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
@@ -42,9 +42,6 @@ ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
-    camDist=1000;
-
-    //camera.setOrientation(ofVec3f(1,-1,1));
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -113,6 +110,7 @@ void RefractiveIndex::setup()
     
     _analysisVector.push_back(new RelaxRateAnalysis());
     
+	
     _analysisVector.push_back(new IResponseAnalysis());
     
     _analysisVector.push_back(new ShapeFromShadingAnalysis());
@@ -135,7 +133,6 @@ void RefractiveIndex::setup()
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
     
-    
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
@@ -151,16 +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);
-    _meshRotation=0;
-    
-    
 }
 
 void RefractiveIndex::stop_analysis()
@@ -224,46 +211,8 @@ void RefractiveIndex::draw()
     // black
     ofBackground(0, 0, 0);
     
-    if(_currentAnalysis){
+    if(_currentAnalysis)
         _currentAnalysis->draw();
-       
-    
-        if(_currentAnalysis->meshIsComplete){
-            
-            fbo.begin();
-            glShadeModel(GL_SMOOTH);  
-            ofClear(0,0,0);
-            
-            camera.begin();
-            ofSetColor(0, 0, 0);
-            //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);
-            ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);
-            
-            
-            ofPopMatrix();
-            ofSetColor(255);
-            
-            float xDiff= (fbo.getWidth()- (_currentAnalysis->_mesh_size_multiplier *_vid_w))/2;
-            float yDiff= (fbo.getHeight()- (_currentAnalysis->_mesh_size_multiplier *_vid_h))/2;
-
-            
-            ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
-            _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!
-
-        }
-       
-    }
 }
 
 void RefractiveIndex::setup_camera()

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;
-    ofLight light;
+    
 };

src/AbstractAnalysis.cpp

@@ -3,34 +3,10 @@
 #include "AbstractAnalysis.h"
 #include "RefractiveIndex.h"
 #include "ofxFileHelper.h"
-#include "ofSystemUtils.h"
-
-void AbstractAnalysis::setup(int camWidth, int camHeight) {
-    
-    meshIsComplete=false;
-    imageForContourAvailable=false;
-    
-    _cam_w = camWidth; _cam_h = camHeight;
-    if(RefractiveIndex::_mode == MODE_DRAWING) {
-        ofFileDialogResult r = ofSystemLoadDialog("choooose da folda", true);
-        if(!r.bSuccess) {
-            ofSystemAlertDialog("OOOOPS.... ERROR...");
-            return;
-        }
-                
-        _whole_file_path_analysis = r.filePath;
-        _whole_file_path_synthesis = r.filePath + "/darwings";        
-    }
-
-}
 
 // this is the main threaded loop for a given analysis
 void AbstractAnalysis::do_synthesize() {
     
-    switch(RefractiveIndex::_mode)
-    {
-        case MODE_ANALYSING:
-        {
     for(int i = 0; i < NUM_RUN; i++) {
         
         cout << "NUM_RUN: " << i << endl;
@@ -48,31 +24,10 @@ void AbstractAnalysis::do_synthesize() {
         displayresults();
         cleanup();
     }
-        }
-            
-        case MODE_DRAWING:
-        {            
-
-
-            ofxFileHelper fileHelperDrawing;
-            if(!fileHelperDrawing.doesDirectoryExist(_whole_file_path_synthesis)){
-                fileHelperDrawing.makeDirectory(_whole_file_path_synthesis);
-            }            
-            
-            read_dir_create_list(_whole_file_path_analysis);
-            _state = STATE_SYNTHESISING;
-            synthesise();
-            if(_state == STATE_STOP) goto exit;
-            _state = STATE_DISPLAY_RESULTS;
-            displayresults();
-            cleanup();            
-        }
-    }
     
     exit:    
     cleanup();
     ofNotifyEvent(_synthesize_cb, _name);
-    
 }
 
 void AbstractAnalysis::create_dir_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)
 {
     
@@ -254,6 +181,5 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
     
     _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);
     
@@ -57,24 +55,9 @@ protected:
         
 public:
     string  _name;    
-    string  _draw_directory;
     
     // event
     ofEvent<string> _synthesize_cb;    
-    bool    meshIsComplete;
-    bool    imageForContourAvailable;
-    ofMesh  aMesh;
-    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;          

src/CamNoiseAnalysis.cpp

@@ -15,8 +15,6 @@ 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;

src/ColorMultiAnalysis.cpp

@@ -14,8 +14,6 @@ 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;
@@ -248,8 +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);

src/ColorSingleAnalysis.cpp

@@ -15,8 +15,6 @@ 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;
@@ -126,7 +124,6 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
-  
     // }
 }
 
@@ -139,11 +136,103 @@ void ColorSingleAnalysis::synthesise()
     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;
@@ -182,7 +271,7 @@ void ColorSingleAnalysis::synthesise()
                 //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? ***//
+                // 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);
@@ -196,7 +285,10 @@ void ColorSingleAnalysis::synthesise()
                 _synth_save_cnt++;
         
            // }
+        
          }
+         */
+        
     }
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
@@ -205,8 +297,23 @@ void ColorSingleAnalysis::synthesise()
     
 }
 
+// 
 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;
@@ -230,6 +337,7 @@ void ColorSingleAnalysis::displayresults()
             _image_shown = false;
         }
     }
+    */
     
 }
 
@@ -240,8 +348,6 @@ void ColorSingleAnalysis::draw()
     switch (_state) {
         case STATE_ACQUIRING:
         {
-            
-            
             if (_frame_cnt < _frame_cnt_max)
             {
                     
@@ -387,8 +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)
             {
@@ -414,10 +560,9 @@ void ColorSingleAnalysis::draw()
             // display results of the synthesis
             _RUN_DONE = true;
             break;
-
+            */
             
         }
-            
         default:
         break;
     }

src/ColorSingleAnalysis.h

@@ -65,5 +65,8 @@ protected:
     //this is the temporary container to allow us to convert and save out greyscale images
     ofxCvColorImage         cvConvertorImage;
     
+    unsigned char * imagePixels;
+    int vectorCount;
+    ofVec2f * vectorField;
     
 };

src/DiffNoiseAnalysis.cpp

@@ -15,8 +15,6 @@ 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;

src/IResponseAnalysis.cpp

@@ -15,8 +15,6 @@ 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;
@@ -25,12 +23,6 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     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=4;
-    
 
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
@@ -131,8 +123,6 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
-    cout<<"SYNTHESISING IRESPONSE";
-    
     
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
@@ -155,48 +145,50 @@ void IResponseAnalysis::synthesise()
             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///////////////
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                ofPixels imagePixels1 = image1.getPixelsRef();
-                ofPixels imagePixels2 = image5.getPixelsRef();
-                ofPixels backgroundPixels = _background.getPixelsRef();
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
-                for(int i=0;i<imagePixels1.size();i++){
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
                 
-                    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;
-                    }
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
                 
-                }
-               
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
+                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                                
                 
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1,image1, aMesh);
-                 //meshPix=make3DZmap(image1, image5, _background);
-                //with jpgs this was refusing to save out
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
-                _saved_filenames_synthesis.push_back(meshFileName);
+                //<---- 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);
                 
-                //flag that we are finished  
-                meshIsComplete=true;
                 _synth_save_cnt++;
                 
+        
+
             }
         }
     }
@@ -413,172 +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>=479){
-                        break;
-                    }
-                }
-             }
-    }
-    /*else{
-           for(int i=0;i<somePixels.getWidth()*(somePixels.getHeight()-1);i++){      
-               
-        
-               ofVec3f U;
-               ofVec3f V;
-                              //tri 1
-               U =ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness() ).operator-  ( ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- somePixels.getColor(x, y).getBrightness()  ) );
-               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ));
-               
-               ofVec3f normal;
-               float mult=5.2;
-               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
-               
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x, y+1).getBrightness() )  ));
-               
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
-
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
-               
-               mesh.addNormal(normal);
-               
-               //tri 2
-               U =ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
-               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- somePixels.getColor(x+1, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
-               
-               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
-               
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
-                 //       mesh.addColor( ofColor(255,10,10)   );
-
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
-
-                 mesh.addColor(meshColour);
-                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,-mult*(1+ somePixels.getColor(x+1, y).getBrightness())   ));
-               
-               mesh.addNormal(normal);
-
-                x++;
-                if(x>=somePixels.getWidth()-1){
-                    x=0;
-                    y++;
-                    if(y>=479){
-                       break;
-                   }
-                }
-             }*/
-         
-     // add colour from current second image of two - this is a hang over from when i was comparing two image
-        
-
-}
-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 colourImage1 = 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(colourImage1.getBrightness()-_presumedBrightness);
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            float multiplier=2.0;
-            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

@@ -62,11 +62,4 @@ 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);
-    //returns ofPixels but these pixels actually hold depth data.
-    //ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    bool _gotFirstImage;
-    ofImage _background;
 };

src/RelaxRateAnalysis.cpp

@@ -12,13 +12,11 @@ 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;
@@ -27,8 +25,8 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     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;
@@ -118,7 +116,7 @@ void RelaxRateAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);            
             cvColorImage1.convertToGrayscalePlanarImage(cvGrayDiff1, 1);
             
-            cvGrayDiff1.threshold(_treshold);
+            cvGrayDiff1.threshold(_threshold);
             
             rfiCvContourFinder* cf = new rfiCvContourFinder();
             

src/RelaxRateAnalysis.h

@@ -39,7 +39,7 @@ 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;

src/ShadowScapesAnalysis.cpp

@@ -19,8 +19,6 @@ 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;

src/ShapeFromShadingAnalysis.cpp

@@ -15,8 +15,6 @@ 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;

src/StrobeAnalysis.cpp

@@ -15,8 +15,6 @@ 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;