuad=="QUAD4") {
+                    
+                    
+                    //with jpgs this was refusing to save out
+                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
+                    _saved_filenames_synthesis.push_back(meshFileName);
+        
+                }
+
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+    }
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);    
+    
+}
+
+void ShapeFromShadingAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+       // cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -175,6 +408,48 @@ void ShapeFromShadingAnalysis::displayresults()
 void ShapeFromShadingAnalysis::draw()
 {
     
+    //rotate light around origin ofviewspace    
+    float xx=cos(ofGetElapsedTimef()*0.4)*150;    
+    float yy=sin(ofGetElapsedTimef()*0.4)*150;    
+    float zz=0;
+    
+    if(fileNameQuad=="QUAD1")
+    {       
+        
+        GLfloat light_position[] = { 1000, 1000, 20, 0.0 };  
+        GLfloat light_position1[] = { 1000, 1000, 20, 0.0 };  
+        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+        
+    } else if(fileNameQuad=="QUAD2")
+    {
+    
+        GLfloat light_position[] = { 1000, -1000, 20, 0.0 };  
+        GLfloat light_position1[] = { 1000, -1000, 20, 0.0 };  
+        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+
+        
+    } else if(fileNameQuad=="QUAD3")
+    {
+      
+        GLfloat light_position[] = {-1000, 1000, 20, 0.0 };  
+        GLfloat light_position1[] = { -1000, 1000, 20, 0.0 };  
+        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+
+        
+    } else if(fileNameQuad=="QUAD4") 
+    {
+        GLfloat light_position[] = { -1000, -1000, 20, 0.0 };  
+        GLfloat light_position1[] = { -1000, -1000, 20, 0.0 };  
+        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+
+    }
+
+    
+    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -477,6 +752,8 @@ void ShapeFromShadingAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {   
+         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -485,50 +762,23 @@ void ShapeFromShadingAnalysis::draw()
             
             _frame_cnt++;
             
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {  
+            //    cout << "_show_image...\n" << endl;
                 
-            image2.bind();        
+                ofEnableAlphaBlending();
                 
-            RefractiveIndex::_shader.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
+                ofDisableAlphaBlending();
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
+            _RUN_DONE = true;
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             break;
             
-            
         }
             
             
@@ -548,3 +798,412 @@ void ShapeFromShadingAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
+
+
+
+void ShapeFromShadingAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> ShapeFromShadingAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            
+            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
+            
+            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
+            
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+        
+            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/ShapeFromShadingAnalysis.h

@@ -31,6 +31,8 @@ public:
 protected:
     
     string quad;
+    string fileNameQuad;
+    
     bool    _RUN_DONE;
     float     _flip, _level;
     int _animation_cnt1;
@@ -55,14 +57,46 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
    
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    int algo;
+    ofxCvColorImage         cvColorImage1;
-    int scale;
+    ofxCvColorImage         cvColorImage2;
-    int draw_style;   
+    ofxCvColorImage         cvColorImage3;
-    float line_width;
+    ofxCvColorImage         cvColorImage4;
-    float point_size;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
     
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 };

src/StrobeAnalysis.cpp

@@ -13,12 +13,6 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    30
 
-const int algo_default = 1;
-const int scale_default = 500;
-const int draw_style_default = 3;
-const int line_width_default = 0.5f;
-const float point_size_default = 0.5f;
-
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
     AbstractAnalysis::setup(camWidth, camHeight);
@@ -27,6 +21,28 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 3;
+    chooseColour            = 2;
+    multiplier              = 4.0;
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+
+    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
@@ -54,24 +70,47 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     
     image1.clear();
     image2.clear();
-    image1.clear();
+    image3.clear();  
-    image2.clear();
+    image4.clear();
+    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
     image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
+   // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+   // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    ////---------
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
-    algo = RefractiveIndex::XML.getValue("config:algorithms:strobe:algo", algo_default);
-    scale = RefractiveIndex::XML.getValue("config:algorithms:strobe:scale", scale_default);
-    draw_style = RefractiveIndex::XML.getValue("config:algorithms:strobe:draw_style", draw_style_default);
-    line_width = RefractiveIndex::XML.getValue("config:algorithms:strobe:line_width", line_width_default);        
-    point_size = RefractiveIndex::XML.getValue("config:algorithms:strobe:point_size", point_size_default);
 
 }
 
@@ -108,45 +147,190 @@ void StrobeAnalysis::acquire()
 
 void StrobeAnalysis::synthesise()
 {
-    // we don't need to synthesise
+   // cout << "StrobeAnalysis::saving synthesis...\n";
-    return;
-    
-    /*
-     
-     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-     _RUN_DONE = false;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+    //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+        
+    //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+    //        cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+            //cvColorImage1.erode();
+            //cvColorImage1.erode();
+                //cvColorImage1.dilate();
+            
+            cvColorImage1.blur(1);
+            cvColorImage2.blur(1);
+            
+            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+            
+            //cvGrayImage1.convertToRange(0.0, 255.0);
+            //cvGrayImage2.convertToRange(0.0, 255.0);
+            
+            //cvGrayImage1.adaptiveThreshold( 200, 0);
+            //cvGrayImage2.adaptiveThreshold( 200, 0);
+            
+            //cvGrayImage1.contrastStretch();
+            //cvGrayImage2.contrastStretch();
+            
+            cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
+
+            cvGrayDiff1.brightnessContrast(1.0,0.5);
+            
+            //cvGrayImage1.brightnessContrast(1.0,0.5);
+            //cvGrayImage2.brightnessContrast(1.0,0.5);
+            
+            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+            
+            //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+            
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+            
+           
+            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+            
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+            // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+            //DIFFERENCING SUBSEQUENT IMAGES
+            /*
+             for(int i=0;i<imagePixels1.size();i++){
+             //unsigned char val=imagePixels1[i];
+             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+             if(imagePixels1[i]-imagePixels2[i]>0){
+             imagePixels1[i]-=imagePixels2[i];
+             }
+             else{
+             imagePixels1[i]=0;
+             }
+             }
+            */ 
+             
+            //DIFFERENCING THE BACKGROUND
+            
+             for(int i=0;i<imagePixels1.size();i++){
+             //unsigned char val=imagePixels1[i];
+             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+             if(imagePixels1[i]-backgroundPixels[i]>0){
+             imagePixels1[i]-=backgroundPixels[i];
+             }
+             else{
+             imagePixels1[i]=0;
+             }
+             }
+            
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
     while(!_RUN_DONE && _state != STATE_STOP)
-     Thread::sleep(3);
+        Thread::sleep(10);
-     */
+
 }
 
 void StrobeAnalysis::displayresults()
 {
     
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
         
-        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+    //    cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
         while(!_image_shown){
             Thread::sleep(2);
             //cout << "!_image_shown" << endl;
         }
         
-        _show_image = false;
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            cout << "didn't load image" << endl;
+      //      cout << "didn't load image" << endl;
         } 
         
-        if(image1.loadImage(_saved_filenames_analysis[i])){
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -160,6 +344,27 @@ void StrobeAnalysis::displayresults()
 void StrobeAnalysis::draw()
 {
     
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+    
+    light.enable();	
+    lightStatic.enable();
+    
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+    
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(5.0f);
+    
+    ofEnableBlendMode(blendMode);
+
+    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -178,7 +383,6 @@ void StrobeAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     //cout <<  "FADE IN STROBE TIME " << endl;
 
-                    
                 }
                 
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max-_fade_in_frames)){
@@ -210,6 +414,7 @@ void StrobeAnalysis::draw()
                 }         
     
                 ofDisableAlphaBlending();
+                
             } else {
                 //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
@@ -306,6 +511,8 @@ void StrobeAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             
+         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -314,47 +521,21 @@ void StrobeAnalysis::draw()
             
             _frame_cnt++;
             
-            ofEnableAlphaBlending();
-            glShadeModel(GL_SMOOTH);
-            glLineWidth(line_width);
-            glPointSize(point_size);
-            glEnable(GL_POINT_SMOOTH);
-            
-            RefractiveIndex::cam.begin();
-            
-            ofTranslate(tx, ty, tz);
-            ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            glScalef(1.5, 1, 1);
-            
             if (_show_image)
-                image2.setFromPixels(image1.getPixels(), image1.width, image1.height, OF_IMAGE_COLOR);
+            {  
+         //       cout << "_show_image...\n" << endl;
                 
-            image2.bind();        
+                ofEnableAlphaBlending();
                 
-            RefractiveIndex::_shader.begin();
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-            RefractiveIndex::_shader.setUniform1i("algo", algo);
+                ofDisableAlphaBlending();
-            RefractiveIndex::_shader.setUniform1f("scale", scale);
-            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-            
-            switch (draw_style) {
-                case VERTS:
-                    RefractiveIndex::_mesh_vbo.drawVertices();
-                    break;
-                case WIRE:
-                    RefractiveIndex::_mesh_vbo.drawWireframe();
-                    break;
-                case FACE:
-                    RefractiveIndex::_mesh_vbo.drawFaces();
-                    break;            
             }
             
-            RefractiveIndex::_shader.end();                
+            // display results of the synthesis
-            
+            _RUN_DONE = true;
-            image2.unbind();
-            
-            RefractiveIndex::cam.end();    
-            
             break;
 
 
@@ -376,3 +557,408 @@ void StrobeAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
+
+void StrobeAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> StrobeAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/StrobeAnalysis.h

@@ -41,14 +41,44 @@ protected:
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
-    int algo;
-    int scale;
-    int draw_style;   
-    float line_width;
-    float point_size; 
 
 };