working on color single and color multi, some openCV implementations in both

still needs work

example/RefractiveIndex.cpp

@@ -107,26 +107,25 @@ void RefractiveIndex::setup()
  
     //TODO:  whichever one of these is first - it always runs twice ?
     
-    _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
+    _analysisVector.push_back(new ShadowScapesAnalysis(V));  //1
-    _analysisVector.push_back(new ShadowScapesAnalysis(H));
+    _analysisVector.push_back(new ShadowScapesAnalysis(H));  //2
-    _analysisVector.push_back(new ShadowScapesAnalysis(D));
+    _analysisVector.push_back(new ShadowScapesAnalysis(D));  //3
 	    
-    _analysisVector.push_back(new RelaxRateAnalysis());
+    _analysisVector.push_back(new RelaxRateAnalysis());   //4
 	
-    _analysisVector.push_back(new IResponseAnalysis());
+    _analysisVector.push_back(new IResponseAnalysis());   //5
     
-    _analysisVector.push_back(new ShapeFromShadingAnalysis());
+    _analysisVector.push_back(new ShapeFromShadingAnalysis());   //6
     
-    _analysisVector.push_back(new StrobeAnalysis());
+    _analysisVector.push_back(new StrobeAnalysis());   //7
     
-    _analysisVector.push_back(new CamNoiseAnalysis());
+    _analysisVector.push_back(new CamNoiseAnalysis());    //8
     
-    _analysisVector.push_back(new ColorSingleAnalysis());
+    _analysisVector.push_back(new ColorSingleAnalysis());    //9
     
-    _analysisVector.push_back(new ColorMultiAnalysis());
+    _analysisVector.push_back(new ColorMultiAnalysis());    //0
-    
-    _analysisVector.push_back(new DiffNoiseAnalysis());	
     
+    _analysisVector.push_back(new DiffNoiseAnalysis());	  //Q
     
     //_currentAnalysisIndx = 0;
     //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
@@ -141,7 +140,6 @@ void RefractiveIndex::setup()
 void RefractiveIndex::analysis_cb(string & analysis)
 {
     assert(analysis == _currentAnalysis->_name);
-    
     _state = ISTATE_STOP;    
 }
 
@@ -160,7 +158,6 @@ void RefractiveIndex::start_analysis()
     camera.setPosition(fbo.getWidth()/2, fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
     _meshRotation=0;
 
-    
 }
 
 void RefractiveIndex::stop_analysis()
@@ -232,25 +229,29 @@ void RefractiveIndex::draw()
             
             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 xDiff= (fbo.getWidth()- (_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
-            float yDiff= (fbo.getHeight()- (_currentAnalysis->_mesh_size_multiplier *_vid_h))/2;
+                float yDiff= (fbo.getHeight()- (_currentAnalysis->_mesh_size_multiplier * _vid_h))/2;
-
                 
                 ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
+                
+                ofEnableBlendMode ( OF_BLENDMODE_ADD ) ;   
                     _currentAnalysis->aMesh.draw();
+                ofDisableBlendMode( ) ;  
+            
                 
             camera.end();
             fbo.end();
@@ -260,9 +261,9 @@ void RefractiveIndex::draw()
           
             ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
             //saving jpgs doesn't work - pngs only!
+            // PNG is fine - better for Final Cut anyway! 
 
         }
-       
     }
 }
 

example/main.cpp

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

src/AbstractAnalysis.cpp

@@ -228,7 +228,6 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
     
 #ifdef TARGET_OSX   
 
-
     ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
     
 #elif defined(TARGET_WIN32)    
@@ -256,4 +255,3 @@ void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels
             
     
 }
-

src/AbstractAnalysis.h

@@ -64,6 +64,7 @@ public:
     bool    meshIsComplete;
     bool    imageForContourAvailable;
     ofMesh  aMesh;
+    
     string  meshFileName;
     //difference between our image size and the size of the fbo
     float   widthScaleFactor;

src/CamNoiseAnalysis.cpp

@@ -21,6 +21,12 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN CamNoiseAnalysis " << 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_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;

src/ColorMultiAnalysis.cpp

@@ -20,6 +20,13 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ColorMultiAnalysis " << 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_colormulti", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
@@ -141,6 +148,7 @@ 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])){
@@ -150,40 +158,75 @@ void ColorMultiAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            cvColorImage1.blur(5);
+            //cvColorImage1.blur(1);
-            cvColorImage1.erode();
+            //cvColorImage1.erode();
-            cvColorImage1.erode();
+            
-            cvColorImage1.dilate();
+            //cvColorImage1.dilate();
-            cvColorImage1.blur(5);
+            //cvColorImage1.dilate();
-            cvColorImage1.dilate();
+            //cvColorImage1.dilate();
-            cvColorImage1.dilate();
+            //cvColorImage1.dilate();
-            cvColorImage1.dilate();
+            
-            cvColorImage1.dilate();
+            //cvFloatImage1 = cvColorImage1;
+            //cvGrayImage1 = cvColorImage1;
+
+            cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 9, 9);
+            cvXorS( cvColorImage1.getCvImage(), cvScalarAll(1), 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;
             
-            file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            //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";
             
-            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            //flag that we are finished  
-            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            meshIsComplete=true;
-            
-            
-            //<---- 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++;
             
             // }
@@ -411,8 +454,149 @@ 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_LINE_STRIP);
+    
+    /*
+     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(255,0,0);
+    
+    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> 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=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/ColorMultiAnalysis.h

@@ -59,4 +59,14 @@ protected:
     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);
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
+
 };

src/ColorSingleAnalysis.cpp

@@ -21,10 +21,23 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ColorSingleAnalysis " << 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_colorsingle", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
 
+    
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=3;
+    
     //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
@@ -97,13 +110,11 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
     cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);    
-    
 }
 
 
 void ColorSingleAnalysis::acquire()
 {
-
     Timer* save_timer;
 
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
@@ -126,8 +137,6 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
-  
-    // }
 }
 
 void ColorSingleAnalysis::synthesise()
@@ -158,41 +167,74 @@ void ColorSingleAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.blur(5);
+                //cvColorImage1.blur(1);
-                cvColorImage1.erode();
+                //cvColorImage1.erode();
-                cvColorImage1.erode();
+                
-                cvColorImage1.dilate();
+                //cvColorImage1.dilate();
-                cvColorImage1.blur(5);
+                //cvColorImage1.dilate();
-                cvColorImage1.erode();
+                //cvColorImage1.dilate();
-                cvColorImage1.erode();
+                //cvColorImage1.dilate();
-                cvColorImage1.erode();
+            
-                cvColorImage1.erode();
+                //cvFloatImage1 = cvColorImage1;
+                //cvGrayImage1 = cvColorImage1;
+            
+                cvXorS( cvColorImage1.getCvImage(), cvScalarAll(255), cvColorImage1.getCvImage(), 0 );
+                //cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 3, 3 );
+                //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;
                 
-                file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                //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 ---->
+                //flag that we are finished  
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                meshIsComplete=true;
-                
-                
-                //<---- 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++;
             
            // }
@@ -433,3 +475,133 @@ 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);
+    
+    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> 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...
+        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.getHue());
+            int thisDiff=abs(imageColor1.getBrightness());
+
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            
+            //red hue: 0
+            //green hue: 120 
+            //blue hue: 240
+            
+            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/ColorSingleAnalysis.h

@@ -60,10 +60,21 @@ 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;
     
     
+    //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);
+    
+    bool _gotFirstImage;
+    ofImage _background;
+
 };

src/IResponseAnalysis.cpp

@@ -31,7 +31,6 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     
     _mesh_size_multiplier=4;
     
-
     //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
@@ -133,7 +132,6 @@ void IResponseAnalysis::synthesise()
 {
     cout<<"SYNTHESISING IRESPONSE";
  
- 
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
@@ -152,7 +150,7 @@ 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){
@@ -164,12 +162,13 @@ void IResponseAnalysis::synthesise()
                 //subtract background begin///////////////
 
                 ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2 = image5.getPixelsRef();
+                //ofPixels imagePixels2       = image5.getPixelsRef();
                 ofPixels backgroundPixels   = _background.getPixelsRef();
 
-                for(int i=0;i<imagePixels1.size();i++){
+                //background subtraction// 
                 
-                    unsigned char val=imagePixels1[i];
+                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];
@@ -177,17 +176,16 @@ void IResponseAnalysis::synthesise()
                     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);
+                
                  //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";
@@ -198,14 +196,12 @@ void IResponseAnalysis::synthesise()
                 _synth_save_cnt++;
                 
             }
-        }
+        //}
     }
 
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-    
-    
 }
 
 
@@ -442,20 +438,21 @@ void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage current
     }
          
     if(chooseColour==1){
+        
             for(int i=0;i<sPixels.size();i++){
-                mesh.addColor(  currentSecondImage.getColor(x, y+1)   );
+                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.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.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.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.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)   );
@@ -472,76 +469,24 @@ void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage current
                 }
             }
     }
-    /*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 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];
+    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;
     
@@ -553,32 +498,36 @@ vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofIma
         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 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=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+           
             //float _presumedBrightness=255;
-            int thisDiff=abs(colourImage1.getBrightness()-_presumedBrightness);
+            
+            int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
+
             //cout<<thisDiff<< " thisDiff "<<endl;
             float multiplier=2.0;
-            differences.push_back(multiplier* thisDiff);
+            
+            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.cpp

@@ -23,6 +23,12 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN RelaxRateAnalysis " << 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_relaxrate", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;

src/ShapeFromShadingAnalysis.cpp

@@ -21,6 +21,13 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN ShapeFromShadingAnalysis " << 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_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;

src/StrobeAnalysis.cpp

@@ -21,6 +21,12 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     cout << "NUM_RUN StrobeAnalysis " << 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_strobe", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;