added triangular mesh and scaling for z axis.

make sure you add the config.refindx to your environment

.gitignore

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

config.refindx

@@ -1,45 +0,0 @@
-<!-- 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            "MIDDLESBOROUGH"
+#define LOCATION            "MANCHESTER"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -42,6 +42,9 @@ ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
+    camDist=1000;
+
+    //camera.setOrientation(ofVec3f(1,-1,1));
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -110,7 +113,6 @@ void RefractiveIndex::setup()
 	    
     _analysisVector.push_back(new RelaxRateAnalysis());
 	
-	
     _analysisVector.push_back(new IResponseAnalysis());
     
     _analysisVector.push_back(new ShapeFromShadingAnalysis());
@@ -133,6 +135,7 @@ void RefractiveIndex::setup()
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
   
+    
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
@@ -148,6 +151,16 @@ 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()
@@ -211,8 +224,46 @@ 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

@@ -10,6 +10,8 @@
 
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
 
 #define MODE_DRAWING        0xEEFF
 #define MODE_ANALYSING      0xFFEE
@@ -54,6 +56,9 @@ protected:
     AnalysisAdaptor*            _analysisAdapator;
     vector<AbstractAnalysis*>   _analysisVector;    
     
+    float                         _meshRotation;
+    float                           camDist;
+    ofEasyCam                     cam;
 public:    
     // acquisition
     static ofPixels         _pixels;    
@@ -68,5 +73,8 @@ public:
     // this should be in xml
     static string           _location;
     static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
-    
+    ofCamera    camera;
+    ofPixels    keepOnScreen;
+    ofFbo fbo;
+    ofLight light;
 };

src/AbstractAnalysis.cpp

@@ -3,10 +3,34 @@
 #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;
@@ -24,10 +48,31 @@ 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()
@@ -112,10 +157,38 @@ 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)
 {
     
@@ -181,5 +254,6 @@ 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){_cam_w = camWidth; _cam_h = camHeight;}  
+    virtual void setup(int camWidth, int camHeight);  
 
     // this is the main threaded loop for a given analysis
     void do_synthesize();
@@ -37,6 +37,8 @@ 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);
     
@@ -55,9 +57,24 @@ 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

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

@@ -14,6 +14,8 @@ 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;
@@ -246,6 +248,8 @@ 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

@@ -15,6 +15,8 @@ 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;
@@ -124,6 +126,7 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
+  
     // }
 }
 
@@ -136,103 +139,11 @@ 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;
@@ -271,7 +182,7 @@ 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);
@@ -285,10 +196,7 @@ void ColorSingleAnalysis::synthesise()
                 _synth_save_cnt++;
             
            // }
-        
         }
-         */
-        
     }
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
@@ -297,23 +205,8 @@ 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;
@@ -337,7 +230,6 @@ void ColorSingleAnalysis::displayresults()
             _image_shown = false;
         }
     }
-    */
     
 }
 
@@ -348,6 +240,8 @@ void ColorSingleAnalysis::draw()
     switch (_state) {
         case STATE_ACQUIRING:
         {
+            
+            
             if (_frame_cnt < _frame_cnt_max)
             {
                     
@@ -493,49 +387,9 @@ void ColorSingleAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             
-            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)
             {
                 _image_shown = true;
@@ -560,9 +414,10 @@ void ColorSingleAnalysis::draw()
             // display results of the synthesis
             _RUN_DONE = true;
             break;
-            */
+
 
         }
+            
         default:
             break;
     }

src/ColorSingleAnalysis.h

@@ -65,8 +65,5 @@ 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

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

@@ -15,6 +15,8 @@ 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;
@@ -23,6 +25,12 @@ 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
     
@@ -123,6 +131,8 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
+    cout<<"SYNTHESISING IRESPONSE";
+    
  
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
@@ -145,50 +155,48 @@ 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;
+                }
                 
-                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                //subtract background begin///////////////
-                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
 
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                ofPixels imagePixels1 = image1.getPixelsRef();
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                ofPixels imagePixels2 = image5.getPixelsRef();
+                ofPixels backgroundPixels = _background.getPixelsRef();
 
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                for(int i=0;i<imagePixels1.size();i++){
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
                     
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                    unsigned char val=imagePixels1[i];
-                string file_name;
+                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                        imagePixels1[i]-=backgroundPixels[i];
+                    }
+                    else{
+                        imagePixels1[i]=0;
+                    }
                   
-                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                }
+               
+                //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 ---->
+                //flag the main app that we aren't read yet
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                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 ---->
+                 //meshPix=make3DZmap(image1, image5, _background);
-                //ofImage image;
+                //with jpgs this was refusing to save out
-                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
-                
+                _saved_filenames_synthesis.push_back(meshFileName);
-                //*** 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++;
                 
-        
-
             }
         }
     }
@@ -405,3 +413,172 @@ 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

@@ -62,4 +62,11 @@ 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

@@ -12,11 +12,13 @@ using Poco::Thread;
 
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
-#define THRESHOLD        80
+#define TRESHOLD        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;
@@ -25,8 +27,8 @@ 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;
     
-    _threshold = RefractiveIndex::XML.getValue("config:relaxrate:threshold", THRESHOLD);
+    _treshold = RefractiveIndex::XML.getValue("config:relaxrate:treshold", TRESHOLD);
-    cout << "THRESHOLD RelaxRateAnalysis " << _threshold << endl;
+    cout << "TRESHOLD RelaxRateAnalysis " << _treshold << endl;
     
     _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
     cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
@@ -116,7 +118,7 @@ void RelaxRateAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);            
             cvColorImage1.convertToGrayscalePlanarImage(cvGrayDiff1, 1);
             
-            cvGrayDiff1.threshold(_threshold);
+            cvGrayDiff1.threshold(_treshold);
             
             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     _threshold;
+    int     _treshold;
     int     _maxblobs;
     
     bool _show_image, _image_shown;

src/ShadowScapesAnalysis.cpp

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

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

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