unloading images

still have problem with image.allocation not letting go of memory
properly... and image.load(image.jpg);

README

@@ -1,10 +1,10 @@
 WARNING: WORK IN PROGRESS...
 
-configuring OpenFrameworks
------------------
+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: {ofxDirList, ofxControlPanel, ofxXmlSettings};  
+(2) Install depedencies: {ofxXmlSettings, ofxOpenCV, ofxFileHelper};  
 (3) Press Play!

config.refindx

@@ -0,0 +1,45 @@
+<!-- THIS FILE NEEDS TO GO IN THE APPLICATION /data/ folder -->
+
+<config>
+	<camera>
+		<id>1</id>
+		<width>640</width>
+		<height>480</height>
+	</camera>
+	<display>
+		<fps>30</fps>
+    </display>
+	<locale>
+		<name>SWANSEA</name>
+	</locale>
+
+    <analysis_NUM_RUN>
+        <NUM_RUN_shadowscapes>          3      </NUM_RUN_shadowscapes>
+        <NUM_RUN_relaxrate>             3      </NUM_RUN_relaxrate>
+        <NUM_RUN_iresponse>             3      </NUM_RUN_iresponse>
+        <NUM_RUN_shapefromshading>      3      </NUM_RUN_shapefromshading>
+        <NUM_RUN_strobe>                5      </NUM_RUN_strobe>
+        <NUM_RUN_camnoise>              5      </NUM_RUN_camnoise>
+        <NUM_RUN_colorsingle>           5      </NUM_RUN_colorsingle>
+        <NUM_RUN_colormulti>            5      </NUM_RUN_colormulti>
+        <NUM_RUN_diffnoise>             3      </NUM_RUN_diffnoise>
+    </analysis_NUM_RUN>
+
+    <analysis_time>
+        <acquiretime_shadowscapes>      30      </acquiretime_shadowscapes>
+        <acquiretime_relaxrate>         30      </acquiretime_relaxrate>
+        <acquiretime_iresponse>         30      </acquiretime_iresponse>
+        <acquiretime_shapefromshading>  30      </acquiretime_shapefromshading>
+        <acquiretime_strobe>            30      </acquiretime_strobe>
+        <acquiretime_camnoise>          30      </acquiretime_camnoise>
+        <acquiretime_colorsingle>       40      </acquiretime_colorsingle>
+        <acquiretime_colormulti>        40      </acquiretime_colormulti>
+        <acquiretime_diffnoise>         30      </acquiretime_diffnoise>
+    </analysis_time>
+    
+    <relaxrate>
+        <treshold>51</treshold>
+        <maxblobs>25</maxblobs>
+    </relaxrate>
+    
+</config>

example/RefractiveIndex.cpp

@@ -15,7 +15,7 @@
 
 #include "ofxXmlSettings.h"
 
-#define CAMERA_ID           1
+#define CAMERA_ID           0
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
@@ -36,7 +36,7 @@ bool             RefractiveIndex::_vid_stream_open;
 bool             RefractiveIndex::_vid_toggle_on;
 string           RefractiveIndex::_location;
 
-ofxXmlSettings   XML;
+ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
@@ -52,6 +52,8 @@ void RefractiveIndex::setup()
         
     // <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);
     
@@ -97,9 +99,10 @@ void RefractiveIndex::setup()
     _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 ShapeFromShadingAnalysis());
@@ -112,11 +115,11 @@ void RefractiveIndex::setup()
     
     _analysisVector.push_back(new ColorMultiAnalysis());
     
-    _analysisVector.push_back(new DiffNoiseAnalysis());
+    _analysisVector.push_back(new DiffNoiseAnalysis());	
+    
 
     //_currentAnalysisIndx = 0;
     //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
-    
     //_state = ISTATE_START;
     
     _currentAnalysis = NULL;
@@ -190,22 +193,11 @@ void RefractiveIndex::update()
 
 void RefractiveIndex::draw()
 {
-    // refractive mauve
+    // refractive mauve - this doesn't work... looks weird in various places.
     //ofBackground(113, 110, 136);
     
     // black
     ofBackground(0, 0, 0);
-    
-    //TODO:  Needs to return to a black screen - not to exit... 
-    
-    // i.e.: operational sequence
-    //    1) starts in a black screen
-    //    2) we 'start' with keypress "s" the entire set of analyses
-    //    3) at any point we need to be able to restart / stop-return-to-black / trigger each analysis individually
-    //    4) should end in black screen as well
-    //    5) final kill button
-    
-    //ofRect(0,0,ofGetWidth(), ofGetHeight());
            
     if(_currentAnalysis)
         _currentAnalysis->draw();
@@ -215,8 +207,9 @@ void RefractiveIndex::setup_camera()
 {
     stop_camera();
     
+    // THIS IS LOADED IN FROM THE XML FILE SETTINGS 
     _vidGrabber.setDeviceID(_vid_id);
-     _vidGrabber.listDevices();
+    _vidGrabber.listDevices();
     
     if(!_vidGrabber.initGrabber(_vid_w, _vid_h)) {
         ofLog(OF_LOG_ERROR) << "RefractiveIndex::setup_camera - could not initialise grabber";
@@ -357,10 +350,53 @@ void RefractiveIndex::keyPressed  (int key)
             _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

@@ -9,6 +9,7 @@
 #include "AnalysisAdaptor.h"
 
 #include "ofxOpenCv.h"
+#include "ofxXmlSettings.h"
 
 class RefractiveIndex : public ofBaseApp
 {
@@ -61,5 +62,6 @@ public:
     
     // this should be in xml
     static string           _location;
+    static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
     
 };

src/AbstractAnalysis.cpp

@@ -9,9 +9,15 @@ void AbstractAnalysis::do_synthesize() {
     
     for(int i = 0; i < NUM_RUN; i++) {
         
-        cout << "i NUM_RUN" << i << endl;
+        cout << "NUM_RUN: " << i << endl;
                 
-        _saved_filenames_analysis.clear();    
+        _saved_filenames_analysis.clear();  
+        _saved_filenames_synthesis.clear();
+        
+        if(_state == STATE_STOP) goto exit;
+        _state = STATE_ALLOCATE;
+        allocate();
+        if(_state == STATE_STOP) goto exit;
         _state = STATE_ACQUIRING;
         acquire();
         if(_state == STATE_STOP) goto exit;
@@ -20,13 +26,16 @@ void AbstractAnalysis::do_synthesize() {
         if(_state == STATE_STOP) goto exit;
         _state = STATE_DISPLAY_RESULTS;
         displayresults();
+        _state = STATE_CLEANUP;
+        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
     
@@ -57,21 +66,125 @@ void AbstractAnalysis::create_dir()
     //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);
+        
+        
     }
     
     _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 //////////////////////////////////////////////////  
+    
+    
+    //////////////////////////////ALLOCATE IMAGES //////////////////////////////////////////////////  
+    
+    myColorImage1.clear();
+    myColorImage1.setUseTexture(false);
+    myColorImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
+
+    myColorImage2.clear();
+    myColorImage2.setUseTexture(false);
+    myColorImage2.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
+    
+    
+    myGrayImage1.clear();
+    myGrayImage1.setUseTexture(false);
+    myGrayImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_GRAYSCALE);
+    
+    //////////////////////////////END ALLOCATE IMAGES //////////////////////////////////////////////////  
+
+}
+
+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);
     
-    //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////    
 }
 

src/AbstractAnalysis.h

@@ -7,15 +7,19 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
+#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
 #define SYNTHESIS_PATH "synthesis/"
 
+#define STATE_ALLOCATE          0x0010
+#define STATE_CLEANUP           0x0001
 #define STATE_ACQUIRING         0x1111
 #define STATE_SYNTHESISING      0x2222
 #define STATE_DISPLAY_RESULTS   0x3333
 #define STATE_STOP              0xDEADBEEF
+#define STATE_DEF               0x0000
 
 class AbstractAnalysis {
     
@@ -34,7 +38,10 @@ public:
         
 protected:
     
-    virtual void create_dir();
+    virtual void create_dir_allocate_images();
+    
+    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;   
@@ -44,6 +51,13 @@ protected:
     
     // display the results from disk
     virtual void displayresults() = 0;   
+
+    // allocate all images
+    virtual void allocate() {;}   
+    
+    // deallocate all images
+    virtual void cleanup() {;}   
+    
         
 public:
     string  _name;    
@@ -59,6 +73,10 @@ protected:
     
     int             _state;
     
+    ofImage         myColorImage1;
+    ofImage         myColorImage2;
+    ofImage         myGrayImage1;
+    
     //int             _run_cnt;
     
     float           DELTA_T_SAVE;

src/CamNoiseAnalysis.cpp

@@ -10,53 +10,88 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
+    cout << "NUM_RUN CamNoiseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
+
+    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
 
-    NUM_RUN = 5;
-    
-    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;
     _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();
+
+    //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);  
+    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);
+
 }
 
 
@@ -69,7 +104,7 @@ void CamNoiseAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
 
     // RUN ROUTINE
     // for(int i = 0; i < NUM_RUN; i++) {
@@ -78,7 +113,7 @@ void CamNoiseAnalysis::acquire()
 
     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);
 
@@ -89,63 +124,83 @@ void CamNoiseAnalysis::acquire()
 }
 
 void CamNoiseAnalysis::synthesise()
-{   
+{
     //cout << "CamNoiseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
-    
+
     for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
-        
+
         //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;
-        } 
-        
+        }
+
         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);
-            
-            cvGrayImage1 = cvColorImage1;
-            //cvGrayImage2 = cvColorImage2;
-            
+            //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);
-            //cvGrayDiff1.erode();
-            //cvGrayDiff1.contrastStretch();
-            //cvGrayDiff1.blur(5);
-            //cvGrayDiff1.dilate();
-            //cvGrayDiff1.contrastStretch();
-            
-            cvGrayImage1.threshold(255.0*i/_saved_filenames_analysis.size());  //random threshold for the moment
-            cvGrayImage1.blur(10);   
-            cvGrayImage1.contrastStretch();
-            cvGrayImage1.blur(10);   
-            
+//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";
-            
-            //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
-            
-            ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            //ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+
+
+            //<---- 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(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);
@@ -154,21 +209,21 @@ void CamNoiseAnalysis::synthesise()
 void CamNoiseAnalysis::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;
@@ -188,30 +243,30 @@ void CamNoiseAnalysis::draw()
             /// *** TODO  *** ///
             // still need to deal with latency frames here - i.e.: there are frames
             /// *** TODO  *** ///
-              
+
             if (_frame_cnt < _frame_cnt_max)
             {
-                
+
                 ofEnableAlphaBlending();
                 ofColor aColour;
-                
+
                 int _fade_in_frames = _frame_cnt_max/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;    
+                    //cout <<  "FADE IN STROBE TIME " << endl;
                 }
                 */
                 //if (_frame_cnt >= _fade_in_frames && _frame_cnt < (_frame_cnt_max)){
-                    
-        
+
+
                     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
@@ -219,11 +274,11 @@ void CamNoiseAnalysis::draw()
                             //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) {
@@ -231,92 +286,92 @@ void CamNoiseAnalysis::draw()
                         ofSetColor(aColour);
                         ofRect(0, 0, ofGetWidth(), ofGetHeight());
                         // cout <<  "FADE OUT STROBE TIME " << endl;
-                }         
+                }
                 */
                 ofDisableAlphaBlending();
-                
-    
+
+
             } else {
                // _state = STATE_SYNTHESISING;
                 _RUN_DONE = true;
             }
-            
+
             _frame_cnt++;
             break;
-       
+
         }
-            
+
         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;
@@ -325,46 +380,46 @@ void CamNoiseAnalysis::draw()
             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_GRAYSCALE);
+                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;
     }
-    
+
 
 }
 
@@ -373,20 +428,7 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
 
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "CamNoiseAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 
+    saveImageAnalysis(file_name);
 }

src/CamNoiseAnalysis.h

@@ -60,4 +60,8 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 };

src/ColorMultiAnalysis.cpp

@@ -9,20 +9,27 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorMultiAnalysis::setup(int camWidth, int 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;
     
-    NUM_RUN = 5;
-    
-    int acq_run_time = 35;  
+    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();
+    //create_dir_allocate_images();
     
     _frame_cnt = 0;
     _run_cnt = 0;
@@ -32,12 +39,15 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
-    //for an ofxOpenCv.h image i would like to use..."
-    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
-   
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -47,9 +57,28 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -57,6 +86,8 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -69,7 +100,7 @@ void ColorMultiAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -117,17 +148,6 @@ void ColorMultiAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            //cvGrayImage1 = cvColorImage1;
-            //cvGrayImage2 = cvColorImage2;
-            
-            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-            //cvGrayDiff1.erode();
-            //cvGrayDiff1.contrastStretch();
-            //cvGrayDiff1.blur(5);
-            //cvGrayDiff1.dilate();
-            //cvGrayDiff1.contrastStretch();
-            
-            cvColorImage1.contrastStretch();
             cvColorImage1.blur(5);
             cvColorImage1.erode();
             cvColorImage1.erode();
@@ -143,10 +163,25 @@ void ColorMultiAnalysis::synthesise()
             
             file_name = ofToString(_synth_save_cnt, 2)+"_ColorMultiAnalysis_"+ofToString(_run_cnt,2)+".jpg";
             
-            //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
             
-            ofSaveImage(cvColorImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+            //<---- 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++;
             
             // }
@@ -351,7 +386,6 @@ void ColorMultiAnalysis::draw()
                 
                 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();
@@ -374,25 +408,9 @@ void ColorMultiAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
-  
     _save_cnt++;
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ColorMultiAnalysis::saving...\n";
-    
+            
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
 
+    saveImageAnalysis(file_name);    
 }

src/ColorMultiAnalysis.h

@@ -54,5 +54,9 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 
 };

src/ColorSingleAnalysis.cpp

@@ -10,20 +10,27 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
+    cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
-    NUM_RUN = 5;
-    
-    int acq_run_time = 25;   // 20 seconds of acquiring per run
+    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();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -42,6 +49,12 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -51,9 +64,28 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -61,6 +93,9 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
 }
 
 
@@ -74,7 +109,7 @@ void ColorSingleAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -121,17 +156,6 @@ void ColorSingleAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                //cvGrayImage1 = cvColorImage1;
-                //cvGrayImage2 = cvColorImage2;
-                
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                //cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
-            
-                cvColorImage1.contrastStretch();
                 cvColorImage1.blur(5);
                 cvColorImage1.erode();
                 cvColorImage1.erode();
@@ -147,12 +171,28 @@ void ColorSingleAnalysis::synthesise()
                 
                 file_name = ofToString(_synth_save_cnt, 2)+"_ColorSingleAnalysis_"+ofToString(_run_cnt,2)+".jpg";
                 
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
                 
-                ofSaveImage(cvColorImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                //<---- 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++;
-                
+            
            // }
         }
     }
@@ -364,7 +404,6 @@ void ColorSingleAnalysis::draw()
                 
                 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();
@@ -388,22 +427,7 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ColorSingleAnalysis::saving...\n";
-    
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
-
+    saveImageAnalysis(file_name);
 }

src/ColorSingleAnalysis.h

@@ -61,5 +61,9 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 
 };

src/DiffNoiseAnalysis.cpp

@@ -10,20 +10,27 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-
-    NUM_RUN = 5;
+    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 = 20;   // 20 seconds of acquiring per run
+    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();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -36,8 +43,11 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    //for an ofxOpenCv.h image i would like to use..."
-    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
+    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
@@ -48,9 +58,28 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -58,8 +87,9 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
-
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
 }
 
 
@@ -71,7 +101,7 @@ void DiffNoiseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -118,34 +148,39 @@ void DiffNoiseAnalysis::synthesise()
             
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
-            
-            //cvGrayImage1 = cvColorImage1;
-            //cvGrayImage2 = cvColorImage2;
-            
-            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-            //cvGrayDiff1.erode();
-            //cvGrayDiff1.contrastStretch();
-            //cvGrayDiff1.blur(5);
-            //cvGrayDiff1.dilate();
-            //cvGrayDiff1.contrastStretch();
-            
-            cvColorImage1.contrastStretch();
+        
             cvColorImage1.invert();
             cvColorImage1.blur(5);
             cvColorImage1.erode();
+            cvColorImage1.erode();
             cvColorImage1.blur(5);
             cvColorImage1.erode();
-            cvColorImage1.contrastStretch();
+            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";
             
-            //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
             
-            ofSaveImage(cvColorImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+            //<---- 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, 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++;
             
             // }
@@ -394,24 +429,8 @@ void DiffNoiseAnalysis::draw()
 void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "DiffNoiseAnalysis::saving...\n";
-    
+            
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-    
-    _save_cnt++;
-
+    saveImageAnalysis(file_name);
 }

src/DiffNoiseAnalysis.h

@@ -59,4 +59,8 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 };

src/IResponseAnalysis.cpp

@@ -10,19 +10,28 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
+
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
+    cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
-    NUM_RUN = 5;
-    
-    int acq_run_time = 20;   // 20 seconds of acquiring per run
+    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;
+
+
+    //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();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -34,6 +43,12 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -43,9 +58,28 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    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);
@@ -54,6 +88,7 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     
 }
 
@@ -67,7 +102,7 @@ void IResponseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
 
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -114,8 +149,8 @@ void IResponseAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.erode();
@@ -129,12 +164,31 @@ void IResponseAnalysis::synthesise()
                 
                 file_name = ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                                
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
                 
-                ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                //<---- 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++;
                 
+        
+
             }
         }
     }
@@ -324,7 +378,7 @@ void IResponseAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
             
                 ofDisableAlphaBlending();
@@ -347,19 +401,7 @@ void IResponseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "IResponseAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+        
+    saveImageAnalysis(file_name);
 }

src/IResponseAnalysis.h

@@ -58,4 +58,8 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 };

src/RelaxRateAnalysis.cpp

@@ -10,19 +10,36 @@ 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)
 {
-    NUM_RUN = 5;
+    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 = 20;   // 20 seconds of acquiring per run
+    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();
+    //create_dir_allocate_images();
     
     _run_cnt = 0;
     _level = 0;
@@ -37,26 +54,19 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    //  images use for drawing the synthesized files to the screen ///
+    image1.clear();
     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
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
     
-    //  images used for re-loading and saving out the synthesized files ///
-    image3.setUseTexture(false);  
-    image4.setUseTexture(false);
-    image5.setUseTexture(false);
-    
-    //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();
+    cvGrayDiff1.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);
-    
+        
 }
 
 
@@ -69,7 +79,7 @@ void RelaxRateAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
 
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -92,47 +102,28 @@ void RelaxRateAnalysis::synthesise()
     //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;
-        
+    cvContourFinderVect.clear();    
+    
+    
+    for(float i=1;i<_saved_filenames_analysis.size();i++){
+                
         if(_state == STATE_STOP) return;
-        
-        if(!image1.loadImage(_saved_filenames_analysis[i])){
-            //couldn't load image
-            cout << "didn't load image" << endl;
-        } 
-        
+                
         if(image1.loadImage(_saved_filenames_analysis[i])){
-            //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);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.erode();
-                cvGrayDiff1.contrastStretch();
-                cvGrayDiff1.blur(5);
-                
-                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
-                string file_name;
-                
-                file_name = ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".jpg";
-                
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
-                
-                ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                _synth_save_cnt++;
-            }
+            ///////////////////////// 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);
+            
         }
     }
     
@@ -144,31 +135,40 @@ void RelaxRateAnalysis::synthesise()
 
 void RelaxRateAnalysis::displayresults()
 {
-    
-    for(float i=1;i<_saved_filenames_synthesis.size();i++){
         
-        if(_state == STATE_STOP) return;
+    //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;
         }
         
-        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-            //couldn't load image
-            // cout << "didn't load image" << endl;
-        } 
+        cvContourFinderVectDisplay.push_back(cvContourFinderVect[i]);    
+        _show_image = true;
+        _image_shown = false;
         
-        if(image3.loadImage(_saved_filenames_synthesis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
-            //cout << "_show_image = true;" << endl;
-            _show_image = true;
-            _image_shown = false;
-        }
-    }
-
+    }     
+    
+    clearcfindervectdisplay();
+    clearcfindervect();
+    
+        
+    //cvContourFinderVectDisplay.clear();
+    //cvContourFinderVect.clear();
+    
     
 }
 
@@ -180,10 +180,8 @@ 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)
             {
                 
@@ -213,6 +211,7 @@ void RelaxRateAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
+            
             // display animation of something while the synthesis in on-going...
             
             //cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
@@ -265,7 +264,7 @@ void RelaxRateAnalysis::draw()
                     }
                 }
                 
-                cout << "_anim_cnt = " << _anim_cnt << endl;
+                //cout << "_anim_cnt = " << _anim_cnt << endl;
                 
                 if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
 
@@ -313,15 +312,10 @@ void RelaxRateAnalysis::draw()
             
             if (_show_image)
             {  
-                //cout << "_show_image...\n" << endl;
-                
-                ofEnableAlphaBlending();
-                
-                ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
-                image2.draw(0,0, ofGetWidth(), ofGetHeight());
-                
-                ofDisableAlphaBlending();
+                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
+                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
+                }
+
             }
             
             // display results of the synthesis
@@ -341,19 +335,34 @@ void RelaxRateAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    //cout << "RelaxRateAnalysis::saving...\n";
-    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    saveImageAnalysis(file_name);
+    
     
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }
+
+void RelaxRateAnalysis::cleanup()
+{
+}
+
+
+void RelaxRateAnalysis::clearcfindervect()
+{
+    for(int i = 0; i < cvContourFinderVect.size(); i++) {
+        rfiCvContourFinder* f = cvContourFinderVect[i];
+
+        // maybe it's erase here?  http://forum.openframeworks.cc/index.php/topic,3016.0.html
+        // cvContourFinderVect.erase(i);
+        
+        delete f;        
+    }
+    cvContourFinderVect.clear();
+    
+}
+
+void RelaxRateAnalysis::clearcfindervectdisplay()
+{
+    cvContourFinderVectDisplay.clear();
+}
+

src/RelaxRateAnalysis.h

@@ -5,8 +5,12 @@
 
 #include "Poco/Timer.h"
 
+#include "rfiCvContourFinder.h"
+
 #include "ofxOpenCv.h"
 
+
+
 class RelaxRateAnalysis : public AbstractAnalysis
 {
 public:
@@ -19,6 +23,7 @@ public:
     void acquire();
     void synthesise(); 
     void displayresults();
+    void cleanup();
 
     void draw();
     
@@ -26,34 +31,24 @@ public:
     
 protected:
     
+    void clearcfindervect();
+    void clearcfindervectdisplay();
+    
     bool    _RUN_DONE;
     float     _flip, _level;
     int     _run_cnt, _save_cnt, _synth_save_cnt, _anim_cnt;
     float   c, _frame_cnt, _frame_cnt_max, _anim_cnt_max;
     
+    int     _treshold;
+    int     _maxblobs;
+    
     bool _show_image, _image_shown;
-    ofImage         image1;
-    ofImage         image2; 
-    ofImage         image3;
-    ofImage         image4;
-    ofImage         image5; 
-    ofImage         image6; 
-    
-    ofxCvColorImage         cvColorImage1;
-    ofxCvColorImage         cvColorImage2;
-    ofxCvColorImage         cvColorImage3;
-    ofxCvColorImage         cvColorImage4;
-    ofxCvColorImage         cvColorImage5;
-    ofxCvColorImage         cvColorImage6;
     
+    ofImage                 image1;    
+    ofxCvColorImage         cvColorImage1;    
     ofxCvGrayscaleImage 	cvGrayDiff1;
-    ofxCvGrayscaleImage 	cvGrayDiff2;
     
-    ofxCvGrayscaleImage 	cvGrayImage1;
-    ofxCvGrayscaleImage 	cvGrayImage2;
-    ofxCvGrayscaleImage 	cvGrayImage3;
-    ofxCvGrayscaleImage 	cvGrayImage4;
-    
-    ofxCvContourFinder      cvContourFinder1;
+    vector<rfiCvContourFinder*>      cvContourFinderVect;
+    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
 
 };

src/ShadowScapesAnalysis.cpp

@@ -5,6 +5,7 @@
 #include "Poco/Thread.h"
 #include "RefractiveIndex.h"
 
+//#include "ofxXmlSettings.h"
 #include "ofxOpenCv.h"
 
 using Poco::Timer;
@@ -13,12 +14,18 @@ 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)
 {
-    NUM_RUN = 5;
+    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 = 15;   // 10 seconds of acquiring per run
+    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();
@@ -32,9 +39,7 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 
     DELTA_T_SAVE = 3*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 100 files
                                             // or 5 times per second = every 200 ms
-        
-    //create_dir();  // this makes both synth and analysis folder structures
-
+    
     _scanLineWidth = 100.0;
     _run_cnt = 0;
     _save_cnt = 0;
@@ -46,6 +51,13 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    /*
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+        
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -55,9 +67,28 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+        
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    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);
@@ -65,6 +96,10 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+     */
+    
 }
 
 void ShadowScapesAnalysis::acquire()
@@ -78,18 +113,14 @@ void ShadowScapesAnalysis::acquire()
     _line = 0;
     _RUN_DONE = false;
 
-    create_dir();
-    
-    //cout << "RUN NUM = " << i;
+    create_dir_allocate_images();
    
     save_timer.start(save_callback);
       
-        while(!_RUN_DONE && _state != STATE_STOP)
-            Thread::sleep(3);
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);
     
     save_timer.stop();
-    
-    //}
 
 }
 
@@ -97,7 +128,7 @@ void ShadowScapesAnalysis::synthesise()
 {
     //cout << "ShadowScapesAnalysis::saving synthesis...\n";
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
+    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
     
       //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
         
@@ -119,15 +150,17 @@ void ShadowScapesAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
+                //cvGrayImage1 = cvColorImage1;
+                //cvGrayImage2 = cvColorImage2;
                 
+                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;
@@ -144,12 +177,29 @@ void ShadowScapesAnalysis::synthesise()
                     file_name = ofToString(_synth_save_cnt, 2)+"_D_ShadowScapesSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 }
                 
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
                 
-                ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                //<---- 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++;
-                
             }
         }
     }
@@ -176,59 +226,116 @@ void ShadowScapesAnalysis::displayresults()
         if(!image3.loadImage(_saved_filenames_synthesis[i])){
             //couldn't load image
             cout << "didn't load image" << endl;
-        } 
-        
+        } else {
+            _show_image = true;
+            _image_shown = false;
+            
+        }
+/*        
         if(image3.loadImage(_saved_filenames_synthesis[i])){
-            image3.loadImage(_saved_filenames_synthesis[i]);
+            //image3.loadImage(_saved_filenames_synthesis[i]);
             //cout << "_show_image = true;" << endl;
             _show_image = true;
             _image_shown = false;
         }
+ */
     }
-    
-    
-    // THE OLD SHIT /// 
-/*
-    for(float i=1;i<_saved_filenames_synthesis.size()-1;i++){
-        
-       // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
-        
-        if(_state == STATE_STOP) return;
-        
-        while(!_image_shown){
-            Thread::sleep(2);
-            //cout << "!_image_shown" << endl;
-        }
-        
-        if(!image1.loadImage(_saved_filenames_synthesis[i])){
-            //couldn't load image
-            cout << "didn't load image" << endl;
-        } 
-        
-            
-        if(image1.loadImage(_saved_filenames_analysis[i])){
-            
-            image1.loadImage(_saved_filenames_analysis[i]);
-            cout << "loaded filenames[i] -  " << _saved_filenames_analysis[i] << endl;
-        
-            image2.setFromPixels(image1.getPixels(),image1.width,image1.height, OF_IMAGE_COLOR);
-          
-            //cout << "_show_image = true;" << endl;
-            _show_image = true;
-            _image_shown = false;
 
-        }
-    }
-*/
-    
 }
 
+void ShadowScapesAnalysis::allocate()
+{
+    _RUN_DONE = false;
+    
+    image1.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
+    image1.setUseTexture(false);         
+    image3.setUseTexture(false);  
+    image4.setUseTexture(false);
+    image5.setUseTexture(false);
+    
+    image1.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);
+    
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);    
+}
+
+void ShadowScapesAnalysis::cleanup()
+{
+    _RUN_DONE = false;
+    
+    image1.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();        
+    
+    while(!_RUN_DONE && _state != STATE_STOP)
+        Thread::sleep(3);    
+}
+
+
 
 // the animation draw - and the output draw
 void ShadowScapesAnalysis::draw()
 {
     
     switch (_state) {
+        case STATE_ALLOCATE:
+        {
+            image2.clear();
+            image2.setUseTexture(true);
+            image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+            
+            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);   
+            
+            _state = STATE_DEF;
+            
+            _RUN_DONE = true;
+            break;
+        }
+        case STATE_CLEANUP:
+        {
+            image2.clear();
+            
+            cvColorImage1.clear();
+            cvGrayImage1.clear();
+            cvGrayDiff1.clear();
+            
+            cvColorImage2.clear();
+            cvGrayImage2.clear();
+            cvGrayDiff2.clear();
+            
+            _state = STATE_DEF;
+            
+            _RUN_DONE = true;
+            break;
+        }
+            
         case STATE_ACQUIRING:
         {
             _line += _step;
@@ -368,9 +475,9 @@ void ShadowScapesAnalysis::draw()
                 
                 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;
+                    //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;
+                    //cout << "fade down = " << fade << endl;
                    
                     for (int i=0; i <= 15; i++){
                         
@@ -399,7 +506,6 @@ void ShadowScapesAnalysis::draw()
         case STATE_DISPLAY_RESULTS:
         {
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
-
             
             if (_frame_cnt > 2)
             {
@@ -416,43 +522,20 @@ void ShadowScapesAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                     ofSetColor(255, 255, 255);
-                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                     image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
                 
-                //cvGrayDiff1.draw(0,0, ofGetWidth(), ofGetHeight());
-                
-                
-                // THE OLD SHIT
-                /*
-                ofEnableAlphaBlending();
-                
-                ofSetColor(255, 255, 255, 200);
-                image3.setFromPixels(image1.getPixels(),image1.width,image1.height, OF_IMAGE_COLOR);
-                image4.setFromPixels(image2.getPixels(),image2.width,image2.height, OF_IMAGE_COLOR);
-                                
-                cvColorImage1.setFromPixels(image3.getPixels(), image3.width, image3.height);
-                cvColorImage2.setFromPixels(image4.getPixels(), image4.width, image4.height);
-                
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
-                
-                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                cvGrayDiff1.contrastStretch();
-                cvGrayDiff1.dilate();
-                
-                cvGrayDiff1.draw(0,0, ofGetWidth(), ofGetHeight());
-                
-                ofDisableAlphaBlending();            
-                */     
-                
-                //image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
             }
             
             // display results of the synthesis
             _RUN_DONE = true;
+            
+            // clear allocated memory...? 
+            
             break;
         }
             
@@ -467,18 +550,7 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
 {
     
     _save_cnt++;
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ShadowScapesAnalysis::saving analysis...\n";
-    
+        
     string file_name;
     
     if(_dir == H) {
@@ -492,9 +564,7 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     if(_dir == D) {
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-    
+        
+    saveImageAnalysis(file_name);
+        
 }

src/ShadowScapesAnalysis.h

@@ -25,6 +25,9 @@ public:
     void acquire();
     void synthesise();   
     void displayresults();
+        
+    void allocate();   
+    void cleanup();    
 
     void draw();
     
@@ -65,5 +68,8 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;    
 
 };

src/ShapeFromShadingAnalysis.cpp

@@ -10,18 +10,28 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    20
+
 void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
-{    
-    NUM_RUN = 5;
+{       
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shapefromshading", NUMBER_RUNS);
+    cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
+    //NUM_RUN = 5;
     
-    int acq_run_time = 20;   // 20 seconds of acquiring per run
+    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();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -30,10 +40,15 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 5;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
     
-    
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -43,9 +58,28 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    cvConvertorImage.clear();    
+    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -53,6 +87,8 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -67,7 +103,7 @@ void ShapeFromShadingAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;    
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     _animation_cnt1 = 0;
     _animation_cnt2 = 0;
@@ -133,8 +169,8 @@ void ShapeFromShadingAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvGrayImage1 = cvColorImage1;
-                cvGrayImage2 = cvColorImage2;
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.erode();
@@ -148,10 +184,27 @@ void ShapeFromShadingAnalysis::synthesise()
                 
                 file_name = ofToString(_synth_save_cnt, 2)+"_ShapeFromShadingSynthesis_"+ofToString(_run_cnt,2)+".jpg";
                 
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
                 
-                ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                //<---- 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++;
                 
             }
@@ -514,7 +567,7 @@ void ShapeFromShadingAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -538,21 +591,8 @@ void ShapeFromShadingAnalysis::draw()
 void ShapeFromShadingAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
-        
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "ShapeFromShadingAnalysis::saving...\n";
-    
+            
     string file_name = ofToString(_save_cnt,2)+"_"+ quad +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
+    saveImageAnalysis(file_name);
 }

src/ShapeFromShadingAnalysis.h

@@ -78,4 +78,8 @@ protected:
     ofxCvGrayscaleImage 	cvGrayImage4;
     
     ofxCvContourFinder      cvContourFinder1;
+    
+    //this is the temporary container to allow us to convert and save out greyscale images
+    ofxCvColorImage         cvConvertorImage;
+    
 };

src/StrobeAnalysis.cpp

@@ -10,22 +10,31 @@ using Poco::Timer;
 using Poco::TimerCallback;
 using Poco::Thread;
 
+#define NUMBER_RUNS     1
+#define ACQUIRE_TIME    30
+
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = 5;
+    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 = 25;   // 20 seconds of acquiring per run
+    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 = 1750;  //every 1 seconds, or every thirty frames 30 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.
     
-    //create_dir();
+    //create_dir_allocate_images();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     
@@ -35,6 +44,12 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
+    image1.clear();
+    image2.clear();
+    image3.clear();  
+    image4.clear();
+    image5.clear();
+    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -44,9 +59,28 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
+    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
+    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
+    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    // that we're getting in OSX/Windows and is maybe crashing Windows
+    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    cvColorImage1.clear();
+	cvGrayImage1.clear();
+    cvGrayDiff1.clear();
+    
+    cvColorImage2.clear();
+	cvGrayImage2.clear();
+    cvGrayDiff2.clear();
+    
+    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);
@@ -54,6 +88,8 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
+    
+    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
 }
 
@@ -67,7 +103,7 @@ void StrobeAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0;  _strobe_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir();
+    create_dir_allocate_images();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -108,40 +144,53 @@ void StrobeAnalysis::synthesise()
         
         if(image1.loadImage(_saved_filenames_analysis[i])){
     //        cout << "LOADED image1!!!" << endl;
-            //if(image5.loadImage(_saved_filenames_analysis[i+1])){
+            if(image5.loadImage(_saved_filenames_analysis[i+1])){
                 
                 ///////////////////////// PROCESS THE SAVED CAMERA IMAGES OF SHIT TO THE IMAGES //////////////////////////
                 
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
+            
+                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
-                cvGrayImage1 = cvColorImage1;
-                //cvGrayImage2 = cvColorImage2;
-                
-                //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-                //cvGrayDiff1.erode();
-                //cvGrayDiff1.contrastStretch();
-                //cvGrayDiff1.blur(5);
-                //cvGrayDiff1.dilate();
-                //cvGrayDiff1.contrastStretch();
-                
-                cvGrayImage1.contrastStretch();
-                cvGrayImage1.blur(10);   
-                cvGrayImage1.dilate();
+                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";
                 
-                //image4.setFromPixels(cvColorImage1.getPixelsRef(),image3.width, image3.height, OF_IMAGE_COLOR);
+        
+                //<---- 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);
                 
-                ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                //ofSaveImage(cvGrayDiff1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                
+                //<---- 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++;
                 
-            //}
+                
+            }
         }
     }
     
@@ -347,7 +396,7 @@ void StrobeAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -370,22 +419,9 @@ void StrobeAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void StrobeAnalysis::save_cb(Timer& timer)
 {
-    _save_cnt++;
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-    
-    //cout << "StrobeAnalysis::saving...\n";
+    _save_cnt++;    
     
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
-
+    saveImageAnalysis(file_name);
 }

src/StrobeAnalysis.h

@@ -64,5 +64,8 @@ protected:
     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