messing around trying to produce the windows error on osx

.gitignore

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

README

@@ -1,10 +1,10 @@
 WARNING: WORK IN PROGRESS...
 
-configuring OpenFrameworks under Xcode
+configuring OpenFrameworks
----------------------------------------
+-----------------
 
 these files are configured according to OpenFrameworks addons - http://ofxaddons.com/howto
 
 (1) drag-drop "ReflectiveIndex" folder into your OpenFrameworks project
-(2) Install depedencies: {ofxXmlSettings, ofxOpenCV, ofxFileHelper};  
+(2) Install depedencies: {ofxDirList, ofxControlPanel, ofxXmlSettings};  
 (3) Press Play!

example/RefractiveIndex.cpp

@@ -15,11 +15,11 @@
 
 #include "ofxXmlSettings.h"
 
-#define CAMERA_ID           0
+#define CAMERA_ID           1
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
-#define LOCATION            "MANCHESTER"
+#define LOCATION            "MIDDLESBOROUGH"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -27,10 +27,8 @@
 #define ISTATE_TRANSITION   0xCCCC
 #define ISTATE_END          0xDDDD
 
-
 int _state = ISTATE_UNDEF;
 
-int              RefractiveIndex::_mode;
 ofPixels         RefractiveIndex::_pixels;
 ofVideoGrabber   RefractiveIndex::_vidGrabber;
 int              RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, RefractiveIndex::_vid_id;
@@ -42,10 +40,6 @@ ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
-    camDist=1000;
-    
-    ofBackground(0, 0, 0);
-    ofSetBackgroundAuto(false);
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -56,10 +50,6 @@ void RefractiveIndex::setup()
         XML.loadFile("config.refindx");
     }
         
-    // <mode>
-    string m = XML.getValue("config:mode", "analysing");
-    _mode = (m == "analysing" ? MODE_ANALYSING : (m == "drawing" ? MODE_DRAWING : MODE_ANALYSING));
-        
     // <camera>
     _vid_id = XML.getValue("config:camera:id", CAMERA_ID);
     cout << "_vid_id: " << _vid_id << endl;
@@ -92,10 +82,8 @@ void RefractiveIndex::setup()
     cout << "* cam width = " << _vid_w << endl;
     cout << "* cam height = " << _vid_h << endl;
     
-    if(_mode == MODE_ANALYSING) {
     _vid_stream_open = false;    
     setup_camera();
-    }
     
     cout << "RRRRRREADY!" << endl;        
 
@@ -105,27 +93,28 @@ 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));  //1
+    _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
-    _analysisVector.push_back(new ShadowScapesAnalysis(H));  //2
+    _analysisVector.push_back(new ShadowScapesAnalysis(H));
-    _analysisVector.push_back(new ShadowScapesAnalysis(D));  //3
+    _analysisVector.push_back(new ShadowScapesAnalysis(D));
     
-    _analysisVector.push_back(new RelaxRateAnalysis());   //4
+    _analysisVector.push_back(new RelaxRateAnalysis());
     
-    _analysisVector.push_back(new IResponseAnalysis());   //5
+    _analysisVector.push_back(new IResponseAnalysis());
     
-    _analysisVector.push_back(new ShapeFromShadingAnalysis());   //6
+    _analysisVector.push_back(new ShapeFromShadingAnalysis());
     
-    _analysisVector.push_back(new StrobeAnalysis());   //7
+    _analysisVector.push_back(new StrobeAnalysis());
     
-    _analysisVector.push_back(new CamNoiseAnalysis());    //8
+    _analysisVector.push_back(new CamNoiseAnalysis());
     
-    _analysisVector.push_back(new ColorSingleAnalysis());    //9
+    _analysisVector.push_back(new ColorSingleAnalysis());
     
-    _analysisVector.push_back(new ColorMultiAnalysis());    //0
+    _analysisVector.push_back(new ColorMultiAnalysis());
     
-    _analysisVector.push_back(new DiffNoiseAnalysis());	  //Q
+    _analysisVector.push_back(new DiffNoiseAnalysis());
 
     //_currentAnalysisIndx = 0;
     //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
@@ -134,12 +123,12 @@ void RefractiveIndex::setup()
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
     
-    
 }
 
 void RefractiveIndex::analysis_cb(string & analysis)
 {
     assert(analysis == _currentAnalysis->_name);
+    
     _state = ISTATE_STOP;    
 }
 
@@ -149,17 +138,6 @@ void RefractiveIndex::start_analysis()
     _analysisAdapator = new AnalysisAdaptor(_currentAnalysis);
     _currentAnalysis->setup(_vid_w, _vid_h);
     _analysisAdapator->start();    
-    
-    //allocate fbo for HD
-    fbo.allocate(1920,1080);
-
-    //    fbo.allocate( _currentAnalysis->_mesh_size_multiplier *_vid_w,_currentAnalysis->_mesh_size_multiplier * _vid_h);
-    //camera.setPosition((fbo.getWidth()/2), fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
-    camera.setPosition(0, (fbo.getHeight()/2)+150,  _currentAnalysis->_mesh_size_multiplier*500);
-    camera.setFov(65.0);
-    camera.setOrientation(ofVec3f(-2,0,0));
-    _meshRotation=0;
-
 }
 
 void RefractiveIndex::stop_analysis()
@@ -193,13 +171,9 @@ void RefractiveIndex::state_analysis()
             break;
         case ISTATE_STOP:
             stop_analysis(); // blocking
-            if(_mode == MODE_DRAWING)
-                _state = ISTATE_UNDEF;
-            else
             _state = ISTATE_TRANSITION;
             break;
         case ISTATE_END:
-            if(_mode == MODE_ANALYSING)
             stop_camera();
             ::exit(1);
             break;
@@ -223,52 +197,8 @@ void RefractiveIndex::draw()
     // black
     ofBackground(0, 0, 0);
            
-    if(_currentAnalysis){
+    if(_currentAnalysis)
-        
         _currentAnalysis->draw();
-       
-        if(_currentAnalysis->meshIsComplete){
-            
-            fbo.begin();
-            ofClear(0,0,0);
-
-            glShadeModel(GL_SMOOTH);  
-            
-            
-            camera.begin();
-            
-                //this is a hack, I don't know how to colour the fbo with black pixels so I'm drawing a massive black rectangle in the  background
-                /*
-                ofPushMatrix();
-                    ofTranslate(0, 0,-500);
-                    ofSetColor(0, 0, 0);
-                    ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);                
-                    ofPopMatrix();
-                ofSetColor(255);
-                */
-                //float xDiff= (fbo.getWidth()- 1.55*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
-                float xDiff= (fbo.getWidth()- 1.33333*(_currentAnalysis->_mesh_size_multiplier * _vid_w))/2;
-                float yDiff= (fbo.getHeight()-(_currentAnalysis->_mesh_size_multiplier * _vid_h))/2;
-                
-                ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
-                    //ofScale(1.33333,1.0,1.0);
-                    //_currentAnalysis->aMesh.drawVertices();     // TODO: tom - why do you have the vertices drawing here? 
-                    _currentAnalysis->aMesh.drawFaces();
-                    _currentAnalysis->aMesh.draw();
-                
-            camera.end();
-            fbo.end();
-
-            ofPixels pixels;
-            fbo.readToPixels(pixels);
-          
-            ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
-            //saving jpgs doesn't work - pngs only!
-            // PNG is fine - better for Final Cut anyway! 
-
-            ofDisableBlendMode() ;  
-        }
-    }
 }
 
 void RefractiveIndex::setup_camera()
@@ -464,7 +394,5 @@ void RefractiveIndex::keyPressed  (int key)
 
 void RefractiveIndex::exit()
 {
-    if(_currentAnalysis)
-        _analysisAdapator->stop();    
     stop_camera();
 }

example/RefractiveIndex.h

@@ -10,11 +10,6 @@
 
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.h"
-#include "ofxOpenCv.h"
-
-
-#define MODE_DRAWING        0xEEFF
-#define MODE_ANALYSING      0xFFEE
 
 class RefractiveIndex : public ofBaseApp
 {
@@ -56,15 +51,10 @@ protected:
     AnalysisAdaptor*            _analysisAdapator;
     vector<AbstractAnalysis*>   _analysisVector;    
     
-    float                         _meshRotation;
-    float                           camDist;
-    ofEasyCam                     cam;
 public:    
     // acquisition
     static ofPixels         _pixels;    
     static ofVideoGrabber   _vidGrabber;
-    static int              _mode;
-    
     vector<string>          videoSourceList;    
     static int              _vid_w, _vid_h, _vid_id;
     static bool             _vid_stream_open;
@@ -73,8 +63,5 @@ public:
     // this should be in xml
     static string           _location;
     static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
-    ofCamera    camera;
-    ofPixels    keepOnScreen;
-    ofFbo fbo;
     
 };

example/main.cpp

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

src/AbstractAnalysis.cpp

@@ -3,37 +3,13 @@
 #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;
+        cout << "i NUM_RUN" << i << endl;
                 
         _saved_filenames_analysis.clear();  
         _saved_filenames_synthesis.clear();    
@@ -46,36 +22,13 @@ void AbstractAnalysis::do_synthesize() {
         if(_state == STATE_STOP) goto exit;
         _state = STATE_DISPLAY_RESULTS;
         displayresults();
-                cleanup();
-            }                    
     }
     
-        case MODE_DRAWING:
+    exit:    
-        {            
-
-
-            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()
+void AbstractAnalysis::create_dir()
 {
     // HERE IS WHERE WE SETUP THE DIRECTORY FOR ALL THE SAVED IMAGES
     
@@ -139,119 +92,7 @@ void AbstractAnalysis::create_dir_allocate_images()
         fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
         
     }
+    
     //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////    
-    
-    
-    //////////////////////////////ALLOCATE IMAGES //////////////////////////////////////////////////  
-    
-    myColorImage1.clear();
-    myColorImage1.setUseTexture(false);
-    myColorImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
-
-    myColorImage2.clear();
-    myColorImage2.setUseTexture(false);
-    myColorImage2.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
-    
-    
-    myGrayImage1.clear();
-    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)
-{
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-        
-#ifdef TARGET_OSX   
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+filename, OF_IMAGE_QUALITY_BEST);
-    
-#elif defined(TARGET_WIN32)    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = appPix.getPixels();
-    myColorImage1.setUseTexture(false);
-    myColorImage1.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myColorImage1.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+filename);
-    myColorImage1.clear();
-    
-#endif
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+filename);
-    
-}
-
-
-void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType)
-{
-    
-#ifdef TARGET_OSX   
-
-    ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
-    
-#elif defined(TARGET_WIN32)    
-    
-    if (newType == OF_IMAGE_COLOR){
-       myColorImage2.setUseTexture(false);
-       myColorImage2.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
-       myColorImage2.saveImage(_whole_file_path_synthesis+"/"+filename);
-    }
-
-    if (newType == OF_IMAGE_GRAYSCALE){
-        myGrayImage1.setUseTexture(false);
-        
-        // THIS IS HOW YOU HAVE TO SAVE OUT THE GREYSCALE IMAGES on WINDOWS FOR SOME REASON --> i.e.: as an OF_IMAGE_COLOR
-        // But they don't save properly - they're spatially translated and generally f'd up
-        myGrayImage1.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
-        myGrayImage1.setImageType(OF_IMAGE_COLOR);
-        myGrayImage1.saveImage(_whole_file_path_synthesis+"/"+filename);
-        //myGrayImage1.clear();
-    }
-        
-#endif
-    
-    _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+filename);
-            
-    
-}

src/AbstractAnalysis.h

@@ -7,7 +7,6 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
-#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
@@ -25,7 +24,7 @@ public:
     virtual ~AbstractAnalysis(){;}
     
     // generic function to set up the camera
-    virtual void setup(int camWidth, int camHeight);  
+    virtual void setup(int camWidth, int camHeight){_cam_w = camWidth; _cam_h = camHeight;}  
 
     // this is the main threaded loop for a given analysis
     void do_synthesize();
@@ -35,12 +34,7 @@ public:
         
 protected:
     
-    virtual void create_dir_allocate_images();
+    virtual void create_dir();
-    
-    virtual void read_dir_create_list(string folder_path);
-    
-    virtual void saveImageAnalysis(string filename);
-    virtual void saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType);
     
     // acquire images - all the children (see - do_synthesize)
     virtual void acquire() = 0;   
@@ -51,33 +45,11 @@ protected:
     // display the results from disk
     virtual void displayresults() = 0;   
         
-    // display the results from disk
-    virtual void cleanup() {;}   
-    
-        
 public:
     string  _name;    
-    string  _draw_directory;
     
     // event
     ofEvent<string> _synthesize_cb;    
-    bool    meshIsComplete;
-    bool    imageForContourAvailable;
-    ofMesh  aMesh;
-    ofLight light;
-    ofLight lightStatic; 
-    
-    string  meshFileName;
-    //difference between our image size and the size of the fbo
-    float   widthScaleFactor;
-    float   heightScaleFactor;
-    ofImage  contourImage;
-    ofPixels meshPix;
-    ofPixels publicColorImage;
-    float    zPlaneAverage;
-    
-    //added Tom 1/5/12 defines the stretch we make to the mesh to make it fit HD proportions
-    float           _mesh_size_multiplier;
 
 protected:    
     int             _cam_w, _cam_h;          
@@ -87,10 +59,6 @@ protected:
     
     int             _state;
     
-    ofImage         myColorImage1;
-    ofImage         myColorImage2;
-    ofImage         myGrayImage1;
-    
     //int             _run_cnt;
     
     float           DELTA_T_SAVE;

src/CamNoiseAnalysis.cpp

@@ -15,73 +15,15 @@ using Poco::Thread;
 
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
     cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
-    
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 1;
-    chooseColour            = 6;
-    multiplier              = 4.0;
-    
-    ofSetLineWidth(5.0f);
-    glPointSize(5.0f);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-   // meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    meshMode = OF_PRIMITIVE_POINTS;
-    
-    ///setup light    
-    ofEnableLighting();    
-    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
-    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
-    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
-    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-    
-    glEnable(GL_LIGHT0);  
-    
-    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
-    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
-    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
-    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-    
-    glEnable(GL_LIGHT1);     
-    glPointSize(9.0f);
-    glEnable(GL_POINT_SMOOTH);
-    glCullFace(GL_BACK);
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_camnoise", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;
     
-
     //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
@@ -98,17 +40,11 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
-    //create_dir_allocate_images();
+    //create_dir();
 
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();
-    image4.clear();
-    image5.clear();
-
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -118,27 +54,9 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage"
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-
-
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -146,6 +64,7 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+
 }
 
 
@@ -158,7 +77,7 @@ void CamNoiseAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
 
     // RUN ROUTINE
     // for(int i = 0; i < NUM_RUN; i++) {
@@ -182,25 +101,10 @@ void CamNoiseAnalysis::synthesise()
     //cout << "CamNoiseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-    _returnAveragePixelValues();
-    vector<vector<float> > averagePixelBrightnessesForEachLevel = averagePixelValuesForAllLevels;
-    float lightLevel=0;
-    float pLightLevel=0;
-    cout<<_listOfLightLevels.size()<<" "<<averagePixelBrightnessesForEachLevel.size()<<" these should be the same";
-    
     for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
         
-        lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
         //cout << "CamNoiseAnalysis::synthesis FOR LOOP...\n";
         
-        //find which list of average pixel values is for THIS light level
-        int _averagePixelVectorIndex;
-        for (int j=0; j<_listOfLightLevels.size(); j+=3) {
-            if(lightLevel==_listOfLightLevels[j]){
-                _averagePixelVectorIndex=j;
-            }
-        }
         //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
         
         if(_state == STATE_STOP) return;
@@ -211,118 +115,49 @@ void CamNoiseAnalysis::synthesise()
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //    cout << "LOADED image1!!!" << endl;
+            //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 //////////////////////////
             
-             /*   cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
-                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+            //cvGrayImage2 = cvColorImage2;
             
             //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
+            cvGrayImage1.erode();
-                
+            cvGrayImage1.erode();
-                cvGrayImage1.dilate();
+            cvGrayImage1.erode();
-                cvGrayImage1.blur(5);
+            cvGrayImage1.blur();
             cvGrayImage1.contrastStretch();
             
             /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+            string file_name;
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
             
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+            file_name = ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
             
             
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
            
-                //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);
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
+            ofImage image;
+            //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
 
-                // convert the CV image 
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            image.setUseTexture(false);  
-                image5.setFromPixels(cvColorImage2.getPixelsRef());  
-                */
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
             
-                //subtract background begin///////////////
+            image.setFromPixels(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
+            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-                ofPixels imagePixels1       = image1.getPixelsRef();
+            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */ 
-                
-                //DIFFERENCING THE BACKGROUND
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-backgroundPixels[i]>0){
-                 imagePixels1[i]-=backgroundPixels[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */
-                
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, averagePixelBrightnessesForEachLevel[_averagePixelVectorIndex], _background), image1, image1, aMesh);
-                
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
-                
-                //with jpgs this was refusing to save out
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
-                _saved_filenames_synthesis.push_back(meshFileName);
-                
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //flag that we are finished  
-                meshIsComplete=true;
             _synth_save_cnt++;
             
+            //}
         }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
-        }
-
     }
     
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
@@ -528,7 +363,7 @@ void CamNoiseAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -552,537 +387,39 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
 
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "CamNoiseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
-}
     
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     
     
-void CamNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    int x=0;
+    unsigned char * somePixels;
-    int y=0;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
     
-    //to do 
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
     
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
     
-    //get rid of all previous vectors and colours
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    mesh.clear();
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    mesh.setMode(meshMode);
     
-    ofColor meshColour=ofColor(255,255,255);
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    if(chooseColour==6){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x++;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y++;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-
-}
-
-
-vector<float> CamNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    int inc=0;
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            if(i<100){
-                
-              //  cout<<" average: "<<averageDepths[inc]<<" actual: "<<imageColor1.getBrightness()<<" ";
-            }
-           // int thisDiff=imageColor1.getBrightness();
-            
-            int thisDiff=-(imageColor1.getBrightness() - averageDepths[inc] );
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-            inc++;
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-
-
-void CamNoiseAnalysis:: _returnAveragePixelValues(){
-    
-    
-    //second number in 15_204.00_2.jpg is the light level
-    
-    float lightLevel=0;
-    float pLightLevel=0;
-    float numberOfImagesActuallyLoaded=0;
-    vector<float> averagePixelValuesForOneLevel;
-
-    for (int j=0; j<RefractiveIndex::_vid_w*RefractiveIndex::_vid_h; j++) {
-        averagePixelValuesForOneLevel.push_back(0.0);
-    }
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        
-        
-        if(_state == STATE_STOP) return;
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
-            //couldn't load image
-            cout << "didn't load image" << endl;
-        }
-        
-        if(image1.loadImage(_saved_filenames_analysis[i])){
-
-            //split file name by under score
-            vector<string> fileNameParts= ofSplitString(_saved_filenames_analysis[i], "_");
-            
-            lightLevel = ofToFloat(fileNameParts[fileNameParts.size()-2]);
-           // cout<<" lightLevel "<<lightLevel;
-
-            ofPixels image1Pixels=image1.getPixelsRef();
-            
-            int x=0;
-            int y=0;
-            int inc=0;
-            for (int j=0; j<image1Pixels.size(); j+=3) {
-                ofColor color=image1Pixels.getColor(x, y);
-                averagePixelValuesForOneLevel[inc]+= color.getBrightness();
-                x++;
-                inc++;
-                if(x>=image1Pixels.getWidth()){ 
-                    x=0;
-                    y++;
-                }
-            }
-           // _listOfLightLevels}
-            numberOfImagesActuallyLoaded++;
-            
-            //if this is a new light level advance
-            if (lightLevel!=pLightLevel) {
-                
-                ///check that this light level is not already in our list
-                
-                
-             _listOfLightLevels.push_back(lightLevel);
-                
-                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
-                    averagePixelValuesForOneLevel[j]/=numberOfImagesActuallyLoaded;
-                    //cout<<" "<<averagePixelValuesForOneLevel[j]<<" ";
-                }
-                averagePixelValuesForAllLevels.push_back(averagePixelValuesForOneLevel);
-                for (int j=0; j<averagePixelValuesForOneLevel.size(); j++) {
-                    averagePixelValuesForOneLevel[j]=0;
-                }
-
-                pLightLevel=lightLevel;
-                numberOfImagesActuallyLoaded=0;
-
-            }
-
-        }
-    }
-    
-    for(int j=0;j<_listOfLightLevels.size();j++){
-        //cout<<_listOfLightLevels[j]<<" lightlevel ";
-    }
 
 }

src/CamNoiseAnalysis.h

@@ -60,30 +60,4 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
-    
-   
-    //mesh making function
-    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
-    
-    //depth map function
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, vector<float> averageDepths, ofImage &backgroundImage);
-    
-    //returns a vector of floats for each distinct light level
-   void _returnAveragePixelValues();
-    //this vector of vectors will be returned
-    vector<vector<float> > averagePixelValuesForAllLevels;
-    
-    vector<float> _listOfLightLevels;
-    
-    int vertexSubsampling;
-    
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
-    
 };

src/ColorMultiAnalysis.cpp

@@ -14,22 +14,13 @@ using Poco::Thread;
 
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
     cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
+    
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    
-    _mesh_size_multiplier=8;
-    vertexSubsampling = 1;
-    chooseColour=1;
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_colormulti", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 35;  
@@ -39,7 +30,7 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _frame_cnt = 0;
     _run_cnt = 0;
@@ -49,15 +40,12 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
+    //for an ofxOpenCv.h image i would like to use..."
+    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
+   
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -67,28 +55,9 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -97,8 +66,6 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 void ColorMultiAnalysis::acquire()
@@ -110,7 +77,7 @@ void ColorMultiAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -149,7 +116,6 @@ void ColorMultiAnalysis::synthesise()
             cout << "didn't load image" << endl;
         } 
         
-        
         if(image1.loadImage(_saved_filenames_analysis[i])){
             //cout << "LOADED image1!!!" << endl;
             //if(image5.loadImage(_saved_filenames_analysis[i+1])){
@@ -159,91 +125,45 @@ void ColorMultiAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            //cvColorImage1.blur(1);
+            cvColorImage1.blur(5);
-            //cvColorImage1.erode();
+            cvColorImage1.erode();
-            
+            cvColorImage1.erode();
-            //cvColorImage1.dilate();
+            cvColorImage1.dilate();
-            //cvColorImage1.dilate();
+            cvColorImage1.blur(5);
-            //cvColorImage1.dilate();
+            cvColorImage1.dilate();
-            //cvColorImage1.dilate();
+            cvColorImage1.dilate();
-            
+            cvColorImage1.dilate();
-            //cvFloatImage1 = cvColorImage1;
+            cvColorImage1.dilate();
-            //cvGrayImage1 = cvColorImage1;
-
-            cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 15, 15);
-            cvXorS( cvColorImage1.getCvImage(), cvScalarAll(2), cvColorImage1.getCvImage(), 0 );
-            
-            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-            
-            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-            
-            // convert the CV image 
-            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-            
-            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-            if(!_gotFirstImage){
-                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                _background=image1;
-                _gotFirstImage=true;
-            }
-            
-            //subtract background begin///////////////
-            
-            ofPixels imagePixels1       = image1.getPixelsRef();
-            //ofPixels imagePixels2       = image5.getPixelsRef();
-            ofPixels backgroundPixels   = _background.getPixelsRef();
-            
-            for(int i=0;i<imagePixels1.size();i++){
-                //unsigned char val=imagePixels1[i];
-                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                if(imagePixels1[i]-backgroundPixels[i]>0){
-                    imagePixels1[i]-=backgroundPixels[i];
-                }
-                else{
-                    imagePixels1[i]=0;
-                }
-            }
-            
-            //update the images with their new background subtracted selves
-            image1.setFromPixels(imagePixels1);
-            
-            //flag the main app that we aren't read yet
-            meshIsComplete=false;
-            
-            //make a mesh - this mesh will be drawn in the main app
-            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
-            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
             
             /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            //string file_name;
+            string file_name;
             
-            //with jpgs this was refusing to save out
+            file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            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";
             
-            //flag that we are finished  
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            meshIsComplete=true;
+            // 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);
             _synth_save_cnt++;
             
             // }
         }
     }
     
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-        _RUN_DONE = true;
-    */
-    
-    meshIsComplete=false;
-    _synth_save_cnt=0;
-    
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
 }
@@ -279,27 +199,6 @@ void ColorMultiAnalysis::displayresults()
 void ColorMultiAnalysis::draw()
 {
     
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();     
-    light.enable();
-	
-    light.setPosition(200,200,-150);
-    lightStatic.enable();
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(2.0f);
-    //glPointSize(4.0f);
-    
-    ofEnableBlendMode ( OF_BLENDMODE_ADD );
-    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
-    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
-    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
-    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
-
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -484,157 +383,42 @@ void ColorMultiAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
+  
     _save_cnt++;
+    
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ColorMultiAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    saveImageAnalysis(file_name);    
+
-}
+
-
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-void ColorMultiAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    
-    int x=0;
+    
-    int y=0;
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    
+    unsigned char * somePixels;
-    //get rid of all previous vectors and colours
+    ofPixels appPix = RefractiveIndex::_pixels;
-    mesh.clear();
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-    
+    somePixels = appPix.getPixels();
-    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    ofImage myImage;
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    //mesh.setMode(OF_PRIMITIVE_LINES);
+    
-    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    myImage.setUseTexture(false);
-    //mesh.setMode(OF_PRIMITIVE_POINTS);
+    
-    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    /*
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-     OF_PRIMITIVE_TRIANGLES,
+    
-     OF_PRIMITIVE_TRIANGLE_STRIP,
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-     OF_PRIMITIVE_TRIANGLE_FAN,
+    
-     OF_PRIMITIVE_LINES,
-     OF_PRIMITIVE_LINE_STRIP,
-     OF_PRIMITIVE_LINE_LOOP,
-     OF_PRIMITIVE_POINTS
-     
-     */
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-   
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-}
-
-
-
-vector<float> ColorMultiAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        //float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            //float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getLightness());
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            float multiplier=15.0*((thisDiff)/255.0);
-            
-            differences.push_back(multiplier* thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
 }

src/ColorMultiAnalysis.h

@@ -55,21 +55,4 @@ protected:
     
     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);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
-
 };

src/ColorSingleAnalysis.cpp

@@ -1,11 +1,9 @@
 #include "ColorSingleAnalysis.h"
 #include "ofMain.h"
+
 #include "Poco/Timer.h"
 #include "Poco/Thread.h"
 
-#include <string>
-#include <iostream>
-
 #include "RefractiveIndex.h"
 
 using Poco::Timer;
@@ -17,24 +15,15 @@ using Poco::Thread;
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
     cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
+    
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier=8;
-    vertexSubsampling = 1;
-    chooseColour=1;
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis: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
@@ -42,7 +31,7 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -57,17 +46,10 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     b = 0;
     
     fileNameTag = "";
-    fileNameColor = "";
 
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -77,28 +59,9 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -106,13 +69,12 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);    
 }
 
 
 void ColorSingleAnalysis::acquire()
 {
+
     Timer* save_timer;
 
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
@@ -120,7 +82,7 @@ void ColorSingleAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -135,6 +97,8 @@ void ColorSingleAnalysis::acquire()
 
     save_timer->stop();
 
+  
+    // }
 }
 
 void ColorSingleAnalysis::synthesise()
@@ -162,121 +126,57 @@ void ColorSingleAnalysis::synthesise()
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                 
-            
-                cout << "_saved_filenames_analysis[i].find(RED): " << _saved_filenames_analysis[i].find("RED") << endl;                
-            
-                if(_saved_filenames_analysis[i].find("RED")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameColor = "RED";
-                    cout<<"FOUND RED"<<endl;
-                } else if (_saved_filenames_analysis[i].find("GREEN")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameColor = "GREEN";
-                    cout<<"FOUND GREEN"<<endl;
-                } else if(_saved_filenames_analysis[i].find("BLUE")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameColor = "BLUE";
-                    cout<<"FOUND BLUE"<<endl;
-                } else if(_saved_filenames_analysis[i].find("FADING")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameColor = "FADING";
-                    cout<<"FOUND FADING"<<endl;
-                }
-                          
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.blur(1);
+                //cvGrayImage1 = cvColorImage1;
+                //cvGrayImage2 = cvColorImage2;
                 
-                //cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 9, 9 );
+                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                //cvGrayDiff1.erode();
+                //cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
             
+                cvColorImage1.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.dilate();
+                cvColorImage1.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.erode();
                 cvColorImage1.erode();
             
-                cvSmooth( cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), CV_GAUSSIAN, 3, 3 );
-            
-                //cvColorImage1.erode();
-            
-                //cvColorImage1.dilate();
-                //cvColorImage1.dilate();
-                //cvColorImage1.dilate();
-                //cvColorImage1.dilate();
-            
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
-            
-                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(255), cvColorImage1.getCvImage(), 0 );
-                
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-            
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-            
-                // convert the CV image 
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-            
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
-                
-                //subtract background begin///////////////
-                
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                for(int i=0;i<imagePixels1.size();i++){
-                    //unsigned char val=imagePixels1[i];
-                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                    if(imagePixels1[i]-backgroundPixels[i]>0){
-                        imagePixels1[i]-=backgroundPixels[i];
-                    }
-                    else{
-                        imagePixels1[i]=0;
-                    }
-                }
-            
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-        
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
+                string file_name;
                 
-                //with jpgs this was refusing to save out
+                file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                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";
                 
-                //flag that we are finished  
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                meshIsComplete=true;
+                // 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);
                 _synth_save_cnt++;
                 
            // }
         }
     }
     
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-     _RUN_DONE = true;
-     */
-    
-    meshIsComplete=false;
-    _synth_save_cnt=0;
-    
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
@@ -313,31 +213,12 @@ void ColorSingleAnalysis::displayresults()
 
 void ColorSingleAnalysis::draw()
 {
-    ofEnableSmoothing();
-
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();     
-    light.enable();
-	
-    light.setPosition(200,200,-150);
-    lightStatic.enable();
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(1.0f);
-    glPointSize(1.0f);
-    
-    ofEnableBlendMode ( OF_BLENDMODE_ADD );
-    //ofEnableBlendMode ( OF_BLENDMODE_MULTIPLY );
-    //ofEnableBlendMode ( OF_BLENDMODE_SUBTRACT );
-    //ofEnableBlendMode ( OF_BLENDMODE_ALPHA );
-    //ofEnableBlendMode ( OF_BLENDMODE_SCREEN );
-    
     
     switch (_state) {
         case STATE_ACQUIRING:
         {
             
+            
             if (_frame_cnt < _frame_cnt_max)
             {
                     
@@ -525,282 +406,40 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ColorSingleAnalysis::saving...\n";
+    
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
-}
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-
+    
-
+    
-void ColorSingleAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    int x=0;
+    unsigned char * somePixels;
-    int y=0;
+    ofPixels appPix = RefractiveIndex::_pixels;
-    
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
-   
+    somePixels = appPix.getPixels();
-    //get rid of all previous vectors and colours
+    
-    mesh.clear();
+    ofImage myImage;
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_STRIP);
+    
-    //mesh.setMode(OF_PRIMITIVE_TRIANGLE_FAN);
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    //mesh.setMode(OF_PRIMITIVE_LINES);
+    myImage.setUseTexture(false);
-    //mesh.setMode(OF_PRIMITIVE_LINE_STRIP);
+    
-    //mesh.setMode(OF_PRIMITIVE_LINE_LOOP);
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    mesh.setMode(OF_PRIMITIVE_POINTS);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-  
+        
-    /*
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-     OF_PRIMITIVE_TRIANGLES,
+
-     OF_PRIMITIVE_TRIANGLE_STRIP,
+
-     OF_PRIMITIVE_TRIANGLE_FAN,
-     OF_PRIMITIVE_LINES,
-     OF_PRIMITIVE_LINE_STRIP,
-     OF_PRIMITIVE_LINE_LOOP,
-     OF_PRIMITIVE_POINTS
-     
-     */
-    
-    ofColor meshColour=ofColor(255,255,255, 255);
-    
-      //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-                
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-             
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-      
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        ofColor currentSecondImageColor;
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            if(fileNameColor=="RED")
-            {
-                currentSecondImageColor.r=255;
-                currentSecondImageColor.g=0;
-                currentSecondImageColor.b=0;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="GREEN")
-            {
-                currentSecondImageColor.r=0;
-                currentSecondImageColor.g=255;
-                currentSecondImageColor.b=0;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="BLUE")
-            {
-                currentSecondImageColor.r=0;
-                currentSecondImageColor.g=0;
-                currentSecondImageColor.b=255;
-                currentSecondImageColor.a=255;
-                
-            } else if(fileNameColor=="FADING")
-            {
-                currentSecondImageColor.r= 255;
-                currentSecondImageColor.g= 255;
-                currentSecondImageColor.b= 255;
-                currentSecondImageColor.a= 255;
-            }
-                       
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-           
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor( currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            //x++;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //y++;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-}
-
-
-vector<float> ColorSingleAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-        
-            int thisDiff;
-            
-            if(fileNameColor=="RED")
-            {   
-                //thisDiff=abs(imageColor1.r);
-
-                thisDiff=abs(255-imageColor1.r);
-            } else if(fileNameColor=="GREEN")
-            {
-                //thisDiff=abs(imageColor1.g);                
-
-                thisDiff=abs(255-imageColor1.g);  
-                
-            } else if(fileNameColor=="BLUE")
-            {
-                //thisDiff=abs(imageColor1.b);
-
-                thisDiff=abs(255-imageColor1.b);
-            
-            } else if(fileNameColor=="FADING") {
-            
-                //thisDiff=imageColor1.getBrightness();
-                thisDiff=255-imageColor1.getBrightness();
-
-            }
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            float multiplier=8.0;
-            
-            differences.push_back(multiplier* thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
 }

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-    /*
+/*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -32,7 +32,6 @@ protected:
 
     bool    _RUN_DONE;
     string  fileNameTag;
-    string  fileNameColor;
     float   r,g,b;
     
     int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
@@ -61,24 +60,6 @@ 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);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
 };

src/DiffNoiseAnalysis.cpp

@@ -15,37 +15,13 @@ using Poco::Thread;
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
- 
     cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 10;
-    vertexSubsampling       = 1;
-    chooseColour            = 5;
-    multiplier              = 4.0;
-
-    blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-        
-    meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    //meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:diffnoise_shadow", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
@@ -55,7 +31,7 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -68,11 +44,8 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
+    //for an ofxOpenCv.h image i would like to use..."
-    image2.clear();
+    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
-    image3.clear();  
-    image4.clear();
-    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
@@ -83,28 +56,9 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -112,8 +66,6 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 }
 
 
@@ -125,7 +77,7 @@ void DiffNoiseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -173,133 +125,42 @@ void DiffNoiseAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
         
-            //cvColorImage1.erode();
+            cvColorImage1.invert();
-            //cvColorImage1.dilate();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
             
-            //cvColorImage1.blur(5);
+            //////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            //cvColorImage2.blur(5);
+            string file_name;
-            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
-            //cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
             
-            //cvGrayImage1.convertToRange(0.0, 255.0);
+            file_name = ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            //cvGrayImage2.convertToRange(0.0, 255.0);
-                
-            //cvGrayImage1.adaptiveThreshold( 200, 0);
-            //cvGrayImage2.adaptiveThreshold( 200, 0);
-                
-            //cvGrayImage1.contrastStretch();
-            //cvGrayImage2.contrastStretch();
-            
-            //cvGrayImage1.brightnessContrast(1.0,0.5);
-            //cvGrayImage2.brightnessContrast(1.0,0.5);
-               
-            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
-                
-            cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
-            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-            //cvFloatImage1 = cvColorImage1;
-            //cvGrayImage1 = cvColorImage1;
-            
-            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
-            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
-            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
-                
-            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-            
-            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
             
             
-             // convert the CV image 
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            //image5.setFromPixels(cvColorImage2.getPixelsRef()); 
             
-            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-            if(!_gotFirstImage){
-                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                _background=image1;
-                _gotFirstImage=true;
-            }
             
-            //subtract background begin///////////////
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            ofImage image;
+            //image.allocate(cvColorImage1.width, cvGrayImage1.height, OF_IMAGE_COLOR);
             
-            ofPixels imagePixels1       = image1.getPixelsRef();
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-            //ofPixels imagePixels2       = image5.getPixelsRef();
+            image.setUseTexture(false);  
-            ofPixels backgroundPixels   = _background.getPixelsRef();
             
-                //DIFFERENCING SUBSEQUENT IMAGES
+            image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-                 /*
+            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-            for(int i=0;i<imagePixels1.size();i++){
-                //unsigned char val=imagePixels1[i];
-                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                if(imagePixels1[i]-imagePixels2[i]>0){
-                    imagePixels1[i]-=imagePixels2[i];
-                }
-                else{
-                    imagePixels1[i]=0;
-                }
-            }
             
-                */ 
+            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                    //DIFFERENCING THE BACKGROUND
-                /*
-            for(int i=0;i<imagePixels1.size();i++){
-                //unsigned char val=imagePixels1[i];
-                // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                if(imagePixels1[i]-backgroundPixels[i]>0){
-                    imagePixels1[i]-=backgroundPixels[i];
-                }
-                else{
-                    imagePixels1[i]=0;
-                }
-            }
-              */                
-             
-            //update the images with their new background subtracted selves
-            image1.setFromPixels(imagePixels1);
-            
-            //flag the main app that we aren't read yet
-            meshIsComplete=false;
-            
-            //make a mesh - this mesh will be drawn in the main app
-            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
-            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
-            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            //string file_name;
-            
-            //with jpgs this was refusing to save out
-            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".png";
-            _saved_filenames_synthesis.push_back(meshFileName);
-            
-            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            
-            //flag that we are finished  
-            meshIsComplete=true;
             _synth_save_cnt++;
             
-            //}
+            // }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
-        
     }
     
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-    _RUN_DONE = true;
-    */
-    
-     meshIsComplete=false;
-    _synth_save_cnt=0;
-    
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
@@ -339,26 +200,6 @@ void DiffNoiseAnalysis::displayresults()
 // this runs at frame rate = 33 ms for 30 FPS
 void DiffNoiseAnalysis::draw()
 {
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();         
-    light.setPointLight();
-
-    light.enable();	
-    lightStatic.enable();
-
-    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
-
-    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(1.0f);
-    glPointSize(5.0f);
-    
-    ofEnableBlendMode(blendMode);
-
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -405,6 +246,7 @@ void DiffNoiseAnalysis::draw()
                     }        
                 }
                 
+                
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
@@ -561,412 +403,39 @@ void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "DiffNoiseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-    saveImageAnalysis(file_name);
-}
     
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     
-void DiffNoiseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
     
-    //get rid of all previous vectors and colours
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    mesh.clear();
+    unsigned char * somePixels;
-    mesh.setMode(meshMode);
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
     
-    ofColor meshColour=ofColor(255,255,255);
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
     
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-    float zPlaneAverage=0;
+    myImage.setUseTexture(false);
     
-    for(int i=0;i<sPixels.size();i++){
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-        zPlaneAverage+=sPixels[i];
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
     
-    else{
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-        
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-        
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-        
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor( currentSecondImageBW.clamp() );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
 
 }
-
-
-vector<float> DiffNoiseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}

src/DiffNoiseAnalysis.h

@@ -59,24 +59,4 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     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);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
 };

src/IResponseAnalysis.cpp

@@ -15,28 +15,15 @@ using Poco::Thread;
 
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-        
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
     cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    
-    _mesh_size_multiplier=4;
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_iresponse", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME IResponseAnalysis " << acq_run_time << endl;
 
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    
-    _mesh_size_multiplier=8;
-    
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
@@ -44,7 +31,7 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -56,12 +43,6 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -71,26 +52,9 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-     
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -98,17 +62,21 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    
 }
 
+
 void IResponseAnalysis::acquire()
 {
+
     Timer* save_timer;
     TimerCallback<IResponseAnalysis> save_callback(*this, &IResponseAnalysis::save_cb);
 
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
 
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -129,7 +97,6 @@ void IResponseAnalysis::acquire()
 
 void IResponseAnalysis::synthesise()
 {
-    cout<<"SYNTHESISING IRESPONSE";
     
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
@@ -149,66 +116,56 @@ void IResponseAnalysis::synthesise()
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
              //cout << "LOADED image1!!!" << endl;
-            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
                 
-                //subtract background begin///////////////
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                ofPixels imagePixels1       = image1.getPixelsRef();
+                cvGrayImage1 = cvColorImage1;
-                //ofPixels imagePixels2       = image5.getPixelsRef();
+                cvGrayImage2 = cvColorImage2;
-                ofPixels backgroundPixels   = _background.getPixelsRef();
                 
-                //background subtraction// 
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                /*
+                cvGrayDiff1.erode();
-                for(int i=0;i<imagePixels1.size();i++){
+                cvGrayDiff1.contrastStretch();
-                    //unsigned char val=imagePixels1[i];
+                //cvGrayDiff1.blur(5);
-                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
+                //cvGrayDiff1.dilate();
-                    if(imagePixels1[i]-backgroundPixels[i]>0){
+                //cvGrayDiff1.contrastStretch();
-                        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
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                meshIsComplete=false;
+                string file_name;
-                //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);
+                file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                //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;
+                //<---- 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);
                 _synth_save_cnt++;
                 
             }
-        //}
         }
-
+    }
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-     _RUN_DONE = true;
-     */
-    
-    meshIsComplete=false;
-    _synth_save_cnt=0;
 
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
+    
+    
 }
 
 
@@ -389,7 +346,7 @@ void IResponseAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
             
                 ofDisableAlphaBlending();
@@ -412,129 +369,38 @@ void IResponseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "IResponseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }
-
-void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
-    
-    ofColor meshColour=ofColor(255,0,0);
-    
-    int chooseColour=1  ;
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-         
-    if(chooseColour==1){
-        
-            for(int i=0;i<sPixels.size();i++){
-                mesh.addColor(  currentSecondImage.getColor(x, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x, y));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-                
-                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-              
-                mesh.addColor(  currentSecondImage.getColor(x, y));
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-                
-                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-
-                x++;
-                if(x>=currentSecondImage.getWidth()-1){
-                    x=0;
-                    y++;
-                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                    if(y>=currentSecondImage.getHeight()-1){
-                        break;
-                    }
-                }
-            }
-    }
-}
-
-vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-        for(int i=0;i<imagePixels1.size();i++){
-            thesePixels[i]=0;
-        }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-           
-            //float _presumedBrightness=255;
-            
-            int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            float multiplier=4.0;
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-
-

src/IResponseAnalysis.h

@@ -58,12 +58,4 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
-    
-    //mesh making function
-    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
-    //returns ofPixels but these pixels actually hold depth data.
-    //ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    bool _gotFirstImage;
-    ofImage _background;
 };

src/RelaxRateAnalysis.cpp

@@ -12,50 +12,18 @@ using Poco::Thread;
 
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
-#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", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_relaxrate", NUMBER_RUNS);
     cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
  
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling_x       = 1; //must be at least '1'
-    vertexSubsampling_y       = 5; //must be at least '1'
-    chooseColour            = 2;
-    multiplier              = 4.0;
-    
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    //meshMode = OF_PRIMITIVE_LINES;
-    meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_relaxrate", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_relaxrate", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
     
-    _treshold = RefractiveIndex::XML.getValue("config:relaxrate:treshold", TRESHOLD);
-    cout << "TRESHOLD RelaxRateAnalysis " << _treshold << endl;
-    
-    _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
-    cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
-
-    
     //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
@@ -63,7 +31,7 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _level = 0;
@@ -78,12 +46,6 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -93,23 +55,8 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
     
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -119,7 +66,6 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
-        
 }
 
 
@@ -132,7 +78,7 @@ void RelaxRateAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
 
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -152,20 +98,20 @@ void RelaxRateAnalysis::acquire()
 
 void RelaxRateAnalysis::synthesise()
 {
-    // cout << "RelaxRate::saving synthesis...\n";
+    //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
     for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
-        //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+        //cout << "IResponseAnalysis::synthesis FOR LOOP...\n";
         
-        //    cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
         
         if(_state == STATE_STOP) return;
         
         if(!image1.loadImage(_saved_filenames_analysis[i])){
             //couldn't load image
-            //        cout << "didn't load image" << endl;
+            cout << "didn't load image" << endl;
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
@@ -177,143 +123,47 @@ void RelaxRateAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                //cvColorImage1.erode();
+                cvGrayImage1 = cvColorImage1;
-                //cvColorImage1.erode();
+                cvGrayImage2 = cvColorImage2;
-                //cvColorImage1.dilate();
                 
-                cvColorImage1.blur(1);
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvColorImage2.blur(1);
+                cvGrayDiff1.erode();
-                
+                cvGrayDiff1.contrastStretch();
-                //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                cvGrayDiff1.blur(5);
-                //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
-                
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
-                
-                //cvGrayImage1.convertToRange(0.0, 255.0);
-                //cvGrayImage2.convertToRange(0.0, 255.0);
-                
-                //cvGrayImage1.adaptiveThreshold( 200, 0);
-                //cvGrayImage2.adaptiveThreshold( 200, 0);
-                
-                //cvGrayImage1.contrastStretch();
-                //cvGrayImage2.contrastStretch();
-                
-                cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
-                
-                //cvGrayDiff1.brightnessContrast(1.0,0.5);
-                
-                //cvGrayImage1.brightnessContrast(1.0,0.5);
-                //cvGrayImage2.brightnessContrast(1.0,0.5);
-                
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
-                
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
-                
-                
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
-                
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-                
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-                
-                // convert the CV image 
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-                image5.setFromPixels(cvColorImage2.getPixelsRef()); 
-                
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
-                
-                //subtract background begin///////////////
-                
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */ 
-                
-                //DIFFERENCING THE BACKGROUND
-                
-                for(int i=0;i<imagePixels1.size();i++){
-                    //unsigned char val=imagePixels1[i];
-                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                    if(imagePixels1[i]-backgroundPixels[i]>0){
-                        imagePixels1[i]-=backgroundPixels[i];
-                    }
-                    else{
-                        imagePixels1[i]=0;
-                    }
-                }
-                
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
                 
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
+                string file_name;
                 
-                //with jpgs this was refusing to save out
+                file_name = ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".png";
-                _saved_filenames_synthesis.push_back(meshFileName);
                 
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
                 
-                //flag that we are finished  
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                meshIsComplete=true;
+                // 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);
                 _synth_save_cnt++;
-                
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
-        
     }
     
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-     _RUN_DONE = true;
-     */
-    
-    meshIsComplete=false;
-    _synth_save_cnt=0;
-    
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    
     while(!_RUN_DONE && _state != STATE_STOP)
-        Thread::sleep(10);
+        Thread::sleep(3);
     
 }
+
 void RelaxRateAnalysis::displayresults()
 {
     
@@ -321,7 +171,7 @@ void RelaxRateAnalysis::displayresults()
         
         if(_state == STATE_STOP) return;
         
-        //    cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
         while(!_image_shown){
             Thread::sleep(2);
@@ -341,6 +191,7 @@ void RelaxRateAnalysis::displayresults()
         }
     }
 
+    
 }
 
 
@@ -348,28 +199,12 @@ void RelaxRateAnalysis::displayresults()
 void RelaxRateAnalysis::draw()
 {
     
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();         
-    light.setPointLight();
-    
-    light.enable();	
-    lightStatic.enable();
-    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
-    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(2.0f);
-    glPointSize(1.0f);
-    
-    ofEnableBlendMode(blendMode);
-        
     switch (_state) {
         case STATE_ACQUIRING:
         {
-            
+            /// *** TODO  *** ///
+            // still need to deal with latency frames here - i.e.: there are frames
+            /// *** TODO  *** ///
            
             if (_frame_cnt < _frame_cnt_max)
             {
@@ -400,7 +235,6 @@ void RelaxRateAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
-            
             // display animation of something while the synthesis in on-going...
             
             //cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
@@ -453,7 +287,7 @@ void RelaxRateAnalysis::draw()
                     }
                 }
                 
-                //cout << "_anim_cnt = " << _anim_cnt << endl;
+                cout << "_anim_cnt = " << _anim_cnt << endl;
                 
                 if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
 
@@ -501,10 +335,15 @@ void RelaxRateAnalysis::draw()
             
             if (_show_image)
             {  
-                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
+                //cout << "_show_image...\n" << endl;
-                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
-                }
                 
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
             }
             
             // display results of the synthesis
@@ -524,441 +363,37 @@ void RelaxRateAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    //cout << "RelaxRateAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     
     
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }
-
-void RelaxRateAnalysis::cleanup()
-{
-}
-
-
-void RelaxRateAnalysis::clearcfindervect()
-{
-    for(int i = 0; i < cvContourFinderVect.size(); i++) {
-        rfiCvContourFinder* f = cvContourFinderVect[i];
-
-        // maybe it's erase here?  http://forum.openframeworks.cc/index.php/topic,3016.0.html
-        // cvContourFinderVect.erase(i);
-        
-        delete f;        
-    }
-    cvContourFinderVect.clear();
-    
-}
-
-void RelaxRateAnalysis::clearcfindervectdisplay()
-{
-    cvContourFinderVectDisplay.clear();
-}
-
-
-
-
-void RelaxRateAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling_x;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling_y;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling_x;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling_y;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling_x;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling_y;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling_x;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling_y;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp() );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling_x;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling_y;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> RelaxRateAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/RelaxRateAnalysis.h

@@ -5,12 +5,8 @@
 
 #include "Poco/Timer.h"
 
-#include "rfiCvContourFinder.h"
-
 #include "ofxOpenCv.h"
 
-
-
 class RelaxRateAnalysis : public AbstractAnalysis
 {
 public:
@@ -23,7 +19,6 @@ public:
     void acquire();
     void synthesise(); 
     void displayresults();
-    void cleanup();
 
     void draw();
     
@@ -31,19 +26,12 @@ public:
     
 protected:
     
-    void clearcfindervect();
-    void clearcfindervectdisplay();
-    
     bool    _RUN_DONE;
     float     _flip, _level;
     int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
-    int     _treshold;
-    int     _maxblobs;
-    
     bool _show_image, _image_shown;
-    
     ofImage         image1;
     ofImage         image2; 
     ofImage         image3;
@@ -66,25 +54,6 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage3;
     ofxCvGrayscaleImage 	cvGrayImage4;
     
-    
+    ofxCvContourFinder      cvContourFinder1;
-    vector<rfiCvContourFinder*>      cvContourFinderVect;
-    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
-    
-    //mesh making function
-    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
-    
-    //depth map function
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    
-    int vertexSubsampling_x;
-    int vertexSubsampling_y;
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-    
 
 };

src/ShadowScapesAnalysis.cpp

@@ -19,65 +19,12 @@ using Poco::Thread;
 
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
     cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 1;
-    chooseColour            = 5;
-    multiplier              = 4.0;
-    
-    ofSetLineWidth(5.0f);
-    glPointSize(5.0f);
-    glEnable(GL_DEPTH_TEST);
-    
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
-    ///setup light    
-    ofEnableLighting();    
-    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
-    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
-    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
-    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-    
-    glEnable(GL_LIGHT0);  
-    
-    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
-    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
-    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
-    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-    
-    glEnable(GL_LIGHT1);     
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shadowscapes", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
     
     int screenSpan;
@@ -92,6 +39,8 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 
     DELTA_T_SAVE = 3*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 100 files
                                             // or 5 times per second = every 200 ms
+    //DELTA_T_SAVE = 1;
+    //create_dir();  // this makes both synth and analysis folder structures
 
     _scanLineWidth = 100.0;
     _run_cnt = 0;
@@ -104,12 +53,6 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-        
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -119,27 +62,9 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-        
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-       
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -147,8 +72,6 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
-    
 }
 
 void ShadowScapesAnalysis::acquire()
@@ -162,7 +85,9 @@ void ShadowScapesAnalysis::acquire()
     _line = 0;
     _RUN_DONE = false;
 
-    create_dir_allocate_images();
+    create_dir();
+    
+    //cout << "RUN NUM = " << i;
    
     save_timer.start(save_callback);
       
@@ -171,13 +96,15 @@ void ShadowScapesAnalysis::acquire()
     
     save_timer.stop();
     
+    //}
+
 }
 
 void ShadowScapesAnalysis::synthesise()
 {
     //cout << "ShadowScapesAnalysis::saving synthesis...\n";
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
     
       //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
         
@@ -191,7 +118,7 @@ void ShadowScapesAnalysis::synthesise()
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //    cout << "LOADED image1!!!" << endl;
+            
             if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
@@ -199,108 +126,50 @@ void ShadowScapesAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                cvGrayImage2 = cvColorImage2;
                 
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
+                cvGrayDiff1.erode();
-                
+                cvGrayDiff1.contrastStretch();
-                cvGrayImage1.dilate();
+                cvGrayDiff1.blur(5);
-                cvGrayImage1.blur(5);
+                cvGrayDiff1.dilate();
-                cvGrayImage1.contrastStretch();
                 
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                string file_name;
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
                 
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                if(_dir == H) {
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
+                    file_name = ofToString(_synth_save_cnt, 2)+"_H_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
-                
-                
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
-                
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-                
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-                
-                // convert the CV image 
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-                image5.setFromPixels(cvColorImage2.getPixelsRef());  
-                
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
                 }
                 
-                //subtract background begin///////////////
+                if(_dir == V) {
-                
+                    file_name = ofToString(_synth_save_cnt, 2)+"_V_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
                 }    
-                 else{
+                
-                 imagePixels1[i]=0;
+                if(_dir == D) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_D_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 }
-                 }
-                 */ 
                 
-                //DIFFERENCING THE BACKGROUND
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-backgroundPixels[i]>0){
-                 imagePixels1[i]-=backgroundPixels[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */
                 
-                //update the images with their new background subtracted selves
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                image1.setFromPixels(imagePixels1);
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
                 
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
                 
-                //make a mesh - this mesh will be drawn in the main app
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
                 
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                image.setUseTexture(false);  
                 
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
                 
-                //with jpgs this was refusing to save out
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShadowScapeAnalysis_"+ofToString(_run_cnt,2)+".png";
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
-                _saved_filenames_synthesis.push_back(meshFileName);
 
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                
-                //flag that we are finished  
-                meshIsComplete=true;
                 _synth_save_cnt++;
                 
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
     }
     
@@ -336,6 +205,41 @@ void ShadowScapesAnalysis::displayresults()
         }
     }
     
+    
+    // THE OLD SHIT /// 
+/*
+    for(float i=1;i<_saved_filenames_synthesis.size()-1;i++){
+        
+       // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image1.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+            
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            
+            image1.loadImage(_saved_filenames_analysis[i]);
+            cout << "loaded filenames[i] -  " << _saved_filenames_analysis[i] << endl;
+        
+            image2.setFromPixels(image1.getPixels(),image1.width,image1.height, OF_IMAGE_COLOR);
+          
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+
+        }
+    }
+*/
+    
 }
 
 
@@ -515,6 +419,7 @@ void ShadowScapesAnalysis::draw()
         {
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
 
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -530,8 +435,7 @@ void ShadowScapesAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                     ofSetColor(255, 255, 255);
-                
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
-                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                     image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -541,9 +445,6 @@ void ShadowScapesAnalysis::draw()
             
             // display results of the synthesis
             _RUN_DONE = true;
-            
-            // clear allocated memory...? 
-            
             break;
         }
             
@@ -559,6 +460,17 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ShadowScapesAnalysis::saving analysis...\n";
+    
     string file_name;
     
     if(_dir == H) {
@@ -573,416 +485,26 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
         
 }
-
-
-
-
-void ShadowScapesAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
-    
-    ofColor meshColour=ofColor(255,255,255);
-    
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
-    float zPlaneAverage=0;
-    
-    for(int i=0;i<sPixels.size();i++){
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-}
-
-
-vector<float> ShadowScapesAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/ShadowScapesAnalysis.h

@@ -66,20 +66,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //mesh making function
-    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
-    
-    //depth map function
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
-
 };

src/ShapeFromShadingAnalysis.cpp

@@ -15,67 +15,16 @@ 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);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
-    //NUM_RUN = 5;
 
-    //flag for main sketch
+   // NUM_RUN = 5;
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 1;
-    chooseColour            = 5;
-    multiplier              = 3.0;
-    
-    ofSetLineWidth(5.0f);
-    glPointSize(5.0f);
-
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    //blendMode = OF_BLENDMODE_SUBTRACT;
-    blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-    
-    ///setup light    
-    ofEnableLighting();    
-    GLfloat light_ambient[] = {0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position[] = { 1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT0, GL_AMBIENT, light_ambient);  
-    glLightfv(GL_LIGHT0, GL_DIFFUSE, light_diffuse);  
-    glLightfv(GL_LIGHT0, GL_SPECULAR, light_specular);  
-    glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-    
-    glEnable(GL_LIGHT0);  
-    
-    GLfloat light_ambient1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_diffuse1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_specular1[] = { 0.5, 0.5, 0.5, 0.5 };  
-    GLfloat light_position1[] = { -1.0, 1.0, 1.0, 0.0 };  
-    
-    glLightfv(GL_LIGHT1, GL_AMBIENT, light_ambient1);  
-    glLightfv(GL_LIGHT1, GL_DIFFUSE, light_diffuse1);  
-    glLightfv(GL_LIGHT1, GL_SPECULAR, light_specular1);  
-    glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-    
-    glEnable(GL_LIGHT1);  
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;
     
-
     //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
@@ -83,7 +32,7 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -92,15 +41,10 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 5;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
     
+    
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -110,28 +54,9 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -140,8 +65,6 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 
@@ -155,7 +78,7 @@ void ShapeFromShadingAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;    
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     _animation_cnt1 = 0;
     _animation_cnt2 = 0;
@@ -216,158 +139,45 @@ void ShapeFromShadingAnalysis::synthesise()
         //    cout << "LOADED image1!!!" << endl;
             if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
-                if(_saved_filenames_analysis[i].find("QUAD1")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD1";
-                    cout<<"FOUND QUAD1"<<endl;
-                } else if (_saved_filenames_analysis[i].find("QUAD2")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD2";
-                    cout<<"FOUND QUAD2"<<endl;
-                } else if(_saved_filenames_analysis[i].find("QUAD3")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD3";
-                    cout<<"FOUND QUAD3"<<endl;
-                } else if(_saved_filenames_analysis[i].find("QUAD4")<_saved_filenames_analysis[i].length())
-                {
-                    fileNameQuad = "QUAD4";
-                    cout<<"FOUND QUAD4"<<endl;
-                }
-                
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                 
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                cvGrayImage2 = cvColorImage2;
                 
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
+                cvGrayDiff1.erode();
-                
+                cvGrayDiff1.contrastStretch();
-                cvGrayImage1.dilate();
+                //cvGrayDiff1.blur(5);
-                cvGrayImage1.blur(5);
+                //cvGrayDiff1.dilate();
-                cvGrayImage1.contrastStretch();
+                //cvGrayDiff1.contrastStretch();
                 
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
+                string file_name;
-                //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
                 
-                //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
+                file_name = ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingSynthesis_"+ofToString(_run_cnt,2)+".jpg";
-                //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-                
-                //cvFloatImage1 = cvColorImage1;
-                //cvGrayImage1 = cvColorImage1;
                 
                 
-                //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-                //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                
-                //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-                //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-                
-                //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-                //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-                
-                // convert the CV image 
-                image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-                image5.setFromPixels(cvColorImage2.getPixelsRef());  
-                
-                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-                if(!_gotFirstImage){
-                    cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                    _background=image1;
-                    _gotFirstImage=true;
-                }
-                
-                //subtract background begin///////////////
-                
-                ofPixels imagePixels1       = image1.getPixelsRef();
-                ofPixels imagePixels2       = image5.getPixelsRef();
-                ofPixels backgroundPixels   = _background.getPixelsRef();
-                
-                //DIFFERENCING SUBSEQUENT IMAGES
-                /*
-                 for(int i=0;i<imagePixels1.size();i++){
-                 //unsigned char val=imagePixels1[i];
-                 // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                 if(imagePixels1[i]-imagePixels2[i]>0){
-                 imagePixels1[i]-=imagePixels2[i];
-                 }
-                 else{
-                 imagePixels1[i]=0;
-                 }
-                 }
-                 */ 
-                
-                //DIFFERENCING THE BACKGROUND
-                /*
-                for(int i=0;i<imagePixels1.size();i++){
-                    //unsigned char val=imagePixels1[i];
-                    // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-                    if(imagePixels1[i]-backgroundPixels[i]>0){
-                        imagePixels1[i]-=backgroundPixels[i];
-                    }
-                    else{
-                        imagePixels1[i]=0;
-                    }
-                }
-                */
-                
-                //update the images with their new background subtracted selves
-                image1.setFromPixels(imagePixels1);
-                
-                //flag the main app that we aren't read yet
-                meshIsComplete=false;
-                
-                //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                //string file_name;
-                
-                if(fileNameQuad=="QUAD1")
-                {       
-                    
-                    //with jpgs this was refusing to save out
-                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
                 
                 
-                } else if(fileNameQuad=="QUAD2")
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                {
+                ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
                 
-                    //with jpgs this was refusing to save out
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
+                image.setUseTexture(false);  
-                    _saved_filenames_synthesis.push_back(meshFileName);
                
-                } else if(fileNameQuad=="QUAD3")
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                {
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
                 
-                    //with jpgs this was refusing to save out
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                   meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-                
-                } else if(fileNameQuad=="QUAD4") {
-                    
-                    
-                    //with jpgs this was refusing to save out
-                    meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingAnalysis_"+fileNameQuad+"_"+ofToString(_run_cnt,2)+".png";
-                    _saved_filenames_synthesis.push_back(meshFileName);
-        
-                }
-
-                //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //flag that we are finished  
-                meshIsComplete=true;
                 _synth_save_cnt++;
                 
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
     }
     
@@ -408,48 +218,6 @@ void ShapeFromShadingAnalysis::displayresults()
 void ShapeFromShadingAnalysis::draw()
 {
     
-    //rotate light around origin ofviewspace    
-    float xx=cos(ofGetElapsedTimef()*0.4)*150;    
-    float yy=sin(ofGetElapsedTimef()*0.4)*150;    
-    float zz=0;
-    
-    if(fileNameQuad=="QUAD1")
-    {       
-        
-        GLfloat light_position[] = { 1000, 1000, 20, 0.0 };  
-        GLfloat light_position1[] = { 1000, 1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-        
-    } else if(fileNameQuad=="QUAD2")
-    {
-    
-        GLfloat light_position[] = { 1000, -1000, 20, 0.0 };  
-        GLfloat light_position1[] = { 1000, -1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-        
-    } else if(fileNameQuad=="QUAD3")
-    {
-      
-        GLfloat light_position[] = {-1000, 1000, 20, 0.0 };  
-        GLfloat light_position1[] = { -1000, 1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-        
-    } else if(fileNameQuad=="QUAD4") 
-    {
-        GLfloat light_position[] = { -1000, -1000, 20, 0.0 };  
-        GLfloat light_position1[] = { -1000, -1000, 20, 0.0 };  
-        glLightfv(GL_LIGHT0, GL_POSITION, light_position);  
-        glLightfv(GL_LIGHT1, GL_POSITION, light_position1);  
-
-    }
-
-    
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -769,7 +537,7 @@ void ShapeFromShadingAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -794,416 +562,39 @@ void ShapeFromShadingAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
         
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ShapeFromShadingAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ quad +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
-}
     
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     
     
-void ShapeFromShadingAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    int x=0;
+    unsigned char * somePixels;
-    int y=0;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
     
-    //get rid of all previous vectors and colours
+    ofImage myImage;
-    mesh.clear();
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    mesh.setMode(meshMode);
     
-    ofColor meshColour=ofColor(255,255,255);
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
     
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    float zPlaneAverage=0;
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
     
-    for(int i=0;i<sPixels.size();i++){
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-        zPlaneAverage+=sPixels[i];
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
-    
-    else{
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
-    }
-    
-    if(chooseColour==1){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
 
 }
-
-
-vector<float> ShapeFromShadingAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            
-            ofColor imageColor2 = imagePixels1.getColor(x+1, y+1);
-            
-            ofColor imageColor3 = imagePixels1.getColor(x+2, y+2);
-            
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-        
-            int thisDiff=-abs(imageColor1.getBrightness()+ofRandom(-50,50));
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/ShapeFromShadingAnalysis.h

@@ -31,8 +31,6 @@ public:
 protected:
     
     string quad;
-    string fileNameQuad;
-    
     bool    _RUN_DONE;
     float     _flip, _level;
     int _animation_cnt1;
@@ -80,23 +78,4 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     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);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
 };

src/StrobeAnalysis.cpp

@@ -15,36 +15,13 @@ using Poco::Thread;
 
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    AbstractAnalysis::setup(camWidth, camHeight);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
-    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
     cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
-    //flag for main sketch
-    meshIsComplete=false;
-    _gotFirstImage=false;
-    _mesh_size_multiplier   = 8;
-    vertexSubsampling       = 3;
-    chooseColour            = 2;
-    multiplier              = 4.0;
-    
-    //blendMode = OF_BLENDMODE_ADD;
-    //blendMode = OF_BLENDMODE_MULTIPLY;
-    blendMode = OF_BLENDMODE_SUBTRACT;
-    //blendMode = OF_BLENDMODE_ALPHA;
-    //blendMode = OF_BLENDMODE_SCREEN;
-    
-    //meshMode = OF_PRIMITIVE_TRIANGLES;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_STRIP;
-    //meshMode = OF_PRIMITIVE_TRIANGLE_FAN;
-    meshMode = OF_PRIMITIVE_LINES;
-    //meshMode = OF_PRIMITIVE_LINE_STRIP;
-    //meshMode = OF_PRIMITIVE_POINTS;
-
-    
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_strobe", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
@@ -58,7 +35,7 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 
     // The British Health and Safety Executive recommend that a net flash rate for a bank of strobe lights does not exceed 5 flashes per second, at which only 5% of photosensitive epileptics are at risk. It also recommends that no strobing effect continue for more than 30 seconds, due to the potential for discomfort and disorientation.
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     
@@ -68,12 +45,6 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -83,26 +54,9 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -111,7 +65,6 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-
 }
 
 
@@ -124,7 +77,7 @@ void StrobeAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0;  _strobe_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -164,7 +117,7 @@ void StrobeAnalysis::synthesise()
         } 
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //cout << "LOADED image1!!!" << endl;
+    //        cout << "LOADED image1!!!" << endl;
             if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
@@ -172,142 +125,44 @@ void StrobeAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            //cvColorImage1.erode();
+                cvGrayImage1 = cvColorImage1;
-            //cvColorImage1.erode();
+                cvGrayImage2 = cvColorImage2;
-                //cvColorImage1.dilate();
             
-            cvColorImage1.blur(1);
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-            cvColorImage2.blur(1);
+                cvGrayDiff1.dilate();
-            
+                cvGrayDiff1.dilate();
-            //cvXorS( cvColorImage1.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
+                cvGrayDiff1.contrastStretch();
-            //cvXorS( cvColorImage2.getCvImage(), cvScalarAll(150), cvColorImage1.getCvImage(), 0 );
-                
-            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
-            cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
-            
-            //cvGrayImage1.convertToRange(0.0, 255.0);
-            //cvGrayImage2.convertToRange(0.0, 255.0);
-            
-            //cvGrayImage1.adaptiveThreshold( 200, 0);
-            //cvGrayImage2.adaptiveThreshold( 200, 0);
-            
-            //cvGrayImage1.contrastStretch();
-            //cvGrayImage2.contrastStretch();
-            
-            cvGrayDiff1.absDiff(cvGrayImage1, cvGrayImage2);
-
-            cvGrayDiff1.brightnessContrast(1.0,0.5);
-            
-            //cvGrayImage1.brightnessContrast(1.0,0.5);
-            //cvGrayImage2.brightnessContrast(1.0,0.5);
-            
-            cvColorImage1.setFromGrayscalePlanarImages(cvGrayImage1, cvGrayImage1, cvGrayImage1);
-            //cvColorImage2.setFromGrayscalePlanarImages(cvGrayImage2, cvGrayImage2, cvGrayImage2);
-            
-            //cvPyrMeanShiftFiltering(cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), 1, 1);
-            //cvPyrMeanShiftFiltering(cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), 1, 1);
-            
-            //cvFloatImage1 = cvColorImage1;
-            //cvGrayImage1 = cvColorImage1;
-            
-           
-            //cvSmooth( cvColorImage1.getCvImage(), cvColorImage1.getCvImage(), CV_GAUSSIAN, 5, 5);
-            //cvSmooth( cvColorImage2.getCvImage(), cvColorImage2.getCvImage(), CV_GAUSSIAN, 5, 5);
-            
-            //cvCanny(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 100, 100, 3);
-            //cvLaplace(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0);
-            
-            //cvGrayImage1 = cvCreateImage(cvSize(image1.width, image1.height),IPL_DEPTH_16S,1);
-            //cvSobel(cvGrayImage1.getCvImage(), cvGrayImage1.getCvImage(), 0, 1, 3);
-            
-            // convert the CV image 
-            image1.setFromPixels(cvColorImage1.getPixelsRef()); 
-            image5.setFromPixels(cvColorImage2.getPixelsRef()); 
-            
-            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
-            if(!_gotFirstImage){
-                cout<<"background image is"<< _saved_filenames_analysis[i]<<endl;
-                _background=image1;
-                _gotFirstImage=true;
-            }
-            
-            //subtract background begin///////////////
-            
-            ofPixels imagePixels1       = image1.getPixelsRef();
-            ofPixels imagePixels2       = image5.getPixelsRef();
-            ofPixels backgroundPixels   = _background.getPixelsRef();
-            
-            //DIFFERENCING SUBSEQUENT IMAGES
-            /*
-             for(int i=0;i<imagePixels1.size();i++){
-             //unsigned char val=imagePixels1[i];
-             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-             if(imagePixels1[i]-imagePixels2[i]>0){
-             imagePixels1[i]-=imagePixels2[i];
-             }
-             else{
-             imagePixels1[i]=0;
-             }
-             }
-            */ 
-             
-            //DIFFERENCING THE BACKGROUND
-            
-             for(int i=0;i<imagePixels1.size();i++){
-             //unsigned char val=imagePixels1[i];
-             // cout<<(int)backgroundPixels[i]<< " thesePixels[i] "<<(int)imagePixels1[i]<<endl;
-             if(imagePixels1[i]-backgroundPixels[i]>0){
-             imagePixels1[i]-=backgroundPixels[i];
-             }
-             else{
-             imagePixels1[i]=0;
-             }
-             }
-            
-            //update the images with their new background subtracted selves
-            image1.setFromPixels(imagePixels1);
-            
-            //flag the main app that we aren't read yet
-            meshIsComplete=false;
-            
-            //make a mesh - this mesh will be drawn in the main app
-            setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
-            
-            //setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1, image1, aMesh);
                
                 /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-            //string file_name;
+                string file_name;
                 
-            //with jpgs this was refusing to save out
+                file_name = ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-            meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".png";
-            _saved_filenames_synthesis.push_back(meshFileName);
                 
-            //file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
         
-            //flag that we are finished  
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-            meshIsComplete=true;
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                ofImage image;
+                //image.allocate(cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);    
+            
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                image.setUseTexture(false);  
+                
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height,OF_IMAGE_GRAYSCALE);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
                 _synth_save_cnt++;
                 
             }
-        } else {
-            cout<<"couldn't load image from "<<_saved_filenames_analysis[i]<<endl;
         }
-        
     }
     
-    // TOM'S fix of why the last file gets overwritten again and again - but seems to prevent the files being written to the screen.
-    /*
-     _RUN_DONE = true;
-     */
-    
-    meshIsComplete=false;
-    _synth_save_cnt=0;
-    
     // _saved_filenames_synthesis has processed all the files in the analysis images folder
-    
     while(!_RUN_DONE && _state != STATE_STOP)
-        Thread::sleep(10);
+        Thread::sleep(3); 
-
 }
 
 void StrobeAnalysis::displayresults()
@@ -344,27 +199,6 @@ void StrobeAnalysis::displayresults()
 void StrobeAnalysis::draw()
 {
     
-    ofEnableSmoothing();
-    
-    ofEnableLighting(); 
-    ofEnableSeparateSpecularLight();         
-    light.setPointLight();
-    
-    light.enable();	
-    lightStatic.enable();
-    
-    light.setPosition(ofGetWidth()/2,ofGetHeight()/2,5);
-    
-    lightStatic.setPosition(ofGetWidth()/2,ofGetHeight()/2,-1);
-    
-    glEnable(GL_DEPTH_TEST);
-    
-    ofSetLineWidth(1.0f);
-    glPointSize(5.0f);
-    
-    ofEnableBlendMode(blendMode);
-
-    
     switch (_state) {
         case STATE_ACQUIRING:
         {
@@ -383,6 +217,7 @@ void StrobeAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     //cout <<  "FADE IN STROBE TIME " << endl;
                     
+                    
                 }
                 
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max-_fade_in_frames)){
@@ -414,7 +249,6 @@ void StrobeAnalysis::draw()
                 }         
             
                 ofDisableAlphaBlending();
-                
             } else {
                 //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
@@ -528,7 +362,7 @@ void StrobeAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -553,412 +387,39 @@ void StrobeAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "StrobeAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
-}
     
-void StrobeAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
-    int x=0;
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    int y=0;
     
-    //get rid of all previous vectors and colours
-    mesh.clear();
-    mesh.setMode(meshMode);
     
-    ofColor meshColour=ofColor(255,255,255);
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
 
-    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    ofImage myImage;
-    float zPlaneAverage=0;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
     
-    for(int i=0;i<sPixels.size();i++){
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
-        zPlaneAverage+=sPixels[i];
+    myImage.setUseTexture(false);
-    }
-    if (sPixels.size()!=0) {
-        zPlaneAverage/=sPixels.size();
-        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
-    }
     
-    else{
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
-    }
     
-    if(chooseColour==1){
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y+1));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x, y));
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==2){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y+1);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x+1, y);
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==3){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            mesh.addColor(  currentSecondImageColor);
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==4){
-        
-        for(int i=0;i<sPixels.size();i++){
-            ofColor currentSecondImageColor;
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            int randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter)    ]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*((y+randomJitter)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+randomJitter),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            mesh.addColor(  currentSecondImageColor.getBrightness());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x+randomJitter)+1),_mesh_size_multiplier*(y+randomJitter),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) +1 ]));
-            
-            ofSeedRandom();
-            
-            currentSecondImageColor.r = ofRandom(0,255);
-            currentSecondImageColor.g = ofRandom(0,255);
-            currentSecondImageColor.b = ofRandom(0,255);
-            
-            randomJitter = ofRandom(0,5);
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
-    
-    if(chooseColour==5){
-        
-        for(int i=0;i<sPixels.size();i++){
-            
-            int randomJitter2 = 0;
-            int randomJitter = 0;
-            
-            ofColor currentSecondImageColor;
-            ofColor currentSecondImageBW;
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*((y)+1),- sPixels[ (currentSecondImage.getWidth()*(y+randomJitter+1))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ] ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1 ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y+1);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor( currentSecondImageBW.clamp() );
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*((y)+1),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)+1))+(x+randomJitter)+1]   ));
-            
-            currentSecondImageColor =  currentSecondImage.getColor(x, y);            
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp());
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter) ]  ));
-            
-            currentSecondImageColor = currentSecondImage.getColor(x+1, y);
-            currentSecondImageBW.r = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.g = currentSecondImageColor.getBrightness()+randomJitter2;
-            currentSecondImageBW.b = currentSecondImageColor.getBrightness()+randomJitter2;
-            
-            mesh.addColor(  currentSecondImageBW.clamp() ); 
-            mesh.addVertex(ofVec3f(_mesh_size_multiplier*((x)+1),_mesh_size_multiplier*(y),- sPixels[(currentSecondImage.getWidth()*((y+randomJitter)))+(x+randomJitter)+1 ]));
-            
-            x=x+vertexSubsampling;
-            if(x>=currentSecondImage.getWidth()-1){
-                x=0;
-                y=y+vertexSubsampling;
-                //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
-                if(y>=currentSecondImage.getHeight()-1){
-                    break;
-                }
-            }
-        }
-    }
 
 }
-
-
-vector<float> StrobeAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    //ofPixels imagePixels2 = image2.getPixelsRef();
-    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    vector<float> differences;
-    
-    ofPixels difference;
-    
-    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
-    unsigned char * thesePixels = new unsigned char[imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
-    for(int i=0;i<imagePixels1.size();i++){
-        thesePixels[i]=0;
-    }
-    
-    int x=0;
-    int y=0;
-    
-    int chooseComparison=1;
-    
-    //comparison here to find out how close each color is to pure RED / GREEN / BLUE
-    
-    if(chooseComparison==1){
-        //for each pixel...
-        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
-        
-        for(int i=0;i<imagePixels1.size();i+=3){
-            
-            ofColor imageColor1 = imagePixels1.getColor(x, y);
-            //ofColor colourImage2 = imagePixels2.getColor(x, y);
-            
-            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
-            float _presumedBrightness=ofMap(sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
-            
-            //int thisDiff=abs(imageColor1.getHue());
-            //int thisDiff=abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getBrightness()-_presumedBrightness);
-            
-            int thisDiff=-abs(imageColor1.getBrightness());
-            //int thisDiff=abs(imageColor1.getLightness());
-            //int thisDiff=-abs(imageColor1.r);
-            
-            //cout<<thisDiff<< " thisDiff "<<endl;
-            
-            //red hue: 0
-            //green hue: 120 
-            //blue hue: 240
-            
-            differences.push_back(multiplier * thisDiff);
-            
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            }
-        }
-    }
-    
-    //difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return differences;
-}
-

src/StrobeAnalysis.h

@@ -65,20 +65,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //mesh making function
-    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
-    
-    //depth map function
-    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
-    
-    int vertexSubsampling;
-    int chooseColour;
-    ofPrimitiveMode meshMode;
-    ofBlendMode blendMode;
-    float multiplier;
-    
-    bool _gotFirstImage;
-    ofImage _background;
-
-
 };

src/rficv/rfiCvContourFinder.cpp

@@ -1,211 +0,0 @@
-
-#include "rfiCvContourFinder.h"
-
-
-
-//--------------------------------------------------------------------------------
-static bool sort_carea_compare( const CvSeq* a, const CvSeq* b) {
-	// use opencv to calc size, then sort based on size
-	float areaa = fabs(cvContourArea(a, CV_WHOLE_SEQ));
-	float areab = fabs(cvContourArea(b, CV_WHOLE_SEQ));
-
-    //return 0;
-	return (areaa > areab);
-}
-
-
-
-
-//--------------------------------------------------------------------------------
-rfiCvContourFinder::rfiCvContourFinder() {
-    _width = 0;
-    _height = 0;
-	myMoments = (CvMoments*)malloc( sizeof(CvMoments) );
-	reset();
-}
-
-//--------------------------------------------------------------------------------
-rfiCvContourFinder::~rfiCvContourFinder() {
-	free( myMoments );
-}
-
-//--------------------------------------------------------------------------------
-void rfiCvContourFinder::reset() {
-    cvSeqBlobs.clear();
-    blobs.clear();
-    nBlobs = 0;
-}
-
-//--------------------------------------------------------------------------------
-int rfiCvContourFinder::findContours( ofxCvGrayscaleImage&  input,
-									  int minArea,
-									  int maxArea,
-									  int nConsidered,
-									  bool bFindHoles,
-                                      bool bUseApproximation) {
-
-    // get width/height disregarding ROI
-    IplImage* ipltemp = input.getCvImage();
-    _width = ipltemp->width;
-    _height = ipltemp->height;
-
-	reset();
-
-	// opencv will clober the image it detects contours on, so we want to
-    // copy it into a copy before we detect contours.  That copy is allocated
-    // if necessary (necessary = (a) not allocated or (b) wrong size)
-	// so be careful if you pass in different sized images to "findContours"
-	// there is a performance penalty, but we think there is not a memory leak
-    // to worry about better to create mutiple contour finders for different
-    // sizes, ie, if you are finding contours in a 640x480 image but also a
-    // 320x240 image better to make two rfiCvContourFinder objects then to use
-    // one, because you will get penalized less.
-
-	if( inputCopy.getWidth() == 0 ) {
-        inputCopy.setUseTexture(false);
-		inputCopy.allocate( _width, _height );
-	} else if( inputCopy.getWidth() != _width || inputCopy.getHeight() != _height ) {
-        // reallocate to new size
-        inputCopy.clear();
-        inputCopy.setUseTexture(false);
-        inputCopy.allocate( _width, _height );
-	}
-
-    inputCopy.setROI( input.getROI() );
-    inputCopy = input;
-
-	CvSeq* contour_list = NULL;
-	contour_storage = cvCreateMemStorage( 1000 );
-	storage	= cvCreateMemStorage( 1000 );
-
-	CvContourRetrievalMode  retrieve_mode
-        = (bFindHoles) ? CV_RETR_LIST : CV_RETR_EXTERNAL;
-	cvFindContours( inputCopy.getCvImage(), contour_storage, &contour_list,
-                    sizeof(CvContour), retrieve_mode, bUseApproximation ? CV_CHAIN_APPROX_SIMPLE : CV_CHAIN_APPROX_NONE );
-	CvSeq* contour_ptr = contour_list;
-
-	// put the contours from the linked list, into an array for sorting
-	while( (contour_ptr != NULL) ) {
-		float area = fabs( cvContourArea(contour_ptr, CV_WHOLE_SEQ) );
-		if( (area > minArea) && (area < maxArea) ) {
-            cvSeqBlobs.push_back(contour_ptr);
-		}
-		contour_ptr = contour_ptr->h_next;
-	}
-
-
-	// sort the pointers based on size
-	if( cvSeqBlobs.size() > 1 ) {
-        sort( cvSeqBlobs.begin(), cvSeqBlobs.end(), sort_carea_compare );
-	}
-
-
-	// now, we have cvSeqBlobs.size() contours, sorted by size in the array
-    // cvSeqBlobs let's get the data out and into our structures that we like
-	for( int i = 0; i < MIN(nConsidered, (int)cvSeqBlobs.size()); i++ ) {
-		blobs.push_back( ofxCvBlob() );
-		float area = cvContourArea( cvSeqBlobs[i], CV_WHOLE_SEQ );
-		CvRect rect	= cvBoundingRect( cvSeqBlobs[i], 0 );
-		cvMoments( cvSeqBlobs[i], myMoments );
-
-		blobs[i].area                     = fabs(area);
-		blobs[i].hole                     = area < 0 ? true : false;
-		blobs[i].length 			      = cvArcLength(cvSeqBlobs[i]);
-		blobs[i].boundingRect.x           = rect.x;
-		blobs[i].boundingRect.y           = rect.y;
-		blobs[i].boundingRect.width       = rect.width;
-		blobs[i].boundingRect.height      = rect.height;
-		blobs[i].centroid.x 			  = (myMoments->m10 / myMoments->m00);
-		blobs[i].centroid.y 			  = (myMoments->m01 / myMoments->m00);
-
-		// get the points for the blob:
-		CvPoint           pt;
-		CvSeqReader       reader;
-		cvStartReadSeq( cvSeqBlobs[i], &reader, 0 );
-
-    	for( int j=0; j < cvSeqBlobs[i]->total; j++ ) {
-			CV_READ_SEQ_ELEM( pt, reader );
-            blobs[i].pts.push_back( ofPoint((float)pt.x, (float)pt.y) );
-		}
-		blobs[i].nPts = blobs[i].pts.size();
-
-	}
-
-    nBlobs = blobs.size();
-
-	// Free the storage memory.
-	// Warning: do this inside this function otherwise a strange memory leak
-	if( contour_storage != NULL ) { cvReleaseMemStorage(&contour_storage); }
-	if( storage != NULL ) { cvReleaseMemStorage(&storage); }
-
-	return nBlobs;
-
-}
-
-//--------------------------------------------------------------------------------
-void rfiCvContourFinder::draw( float x, float y, float w, float h ) {
-
-    float scalex = 0.0f;
-    float scaley = 0.0f;
-    if( _width != 0 ) { scalex = w/_width; } else { scalex = 1.0f; }
-    if( _height != 0 ) { scaley = h/_height; } else { scaley = 1.0f; }
-
-    if(bAnchorIsPct){
-        x -= anchor.x * w;
-        y -= anchor.y * h;
-    }else{
-        x -= anchor.x;
-        y -= anchor.y;
-    }
-
-    ofPushStyle();
-    glPushMatrix();
-    glTranslatef( x, y, 0.0 );
-    glScalef( scalex, scaley, 0.0 );
-	ofSetHexColor(0xFFFFFF);
-
-	for( int i=0; i<(int)blobs.size(); i++ ) {
-		ofNoFill();
-		ofBeginShape();
-		for( int j=0; j<blobs[i].nPts; j++ ) {
-			ofVertex( blobs[i].pts[j].x, blobs[i].pts[j].y );
-		}
-		ofEndShape();
-
-	}
-	glPopMatrix();
-	ofPopStyle();
-}
-
-
-//----------------------------------------------------------
-void rfiCvContourFinder::draw(const ofPoint & point){
-	draw(point.x, point.y);
-}
-
-//----------------------------------------------------------
-void rfiCvContourFinder::draw(const ofRectangle & rect){
-	draw(rect.x, rect.y, rect.width, rect.height);
-}
-
-//--------------------------------------------------------------------------------
-void rfiCvContourFinder::setAnchorPercent( float xPct, float yPct ){
-    anchor.x = xPct;
-    anchor.y = yPct;
-    bAnchorIsPct = true;
-}
-
-//--------------------------------------------------------------------------------
-void rfiCvContourFinder::setAnchorPoint( int x, int y ){
-    anchor.x = x;
-    anchor.y = y;
-    bAnchorIsPct = false;
-}
-
-//--------------------------------------------------------------------------------
-void rfiCvContourFinder::resetAnchor(){
-    anchor.set(0,0);
-    bAnchorIsPct = false;
-}
-
-

src/rficv/rfiCvContourFinder.h

@@ -1,73 +0,0 @@
-/*
-* rfiCvContourFinder.h
-*
-* Finds white blobs in binary images and identifies
-* centroid, bounding box, area, length and polygonal contour
-* The result is placed in a vector of ofxCvBlob objects.
-*
-*/
-
-#ifndef RFI_CV_CONTOUR_FINDER
-#define RFI_CV_CONTOUR_FINDER
-
-
-
-#include "ofxCvConstants.h"
-#include "ofxCvBlob.h"
-#include "ofxCvGrayscaleImage.h"
-#include <algorithm>
-
-class rfiCvContourFinder : public ofBaseDraws {
-
-  public:
-  
-    vector<ofxCvBlob>  blobs;
-    int                nBlobs;    // DEPRECATED: use blobs.size() instead
-      
-
-    rfiCvContourFinder();
-    virtual  ~rfiCvContourFinder();
-    
-	virtual float getWidth() { return _width; };    //set after first findContours call
-	virtual float getHeight() { return _height; };  //set after first findContours call
-    
-    virtual int  findContours( ofxCvGrayscaleImage& input,
-                               int minArea, int maxArea,
-                               int nConsidered, bool bFindHoles,
-                               bool bUseApproximation = true);
-                               // approximation = don't do points for all points 
-                               // of the contour, if the contour runs
-                               // along a straight line, for example...
-
-    virtual void  draw() { draw(0,0, _width, _height); };
-    virtual void  draw( float x, float y ) { draw(x,y, _width, _height); };
-    virtual void  draw( float x, float y, float w, float h );
-	virtual void  draw(const ofPoint & point);
-	virtual void  draw(const ofRectangle & rect);
-	virtual void setAnchorPercent(float xPct, float yPct);
-    virtual void setAnchorPoint(int x, int y);
-	virtual void resetAnchor();      
-    //virtual ofxCvBlob  getBlob(int num);
-
-
-
-  protected:
-
-    int  _width;
-    int  _height;
-    ofxCvGrayscaleImage     inputCopy;
-    CvMemStorage*           contour_storage;
-    CvMemStorage*           storage;
-    CvMoments*              myMoments;
-    vector<CvSeq*>          cvSeqBlobs;  //these will become blobs
-    
-    ofPoint  anchor;
-    bool  bAnchorIsPct;      
-
-    virtual void reset();
-
-};
-
-
-
-#endif