beginning to integrate dviid's code

colorsingleanalysis has some initial vectorisation code

.gitignore

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

config.refindx

@@ -0,0 +1,45 @@
+<!-- THIS FILE NEEDS TO GO IN THE APPLICATION /data/ folder -->
+
+<config>
+<camera>
+<id>1</id>
+<width>640</width>
+<height>480</height>
+</camera>
+<display>
+<fps>30</fps>
+</display>
+<locale>
+<name>SWANSEA</name>
+</locale>
+
+<analysis_NUM_RUN>
+<NUM_RUN_shadowscapes>          3      </NUM_RUN_shadowscapes>
+<NUM_RUN_relaxrate>             3      </NUM_RUN_relaxrate>
+<NUM_RUN_iresponse>             3      </NUM_RUN_iresponse>
+<NUM_RUN_shapefromshading>      3      </NUM_RUN_shapefromshading>
+<NUM_RUN_strobe>                5      </NUM_RUN_strobe>
+<NUM_RUN_camnoise>              5      </NUM_RUN_camnoise>
+<NUM_RUN_colorsingle>           5      </NUM_RUN_colorsingle>
+<NUM_RUN_colormulti>            5      </NUM_RUN_colormulti>
+<NUM_RUN_diffnoise>             3      </NUM_RUN_diffnoise>
+</analysis_NUM_RUN>
+
+<analysis_time>
+<acquiretime_shadowscapes>      30      </acquiretime_shadowscapes>
+<acquiretime_relaxrate>         30      </acquiretime_relaxrate>
+<acquiretime_iresponse>         30      </acquiretime_iresponse>
+<acquiretime_shapefromshading>  30      </acquiretime_shapefromshading>
+<acquiretime_strobe>            30      </acquiretime_strobe>
+<acquiretime_camnoise>          30      </acquiretime_camnoise>
+<acquiretime_colorsingle>       40      </acquiretime_colorsingle>
+<acquiretime_colormulti>        40      </acquiretime_colormulti>
+<acquiretime_diffnoise>         30      </acquiretime_diffnoise>
+</analysis_time>
+
+<relaxrate>
+<threshold>51</threshold>
+<maxblobs>25</maxblobs>
+</relaxrate>
+
+</config>

example/RefractiveIndex.cpp

@@ -19,7 +19,7 @@
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
-#define LOCATION            "MANCHESTER"
+#define LOCATION            "MIDDLESBOROUGH"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -42,10 +42,6 @@ ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
-    camDist=1000;
-    
-    ofBackground(0, 0, 0);
-    ofSetBackgroundAuto(false);
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -59,7 +55,7 @@ void RefractiveIndex::setup()
     // <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;
@@ -69,12 +65,12 @@ void RefractiveIndex::setup()
     
     // <display>
     int fps = XML.getValue("config:display:fps", 30);
-            
+    
     // <location>
     _location = XML.getValue("config:locale:name", LOCATION);
-        
+    
     cout << "Configuring..." << endl;
-
+    
     // display
     cout << "> display" << endl;
     ofSetFrameRate(fps);
@@ -98,34 +94,37 @@ void RefractiveIndex::setup()
     }
     
     cout << "RRRRRREADY!" << endl;        
-
+    
     _analysisAdapator = NULL;
-
+    
     //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));  //1
-    _analysisVector.push_back(new ShadowScapesAnalysis(H));  //2
-    _analysisVector.push_back(new ShadowScapesAnalysis(D));  //3
-	    
-    _analysisVector.push_back(new RelaxRateAnalysis());   //4
+    _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
+    _analysisVector.push_back(new ShadowScapesAnalysis(H));
+    _analysisVector.push_back(new ShadowScapesAnalysis(D));
+    
+    _analysisVector.push_back(new RelaxRateAnalysis());
+    
 	
-    _analysisVector.push_back(new IResponseAnalysis());   //5
+    _analysisVector.push_back(new IResponseAnalysis());
     
-    _analysisVector.push_back(new ShapeFromShadingAnalysis());   //6
+    _analysisVector.push_back(new ShapeFromShadingAnalysis());
     
-    _analysisVector.push_back(new StrobeAnalysis());   //7
+    _analysisVector.push_back(new StrobeAnalysis());
     
-    _analysisVector.push_back(new CamNoiseAnalysis());    //8
+    _analysisVector.push_back(new CamNoiseAnalysis());
     
-    _analysisVector.push_back(new ColorSingleAnalysis());    //9
+    _analysisVector.push_back(new ColorSingleAnalysis());
     
-    _analysisVector.push_back(new ColorMultiAnalysis());    //0
+    _analysisVector.push_back(new ColorMultiAnalysis());
+    
+    _analysisVector.push_back(new DiffNoiseAnalysis());	
     
-    _analysisVector.push_back(new DiffNoiseAnalysis());	  //Q
     
     //_currentAnalysisIndx = 0;
     //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
@@ -133,13 +132,13 @@ void RefractiveIndex::setup()
     
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
-  
     
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
 {
     assert(analysis == _currentAnalysis->_name);
+    
     _state = ISTATE_STOP;    
 }
 
@@ -149,17 +148,6 @@ 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()
@@ -222,53 +210,9 @@ void RefractiveIndex::draw()
     
     // 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()
@@ -327,7 +271,7 @@ void RefractiveIndex::keyPressed  (int key)
         if(!_currentAnalysis)
             _state = ISTATE_TRANSITION;            
     }
-
+    
     else if(key == '2')
     {
         if(_currentAnalysis)
@@ -336,7 +280,7 @@ void RefractiveIndex::keyPressed  (int key)
         if(!_currentAnalysis)
             _state = ISTATE_TRANSITION;            
     }
-
+    
     else if(key == '3')
     {        
         if(_currentAnalysis)
@@ -408,7 +352,7 @@ void RefractiveIndex::keyPressed  (int key)
         if(!_currentAnalysis)
             _state = ISTATE_TRANSITION;            
     }
-
+    
     else if(key == 'q')
     {
         if(_currentAnalysis)
@@ -422,42 +366,42 @@ void RefractiveIndex::keyPressed  (int key)
      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;
-    */
+     >> 		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;
+     */
     
     
 }

example/RefractiveIndex.h

@@ -10,8 +10,6 @@
 
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.h"
-#include "ofxOpenCv.h"
-
 
 #define MODE_DRAWING        0xEEFF
 #define MODE_ANALYSING      0xFFEE
@@ -56,9 +54,6 @@ protected:
     AnalysisAdaptor*            _analysisAdapator;
     vector<AbstractAnalysis*>   _analysisVector;    
     
-    float                         _meshRotation;
-    float                           camDist;
-    ofEasyCam                     cam;
 public:    
     // acquisition
     static ofPixels         _pixels;    
@@ -73,8 +68,5 @@ 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

@@ -1,8 +1,8 @@
 #include "ofAppGlutWindow.h"
 #include "RefractiveIndex.h"
 
-#define SCREEN_WIDTH        1280
-#define SCREEN_HEIGHT       800
+#define SCREEN_WIDTH        800
+#define SCREEN_HEIGHT       600
 
 int main() {
     

src/AbstractAnalysis.cpp

@@ -3,76 +3,31 @@
 #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++) {
+    for(int i = 0; i < NUM_RUN; i++) {
+        
+        cout << "NUM_RUN: " << i << endl;
                 
-                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:
-        {            
+        _saved_filenames_analysis.clear();  
+        _saved_filenames_synthesis.clear(); 
 
-
-            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();            
-        }
+        _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();
     }
     
-exit:    
+    exit:    
     cleanup();
-    ofNotifyEvent(_synthesize_cb, _name);    
-    
+    ofNotifyEvent(_synthesize_cb, _name);
 }
 
 void AbstractAnalysis::create_dir_allocate_images()
@@ -157,38 +112,10 @@ void AbstractAnalysis::create_dir_allocate_images()
     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)
 {
     
@@ -227,6 +154,7 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
 {
     
 #ifdef TARGET_OSX   
+    
 
     ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
     
@@ -252,6 +180,6 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
 #endif
     
     _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+filename);
-            
     
 }
+

src/AbstractAnalysis.h

@@ -25,7 +25,7 @@ public:
     virtual ~AbstractAnalysis(){;}
     
     // generic function to set up the camera
-    virtual void setup(int camWidth, int camHeight);  
+    virtual void setup(int camWidth, int camHeight){_cam_w = camWidth; _cam_h = camHeight;}  
 
     // this is the main threaded loop for a given analysis
     void do_synthesize();
@@ -37,8 +37,6 @@ protected:
     
     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);
     
@@ -56,29 +54,11 @@ protected:
     
         
 public:
-    string  _name;       
-    string  _draw_directory;
+    string  _name;    
     
     // 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_analysis, _whole_file_path_synthesis;

src/CamNoiseAnalysis.cpp

@@ -15,68 +15,10 @@ using Poco::Thread;
 
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
     cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
 
-    
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 1;
-    chooseColour            = 6;
-    multiplier              = 4.0;
-    
-    ofSetLineWidth(5.0f);
-    glPointSize(5.0f);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-   // meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    meshMode = OF_PRIMITIVE_POINTS;
-    
-    ///setup light    
-    ofEnableLighting();    
-    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
-    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
-    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
-    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-    
-    glEnable(GL_LIGHT0);  
-    
-    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
-    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
-    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
-    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-    
-    glEnable(GL_LIGHT1);     
-    glPointSize(9.0f);
-    glEnable(GL_POINT_SMOOTH);
-    glCullFace(GL_BACK);
-    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;
@@ -138,6 +80,7 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.clear();
     cvGrayDiff2.clear();
 
+    cvConvertorImage.clear();
 
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -146,6 +89,9 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     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);
+
 }
 
 
@@ -181,26 +127,11 @@ void CamNoiseAnalysis::synthesise()
 {
     //cout << "CamNoiseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
-    
-    _returnAveragePixelValues();
-    vector<vector<float> > averagePixelBrightnessesForEachLevel = averagePixelValuesForAllLevels;
-    float lightLevel=0;
-    float pLightLevel=0;
-    cout<<_listOfLightLevels.size()<<" "<<averagePixelBrightnessesForEachLevel.size()<<" these should be the same";
-    
+
     for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
-        
-        lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
+
         //cout << "CamNoiseAnalysis::synthesis FOR LOOP...\n";
-        
-        //find which list of average pixel values is for THIS light level
-        int _averagePixelVectorIndex;
-        for (int j=0; j<_listOfLightLevels.size(); j+=3) {
-            if(lightLevel==_listOfLightLevels[j]){
-                _averagePixelVectorIndex=j;
-            }
-        }
+
         //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
 
         if(_state == STATE_STOP) return;
@@ -211,118 +142,63 @@ void CamNoiseAnalysis::synthesise()
         }
 
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //    cout << "LOADED image1!!!" << endl;
-            if(image5.loadImage(_saved_filenames_analysis[i+1])){
-                
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                
-             /*   cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
-                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
-                
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
-                
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                
-                cvGrayImage1.dilate();
-                cvGrayImage1.blur(5);
-                cvGrayImage1.contrastStretch();
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
-                
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
-                
-                
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
-                
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-                
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-                
-                // convert the CV image 
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-                image5.setFromPixels(cvColorImage2.getPixelsRef());  
-                */
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
-                
-                //subtract background begin///////////////
-                
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */ 
-                
-                //DIFFERENCING THE BACKGROUND
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-backgroundPixels[i]>0){
-                 imagePixels1[i]-=backgroundPixels[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */
-                
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, averagePixelBrightnessesForEachLevel[_averagePixelVectorIndex], _background), image1, image1, aMesh);
-                
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
-                
-                //with jpgs this was refusing to save out
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
-                _saved_filenames_synthesis.push_back(meshFileName);
-                
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //flag that we are finished  
-                meshIsComplete=true;
-                _synth_save_cnt++;
-                
-            }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
-        }
+            //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);
+            //added by tom we weren't actually setting cvgrayimage1 anywhere
+           // cvGrayImage1.setFromPixels(cvColorImage1.getPixels(),cvColorImage1.width,cvColorImage1.height);
+            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+//cvGrayImage1=cvColorImage1;
+
+            cvGrayImage1.erode();
+            cvGrayImage1.erode();
+            cvGrayImage1.erode();
+            cvGrayImage1.blur();
+            cvGrayImage1.contrastStretch();
+           /* cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.blur();
+            cvColorImage1.contrastStretch();*/
+
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
+
+            file_name = ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+
+
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+
+
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
+
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);
+
+            //image.setFromPixels(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            cvConvertorImage.setFromGrayscalePlanarImages(cvGrayImage1,cvGrayImage1,cvGrayImage1);
+            //cvConvertorImage.setFromGrayscalePlanarImages(cvColorImage1,cvColorImage1,cvColorImage1);
+            saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+            _synth_save_cnt++;
+
+
+            //}
+        }
     }
 
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
@@ -556,533 +432,3 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 
     saveImageAnalysis(file_name);
 }
-
-
-
-void CamNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //to do 
-    
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    if(chooseColour==6){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x++;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y++;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-
-}
-
-
-vector<float> CamNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    int inc=0;
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            if(i<100){
-                
-              //  cout<<" average: "<<averageDepths[inc]<<" actual: "<<imageColor1.getBrightness()<<" ";
-            }
-           // int thisDiff=imageColor1.getBrightness();
-            
-            int thisDiff=-(imageColor1.getBrightness() - averageDepths[inc] );
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-            inc++;
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-
-
-void CamNoiseAnalysis:: _returnAveragePixelValues(){
-    
-    
-    //second number in 15_204.00_2.jpg is the light level
-    
-    float lightLevel=0;
-    float pLightLevel=0;
-    float numberOfImagesActuallyLoaded=0;
-    vector<float> averagePixelValuesForOneLevel;
-
-    for (int j=0; j<RefractiveIndex::_vid_w*RefractiveIndex::_vid_h; j++) {
-        averagePixelValuesForOneLevel.push_back(0.0);
-    }
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        
-        
-        if(_state == STATE_STOP) return;
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
-            //couldn't load image
-            cout << "didn't load image" << endl;
-        }
-        
-        if(image1.loadImage(_saved_filenames_analysis[i])){
-
-            //split file name by under score
-            vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
-            
-            lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
-           // cout<<" lightLevel "<<lightLevel;
-
-            ofPixels image1Pixels=image1.getPixelsRef();
-            
-            int x=0;
-            int y=0;
-            int inc=0;
-            for (int j=0; j<image1Pixels.size(); j+=3) {
-                ofColor color=image1Pixels.getColor(x, y);
-                averagePixelValuesForOneLevel[inc]+= color.getBrightness();
-                x++;
-                inc++;
-                if(x>=image1Pixels.getWidth()){ 
-                    x=0;
-                    y++;
-                }
-            }
-           // _listOfLightLevels}
-            numberOfImagesActuallyLoaded++;
-            
-            //if this is a new light level advance
-            if (lightLevel!=pLightLevel) {
-                
-                ///check that this light level is not already in our list
-                
-                
-             _listOfLightLevels.push_back(lightLevel);
-                
-                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
-                    averagePixelValuesForOneLevel[j]/=numberOfImagesActuallyLoaded;
-                    //cout<<" "<<averagePixelValuesForOneLevel[j]<<" ";
-                }
-                averagePixelValuesForAllLevels.push_back(averagePixelValuesForOneLevel);
-                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
-                    averagePixelValuesForOneLevel[j]=0;
-                }
-
-                pLightLevel=lightLevel;
-                numberOfImagesActuallyLoaded=0;
-
-            }
-
-        }
-    }
-    
-    for(int j=0;j<_listOfLightLevels.size();j++){
-        //cout<<_listOfLightLevels[j]<<" lightlevel ";
-    }
-    
-}

src/CamNoiseAnalysis.h

@@ -61,29 +61,7 @@ protected:
     
     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;
-
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
     
 };

src/ColorMultiAnalysis.cpp

@@ -14,20 +14,10 @@ using Poco::Thread;
 
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
     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;
@@ -149,7 +139,6 @@ void ColorMultiAnalysis::synthesise()
             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])){
@@ -159,91 +148,47 @@ void ColorMultiAnalysis::synthesise()
             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);
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.dilate();
+            cvColorImage1.blur(5);
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
             
             /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            //string file_name;
+            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";
             
-            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
             
-            //flag that we are finished  
-            meshIsComplete=true;
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            
+            
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);  
+           
+            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+            
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
             _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);
 }
@@ -279,27 +224,6 @@ void ColorMultiAnalysis::displayresults()
 void ColorMultiAnalysis::draw()
 {
     
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();     
-    light.enable();
-	
-    light.setPosition(200,200,-150);
-    lightStatic.enable();
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(2.0f);
-    //glPointSize(4.0f);
-    
-    ofEnableBlendMode ( OF_BLENDMODE_ADD );
-    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
-    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
-    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
-    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
-
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -322,8 +246,6 @@ void ColorMultiAnalysis::draw()
                     //cout << "FADING IN..." << endl;
                 }
                 
-                
-                
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < _frame_cnt_max-_fade_in_frames){
                     
                     aColor.setHsb(c, 255, 255);
@@ -485,156 +407,8 @@ void ColorMultiAnalysis::draw()
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
+            
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
+
     saveImageAnalysis(file_name);    
 }
-
-
-void ColorMultiAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    
-    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
-    //mesh.setMode(OF_PRIMITIVE_LINES);
-    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
-    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
-    //mesh.setMode(OF_PRIMITIVE_POINTS);
-    
-    /*
-     OF_PRIMITIVE_TRIANGLES,
-     OF_PRIMITIVE_TRIANGLE_STRIP,
-     OF_PRIMITIVE_TRIANGLE_FAN,
-     OF_PRIMITIVE_LINES,
-     OF_PRIMITIVE_LINE_STRIP,
-     OF_PRIMITIVE_LINE_LOOP,
-     OF_PRIMITIVE_POINTS
-     
-     */
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-   
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-}
-
-
-
-vector<float> ColorMultiAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        //float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            //float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getLightness());
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            float multiplier=15.0*((thisDiff)/255.0);
-            
-            differences.push_back(multiplier* thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}

src/ColorMultiAnalysis.h

@@ -58,18 +58,5 @@ protected:
     //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

@@ -1,11 +1,9 @@
 #include "ColorSingleAnalysis.h"
 #include "ofMain.h"
+
 #include "Poco/Timer.h"
 #include "Poco/Thread.h"
 
-#include <string>
-#include <iostream>
-
 #include "RefractiveIndex.h"
 
 using Poco::Timer;
@@ -17,24 +15,14 @@ using Poco::Thread;
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     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
@@ -57,8 +45,7 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     b = 0;
     
     fileNameTag = "";
-    fileNameColor = "";
-    
+
     _show_image = false;
     _image_shown = false;
     
@@ -107,16 +94,18 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
-    cvConvertorImage.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;
@@ -135,6 +124,7 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
+    // }
 }
 
 void ColorSingleAnalysis::synthesise()
@@ -144,146 +134,186 @@ void ColorSingleAnalysis::synthesise()
     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;
         
+        image1.loadImage("Mar_02_19_00_47_2/194_9.72_1.jpg");
+        image1.resize(image1.width/20, image1.height/20);
+        
+        int width = image1.width;
+        int height = image1.height;
+        
+        // get the pixels from the image
+        imagePixels = image1.getPixels();
+        
+        // ------------------- create the vector field ------------------------------------
+        
+        vectorCount = width * height;
+        
+        // create a 2d vector field
+        vectorField = new ofVec2f[vectorCount];
+        
+        // set all values in vector field to 0.0
+        for(int i=0; i<vectorCount; i++){
+            
+            vectorField[i].x = 0.0;
+            vectorField[i].y = 0.0;
+        }
+        
+        
+        // ------------------- calculate the vectors ------------------------------------
+        
+        // loop through all of the pixels
+        for(int x=1; x< width-1; x++){
+            for(int y=1; y< height-1; y++){
+                
+                char areaPixels[9];
+                
+                // loop through the area pixels
+                for(int i=-1; i<=1; i++){
+                    for(int j=-1; j<=1; j++){
+                        
+                        // determine where to read from in the area (not optimized)
+                        int readPos = ((y + j) * width + (x + i)) * 3;
+                        
+                        unsigned char R = imagePixels[readPos];
+                        unsigned char G = imagePixels[readPos+1];
+                        unsigned char B = imagePixels[readPos+2];
+                        
+                        unsigned char BR = (0.299 * R) + (.587 * G) + (.114 * B);
+                        
+                        int writePos = (j+1) * 3 + (i + 1);
+                        
+                        areaPixels[writePos] = BR;
+                    }
+                }
+                
+                
+                
+                float dX = (areaPixels[0] + areaPixels[3] + areaPixels[6])/3 - (areaPixels[2] + areaPixels[5] + areaPixels[8])/3;
+                float dY = (areaPixels[0] + areaPixels[1] + areaPixels[2])/3 - (areaPixels[6] + areaPixels[7] + areaPixels[8])/3;
+                
+                int vectorPos = y * width + x;
+                
+                //printf("dx %f\n", dX);
+                
+                vectorField[vectorPos].x = dX;
+                vectorField[vectorPos].y = dY;
+                
+                //vectorField[vectorPos].x = -dY;
+                //vectorField[vectorPos].y = dX;
+                
+            }
+        }
+        
+        
+        
+        // ------------------- normalize the vectors ------------------------------------
+        
+        // variables for the maximum magnitude (absolute) in x and y
+        float maxMagX = 1.0;
+        float maxMagY = 1.0;
+        
+        // loop through the vector field to find the maximum x and y values
+        for(int i=0; i< vectorCount; i++){
+            
+            if(fabs(vectorField[i].x) > maxMagX)  maxMagX = fabs(vectorField[i].x);
+            if(fabs(vectorField[i].y) > maxMagY)  maxMagY = fabs(vectorField[i].y);
+        }
+        
+        // loop through the vector field to normalize the values
+        for(int i=0; i< vectorCount; i++){
+            
+            vectorField[i].x /= maxMagX;
+            vectorField[i].y /= maxMagY;
+        }
+        
+        // COMMENTING OUT THE FILLER SYNTH ALGORITHM
+        /*  
         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])){
+            //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.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.dilate();
+                cvColorImage1.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.erode();
                 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;
+                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";
+                
+                
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+                
+                // This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? 
+                //image.setUseTexture(false);  
+                
+                //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
             
-                //flag that we are finished  
-                meshIsComplete=true;
+                saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
                 _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()
 {
+    
+    if(_state == STATE_STOP) return;
+    
+    _show_image = true;
+    _image_shown = false;
+    
+    //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+    
+    while(!_image_shown){
+        Thread::sleep(2);
+        //cout << "!_image_shown" << endl;
+    }
+    
+    /*
     for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
         if(_state == STATE_STOP) return;
@@ -307,37 +337,17 @@ void ColorSingleAnalysis::displayresults()
             _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)
             {
                     
@@ -483,8 +493,48 @@ void ColorSingleAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             
-            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            cout << "case STATE_DISPLAY_RESULTS = true" << endl;
+
+            int width = image1.width;
+            int height = image1.height;
+            float spacing = 10;
             
+            if (_frame_cnt > 2000)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+
+            if (_show_image)
+            {  
+                
+                
+                cout << "_show_image = true" << endl;
+               
+                for(int x=0; x<width; x++){
+                    
+                    float xPos = (float) x * spacing + 5;
+                    
+                    for(int y=0; y<height; y++){
+                        float yPos = (float)y * spacing + 5;
+                        glPushMatrix();
+                            ofLine(xPos, yPos, xPos+(vectorField[y*width+x].x*spacing), yPos+(vectorField[y*width+x].y*spacing));
+                        glPopMatrix();
+                    }
+                }
+                
+                //this is where we save the full-frame software output to file... after the vectors, etc. are rendered... 
+                //saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
+                
+            }
+            
+            _RUN_DONE = true;
+            break;
+
+            /*
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
             if (_frame_cnt > 2)
             {
@@ -500,9 +550,9 @@ void ColorSingleAnalysis::draw()
                 
                 ofEnableAlphaBlending();
                 
-                ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                    ofSetColor(255, 255, 255);
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                    image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
             }
@@ -510,12 +560,11 @@ void ColorSingleAnalysis::draw()
             // display results of the synthesis
             _RUN_DONE = true;
             break;
-
-
-        }
+            */
             
+        }
         default:
-            break;
+        break;
     }
     
 }
@@ -529,278 +578,3 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
-
-
-
-void ColorSingleAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-   
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLES);
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
-    //mesh.setMode(OF_PRIMITIVE_LINES);
-    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
-    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
-    mesh.setMode(OF_PRIMITIVE_POINTS);
-  
-    /*
-     OF_PRIMITIVE_TRIANGLES,
-     OF_PRIMITIVE_TRIANGLE_STRIP,
-     OF_PRIMITIVE_TRIANGLE_FAN,
-     OF_PRIMITIVE_LINES,
-     OF_PRIMITIVE_LINE_STRIP,
-     OF_PRIMITIVE_LINE_LOOP,
-     OF_PRIMITIVE_POINTS
-     
-     */
-    
-    ofColor meshColour=ofColor(255,255,255, 255);
-    
-      //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-                
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-             
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-      
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        ofColor currentSecondImageColor;
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            if(fileNameColor=="RED")
-            {
-                currentSecondImageColor.r=255;
-                currentSecondImageColor.g=0;
-                currentSecondImageColor.b=0;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="GREEN")
-            {
-                currentSecondImageColor.r=0;
-                currentSecondImageColor.g=255;
-                currentSecondImageColor.b=0;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="BLUE")
-            {
-                currentSecondImageColor.r=0;
-                currentSecondImageColor.g=0;
-                currentSecondImageColor.b=255;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="FADING")
-            {
-                currentSecondImageColor.r= 255;
-                currentSecondImageColor.g= 255;
-                currentSecondImageColor.b= 255;
-                currentSecondImageColor.a= 255;
-            }
-                       
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-           
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor( currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            //x++;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //y++;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-}
-
-
-vector<float> ColorSingleAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-        
-            int thisDiff;
-            
-            if(fileNameColor=="RED")
-            {   
-                //thisDiff=abs(imageColor1.r);
-
-                thisDiff=abs(255-imageColor1.r);
-            } else if(fileNameColor=="GREEN")
-            {
-                //thisDiff=abs(imageColor1.g);                
-
-                thisDiff=abs(255-imageColor1.g);  
-                
-            } else if(fileNameColor=="BLUE")
-            {
-                //thisDiff=abs(imageColor1.b);
-
-                thisDiff=abs(255-imageColor1.b);
-            
-            } else if(fileNameColor=="FADING") {
-            
-                //thisDiff=imageColor1.getBrightness();
-                thisDiff=255-imageColor1.getBrightness();
-
-            }
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            float multiplier=8.0;
-            
-            differences.push_back(multiplier* thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-    /*
+/*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -32,7 +32,6 @@ protected:
 
     bool    _RUN_DONE;
     string  fileNameTag;
-    string  fileNameColor;
     float   r,g,b;
     
     int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
@@ -61,24 +60,13 @@ protected:
     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;
     
+    unsigned char * imagePixels;
+    int vectorCount;
+    ofVec2f * vectorField;
     
-    //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

@@ -15,35 +15,10 @@ using Poco::Thread;
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
- 
     cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 10;
-    vertexSubsampling       = 1;
-    chooseColour            = 5;
-    multiplier              = 4.0;
-
-    blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-        
-    meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    //meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
-    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
@@ -114,6 +89,7 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
     cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
 }
 
 
@@ -173,133 +149,45 @@ void DiffNoiseAnalysis::synthesise()
             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();
+            cvColorImage1.invert();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
             
-            //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;
+            //////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
             
-            //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);
+            file_name = ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
             
-            //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;
-            }
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
             
-            //subtract background begin///////////////
             
-            ofPixels imagePixels1       = image1.getPixelsRef();
-            //ofPixels imagePixels2       = image5.getPixelsRef();
-            ofPixels backgroundPixels   = _background.getPixelsRef();
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvColorImage1.width, cvGrayImage1.height, OF_IMAGE_COLOR);
             
-                //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);
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);  
             
-            //flag the main app that we aren't read yet
-            meshIsComplete=false;
+            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-            //make a mesh - this mesh will be drawn in the main app
-            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
             
-            //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;
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
             _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);
     
@@ -338,27 +226,7 @@ void DiffNoiseAnalysis::displayresults()
 
 // 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:
         {
@@ -405,6 +273,7 @@ void DiffNoiseAnalysis::draw()
                     }        
                 }
                 
+                
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
@@ -565,408 +434,3 @@ void DiffNoiseAnalysis::save_cb(Timer& timer)
 
     saveImageAnalysis(file_name);
 }
-
-
-void DiffNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-        
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-        
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-        
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-        
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor( currentSecondImageBW.clamp() );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> DiffNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}

src/DiffNoiseAnalysis.h

@@ -63,20 +63,4 @@ protected:
     //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

@@ -15,28 +15,15 @@ using Poco::Thread;
 
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-        
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
     cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
-
-    //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
@@ -90,7 +77,9 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     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);
@@ -98,10 +87,15 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     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 IResponseAnalysis::acquire()
 {
+
     Timer* save_timer;
     TimerCallback<IResponseAnalysis> save_callback(*this, &IResponseAnalysis::save_cb);
 
@@ -129,8 +123,7 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
-    cout<<"SYNTHESISING IRESPONSE";
- 
+    
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
@@ -149,66 +142,62 @@ void IResponseAnalysis::synthesise()
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
              //cout << "LOADED image1!!!" << endl;
-            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            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);
+                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();
+                cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                               
+                
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
                 
-                 //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);
+    
+    
 }
 
 
@@ -416,125 +405,3 @@ void IResponseAnalysis::save_cb(Timer& timer)
         
     saveImageAnalysis(file_name);
 }
-
-void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
-    
-    ofColor meshColour=ofColor(255,0,0);
-    
-    int chooseColour=1  ;
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-         
-    if(chooseColour==1){
-        
-            for(int i=0;i<sPixels.size();i++){
-                mesh.addColor(  currentSecondImage.getColor(x, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x, y));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-                
-                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x, y));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-                
-                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-
-                x++;
-                if(x>=currentSecondImage.getWidth()-1){
-                    x=0;
-                    y++;
-                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                    if(y>=currentSecondImage.getHeight()-1){
-                        break;
-                    }
-                }
-            }
-    }
-}
-
-vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-        for(int i=0;i<imagePixels1.size();i++){
-            thesePixels[i]=0;
-        }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-           
-            //float _presumedBrightness=255;
-            
-            int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            float multiplier=4.0;
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-
-

src/IResponseAnalysis.h

@@ -59,11 +59,7 @@ protected:
     
     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;
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 };

src/RelaxRateAnalysis.cpp

@@ -12,45 +12,21 @@ using Poco::Thread;
 
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
-#define TRESHOLD        80
+#define THRESHOLD        80
 #define MAXBLOBS        15
 
 void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     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;
+    _threshold = RefractiveIndex::XML.getValue("config:relaxrate:threshold", THRESHOLD);
+    cout << "THRESHOLD RelaxRateAnalysis " << _threshold << endl;
     
     _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
     cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
@@ -79,46 +55,17 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     _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);
-    
         
 }
 
@@ -152,194 +99,76 @@ void RelaxRateAnalysis::acquire()
 
 void RelaxRateAnalysis::synthesise()
 {
-    // cout << "RelaxRate::saving synthesis...\n";
+    //cout << "IResponseAnalysis::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;
-        
+    cvContourFinderVect.clear();    
+    
+    
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
+                
         if(_state == STATE_STOP) return;
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
-            //couldn't load image
-            //        cout << "didn't load image" << endl;
-        } 
-        
+                
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //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;
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);            
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayDiff1, 1);
+            
+            cvGrayDiff1.threshold(_threshold);
+            
+            rfiCvContourFinder* cf = new rfiCvContourFinder();
+            
+            cf->findContours(cvGrayDiff1, 20, (image1.width * image1.height) / 4, _maxblobs, true);
+            
+            cvContourFinderVect.push_back(cf);
+            
         }
-        
     }
     
-    // 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);
+        Thread::sleep(3);
     
 }
+
 void RelaxRateAnalysis::displayresults()
 {
         
-    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+    //cvContourFinderVectDisplay.clear();
+    clearcfindervectdisplay();
+    
+    for(int i=1;i<cvContourFinderVect.size();i++){
         
-        if(_state == STATE_STOP) return;
+        if(_state == STATE_STOP){
+            clearcfindervectdisplay();
+            clearcfindervect();
+            return;
+        }        
         
-        //    cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
         while(!_image_shown){
             Thread::sleep(2);
+            if(_state == STATE_STOP) return;
             //cout << "!_image_shown" << endl;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-            //couldn't load image
-            //      cout << "didn't load image" << endl;
-        } 
+        cvContourFinderVectDisplay.push_back(cvContourFinderVect[i]);    
+        _show_image = true;
+        _image_shown = false;
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
-            //cout << "_show_image = true;" << endl;
-            _show_image = true;
-            _image_shown = false;
-        }
-    }
+    }     
+    
+    clearcfindervectdisplay();
+    clearcfindervect();
+    
+        
+    //cvContourFinderVectDisplay.clear();
+    //cvContourFinderVect.clear();
+    
     
 }
 
@@ -347,25 +176,7 @@ void RelaxRateAnalysis::displayresults()
 // 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:
         {
@@ -555,410 +366,3 @@ 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

@@ -39,52 +39,16 @@ protected:
     int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
-    int     _treshold;
+    int     _threshold;
     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;
-    
+    ofImage                 image1;    
+    ofxCvColorImage         cvColorImage1;    
     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

@@ -19,63 +19,10 @@ using Poco::Thread;
 
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
     cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
-    //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;
@@ -138,7 +85,8 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.clear();
 	cvGrayImage2.clear();
     cvGrayDiff2.clear();
-       
+    
+    cvConvertorImage.clear();    
     
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -148,6 +96,7 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
 }
 
@@ -191,116 +140,65 @@ void ShadowScapesAnalysis::synthesise()
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //    cout << "LOADED image1!!!" << endl;
+            
             if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                
+                               
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
+                //cvGrayImage1 = cvColorImage1;
+                //cvGrayImage2 = cvColorImage2;
+                
                 cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
                 cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
-                
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                
-                cvGrayImage1.dilate();
-                cvGrayImage1.blur(5);
-                cvGrayImage1.contrastStretch();
+      
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                cvGrayDiff1.blur(5);
+                cvGrayDiff1.dilate();
                 
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                string file_name;
                 
-                //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;
+                if(_dir == H) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_H_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 }
                 
-                //subtract background begin///////////////
+                if(_dir == V) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_V_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                }    
                 
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
+                if(_dir == D) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_D_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                }
                 
-                //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);
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
                 
-                //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);
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
                 
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
                 
-                /////////////////////////////////// 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);
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                               
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
                 
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //flag that we are finished  
-                meshIsComplete=true;
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
                 _synth_save_cnt++;
-                
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
     }
     
@@ -576,413 +474,3 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     saveImageAnalysis(file_name);
         
 }
-
-
-
-
-void ShadowScapesAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> ShadowScapesAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/ShadowScapesAnalysis.h

@@ -66,20 +66,7 @@ protected:
     
     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;
-
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;    
 
 };

src/ShapeFromShadingAnalysis.cpp

@@ -15,62 +15,10 @@ using Poco::Thread;
 
 void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 {       
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shapefromshading", NUMBER_RUNS);
     cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 1;
-    chooseColour            = 5;
-    multiplier              = 3.0;
-    
-    ofSetLineWidth(5.0f);
-    glPointSize(5.0f);
-
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
-    ///setup light    
-    ofEnableLighting();    
-    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
-    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
-    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
-    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-    
-    glEnable(GL_LIGHT0);  
-    
-    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
-    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
-    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
-    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-    
-    glEnable(GL_LIGHT1);  
-    
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;
@@ -216,24 +164,6 @@ void ShapeFromShadingAnalysis::synthesise()
         //    cout << "LOADED image1!!!" << endl;
             if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
-                if(_saved_filenames_analysis[i].find("QUAD1")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD1";
-                    cout<<"FOUND QUAD1"<<endl;
-                } else if (_saved_filenames_analysis[i].find("QUAD2")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD2";
-                    cout<<"FOUND QUAD2"<<endl;
-                } else if(_saved_filenames_analysis[i].find("QUAD3")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD3";
-                    cout<<"FOUND QUAD3"<<endl;
-                } else if(_saved_filenames_analysis[i].find("QUAD4")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD4";
-                    cout<<"FOUND QUAD4"<<endl;
-                }
-                
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                 
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
@@ -242,132 +172,42 @@ void ShapeFromShadingAnalysis::synthesise()
                 cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
                 cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                
-                cvGrayImage1.dilate();
-                cvGrayImage1.blur(5);
-                cvGrayImage1.contrastStretch();
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
                 
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
+                string file_name;
                 
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
+                file_name = ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 
                 
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
                 
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+               
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
                 
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
                 
-                // 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;
-                }
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
                 
-                //subtract background begin///////////////
-                
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */ 
-                
-                //DIFFERENCING THE BACKGROUND
-                /*
-                for(int i=0;i<imagePixels1.size();i++){
-                    //unsigned char val=imagePixels1[i];
-                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                    if(imagePixels1[i]-backgroundPixels[i]>0){
-                        imagePixels1[i]-=backgroundPixels[i];
-                    }
-                    else{
-                        imagePixels1[i]=0;
-                    }
-                }
-                */
-                
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
-                
-                if(fileNameQuad=="QUAD1")
-                {       
-                    
-                    //with jpgs this was refusing to save out
-                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-                    
-                    
-                } else if(fileNameQuad=="QUAD2")
-                {
-                    
-                    //with jpgs this was refusing to save out
-                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-                    
-                } else if(fileNameQuad=="QUAD3")
-                {
-                    
-                    //with jpgs this was refusing to save out
-                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-                
-                } else if(fileNameQuad=="QUAD4") {
-                    
-                    
-                    //with jpgs this was refusing to save out
-                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-        
-                }
-
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //flag that we are finished  
-                meshIsComplete=true;
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
                 _synth_save_cnt++;
-
+                
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
     }
     
@@ -408,48 +248,6 @@ void ShapeFromShadingAnalysis::displayresults()
 void ShapeFromShadingAnalysis::draw()
 {
     
-    //rotate light around origin ofviewspace    
-    float xx=cos(ofGetElapsedTimef()*0.4)*150;    
-    float yy=sin(ofGetElapsedTimef()*0.4)*150;    
-    float zz=0;
-    
-    if(fileNameQuad=="QUAD1")
-    {       
-        
-        GLfloat light_position[] = { 1000, 1000, 20, 0.0 };  
-        GLfloat light_position1[] = { 1000, 1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-        
-    } else if(fileNameQuad=="QUAD2")
-    {
-    
-        GLfloat light_position[] = { 1000, -1000, 20, 0.0 };  
-        GLfloat light_position1[] = { 1000, -1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-        
-    } else if(fileNameQuad=="QUAD3")
-    {
-      
-        GLfloat light_position[] = {-1000, 1000, 20, 0.0 };  
-        GLfloat light_position1[] = { -1000, 1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-        
-    } else if(fileNameQuad=="QUAD4") 
-    {
-        GLfloat light_position[] = { -1000, -1000, 20, 0.0 };  
-        GLfloat light_position1[] = { -1000, -1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-    }
-
-    
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -798,412 +596,3 @@ void ShapeFromShadingAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
-
-
-
-void ShapeFromShadingAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> ShapeFromShadingAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-        
-            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/ShapeFromShadingAnalysis.h

@@ -31,8 +31,6 @@ public:
 protected:
     
     string quad;
-    string fileNameQuad;
-    
     bool    _RUN_DONE;
     float     _flip, _level;
     int _animation_cnt1;
@@ -84,19 +82,4 @@ protected:
     //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

@@ -15,34 +15,10 @@ using Poco::Thread;
 
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
-    
     NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
     cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
-    //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;
@@ -102,7 +78,9 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     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);
@@ -111,6 +89,7 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -164,150 +143,60 @@ void StrobeAnalysis::synthesise()
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //cout << "LOADED image1!!!" << endl;
+    //        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);
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            //cvGrayImage1.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;
-        }
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.dilate();
+                cvGrayDiff1.dilate();
+                cvGrayDiff1.contrastStretch();
+               
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
         
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);    
+            
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+                
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height,OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+              
+                
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+                _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(10);
-
+        Thread::sleep(3); 
 }
 
 void StrobeAnalysis::displayresults()
@@ -344,27 +233,6 @@ void StrobeAnalysis::displayresults()
 void StrobeAnalysis::draw()
 {
     
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();         
-    light.setPointLight();
-    
-    light.enable();	
-    lightStatic.enable();
-    
-    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
-    
-    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(1.0f);
-    glPointSize(5.0f);
-    
-    ofEnableBlendMode(blendMode);
-
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -382,7 +250,8 @@ void StrobeAnalysis::draw()
                     ofSetColor(aColour);
                     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)){
@@ -412,9 +281,8 @@ void StrobeAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     // cout <<  "FADE OUT STROBE TIME " << endl;
                 }         
-    
+            
                 ofDisableAlphaBlending();
-                
             } else {
                 //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
@@ -557,408 +425,3 @@ void StrobeAnalysis::save_cb(Timer& timer)
     
     saveImageAnalysis(file_name);
 }
-
-void StrobeAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp() );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> StrobeAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/StrobeAnalysis.h

@@ -65,20 +65,7 @@ protected:
     
     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;
-
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;    
 
 };