post future everything commit

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

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

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

.gitignore

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

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!

example/RefractiveIndex.cpp

@@ -1,12 +1,5 @@
-/*
 
- todo:
+////also the new shit////
- (1) Look at warinings about the #define which get over written
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
 
 #include "RefractiveIndex.h"
 
@@ -22,11 +15,11 @@
 
 #include "ofxXmlSettings.h"
 
-#define CAMERA_ID           1
+#define CAMERA_ID           0
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
-#define LOCATION            "MIDDLESBOROUGH"
+#define LOCATION            "MANCHESTER"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -34,8 +27,10 @@
 #define ISTATE_TRANSITION   0xCCCC
 #define ISTATE_END          0xDDDD
 
+
 int _state = ISTATE_UNDEF;
 
+int              RefractiveIndex::_mode;
 ofPixels         RefractiveIndex::_pixels;
 ofVideoGrabber   RefractiveIndex::_vidGrabber;
 int              RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, RefractiveIndex::_vid_id;
@@ -43,20 +38,32 @@ bool             RefractiveIndex::_vid_stream_open;
 bool             RefractiveIndex::_vid_toggle_on;
 string           RefractiveIndex::_location;
 
-ofxXmlSettings   XML;
+ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
+    camDist=1000;
+    
+    ofBackground(0, 0, 0);
+    ofSetBackgroundAuto(false);
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
-    if(!XML.loadFile("../data/config.refindx")) {
+    if(XML.loadFile("config.refindx") == false) {
         ofLog(OF_LOG_ERROR) << "error loading config - using default.";
         save_config = true;                
+    } 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);
+    cout << "_vid_id: " << _vid_id << endl;
+    
     _vid_w  = XML.getValue("config:camera:width", CAMERA_ACQU_WIDTH);
     _vid_h  = XML.getValue("config:camera:height", CAMERA_ACQU_HEIGHT);
     
@@ -71,6 +78,7 @@ void RefractiveIndex::setup()
     // display
     cout << "> display" << endl;
     ofSetFrameRate(fps);
+    
     if(fps > 30) {
         ofSetVerticalSync(FALSE);            
     } else {        
@@ -84,8 +92,10 @@ void RefractiveIndex::setup()
     cout << "* cam width = " << _vid_w << endl;
     cout << "* cam height = " << _vid_h << endl;
     
+    if(_mode == MODE_ANALYSING) {
         _vid_stream_open = false;    
         setup_camera();
+    }
     
     cout << "RRRRRREADY!" << endl;        
 
@@ -93,42 +103,43 @@ void RefractiveIndex::setup()
 
     //getting a warning from the OFlog that the pixels aren't allocated
     //void ofPixels::allocate(int w, int h, ofImageType type)    
-    
+    _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR); 
     
     //TODO:  whichever one of these is first - it always runs twice ?
     
-    _analysisVector.push_back(new ShadowScapesAnalysis(V));
+    _analysisVector.push_back(new ShadowScapesAnalysis(V));  //1
-    _analysisVector.push_back(new ShadowScapesAnalysis(H));
+    _analysisVector.push_back(new ShadowScapesAnalysis(H));  //2
-    _analysisVector.push_back(new ShadowScapesAnalysis(D));
+    _analysisVector.push_back(new ShadowScapesAnalysis(D));  //3
 	    
-    _analysisVector.push_back(new RelaxRateAnalysis());
+    _analysisVector.push_back(new RelaxRateAnalysis());   //4
 	
-    _analysisVector.push_back(new IResponseAnalysis());
+    _analysisVector.push_back(new IResponseAnalysis());   //5
     
-    _analysisVector.push_back(new ShapeFromShadingAnalysis());
+    _analysisVector.push_back(new ShapeFromShadingAnalysis());   //6
     
-    _analysisVector.push_back(new StrobeAnalysis());
+    _analysisVector.push_back(new StrobeAnalysis());   //7
     
-    _analysisVector.push_back(new CamNoiseAnalysis());
+    _analysisVector.push_back(new CamNoiseAnalysis());    //8
     
-    _analysisVector.push_back(new ColorSingleAnalysis());
+    _analysisVector.push_back(new ColorSingleAnalysis());    //9
     
-    _analysisVector.push_back(new ColorMultiAnalysis());
+    _analysisVector.push_back(new ColorMultiAnalysis());    //0
     
-    _analysisVector.push_back(new DiffNoiseAnalysis());
+    _analysisVector.push_back(new DiffNoiseAnalysis());	  //Q
     
+    //_currentAnalysisIndx = 0;
+    //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
+    //_state = ISTATE_START;
     
-    _currentAnalysisIndx = 0;
+    _currentAnalysis = NULL;
-    _currentAnalysis = _analysisVector.at(_currentAnalysisIndx); 
+    _state = ISTATE_UNDEF;
   
-    _state = ISTATE_START;
     
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
 {
     assert(analysis == _currentAnalysis->_name);
-    
     _state = ISTATE_STOP;    
 }
 
@@ -138,6 +149,17 @@ void RefractiveIndex::start_analysis()
     _analysisAdapator = new AnalysisAdaptor(_currentAnalysis);
     _currentAnalysis->setup(_vid_w, _vid_h);
     _analysisAdapator->start();    
+    
+    //allocate fbo for HD
+    fbo.allocate(1920,1080);
+
+    //    fbo.allocate( _currentAnalysis->_mesh_size_multiplier *_vid_w,_currentAnalysis->_mesh_size_multiplier * _vid_h);
+    //camera.setPosition((fbo.getWidth()/2), fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
+    camera.setPosition(0, (fbo.getHeight()/2)+150,  _currentAnalysis->_mesh_size_multiplier*500);
+    camera.setFov(65.0);
+    camera.setOrientation(ofVec3f(-2,0,0));
+    _meshRotation=0;
+
 }
 
 void RefractiveIndex::stop_analysis()
@@ -161,7 +183,9 @@ void RefractiveIndex::state_analysis()
         case ISTATE_TRANSITION:            
             if(_currentAnalysisIndx >= _analysisVector.size()) {
                 _currentAnalysisIndx = 0;
-                _state = ISTATE_END;
+                _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
+                _state = ISTATE_START;                
+                //_state = ISTATE_END;
             } else {
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;
@@ -169,9 +193,13 @@ void RefractiveIndex::state_analysis()
             break;
         case ISTATE_STOP:
             stop_analysis(); // blocking
+            if(_mode == MODE_DRAWING)
+                _state = ISTATE_UNDEF;
+            else
                 _state = ISTATE_TRANSITION;
             break;
         case ISTATE_END:
+            if(_mode == MODE_ANALYSING)
                 stop_camera();
             ::exit(1);
             break;
@@ -185,34 +213,82 @@ void RefractiveIndex::state_analysis()
 void RefractiveIndex::update()
 {    
     state_analysis();
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-
-    if (_vidGrabber.isFrameNew())
-    {
-        _pixels = _vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    }
 }
 
 void RefractiveIndex::draw()
 {
+    // refractive mauve - this doesn't work... looks weird in various places.
+    //ofBackground(113, 110, 136);
+    
+    // black
     ofBackground(0, 0, 0);
-    if(_currentAnalysis)
+   
+    if(_currentAnalysis){
+        
         _currentAnalysis->draw();
+       
+        if(_currentAnalysis->meshIsComplete){
+            
+            fbo.begin();
+            ofClear(0,0,0);
+
+            glShadeModel(GL_SMOOTH);  
+            
+            
+            camera.begin();
+            
+                //this is a hack, I don't know how to colour the fbo with black pixels so I'm drawing a massive black rectangle in the  background
+                /*
+                ofPushMatrix();
+                    ofTranslate(0, 0,-500);
+                    ofSetColor(0, 0, 0);
+                    ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);                
+                    ofPopMatrix();
+                ofSetColor(255);
+                */
+                //float xDiff= (fbo.getWidth()- 1.55*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
+                float xDiff= (fbo.getWidth()- 1.33333*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
+                float yDiff= (fbo.getHeight()-(_currentAnalysis->_mesh_size_multiplier * _vid_h))/2;
+                
+                ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
+                    //ofScale(1.33333,1.0,1.0);
+                    //_currentAnalysis->aMesh.drawVertices();     // TODO: tom - why do you have the vertices drawing here? 
+                    _currentAnalysis->aMesh.drawFaces();
+                    _currentAnalysis->aMesh.draw();
+                
+            camera.end();
+            fbo.end();
+
+            ofPixels pixels;
+            fbo.readToPixels(pixels);
+          
+            ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
+            //saving jpgs doesn't work - pngs only!
+            // PNG is fine - better for Final Cut anyway! 
+
+            ofDisableBlendMode() ;  
+        }
+    }
 }
 
 void RefractiveIndex::setup_camera()
 {
     stop_camera();
     
+    // THIS IS LOADED IN FROM THE XML FILE SETTINGS 
+    _vidGrabber.setDeviceID(_vid_id);
+    _vidGrabber.listDevices();
+    
     if(!_vidGrabber.initGrabber(_vid_w, _vid_h)) {
         ofLog(OF_LOG_ERROR) << "RefractiveIndex::setup_camera - could not initialise grabber";
         return;
     }
-    _vidGrabber.listDevices();
+    
     _vidGrabber.setVerbose(true);
+    _vidGrabber.setUseTexture(false);
     _vid_stream_open = true;
-    _vidGrabber.setDeviceID(_vid_id);
+    cout << "CAMERA SETUP " << endl;
+    return;
 	
 }
 
@@ -228,9 +304,167 @@ 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)
+            _analysisAdapator->stop();
+        _currentAnalysis = NULL;
+        _state = ISTATE_UNDEF;
+    }    
+    
+    else if(key == '1')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 0;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == '2')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 1;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == '3')
+    {        
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 2;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '4')
+    {     
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 3;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '5')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 4;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '6')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 5;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '7')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 6;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '8')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 7;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '9')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 8;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '0')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 9;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == 'q')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _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

@@ -1,8 +1,3 @@
-/*
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #pragma once
 
@@ -13,6 +8,13 @@
 #include "AbstractAnalysis.h"
 #include "AnalysisAdaptor.h"
 
+#include "ofxOpenCv.h"
+#include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
+
+#define MODE_DRAWING        0xEEFF
+#define MODE_ANALYSING      0xFFEE
 
 class RefractiveIndex : public ofBaseApp
 {
@@ -54,10 +56,15 @@ protected:
     AnalysisAdaptor*            _analysisAdapator;
     vector<AbstractAnalysis*>   _analysisVector;    
     
+    float                         _meshRotation;
+    float                           camDist;
+    ofEasyCam                     cam;
 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;
@@ -65,6 +72,9 @@ public:
     
     // this should be in xml
     static string           _location;
-    
+    static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
+    ofCamera    camera;
+    ofPixels    keepOnScreen;
+    ofFbo fbo;
    
 };

example/main.cpp

@@ -1,35 +1,27 @@
 #include "ofAppGlutWindow.h"
 #include "RefractiveIndex.h"
-#include "ofxXmlSettings.h"
-
-#define SCREEN_WIDTH        800
-#define SCREEN_HEIGHT       600
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
 
+#define SCREEN_WIDTH        1280
+#define SCREEN_HEIGHT       800
 
 int main() {
+    
 	ofAppGlutWindow window;
    
-    ofxXmlSettings   XML;
+    bool fullscreen;
-    XML.loadFile("../data/config.refindx");
+    
-    bool fullscreen = (XML.getValue("config:display:fullscreen", "false") == "true" ? true : false);
+    //fullscreen = true; 
-    int screen_w = XML.getValue("config:display:width", SCREEN_WIDTH);
+    fullscreen = false;
-    int screen_h = XML.getValue("config:display:height", SCREEN_HEIGHT);     
     
     cout << "> display configuration" << endl;
     cout << "* fullscreen: " << (fullscreen ? "yes" : "no") << endl;
+ 
     if(!fullscreen) {
-        cout << "* screen width: " << screen_w << endl;
+        cout << "* screen width: " << SCREEN_WIDTH << endl;
-        cout << "* screen height: " << screen_h << endl;
+        cout << "* screen height: " << SCREEN_HEIGHT << endl;
     }
     
-	ofSetupOpenGL(&window, screen_w, screen_h, (fullscreen ? OF_FULLSCREEN : OF_WINDOW));
+	ofSetupOpenGL(&window, SCREEN_WIDTH, SCREEN_HEIGHT, (fullscreen ? OF_FULLSCREEN : OF_WINDOW));
 	ofRunApp(new RefractiveIndex());
 
 }

src/AbstractAnalysis.cpp

@@ -1,50 +1,81 @@
-/*
+/* */
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
- 
- + 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.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #include "AbstractAnalysis.h"
 #include "RefractiveIndex.h"
 #include "ofxFileHelper.h"
+#include "ofSystemUtils.h"
+
+void AbstractAnalysis::setup(int camWidth, int camHeight) {
+    
+    meshIsComplete=false;
+    imageForContourAvailable=false;
+    
+    _cam_w = camWidth; _cam_h = camHeight;
+    if(RefractiveIndex::_mode == MODE_DRAWING) {
+        ofFileDialogResult r = ofSystemLoadDialog("choooose da folda", true);
+        if(!r.bSuccess) {
+            ofSystemAlertDialog("OOOOPS.... ERROR...");
+            return;
+        }
+                
+        _whole_file_path_analysis = r.filePath;
+        _whole_file_path_synthesis = r.filePath + "/darwings";        
+    }
+
+}
 
 // this is the main threaded loop for a given analysis
 void AbstractAnalysis::do_synthesize() {
+    
+    switch(RefractiveIndex::_mode)
+    {
+        case MODE_ANALYSING:
+        {
+            for(int i = 0; i < NUM_RUN; i++) {
+                
+                cout << "NUM_RUN: " << i << endl;
+                
+                _saved_filenames_analysis.clear();  
+                _saved_filenames_synthesis.clear(); 
+                
                 _state = STATE_ACQUIRING;
                 acquire();
+                if(_state == STATE_STOP) goto exit;
                 _state = STATE_SYNTHESISING;
                 synthesise();
+                if(_state == STATE_STOP) goto exit;
                 _state = STATE_DISPLAY_RESULTS;
+                displayresults();
+                cleanup();
+            }                    
+        }
+            
+        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();
+            cleanup();            
+        }
+    }
+    
+exit:    
+    cleanup();
     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
     
@@ -67,17 +98,160 @@ void AbstractAnalysis::create_dir()
         }
     }
 
-    ofxFileHelper fileHelper;
+    ofxFileHelper fileHelperAnalysis;
-    _whole_file_path = ANALYSIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime ;
+    ofxFileHelper fileHelperSynthesis;
-    //cout << "_whole_file_path = " << _whole_file_path << endl;
+    
+    _whole_file_path_analysis = ANALYSIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime ;
+  
+    //cout << "_whole_file_path_analysis = " << _whole_file_path_analysis << endl;
+    
+    if(!fileHelperAnalysis.doesDirectoryExist(_whole_file_path_analysis)){
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location);
+
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
+        
         
-    if(!fileHelper.doesDirectoryExist(_whole_file_path)){
-        fileHelper.makeDirectory(ANALYSIS_PATH);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
     }
     
+    _whole_file_path_synthesis = SYNTHESIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime;
+    
+    if(!fileHelperSynthesis.doesDirectoryExist(_whole_file_path_synthesis)){
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location);
+
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
+        
+    }
     //////////////////////////////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);
+                        
+            cout << list[i] << endl; 
+            
+        }                
+    }
+}
+
+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

@@ -7,9 +7,11 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
+#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
+#define SYNTHESIS_PATH "synthesis/"
 
 #define STATE_ACQUIRING         0x1111
 #define STATE_SYNTHESISING      0x2222
@@ -23,16 +25,22 @@ 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();
                         
-    // ofx
+    // show the results to the screen
     virtual void draw() = 0;    
         
 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;   
@@ -40,20 +48,51 @@ protected:
     // analysis + synthesize images - all the children (see - do_synthesize)
     virtual void synthesise() = 0;   
     
+    // display the results from disk
+    virtual void displayresults() = 0;   
+    
+    // display the results from disk
+    virtual void cleanup() {;}   
+    
         
 public:
     string  _name;       
+    string  _draw_directory;
     
     // event
     ofEvent<string> _synthesize_cb;    
+    bool    meshIsComplete;
+    bool    imageForContourAvailable;
+    ofMesh  aMesh;
+    ofLight light;
+    ofLight lightStatic; 
+    
+    string  meshFileName;
+    //difference between our image size and the size of the fbo
+    float   widthScaleFactor;
+    float   heightScaleFactor;
+    ofImage  contourImage;
+    ofPixels meshPix;
+    ofPixels publicColorImage;
+    float    zPlaneAverage;
+    
+    //added Tom 1/5/12 defines the stretch we make to the mesh to make it fit HD proportions
+    float           _mesh_size_multiplier;
     
 protected:    
     int             _cam_w, _cam_h;          
-    string          _whole_file_path;
+    string          _whole_file_path_analysis, _whole_file_path_synthesis;
-    vector<string>  _saved_filenames;
+    vector<string>  _saved_filenames_analysis;
+    vector<string>  _saved_filenames_synthesis;
     
     int             _state;
     
+    ofImage         myColorImage1;
+    ofImage         myColorImage2;
+    ofImage         myGrayImage1;
+    
+    //int             _run_cnt;
+    
     float           DELTA_T_SAVE;
     int             NUM_PHASE;
     int             NUM_RUN;

src/AnalysisAdaptor.h

@@ -21,12 +21,15 @@ public:
     
     void start()
     {
+        _stopping = false;
         _runnable = new RunnableAdapter<AbstractAnalysis>(*_analysis, &AbstractAnalysis::do_synthesize);
         _worker.start(*_runnable);
     }
     
     void stop() 
     {
+        if(_stopping) return;
+        _stopping = true;
         _analysis->_state = STATE_STOP;
         _worker.join();        
     }
@@ -35,5 +38,6 @@ protected:
     AbstractAnalysis*                   _analysis;
     Thread                              _worker;    //   
     RunnableAdapter<AbstractAnalysis>*  _runnable;  
+    bool                                _stopping;
 };
 

src/CamNoiseAnalysis.h

@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class CamNoiseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,6 +23,8 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();    
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -27,8 +32,58 @@ public:
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt;
+  
-    float   c, _frame_cnt, _frame_cnt_max,_save_cnt_max ;
+    int     _run_cnt, _save_cnt, _synth_save_cnt,_anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+   
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImage);
+    
+    //returns a vector of floats for each distinct light level
+   void _returnAveragePixelValues();
+    //this vector of vectors will be returned
+    vector<vector<float> > averagePixelValuesForAllLevels;
+    
+    vector<float> _listOfLightLevels;
+    
+    int vertexSubsampling;
+    
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
     
 };

src/ColorMultiAnalysis.cpp

@@ -1,35 +1,3 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
-
- + 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.
-
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ColorMultiAnalysis.h"
 #include "ofMain.h"
 
@@ -41,82 +9,323 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
-
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 150; // the right number is about 300
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
+    
-    NUM_RUN = 1;
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
-    NUM_SAVE_PER_RUN = 300;    
+    cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=8;
+    vertexSubsampling = 1;
+    chooseColour=1;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
+
+    //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
+                                            // 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_allocate_images();
     
-    create_dir();
     _frame_cnt = 0;
-    _fade_cnt=0;
+    _run_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _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
+        
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+
 }
 
 void ColorMultiAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<ColorMultiAnalysis> save_callback(*this, &ColorMultiAnalysis::save_cb);
 
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
+      //  _run_cnt = i;
 
-        cout << "RUN NUM = " << i;
+        //cout << "RUN NUM = " << i;
     
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
 
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
    
+    //}
 }
 
 void ColorMultiAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+    
+    //cout << "ColorMultiAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorMultiAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+            //cvColorImage1.blur(1);
+            //cvColorImage1.erode();
+            
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            //cvColorImage1.dilate();
+            
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+
+            cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 15, 15);
+            cvXorS( cvColorImage1.getCvImage(), cvScalarAll(2), cvColorImage1.getCvImage(), 0 );
+            
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+            // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            //ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-backgroundPixels[i]>0){
+                    imagePixels1[i]-=backgroundPixels[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+            
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            // }
+        }
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+        _RUN_DONE = true;
+    */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+}
+
+void ColorMultiAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_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;
+        }
+    }    
 }
 
 
 void ColorMultiAnalysis::draw()
 {
     
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();     
+    light.enable();
+	
+    light.setPosition(200,200,-150);
+    lightStatic.enable();
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(2.0f);
+    //glPointSize(4.0f);
+    
+    ofEnableBlendMode ( OF_BLENDMODE_ADD );
+    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
+    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
+    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
+    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
+
+    
     switch (_state) {
         case STATE_ACQUIRING:
         {
+            ofEnableAlphaBlending();
             
             if (_frame_cnt < _frame_cnt_max)
             {
 
-                
                 int _fade_in_frames = _frame_cnt_max/50;
+                ofColor aColor;
                 
                 if (_frame_cnt < _fade_in_frames) {
-                    ofColor aColor;
+                   
                     
                     aColor.setHsb(c, ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255), ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
                     
                     ofSetColor(aColor);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     
-                    cout << "FADING IN..." << endl;
+                    //cout << "FADING IN..." << endl;
                 }
                 
+                
+                
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < _frame_cnt_max-_fade_in_frames){
                     
-                    ofColor aColor;
                     aColor.setHsb(c, 255, 255);
                     ofSetColor(aColor);
                     
@@ -126,41 +335,142 @@ void ColorMultiAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                 }
                 
-                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
+                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
-                    ofColor aColor;
+                    aColor.set(c, c, c, 255-int(ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255)));
                     
-                    aColor.setHsb(c, 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255), 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255));
+                    //aColor.setHsb(c, 255-ofMap(_fade_cnt- (_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255), 255-(ofMap(_fade_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255)));
                     
                     ofSetColor(aColor);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
-                    
+                    //cout << "FADING OUT..." << endl;
-                    _fade_cnt++;
-                    cout << "FADING OUT..." << endl;
                     
                 }
                 
+                
             } else {
-                 
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
-            
             }
             
             _frame_cnt++;            
-            
+            ofDisableAlphaBlending();
             break;
         }
             
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "ColorMultiAnalysis = 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 << "ColorMultiAnalysis 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 {
+                _state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
+            
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
             // display results of the synthesis
+            _RUN_DONE = true;
             break;
+            
         }
             
             
@@ -175,18 +485,156 @@ void ColorMultiAnalysis::draw()
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-    
-    // UPDATE THE COLOR ON THE SCREEN
-    //float c_last = c;
-    
-    // cout << "COLORMULTIANALYSIS::saving...\n";
-    // cout << "c_last... " << c << endl;
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
+    saveImageAnalysis(file_name);    
-    // cout<<_whole_file_path<<endl;
+}
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+
-    
+
-    //if(_save_cnt >= NUM_SAVE_PER_RUN){
+void ColorMultiAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    //    _RUN_DONE = true;
+    int x=0;
-    //}
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //mesh.setMode(OF_PRIMITIVE_LINES);
+    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    //mesh.setMode(OF_PRIMITIVE_POINTS);
+    
+    /*
+     OF_PRIMITIVE_TRIANGLES,
+     OF_PRIMITIVE_TRIANGLE_STRIP,
+     OF_PRIMITIVE_TRIANGLE_FAN,
+     OF_PRIMITIVE_LINES,
+     OF_PRIMITIVE_LINE_STRIP,
+     OF_PRIMITIVE_LINE_LOOP,
+     OF_PRIMITIVE_POINTS
+     
+     */
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+   
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+}
+
+
+
+vector<float> ColorMultiAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        //float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            //float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getLightness());
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            float multiplier=15.0*((thisDiff)/255.0);
+            
+            differences.push_back(multiplier* thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
 }

src/ColorMultiAnalysis.h

@@ -4,6 +4,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class ColorMultiAnalysis : public AbstractAnalysis
 {
 public:
@@ -15,6 +18,7 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -22,6 +26,50 @@ public:
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt, _fade_cnt;
+    
-    float   c, _frame_cnt, _frame_cnt_max;
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
+
 };

src/ColorSingleAnalysis.cpp

@@ -1,80 +1,343 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ColorSingleAnalysis.h"
 #include "ofMain.h"
-
 #include "Poco/Timer.h"
 #include "Poco/Thread.h"
 
+#include <string>
+#include <iostream>
+
 #include "RefractiveIndex.h"
 
 using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 300;
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
+    cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier=8;
+    vertexSubsampling = 1;
+    chooseColour=1;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
+
+    
+    //int acq_run_time = 25;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 1*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
+                                            // 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_allocate_images();
+    
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _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
+    
     r = 0;
     g = 0;
     b = 0;
     
-    _fade_cnt=0;
     fileNameTag = "";
+    fileNameColor = "";
+    
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);    
 }
 
 
 void ColorSingleAnalysis::acquire()
 {
-
     Timer* save_timer;
 
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
-
+      //  _run_cnt = i;
-        _run_cnt = i;
+        //cout << "RUN NUM = " << i;
-
-        cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
         
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+
 }
 
 void ColorSingleAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+    
+    //cout << "ColorSingleAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorSingleAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+                //cout << "LOADED image1!!!" << endl;
+                //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+
+            
+                cout << "_saved_filenames_analysis[i].find(RED): " << _saved_filenames_analysis[i].find("RED") << endl;                
+            
+                if(_saved_filenames_analysis[i].find("RED")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "RED";
+                    cout<<"FOUND RED"<<endl;
+                } else if (_saved_filenames_analysis[i].find("GREEN")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "GREEN";
+                    cout<<"FOUND GREEN"<<endl;
+                } else if(_saved_filenames_analysis[i].find("BLUE")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "BLUE";
+                    cout<<"FOUND BLUE"<<endl;
+                } else if(_saved_filenames_analysis[i].find("FADING")<_saved_filenames_analysis[i].length())
+                {
+                    fileNameColor = "FADING";
+                    cout<<"FOUND FADING"<<endl;
+                }
+                          
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.blur(1);
+            
+                //cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 9, 9 );
+                
+                cvColorImage1.erode();
+                
+                cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 3, 3 );
+            
+                //cvColorImage1.erode();
+            
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+                //cvColorImage1.dilate();
+            
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+            
+                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(255), cvColorImage1.getCvImage(), 0 );
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+            
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+        
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+            
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+            
+           // }
+        }
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+    
+}
+
+void ColorSingleAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_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;
+        }
+    }
+    
 }
 
 
 void ColorSingleAnalysis::draw()
 {
+    ofEnableSmoothing();
+
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();     
+    light.enable();
+	
+    light.setPosition(200,200,-150);
+    lightStatic.enable();
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(1.0f);
+    
+    ofEnableBlendMode ( OF_BLENDMODE_ADD );
+    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
+    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
+    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
+    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
+    
     
     switch (_state) {
         case STATE_ACQUIRING:
         {
 
-            
             if (_frame_cnt < _frame_cnt_max)
             {
                     
@@ -116,8 +379,8 @@ void ColorSingleAnalysis::draw()
                 
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max){
                    
-                    ofSetColor(0, 0, 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255));
+                    int fade = ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255);
-                    cout << "255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255)"<< 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255) << endl;
+                    ofSetColor(0, 0, 255-fade);
         
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     _fade_cnt++;
@@ -125,6 +388,7 @@ void ColorSingleAnalysis::draw()
                 }
             
             } else {
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
             
@@ -136,13 +400,118 @@ void ColorSingleAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "ColorSingleAnalysis = 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 << "ColorSingleAnalysis 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;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
+            
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
             // display results of the synthesis
+            _RUN_DONE = true;
             break;
+
+
         }
             
         default:
@@ -156,15 +525,282 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    //    cout << "ColorSingleAnalysis::saving...\n";
-    
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    saveImageAnalysis(file_name);
-    
+}
-    //cout<<_whole_file_path+"/"+file_name<<endl;
+
-    
+
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
+
-    //    _RUN_DONE = true;
+void ColorSingleAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-
+    int x=0;
+    int y=0;
+    
+   
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //mesh.setMode(OF_PRIMITIVE_LINES);
+    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    mesh.setMode(OF_PRIMITIVE_POINTS);
+  
+    /*
+     OF_PRIMITIVE_TRIANGLES,
+     OF_PRIMITIVE_TRIANGLE_STRIP,
+     OF_PRIMITIVE_TRIANGLE_FAN,
+     OF_PRIMITIVE_LINES,
+     OF_PRIMITIVE_LINE_STRIP,
+     OF_PRIMITIVE_LINE_LOOP,
+     OF_PRIMITIVE_POINTS
+     
+     */
+    
+    ofColor meshColour=ofColor(255,255,255, 255);
+    
+      //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+                
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+             
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+      
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        ofColor currentSecondImageColor;
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            if(fileNameColor=="RED")
+            {
+                currentSecondImageColor.r=255;
+                currentSecondImageColor.g=0;
+                currentSecondImageColor.b=0;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="GREEN")
+            {
+                currentSecondImageColor.r=0;
+                currentSecondImageColor.g=255;
+                currentSecondImageColor.b=0;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="BLUE")
+            {
+                currentSecondImageColor.r=0;
+                currentSecondImageColor.g=0;
+                currentSecondImageColor.b=255;
+                currentSecondImageColor.a=255;
+                
+            } else if(fileNameColor=="FADING")
+            {
+                currentSecondImageColor.r= 255;
+                currentSecondImageColor.g= 255;
+                currentSecondImageColor.b= 255;
+                currentSecondImageColor.a= 255;
+            }
+                       
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+           
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor( currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            //x++;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //y++;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+}
+
+
+vector<float> ColorSingleAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+        
+            int thisDiff;
+            
+            if(fileNameColor=="RED")
+            {   
+                //thisDiff=abs(imageColor1.r);
+
+                thisDiff=abs(255-imageColor1.r);
+            } else if(fileNameColor=="GREEN")
+            {
+                //thisDiff=abs(imageColor1.g);                
+
+                thisDiff=abs(255-imageColor1.g);  
+                
+            } else if(fileNameColor=="BLUE")
+            {
+                //thisDiff=abs(imageColor1.b);
+
+                thisDiff=abs(255-imageColor1.b);
+            
+            } else if(fileNameColor=="FADING") {
+            
+                //thisDiff=imageColor1.getBrightness();
+                thisDiff=255-imageColor1.getBrightness();
+
+            }
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            float multiplier=8.0;
+            
+            differences.push_back(multiplier* thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
 }

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-/*
+    /*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class ColorSingleAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,6 +23,7 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -28,6 +32,53 @@ protected:
 
     bool    _RUN_DONE;
     string  fileNameTag;
-    int     _run_cnt, _save_cnt, _fade_cnt;
+    string  fileNameColor;
-    float   r,g,b, _frame_cnt, _frame_cnt_max;
+    float   r,g,b;
+    
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvFloatImage       	cvFloatImage1;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
 };

src/DiffNoiseAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "DiffNoiseAnalysis.h"
 #include "ofMain.h"
 
@@ -15,57 +10,355 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 600;  // right number is about 450
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 50;    
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
-    _fade_cnt=0;
+ 
+    cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 10;
+    vertexSubsampling       = 1;
+    chooseColour            = 5;
+    multiplier              = 4.0;
+
+    blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+        
+    meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    //meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
+    
+    //int acq_run_time = 20;   // 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
+    // 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_allocate_images();
+    
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _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
+    
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
 
 void DiffNoiseAnalysis::acquire()
 {
-
     Timer* save_timer;
-
     TimerCallback<DiffNoiseAnalysis> save_callback(*this, &DiffNoiseAnalysis::save_cb);
 
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
+    //  _run_cnt = i;
-
+    //cout << "RUN NUM = " << i;
-        cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
     
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+    
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+
+    //}
 }
 
 void DiffNoiseAnalysis::synthesise()
 {   
-    // _saved_filenames has all the file names of all the saved images
+    
+    //cout << "DiffNoiseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "DiffNoiseAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+        
+            //cvColorImage1.erode();
+            //cvColorImage1.dilate();
+                     
+            //cvColorImage1.blur(5);
+            //cvColorImage2.blur(5);
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            //cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+            //cvGrayImage1.convertToRange(0.0, 255.0);
+            //cvGrayImage2.convertToRange(0.0, 255.0);
+                
+            //cvGrayImage1.adaptiveThreshold( 200, 0);
+            //cvGrayImage2.adaptiveThreshold( 200, 0);
+                
+            //cvGrayImage1.contrastStretch();
+            //cvGrayImage2.contrastStretch();
+            
+            //cvGrayImage1.brightnessContrast(1.0,0.5);
+            //cvGrayImage2.brightnessContrast(1.0,0.5);
+               
+            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+            cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+            
+            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+                
+             // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            //image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+                
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            //ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+                //DIFFERENCING SUBSEQUENT IMAGES
+                 /*
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-imagePixels2[i]>0){
+                    imagePixels1[i]-=imagePixels2[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+                 
+                */ 
+                    //DIFFERENCING THE BACKGROUND
+                /*
+            for(int i=0;i<imagePixels1.size();i++){
+                //unsigned char val=imagePixels1[i];
+                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                if(imagePixels1[i]-backgroundPixels[i]>0){
+                    imagePixels1[i]-=backgroundPixels[i];
+                }
+                else{
+                    imagePixels1[i]=0;
+                }
+            }
+              */                
+             
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            //}
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+    _RUN_DONE = true;
+    */
+    
+     meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+    
+}
+
+void DiffNoiseAnalysis::displayresults()
+{
+    
+    for(float i=1;i<_saved_filenames_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
 void DiffNoiseAnalysis::draw()
 {    
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+
+    light.enable();	
+    lightStatic.enable();
+
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(5.0f);
+    
+    ofEnableBlendMode(blendMode);
+
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -92,12 +385,12 @@ void DiffNoiseAnalysis::draw()
                         }
                     }        
                     
-                    cout << "FADING IN..." << endl;
+                    //cout << "FADING IN..." << endl;
                 }
                 
                 
                 
-                if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max-_fade_in_frames)){
+                if (_frame_cnt >= _fade_in_frames && _frame_cnt <= (_frame_cnt_max-_fade_in_frames)){
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
                     {
@@ -112,30 +405,27 @@ void DiffNoiseAnalysis::draw()
                     }        
                 }
                 
-                
+                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
-                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
                     {
                         for (int j=1; j < ofGetWidth(); j=j+rectSize)
                         {
                             c = ofRandom(0,255);
-                            aColour.set(c, c, c, 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                            aColour.set(c, c, c, 255-ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
                             ofSetColor(aColour);
                             ofRect(j, i, rectSize, rectSize);
                         } 
                     }
                     
-                    _fade_cnt++;
+                    //_fade_cnt++;
-                    cout << "FADING OUT..." << endl;
+                    //cout << "FADING OUT..." << endl;
-                    
                 }
             
-                
                 ofDisableAlphaBlending();
            
             } else {
-            
+               // _state  = STATE_SYNTHESISING;
                _RUN_DONE = true;
             
             }
@@ -148,51 +438,535 @@ void DiffNoiseAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "DiffNoiseAnalysis = 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 << "DiffNoiseAnalysis 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;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            break;
+            
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
             
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                //image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
+            break;
+            
+        }
         default:
             break;
     }
-
 }
 
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
-
+    _save_cnt++;
-
-    float rand10 = ofRandom(0,10);
-
-    if (rand10 > 5.0) {
-
-    cout << "DiffNoiseAnalysis::saving...\n";
-    cout << "c_last... " << c << endl;
-    cout<<"rand10... " <<rand10<<endl;
             
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    string thisLocation = RefractiveIndex::_location;
 
-    //RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    saveImageAnalysis(file_name);
-    //    fileName = imageSaveFolderPath+whichAnalysis+"_"+ofToString(100.0*i*scanLineSpeed/ofGetHeight(),2)+"%_"+ofToString(i)+".jpg";
+}
-    //ofSaveImage(vectorOfPixels[i], fileName, OF_IMAGE_QUALITY_BEST);
 
-    string file = _whole_file_path+"/"+file_name;
 
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+void DiffNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
     
-    _saved_filenames.push_back(file);
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
     
+    ofColor meshColour=ofColor(255,255,255);
+        
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+        
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+        
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+        
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
     }
-    _save_cnt++;
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
     
 }
+
+
+vector<float> DiffNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}

src/DiffNoiseAnalysis.h

@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class DiffNoiseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,6 +23,7 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -27,7 +31,52 @@ public:
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt, _fade_cnt;
+
-    float   c, _frame_cnt, _frame_cnt_max;
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 
 };

src/IResponseAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "IResponseAnalysis.h"
 #include "ofMain.h"
 
@@ -15,49 +10,233 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
+
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
         
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
+    cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=4;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME IResponseAnalysis " << acq_run_time << endl;
+
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=8;
+    
+    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    
+    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_allocate_images();
+    _synth_save_cnt = 0;
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
     c = 0;
-}
     
+    int anim_time = 10;   // 10 seconds
+    _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
+
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+     
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+}
 
 void IResponseAnalysis::acquire()
 {
-
     Timer* save_timer;
-
     TimerCallback<IResponseAnalysis> save_callback(*this, &IResponseAnalysis::save_cb);
 
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
-
+    //_run_cnt = i;
-        _run_cnt = i;
+    //cout << "RUN NUM = " << i;
-
-        cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
    
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+    
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+   
+    //}
 }
 
 void IResponseAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+    cout<<"SYNTHESISING IRESPONSE";
+ 
+    //cout << "IResponseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) 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 //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                //ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+
+                //background subtraction// 
+                /*
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+               */
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                 //meshPix=make3DZmap(image1, image5, _background);
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        //}
+    }
+
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+}
+
+
+void IResponseAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_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;
+        }
+    }
 }
 
 
@@ -70,9 +249,18 @@ void IResponseAnalysis::draw()
             
         case STATE_ACQUIRING:
         {
-            /// *** TODO  *** ///
+            ofEnableAlphaBlending();
-            // still need to deal with latency frames here - i.e.: there are frames
+            ofColor aColour;
-            /// *** TODO  *** ///
+            int _fade_in_frames = _frame_cnt_max/10;
+            //cout<< "_fade_in_frames" << _fade_in_frames<< endl;
+            
+            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());
+            
+            }
             
             if (_frame_cnt < _frame_cnt_max)
             {
@@ -80,9 +268,18 @@ void IResponseAnalysis::draw()
                 ofRect(0, 0, ofGetWidth(), ofGetHeight());
                 c  = 255.0 * (_frame_cnt_max*_frame_cnt_max - _frame_cnt*_frame_cnt)/(_frame_cnt_max*_frame_cnt_max);
             } else {
+                
                 _RUN_DONE = true;
             }
             
+            if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
+                aColour.set(0, 0, 0, ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
+                ofSetColor(aColour);
+                ofRect(0, 0, ofGetWidth(), ofGetHeight());
+                // cout <<  "FADE OUT STROBE TIME " << endl;
+            }         
+            
+            ofDisableAlphaBlending();
             _frame_cnt++;
 
             break;
@@ -91,15 +288,118 @@ void IResponseAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            // cout << "IResponse = 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 << "IResponse 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;
+                _anim_cnt=0;
+            }
+            
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
          
+            
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-            break;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
+            break;
+            
+        }
         
         default:
             break;
@@ -112,17 +412,129 @@ void IResponseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    cout << "IResponseAnalysis::saving...\n";
-    //cout << "c_last... " << c << endl;
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    string thisLocation = RefractiveIndex::_location;
         
-    //RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    saveImageAnalysis(file_name);
-    //    fileName = imageSaveFolderPath+whichAnalysis+"_"+ofToString(100.0*i*scanLineSpeed/ofGetHeight(),2)+"%_"+ofToString(i)+".jpg";
-    //ofSaveImage(vectorOfPixels[i], fileName, OF_IMAGE_QUALITY_BEST);
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
 }
+
+void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    
+    ofColor meshColour=ofColor(255,0,0);
+    
+    int chooseColour=1  ;
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+         
+    if(chooseColour==1){
+        
+            for(int i=0;i<sPixels.size();i++){
+                mesh.addColor(  currentSecondImage.getColor(x, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y));
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+
+                x++;
+                if(x>=currentSecondImage.getWidth()-1){
+                    x=0;
+                    y++;
+                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                    if(y>=currentSecondImage.getHeight()-1){
+                        break;
+                    }
+                }
+            }
+    }
+}
+
+vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+        for(int i=0;i<imagePixels1.size();i++){
+            thesePixels[i]=0;
+        }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+           
+            //float _presumedBrightness=255;
+            
+            int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            float multiplier=4.0;
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+
+

src/IResponseAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 class IResponseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,6 +22,8 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -27,8 +31,39 @@ public:
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt;
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
-    float   c, _frame_cnt, _frame_cnt_max;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
   
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    //returns ofPixels but these pixels actually hold depth data.
+    //ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    bool _gotFirstImage;
+    ofImage _background;
 };

src/RelaxRateAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "RelaxRateAnalysis.h"
 #include "ofMain.h"
 
@@ -15,65 +10,366 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
+#define TRESHOLD        80
+#define MAXBLOBS        15
 
 void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 300;
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
-    NUM_RUN = 3;
-    NUM_SAVE_PER_RUN = 100;    
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_relaxrate", NUMBER_RUNS);
+    cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling_x       = 1; //must be at least '1'
+    vertexSubsampling_y       = 5; //must be at least '1'
+    chooseColour            = 2;
+    multiplier              = 4.0;
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    //meshMode = OF_PRIMITIVE_LINES;
+    meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_relaxrate", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
+    
+    _treshold = RefractiveIndex::XML.getValue("config:relaxrate:treshold", TRESHOLD);
+    cout << "TRESHOLD RelaxRateAnalysis " << _treshold << endl;
+    
+    _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
+    cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
+
+    
+    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
+    // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    
+    _run_cnt = 0;
     _level = 0;
     _flip = 1;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
     c = 0;
+    _synth_save_cnt = 0;
+    
+    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;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+        
 }
 
 
 void RelaxRateAnalysis::acquire()
 {
-
     Timer* save_timer;
-
     TimerCallback<RelaxRateAnalysis> save_callback(*this, &RelaxRateAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
-
+    //_run_cnt = i;
-        _run_cnt = i;
+    //cout << "RUN NUM = " << i;
-
-        cout << "RUN NUM = " << i;
     
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
   
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+  
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
     
     save_timer->stop();
-    }
+        
 }
 
 void RelaxRateAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+    // cout << "RelaxRate::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+        
+        //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            //        cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                //cvColorImage1.erode();
+                //cvColorImage1.erode();
+                //cvColorImage1.dilate();
+                
+                cvColorImage1.blur(1);
+                cvColorImage2.blur(1);
+                
+                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayImage1.convertToRange(0.0, 255.0);
+                //cvGrayImage2.convertToRange(0.0, 255.0);
+                
+                //cvGrayImage1.adaptiveThreshold( 200, 0);
+                //cvGrayImage2.adaptiveThreshold( 200, 0);
+                
+                //cvGrayImage1.contrastStretch();
+                //cvGrayImage2.contrastStretch();
+                
+                cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
+                
+                //cvGrayDiff1.brightnessContrast(1.0,0.5);
+                
+                //cvGrayImage1.brightnessContrast(1.0,0.5);
+                //cvGrayImage2.brightnessContrast(1.0,0.5);
+                
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */ 
+                
+                //DIFFERENCING THE BACKGROUND
+                
+                for(int i=0;i<imagePixels1.size();i++){
+                    //unsigned char val=imagePixels1[i];
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
+                }
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+                
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+                
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(10);
+    
 }
+void RelaxRateAnalysis::displayresults()
+{
+        
+    for(float i=1;i<_saved_filenames_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
 void RelaxRateAnalysis::draw()
 {
 
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+    
+    light.enable();	
+    lightStatic.enable();
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(2.0f);
+    glPointSize(1.0f);
+    
+    ofEnableBlendMode(blendMode);
+        
     switch (_state) {
         case STATE_ACQUIRING:
         {
-            /// *** TODO  *** ///
+            
-            // still need to deal with latency frames here - i.e.: there are frames
-            /// *** TODO  *** ///
             
             if (_frame_cnt < _frame_cnt_max)
             {
@@ -92,54 +388,577 @@ void RelaxRateAnalysis::draw()
                 }
                 
             } else {
-                cout << "RELAXRATE RUN COMPLETED" << endl;
+              
-                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
             
             _frame_cnt++;
-            cout << "_frame_cnt:" << _frame_cnt << endl;
+            //cout << "_frame_cnt:" << _frame_cnt << endl;
             
             break;
         }
             
         case STATE_SYNTHESISING:
         {
+            
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "RelaxRateAnalysis = 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 << "ShadowScapesAnalysis 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)){
+                    
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = MIDDLE OF ANIMATION...\n";
+                    
+                    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);
+                    }
+                }
+                
+                //cout << "_anim_cnt = " << _anim_cnt << endl;
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = FADE OUT OF ANIMATION...\n";
+                    
+                    //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);
+                        //cout << "c_anim = " << c_anim << endl;
+                        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;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
+            
-            break;
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
+                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
+                }
+
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
+            break;
+        
+        }
             
         default:
             break;
     }
 
-
-
 }
 
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void RelaxRateAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-    cout << "RelaxRateAnalysis::saving...\n";
+    
-    //cout << "c_last... " << c << endl;
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    string thisLocation = RefractiveIndex::_location;
     
-    string file = _whole_file_path+"/"+file_name;
+    saveImageAnalysis(file_name);
     
-    ofSaveImage(RefractiveIndex::_pixels, file, OF_IMAGE_QUALITY_BEST);
-    
-    _saved_filenames.push_back(file);
-
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-     //   _RUN_DONE = true;
     
 }
+
+void RelaxRateAnalysis::cleanup()
+{
+}
+
+
+void RelaxRateAnalysis::clearcfindervect()
+{
+    for(int i = 0; i < cvContourFinderVect.size(); i++) {
+        rfiCvContourFinder* f = cvContourFinderVect[i];
+
+        // maybe it's erase here?  http://forum.openframeworks.cc/index.php/topic,3016.0.html
+        // cvContourFinderVect.erase(i);
+        
+        delete f;        
+    }
+    cvContourFinderVect.clear();
+    
+}
+
+void RelaxRateAnalysis::clearcfindervectdisplay()
+{
+    cvContourFinderVectDisplay.clear();
+}
+
+
+
+
+void RelaxRateAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling_x;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling_y;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> RelaxRateAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/RelaxRateAnalysis.h

@@ -1,7 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #pragma once
 
@@ -9,6 +5,11 @@
 
 #include "Poco/Timer.h"
 
+#include "rfiCvContourFinder.h"
+
+#include "ofxOpenCv.h"
+
+
 
 class RelaxRateAnalysis : public AbstractAnalysis
 {
@@ -21,15 +22,69 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
+    void displayresults();
+    void cleanup();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
     
 protected:
     
+    void clearcfindervect();
+    void clearcfindervectdisplay();
+    
     bool    _RUN_DONE;
     float     _flip, _level;
-    int     _run_cnt, _save_cnt;
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
-    float   c, _frame_cnt, _frame_cnt_max;
+    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;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    
+    vector<rfiCvContourFinder*>      cvContourFinderVect;
+    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling_x;
+    int vertexSubsampling_y;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+    
 
 };

src/ShadowScapesAnalysis.cpp

@@ -1,35 +1,3 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
-
- + 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.
-
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ShadowScapesAnalysis.h"
 #include "ofMain.h"
 
@@ -37,59 +5,337 @@
 #include "Poco/Thread.h"
 #include "RefractiveIndex.h"
 
+//#include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
 using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
 #define STATE_SCAN      0
 #define STATE_ANALYSIS  1
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_PHASE = 1;
+    
-    NUM_RUN = 1;
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
-    NUM_SAVE_PER_RUN = 100;  
+    cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 1;
+    chooseColour            = 5;
+    multiplier              = 4.0;
+    
+    ofSetLineWidth(5.0f);
+    glPointSize(5.0f);
+    glEnable(GL_DEPTH_TEST);
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    //blendMode = OF_BLENDMODE_SUBTRACT;
+    blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+    
+    ///setup light    
+    ofEnableLighting();    
+    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
+    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
+    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
+    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
+    
+    glEnable(GL_LIGHT0);  
+    
+    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
+    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
+    
+    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
+    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
+    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
+    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
+    
+    glEnable(GL_LIGHT1);     
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
+    
+    int screenSpan;
+    if (_dir == V) screenSpan = ofGetHeight();
+    if (_dir == H) screenSpan = ofGetWidth();
+    if (_dir == D) screenSpan = ofGetHeight();
+    
+    _step = (screenSpan/acq_run_time)/(ofGetFrameRate());
+            // pixel per frame = (pixels / sec) / (frame / sec)
+    
+    // 40 pixels per second should give us a 20 second scan at 800 pixels wide
+
+    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
     
-    create_dir();
-    _speed = 900.0;  // 900.0 is the correct number
     _scanLineWidth = 100.0;
     _run_cnt = 0;
     _save_cnt = 0;
+    _synth_save_cnt = 0;
+
+    int anim_time = 10;   // 10 seconds
+    _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
+    
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+        
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+   
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+        
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+       
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    
 }
 
 void ShadowScapesAnalysis::acquire()
 {
-    int w;
-    if (_dir == V) w = ofGetHeight();
-    if (_dir == H) w = ofGetWidth();
-    if (_dir == D) w = ofGetHeight();
-    
-    _step = ((w/_speed) * 1000.0) / 500.0;
-    _line = 0;
-    
-    // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
         
     Timer save_timer(0, DELTA_T_SAVE);  
     TimerCallback<ShadowScapesAnalysis> save_callback(*this, &ShadowScapesAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _line = 0;
     _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
+
+    create_dir_allocate_images();
    
     save_timer.start(save_callback);
       
-        while(!_RUN_DONE)
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
     save_timer.stop();
-    }
 
 }
 
 void ShadowScapesAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+    //cout << "ShadowScapesAnalysis::saving synthesis...\n";
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
+    
+      //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
+        
+        // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+                
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //    cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                //cvGrayDiff1.erode();
+                
+                cvGrayImage1.dilate();
+                cvGrayImage1.blur(5);
+                cvGrayImage1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                
+                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+                
+                
+                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                
+                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                
+                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                
+                // convert the CV image 
+                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+                image5.setFromPixels(cvColorImage2.getPixelsRef());  
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                if(!_gotFirstImage){
+                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                    _background=image1;
+                    _gotFirstImage=true;
+                }
+                
+                //subtract background begin///////////////
+                
+                ofPixels imagePixels1       = image1.getPixelsRef();
+                ofPixels imagePixels2       = image5.getPixelsRef();
+                ofPixels backgroundPixels   = _background.getPixelsRef();
+                
+                //DIFFERENCING SUBSEQUENT IMAGES
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-imagePixels2[i]>0){
+                 imagePixels1[i]-=imagePixels2[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */ 
+                
+                //DIFFERENCING THE BACKGROUND
+                /*
+                 for(int i=0;i<imagePixels1.size();i++){
+                 //unsigned char val=imagePixels1[i];
+                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                 if(imagePixels1[i]-backgroundPixels[i]>0){
+                 imagePixels1[i]-=backgroundPixels[i];
+                 }
+                 else{
+                 imagePixels1[i]=0;
+                 }
+                 }
+                 */
+                
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
+                
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                //string file_name;
+        
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShadowScapeAnalysis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
+                
+                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+    }
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+     while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+}
+
+
+void ShadowScapesAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+       // cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
+
 }
 
 
@@ -163,24 +409,22 @@ void ShadowScapesAnalysis::draw()
             }
             
             
-            
             if(_dir == V && int(_line) >= (ofGetHeight()+4*_scanLineWidth)){
-                cout << "VERTICAL IS DONE - _line >= (ofGetHeight()+4*_scanLineWidth) is TRUE" << endl;
+                //cout << "VERTICAL IS DONE - _line >= (ofGetHeight()+4*_scanLineWidth) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
+                
             }
             
             if(_dir == H && int(_line) >= (ofGetWidth()+4*_scanLineWidth)) {
                 
                 //cout << "HORIZONTAL IS DONE -  _line >= (ofGetWidth()+4*_scanLineWidth)) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
                 
             }
             
             if(_dir == D && int(_line) >= (1.5*ofGetHeight()+4*_scanLineWidth)) {
                 //cout << "DIAGONAL IS DONE - _line >= (1.5*ofGetHeight()+4*_scanLineWidth)) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
+            
                 _RUN_DONE = true;
             }
         
@@ -189,15 +433,117 @@ void ShadowScapesAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
-            // display animation of something while the synthesis in on-going...
+           // cout << "ShadowScapesAnalysis = STATE_SYNTHESISING...\n";
 
-            _state = STATE_DISPLAY_RESULTS;
+            // 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 << "ShadowScapesAnalysis 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;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
             break;
+      
         }
             
         case STATE_DISPLAY_RESULTS:
         {
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+              //  cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                    ofSetColor(255, 255, 255);
+                
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                    image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+                
+                
+            }
+            
             // display results of the synthesis
+            _RUN_DONE = true;
+            
+            // clear allocated memory...? 
+            
             break;
         }
             
@@ -211,7 +557,8 @@ void ShadowScapesAnalysis::draw()
 void ShadowScapesAnalysis::save_cb(Timer& timer)
 {
     
-    cout << "ShadowScapesAnalysis::saving...\n";
+    _save_cnt++;
+        
     string file_name;
     
     if(_dir == H) {
@@ -226,7 +573,416 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
         
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    saveImageAnalysis(file_name);
-    _save_cnt++;    
         
 }
+
+
+
+
+void ShadowScapesAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+}
+
+
+vector<float> ShadowScapesAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            
+            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
+            
+            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
+            
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/ShadowScapesAnalysis.h

@@ -1,34 +1,4 @@
-/*
+/* */
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
- 
- + 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.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #pragma once
 
@@ -36,6 +6,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 enum shadow_type {
     H, V, D,
 };
@@ -52,6 +24,8 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -64,7 +38,48 @@ protected:
     float    _scanLineWidth; // pix per second
     float     _step;
     shadow_type _dir;
-    int     _run_cnt, _save_cnt;
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
-    float   c, _frame_cnt, _frame_cnt_max;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
 
 };

src/ShapeFromShadingAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 
 class ShapeFromShadingAnalysis : public AbstractAnalysis
 {
@@ -21,6 +23,7 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();    
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -28,9 +31,10 @@ public:
 protected:
     
     string quad;
+    string fileNameQuad;
+    
     bool    _RUN_DONE;
     float     _flip, _level;
-    int     _run_cnt, _save_cnt;
     int _animation_cnt1;
     int _animation_cnt2;
     int _animation_cnt3;
@@ -48,6 +52,51 @@ protected:
     int _animation_cnt15;
     int _animation_cnt16;
     int _animation_reset;  // this reset part didn't get working - so using 16 different counters! yay! 
-    float   c, _frame_cnt, _frame_cnt_max;
    
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+   
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
 };

src/StrobeAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "StrobeAnalysis.h"
 #include "ofMain.h"
 
@@ -15,22 +10,108 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    30
+
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
+    AbstractAnalysis::setup(camWidth, camHeight);
-    NUM_RUN = 1;
     
-    _strobe_cnt = 0;
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
-    _strobe_cnt_max = 20;  // 40 x 500 ms = 20000 ms = 20 seconds run time
+    cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
-    _strobe_interval = 1000;  //every 0.5seconds = 15 frames
+    //NUM_RUN = 5;
-    _frame_cnt_max = _strobe_cnt_max * _strobe_interval * ofGetFrameRate()/1000;
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    _mesh_size_multiplier   = 8;
+    vertexSubsampling       = 3;
+    chooseColour            = 2;
+    multiplier              = 4.0;
+    
+    //blendMode = OF_BLENDMODE_ADD;
+    //blendMode = OF_BLENDMODE_MULTIPLY;
+    blendMode = OF_BLENDMODE_SUBTRACT;
+    //blendMode = OF_BLENDMODE_ALPHA;
+    //blendMode = OF_BLENDMODE_SCREEN;
+    
+    //meshMode = OF_PRIMITIVE_TRIANGLES;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
+    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
+    meshMode = OF_PRIMITIVE_LINES;
+    //meshMode = OF_PRIMITIVE_LINE_STRIP;
+    //meshMode = OF_PRIMITIVE_POINTS;
+
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
+
+    //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
+                                          // 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
+    
+    _strobe_interval = 2000;  //every 1 seconds, or every thirty frames 30 frames
 
     // 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.
     
-    //or 20 times, every one second... 
+    //create_dir_allocate_images();
-    _save_cnt_max = _strobe_cnt_max*_strobe_interval/DELTA_T_SAVE;
+    _synth_save_cnt = 0;
+    _run_cnt = 0;
+    
+    int anim_time = 5;   // 5 seconds for the animation
+    _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
+    
+    _show_image = false;
+    _image_shown = false;
+    
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    //  images use for drawing the synthesized files to the screen ///
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
+   // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+   // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
+    
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    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);
+    
 
-    create_dir();
 }
 
 
@@ -38,39 +119,252 @@ void StrobeAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<StrobeAnalysis> save_callback(*this, &StrobeAnalysis::save_cb);
     
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0;  _strobe_cnt = 0, _synth_save_cnt = 0;
+    _run_cnt++;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
+    //_run_cnt = i;
-        _save_cnt = 0;
-        _frame_cnt = 0;
     
-        cout << "RUN NUM = " << i;
+    //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
     
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+  
+    
+    //}
 }
 
 void StrobeAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
+   // cout << "StrobeAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+    //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+        
+    //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+    //        cout << "didn't load image" << endl;
+        } 
+        
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+            //cvColorImage1.erode();
+            //cvColorImage1.erode();
+                //cvColorImage1.dilate();
+            
+            cvColorImage1.blur(1);
+            cvColorImage2.blur(1);
+            
+            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+            
+            //cvGrayImage1.convertToRange(0.0, 255.0);
+            //cvGrayImage2.convertToRange(0.0, 255.0);
+            
+            //cvGrayImage1.adaptiveThreshold( 200, 0);
+            //cvGrayImage2.adaptiveThreshold( 200, 0);
+            
+            //cvGrayImage1.contrastStretch();
+            //cvGrayImage2.contrastStretch();
+            
+            cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
+
+            cvGrayDiff1.brightnessContrast(1.0,0.5);
+            
+            //cvGrayImage1.brightnessContrast(1.0,0.5);
+            //cvGrayImage2.brightnessContrast(1.0,0.5);
+            
+            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+            
+            //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+            
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+            
+           
+            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+            
+            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
+            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+            
+            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
+            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            
+            // convert the CV image 
+            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            image5.setFromPixels(cvColorImage2.getPixelsRef()); 
+            
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            if(!_gotFirstImage){
+                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
+                _background=image1;
+                _gotFirstImage=true;
+            }
+            
+            //subtract background begin///////////////
+            
+            ofPixels imagePixels1       = image1.getPixelsRef();
+            ofPixels imagePixels2       = image5.getPixelsRef();
+            ofPixels backgroundPixels   = _background.getPixelsRef();
+            
+            //DIFFERENCING SUBSEQUENT IMAGES
+            /*
+             for(int i=0;i<imagePixels1.size();i++){
+             //unsigned char val=imagePixels1[i];
+             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+             if(imagePixels1[i]-imagePixels2[i]>0){
+             imagePixels1[i]-=imagePixels2[i];
+             }
+             else{
+             imagePixels1[i]=0;
+             }
+             }
+            */ 
+             
+            //DIFFERENCING THE BACKGROUND
+            
+             for(int i=0;i<imagePixels1.size();i++){
+             //unsigned char val=imagePixels1[i];
+             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+             if(imagePixels1[i]-backgroundPixels[i]>0){
+             imagePixels1[i]-=backgroundPixels[i];
+             }
+             else{
+             imagePixels1[i]=0;
+             }
+             }
+            
+            //update the images with their new background subtracted selves
+            image1.setFromPixels(imagePixels1);
+            
+            //flag the main app that we aren't read yet
+            meshIsComplete=false;
+            
+            //make a mesh - this mesh will be drawn in the main app
+            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            //string file_name;
+            
+            //with jpgs this was refusing to save out
+            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".png";
+            _saved_filenames_synthesis.push_back(meshFileName);
+            
+            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            //flag that we are finished  
+            meshIsComplete=true;
+            _synth_save_cnt++;
+            
+            }
+        } else {
+            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
+        }
+        
+    }
+    
+    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
+    /*
+     _RUN_DONE = true;
+     */
+    
+    meshIsComplete=false;
+    _synth_save_cnt=0;
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(10);
+
 }
 
+void StrobeAnalysis::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
 void StrobeAnalysis::draw()
 {
     
+    ofEnableSmoothing();
+    
+    ofEnableLighting(); 
+    ofEnableSeparateSpecularLight();         
+    light.setPointLight();
+    
+    light.enable();	
+    lightStatic.enable();
+    
+    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
+    
+    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
+    
+    glEnable(GL_DEPTH_TEST);
+    
+    ofSetLineWidth(1.0f);
+    glPointSize(5.0f);
+    
+    ofEnableBlendMode(blendMode);
+
+    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -80,7 +374,7 @@ void StrobeAnalysis::draw()
                 ofEnableAlphaBlending();
                 ofColor aColour;
                 int _fade_in_frames = _frame_cnt_max/10;
-                cout<< "_fade_in_frames" << _fade_in_frames<< endl;
+           //     cout<< "_fade_in_frames" << _fade_in_frames<< endl;
                 
                 if (_frame_cnt < _fade_in_frames) {
                     
@@ -89,7 +383,6 @@ void StrobeAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     //cout <<  "FADE IN STROBE TIME " << endl;
 
-                    
                 }
                 
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max-_fade_in_frames)){
@@ -98,13 +391,13 @@ void StrobeAnalysis::draw()
                     //cout <<  "frame_cnt % 15: " << _frame_cnt%15 << endl;
                     //cout <<  "MAIN STROBE TIME " << endl;
                     
-                    if (_frame_cnt%int(ofGetFrameRate()*_strobe_interval/1000) < (ofGetFrameRate()*_strobe_interval/1000)/2)
+                    if (int(_frame_cnt)%int(ofGetFrameRate()*_strobe_interval/1000) < (ofGetFrameRate()*_strobe_interval/1000)/2)
                     {
                         ofSetColor(255, 255, 255);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                         _strobe_cnt++;
                         _strobe_on = 1;
-                    } else if (_frame_cnt%int(ofGetFrameRate()*_strobe_interval/1000) >= (ofGetFrameRate()*_strobe_interval/1000)/2)
+                    } else if (int(_frame_cnt)%int(ofGetFrameRate()*_strobe_interval/1000) >= (ofGetFrameRate()*_strobe_interval/1000)/2)
                     {
                         ofSetColor(0, 0, 0);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
@@ -114,14 +407,16 @@ void StrobeAnalysis::draw()
                 }
                 
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
-                    aColour.set(255, 255, 255, 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                    aColour.set(255, 255, 255, 255-ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
                     ofSetColor(aColour);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     // cout <<  "FADE OUT STROBE TIME " << endl;
                 }         
     
                 ofDisableAlphaBlending();
+                
             } else {
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
             
@@ -133,13 +428,117 @@ void StrobeAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+          //  cout << "StrobeAnalysis = 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 << "StrobeAnalysis 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;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
+            
+         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+         //       cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
             // display results of the synthesis
+            _RUN_DONE = true;
             break;
+
+
         }
             
             
@@ -152,17 +551,414 @@ void StrobeAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void StrobeAnalysis::save_cb(Timer& timer)
 {
-    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     _save_cnt++;    
     
-    cout << "_save_cnt" << _save_cnt << endl;
+    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    cout << "_save_cnt_max" << _save_cnt_max << endl;
+    saveImageAnalysis(file_name);
+}
 
-    //TODO:  something fucked here with my calc of _save_cnt_max - new structure should fix it?   
+void StrobeAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    //if(_save_cnt >= _save_cnt_max-10) {
+    int x=0;
-    //    _RUN_DONE = true;
+    int y=0;
-    //}
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(meshMode);
+    
+    ofColor meshColour=ofColor(255,255,255);
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
+    }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+    
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+    
+    if(chooseColour==1){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x, y));
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==2){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==3){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            mesh.addColor(  currentSecondImageColor);
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==4){
+        
+        for(int i=0;i<sPixels.size();i++){
+            ofColor currentSecondImageColor;
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            int randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            mesh.addColor(  currentSecondImageColor.getBrightness());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
+            
+            ofSeedRandom();
+            
+            currentSecondImageColor.r = ofRandom(0,255);
+            currentSecondImageColor.g = ofRandom(0,255);
+            currentSecondImageColor.b = ofRandom(0,255);
+            
+            randomJitter = ofRandom(0,5);
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
+    
+    if(chooseColour==5){
+        
+        for(int i=0;i<sPixels.size();i++){
+            
+            int randomJitter2 = 0;
+            int randomJitter = 0;
+            
+            ofColor currentSecondImageColor;
+            ofColor currentSecondImageBW;
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor( currentSecondImageBW.clamp() );
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
+            
+            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp());
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
+            
+            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
+            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
+            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
+            
+            mesh.addColor(  currentSecondImageBW.clamp() ); 
+            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
+            
+            x=x+vertexSubsampling;
+            if(x>=currentSecondImage.getWidth()-1){
+                x=0;
+                y=y+vertexSubsampling;
+                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                if(y>=currentSecondImage.getHeight()-1){
+                    break;
+                }
+            }
+        }
+    }
     
 }
+
+
+vector<float> StrobeAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    //ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
+    
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor imageColor1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            
+            //int thisDiff=abs(imageColor1.getHue());
+            //int thisDiff=abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=-abs(imageColor1.getBrightness());
+            //int thisDiff=abs(imageColor1.getLightness());
+            //int thisDiff=-abs(imageColor1.r);
+            
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            differences.push_back(multiplier * thisDiff);
+            
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+            }
+        }
+    }
+    
+    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+}
+

src/StrobeAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 
 class StrobeAnalysis : public AbstractAnalysis
 {
@@ -21,6 +23,8 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
@@ -28,10 +32,53 @@ public:
 protected:
     
     bool    _RUN_DONE;
-    int     _strobe_cnt, _run_cnt, _strobe_cnt_max;
+    int     _strobe_cnt, _strobe_cnt_max;
-    int     _save_cnt;
     
-    int     _frame_cnt, _frame_cnt_max, _save_cnt_max ;
     int     _strobe_interval;
     bool    _strobe_on;
+    
+    int     _run_cnt, _save_cnt,_synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //mesh making function
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    
+    //depth map function
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    
+    int vertexSubsampling;
+    int chooseColour;
+    ofPrimitiveMode meshMode;
+    ofBlendMode blendMode;
+    float multiplier;
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
+
 };

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