added file name sorting code to abrastract analysis

there does seem to be some kind of strange file saving ordering problem
going on... into the 'drawing' --> folder. will look at it and try and
see what its doing wrong

.gitignore

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

config.refindx

@@ -0,0 +1,46 @@
+<!-- THIS FILE NEEDS TO GO IN THE APPLICATION /data/ folder -->
+
+<config>
+    <mode>drawing</mode>
+	<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>
+        <treshold>51</treshold>
+        <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;
@@ -104,7 +101,7 @@ void RefractiveIndex::setup()
     //void ofPixels::allocate(int w, int h, ofImageType type)    
     _pixels.allocate(_vid_w, _vid_h, OF_IMAGE_COLOR); 
     
- 
+    
     //TODO:  whichever one of these is first - it always runs twice ?
     
     _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
@@ -112,6 +109,7 @@ void RefractiveIndex::setup()
     _analysisVector.push_back(new ShadowScapesAnalysis(D));
 	    
     _analysisVector.push_back(new RelaxRateAnalysis());
+    
 	
     _analysisVector.push_back(new IResponseAnalysis());
     
@@ -134,7 +132,6 @@ void RefractiveIndex::setup()
     
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
-  
     
 }
 
@@ -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()
@@ -223,47 +210,9 @@ 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

@@ -7,10 +7,8 @@
 
 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) {
@@ -21,7 +19,7 @@ void AbstractAnalysis::setup(int camWidth, int camHeight) {
         _whole_file_path_analysis = r.filePath;
         _whole_file_path_synthesis = r.filePath + "/darwings";        
     }
-
+    
 }
 
 // this is the main threaded loop for a given analysis
@@ -52,8 +50,6 @@ void AbstractAnalysis::do_synthesize() {
             
         case MODE_DRAWING:
         {            
-
-
             ofxFileHelper fileHelperDrawing;
             if(!fileHelperDrawing.doesDirectoryExist(_whole_file_path_synthesis)){
                 fileHelperDrawing.makeDirectory(_whole_file_path_synthesis);
@@ -157,38 +153,61 @@ 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)
 {
     

src/AbstractAnalysis.h

@@ -61,21 +61,7 @@ public:
     
     // 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;          
     string          _whole_file_path_analysis, _whole_file_path_synthesis;

src/ColorSingleAnalysis.cpp

@@ -24,11 +24,11 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     int acq_run_time;   // 10 seconds of acquiring per run
     acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
-
+    
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 1*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
-                                            // or 10 times per second = every 100 ms
+    // or 10 times per second = every 100 ms
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
@@ -47,7 +47,7 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     b = 0;
     
     fileNameTag = "";
-
+    
     _show_image = false;
     _image_shown = false;
     
@@ -103,9 +103,9 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 
 void ColorSingleAnalysis::acquire()
 {
-
+    
     Timer* save_timer;
-
+    
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
     
     _run_cnt++;
@@ -115,18 +115,18 @@ void ColorSingleAnalysis::acquire()
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
-      //  _run_cnt = i;
-        //cout << "RUN NUM = " << i;
-
+    //  _run_cnt = i;
+    //cout << "RUN NUM = " << i;
+    
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        
-        while(!_RUN_DONE && _state != STATE_STOP)
-            Thread::sleep(3);
-
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+    
     save_timer->stop();
-
-  
+    
+    
     // }
 }
 
@@ -152,50 +152,50 @@ void ColorSingleAnalysis::synthesise()
         if(image1.loadImage(_saved_filenames_analysis[i])){
             //cout << "LOADED image1!!!" << endl;
             //if(image5.loadImage(_saved_filenames_analysis[i+1])){
-                
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                
-                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
-                //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
-                
-                cvColorImage1.blur(5);
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.dilate();
-                cvColorImage1.blur(5);
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.erode();
-                cvColorImage1.erode();
             
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                
-                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                
-                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                //ofImage image;
-                //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
-                
-                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                //image.setUseTexture(false);  
-                
-                //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
             
-                //_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> ///
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-                saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
-                _synth_save_cnt++;
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.dilate();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.erode();
             
-           // }
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
+            
+            file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            
+            
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);  
+            
+            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            
+            //_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++;
+            
+            // }
         }
     }
     
@@ -244,7 +244,7 @@ void ColorSingleAnalysis::draw()
             
             if (_frame_cnt < _frame_cnt_max)
             {
-                    
+                
                 float one_third_of_frame_count_max=_frame_cnt_max/3;
                 int _fade_in_frames = one_third_of_frame_count_max/10;
                 
@@ -282,15 +282,15 @@ void ColorSingleAnalysis::draw()
                 }
                 
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max){
-                   
+                    
                     int fade = ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255);
                     ofSetColor(0, 0, 255-fade);
-        
+                    
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     _fade_cnt++;
                     fileNameTag = "FADING";
                 }
-            
+                
             } else {
                 //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
@@ -326,7 +326,7 @@ void ColorSingleAnalysis::draw()
                 //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
                 
                 if (_anim_cnt < _fade_in_frames) {
-                   // cout << "ColorSingleAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    // cout << "ColorSingleAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
                     
                     fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
                     
@@ -414,8 +414,8 @@ void ColorSingleAnalysis::draw()
             // display results of the synthesis
             _RUN_DONE = true;
             break;
-
-
+            
+            
         }
             
         default:
@@ -432,4 +432,4 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
     saveImageAnalysis(file_name);
-}
+}

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-    /*
+/*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -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/IResponseAnalysis.cpp

@@ -25,12 +25,6 @@ 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
     
@@ -131,9 +125,7 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
-    cout<<"SYNTHESISING IRESPONSE";
     
- 
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
@@ -155,48 +147,50 @@ 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///////////////
-
-                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);
-
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+                
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                               
+                
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
                 
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1,image1, aMesh);
-                 //meshPix=make3DZmap(image1, image5, _background);
-                //with jpgs this was refusing to save out
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
-                _saved_filenames_synthesis.push_back(meshFileName);
-
-                //flag that we are finished  
-                meshIsComplete=true;
                 _synth_save_cnt++;
                 
+        
+
             }
         }
     }
@@ -413,172 +407,3 @@ 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;
 };