added triangular mesh and scaling for z axis.

make sure you add the config.refindx to your environment

.gitignore

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

README

@@ -0,0 +1,10 @@
+WARNING: WORK IN PROGRESS...
+
+configuring OpenFrameworks under Xcode
+---------------------------------------
+
+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};  
+(3) Press Play!

README.md

@@ -1,2 +0,0 @@
-<img src="https://davidgauthier.info/rfi/img-resize/rfi3.jpg" width="100%">
-<img src="https://davidgauthier.info/rfi/img-resize/rfi4.jpg" width="100%">

example/RefractiveIndex.cpp

@@ -1,12 +1,5 @@
-/*
 
- todo:
- (1) Look at warinings about the #define which get over written
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
+////also the new shit////
 
 #include "RefractiveIndex.h"
 
@@ -22,11 +15,11 @@
 
 #include "ofxXmlSettings.h"
 
-#define CAMERA_ID           1
+#define CAMERA_ID           0
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
-#define LOCATION            "MIDDLESBOROUGH"
+#define LOCATION            "MANCHESTER"
 
 #define ISTATE_UNDEF        0xEEEE
 #define ISTATE_START        0xAAAA
@@ -34,8 +27,10 @@
 #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;
@@ -43,20 +38,31 @@ bool             RefractiveIndex::_vid_stream_open;
 bool             RefractiveIndex::_vid_toggle_on;
 string           RefractiveIndex::_location;
 
-ofxXmlSettings   XML;
+ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
+    camDist=1000;
+
+    //camera.setOrientation(ofVec3f(1,-1,1));
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
-    if(!XML.loadFile("../data/config.refindx")) {
+    if(XML.loadFile("config.refindx") == false) {
         ofLog(OF_LOG_ERROR) << "error loading config - using default.";
         save_config = true;                
+    } else {
+        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;
+    
     _vid_w  = XML.getValue("config:camera:width", CAMERA_ACQU_WIDTH);
     _vid_h  = XML.getValue("config:camera:height", CAMERA_ACQU_HEIGHT);
     
@@ -71,6 +77,7 @@ void RefractiveIndex::setup()
     // display
     cout << "> display" << endl;
     ofSetFrameRate(fps);
+    
     if(fps > 30) {
         ofSetVerticalSync(FALSE);            
     } else {        
@@ -84,8 +91,10 @@ 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;        
 
@@ -93,35 +102,39 @@ void RefractiveIndex::setup()
 
     //getting a warning from the OFlog that the pixels aren't allocated
     //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));
-    //_analysisVector.push_back(new ShadowScapesAnalysis(H));
-    //_analysisVector.push_back(new ShadowScapesAnalysis(D));
+    _analysisVector.push_back(new ShadowScapesAnalysis(V)); 
+    _analysisVector.push_back(new ShadowScapesAnalysis(H));
+    _analysisVector.push_back(new ShadowScapesAnalysis(D));
 	    
     _analysisVector.push_back(new RelaxRateAnalysis());
 	
-    //_analysisVector.push_back(new IResponseAnalysis());
+    _analysisVector.push_back(new IResponseAnalysis());
     
-    //_analysisVector.push_back(new ShapeFromShadingAnalysis());
+    _analysisVector.push_back(new ShapeFromShadingAnalysis());
     
-    //_analysisVector.push_back(new StrobeAnalysis());
+    _analysisVector.push_back(new StrobeAnalysis());
     
-    //_analysisVector.push_back(new CamNoiseAnalysis());
+    _analysisVector.push_back(new CamNoiseAnalysis());
     
-    //_analysisVector.push_back(new ColorSingleAnalysis());
+    _analysisVector.push_back(new ColorSingleAnalysis());
     
-    //_analysisVector.push_back(new ColorMultiAnalysis());
+    _analysisVector.push_back(new ColorMultiAnalysis());
     
-    //_analysisVector.push_back(new DiffNoiseAnalysis());
+    _analysisVector.push_back(new DiffNoiseAnalysis());	
     
 
-    _currentAnalysisIndx = 0;
-    _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
+    //_currentAnalysisIndx = 0;
+    //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
+    //_state = ISTATE_START;
+    
+    _currentAnalysis = NULL;
+    _state = ISTATE_UNDEF;
   
-    _state = ISTATE_START;
     
 }
 
@@ -138,6 +151,16 @@ void RefractiveIndex::start_analysis()
     _analysisAdapator = new AnalysisAdaptor(_currentAnalysis);
     _currentAnalysis->setup(_vid_w, _vid_h);
     _analysisAdapator->start();    
+    
+    
+    //allocate fbo for HD
+    fbo.allocate(1920,1080);
+
+//    fbo.allocate( _currentAnalysis->_mesh_size_multiplier *_vid_w,_currentAnalysis->_mesh_size_multiplier * _vid_h);
+    camera.setPosition(fbo.getWidth()/2, fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
+    _meshRotation=0;
+    
+    
 }
 
 void RefractiveIndex::stop_analysis()
@@ -161,7 +184,9 @@ void RefractiveIndex::state_analysis()
         case ISTATE_TRANSITION:            
             if(_currentAnalysisIndx >= _analysisVector.size()) {
                 _currentAnalysisIndx = 0;
-                _state = ISTATE_END;
+                _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
+                _state = ISTATE_START;                
+                //_state = ISTATE_END;
             } else {
                 _currentAnalysis = _analysisVector.at(_currentAnalysisIndx++);
                 _state = ISTATE_START;
@@ -169,9 +194,13 @@ 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;
@@ -185,35 +214,76 @@ void RefractiveIndex::state_analysis()
 void RefractiveIndex::update()
 {    
     state_analysis();
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-
-    if (_vidGrabber.isFrameNew())
-    {
-        _pixels = _vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    }
 }
 
 void RefractiveIndex::draw()
 {
+    // refractive mauve - this doesn't work... looks weird in various places.
+    //ofBackground(113, 110, 136);
+    
+    // black
     ofBackground(0, 0, 0);
-    if(_currentAnalysis)
+   
+    if(_currentAnalysis){
         _currentAnalysis->draw();
+       
+    
+        if(_currentAnalysis->meshIsComplete){
+            
+            fbo.begin();
+            glShadeModel(GL_SMOOTH);  
+            ofClear(0,0,0);
+            
+            camera.begin();
+            ofSetColor(0, 0, 0);
+            //this is a hack, I don't know how to colour the fbo with black pixels so I'm drawing a massive black rectangle in the  background
+            ofPushMatrix();
+            ofTranslate(0, 0,-500);
+            ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);
+            
+            
+            ofPopMatrix();
+            ofSetColor(255);
+            
+            float xDiff= (fbo.getWidth()- (_currentAnalysis->_mesh_size_multiplier *_vid_w))/2;
+            float yDiff= (fbo.getHeight()- (_currentAnalysis->_mesh_size_multiplier *_vid_h))/2;
+
+            
+            ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
+            _currentAnalysis->aMesh.draw();
+            
+            camera.end();
+            fbo.end();
+            
+            ofPixels pixels;
+            fbo.readToPixels(pixels);
+          
+            ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
+            //saving jpgs doesn't work - pngs only!
+
+        }
+       
+    }
 }
 
 void RefractiveIndex::setup_camera()
 {
     stop_camera();
     
+    // THIS IS LOADED IN FROM THE XML FILE SETTINGS 
+    _vidGrabber.setDeviceID(_vid_id);
+    _vidGrabber.listDevices();
+    
     if(!_vidGrabber.initGrabber(_vid_w, _vid_h)) {
         ofLog(OF_LOG_ERROR) << "RefractiveIndex::setup_camera - could not initialise grabber";
         return;
     }
-    _vidGrabber.setUseTexture(false);
-    _vidGrabber.listDevices();
+    
     _vidGrabber.setVerbose(true);
+    _vidGrabber.setUseTexture(false);
     _vid_stream_open = true;
-    _vidGrabber.setDeviceID(_vid_id);
+    cout << "CAMERA SETUP " << endl;
+    return;
 	
 }
 
@@ -229,9 +299,167 @@ void RefractiveIndex::keyPressed  (int key)
 {
     if( key =='f')
         ofToggleFullscreen();
+    
+    /*  TODO:  complete the below... would be good to trigger the Analysis from keypresses if needed... */
+    // currently this doesn't work... the save_cb's in the individual 
+    // tried to add a  stop_analysis(); call but it blocks the whole programme
+    
+    // i.e.: ask david how to shut off the prior Analysis if it's not finished running from here? 
+    
+    if(key == 'x')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysis = NULL;
+        _state = ISTATE_UNDEF;
+    }    
+    
+    else if(key == '1')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 0;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == '2')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 1;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == '3')
+    {        
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 2;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '4')
+    {     
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 3;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '5')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 4;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '6')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 5;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '7')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 6;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '8')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 7;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '9')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 8;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    else if(key == '0')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 9;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+
+    else if(key == 'q')
+    {
+        if(_currentAnalysis)
+            _analysisAdapator->stop();
+        _currentAnalysisIndx = 10;
+        if(!_currentAnalysis)
+            _state = ISTATE_TRANSITION;            
+    }
+    
+    /*
+     TO DO:  add a file dialog so we can save images to another hard drive...
+     e.g.: http://dev.openframeworks.cc/pipermail/of-dev-openframeworks.cc/2011-April/003125.html
+     
+>> 		case 's':
+>> 			doSave ^= true;
+>> 			doLoad = false;
+>> 			if(doSave) {
+>> 				ofFileDialogResult r = ofSystemLoadDialog("Select path to save to", true);
+>> 				if(r.bSuccess) {
+>> 					saveCounter = 0;
+>> 					savePath = r.getPath();
+>> 					ofDirectory::createDirectory(savePath + "/color/");
+>> 					ofDirectory::createDirectory(savePath + "/depth/");
+>> 					printf("SAVE %s %s\n", r.getPath().c_str(), r.getName().c_str());
+>> 				} else {
+>> 					doSave = false;
+>> 				}
+>> 				
+>> 			}
+>> 			break;
+>> 			
+>> 		case 'l':
+>> 			doLoad ^= true;
+>> 			doSave = false;
+>> 			if(doLoad) {
+>> 				ofFileDialogResult r = ofSystemLoadDialog("Select path to load from", true);
+>> 				if(r.bSuccess) {
+>> 					loadCounter = 0;
+>> 					loadPath = r.getPath();
+>> 					ofDirectory dir;
+>> 					loadMaxFiles = MAX(dir.listDir(loadPath + "/color"), dir.listDir(loadPath + "/depth"));
+>> 					printf("LOAD %i %s %s\n", loadMaxFiles, r.getPath().c_str(), r.getName().c_str());
+>> 				} else {
+>> 					doLoad = false;
+>> 				}
+>> 				
+>> 			}
+>> 			break;
+    */
+    
+    
 }
 
 void RefractiveIndex::exit()
 {
+    if(_currentAnalysis)
+        _analysisAdapator->stop();    
     stop_camera();
 }

example/RefractiveIndex.h

@@ -1,8 +1,3 @@
-/*
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #pragma once
 
@@ -13,6 +8,13 @@
 #include "AbstractAnalysis.h"
 #include "AnalysisAdaptor.h"
 
+#include "ofxOpenCv.h"
+#include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
+
+#define MODE_DRAWING        0xEEFF
+#define MODE_ANALYSING      0xFFEE
 
 class RefractiveIndex : public ofBaseApp
 {
@@ -54,10 +56,15 @@ 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;
@@ -65,6 +72,9 @@ public:
     
     // this should be in xml
     static string           _location;
-    
-    
+    static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
+    ofCamera    camera;
+    ofPixels    keepOnScreen;
+    ofFbo fbo;
+    ofLight light;
 };

example/main.cpp

@@ -1,35 +1,27 @@
 #include "ofAppGlutWindow.h"
 #include "RefractiveIndex.h"
-#include "ofxXmlSettings.h"
 
 #define SCREEN_WIDTH        800
 #define SCREEN_HEIGHT       600
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
-
-/////////////////////////dis is the new shit///////////
-
 
 int main() {
+    
 	ofAppGlutWindow window;
    
-    ofxXmlSettings   XML;
-    XML.loadFile("../data/config.refindx");
-    bool fullscreen = (XML.getValue("config:display:fullscreen", "false") == "true" ? true : false);
-    int screen_w = XML.getValue("config:display:width", SCREEN_WIDTH);
-    int screen_h = XML.getValue("config:display:height", SCREEN_HEIGHT);     
+    bool fullscreen;
+    
+    //fullscreen = true; 
+    fullscreen = false;
     
     cout << "> display configuration" << endl;
     cout << "* fullscreen: " << (fullscreen ? "yes" : "no") << endl;
+ 
     if(!fullscreen) {
-        cout << "* screen width: " << screen_w << endl;
-        cout << "* screen height: " << screen_h << endl;
+        cout << "* screen width: " << SCREEN_WIDTH << endl;
+        cout << "* screen height: " << SCREEN_HEIGHT << endl;
     }
     
-	ofSetupOpenGL(&window, screen_w, screen_h, (fullscreen ? OF_FULLSCREEN : OF_WINDOW));
+	ofSetupOpenGL(&window, SCREEN_WIDTH, SCREEN_HEIGHT, (fullscreen ? OF_FULLSCREEN : OF_WINDOW));
 	ofRunApp(new RefractiveIndex());
 
 }

src/AbstractAnalysis.cpp

@@ -1,54 +1,81 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
- 
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
- 
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
+/* */
 
 #include "AbstractAnalysis.h"
 #include "RefractiveIndex.h"
 #include "ofxFileHelper.h"
+#include "ofSystemUtils.h"
 
+void AbstractAnalysis::setup(int camWidth, int camHeight) {
     
-vector<ofMesh>  AbstractAnalysis::meshes;
+    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;
+                
+                _saved_filenames_analysis.clear();  
+                _saved_filenames_synthesis.clear(); 
+                
                 _state = STATE_ACQUIRING;
                 acquire();
+                if(_state == STATE_STOP) goto exit;
                 _state = STATE_SYNTHESISING;
                 synthesise();
+                if(_state == STATE_STOP) goto exit;
                 _state = STATE_DISPLAY_RESULTS;
-    display_results();
+                displayresults();
+                cleanup();
+            }                    
+        }
+            
+        case MODE_DRAWING:
+        {            
+
+
+            ofxFileHelper fileHelperDrawing;
+            if(!fileHelperDrawing.doesDirectoryExist(_whole_file_path_synthesis)){
+                fileHelperDrawing.makeDirectory(_whole_file_path_synthesis);
+            }            
+            
+            read_dir_create_list(_whole_file_path_analysis);
+            _state = STATE_SYNTHESISING;
+            synthesise();
+            if(_state == STATE_STOP) goto exit;
+            _state = STATE_DISPLAY_RESULTS;
+            displayresults();
+            cleanup();            
+        }
+    }
+    
+exit:    
+    cleanup();
     ofNotifyEvent(_synthesize_cb, _name);    
+    
 }
 
-void AbstractAnalysis::create_dir()
+void AbstractAnalysis::create_dir_allocate_images()
 {
     // HERE IS WHERE WE SETUP THE DIRECTORY FOR ALL THE SAVED IMAGES
     
@@ -71,266 +98,162 @@ void AbstractAnalysis::create_dir()
         }
     }
 
-    ofxFileHelper fileHelper;
-    _whole_file_path = ofToDataPath("") + ANALYSIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime ;
-    cout << "_whole_file_path = " << _whole_file_path << endl;
+    ofxFileHelper fileHelperAnalysis;
+    ofxFileHelper fileHelperSynthesis;
+    
+    _whole_file_path_analysis = ANALYSIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime ;
+  
+    //cout << "_whole_file_path_analysis = " << _whole_file_path_analysis << endl;
+    
+    if(!fileHelperAnalysis.doesDirectoryExist(_whole_file_path_analysis)){
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location);
+
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime))
+        fileHelperAnalysis.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
+        
         
-    if(!fileHelper.doesDirectoryExist(_whole_file_path)){
-        fileHelper.makeDirectory(ANALYSIS_PATH);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name);
-        fileHelper.makeDirectory(ANALYSIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
     }
     
+    _whole_file_path_synthesis = SYNTHESIS_PATH + RefractiveIndex::_location + "/" + _name + "/"+replaceTime;
+    
+    if(!fileHelperSynthesis.doesDirectoryExist(_whole_file_path_synthesis)){
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location);
+
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name);
+        
+        if(!fileHelperAnalysis.doesDirectoryExist(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime))
+        fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
+        
+    }
     //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////  
-}
-ofPixels AbstractAnalysis::calculateListOfZValues(ofImage image1, ofImage image2, int whichComparison){
-    //zScale is the mapping factor from pixel difference to shift on the zPlane
-    int zScale=200;
     
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    ofPixels imagePixels2 = image2.getPixelsRef();
     
-    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];
+    //////////////////////////////ALLOCATE IMAGES //////////////////////////////////////////////////  
     
-    //where are we in the image pixel array
-    int x=0;
-    int y=0;
+    myColorImage1.clear();
+    myColorImage1.setUseTexture(false);
+    myColorImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
 
-    //for each pixel...
-    for(int i=0;i<imagePixels1.size();i+=3){
+    myColorImage2.clear();
+    myColorImage2.setUseTexture(false);
+    myColorImage2.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
     
-        //get the colour of each image at this x y location - we will use these colours for comparison according to the below criteria
-        ofColor colourImage1 = imagePixels1.getColor(x, y);
-        ofColor colourImage2 = imagePixels2.getColor(x, y);
     
-        //COMPARE THIS PIXEL'S VALUES with the first image in the sequence
-        int thisDiff;
-        //compare Red
-        if (whichComparison==1) {
-            thisDiff=ofMap((colourImage1.r-colourImage2.r),-255,255,0,zScale);
-        }
-        //compare blue
-        if (whichComparison==2) {
-            thisDiff=ofMap((colourImage1.g-colourImage2.g),-255,255,0,zScale);
-        }
-        //compare green
-        if (whichComparison==3) {
-            thisDiff=ofMap((colourImage1.b-colourImage2.b),-255,255,0,zScale);
-        }
-        //compare hue
-        if (whichComparison==4) {
-            thisDiff=ofMap((colourImage1.getHue()-colourImage2.getHue()),-255,255,0,zScale);
-        }
-        //compare brightness
-        if (whichComparison==5) {
-            thisDiff=ofMap((colourImage1.getBrightness()-colourImage2.getBrightness()),-255,255,0,zScale);
-        }
-        thesePixels[i]=thisDiff;
-        thesePixels[i+1]=thisDiff;
-        thesePixels[i+2]=thisDiff;
+    myGrayImage1.clear();
+    myGrayImage1.setUseTexture(false);
+    myGrayImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_GRAYSCALE);
     
-        x++;
-        //new line
-        if(x>imagePixels1.getWidth()){
-            x=0;
-            y++;
 
-        }
-    }
-    
-    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    
-    return difference;
+    //////////////////////////////END ALLOCATE IMAGES //////////////////////////////////////////////////  
 
 }
 
-ofPixels AbstractAnalysis::calculateListOfZValues(ofImage image1, ofImage image2, int whichComparison, int colourValue){
-    //zScale is the mapping factor from pixel difference to shift on the zPlane
-    int zScale=200;
-    
-    ofPixels imagePixels1 = image1.getPixelsRef();
-    ofPixels imagePixels2 = image2.getPixelsRef();
-    
-    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];
-    
-    //where are we in the image pixel array
-    int x=0;
-    int y=0;
-    
-    //for each pixel...
-    //for(int i=0;i<imagePixels1.size();i+=3){
-    for(int i=0;i<20;i+=3){
-        
-        //get the colour of each image at this x y location - we will use these colours for comparison according to the below criteria
-        ofColor colourImage1 = imagePixels1.getColor(x, y);
-        ofColor colourImage2 = imagePixels2.getColor(x, y);
-        
-        //COMPARE THIS PIXEL'S VALUES with the first image in the sequence
-        int thisDiff;
-        //compare Red
-        if (whichComparison==1) {
-            thisDiff=ofMap((colourImage1.r-colourImage2.r),-255,255,0,zScale);
-        }
-        //compare blue
-        if (whichComparison==2) {
-            thisDiff=ofMap((colourImage1.g-colourImage2.g),-255,255,0,zScale);
-        }
-        //compare green
-        if (whichComparison==3) {
-            thisDiff=ofMap((colourImage1.b-colourImage2.b),-255,255,0,zScale);
-        }
-        //compare hue
-        if (whichComparison==4) {
-            thisDiff=ofMap((colourImage1.getHue()-colourImage2.getHue()),-255,255,0,zScale);
-        }
-        //compare brightness
-        if (whichComparison==5) {
-            thisDiff=ofMap((colourImage1.getBrightness()-colourImage2.getBrightness()),-255,255,0,zScale);
-        }
-        thesePixels[i]=thisDiff;
-        thesePixels[i+1]=thisDiff;
-        thesePixels[i+2]=thisDiff;
-        
-        x++;
-        //new line
-        if(x>imagePixels1.getWidth()){
-            x=0;
-            y++;
-            
-        }
-    }
-    
-    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    
-    return difference;
-    
-}
-
-void AbstractAnalysis::setMeshFromPixels(ofPixels somePixels, ofImage currentSecondImage, ofMesh * someMesh){
-    int x=0;
-    int y=0;
-    
-    //get rid of all previous vectors and colours - uncomment if re-setting the mesh on the fly - ie live rather than saving it first
-    //someMesh->clear();
-    
-    unsigned char * thesePixels =currentSecondImage.getPixels();
-    
-    for(int i=0;i<somePixels.size();i+=3){
-        someMesh->addVertex(ofVec3f(x,y,- somePixels.getColor(x, y).getBrightness()   ));
-        // add colour from current second image of two 
-        someMesh->addColor(  currentSecondImage.getColor(x, y)   );
-        x++;
-        if(x>somePixels.getWidth()){
-            x=0;
-            y++;
-        }
-        
-    }
-    
-}
-
-vector<string>AbstractAnalysis:: getListOfImageFilePaths(string location, string whichAnalysis){
-    
-    string path = ofToDataPath("")+"debug_analysis/"+location+"/"+whichAnalysis;
-    //ofxDirList dirList;
-    ofDirectory dirList;
-    int numDirs = dirList.listDir(path);
-    
-    vector<string>directoryNames;
-    
-    //get the last folder alphabetically - this should probably change to do something fancy with date to find most recent but don't want to code that until we are sure
-    string dirName=dirList.getName(numDirs-1);
-    
-    
-    const char *results=dirName.c_str();
-    
-    ofFile file=ofFile(path+"/"+dirName);
-    vector<string>fileNamesToReturn;
-    
-    
-    // get 
-    if(file.isDirectory()){
-        dirList.listDir(path+"/"+dirName);
-        //if there are no files, exit here
-        if(dirList.size()==0){
-            //if it's empty return an error warning
-            fileNamesToReturn.push_back("NO FILE HERE!");
-            cout<<"NO FILE HERE!";
-            return fileNamesToReturn;
-        }
-        for (int i=0; i<dirList.size(); i++) {
-            
-            string fname=dirList.getName(i);
-            const char *results=fname.c_str();
-            
-            //full path is what actually gets written into the vector
-            string fullPath=path+"/"+dirName+"/"+fname;
-            
-            
-            fileNamesToReturn.push_back(fullPath);
-        }
-    }
-    else{
-        cout<<"WARNING, DIRECTORY NOT FOUND";
-        fileNamesToReturn.push_back("NO FILE HERE!");
-    }
-    
-    
-    
-    
-    return fileNamesToReturn;
-}
-int AbstractAnalysis::getRecordedValueFromFileName(string str){
-    //split filename by underscore - there HAS to be a quicker way of doing things - its ONE LINE in java :(
-    char * cstr, *p;
-    vector<char *>tokens;
-    //string str ("Please split this phrase into tokens");
-    
-    //make char pointer array
-    cstr = new char [str.size()+1];
-    //copy string to char pointer array
-    strcpy (cstr, str.c_str());
-    
-    //tokenise char p array and put first results into pointer?
-    p=strtok (cstr,"_");
-    
-    while (p!=NULL)
-    {
-        p=strtok(NULL,"_");
-        //push tokenised char into vector
-        tokens.push_back(p);
-        
-    }
-    delete[] cstr; 
-    char *p1;
-    //cstr = new char [str.size()+1];
-    //strcpy (cstr, str.c_str());
-    
-    p1=strtok (tokens[tokens.size()-2],".");
-    
-    return ofToInt(p1);
-}
-
-
-void AbstractAnalysis::saveimage(string filename) 
+bool cmp_file(string f0, string f1)
 {
-    if(RefractiveIndex::_pixels.isAllocated()) {
+    int v0 = atoi(f0.substr(0, f0.find("_")).c_str());
+    int v1 = atoi(f1.substr(0, f1.find("_")).c_str());    
+    return v0 < v1;
+}
 
-        string fname = _whole_file_path + "/" + filename;
+void AbstractAnalysis::read_dir_create_list(string folder_path)
+{
+    File dir(folder_path);
     
-        cout << "saving - " << fname << endl;
+    if(dir.exists() && dir.isDirectory()) {
+        vector<string> list;
+        dir.list(list);   
         
-        ofSaveImage(RefractiveIndex::_pixels, fname, OF_IMAGE_QUALITY_BEST);
+        std::sort(list.begin(), list.end(), cmp_file);
         
-        _saved_filenames.push_back(fname);
+        for(int i = 0; i < list.size(); i++) {
+            string filepath = folder_path + "/" + list[i]; 
+            _saved_filenames_analysis.push_back(filepath);
                         
-    } else {
-        ofLog(OF_LOG_ERROR) << "RefractiveIndex::_pixels NOT allocated...";
+            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

@@ -7,21 +7,17 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
+#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
+#define SYNTHESIS_PATH "synthesis/"
 
 #define STATE_ACQUIRING         0x1111
 #define STATE_SYNTHESISING      0x2222
 #define STATE_DISPLAY_RESULTS   0x3333
 #define STATE_STOP              0xDEADBEEF
 
-#define COMPARE_RED 1
-#define COMPARE_BLUE 2
-#define COMPARE_GREEN 3
-#define  COMPARE_HUE 4
-#define COMPARE_BRIGHTNESS 5
-
 class AbstractAnalysis {
     
 public:
@@ -29,17 +25,22 @@ public:
     virtual ~AbstractAnalysis(){;}
     
     // generic function to set up the camera
-    virtual void setup(int camWidth, int camHeight){_cam_w = camWidth; _cam_h = camHeight;}  
+    virtual void setup(int camWidth, int camHeight);  
+
     // this is the main threaded loop for a given analysis
     void do_synthesize();
                         
-    // ofx
+    // show the results to the screen
     virtual void draw() = 0;    
         
 protected:
     
-    virtual void create_dir();
-    virtual void saveimage(string filename);
+    virtual void create_dir_allocate_images();
+    
+    virtual void read_dir_create_list(string folder_path);
+    
+    virtual void saveImageAnalysis(string filename);
+    virtual void saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType);
     
     // acquire images - all the children (see - do_synthesize)
     virtual void acquire() = 0;   
@@ -47,51 +48,52 @@ protected:
     // analysis + synthesize images - all the children (see - do_synthesize)
     virtual void synthesise() = 0;   
     
-    //added tom s 19/2 function runs a call back exactly like acquire.
-    virtual void display_results() = 0;   
+    // display the results from disk
+    virtual void displayresults() = 0;   
     
-    //returns ofPixels which contain the color differences between the two images. Is overloaded to include comparison with values written in to file names for some analyses
-    virtual ofPixels calculateListOfZValues(ofImage image1, ofImage image2, int whichComparison);
-    virtual ofPixels calculateListOfZValues(ofImage image1, ofImage image2, int whichComparison, int colourValue);
-    
-    //uses the returned pixels from make3DZmap to make a mesh of points whose Z positions are set by the brightness values in ofPixels - ofPixels is being used as a convenient container for a bunch of z coordinates
-    virtual void setMeshFromPixels(ofPixels somePixels, ofImage currentSecondImage, ofMesh * someMesh);
-    //HELPER FUNCTIONS
-    
-    //this is purely for debug/viewing purposes and loads old images from middlesborough test
-    virtual vector<string> getListOfImageFilePaths(string location, string whichAnalysis);
-    
-    //splits up the filename and returns the recorded value eg brightness
-    //EG FILENAME : DIFF_NOISE_7_85.7322.jpg RETURNS : 85.7322
-    virtual int getRecordedValueFromFileName(string str);
-    
-    static vector<ofMesh>meshes;
+    // 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;
+    string  meshFileName;
+    //difference between our image size and the size of the fbo
+    float   widthScaleFactor;
+    float   heightScaleFactor;
+    ofImage  contourImage;
+    ofPixels meshPix;
+    ofPixels publicColorImage;
+    float    zPlaneAverage;
+    
+    //added Tom 1/5/12 defines the stretch we make to the mesh to make it fit HD proportions
+    float           _mesh_size_multiplier;
     
 protected:    
     int             _cam_w, _cam_h;          
-    string          _whole_file_path;
-    vector<string>  _saved_filenames;
+    string          _whole_file_path_analysis, _whole_file_path_synthesis;
+    vector<string>  _saved_filenames_analysis;
+    vector<string>  _saved_filenames_synthesis;
     
     int             _state;
     
+    ofImage         myColorImage1;
+    ofImage         myColorImage2;
+    ofImage         myGrayImage1;
+    
+    //int             _run_cnt;
+    
     float           DELTA_T_SAVE;
     int             NUM_PHASE;
     int             NUM_RUN;
     int             NUM_SAVE_PER_RUN;    
     
-    //added Tom S 19/2/12
-    //each mesh in the vector is a seperate 3D point cloud which is coloured with pixel data and shifted in the z plane according to the specified type of colour difference eg red value or hue
-    //make this vector were static
-    //how fast to move from one mesh to the next
-    float speed;
-    //the index (inside the vector of meshes) of the current mesh being displayed
-    float whichMesh;
     friend class AnalysisAdaptor;
 };

src/AnalysisAdaptor.h

@@ -21,12 +21,15 @@ public:
     
     void start()
     {
+        _stopping = false;
         _runnable = new RunnableAdapter<AbstractAnalysis>(*_analysis, &AbstractAnalysis::do_synthesize);
         _worker.start(*_runnable);
     }
     
     void stop() 
     {
+        if(_stopping) return;
+        _stopping = true;
         _analysis->_state = STATE_STOP;
         _worker.join();        
     }
@@ -35,5 +38,6 @@ protected:
     AbstractAnalysis*                   _analysis;
     Thread                              _worker;    //   
     RunnableAdapter<AbstractAnalysis>*  _runnable;  
+    bool                                _stopping;
 };
 

src/CamNoiseAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "CamNoiseAnalysis.h"
 #include "ofMain.h"
 
@@ -15,19 +10,90 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 200;
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
+    cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_camnoise", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;
+
+
+    //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
+                                                // or 5 times per second = every 200 ms
+
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
 
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _run_cnt = 0;
+    _synth_save_cnt = 0;
+
     c = 0;
+
+    int anim_time = 10;   // 10 seconds
+    _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
+
+    //create_dir_allocate_images();
+
+    _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
+
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);
+    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);
+
+    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);
+
 }
 
 
@@ -35,91 +101,138 @@ void CamNoiseAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<CamNoiseAnalysis> save_callback(*this, &CamNoiseAnalysis::save_cb);
 
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _run_cnt++;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
-
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
+    // for(int i = 0; i < NUM_RUN; i++) {
+    // _run_cnt = i;
+    //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
 
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+
+
+   // }
 }
 
 void CamNoiseAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+    //cout << "CamNoiseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
 
-    int index=0;
-    float iterator=1;
-    //if you want to see what this looks like with real data ignore the new filenames and load teh old ones.
-    bool debug=true;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
 
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+        //cout << "CamNoiseAnalysis::synthesis FOR LOOP...\n";
+
+        //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;
         }
 
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
 
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+            ///////////////////////// 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);
+            // cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+            //added by tom we weren't actually setting cvgrayimage1 anywhere
+           // cvGrayImage1.setFromPixels(cvColorImage1.getPixels(),cvColorImage1.width,cvColorImage1.height);
+            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+//cvGrayImage1=cvColorImage1;
+
+            cvGrayImage1.erode();
+            cvGrayImage1.erode();
+            cvGrayImage1.erode();
+            cvGrayImage1.blur();
+            cvGrayImage1.contrastStretch();
+           /* cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.blur();
+            cvColorImage1.contrastStretch();*/
+
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
+
+            file_name = ofToString(_synth_save_cnt, 2)+"_CamNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
 
 
-        ofImage image1;
-        ofImage image2;
+            //<---- 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);
 
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_hue_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_HUE,_recorded_hue_value), image2, &meshes[index]);            
-            index++;
+
+            //<---- 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(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            cvConvertorImage.setFromGrayscalePlanarImages(cvGrayImage1,cvGrayImage1,cvGrayImage1);
+            //cvConvertorImage.setFromGrayscalePlanarImages(cvColorImage1,cvColorImage1,cvColorImage1);
+            saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+            _synth_save_cnt++;
+
+
+            //}
         }
     }
 
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
 }
 
-void CamNoiseAnalysis::display_results(){
+void CamNoiseAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
 
-    Timer* display_results_timer;
+        if(_state == STATE_STOP) return;
 
-    TimerCallback<CamNoiseAnalysis> display_results_callback(*this, &CamNoiseAnalysis::display_results_cb);
-    // display results of the synthesis
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
 
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
 
-    while(!_RUN_DONE)
-        Thread::sleep(3);
-    
-    display_results_timer->stop();
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        }
 
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
 }
 
 
@@ -140,44 +253,48 @@ void CamNoiseAnalysis::draw()
                 ofColor aColour;
 
                 int _fade_in_frames = _frame_cnt_max/10;
-                float _number_of_grey_levels=10;
+                float _number_of_grey_levels=5;
 
                 float _frames_per_level = _frame_cnt_max / _number_of_grey_levels;
                 ofColor someColor;
 
+                 /*
                 if (_frame_cnt < _fade_in_frames) {
                     aColour.set(255, 255, 255, ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
                     ofSetColor(aColour);
                     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)){
+                */
+                //if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max)){
 
 
-                    for(int i=0;i<_number_of_grey_levels;i++){
-                        if (_frame_cnt>= _frames_per_level *( i-1) && +_frame_cnt < _frames_per_level * (i) ) {
+                    for(int i=1;i<_number_of_grey_levels;i++){
+                        if ( _frame_cnt >= _frames_per_level*(i-1) && +_frame_cnt < _frames_per_level * (i+1) ) {
                             //set colour to current grey level
                             c=255-( 255.0 * ( i /_number_of_grey_levels));
+                            //cout << "c: " << c << endl;
                             someColor.set(c);
                         }
+
                         ofSetColor(someColor);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     }
 
-                }
-                
+                //}
+                /*
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
-                        aColour.set(0, 0, 0, 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                        aColour.set(0, 0, 0, ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
                         ofSetColor(aColour);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                         // cout <<  "FADE OUT STROBE TIME " << endl;
                 }
-                
+                */
                 ofDisableAlphaBlending();
 
 
             } else {
+               // _state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
 
@@ -189,36 +306,117 @@ void CamNoiseAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+
+            //cout << "CamNoiseAnalysis = STATE_SYNTHESISING...\n";
+
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+
+            if(_anim_cnt < _anim_cnt_max){
+
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+
+                int c_anim = 10;
+                int fade;
+
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "CamNoiseAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+
+                    for (int i=0; i <= 15; i++){
+
+                        c_anim = (17*i);
+
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+
+                }
+                _anim_cnt++;
+
+            } else {
+                _RUN_DONE = true;
+                //_state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+
             break;
         }
 
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
 
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
 
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
 
+            _frame_cnt++;
+
+            if (_show_image)
+            {
+                //cout << "_show_image...\n" << endl;
+
+                ofEnableAlphaBlending();
+
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+
+                ofDisableAlphaBlending();
+            }
+
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
-        }
 
+        }
 
         default:
             break;
@@ -233,15 +431,6 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
     _save_cnt++;
 
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    saveimage(file_name);
-    
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
 
-}
-void CamNoiseAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
+    saveImageAnalysis(file_name);
 }

src/CamNoiseAnalysis.h

@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class CamNoiseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,17 +23,45 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();    
-    void display_results();
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
   
+    int     _run_cnt, _save_cnt, _synth_save_cnt,_anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
     
 };

src/ColorMultiAnalysis.cpp

@@ -1,35 +1,3 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
-
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
-
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
-
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ColorMultiAnalysis.h"
 #include "ofMain.h"
 
@@ -41,136 +9,249 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
-
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;//150; // the right number is about 300
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;//;    
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
+    cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
+
+    //int acq_run_time = 35;  
+    
+    DELTA_T_SAVE = 1*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 200 files
+                                            // or 10 times per second = every 100 ms
+    
+    _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;
-    _fade_cnt=0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _run_cnt = 0;
+    _synth_save_cnt = 0;
     c = 0;
+    
+    int anim_time = 10;   // 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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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 ColorMultiAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<ColorMultiAnalysis> save_callback(*this, &ColorMultiAnalysis::save_cb);
 
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
+      //  _run_cnt = i;
 
-        cout << "RUN NUM = " << i;
+        //cout << "RUN NUM = " << i;
     
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
 
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
    
+    //}
 }
 
 void ColorMultiAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    //cout << "ColorMultiAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorMultiAnalysis::synthesis FOR LOOP...\n";
+        
+        //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;
         } 
         
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
             
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
             
-        ofImage image1;
-        ofImage image2;
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+            //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[0]) && image2.loadImage(_saved_filenames[i+1])){
-            cout<<"setting mesh"<<endl;
-            meshes.push_back(ofMesh());
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_HUE), image2, &meshes[index]);            
-            index++;
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.dilate();
+            cvColorImage1.blur(5);
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
+            cvColorImage1.dilate();
+            
+            /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
+            
+            file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+            
+            
+            //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+            // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            
+            
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);  
+           
+            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+            
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
+            _synth_save_cnt++;
+            
+            // }
         }
     }
-}
     
-void ColorMultiAnalysis::display_results(){
-   
-    Timer* display_results_timer;
-    
-    TimerCallback<ColorMultiAnalysis> display_results_callback(*this, &ColorMultiAnalysis::display_results_cb);
-    // display results of the synthesis
-    
-    display_results_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=500;
-    
-    while(!_RUN_DONE)
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
-    
-    display_results_timer->stop();
-    
 }
+
+void ColorMultiAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }    
+}
+
+
 void ColorMultiAnalysis::draw()
 {
     
     switch (_state) {
         case STATE_ACQUIRING:
         {
+            ofEnableAlphaBlending();
             
             if (_frame_cnt < _frame_cnt_max)
             {
 
-                
                 int _fade_in_frames = _frame_cnt_max/50;
+                ofColor aColor;
                 
                 if (_frame_cnt < _fade_in_frames) {
-                    ofColor aColor;
+                   
                     
                     aColor.setHsb(c, ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255), ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
                     
                     ofSetColor(aColor);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     
-                    cout << "FADING IN..." << endl;
+                    //cout << "FADING IN..." << endl;
                 }
                 
+                
+                
                 if (_frame_cnt >= _fade_in_frames && _frame_cnt < _frame_cnt_max-_fade_in_frames){
                     
-                    ofColor aColor;
                     aColor.setHsb(c, 255, 255);
                     ofSetColor(aColor);
                     
@@ -180,28 +261,26 @@ void ColorMultiAnalysis::draw()
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                 }
                 
-                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
+                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
-                    ofColor aColor;
+                    aColor.set(c, c, c, 255-int(ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255)));
                     
-                    aColor.setHsb(c, 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255), 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255));
+                    //aColor.setHsb(c, 255-ofMap(_fade_cnt- (_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255), 255-(ofMap(_fade_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255)));
                     
                     ofSetColor(aColor);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
-                    
-                    _fade_cnt++;
-                    cout << "FADING OUT..." << endl;
+                    //cout << "FADING OUT..." << endl;
                     
                 }
                 
+                
             } else {
-                 
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
-            
             }
             
             _frame_cnt++;            
-            
+            ofDisableAlphaBlending();
             break;
         }
             
@@ -209,31 +288,115 @@ void ColorMultiAnalysis::draw()
         {
             // display animation of something while the synthesis in on-going...
             
+            //cout << "ColorMultiAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "ColorMultiAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                _state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
             
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
+            
         }
             
             
@@ -247,20 +410,9 @@ void ColorMultiAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
-    
-    // cout << "COLORMULTIANALYSIS::saving...\n";
-    
-    string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    saveimage(file_name);
-    
     _save_cnt++;
             
-}
+    string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-void ColorMultiAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
+    saveImageAnalysis(file_name);    
 }
-

src/ColorMultiAnalysis.h

@@ -4,6 +4,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class ColorMultiAnalysis : public AbstractAnalysis
 {
 public:
@@ -15,15 +18,45 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
-    void display_results();
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt, _fade_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+    
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+
 };

src/ColorSingleAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ColorSingleAnalysis.h"
 #include "ofMain.h"
 
@@ -15,23 +10,94 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;//300;
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
+    cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
+
+    //int acq_run_time = 25;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 1*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
+                                            // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _synth_save_cnt = 0;
+    c = 0;
+    
+    int anim_time = 10;   // 10 seconds
+    _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
+    
     r = 0;
     g = 0;
     b = 0;
     
-    _fade_cnt=0;
     fileNameTag = "";
+
+    _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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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);
+    
 }
 
 
@@ -42,94 +108,132 @@ void ColorSingleAnalysis::acquire()
 
     TimerCallback<ColorSingleAnalysis> save_callback(*this, &ColorSingleAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
-
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
+    //for(int i = 0; i < NUM_RUN; i++) {
+      //  _run_cnt = i;
+        //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
         
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+
+  
+    // }
 }
 
 void ColorSingleAnalysis::synthesise()
 {
-    // _saved_filenames has all the file names of all the saved images
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    //cout << "ColorSingleAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "ColorSingleAnalysis::synthesis FOR LOOP...\n";
+        
+        //cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        if(!image1.loadImage(_saved_filenames_analysis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
         } 
         
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                 
-        ofImage image1;
-        ofImage image2;
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
+                cvColorImage1.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.dilate();
+                cvColorImage1.blur(5);
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.erode();
+                cvColorImage1.erode();
             
-            if(i<_saved_filenames.size()/3){
-                setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_RED), image2, &meshes[index]);
-            }
-            if(i>=_saved_filenames.size()/3 && i<2* _saved_filenames.size()/3){
-                setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_GREEN), image2, &meshes[index]);   
-            }
-            if(i>= 2* _saved_filenames.size()/3 && i<_saved_filenames.size()){
-                setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BLUE), image2, &meshes[index]);            
-            }
-            index++;
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+                
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+                
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+                
+                //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            
+                saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
+                _synth_save_cnt++;
+            
+           // }
         }
     }
-}
     
-void ColorSingleAnalysis::display_results(){
-    
-    Timer* display_results_timer;
-    
-    TimerCallback<ColorSingleAnalysis> display_results_callback(*this, &ColorSingleAnalysis::display_results_cb);
-    // display results of the synthesis
-    
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=500;
-    
-    while(!_RUN_DONE)
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
-    display_results_timer->stop();
+}
+
+void ColorSingleAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
     
 }
+
+
 void ColorSingleAnalysis::draw()
 {
     
@@ -179,8 +283,8 @@ void ColorSingleAnalysis::draw()
                 
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max){
                    
-                    ofSetColor(0, 0, 255-ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255));
-                    cout << "255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255)"<< 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255) << endl;
+                    int fade = ofMap(_fade_cnt, 0, _fade_in_frames, 0, 255);
+                    ofSetColor(0, 0, 255-fade);
         
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     _fade_cnt++;
@@ -188,6 +292,7 @@ void ColorSingleAnalysis::draw()
                 }
             
             } else {
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
             
@@ -199,32 +304,118 @@ void ColorSingleAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "ColorSingleAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                   // cout << "ColorSingleAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                _RUN_DONE = true;
+                //_state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
             
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
+
+
         }
             
         default:
@@ -236,22 +427,9 @@ void ColorSingleAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorSingleAnalysis::save_cb(Timer& timer)
 {
-        
-    //cout << "ColorSingleAnalysis::saving...\n";
-    
-    string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";    
-    saveimage(file_name);
-    
     _save_cnt++;
     
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
+    string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
+    saveImageAnalysis(file_name);
 }
-void ColorSingleAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
-}
-

src/ColorSingleAnalysis.h

@@ -1,4 +1,4 @@
-/*
+    /*
  ~ author: dviid
  ~ contact: dviid@labs.ciid.dk 
  */
@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class ColorSingleAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,16 +23,47 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
-    void display_results();
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
 
     bool    _RUN_DONE;
     string  fileNameTag;
-    int     _run_cnt, _save_cnt, _fade_cnt;
-    float   r,g,b, _frame_cnt, _frame_cnt_max , _results_cnt, _results_cnt_max;
+    float   r,g,b;
+    
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
+
 };

src/DiffNoiseAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "DiffNoiseAnalysis.h"
 #include "ofMain.h"
 
@@ -15,112 +10,223 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 600;  // right number is about 450
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 50;    
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    create_dir();
-    _fade_cnt=0;
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
+    cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
+    
+    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 1*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
+    // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
+    _synth_save_cnt = 0;
     c = 0;
+    
+    int anim_time = 10;   // 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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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 DiffNoiseAnalysis::acquire()
 {
-
     Timer* save_timer;
-
     TimerCallback<DiffNoiseAnalysis> save_callback(*this, &DiffNoiseAnalysis::save_cb);
 
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
+    //  _run_cnt = i;
+    //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
     
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+    
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+
+    //}
 }
 
 void DiffNoiseAnalysis::synthesise()
 {   
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    //cout << "DiffNoiseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "DiffNoiseAnalysis::synthesis FOR LOOP...\n";
+        
+        //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;
         } 
         
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            //cout << "LOADED image1!!!" << endl;
+            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
             
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+            ///////////////////////// 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.invert();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            cvColorImage1.blur(5);
+            cvColorImage1.erode();
+            cvColorImage1.erode();
+            
+            //////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+            string file_name;
+            
+            file_name = ofToString(_synth_save_cnt, 2)+"_DiffNoiseAnalysis_"+ofToString(_run_cnt,2)+".jpg";
             
             
-        ofImage image1;
-        ofImage image2;
+            //<---- 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);
             
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_brightness_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_HUE,_recorded_brightness_value), image2, &meshes[index]);            
-            index++;
+            
+            //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+            //ofImage image;
+            //image.allocate(cvColorImage1.width, cvGrayImage1.height, OF_IMAGE_COLOR);
+            
+            //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+            //image.setUseTexture(false);  
+            
+            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            
+            //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+            
+            // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+            saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
+            _synth_save_cnt++;
+            
+            // }
         }
     }
     
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
+    
 }
 
-void DiffNoiseAnalysis::display_results(){
+void DiffNoiseAnalysis::displayresults()
+{
     
-    Timer* display_results_timer;
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
-    TimerCallback<DiffNoiseAnalysis> display_results_callback(*this, &DiffNoiseAnalysis::display_results_cb);
-    // display results of the synthesis
+        if(_state == STATE_STOP) return;
         
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
-    while(!_RUN_DONE)
-        Thread::sleep(3);
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
         
-    display_results_timer->stop();
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
         
-}// this runs at frame rate = 33 ms for 30 FPS
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }    
     
+    
+}
+
+
+// this runs at frame rate = 33 ms for 30 FPS
 void DiffNoiseAnalysis::draw()
 {
     switch (_state) {
@@ -149,12 +255,12 @@ void DiffNoiseAnalysis::draw()
                         }
                     }        
                     
-                    cout << "FADING IN..." << endl;
+                    //cout << "FADING IN..." << endl;
                 }
                 
                 
                 
-                if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max-_fade_in_frames)){
+                if (_frame_cnt >= _fade_in_frames && _frame_cnt <= (_frame_cnt_max-_fade_in_frames)){
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
                     {
@@ -170,29 +276,27 @@ void DiffNoiseAnalysis::draw()
                 }
                 
                 
-                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
+                if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt <= _frame_cnt_max) {
                     
                     for (int i=1; i < ofGetHeight() ; i=i+rectSize)
                     {
                         for (int j=1; j < ofGetWidth(); j=j+rectSize)
                         {
                             c = ofRandom(0,255);
-                            aColour.set(c, c, c, 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                            aColour.set(c, c, c, 255-ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
                             ofSetColor(aColour);
                             ofRect(j, i, rectSize, rectSize);
                         } 
                     }
                     
-                    _fade_cnt++;
-                    cout << "FADING OUT..." << endl;
-                    
+                    //_fade_cnt++;
+                    //cout << "FADING OUT..." << endl;
                 }
             
-                
                 ofDisableAlphaBlending();
            
             } else {
-            
+               // _state  = STATE_SYNTHESISING;
                _RUN_DONE = true;
             
             }
@@ -205,73 +309,130 @@ void DiffNoiseAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "DiffNoiseAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "DiffNoiseAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                
+                _RUN_DONE = true;
+                //_state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
             
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
             
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                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();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
+            
         }
-            
-            
         default:
             break;
     }
-
 }
 
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
-
-
-    float rand10 = ofRandom(0,10);
-
-    if (rand10 > 5.0) {
-
-        cout << "DiffNoiseAnalysis::saving...\n";
-        cout << "c_last... " << c << endl;
-        cout<<"rand10... " <<rand10<<endl;
-
-        string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-        saveimage(file_name);
-
-    }
-    
     _save_cnt++;
             
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
+    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
+    saveImageAnalysis(file_name);
 }
-void DiffNoiseAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
-}
-
-

src/DiffNoiseAnalysis.h

@@ -9,6 +9,9 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
+
 class DiffNoiseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,16 +23,44 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
-    void display_results();
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt, _fade_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+
+    int     _run_cnt, _save_cnt, _fade_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
     
 };

src/IResponseAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "IResponseAnalysis.h"
 #include "ofMain.h"
 
@@ -15,19 +10,94 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
-
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
+    AbstractAnalysis::setup(camWidth, camHeight);
         
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
+    cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME IResponseAnalysis " << acq_run_time << endl;
+
+    //flag for main sketch
+    meshIsComplete=false;
+    _gotFirstImage=false;
+    
+    _mesh_size_multiplier=4;
+    
+
+    //int acq_run_time = 20;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
+    // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    _synth_save_cnt = 0;
+    _run_cnt = 0;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
     c = 0;
+    
+    int anim_time = 10;   // 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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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);
+    
 }
 
 
@@ -35,94 +105,139 @@ 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();
+
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
-
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
+    //for(int i = 0; i < NUM_RUN; i++) {
+    //_run_cnt = i;
+    //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
    
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+    
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
-}
    
+    //}
+}
 
 void IResponseAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+    cout<<"SYNTHESISING IRESPONSE";
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
  
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    //cout << "IResponseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
+    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+        
+        //cout << "IResponseAnalysis::synthesis FOR LOOP...\n";
+    
+        //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;
+        } 
+        
+        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 //////////////////////////
+                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;
                     }
                   
                 }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
                
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+                //update the images with their new background subtracted selves
+                image1.setFromPixels(imagePixels1);
 
                 
-        ofImage image1;
-        ofImage image2;
+                //flag the main app that we aren't read yet
+                meshIsComplete=false;
+                //make a mesh - this mesh will be drawn in the main app
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1,image1, aMesh);
+                 //meshPix=make3DZmap(image1, image5, _background);
+                //with jpgs this was refusing to save out
+                meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
+                _saved_filenames_synthesis.push_back(meshFileName);
 
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_brightness_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BRIGHTNESS,_recorded_brightness_value), image2, &meshes[index]);            
-            index++;
+                //flag that we are finished  
+                meshIsComplete=true;
+                _synth_save_cnt++;
+                
+            }
         }
     }
 
-}
-
-void IResponseAnalysis::display_results(){
-    
-    Timer* display_results_timer;
-    
-    TimerCallback<IResponseAnalysis> display_results_callback(*this, &IResponseAnalysis::display_results_cb);
-    // display results of the synthesis
-    
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
-    
-    while(!_RUN_DONE)
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
-    display_results_timer->stop();
     
 }
 
 
+void IResponseAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            // cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
+}
+
+
+
 // this runs at frame rate = 33 ms for 30 FPS
 void IResponseAnalysis::draw()
 {
@@ -131,9 +246,18 @@ void IResponseAnalysis::draw()
             
         case STATE_ACQUIRING:
         {
-            /// *** TODO  *** ///
-            // still need to deal with latency frames here - i.e.: there are frames
-            /// *** TODO  *** ///
+            ofEnableAlphaBlending();
+            ofColor aColour;
+            int _fade_in_frames = _frame_cnt_max/10;
+            //cout<< "_fade_in_frames" << _fade_in_frames<< endl;
+            
+            if (_frame_cnt < _fade_in_frames) {
+                
+                aColour.set(255, 255, 255, ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                ofSetColor(aColour);
+                ofRect(0, 0, ofGetWidth(), ofGetHeight());
+            
+            }
             
             if (_frame_cnt < _frame_cnt_max)
             {
@@ -141,9 +265,18 @@ void IResponseAnalysis::draw()
                 ofRect(0, 0, ofGetWidth(), ofGetHeight());
                 c  = 255.0 * (_frame_cnt_max*_frame_cnt_max - _frame_cnt*_frame_cnt)/(_frame_cnt_max*_frame_cnt_max);
             } else {
+                
                 _RUN_DONE = true;
             }
             
+            if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
+                aColour.set(0, 0, 0, ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
+                ofSetColor(aColour);
+                ofRect(0, 0, ofGetWidth(), ofGetHeight());
+                // cout <<  "FADE OUT STROBE TIME " << endl;
+            }         
+            
+            ofDisableAlphaBlending();
             _frame_cnt++;
 
             break;
@@ -151,37 +284,119 @@ void IResponseAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
+            // display animation of something while the synthesis in on-going...
+            
+            // cout << "IResponse = STATE_SYNTHESISING...\n";
             
             // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "IResponse STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                
+                _RUN_DONE = true;
+                _anim_cnt=0;
+            }
+            
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
          
+            
         case STATE_DISPLAY_RESULTS:
         {
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                //cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+            
+                ofDisableAlphaBlending();
+            }
+            
             // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
-            
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
-                
-            }
-
+            _RUN_DONE = true;
             break;
-        }
             
+        }
         
         default:
             break;
@@ -192,21 +407,178 @@ void IResponseAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void IResponseAnalysis::save_cb(Timer& timer)
 {
-    //cout << "IResponseAnalysis::saving...\n";
-    //cout << "c_last... " << c << endl;
-    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    saveimage(file_name);
-    
     _save_cnt++;
     
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
+    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
+        
+    saveImageAnalysis(file_name);
 }
-void IResponseAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
+
+void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+    int x=0;
+    int y=0;
+    
+    //get rid of all previous vectors and colours
+    mesh.clear();
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
+    
+    ofColor meshColour=ofColor(255,0,0);
+    
+    int chooseColour=1  ;
+    
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
     }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+         
+    if(chooseColour==1){
+            for(int i=0;i<sPixels.size();i++){
+                mesh.addColor(  currentSecondImage.getColor(x, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+
+                x++;
+                if(x>=currentSecondImage.getWidth()-1){
+                    x=0;
+                    y++;
+                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                    if(y>=479){
+                        break;
+                    }
+                }
+             }
+    }
+    /*else{
+           for(int i=0;i<somePixels.getWidth()*(somePixels.getHeight()-1);i++){      
+               
+        
+               ofVec3f U;
+               ofVec3f V;
+                              //tri 1
+               U =ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness() ).operator-  ( ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- somePixels.getColor(x, y).getBrightness()  ) );
+               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ));
+               
+               ofVec3f normal;
+               float mult=5.2;
+               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x, y+1).getBrightness() )  ));
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
+               
+               mesh.addNormal(normal);
+               
+               //tri 2
+               U =ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
+               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- somePixels.getColor(x+1, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
+               
+               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
+                 //       mesh.addColor( ofColor(255,10,10)   );
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,-mult*(1+ somePixels.getColor(x+1, y).getBrightness())   ));
+               
+               mesh.addNormal(normal);
+
+                x++;
+                if(x>=somePixels.getWidth()-1){
+                    x=0;
+                    y++;
+                    if(y>=479){
+                       break;
+                   }
+                }
+             }*/
+         
+     // add colour from current second image of two - this is a hang over from when i was comparing two image
+        
+
+}
+vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+    
+    ofPixels imagePixels1 = image1.getPixelsRef();
+    ofPixels imagePixels2 = image2.getPixelsRef();
+    ofPixels backgroundPixels = backgroundImag.getPixelsRef();
+    vector<float> differences;
+    
+    ofPixels difference;
+    //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
+    unsigned char * thesePixels = new unsigned char[ imagePixels1.getWidth()*imagePixels1.getHeight()*3];
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
+    int x=0;
+    int y=0;
+    
+    int chooseComparison=1;
+    
+    //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
+    if(chooseComparison==1){
+        //for each pixel...
+        float _maxPossibleDistanceToCentre=ofDist(0,0,imagePixels1.getWidth()/2, imagePixels1.getHeight()/2);
+        for(int i=0;i<imagePixels1.size();i+=3){
+            
+            ofColor colourImage1 = imagePixels1.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
+            
+            float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
+            float _presumedBrightness=ofMap( sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
+            //float _presumedBrightness=255;
+            int thisDiff=abs(colourImage1.getBrightness()-_presumedBrightness);
+            //cout<<thisDiff<< " thisDiff "<<endl;
+            float multiplier=2.0;
+            differences.push_back(multiplier* thisDiff);
+            thesePixels[i]=thisDiff;
+            thesePixels[i+1]=thisDiff;
+            thesePixels[i+2]=thisDiff;
+            x++;
+            if(x>=imagePixels1.getWidth()){
+                x=0;
+                y++;
+                
+            }
+            
+        }
+    }
+    
+    difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
+    return differences;
+    
 }
 
 

src/IResponseAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 class IResponseAnalysis : public AbstractAnalysis
 {
 public:
@@ -20,17 +22,51 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();
-    void display_results();
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
     bool    _RUN_DONE;
-    int     _run_cnt, _save_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
   
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    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);
+    //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

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "RelaxRateAnalysis.h"
 #include "ofMain.h"
 
@@ -15,115 +10,167 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
+#define TRESHOLD        80
+#define MAXBLOBS        15
 
 void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 130;
-    NUM_PHASE = 1;
-    NUM_RUN = 3;
-    NUM_SAVE_PER_RUN = 100;    
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_relaxrate", NUMBER_RUNS);
+    cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_relaxrate", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
+    
+    _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
+    // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    
+    _run_cnt = 0;
     _level = 0;
     _flip = 1;
     _frame_cnt = 0;
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
     c = 0;
+    _synth_save_cnt = 0;
+    
+    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();
+    image1.setUseTexture(false);  // the non texture image that is needed to first load the image
+    image1.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();
+    cvGrayDiff1.clear();
+    
+    cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+        
 }
 
 
 void RelaxRateAnalysis::acquire()
 {
-
     Timer* save_timer;
-
     TimerCallback<RelaxRateAnalysis> save_callback(*this, &RelaxRateAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _RUN_DONE = false;
+
+    create_dir_allocate_images();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
-
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
+    //for(int i = 0; i < NUM_RUN; i++) {
+    //_run_cnt = i;
+    //cout << "RUN NUM = " << i;
     
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
   
-        while(!_RUN_DONE)
+    save_timer->start(save_callback);
+  
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
     
     save_timer->stop();
-    }
+        
 }
 
 void RelaxRateAnalysis::synthesise()
 {
-    /*
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+    //cout << "IResponseAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    cvContourFinderVect.clear();    
     
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
-        }
+    
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
+                
+        if(_state == STATE_STOP) return;
+                
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+                
+            ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+            
+            cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);            
+            cvColorImage1.convertToGrayscalePlanarImage(cvGrayDiff1, 1);
+            
+            cvGrayDiff1.threshold(_treshold);
+            
+            rfiCvContourFinder* cf = new rfiCvContourFinder();
+            
+            cf->findContours(cvGrayDiff1, 20, (image1.width * image1.height) / 4, _maxblobs, true);
+            
+            cvContourFinderVect.push_back(cf);
             
         }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
-    
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
-        
-        
-        ofImage image1;
-        ofImage image2;
-        
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_brightness_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BRIGHTNESS,_recorded_brightness_value), image2, &meshes[index]);            
-            index++;
     }
-    }
-     */
     
-}
-void RelaxRateAnalysis::display_results(){
-    
-    /*
-    
-    Timer* display_results_timer;
-    
-    TimerCallback<RelaxRateAnalysis> display_results_callback(*this, &RelaxRateAnalysis::display_results_cb);
-    // display results of the synthesis
-    
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
-    
-    while(!_RUN_DONE)
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
-    display_results_timer->stop();
-     */
+}
+
+void RelaxRateAnalysis::displayresults()
+{
+        
+    //cvContourFinderVectDisplay.clear();
+    clearcfindervectdisplay();
+    
+    for(int i=1;i<cvContourFinderVect.size();i++){
+        
+        if(_state == STATE_STOP){
+            clearcfindervectdisplay();
+            clearcfindervect();
+            return;
+        }        
+        
+        
+        //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            if(_state == STATE_STOP) return;
+            //cout << "!_image_shown" << endl;
+        }
+        
+        cvContourFinderVectDisplay.push_back(cvContourFinderVect[i]);    
+        _show_image = true;
+        _image_shown = false;
+        
+    }     
+    
+    clearcfindervectdisplay();
+    clearcfindervect();
+    
+        
+    //cvContourFinderVectDisplay.clear();
+    //cvContourFinderVect.clear();
+    
     
 }
 
@@ -135,9 +182,7 @@ void RelaxRateAnalysis::draw()
     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)
             {
@@ -156,81 +201,170 @@ void RelaxRateAnalysis::draw()
                 }
                 
             } else {
-                cout << "RELAXRATE RUN COMPLETED" << endl;
-                //_state = STATE_SYNTHESISING;
+              
                 _RUN_DONE = true;
             }
             
             _frame_cnt++;
-            cout << "_frame_cnt:" << _frame_cnt << endl;
+            //cout << "_frame_cnt:" << _frame_cnt << endl;
             
             break;
         }
             
         case STATE_SYNTHESISING:
         {
+            
             // display animation of something while the synthesis in on-going...
+            
+            //cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = MIDDLE OF ANIMATION...\n";
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                //cout << "_anim_cnt = " << _anim_cnt << endl;
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = FADE OUT OF ANIMATION...\n";
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        //cout << "c_anim = " << c_anim << endl;
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                
+                _anim_cnt++;
+                
+            } else {
+                _RUN_DONE = true;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            /*
-            // display results of the synthesis
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
             
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
+                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
+                }
 
             }
-             */
             
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
-        }
         
+        }
             
         default:
             break;
     }
 
-
-
 }
 
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void RelaxRateAnalysis::save_cb(Timer& timer)
 {
-    //cout << "RelaxRateAnalysis::saving...\n";
-    //cout << "c_last... " << c << endl;
-    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-
-    saveimage(file_name);
-    
     _save_cnt++;
     
+    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
+    
+    saveImageAnalysis(file_name);
     
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-     //   _RUN_DONE = true;
     
 }
-void RelaxRateAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
+
+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();
 }
 

src/RelaxRateAnalysis.h

@@ -1,7 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
 
 #pragma once
 
@@ -9,6 +5,11 @@
 
 #include "Poco/Timer.h"
 
+#include "rfiCvContourFinder.h"
+
+#include "ofxOpenCv.h"
+
+
 
 class RelaxRateAnalysis : public AbstractAnalysis
 {
@@ -21,17 +22,33 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise(); 
-    void display_results();
+    void displayresults();
+    void cleanup();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
+    void clearcfindervect();
+    void clearcfindervectdisplay();
+    
     bool    _RUN_DONE;
     float     _flip, _level;
-    int     _run_cnt, _save_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+    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;    
+    ofxCvColorImage         cvColorImage1;    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    
+    vector<rfiCvContourFinder*>      cvContourFinderVect;
+    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
 
 };

src/ShadowScapesAnalysis.cpp

@@ -1,35 +1,3 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
-
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
-
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
-
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ShadowScapesAnalysis.h"
 #include "ofMain.h"
 
@@ -37,130 +5,240 @@
 #include "Poco/Thread.h"
 #include "RefractiveIndex.h"
 
+//#include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
 using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
 #define STATE_SCAN      0
 #define STATE_ANALYSIS  1
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;  
+    AbstractAnalysis::setup(camWidth, camHeight);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
+    cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
+    
+    int screenSpan;
+    if (_dir == V) screenSpan = ofGetHeight();
+    if (_dir == H) screenSpan = ofGetWidth();
+    if (_dir == D) screenSpan = ofGetHeight();
+    
+    _step = (screenSpan/acq_run_time)/(ofGetFrameRate());
+            // pixel per frame = (pixels / sec) / (frame / sec)
+    
+    // 40 pixels per second should give us a 20 second scan at 800 pixels wide
+
+    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
     
-    create_dir();
-    _speed = 900.0;  // 900.0 is the correct number
     _scanLineWidth = 100.0;
     _run_cnt = 0;
     _save_cnt = 0;
+    _synth_save_cnt = 0;
+
+    int anim_time = 10;   // 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
+   
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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 ShadowScapesAnalysis::acquire()
 {
-    int w;
-    if (_dir == V) w = ofGetHeight();
-    if (_dir == H) w = ofGetWidth();
-    if (_dir == D) w = ofGetHeight();
-    
-    _step = ((w/_speed) * 1000.0) / 500.0;
-    _line = 0;
-    
-    // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
         
     Timer save_timer(0, DELTA_T_SAVE);  
     TimerCallback<ShadowScapesAnalysis> save_callback(*this, &ShadowScapesAnalysis::save_cb);
     
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
+    _line = 0;
     _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
+
+    create_dir_allocate_images();
    
     save_timer.start(save_callback);
       
-        while(!_RUN_DONE)
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
     
     save_timer.stop();
-    }
 
 }
 
 void ShadowScapesAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+    //cout << "ShadowScapesAnalysis::saving synthesis...\n";
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
     
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+      //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
+        
+        // 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;
         } 
         
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
             
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                                
-        ofImage image1;
-        ofImage image2;
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
+                //cvGrayImage1 = cvColorImage1;
+                //cvGrayImage2 = cvColorImage2;
                 
-        string fnamei = _saved_filenames[i];
-        string fnameii = _saved_filenames[i + 1];
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
       
-        bool l1 = image1.loadImage(_saved_filenames[i]);
-        bool l2 = image2.loadImage(_saved_filenames[i+1]);        
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                cvGrayDiff1.blur(5);
+                cvGrayDiff1.dilate();
                 
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
                 
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BRIGHTNESS), image2, &meshes[index]);            
-            index++;
+                if(_dir == H) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_H_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 }
                 
-        image1.clear();
-        image2.clear();
+                if(_dir == V) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_V_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 }    
                 
-}
+                if(_dir == D) {
+                    file_name = ofToString(_synth_save_cnt, 2)+"_D_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
+                }
                 
                 
-void ShadowScapesAnalysis::display_results(){
                 
-    Timer* display_results_timer;
+                //<---- 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);
                 
-    TimerCallback<ShadowScapesAnalysis> display_results_callback(*this, &ShadowScapesAnalysis::display_results_cb);
-    // display results of the synthesis
                 
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
                 
-    while(!_RUN_DONE)
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+                
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                               
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+                _synth_save_cnt++;
+            }
+        }
+    }
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+     while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3);
+}
 
-    display_results_timer->stop();
+
+void ShadowScapesAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+       // cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
 
 }
+
+
 // the animation draw - and the output draw
 void ShadowScapesAnalysis::draw()
 {
@@ -231,24 +309,22 @@ void ShadowScapesAnalysis::draw()
             }
             
             
-            
             if(_dir == V && int(_line) >= (ofGetHeight()+4*_scanLineWidth)){
-                cout << "VERTICAL IS DONE - _line >= (ofGetHeight()+4*_scanLineWidth) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
+                //cout << "VERTICAL IS DONE - _line >= (ofGetHeight()+4*_scanLineWidth) is TRUE" << endl;
                 _RUN_DONE = true;
+                
             }
             
             if(_dir == H && int(_line) >= (ofGetWidth()+4*_scanLineWidth)) {
                 
                 //cout << "HORIZONTAL IS DONE -  _line >= (ofGetWidth()+4*_scanLineWidth)) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
                 
             }
             
             if(_dir == D && int(_line) >= (1.5*ofGetHeight()+4*_scanLineWidth)) {
                 //cout << "DIAGONAL IS DONE - _line >= (1.5*ofGetHeight()+4*_scanLineWidth)) is TRUE" << endl;
-                //_state = STATE_SYNTHESISING;
+            
                 _RUN_DONE = true;
             }
         
@@ -257,35 +333,117 @@ void ShadowScapesAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
-            // display animation of something while the synthesis in on-going...
+           // cout << "ShadowScapesAnalysis = STATE_SYNTHESISING...\n";
 
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                         
+                if (_anim_cnt < _fade_in_frames) {
+                  //  cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+            
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                   
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+        
+                }
+                _anim_cnt++;
+                
+            } else {
+                _RUN_DONE = true;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
             break;
+      
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
+            //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
+            
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
+            }
+            
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+              //  cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                    ofSetColor(255, 255, 255);
+                
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                    image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
                 
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
                 
             }
             
+            // display results of the synthesis
+            _RUN_DONE = true;
+            
+            // clear allocated memory...? 
+            
             break;
         }
             
@@ -299,15 +457,8 @@ void ShadowScapesAnalysis::draw()
 void ShadowScapesAnalysis::save_cb(Timer& timer)
 {
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    _save_cnt++;
         
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    }
-    
-    
-    cout << "ShadowScapesAnalysis::saving...\n";
     string file_name;
     
     if(_dir == H) {
@@ -322,15 +473,6 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
         
-    saveimage(file_name);
-    
-    _save_cnt++;    
+    saveImageAnalysis(file_name);
         
 }
-void ShadowScapesAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
-}
-

src/ShadowScapesAnalysis.h

@@ -1,34 +1,4 @@
-/*
- - copyright (c) 2011 Copenhagen Institute of Interaction Design (CIID)
- - all rights reserved.
- 
- + redistribution and use in source and binary forms, with or without
- + modification, are permitted provided that the following conditions
- + are met:
- +  > redistributions of source code must retain the above copyright
- +    notice, this list of conditions and the following disclaimer.
- +  > redistributions in binary form must reproduce the above copyright
- +    notice, this list of conditions and the following disclaimer in
- +    the documentation and/or other materials provided with the
- +    distribution.
- 
- + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
- + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
- + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
- + FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
- + COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
- + INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
- + BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
- + OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED
- + AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
- + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT
- + OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF
- + SUCH DAMAGE.
- 
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk 
- */
+/* */
 
 #pragma once
 
@@ -36,6 +6,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 enum shadow_type {
     H, V, D,
 };
@@ -52,11 +24,11 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
-    void display_results();
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
@@ -66,7 +38,35 @@ protected:
     float    _scanLineWidth; // pix per second
     float     _step;
     shadow_type _dir;
-    int     _run_cnt, _save_cnt;
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;    
 
 };

src/ShapeFromShadingAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "ShapeFromShadingAnalysis.h"
 #include "ofMain.h"
 
@@ -15,43 +10,103 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 {       
-    DELTA_T_SAVE = 300;
-    NUM_PHASE = 1;
-    NUM_RUN = 1;
-    NUM_SAVE_PER_RUN = 100;    
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    create_dir();
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shapefromshading", NUMBER_RUNS);
+    cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
-    _level = 0;
-    _flip = 1;
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;
+
+
+    //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
+    // or 10 times per second = every 100 ms
+    
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    //create_dir_allocate_images();
+    _synth_save_cnt = 0;
+    _run_cnt = 0;
     _frame_cnt = 0;
-    
-    _frame_cnt_max = ofGetFrameRate() * ((DELTA_T_SAVE * NUM_SAVE_PER_RUN) / 1000);
     c = 0;
+    
+    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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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 ShapeFromShadingAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<ShapeFromShadingAnalysis> save_callback(*this, &ShapeFromShadingAnalysis::save_cb);
 
-    // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
-
-        _run_cnt = i;
-
-        cout << "RUN NUM = " << i;
-
-        save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
-        save_timer->start(save_callback);
+    _run_cnt++;
+    _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;    
     _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
+    create_dir_allocate_images();
+    
     _animation_cnt1 = 0;
     _animation_cnt2 = 0;
     _animation_cnt3 = 0;
@@ -70,76 +125,125 @@ void ShapeFromShadingAnalysis::acquire()
     _animation_cnt16 = 0;
     _animation_reset = false;  // coundn't get this to work - so using seperate counters - shitty!
     
-        while(!_RUN_DONE)
+    // RUN ROUTINE
+    //for(int i = 0; i < NUM_RUN; i++) {
+
+      //  _run_cnt = i;
+
+        //cout << "RUN NUM = " << i;
+
+    save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
+   
+    save_timer->start(save_callback);
+     
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
-}
     
+   // }
+}
 
 void ShapeFromShadingAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+   // cout << "ShapeFromShadingAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    //    cout << "ShapeFromShadingAnalysis::synthesis FOR LOOP...\n";
+        
+     //   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;
         } 
         
-    }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+        //    cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
+                ///////////////////////// 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);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                //cvGrayDiff1.blur(5);
+                //cvGrayDiff1.dilate();
+                //cvGrayDiff1.contrastStretch();
+                
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 
                 
-        ofImage image1;
-        ofImage image2;
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+            
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                //image.setUseTexture(false);  
+               
+                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                
+                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+                _synth_save_cnt++;
                 
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_brightness_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BRIGHTNESS,_recorded_brightness_value), image2, &meshes[index]);            
-            index++;
             }
         }
+    }
+    
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);    
     
 }
 
-void ShapeFromShadingAnalysis::display_results(){
+void ShapeFromShadingAnalysis::displayresults()
+{
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
-    Timer* display_results_timer;
+        if(_state == STATE_STOP) return;
         
-    TimerCallback<ShapeFromShadingAnalysis> display_results_callback(*this, &ShapeFromShadingAnalysis::display_results_cb);
-    // display results of the synthesis
+       // cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
         
-    while(!_RUN_DONE)
-        Thread::sleep(3);
-    
-    display_results_timer->stop();
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
         
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
 }
 
 // this runs at frame rate = 33 ms for 30 FPS
@@ -154,23 +258,10 @@ void ShapeFromShadingAnalysis::draw()
                 
                 ofEnableAlphaBlending();
                 
-                
                 int _quarter_frame_cnt_max = _frame_cnt_max/4;
                 int _half_frame_cnt_max = _frame_cnt_max/2;
                 int _threequarters_frame_cnt_max = 3*_frame_cnt_max/4;
                 
-                //TODO:  put in CROSS FADES, ETC§E 
-                
-                /*
-                 if (_animation_reset == true)
-                 {
-                 _animation_cnt1 = 0;
-                 _animation_cnt2 = 0;
-                 _animation_cnt3 = 0;
-                 _animation_cnt4 = 0;
-                 }
-                 */
-                
                 if(_frame_cnt < _quarter_frame_cnt_max) {
                     
                     quad =  "QUAD1";
@@ -311,10 +402,6 @@ void ShapeFromShadingAnalysis::draw()
                         _animation_cnt12++;
                     }  
                 
-                    
-                    
-                    
-                    
                 }
                 
                 
@@ -366,6 +453,10 @@ void ShapeFromShadingAnalysis::draw()
                 }
                 
                 ofDisableAlphaBlending();
+            } else {
+                //_state = STATE_SYNTHESISING;
+                _frame_cnt = 0;
+                _RUN_DONE = true;
             }
             
             _frame_cnt++;
@@ -377,33 +468,117 @@ void ShapeFromShadingAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+           // cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+                    //cout << "ShadowScapesAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+                    //cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+                    //cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                _RUN_DONE = true;
+                //_state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
+        
+            
         case STATE_DISPLAY_RESULTS:
         {   
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
-            
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+            //    cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
+            
         }
             
             
@@ -417,23 +592,9 @@ void ShapeFromShadingAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ShapeFromShadingAnalysis::save_cb(Timer& timer)
 {
-    //cout << "ShapeFromShadingAnalysis::saving...\n";
+    _save_cnt++;
             
     string file_name = ofToString(_save_cnt,2)+"_"+ quad +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveimage(file_name);
-    
-    _save_cnt++;
-    
-    //if(_save_cnt >= NUM_SAVE_PER_RUN)
-    //    _RUN_DONE = true;
-
+    saveImageAnalysis(file_name);
 }
-void ShapeFromShadingAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
-}
-
-

src/ShapeFromShadingAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 
 class ShapeFromShadingAnalysis : public AbstractAnalysis
 {
@@ -21,18 +23,16 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();    
-    void display_results();
+    void displayresults();
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);
     
 protected:
     
     string quad;
     bool    _RUN_DONE;
     float     _flip, _level;
-    int     _run_cnt, _save_cnt;
     int _animation_cnt1;
     int _animation_cnt2;
     int _animation_cnt3;
@@ -50,6 +50,36 @@ protected:
     int _animation_cnt15;
     int _animation_cnt16;
     int _animation_reset;  // this reset part didn't get working - so using 16 different counters! yay! 
-    float   c, _frame_cnt, _frame_cnt_max, _results_cnt, _results_cnt_max;
+   
+    int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+   
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
     
 };

src/StrobeAnalysis.cpp

@@ -1,8 +1,3 @@
-/*
- ~ author: dviid
- ~ contact: dviid@labs.ciid.dk
- */
-
 #include "StrobeAnalysis.h"
 #include "ofMain.h"
 
@@ -15,22 +10,89 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    30
+
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    DELTA_T_SAVE = 100;
-    NUM_RUN = 1;
+    AbstractAnalysis::setup(camWidth, camHeight);
     
-    _strobe_cnt = 0;
-    _strobe_cnt_max = 20;  // 40 x 500 ms = 20000 ms = 20 seconds run time
-    _strobe_interval = 1000;  //every 0.5seconds = 15 frames
-    _frame_cnt_max = _strobe_cnt_max * _strobe_interval * ofGetFrameRate()/1000;
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
+    cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+    
+    int acq_run_time;   // 10 seconds of acquiring per run
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
+    cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
+
+    //int acq_run_time = 25;   // 20 seconds of acquiring per run
+    
+    DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 100 files
+                                          // or 5 times per second = every 200 ms
+   
+    _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
+    
+    _strobe_interval = 2000;  //every 1 seconds, or every thirty frames 30 frames
 
     // 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.
     
-    //or 20 times, every one second... 
-    _save_cnt_max = _strobe_cnt_max*_strobe_interval/DELTA_T_SAVE;
+    //create_dir_allocate_images();
+    _synth_save_cnt = 0;
+    _run_cnt = 0;
+    
+    int anim_time = 5;   // 5 seconds for the animation
+    _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
+    
+    //  images used for re-loading and saving out the synthesized files ///
+    image3.setUseTexture(false);  
+    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);
+    
+    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);
 
-    create_dir();
 }
 
 
@@ -38,94 +100,137 @@ void StrobeAnalysis::acquire()
 {
 
     Timer* save_timer;
-
     TimerCallback<StrobeAnalysis> save_callback(*this, &StrobeAnalysis::save_cb);
     
+    _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();
+    
     // RUN ROUTINE
-    for(int i = 0; i < NUM_RUN; i++) {
+    //for(int i = 0; i < NUM_RUN; i++) {
 
-        _run_cnt = i;
-        _save_cnt = 0;
-        _frame_cnt = 0;
+    //_run_cnt = i;
     
-        cout << "RUN NUM = " << i;
+    //cout << "RUN NUM = " << i;
 
     save_timer = new Timer(0, DELTA_T_SAVE); // timing interval for saving files
     save_timer->start(save_callback);
-        _RUN_DONE = false;
-        _frame_cnt = 0; _save_cnt = 0;
     
-        while(!_RUN_DONE)
+        while(!_RUN_DONE && _state != STATE_STOP)
             Thread::sleep(3);
 
     save_timer->stop();
-    }
+  
+    
+    //}
 }
 
 void StrobeAnalysis::synthesise()
 {
-    //incrementer to whichMesh
-    speed=0.2;
-    //whichMesh is the index in the vector of meshes
-    whichMesh=0;
+   // cout << "StrobeAnalysis::saving synthesis...\n";
+    if(_state == STATE_STOP) return;
     
-    int index=0;
-    float iterator=1;
-    bool debug=false;
-    if(debug){
-        _saved_filenames.clear();
-        _saved_filenames=getListOfImageFilePaths("MIDDLESBOROUGH", _name);
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
-        //hack to limit number of meshes.
-        if(_saved_filenames.size()>100){
-            iterator= _saved_filenames.size() /100;
+    //    cout << "StrobeAnalysis::synthesis FOR LOOP...\n";
+        
+    //    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;
         } 
         
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+    //        cout << "LOADED image1!!!" << endl;
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
+                
+                ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
+                
+                cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.dilate();
+                cvGrayDiff1.dilate();
+                cvGrayDiff1.contrastStretch();
+               
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
+                
+                file_name = ofToString(_synth_save_cnt, 2)+"_StrobeAnalysis_"+ofToString(_run_cnt,2)+".jpg";
+                
+        
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                //ofImage image;
+                //image.allocate(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);
+              
+                
+                
+                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
+                
+                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
+                _synth_save_cnt++;
+                
+                
             }
-    //clear vector so we don't add to it on successive runs
-    meshes.clear();
-    
-    for(float i=0;i<_saved_filenames.size()-1;i+=iterator){
-        
-        
-        ofImage image1;
-        ofImage image2;
-        
-        //there is a known issue with using loadImage inside classes in other directories. the fix is to call setUseTExture(false)
-        image1.setUseTexture(false);
-        image2.setUseTexture(false);
-        //some of the textures are not loading correctly so only make mesh if both the images load
-        if(image1.loadImage(_saved_filenames[i]) && image2.loadImage(_saved_filenames[i+1])){
-            meshes.push_back(ofMesh());
-            cout<<"setting mesh"<<endl;
-            int _recorded_brightness_value=getRecordedValueFromFileName(_saved_filenames[i]);
-            setMeshFromPixels( calculateListOfZValues(image1,image2, COMPARE_BRIGHTNESS,_recorded_brightness_value), image2, &meshes[index]);            
-            index++;
         }
     }
     
-}
-
-void StrobeAnalysis::display_results(){
-    
-    Timer* display_results_timer;
-    
-    TimerCallback<StrobeAnalysis> display_results_callback(*this, &StrobeAnalysis::display_results_cb);
-    // display results of the synthesis
-    
-    display_results_timer = new Timer(0, 20); // timing interval for saving files
-    display_results_timer->start(display_results_callback);
-    _RUN_DONE = false;
-    _results_cnt=0;
-    _results_cnt_max=300;
-    
-    while(!_RUN_DONE)
+    // _saved_filenames_synthesis has processed all the files in the analysis images folder
+    while(!_RUN_DONE && _state != STATE_STOP)
         Thread::sleep(3); 
+}
 
-    display_results_timer->stop();
+void StrobeAnalysis::displayresults()
+{
+    
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
+        
+        if(_state == STATE_STOP) return;
+        
+    //    cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+      //      cout << "didn't load image" << endl;
+        } 
+        
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
+            image3.loadImage(_saved_filenames_synthesis[i]);
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+        }
+    }
     
 }
 
+
 // this runs at frame rate = 33 ms for 30 FPS
 void StrobeAnalysis::draw()
 {
@@ -139,7 +244,7 @@ void StrobeAnalysis::draw()
                 ofEnableAlphaBlending();
                 ofColor aColour;
                 int _fade_in_frames = _frame_cnt_max/10;
-                cout<< "_fade_in_frames" << _fade_in_frames<< endl;
+           //     cout<< "_fade_in_frames" << _fade_in_frames<< endl;
                 
                 if (_frame_cnt < _fade_in_frames) {
                     
@@ -157,13 +262,13 @@ void StrobeAnalysis::draw()
                     //cout <<  "frame_cnt % 15: " << _frame_cnt%15 << endl;
                     //cout <<  "MAIN STROBE TIME " << endl;
                     
-                    if (_frame_cnt%int(ofGetFrameRate()*_strobe_interval/1000) < (ofGetFrameRate()*_strobe_interval/1000)/2)
+                    if (int(_frame_cnt)%int(ofGetFrameRate()*_strobe_interval/1000) < (ofGetFrameRate()*_strobe_interval/1000)/2)
                     {
                         ofSetColor(255, 255, 255);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                         _strobe_cnt++;
                         _strobe_on = 1;
-                    } else if (_frame_cnt%int(ofGetFrameRate()*_strobe_interval/1000) >= (ofGetFrameRate()*_strobe_interval/1000)/2)
+                    } else if (int(_frame_cnt)%int(ofGetFrameRate()*_strobe_interval/1000) >= (ofGetFrameRate()*_strobe_interval/1000)/2)
                     {
                         ofSetColor(0, 0, 0);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
@@ -173,7 +278,7 @@ void StrobeAnalysis::draw()
                 }
                 
                 if (_frame_cnt >= (_frame_cnt_max-_fade_in_frames) && _frame_cnt < _frame_cnt_max) {
-                    aColour.set(255, 255, 255, 255-ofMap(_frame_cnt, 0, _fade_in_frames, 0, 255));
+                    aColour.set(255, 255, 255, 255-ofMap(_frame_cnt-(_frame_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255));
                     ofSetColor(aColour);
                     ofRect(0, 0, ofGetWidth(), ofGetHeight());
                     // cout <<  "FADE OUT STROBE TIME " << endl;
@@ -181,6 +286,7 @@ void StrobeAnalysis::draw()
             
                 ofDisableAlphaBlending();
             } else {
+                //_state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
             
@@ -192,33 +298,117 @@ void StrobeAnalysis::draw()
         case STATE_SYNTHESISING:
         {
             // display animation of something while the synthesis in on-going...
+            
+          //  cout << "StrobeAnalysis = STATE_SYNTHESISING...\n";
+            
+            // display animation of something while the synthesis in on-going...
+            ofEnableAlphaBlending();
+            ofSetRectMode(OF_RECTMODE_CENTER);
+            ofPushMatrix();
+            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
+            
+            if(_anim_cnt < _anim_cnt_max){
+                
+                ofColor aColour;
+                int rectSizeW = ofGetWidth()/4;
+                int rectSizeH = ofGetHeight()/4;
+                int _fade_in_frames = _anim_cnt_max/2;
+                
+                int c_anim = 10;
+                int fade;
+                
+                //ofRotate(ofMap(_anim_cnt/2.0, 0, _anim_cnt_max, 0, 360));
+                
+                if (_anim_cnt < _fade_in_frames) {
+            //        cout << "StrobeAnalysis STATE_SYNTHESIZING = FADING IN ANIMATION...\n";
+                    
+                    fade = ofMap(_anim_cnt, 0, _fade_in_frames, 0, 255);
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 0+17*i;
+                        
+                        aColour.set(c_anim, c_anim, c_anim, fade);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt >= _fade_in_frames && _anim_cnt <= (_anim_cnt_max-_fade_in_frames)){
+                    
+                    for (int i=0; i <= 15; i++){
+                        c_anim = 255;
+                        aColour.set(c_anim, c_anim, c_anim, 255);
+                        ofSetColor(aColour);
+                        
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                }
+                
+                if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
+                    
+             //       cout << "_anim_cnt = " << _anim_cnt-(_anim_cnt_max-_fade_in_frames) << endl;
+                    fade = ofMap(_anim_cnt-(_anim_cnt_max-_fade_in_frames), 0, _fade_in_frames, 0, 255);
+             //       cout << "fade down = " << fade << endl;
+                    
+                    for (int i=0; i <= 15; i++){
+                        
+                        c_anim = (17*i);
+                        
+                        aColour.set(c_anim, c_anim, c_anim, 255-fade);
+                        ofSetColor(aColour);
+                        ofRect(0, 0, rectSizeW+10*i, rectSizeH+10*i);
+                        ofRect(0, 0, rectSizeW-10*i, rectSizeH-10*i);
+                    }
+                    
+                }
+                _anim_cnt++;
+                
+            } else {
+                _RUN_DONE = true;
+                //_state = STATE_DISPLAY_RESULTS;
+                _anim_cnt=0;
+            }
+            ofPopMatrix();
+            ofSetRectMode(OF_RECTMODE_CORNER);
+            ofDisableAlphaBlending();
+            
             break;
         }
             
         case STATE_DISPLAY_RESULTS:
         {
-            // display results of the synthesis
-            int imageWidth=640;
-            int imageHeight =480;
-            ofPushMatrix();
-            ofTranslate(ofGetWidth()/2, ofGetHeight()/2);
-            ofRotateY(_results_cnt*0.3);
-            //ofRotateX(90);
-            //ofRotateZ(whichMesh);
-            ofTranslate(-ofGetWidth()/2, -ofGetHeight()/2),-400;
-            ofTranslate((ofGetWidth()/2)-(imageWidth/2),0,0 );
             
-            meshes[whichMesh].drawVertices();
-            ofPopMatrix();
-            whichMesh+=speed;
-            cout<<whichMesh<<" size of meshes "<<meshes.size()<<endl;
-            if(whichMesh>meshes.size() -1 || whichMesh<0){
-                speed*=-1;
-                whichMesh+=speed;
+         //   cout << "STATE_DISPLAY_RESULTS...\n" << endl;
             
+            if (_frame_cnt > 2)
+            {
+                _image_shown = true;
+                _frame_cnt=0;
             }
             
+            _frame_cnt++;
+            
+            if (_show_image)
+            {  
+         //       cout << "_show_image...\n" << endl;
+                
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
+            }
+            
+            // display results of the synthesis
+            _RUN_DONE = true;
             break;
+
+
         }
             
             
@@ -231,27 +421,9 @@ void StrobeAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void StrobeAnalysis::save_cb(Timer& timer)
 {
-    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
-    saveimage(file_name);
-    
     _save_cnt++;    
     
-    cout << "_save_cnt" << _save_cnt << endl;
-    
-    cout << "_save_cnt_max" << _save_cnt_max << endl;
-    
-    //TODO:  something fucked here with my calc of _save_cnt_max - new structure should fix it?   
-    //if(_save_cnt >= _save_cnt_max-10) {
-    //    _RUN_DONE = true;
-    //}
+    string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
+    saveImageAnalysis(file_name);
 }
-
-void StrobeAnalysis::display_results_cb(Timer& timer){
-    _results_cnt++;
-    if (_results_cnt>_results_cnt_max) {
-        _RUN_DONE=true;
-    }
-}
-
-

src/StrobeAnalysis.h

@@ -9,6 +9,8 @@
 
 #include "Poco/Timer.h"
 
+#include "ofxOpenCv.h"
+
 
 class StrobeAnalysis : public AbstractAnalysis
 {
@@ -21,21 +23,49 @@ public:
     void setup(int camWidth, int camHeight);
     void acquire();
     void synthesise();   
-    void display_results();
+    void displayresults();
+
     void draw();
     
     void save_cb(Poco::Timer& timer);
-    void display_results_cb(Poco::Timer& timer);    
     
 protected:
     
     bool    _RUN_DONE;
-    int     _strobe_cnt, _run_cnt, _strobe_cnt_max;
-    int     _save_cnt;
-    
-    int     _frame_cnt, _frame_cnt_max, _save_cnt_max ;
-    float   _results_cnt, _results_cnt_max;
+    int     _strobe_cnt, _strobe_cnt_max;
     
     int     _strobe_interval;
     bool    _strobe_on;
+    
+    int     _run_cnt, _save_cnt,_synth_save_cnt, _anim_cnt;
+    float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
+    
+    bool _show_image, _image_shown;
+    ofImage         image1;
+    ofImage         image2; 
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
+    
+    ofxCvColorImage         cvColorImage1;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;    
+
 };

src/rficv/rfiCvContourFinder.cpp

@@ -0,0 +1,211 @@
+
+#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

@@ -0,0 +1,73 @@
+/*
+* 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