shaders all analysis

all analysis are now shadered

README

@@ -1,10 +1,10 @@
 WARNING: WORK IN PROGRESS...
 
-configuring OpenFrameworks
+configuring OpenFrameworks under Xcode
------------------
+---------------------------------------
 
 these files are configured according to OpenFrameworks addons - http://ofxaddons.com/howto
 
 (1) drag-drop "ReflectiveIndex" folder into your OpenFrameworks project
-(2) Install depedencies: {ofxDirList, ofxControlPanel, ofxXmlSettings};  
+(2) Install depedencies: {ofxXmlSettings, ofxOpenCV, ofxFileHelper};  
 (3) Press Play!

config.refindx

@@ -0,0 +1,115 @@
+<!-- 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

@@ -0,0 +1,372 @@
+/*
+ ~ 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

@@ -0,0 +1,148 @@
+/*
+ ~ 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

@@ -0,0 +1,130 @@
+/*
+ ~ 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

@@ -0,0 +1,18 @@
+#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

@@ -0,0 +1,127 @@
+#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

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

example/RefractiveIndex.cpp

@@ -15,7 +15,12 @@
 
 #include "ofxXmlSettings.h"
 
-#define CAMERA_ID           1
+#include "ofxArcBall.h"
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#define CAMERA_ID           0
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
@@ -27,8 +32,26 @@
 #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;
 
+int              RefractiveIndex::_mode;
 ofPixels         RefractiveIndex::_pixels;
 ofVideoGrabber   RefractiveIndex::_vidGrabber;
 int              RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, RefractiveIndex::_vid_id;
@@ -38,8 +61,64 @@ 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);
+    
+    ofHideCursor();
+    
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -49,6 +128,10 @@ void RefractiveIndex::setup()
     } else {
         XML.loadFile("config.refindx");
     }
+    
+    // <mode>
+    string m = XML.getValue("config:mode", "analysing");
+    _mode = (m == "analysing" ? MODE_ANALYSING : (m == "drawing" ? MODE_DRAWING : MODE_ANALYSING));
         
     // <camera>
     _vid_id = XML.getValue("config:camera:id", CAMERA_ID);
@@ -82,47 +165,41 @@ void RefractiveIndex::setup()
     cout << "* cam width = " << _vid_w << endl;
     cout << "* cam height = " << _vid_h << endl;
     
-    _vid_stream_open = false;    
+    if(_mode == MODE_ANALYSING) {
-    setup_camera();
+        _vid_stream_open = false;    
+        setup_camera();
+    }
     
     cout << "RRRRRREADY!" << endl;        
 
     _analysisAdapator = NULL;
 
-    //getting a warning from the OFlog that the pixels aren't allocated
+    _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR_ALPHA); 
-    //void ofPixels::allocate(int w, int h, ofImageType type)    
-    _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR); 
     
     
-    //TODO:  whichever one of these is first - it always runs twice ?
+    setup_shader_vbo();
     
-    _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
-    _analysisVector.push_back(new ShadowScapesAnalysis(H));
-    _analysisVector.push_back(new ShadowScapesAnalysis(D));
     
-    _analysisVector.push_back(new RelaxRateAnalysis());
+    //TODO:  whichever one of these is first - it always runs twice ?    
     
-    _analysisVector.push_back(new IResponseAnalysis());
+    _analysisVector.push_back(new ShadowScapesAnalysis(V)); //1
-    
+    _analysisVector.push_back(new ShadowScapesAnalysis(H)); //2
-    _analysisVector.push_back(new ShapeFromShadingAnalysis());
+    _analysisVector.push_back(new ShadowScapesAnalysis(D)); //3
-    
+    _analysisVector.push_back(new RelaxRateAnalysis());     //4
-    _analysisVector.push_back(new StrobeAnalysis());
+    _analysisVector.push_back(new IResponseAnalysis());     //5
-    
+    _analysisVector.push_back(new ShapeFromShadingAnalysis()); //6   
-    _analysisVector.push_back(new CamNoiseAnalysis());
+    _analysisVector.push_back(new StrobeAnalysis());        //7
-    
+    _analysisVector.push_back(new CamNoiseAnalysis());      //8
-    _analysisVector.push_back(new ColorSingleAnalysis());
+    _analysisVector.push_back(new ColorSingleAnalysis());   //9
-    
+    _analysisVector.push_back(new ColorMultiAnalysis());    //10
-    _analysisVector.push_back(new ColorMultiAnalysis());
+    _analysisVector.push_back(new DiffNoiseAnalysis());	    //11
-    
-    _analysisVector.push_back(new DiffNoiseAnalysis());
-
-    //_currentAnalysisIndx = 0;
-    //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
-    //_state = ISTATE_START;
     
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
     
+    // disbale <ESC> ?
+    //ofSetEscapeQuitsApp(false);
+    
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
@@ -163,7 +240,6 @@ void RefractiveIndex::state_analysis()
                 _currentAnalysisIndx = 0;
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;                
-                //_state = ISTATE_END;
             } else {
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;
@@ -171,10 +247,14 @@ void RefractiveIndex::state_analysis()
             break;
         case ISTATE_STOP:
             stop_analysis(); // blocking
-            _state = ISTATE_TRANSITION;
+            if(_mode == MODE_DRAWING)
+                _state = ISTATE_UNDEF;
+            else
+                _state = ISTATE_TRANSITION;
             break;
         case ISTATE_END:
-            stop_camera();
+            if(_mode == MODE_ANALYSING)
+                stop_camera();
             ::exit(1);
             break;
         case ISTATE_UNDEF:
@@ -190,10 +270,7 @@ 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);
            
@@ -232,15 +309,10 @@ 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)
@@ -346,53 +418,13 @@ void RefractiveIndex::keyPressed  (int key)
         _currentAnalysisIndx = 10;
         if(!_currentAnalysis)
             _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()
 {
+    if(_currentAnalysis)
+        _analysisAdapator->stop();    
     stop_camera();
 }

example/RefractiveIndex.h

@@ -11,6 +11,15 @@
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.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:
@@ -29,6 +38,8 @@ public:
     void stop_analysis();
     void state_analysis();
     
+    void setup_shader_vbo();
+    
     // ofx
     void keyPressed  (int key);
     void keyReleased(int key){;}
@@ -55,6 +66,8 @@ public:
     // acquisition
     static ofPixels         _pixels;    
     static ofVideoGrabber   _vidGrabber;
+    static int              _mode;
+    
     vector<string>          videoSourceList;    
     static int              _vid_w, _vid_h, _vid_id;
     static bool             _vid_stream_open;
@@ -64,4 +77,16 @@ public:
     static string           _location;
     static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
     
+    
+    static ofVboMesh       _mesh_vbo;
+    
+    vector<ofVec3f> _verts;
+    vector<ofVec2f> _tex;
+    vector<unsigned int> _ind;
+    
+    static ofxArcBall cam;
+    
+    static ofShader        _shader;
+    
+    
 };

example/main.cpp

@@ -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

@@ -3,32 +3,88 @@
 #include "AbstractAnalysis.h"
 #include "RefractiveIndex.h"
 #include "ofxFileHelper.h"
+#include "ofSystemUtils.h"
+
+void AbstractAnalysis::setup(int camWidth, int camHeight) {
+    
+    _cam_w = camWidth; _cam_h = camHeight;
+    
+    if(RefractiveIndex::_mode == MODE_DRAWING) {
+        ofFileDialogResult r = ofSystemLoadDialog("choooose da folda", true);
+        if(!r.bSuccess) {
+            ofSystemAlertDialog("OOOOPS.... ERROR...");
+            return;
+        }
+                
+        _whole_file_path_analysis = r.filePath;
+        _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
 void AbstractAnalysis::do_synthesize() {
     
-    for(int i = 0; i < NUM_RUN; i++) {
+    switch(RefractiveIndex::_mode)
-        
+    {
-        cout << "i NUM_RUN" << i << endl;
+        case MODE_ANALYSING:
+        {
+            for(int i = 0; i < NUM_RUN; i++) {
                 
-        _saved_filenames_analysis.clear();  
+                cout << "NUM_RUN: " << i << endl;
-        _saved_filenames_synthesis.clear();    
+                
-        
+                _saved_filenames_analysis.clear();  
-        _state = STATE_ACQUIRING;
+                _saved_filenames_synthesis.clear(); 
-        acquire();
+                
-        if(_state == STATE_STOP) goto exit;
+                _state = STATE_ACQUIRING;
-        _state = STATE_SYNTHESISING;
+                acquire();
-        synthesise();
+                if(_state == STATE_STOP) goto exit;
-        if(_state == STATE_STOP) goto exit;
+                _state = STATE_SYNTHESISING;
-        _state = STATE_DISPLAY_RESULTS;
+                synthesise();
-        displayresults();
+                if(_state == STATE_STOP) goto exit;
+                _state = STATE_DISPLAY_RESULTS;
+                displayresults();
+            }       
+            
+            break;
+        }
+            
+        case MODE_DRAWING:
+        {            
+            ofxFileHelper fileHelperDrawing;
+            if(!fileHelperDrawing.doesDirectoryExist(_whole_file_path_synthesis)){
+                fileHelperDrawing.makeDirectory(_whole_file_path_synthesis);
+            }            
+            
+            read_dir_create_list(_whole_file_path_analysis);
+            _state = STATE_SYNTHESISING;
+            synthesise();
+            if(_state == STATE_STOP) goto exit;
+            _state = STATE_DISPLAY_RESULTS;
+            displayresults();   
+            
+            break;
+        }
     }
     
-    exit:    
+exit:    
-    ofNotifyEvent(_synthesize_cb, _name);
+    cleanup();
+    ofxFileHelper::deleteFolder(_whole_file_path_analysis);
+    ofNotifyEvent(_synthesize_cb, _name);    
+    
 }
 
-void AbstractAnalysis::create_dir()
+void AbstractAnalysis::create_dir_allocate_images()
 {
     // HERE IS WHERE WE SETUP THE DIRECTORY FOR ALL THE SAVED IMAGES
     
@@ -75,6 +131,7 @@ void AbstractAnalysis::create_dir()
         
     }
     
+    
     _whole_file_path_synthesis = SYNTHESIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime;
     
     if(!fileHelperSynthesis.doesDirectoryExist(_whole_file_path_synthesis)){
@@ -93,6 +150,118 @@ void AbstractAnalysis::create_dir()
         
     }
     
-    //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////    
+    //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////  
+    
+    
+    //////////////////////////////ALLOCATE IMAGES //////////////////////////////////////////////////  
+    
+    myColorImage1.clear();
+    myColorImage1.setUseTexture(false);
+    myColorImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
+
+    myColorImage2.clear();
+    myColorImage2.setUseTexture(false);
+    myColorImage2.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
+    
+    
+    myGrayImage1.clear();
+    myGrayImage1.setUseTexture(false);
+    myGrayImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_GRAYSCALE);
+    
+    //////////////////////////////END ALLOCATE IMAGES //////////////////////////////////////////////////  
+
+}
+
+bool cmp_file(string f0, string f1)
+{
+    int v0 = atoi(f0.substr(0, f0.find("_")).c_str());
+    int v1 = atoi(f1.substr(0, f1.find("_")).c_str());    
+    return v0 < v1;
+}
+
+void AbstractAnalysis::read_dir_create_list(string folder_path)
+{
+    File dir(folder_path);
+    
+    if(dir.exists() && dir.isDirectory()) {
+        vector<string> list;
+        dir.list(list);   
+        
+        std::sort(list.begin(), list.end(), cmp_file);
+        
+        for(int i = 0; i < list.size(); i++) {
+            string filepath = folder_path + "/" + list[i]; 
+            _saved_filenames_analysis.push_back(filepath);
+        }                
+    }
+}
+
+void AbstractAnalysis::saveImageAnalysis(string filename)
+{
+    
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+        
+    } else {
+        return;
+    }
+        
+#ifdef TARGET_OSX   
+    
+    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+filename, OF_IMAGE_QUALITY_BEST);
+    
+#elif defined(TARGET_WIN32)    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = appPix.getPixels();
+    myColorImage1.setUseTexture(false);
+    myColorImage1.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myColorImage1.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+filename);
+    myColorImage1.clear();
+    
+#endif
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+filename);
+    
+}
+
+
+void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType)
+{
+    
+#ifdef TARGET_OSX   
+    
+
+    ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
+    
+#elif defined(TARGET_WIN32)    
+    
+    if (newType == OF_IMAGE_COLOR){
+       myColorImage2.setUseTexture(false);
+       myColorImage2.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
+       myColorImage2.saveImage(_whole_file_path_synthesis+"/"+filename);
+    }
+
+    if (newType == OF_IMAGE_GRAYSCALE){
+        myGrayImage1.setUseTexture(false);
+        
+        // THIS IS HOW YOU HAVE TO SAVE OUT THE GREYSCALE IMAGES on WINDOWS FOR SOME REASON --> i.e.: as an OF_IMAGE_COLOR
+        // But they don't save properly - they're spatially translated and generally f'd up
+        myGrayImage1.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
+        myGrayImage1.setImageType(OF_IMAGE_COLOR);
+        myGrayImage1.saveImage(_whole_file_path_synthesis+"/"+filename);
+        //myGrayImage1.clear();
+    }
+        
+#endif
+    
+    _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+filename);
+            
+    
 }
 

src/AbstractAnalysis.h

@@ -7,6 +7,7 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
+#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
@@ -24,7 +25,7 @@ public:
     virtual ~AbstractAnalysis(){;}
     
     // generic function to set up the camera
-    virtual void setup(int camWidth, int camHeight){_cam_w = camWidth; _cam_h = camHeight;}  
+    virtual void setup(int camWidth, int camHeight);  
 
     // this is the main threaded loop for a given analysis
     void do_synthesize();
@@ -34,7 +35,12 @@ public:
         
 protected:
     
-    virtual void create_dir();
+    virtual void create_dir_allocate_images();
+    
+    virtual void read_dir_create_list(string folder_path);
+    
+    virtual void saveImageAnalysis(string filename);
+    virtual void saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType);
     
     // acquire images - all the children (see - do_synthesize)
     virtual void acquire() = 0;   
@@ -44,9 +50,14 @@ protected:
     
     // display the results from disk
     virtual void displayresults() = 0;   
+    
+    // display the results from disk
+    virtual void cleanup() {;}   
+    
         
 public:
-    string  _name;    
+    string  _name;       
+    string  _draw_directory;
     
     // event
     ofEvent<string> _synthesize_cb;    
@@ -59,12 +70,20 @@ protected:
     
     int             _state;
     
+    ofImage         myColorImage1;
+    ofImage         myColorImage2;
+    ofImage         myGrayImage1;
+    
     //int             _run_cnt;
     
     float           DELTA_T_SAVE;
     int             NUM_PHASE;
     int             NUM_RUN;
-    int             NUM_SAVE_PER_RUN;    
+    int             NUM_SAVE_PER_RUN;  
+    
+    //viewport
+    
+    float tx, ty, tz, rx, ry, rz;    
     
     friend class AnalysisAdaptor;
 };

src/CamNoiseAnalysis.cpp

@@ -13,57 +13,66 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
     cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
-
     //NUM_RUN = 5;
-    
+
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_camnoise", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << 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 5 times per second = every 200 ms
-    
+
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
-    
+
     _frame_cnt = 0;
     _run_cnt = 0;
     _synth_save_cnt = 0;
-    
+
     c = 0;
-    
+
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
-        
+
-    //create_dir();
+    //create_dir_allocate_images();
 
     _show_image = false;
     _image_shown = false;
+
+    
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    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);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:camnoise:algo", algo_default);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:camnoise:scale", scale_default);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    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);
 
 }
 
@@ -77,7 +86,7 @@ void CamNoiseAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
 
     // RUN ROUTINE
     // for(int i = 0; i < NUM_RUN; i++) {
@@ -86,7 +95,7 @@ void CamNoiseAnalysis::acquire()
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-    
+
         while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
@@ -97,77 +106,28 @@ void CamNoiseAnalysis::acquire()
 }
 
 void CamNoiseAnalysis::synthesise()
-{   
+{
-    //cout << "CamNoiseAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
+    
+    /*
+     
+     //cout << "IResponseAnalysis::saving synthesis...\n";
+     if(_state == STATE_STOP) return;
+     
+     _RUN_DONE = false;
+     
+     // _saved_filenames_synthesis has processed all the files in the analysis images folder
+     while(!_RUN_DONE && _state != STATE_STOP)
+     Thread::sleep(3);
+     */
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        
-        //cout << "CamNoiseAnalysis::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);
-            
-            cvGrayImage1 = cvColorImage1;
-            //cvGrayImage2 = cvColorImage2;
-            
-            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-            cvGrayImage1.erode();
-            cvGrayImage1.erode();
-            cvGrayImage1.erode();
-            cvGrayImage1.blur();
-            cvGrayImage1.contrastStretch();
-            
-            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            string file_name;
-            
-            file_name = ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            
-            
-            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-           
-            
-            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            ofImage image;
-            //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
 
-            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-            image.setUseTexture(false);  
-            
-            image.setFromPixels(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
-            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-            
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-            _synth_save_cnt++;
-            
-            //}
-        }
-    }
-    
-    // _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_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -178,18 +138,20 @@ void CamNoiseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }
+    }        
 }
 
 
@@ -202,30 +164,30 @@ void CamNoiseAnalysis::draw()
             /// *** TODO  *** ///
             // still need to deal with latency frames here - i.e.: there are frames
             /// *** TODO  *** ///
-              
+
             if (_frame_cnt < _frame_cnt_max)
             {
-                
+
                 ofEnableAlphaBlending();
                 ofColor aColour;
-                
+
                 int _fade_in_frames = _frame_cnt_max/10;
                 float _number_of_grey_levels=5;
-                
+
                 float _frames_per_level = _frame_cnt_max / _number_of_grey_levels;
                 ofColor someColor;
-                
+
                  /*
                 if (_frame_cnt < _fade_in_frames) {
                     aColour.set(255, 255, 255, ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
                     ofSetColor(aColour);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
-                    //cout <<  "FADE IN STROBE TIME " << endl;    
+                    //cout <<  "FADE IN STROBE TIME " << endl;
                 }
                 */
                 //if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max)){
-                    
+
-        
+
                     for(int i=1;i<_number_of_grey_levels;i++){
                         if ( _frame_cnt >= _frames_per_level*(i-1) && +_frame_cnt < _frames_per_level * (i+1) ) {
                             //set colour to current grey level
@@ -233,11 +195,11 @@ void CamNoiseAnalysis::draw()
                             //cout << "c: " << c << endl;
                             someColor.set(c);
                         }
-                        
+
                         ofSetColor(someColor);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     }
-                    
+
                 //}
                 /*
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
@@ -245,92 +207,92 @@ void CamNoiseAnalysis::draw()
                         ofSetColor(aColour);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                         // cout <<  "FADE OUT STROBE TIME " << endl;
-                }         
+                }
                 */
                 ofDisableAlphaBlending();
-                
+
-    
+
             } else {
                // _state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
-            
+
             _frame_cnt++;
             break;
-       
+
         }
-            
+
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
-            
+
             //cout << "CamNoiseAnalysis = STATE_SYNTHESISING...\n";
-            
+
             // display animation of something while the synthesis in on-going...
             ofEnableAlphaBlending();
             ofSetRectMode(OF_RECTMODE_CENTER);
             ofPushMatrix();
             ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            
+
             if(_anim_cnt < _anim_cnt_max){
-                
+
                 ofColor aColour;
                 int rectSizeW = ofGetWidth()/4;
                 int rectSizeH = ofGetHeight()/4;
                 int _fade_in_frames = _anim_cnt_max/2;
-                
+
                 int c_anim = 10;
                 int fade;
-                
+
                 //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
-                
+
                 if (_anim_cnt < _fade_in_frames) {
                     //cout << "CamNoiseAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
-                    
+
                     fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
-                    
+
                     for (int i=0; i <= 15; i++){
                         c_anim = 0+17*i;
-                        
+
                         aColour.set(c_anim, c_anim, c_anim, fade);
                         ofSetColor(aColour);
-                        
+
                         ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
                         ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
                     }
                 }
-                
+
                 if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
-                    
+
                     for (int i=0; i <= 15; i++){
                         c_anim = 255;
                         aColour.set(c_anim, c_anim, c_anim, 255);
                         ofSetColor(aColour);
-                        
+
                         ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
                         ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
                     }
                 }
-                
+
                 if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
-                    
+
                     //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
                     fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
                     //cout << "fade down = " << fade << endl;
-                    
+
                     for (int i=0; i <= 15; i++){
-                        
+
                         c_anim = (17*i);
-                        
+
                         aColour.set(c_anim, c_anim, c_anim, 255-fade);
                         ofSetColor(aColour);
                         ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
                         ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
                     }
-                    
+
                 }
                 _anim_cnt++;
-                
+
             } else {
                 _RUN_DONE = true;
                 //_state = STATE_DISPLAY_RESULTS;
@@ -339,15 +301,13 @@ void CamNoiseAnalysis::draw()
             ofPopMatrix();
             ofSetRectMode(OF_RECTMODE_CORNER);
             ofDisableAlphaBlending();
-            
+
             break;
         }
-            
+
         case STATE_DISPLAY_RESULTS:
         {
-            
+
-            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -356,29 +316,55 @@ 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_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
-            break;
-        
-        }
             
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
+            break;
+
+        }
+
         default:
             break;
     }
-    
+
 
 }
 
@@ -387,39 +373,7 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
 
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "CamNoiseAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
-    
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 
+    saveImageAnalysis(file_name);
 }

src/CamNoiseAnalysis.h

@@ -37,27 +37,13 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size;    
-    ofxCvColorImage         cvColorImage6;
-    
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 };

src/ColorMultiAnalysis.cpp

@@ -12,17 +12,23 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
-    cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
     
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
+    cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_colormulti", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
-    
+
     //int acq_run_time = 35;  
     
     DELTA_T_SAVE = 1*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 200 files
@@ -30,7 +36,7 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     
     _frame_cnt = 0;
     _run_cnt = 0;
@@ -40,31 +46,26 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
-    //for an ofxOpenCv.h image i would like to use..."
-    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
-   
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    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);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:colormulti:algo", algo_default);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:colormulti:scale", scale_default);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    draw_style = RefractiveIndex::XML.getValue("config:algorithms:colormulti:draw_style", draw_style_default);
+    line_width = RefractiveIndex::XML.getValue("config:algorithms:colormulti:line_width", line_width_default);
 
 }
 
@@ -77,7 +78,7 @@ void ColorMultiAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -100,77 +101,25 @@ void ColorMultiAnalysis::acquire()
 void ColorMultiAnalysis::synthesise()
 {
     
-    //cout << "ColorMultiAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-        
+     
-        //cout << "ColorMultiAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
-        
+     _RUN_DONE = false;
-        if(_state == STATE_STOP) return;
+     
-        
+     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
+     while(!_RUN_DONE && _state != STATE_STOP)
-            //couldn't load image
+     Thread::sleep(3);
-            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(5);
-            cvColorImage1.erode();
-            cvColorImage1.erode();
-            cvColorImage1.dilate();
-            cvColorImage1.blur(5);
-            cvColorImage1.dilate();
-            cvColorImage1.dilate();
-            cvColorImage1.dilate();
-            cvColorImage1.dilate();
-            
-            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            string file_name;
-            
-            file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            
-            
-            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            
-            
-            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            ofImage image;
-            //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
-            
-            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-            image.setUseTexture(false);  
-           
-            image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-            
-            
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-            _synth_save_cnt++;
-            
-            // }
-        }
-    }
-    
-    // _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_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -181,13 +130,15 @@ void ColorMultiAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
@@ -329,8 +280,9 @@ 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);
@@ -344,7 +296,6 @@ void ColorMultiAnalysis::draw()
             
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -353,22 +304,48 @@ void ColorMultiAnalysis::draw()
             
             _frame_cnt++;
             
-            if (_show_image)
-            {  
-                //cout << "_show_image...\n" << endl;
                 
-                ofEnableAlphaBlending();
+            ofEnableAlphaBlending();
+            glShadeModel(GL_SMOOTH);
+            glLineWidth(line_width);              
                 
-                ofSetColor(255, 255, 255);
+                RefractiveIndex::cam.begin();
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
-                ofDisableAlphaBlending();
+                ofTranslate(tx, ty, tz);
-            }
+                ofRotateX(rx); ofRotateY(ry); ofRotateZ(rz);
-            
+                glScalef(1.5, 1, 1);
-            // display results of the synthesis
+                
-            _RUN_DONE = true;
+                if (_show_image)
-            break;
+                    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();                
+                
+                image2.unbind();
+                
+                RefractiveIndex::cam.end();    
+                
+                _RUN_DONE = true;
+                break;
             
         }
             
@@ -383,42 +360,9 @@ void ColorMultiAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
-  
     _save_cnt++;
-    
+            
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ColorMultiAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-
+    saveImageAnalysis(file_name);    
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-    
 }

src/ColorMultiAnalysis.h

@@ -31,28 +31,14 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
-    ofxCvColorImage         cvColorImage6;
     
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 
 };

src/ColorSingleAnalysis.cpp

@@ -13,17 +13,23 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
-    cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
     
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
+    cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_colorsingle", ACQUIRE_TIME);
+    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
@@ -31,7 +37,7 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -50,25 +56,24 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    ////---------
-	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
-    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:algo", algo_default);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:scale", scale_default);
+    draw_style = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:draw_style", draw_style_default);
+    line_width = RefractiveIndex::XML.getValue("config:algorithms:colorsingle:line_width", line_width_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);
 }
 
 
@@ -82,7 +87,7 @@ void ColorSingleAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -104,87 +109,26 @@ void ColorSingleAnalysis::acquire()
 void ColorSingleAnalysis::synthesise()
 {
     
-    //cout << "ColorSingleAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-        
+     
-        //cout << "ColorSingleAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
-        
+     _RUN_DONE = false;
-        if(_state == STATE_STOP) return;
+     
-        
+     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
+     while(!_RUN_DONE && _state != STATE_STOP)
-            //couldn't load image
+     Thread::sleep(3);
-            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);
-                
-                //cvGrayImage1 = cvColorImage1;
-                //cvGrayImage2 = cvColorImage2;
-                
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                //cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
-            
-                cvColorImage1.blur(5);
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.dilate();
-                cvColorImage1.blur(5);
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-            
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-                
-                image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-            
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-                
-           // }
-        }
-    }
-    
-    // _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_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -195,18 +139,20 @@ void ColorSingleAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }
+    }    
     
 }
 
@@ -366,7 +312,6 @@ void ColorSingleAnalysis::draw()
             
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -375,20 +320,46 @@ void ColorSingleAnalysis::draw()
             
             _frame_cnt++;
             
+            
+            ofEnableAlphaBlending();
+            glShadeModel(GL_SMOOTH);
+            glLineWidth(line_width);              
+            
+            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);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             _RUN_DONE = true;
             break;
 
@@ -406,40 +377,7 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ColorSingleAnalysis::saving...\n";
-    
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-        
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
-
 }

src/ColorSingleAnalysis.h

@@ -38,28 +38,13 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;
-    ofxCvColorImage         cvColorImage4;
+    float line_width;    
-    ofxCvColorImage         cvColorImage5;
-    ofxCvColorImage         cvColorImage6;
-    
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 
 };

src/DiffNoiseAnalysis.cpp

@@ -13,15 +13,22 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    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;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:diffnoise_shadow", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
@@ -31,7 +38,7 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -44,28 +51,25 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    //for an ofxOpenCv.h image i would like to use..."
+    image1.clear();
-    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    ////---------
-	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
-    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:algo", algo_default);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:scale", scale_default);
+    draw_style = RefractiveIndex::XML.getValue("config:algorithms:diffnoise:draw_style", draw_style_default);
+    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);
     
-    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
 
@@ -77,7 +81,7 @@ void DiffNoiseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -100,76 +104,27 @@ void DiffNoiseAnalysis::acquire()
 void DiffNoiseAnalysis::synthesise()
 {   
     
-    //cout << "DiffNoiseAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-        
+     
-        //cout << "DiffNoiseAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
-        
+     _RUN_DONE = false;
-        if(_state == STATE_STOP) return;
+     
-        
+     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
+     while(!_RUN_DONE && _state != STATE_STOP)
-            //couldn't load image
+     Thread::sleep(3);
-            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.invert();
-            cvColorImage1.blur(5);
-            cvColorImage1.erode();
-            cvColorImage1.erode();
-            cvColorImage1.blur(5);
-            cvColorImage1.erode();
-            cvColorImage1.erode();
-            
-            //////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            string file_name;
-            
-            file_name = ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            
-            
-            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            
-            
-            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            ofImage image;
-            //image.allocate(cvColorImage1.width, cvGrayImage1.height, OF_IMAGE_COLOR);
-            
-            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-            image.setUseTexture(false);  
-            
-            image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-            
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-            _synth_save_cnt++;
-            
-            // }
-        }
-    }
-    
-    // _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_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -180,19 +135,20 @@ void DiffNoiseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }    
+    }         
-    
     
 }
 
@@ -363,9 +319,6 @@ void DiffNoiseAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {
-            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -374,22 +327,47 @@ 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);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                //image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                
+            
-                ofDisableAlphaBlending();
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             break;
             
         }
@@ -402,40 +380,8 @@ void DiffNoiseAnalysis::draw()
 void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-    
+            
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "DiffNoiseAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
 }

src/DiffNoiseAnalysis.h

@@ -36,27 +36,14 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size;
-    ofxCvColorImage         cvColorImage6;
     
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 };

src/IResponseAnalysis.cpp

@@ -13,17 +13,26 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
+        
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
     cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
-
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_iresponse", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME IResponseAnalysis " << acq_run_time << 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
@@ -31,7 +40,7 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -43,27 +52,24 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
-    
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
-    
-    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:iresponse:algo", algo_default);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:iresponse:scale", scale_default);
+    draw_style = RefractiveIndex::XML.getValue("config:algorithms:iresponse:draw_style", draw_style_default);
+    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);    
 }
 
 
@@ -76,7 +82,7 @@ void IResponseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
 
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -98,80 +104,27 @@ void IResponseAnalysis::acquire()
 void IResponseAnalysis::synthesise()
 {
     
-    //cout << "IResponseAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
-    
-    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 //////////////////////////
-                
-                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
-                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                               
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-                
-                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-                
-                
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-                
-            }
-        }
-    }
-
-    // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    while(!_RUN_DONE && _state != STATE_STOP)
-        Thread::sleep(3);
     
+    /*
+     
+     //cout << "IResponseAnalysis::saving synthesis...\n";
+     if(_state == STATE_STOP) return;
+     
+     _RUN_DONE = false;
+     
+     // _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_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -182,18 +135,20 @@ void IResponseAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            // cout << "didn't load image" << endl;
+            cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }
+    }        
 }
 
 
@@ -329,8 +284,6 @@ void IResponseAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {
-            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -339,21 +292,47 @@ void IResponseAnalysis::draw()
             
             _frame_cnt++;
             
-            if (_show_image)
+            ofEnableAlphaBlending();
-            {  
+            glShadeModel(GL_SMOOTH);
-                //cout << "_show_image...\n" << endl;
+            glLineWidth(line_width);
-                
+            glPointSize(point_size);
-                ofEnableAlphaBlending();
+            glEnable(GL_POINT_SMOOTH);
-                
-                ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
             
-                ofDisableAlphaBlending();
+            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);
+            
+            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;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             break;
             
         }
@@ -369,38 +348,7 @@ void IResponseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "IResponseAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
+        
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }

src/IResponseAnalysis.h

@@ -35,27 +35,14 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size;
-    ofxCvColorImage         cvColorImage6;
     
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 };

src/RelaxRateAnalysis.cpp

@@ -13,25 +13,30 @@ 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 RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
-    cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
-
-    //NUM_RUN = 5;
- 
-    int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_relaxrate", ACQUIRE_TIME);
-    cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
     
-    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_relaxrate", NUMBER_RUNS);
+    cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    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;
     
     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
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _level = 0;
@@ -46,25 +51,24 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    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);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:algo", algo_default);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:relaxrate:scale", scale_default);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    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);
     
 }
 
@@ -78,7 +82,7 @@ void RelaxRateAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
 
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -98,76 +102,28 @@ void RelaxRateAnalysis::acquire()
 
 void RelaxRateAnalysis::synthesise()
 {
+    // we don't need to synthesise
+    return;
+    
+    /*
+    
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    _RUN_DONE = false;
-        
-        //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 //////////////////////////
-                
-                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
-                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                cvGrayDiff1.blur(5);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-                
-                
-                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-                
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-            }
-        }
-    }
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
+     */
+
     
 }
 
 void RelaxRateAnalysis::displayresults()
 {
-    
+        
-    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
         
         if(_state == STATE_STOP) return;
         
@@ -178,19 +134,20 @@ void RelaxRateAnalysis::displayresults()
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            // cout << "didn't load image" << endl;
+            cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }
+    }        
-
     
 }
 
@@ -202,10 +159,8 @@ void RelaxRateAnalysis::draw()
     switch (_state) {
         case STATE_ACQUIRING:
         {
-            /// *** TODO  *** ///
+            
-            // still need to deal with latency frames here - i.e.: there are frames
+            
-            /// *** TODO  *** ///
-           
             if (_frame_cnt < _frame_cnt_max)
             {
                 
@@ -235,6 +190,7 @@ void RelaxRateAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
+            
             // display animation of something while the synthesis in on-going...
             
             //cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
@@ -287,7 +243,7 @@ void RelaxRateAnalysis::draw()
                     }
                 }
                 
-                cout << "_anim_cnt = " << _anim_cnt << endl;
+                //cout << "_anim_cnt = " << _anim_cnt << endl;
                 
                 if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
 
@@ -332,22 +288,48 @@ 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);
-                //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_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             break;
         
         }
@@ -363,37 +345,8 @@ void RelaxRateAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    //cout << "RelaxRateAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    
+    saveImageAnalysis(file_name);        
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }
+

src/RelaxRateAnalysis.h

@@ -5,8 +5,12 @@
 
 #include "Poco/Timer.h"
 
+#include "rfiCvContourFinder.h"
+
 #include "ofxOpenCv.h"
 
+
+
 class RelaxRateAnalysis : public AbstractAnalysis
 {
 public:
@@ -26,34 +30,24 @@ public:
     
 protected:
     
+    
     bool    _RUN_DONE;
     float     _flip, _level;
     int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
+    int     _treshold;
+    int     _maxblobs;
+    
     bool _show_image, _image_shown;
+    
     ofImage         image1;
     ofImage         image2; 
-    ofImage         image3;
-    ofImage         image4;
-    ofImage         image5; 
-    ofImage         image6; 
     
-    ofxCvColorImage         cvColorImage1;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size;
-    ofxCvColorImage         cvColorImage6;
-    
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 
 };

src/ShadowScapesAnalysis.cpp

@@ -17,14 +17,21 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
     cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shadowscapes", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
     
     int screenSpan;
@@ -39,10 +46,8 @@ 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
-    //DELTA_T_SAVE = 1;
+    
-    //create_dir();  // this makes both synth and analysis folder structures
+    _scanLineWidth = 300.0;
-
-    _scanLineWidth = 100.0;
     _run_cnt = 0;
     _save_cnt = 0;
     _synth_save_cnt = 0;
@@ -53,25 +58,24 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.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);
     
-    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
-    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);
+    
 }
 
 void ShadowScapesAnalysis::acquire()
@@ -85,161 +89,63 @@ void ShadowScapesAnalysis::acquire()
     _line = 0;
     _RUN_DONE = false;
 
-    create_dir();
+    create_dir_allocate_images();
-    
-    //cout << "RUN NUM = " << i;
    
     save_timer.start(save_callback);
       
-        while(!_RUN_DONE && _state != STATE_STOP)
+    while(!_RUN_DONE && _state != STATE_STOP)
-            Thread::sleep(3);
+        Thread::sleep(3);
     
     save_timer.stop();
-    
-    //}
 
 }
 
 void ShadowScapesAnalysis::synthesise()
 {
-    //cout << "ShadowScapesAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-    
+     
-      //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-        // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
+     _RUN_DONE = false;
+     
+     // _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])){
-            
-            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);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                cvGrayDiff1.blur(5);
-                cvGrayDiff1.dilate();
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                if(_dir == H) {
-                    file_name = ofToString(_synth_save_cnt, 2)+"_H_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                }
-                
-                if(_dir == V) {
-                    file_name = ofToString(_synth_save_cnt, 2)+"_V_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                }    
-                
-                if(_dir == D) {
-                    file_name = ofToString(_synth_save_cnt, 2)+"_D_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                }
-                
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-                
-                
-                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-                
-            }
-        }
-    }
-    
-    // _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;
         }
-    }
+    }    
-    
-    
-    // THE OLD SHIT /// 
-/*
-    for(float i=1;i<_saved_filenames_synthesis.size()-1;i++){
-        
-       // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
-        
-        if(_state == STATE_STOP) return;
-        
-        while(!_image_shown){
-            Thread::sleep(2);
-            //cout << "!_image_shown" << endl;
-        }
-        
-        if(!image1.loadImage(_saved_filenames_synthesis[i])){
-            //couldn't load image
-            cout << "didn't load image" << endl;
-        } 
-        
-            
-        if(image1.loadImage(_saved_filenames_analysis[i])){
-            
-            image1.loadImage(_saved_filenames_analysis[i]);
-            cout << "loaded filenames[i] -  " << _saved_filenames_analysis[i] << endl;
-        
-            image2.setFromPixels(image1.getPixels(),image1.width,image1.height, OF_IMAGE_COLOR);
-          
-            //cout << "_show_image = true;" << endl;
-            _show_image = true;
-            _image_shown = false;
-
-        }
-    }
-*/
-    
 }
 
 
@@ -418,7 +324,6 @@ void ShadowScapesAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-
             
             if (_frame_cnt > 2)
             {
@@ -428,22 +333,46 @@ void ShadowScapesAnalysis::draw()
             
             _frame_cnt++;
             
+            
+            ofEnableAlphaBlending();
+            glShadeModel(GL_SMOOTH);
+            glLineWidth(line_width);
+            
+            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_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                    image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
-                
+            switch (draw_style) {
-                
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             _RUN_DONE = true;
             break;
         }
@@ -459,18 +388,7 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
 {
     
     _save_cnt++;
-    
+        
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ShadowScapesAnalysis::saving analysis...\n";
-    
     string file_name;
     
     if(_dir == H) {
@@ -484,27 +402,7 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     if(_dir == D) {
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
-    
+        
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
         
 }

src/ShadowScapesAnalysis.h

@@ -42,28 +42,13 @@ 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;
+    int algo;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
+    int scale;
-    
+    int draw_style;    
-    ofxCvGrayscaleImage 	cvGrayImage1;
+    double line_width;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 
 };

src/ShapeFromShadingAnalysis.cpp

@@ -13,18 +13,26 @@ using Poco::Thread;
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
 
-void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
+const int algo_default = 1;
-{    
+const int scale_default = 500;
-    
+const int draw_style_default = 3;
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+const int line_width_default = 0.5f;
-    cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
+const float point_size_default = 0.5f;
 
-   // NUM_RUN = 5;
+
+void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
+{       
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shapefromshading", NUMBER_RUNS);
+    cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shapefromshading", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << 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
@@ -32,7 +40,7 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -41,29 +49,26 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 5;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
     
-    
     _show_image = false;
     _image_shown = false;
     
-    //  images use for drawing the synthesized files to the screen ///
+    image1.clear();
-    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.clear();
-    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 ///
+    image1.setUseTexture(false);  
-    image3.setUseTexture(false);  
+    image2.setUseTexture(true);  
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-   // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-   // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
-    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);
+    algo = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:algo", algo_default);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    scale = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:scale", scale_default);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    draw_style = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:draw_style", draw_style_default);
+    line_width = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:line_width", line_width_default);        
+    point_size = RefractiveIndex::XML.getValue("config:algorithms:shapeshade:point_size", point_size_default);
+
 
 }
 
@@ -78,7 +83,7 @@ void ShapeFromShadingAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;    
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     _animation_cnt1 = 0;
     _animation_cnt2 = 0;
@@ -119,99 +124,51 @@ void ShapeFromShadingAnalysis::acquire()
 
 void ShapeFromShadingAnalysis::synthesise()
 {
-   // cout << "ShapeFromShadingAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-        
+     
-    //    cout << "ShapeFromShadingAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-     //   cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
+     _RUN_DONE = false;
+     
+     // _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_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);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-               
-                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-                
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-                
-            }
-        }
-    }
-    
-    // _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;
         }
-    }
+    }        
 }
 
 // this runs at frame rate = 33 ms for 30 FPS
@@ -520,8 +477,6 @@ void ShapeFromShadingAnalysis::draw()
             
         case STATE_DISPLAY_RESULTS:
         {   
-         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -530,22 +485,49 @@ 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_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
+            
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
             break;
+
             
         }
             
@@ -561,40 +543,8 @@ void ShapeFromShadingAnalysis::draw()
 void ShapeFromShadingAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-        
+            
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ShapeFromShadingAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ quad +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-    
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
 }

src/ShapeFromShadingAnalysis.h

@@ -55,27 +55,14 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size;
-    ofxCvColorImage         cvColorImage6;
     
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 };

src/StrobeAnalysis.cpp

@@ -13,17 +13,24 @@ 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)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
     cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
-
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_strobe", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
-    
+
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 100 files
@@ -35,7 +42,7 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 
     // The British Health and Safety Executive recommend that a net flash rate for a bank of strobe lights does not exceed 5 flashes per second, at which only 5% of photosensitive epileptics are at risk. It also recommends that no strobing effect continue for more than 30 seconds, due to the potential for discomfort and disorientation.
     
-    //create_dir();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     
@@ -45,26 +52,27 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image1.clear();
+    image2.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 ///
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.setUseTexture(false);  
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
     
-   // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-   // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    ////---------
-	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
-    cvGrayDiff1.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);
     
-    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 
@@ -77,7 +85,7 @@ void StrobeAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0;  _strobe_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -100,97 +108,50 @@ void StrobeAnalysis::acquire()
 
 void StrobeAnalysis::synthesise()
 {
-   // cout << "StrobeAnalysis::saving synthesis...\n";
+    // we don't need to synthesise
-    if(_state == STATE_STOP) return;
+    return;
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    /*
-        
+     
-    //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+     //cout << "IResponseAnalysis::saving synthesis...\n";
-        
+     if(_state == STATE_STOP) return;
-    //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+     
-        
+     _RUN_DONE = false;
-        if(_state == STATE_STOP) return;
+     
-        
+     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
+     while(!_RUN_DONE && _state != STATE_STOP)
-            //couldn't load image
+     Thread::sleep(3);
-    //        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);
-            
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-            
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.dilate();
-                cvGrayDiff1.dilate();
-                cvGrayDiff1.contrastStretch();
-               
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-        
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                ofImage image;
-                //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);    
-            
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image.setUseTexture(false);  
-                
-                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height,OF_IMAGE_GRAYSCALE);
-                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-                
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-                
-            }
-        }
-    }
-    
-    // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    while(!_RUN_DONE && _state != STATE_STOP)
-        Thread::sleep(3); 
 }
 
 void StrobeAnalysis::displayresults()
 {
     
-    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+    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;
+        //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])){
+        _show_image = false;
+        
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-      //      cout << "didn't load image" << endl;
+            cout << "didn't load image" << endl;
         } 
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
+        if(image1.loadImage(_saved_filenames_analysis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
-    }
+    }        
     
 }
 
@@ -345,8 +306,6 @@ void StrobeAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             
-         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -355,22 +314,48 @@ 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_GRAYSCALE);
+            RefractiveIndex::_shader.setUniform1i("algo", algo);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            RefractiveIndex::_shader.setUniform1f("scale", scale);
-                
+            RefractiveIndex::_shader.setUniform1i("tex0", 0);
-                ofDisableAlphaBlending();
+            
+            switch (draw_style) {
+                case VERTS:
+                    RefractiveIndex::_mesh_vbo.drawVertices();
+                    break;
+                case WIRE:
+                    RefractiveIndex::_mesh_vbo.drawWireframe();
+                    break;
+                case FACE:
+                    RefractiveIndex::_mesh_vbo.drawFaces();
+                    break;            
             }
             
-            // display results of the synthesis
+            RefractiveIndex::_shader.end();                
-            _RUN_DONE = true;
+            
-            break;
+            image2.unbind();
+            
+            RefractiveIndex::cam.end();    
+            
+            break;            
 
 
         }
@@ -385,41 +370,9 @@ void StrobeAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void StrobeAnalysis::save_cb(Timer& timer)
 {
-    _save_cnt++;
+    _save_cnt++;    
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "StrobeAnalysis::saving...\n";
     
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    
+    saveImageAnalysis(file_name);
-    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    somePixels = appPix.getPixels();
-
-    ofImage myImage;
-    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    
-    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    myImage.setUseTexture(false);
-    
-    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
 }

src/StrobeAnalysis.h

@@ -41,28 +41,14 @@ 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;
+    int algo;
-    ofxCvColorImage         cvColorImage2;
+    int scale;
-    ofxCvColorImage         cvColorImage3;
+    int draw_style;   
-    ofxCvColorImage         cvColorImage4;
+    float line_width;
-    ofxCvColorImage         cvColorImage5;
+    float point_size; 
-    ofxCvColorImage         cvColorImage6;
-    
-    ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
-    
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
 
 };

src/rficv/rfiCvContourFinder.cpp

@@ -0,0 +1,211 @@
+
+#include "rfiCvContourFinder.h"
+
+
+
+//--------------------------------------------------------------------------------
+static bool sort_carea_compare( const CvSeq* a, const CvSeq* b) {
+	// use opencv to calc size, then sort based on size
+	float areaa = fabs(cvContourArea(a, CV_WHOLE_SEQ));
+	float areab = fabs(cvContourArea(b, CV_WHOLE_SEQ));
+
+    //return 0;
+	return (areaa > areab);
+}
+
+
+
+
+//--------------------------------------------------------------------------------
+rfiCvContourFinder::rfiCvContourFinder() {
+    _width = 0;
+    _height = 0;
+	myMoments = (CvMoments*)malloc( sizeof(CvMoments) );
+	reset();
+}
+
+//--------------------------------------------------------------------------------
+rfiCvContourFinder::~rfiCvContourFinder() {
+	free( myMoments );
+}
+
+//--------------------------------------------------------------------------------
+void rfiCvContourFinder::reset() {
+    cvSeqBlobs.clear();
+    blobs.clear();
+    nBlobs = 0;
+}
+
+//--------------------------------------------------------------------------------
+int rfiCvContourFinder::findContours( ofxCvGrayscaleImage&  input,
+									  int minArea,
+									  int maxArea,
+									  int nConsidered,
+									  bool bFindHoles,
+                                      bool bUseApproximation) {
+
+    // get width/height disregarding ROI
+    IplImage* ipltemp = input.getCvImage();
+    _width = ipltemp->width;
+    _height = ipltemp->height;
+
+	reset();
+
+	// opencv will clober the image it detects contours on, so we want to
+    // copy it into a copy before we detect contours.  That copy is allocated
+    // if necessary (necessary = (a) not allocated or (b) wrong size)
+	// so be careful if you pass in different sized images to "findContours"
+	// there is a performance penalty, but we think there is not a memory leak
+    // to worry about better to create mutiple contour finders for different
+    // sizes, ie, if you are finding contours in a 640x480 image but also a
+    // 320x240 image better to make two rfiCvContourFinder objects then to use
+    // one, because you will get penalized less.
+
+	if( inputCopy.getWidth() == 0 ) {
+        inputCopy.setUseTexture(false);
+		inputCopy.allocate( _width, _height );
+	} else if( inputCopy.getWidth() != _width || inputCopy.getHeight() != _height ) {
+        // reallocate to new size
+        inputCopy.clear();
+        inputCopy.setUseTexture(false);
+        inputCopy.allocate( _width, _height );
+	}
+
+    inputCopy.setROI( input.getROI() );
+    inputCopy = input;
+
+	CvSeq* contour_list = NULL;
+	contour_storage = cvCreateMemStorage( 1000 );
+	storage	= cvCreateMemStorage( 1000 );
+
+	CvContourRetrievalMode  retrieve_mode
+        = (bFindHoles) ? CV_RETR_LIST : CV_RETR_EXTERNAL;
+	cvFindContours( inputCopy.getCvImage(), contour_storage, &contour_list,
+                    sizeof(CvContour), retrieve_mode, bUseApproximation ? CV_CHAIN_APPROX_SIMPLE : CV_CHAIN_APPROX_NONE );
+	CvSeq* contour_ptr = contour_list;
+
+	// put the contours from the linked list, into an array for sorting
+	while( (contour_ptr != NULL) ) {
+		float area = fabs( cvContourArea(contour_ptr, CV_WHOLE_SEQ) );
+		if( (area > minArea) && (area < maxArea) ) {
+            cvSeqBlobs.push_back(contour_ptr);
+		}
+		contour_ptr = contour_ptr->h_next;
+	}
+
+
+	// sort the pointers based on size
+	if( cvSeqBlobs.size() > 1 ) {
+        sort( cvSeqBlobs.begin(), cvSeqBlobs.end(), sort_carea_compare );
+	}
+
+
+	// now, we have cvSeqBlobs.size() contours, sorted by size in the array
+    // cvSeqBlobs let's get the data out and into our structures that we like
+	for( int i = 0; i < MIN(nConsidered, (int)cvSeqBlobs.size()); i++ ) {
+		blobs.push_back( ofxCvBlob() );
+		float area = cvContourArea( cvSeqBlobs[i], CV_WHOLE_SEQ );
+		CvRect rect	= cvBoundingRect( cvSeqBlobs[i], 0 );
+		cvMoments( cvSeqBlobs[i], myMoments );
+
+		blobs[i].area                     = fabs(area);
+		blobs[i].hole                     = area < 0 ? true : false;
+		blobs[i].length 			      = cvArcLength(cvSeqBlobs[i]);
+		blobs[i].boundingRect.x           = rect.x;
+		blobs[i].boundingRect.y           = rect.y;
+		blobs[i].boundingRect.width       = rect.width;
+		blobs[i].boundingRect.height      = rect.height;
+		blobs[i].centroid.x 			  = (myMoments->m10 / myMoments->m00);
+		blobs[i].centroid.y 			  = (myMoments->m01 / myMoments->m00);
+
+		// get the points for the blob:
+		CvPoint           pt;
+		CvSeqReader       reader;
+		cvStartReadSeq( cvSeqBlobs[i], &reader, 0 );
+
+    	for( int j=0; j < cvSeqBlobs[i]->total; j++ ) {
+			CV_READ_SEQ_ELEM( pt, reader );
+            blobs[i].pts.push_back( ofPoint((float)pt.x, (float)pt.y) );
+		}
+		blobs[i].nPts = blobs[i].pts.size();
+
+	}
+
+    nBlobs = blobs.size();
+
+	// Free the storage memory.
+	// Warning: do this inside this function otherwise a strange memory leak
+	if( contour_storage != NULL ) { cvReleaseMemStorage(&contour_storage); }
+	if( storage != NULL ) { cvReleaseMemStorage(&storage); }
+
+	return nBlobs;
+
+}
+
+//--------------------------------------------------------------------------------
+void rfiCvContourFinder::draw( float x, float y, float w, float h ) {
+
+    float scalex = 0.0f;
+    float scaley = 0.0f;
+    if( _width != 0 ) { scalex = w/_width; } else { scalex = 1.0f; }
+    if( _height != 0 ) { scaley = h/_height; } else { scaley = 1.0f; }
+
+    if(bAnchorIsPct){
+        x -= anchor.x * w;
+        y -= anchor.y * h;
+    }else{
+        x -= anchor.x;
+        y -= anchor.y;
+    }
+
+    ofPushStyle();
+    glPushMatrix();
+    glTranslatef( x, y, 0.0 );
+    glScalef( scalex, scaley, 0.0 );
+	ofSetHexColor(0xFFFFFF);
+
+	for( int i=0; i<(int)blobs.size(); i++ ) {
+		ofNoFill();
+		ofBeginShape();
+		for( int j=0; j<blobs[i].nPts; j++ ) {
+			ofVertex( blobs[i].pts[j].x, blobs[i].pts[j].y );
+		}
+		ofEndShape();
+
+	}
+	glPopMatrix();
+	ofPopStyle();
+}
+
+
+//----------------------------------------------------------
+void rfiCvContourFinder::draw(const ofPoint & point){
+	draw(point.x, point.y);
+}
+
+//----------------------------------------------------------
+void rfiCvContourFinder::draw(const ofRectangle & rect){
+	draw(rect.x, rect.y, rect.width, rect.height);
+}
+
+//--------------------------------------------------------------------------------
+void rfiCvContourFinder::setAnchorPercent( float xPct, float yPct ){
+    anchor.x = xPct;
+    anchor.y = yPct;
+    bAnchorIsPct = true;
+}
+
+//--------------------------------------------------------------------------------
+void rfiCvContourFinder::setAnchorPoint( int x, int y ){
+    anchor.x = x;
+    anchor.y = y;
+    bAnchorIsPct = false;
+}
+
+//--------------------------------------------------------------------------------
+void rfiCvContourFinder::resetAnchor(){
+    anchor.set(0,0);
+    bAnchorIsPct = false;
+}
+
+

src/rficv/rfiCvContourFinder.h

@@ -0,0 +1,73 @@
+/*
+* rfiCvContourFinder.h
+*
+* Finds white blobs in binary images and identifies
+* centroid, bounding box, area, length and polygonal contour
+* The result is placed in a vector of ofxCvBlob objects.
+*
+*/
+
+#ifndef RFI_CV_CONTOUR_FINDER
+#define RFI_CV_CONTOUR_FINDER
+
+
+
+#include "ofxCvConstants.h"
+#include "ofxCvBlob.h"
+#include "ofxCvGrayscaleImage.h"
+#include <algorithm>
+
+class rfiCvContourFinder : public ofBaseDraws {
+
+  public:
+  
+    vector<ofxCvBlob>  blobs;
+    int                nBlobs;    // DEPRECATED: use blobs.size() instead
+      
+
+    rfiCvContourFinder();
+    virtual  ~rfiCvContourFinder();
+    
+	virtual float getWidth() { return _width; };    //set after first findContours call
+	virtual float getHeight() { return _height; };  //set after first findContours call
+    
+    virtual int  findContours( ofxCvGrayscaleImage& input,
+                               int minArea, int maxArea,
+                               int nConsidered, bool bFindHoles,
+                               bool bUseApproximation = true);
+                               // approximation = don't do points for all points 
+                               // of the contour, if the contour runs
+                               // along a straight line, for example...
+
+    virtual void  draw() { draw(0,0, _width, _height); };
+    virtual void  draw( float x, float y ) { draw(x,y, _width, _height); };
+    virtual void  draw( float x, float y, float w, float h );
+	virtual void  draw(const ofPoint & point);
+	virtual void  draw(const ofRectangle & rect);
+	virtual void setAnchorPercent(float xPct, float yPct);
+    virtual void setAnchorPoint(int x, int y);
+	virtual void resetAnchor();      
+    //virtual ofxCvBlob  getBlob(int num);
+
+
+
+  protected:
+
+    int  _width;
+    int  _height;
+    ofxCvGrayscaleImage     inputCopy;
+    CvMemStorage*           contour_storage;
+    CvMemStorage*           storage;
+    CvMoments*              myMoments;
+    vector<CvSeq*>          cvSeqBlobs;  //these will become blobs
+    
+    ofPoint  anchor;
+    bool  bAnchorIsPct;      
+
+    virtual void reset();
+
+};
+
+
+
+#endif