messing around trying to produce the windows error on osx

README

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

config.refindx

@@ -1,45 +0,0 @@
-<!-- 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           0
+#define CAMERA_ID           1
 #define CAMERA_ACQU_WIDTH   640
 #define CAMERA_ACQU_HEIGHT  480
 
@@ -102,7 +102,6 @@ void RefractiveIndex::setup()
     
     _analysisVector.push_back(new RelaxRateAnalysis());
     
-	
     _analysisVector.push_back(new IResponseAnalysis());
     
     _analysisVector.push_back(new ShapeFromShadingAnalysis());
@@ -117,7 +116,6 @@ void RefractiveIndex::setup()
     
     _analysisVector.push_back(new DiffNoiseAnalysis());
 
-
     //_currentAnalysisIndx = 0;
     //_currentAnalysis = _analysisVector.at(_currentAnalysisIndx++); 
     //_state = ISTATE_START;
@@ -396,7 +394,5 @@ void RefractiveIndex::keyPressed  (int key)
 
 void RefractiveIndex::exit()
 {
-    if(_currentAnalysis)
-        _analysisAdapator->stop();    
     stop_camera();
 }

src/AbstractAnalysis.cpp

@@ -9,7 +9,7 @@ void AbstractAnalysis::do_synthesize() {
     
     for(int i = 0; i < NUM_RUN; i++) {
         
-        cout << "NUM_RUN: " << i << endl;
+        cout << "i NUM_RUN" << i << endl;
                 
         _saved_filenames_analysis.clear();  
         _saved_filenames_synthesis.clear();    
@@ -22,15 +22,13 @@ void AbstractAnalysis::do_synthesize() {
         if(_state == STATE_STOP) goto exit;
         _state = STATE_DISPLAY_RESULTS;
         displayresults();
-        cleanup();
     }
     
     exit:    
-    cleanup();
     ofNotifyEvent(_synthesize_cb, _name);
 }
 
-void AbstractAnalysis::create_dir_allocate_images()
+void AbstractAnalysis::create_dir()
 {
     // HERE IS WHERE WE SETUP THE DIRECTORY FOR ALL THE SAVED IMAGES
     
@@ -94,92 +92,7 @@ void AbstractAnalysis::create_dir_allocate_images()
         fileHelperSynthesis.makeDirectory(SYNTHESIS_PATH+RefractiveIndex::_location+"/"+_name+"/"+replaceTime);
         
     }
+    
     //////////////////////////////END DIRECTORY CREATION //////////////////////////////////////////////////    
-    
-    
-    //////////////////////////////ALLOCATE IMAGES //////////////////////////////////////////////////  
-    
-    myColorImage1.clear();
-    myColorImage1.setUseTexture(false);
-    myColorImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
-
-    myColorImage2.clear();
-    myColorImage2.setUseTexture(false);
-    myColorImage2.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_COLOR);
-    
-    
-    myGrayImage1.clear();
-    myGrayImage1.setUseTexture(false);
-    myGrayImage1.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h, OF_IMAGE_GRAYSCALE);
-    
-    //////////////////////////////END ALLOCATE IMAGES //////////////////////////////////////////////////  
-
-}
-
-void AbstractAnalysis::saveImageAnalysis(string filename)
-{
-    
-    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
-    
-    if (RefractiveIndex::_vidGrabber.isFrameNew())
-    {
-        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
-    } else {
-        return;
-    }
-        
-#ifdef TARGET_OSX   
-    
-    ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+filename, OF_IMAGE_QUALITY_BEST);
-    
-#elif defined(TARGET_WIN32)    
-    
-    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-    unsigned char * somePixels;
-    ofPixels appPix = RefractiveIndex::_pixels;
-    somePixels = appPix.getPixels();
-    myColorImage1.setUseTexture(false);
-    myColorImage1.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
-    myColorImage1.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+filename);
-    myColorImage1.clear();
-    
-#endif
-    
-    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+filename);
-    
-}
-
-
-void AbstractAnalysis::saveImageSynthesis(string filename, ofxCvImage* newPixels, ofImageType newType)
-{
-    
-#ifdef TARGET_OSX   
-    
-
-    ofSaveImage(newPixels->getPixelsRef(), _whole_file_path_synthesis+"/"+filename, OF_IMAGE_QUALITY_BEST);
-    
-#elif defined(TARGET_WIN32)    
-    
-    if (newType == OF_IMAGE_COLOR){
-       myColorImage2.setUseTexture(false);
-       myColorImage2.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
-       myColorImage2.saveImage(_whole_file_path_synthesis+"/"+filename);
-    }
-
-    if (newType == OF_IMAGE_GRAYSCALE){
-        myGrayImage1.setUseTexture(false);
-        
-        // THIS IS HOW YOU HAVE TO SAVE OUT THE GREYSCALE IMAGES on WINDOWS FOR SOME REASON --> i.e.: as an OF_IMAGE_COLOR
-        // But they don't save properly - they're spatially translated and generally f'd up
-        myGrayImage1.setFromPixels(newPixels->getPixels(), newPixels->getWidth(), newPixels->getHeight(), OF_IMAGE_COLOR);
-        myGrayImage1.setImageType(OF_IMAGE_COLOR);
-        myGrayImage1.saveImage(_whole_file_path_synthesis+"/"+filename);
-        //myGrayImage1.clear();
-    }
-        
-#endif
-    
-    _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+filename);
-    
 }
 

src/AbstractAnalysis.h

@@ -7,7 +7,6 @@
 
 #include "ofMain.h"
 #include "ofEvents.h"
-#include "ofxOpenCv.h"
 #include <string>
 
 #define ANALYSIS_PATH "analysis/"
@@ -35,10 +34,7 @@ public:
         
 protected:
     
-    virtual void create_dir_allocate_images();
+    virtual void create_dir();
-    
-    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;   
@@ -49,10 +45,6 @@ protected:
     // display the results from disk
     virtual void displayresults() = 0;   
         
-    // display the results from disk
-    virtual void cleanup() {;}   
-    
-        
 public:
     string  _name;    
     
@@ -67,10 +59,6 @@ protected:
     
     int             _state;
     
-    ofImage         myColorImage1;
-    ofImage         myColorImage2;
-    ofImage         myGrayImage1;
-    
     //int             _run_cnt;
     
     float           DELTA_T_SAVE;

src/CamNoiseAnalysis.cpp

@@ -15,15 +15,15 @@ using Poco::Thread;
 
 void CamNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_camnoise", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", 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);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_camnoise", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME CamNoiseAnalysis " << acq_run_time << endl;
     
-
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 2*(10*acq_run_time/2);       // for 20 seconds, we want this to be around 200 files
@@ -40,17 +40,11 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
-    //create_dir_allocate_images();
+    //create_dir();
 
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();
-    image4.clear();
-    image5.clear();
-
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -60,28 +54,9 @@ void CamNoiseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage"
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-
-    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);
@@ -90,8 +65,6 @@ void CamNoiseAnalysis::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);
-
 }
 
 
@@ -104,7 +77,7 @@ void CamNoiseAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
 
     // RUN ROUTINE
     // for(int i = 0; i < NUM_RUN; i++) {
@@ -150,23 +123,15 @@ void CamNoiseAnalysis::synthesise()
             cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
             //cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-            cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+            cvGrayImage1 = cvColorImage1;
-            // cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+            //cvGrayImage2 = cvColorImage2;
-            //added by tom we weren't actually setting cvgrayimage1 anywhere
-           // cvGrayImage1.setFromPixels(cvColorImage1.getPixels(),cvColorImage1.width,cvColorImage1.height);
-            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
-//cvGrayImage1=cvColorImage1;
             
+            //cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
             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;
@@ -179,24 +144,18 @@ void CamNoiseAnalysis::synthesise()
            
             
             //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            //ofImage image;
+            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.setUseTexture(false);  
             
-            //image.setFromPixels(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
+            image.setFromPixels(cvGrayImage1.getPixels(), cvGrayImage1.width, cvGrayImage1.height, OF_IMAGE_GRAYSCALE);
-            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-            //_saved_filenames_synthesis.push_back(_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++;
             
-
             //}
         }
     }
@@ -404,7 +363,7 @@ void CamNoiseAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -428,7 +387,39 @@ void CamNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
 
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "CamNoiseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+
 }

src/CamNoiseAnalysis.h

@@ -60,8 +60,4 @@ 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

@@ -14,12 +14,13 @@ using Poco::Thread;
 
 void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colormulti", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN ColorMultiAnalysis " << NUM_RUN << endl;
+    
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colormulti", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_colormulti", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorMultiAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 35;  
@@ -29,7 +30,7 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _frame_cnt = 0;
     _run_cnt = 0;
@@ -39,15 +40,12 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 10;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
         
+    //for an ofxOpenCv.h image i would like to use..."
+    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
+   
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -57,28 +55,9 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -87,8 +66,6 @@ void ColorMultiAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 void ColorMultiAnalysis::acquire()
@@ -100,7 +77,7 @@ void ColorMultiAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -169,19 +146,17 @@ void ColorMultiAnalysis::synthesise()
             
             
             //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            //ofImage image;
+            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.setUseTexture(false);  
            
-            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+            image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            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> ///
+            _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-            saveImageSynthesis(file_name, &cvColorImage1, OF_IMAGE_COLOR);
             _synth_save_cnt++;
             
             // }
@@ -408,9 +383,42 @@ void ColorMultiAnalysis::draw()
 // this runs at save_cb timer rate = DELTA_T_SAVE
 void ColorMultiAnalysis::save_cb(Timer& timer)
 {
+  
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ColorMultiAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-    saveImageAnalysis(file_name);    
+
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+    
 }

src/ColorMultiAnalysis.h

@@ -55,8 +55,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //this is the temporary container to allow us to convert and save out greyscale images
-    ofxCvColorImage         cvConvertorImage;
-    
-
 };

src/ColorSingleAnalysis.cpp

@@ -15,12 +15,13 @@ using Poco::Thread;
 
 void ColorSingleAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_colorsingle", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN ColorSingleAnalysis " << NUM_RUN << endl;
+    
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_colorsingle", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_colorsingle", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ColorSingleAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
@@ -30,7 +31,7 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -49,12 +50,6 @@ 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
@@ -64,28 +59,9 @@ void ColorSingleAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -93,9 +69,6 @@ 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);
-    
 }
 
 
@@ -109,7 +82,7 @@ void ColorSingleAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -156,6 +129,16 @@ 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.blur(5);
                 cvColorImage1.erode();
                 cvColorImage1.erode();
@@ -177,20 +160,16 @@ void ColorSingleAnalysis::synthesise()
                 
                 
                 //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                //ofImage image;
+                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.setUseTexture(false);  
                 
-                //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
+                image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-                //_saved_filenames_synthesis.push_back(_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++;
                 
            // }
@@ -427,7 +406,40 @@ void ColorSingleAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ColorSingleAnalysis::saving...\n";
+    
     string file_name =ofToString(_save_cnt,2)+"_"+fileNameTag+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+        
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+
+
 }

src/ColorSingleAnalysis.h

@@ -62,8 +62,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //this is the temporary container to allow us to convert and save out greyscale images
-    ofxCvColorImage         cvConvertorImage;
-    
-
 };

src/DiffNoiseAnalysis.cpp

@@ -15,12 +15,13 @@ using Poco::Thread;
 
 void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_diffnoise", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN DiffNoiseAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_diffnoise", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:diffnoise_shadow", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME DiffNoiseAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
@@ -30,7 +31,7 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -43,11 +44,8 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
+    //for an ofxOpenCv.h image i would like to use..."
-    image2.clear();
+    //image3.allocate(RefractiveIndex::_vid_w, RefractiveIndex::_vid_h);
-    image3.clear();  
-    image4.clear();
-    image5.clear();
     
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
@@ -58,28 +56,9 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -87,9 +66,6 @@ void DiffNoiseAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
 }
 
 
@@ -101,7 +77,7 @@ void DiffNoiseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -168,19 +144,16 @@ void DiffNoiseAnalysis::synthesise()
             
             
             //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-            //ofImage image;
+            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.setUseTexture(false);  
             
-            //image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height, OF_IMAGE_COLOR);
+            image.setFromPixels(cvColorImage1.getPixels(), cvColorImage1.width, cvColorImage1.height,OF_IMAGE_COLOR);
-            //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+            image.saveImage(_whole_file_path_synthesis+"/"+file_name);
             
-            //_saved_filenames_synthesis.push_back(_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++;
             
             // }
@@ -430,7 +403,39 @@ void DiffNoiseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "DiffNoiseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
 
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+
 }

src/DiffNoiseAnalysis.h

@@ -59,8 +59,4 @@ 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

@@ -15,15 +15,15 @@ using Poco::Thread;
 
 void IResponseAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_iresponse", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN IResponseAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_iresponse", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis: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
@@ -31,7 +31,7 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -43,12 +43,6 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -58,28 +52,9 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    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);
@@ -88,7 +63,6 @@ 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);
     
 }
 
@@ -102,7 +76,7 @@ void IResponseAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
 
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -149,8 +123,8 @@ void IResponseAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                cvGrayImage2 = cvColorImage2;
                 
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.erode();
@@ -170,25 +144,19 @@ void IResponseAnalysis::synthesise()
                 
                 
                 //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                //ofImage image;
+                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.setUseTexture(false);  
-                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                
-                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                //_saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
                 
                 
-                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
-                
-                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
-                
                 _synth_save_cnt++;
                 
-        
-
             }
         }
     }
@@ -378,7 +346,7 @@ void IResponseAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
             
                 ofDisableAlphaBlending();
@@ -401,7 +369,38 @@ void IResponseAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "IResponseAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }

src/IResponseAnalysis.h

@@ -58,8 +58,4 @@ 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

@@ -12,26 +12,18 @@ using Poco::Thread;
 
 #define NUMBER_RUNS     1
 #define ACQUIRE_TIME    20
-#define TRESHOLD        80
-#define MAXBLOBS        15
 
 void RelaxRateAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_relaxrate", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN RelaxRateAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
  
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_relaxrate", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_relaxrate", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME RelaxRateAnalysis " << acq_run_time << endl;
     
-    _treshold = RefractiveIndex::XML.getValue("config:relaxrate:treshold", TRESHOLD);
-    cout << "TRESHOLD RelaxRateAnalysis " << _treshold << endl;
-    
-    _maxblobs = RefractiveIndex::XML.getValue("config:relaxrate:maxblobs", MAXBLOBS);
-    cout << "MAXBLOBS RelaxRateAnalysis " << _maxblobs << endl;
-
-    
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
@@ -39,7 +31,7 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     
     _run_cnt = 0;
     _level = 0;
@@ -54,19 +46,26 @@ void RelaxRateAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.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
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
+    image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
+    //  images used for re-loading and saving out the synthesized files ///
-    // that we're getting in OSX/Windows and is maybe crashing Windows
+    image3.setUseTexture(false);  
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
+    image4.setUseTexture(false);
-    cvColorImage1.clear();
+    image5.setUseTexture(false);
-    cvGrayDiff1.clear();
+    
+    //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
+    //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
     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);
+    
 }
 
 
@@ -79,7 +78,7 @@ void RelaxRateAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;
     _RUN_DONE = false;
 
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -102,28 +101,60 @@ void RelaxRateAnalysis::synthesise()
     //cout << "IResponseAnalysis::saving synthesis...\n";
     if(_state == STATE_STOP) return;
     
-    cvContourFinderVect.clear();    
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
         
+        //cout << "IResponseAnalysis::synthesis FOR LOOP...\n";
         
-    for(float i=1;i<_saved_filenames_analysis.size();i++){
+        //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);
-            cvColorImage1.convertToGrayscalePlanarImage(cvGrayDiff1, 1);
+                cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-            cvGrayDiff1.threshold(_treshold);
+                cvGrayImage1 = cvColorImage1;
+                cvGrayImage2 = cvColorImage2;
                 
-            rfiCvContourFinder* cf = new rfiCvContourFinder();
+                cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
+                cvGrayDiff1.erode();
+                cvGrayDiff1.contrastStretch();
+                cvGrayDiff1.blur(5);
                 
-            cf->findContours(cvGrayDiff1, 20, (image1.width * image1.height) / 4, _maxblobs, true);
+                /////////////////////////////////// SAVE TO DISK IN THE SYNTHESIS FOLDER ////////////////////////////////
+                string file_name;
                 
-            cvContourFinderVect.push_back(cf);
+                file_name = ofToString(_synth_save_cnt, 2)+"_RelaxRateAnalysis_"+ofToString(_run_cnt,2)+".jpg";
                 
+                
+                //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+                // ofSaveImage(cvGrayImage1.getPixelsRef(),_whole_file_path_synthesis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+                
+                
+                //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+                ofImage image;
+                //image.allocate(cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                
+                //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+                image.setUseTexture(false);  
+                
+                
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
+                _synth_save_cnt++;
+            }
         }
     }
     
@@ -136,38 +167,29 @@ void RelaxRateAnalysis::synthesise()
 void RelaxRateAnalysis::displayresults()
 {
     
-    //cvContourFinderVectDisplay.clear();
+    for(float i=1;i<_saved_filenames_synthesis.size();i++){
-    clearcfindervectdisplay();
-    
-    for(int i=1;i<cvContourFinderVect.size();i++){
-        
-        if(_state == STATE_STOP){
-            clearcfindervectdisplay();
-            clearcfindervect();
-            return;
-        }        
         
+        if(_state == STATE_STOP) return;
         
         //cout << "_saved_filenames_analysis[i] - " << _saved_filenames_synthesis[i] << endl;
         
         while(!_image_shown){
             Thread::sleep(2);
-            if(_state == STATE_STOP) return;
             //cout << "!_image_shown" << endl;
         }
         
-        cvContourFinderVectDisplay.push_back(cvContourFinderVect[i]);    
+        if(!image3.loadImage(_saved_filenames_synthesis[i])){
-        _show_image = true;
+            //couldn't load image
-        _image_shown = false;
+            // cout << "didn't load image" << endl;
-        
         } 
         
-    clearcfindervectdisplay();
+        if(image3.loadImage(_saved_filenames_synthesis[i])){
-    clearcfindervect();
+            image3.loadImage(_saved_filenames_synthesis[i]);
-    
+            //cout << "_show_image = true;" << endl;
-        
+            _show_image = true;
-    //cvContourFinderVectDisplay.clear();
+            _image_shown = false;
-    //cvContourFinderVect.clear();
+        }
+    }
 
     
 }
@@ -180,7 +202,9 @@ 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)
             {
@@ -211,7 +235,6 @@ void RelaxRateAnalysis::draw()
             
         case STATE_SYNTHESISING:
         {
-            
             // display animation of something while the synthesis in on-going...
             
             //cout << "RelaxRateAnalysis = STATE_SYNTHESISING...\n";
@@ -264,7 +287,7 @@ void RelaxRateAnalysis::draw()
                     }
                 }
                 
-                //cout << "_anim_cnt = " << _anim_cnt << endl;
+                cout << "_anim_cnt = " << _anim_cnt << endl;
                 
                 if (_anim_cnt > (_anim_cnt_max-_fade_in_frames) && _anim_cnt <= _anim_cnt_max) {
 
@@ -312,10 +335,15 @@ void RelaxRateAnalysis::draw()
             
             if (_show_image)
             {  
-                for(int i=0;i<cvContourFinderVectDisplay.size();i++){
+                //cout << "_show_image...\n" << endl;
-                    cvContourFinderVectDisplay[i]->draw(0,0, ofGetWidth(), ofGetHeight());
-                }
                 
+                ofEnableAlphaBlending();
+                
+                ofSetColor(255, 255, 255);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
+                image2.draw(0,0, ofGetWidth(), ofGetHeight());
+                
+                ofDisableAlphaBlending();
             }
             
             // display results of the synthesis
@@ -335,34 +363,37 @@ void RelaxRateAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    //cout << "RelaxRateAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(c,2)+"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
     
     
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
 }
-
-void RelaxRateAnalysis::cleanup()
-{
-}
-
-
-void RelaxRateAnalysis::clearcfindervect()
-{
-    for(int i = 0; i < cvContourFinderVect.size(); i++) {
-        rfiCvContourFinder* f = cvContourFinderVect[i];
-
-        // maybe it's erase here?  http://forum.openframeworks.cc/index.php/topic,3016.0.html
-        // cvContourFinderVect.erase(i);
-        
-        delete f;        
-    }
-    cvContourFinderVect.clear();
-    
-}
-
-void RelaxRateAnalysis::clearcfindervectdisplay()
-{
-    cvContourFinderVectDisplay.clear();
-}
-

src/RelaxRateAnalysis.h

@@ -5,12 +5,8 @@
 
 #include "Poco/Timer.h"
 
-#include "rfiCvContourFinder.h"
-
 #include "ofxOpenCv.h"
 
-
-
 class RelaxRateAnalysis : public AbstractAnalysis
 {
 public:
@@ -23,7 +19,6 @@ public:
     void acquire();
     void synthesise(); 
     void displayresults();
-    void cleanup();
 
     void draw();
     
@@ -31,24 +26,34 @@ 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;
-    ofxCvColorImage         cvColorImage1;    
+    ofImage         image2; 
-    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofImage         image3;
+    ofImage         image4;
+    ofImage         image5; 
+    ofImage         image6; 
     
-    vector<rfiCvContourFinder*>      cvContourFinderVect;
+    ofxCvColorImage         cvColorImage1;
-    vector<rfiCvContourFinder*>      cvContourFinderVectDisplay;
+    ofxCvColorImage         cvColorImage2;
+    ofxCvColorImage         cvColorImage3;
+    ofxCvColorImage         cvColorImage4;
+    ofxCvColorImage         cvColorImage5;
+    ofxCvColorImage         cvColorImage6;
+    
+    ofxCvGrayscaleImage 	cvGrayDiff1;
+    ofxCvGrayscaleImage 	cvGrayDiff2;
+    
+    ofxCvGrayscaleImage 	cvGrayImage1;
+    ofxCvGrayscaleImage 	cvGrayImage2;
+    ofxCvGrayscaleImage 	cvGrayImage3;
+    ofxCvGrayscaleImage 	cvGrayImage4;
+    
+    ofxCvContourFinder      cvContourFinder1;
 
 };

src/ShadowScapesAnalysis.cpp

@@ -19,12 +19,12 @@ using Poco::Thread;
 
 void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shadowscapes", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN ShadowScapesAnalysis " << NUM_RUN << endl;
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shadowscapes", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shadowscapes", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShadowScapesAnalysis " << acq_run_time << endl;
     
     int screenSpan;
@@ -39,6 +39,8 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
 
     DELTA_T_SAVE = 3*(10*acq_run_time/2);   // for 20 seconds, we want this to be around 100 files
                                             // or 5 times per second = every 200 ms
+    //DELTA_T_SAVE = 1;
+    //create_dir();  // this makes both synth and analysis folder structures
 
     _scanLineWidth = 100.0;
     _run_cnt = 0;
@@ -51,12 +53,6 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-        
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -66,28 +62,9 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-        
     //cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
     //cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    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);
@@ -95,9 +72,6 @@ void ShadowScapesAnalysis::setup(int camWidth, int camHeight)
     cvColorImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-    
 }
 
 void ShadowScapesAnalysis::acquire()
@@ -111,7 +85,9 @@ void ShadowScapesAnalysis::acquire()
     _line = 0;
     _RUN_DONE = false;
 
-    create_dir_allocate_images();
+    create_dir();
+    
+    //cout << "RUN NUM = " << i;
    
     save_timer.start(save_callback);
       
@@ -120,13 +96,15 @@ void ShadowScapesAnalysis::acquire()
     
     save_timer.stop();
     
+    //}
+
 }
 
 void ShadowScapesAnalysis::synthesise()
 {
     //cout << "ShadowScapesAnalysis::saving synthesis...\n";
     
-    for(float i=1;i<_saved_filenames_analysis.size()-1; i++){
+    for(float i=1;i<_saved_filenames_analysis.size()-1;i++){
     
       //  cout << "ShadowScapesAnalysis::synthesis FOR LOOP...\n";
         
@@ -148,11 +126,8 @@ void ShadowScapesAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                //cvGrayImage1 = cvColorImage1;
+                cvGrayImage1 = cvColorImage1;
-                //cvGrayImage2 = cvColorImage2;
+                cvGrayImage2 = cvColorImage2;
-                
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
                 
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.erode();
@@ -176,28 +151,24 @@ void ShadowScapesAnalysis::synthesise()
                 }
                 
                 
-                
                 //<---- 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;
+                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.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);
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
 
-                // <--- REALLY NEW SAVING METHOD --- 26 feb 2012 --- consolidated the save function into Abstract Analysis> ///
+                _saved_filenames_synthesis.push_back(_whole_file_path_synthesis+"/"+file_name);
-                cvConvertorImage.setFromGrayscalePlanarImages(cvGrayDiff1,cvGrayDiff1,cvGrayDiff1);
-                
-                saveImageSynthesis(file_name, &cvConvertorImage, OF_IMAGE_GRAYSCALE);
                 _synth_save_cnt++;
+                
             }
         }
     }
@@ -234,6 +205,41 @@ void ShadowScapesAnalysis::displayresults()
         }
     }
     
+    
+    // THE OLD SHIT /// 
+/*
+    for(float i=1;i<_saved_filenames_synthesis.size()-1;i++){
+        
+       // cout << "_saved_filenames_analysis[i]" << _saved_filenames_analysis[i] << endl;
+        
+        if(_state == STATE_STOP) return;
+        
+        while(!_image_shown){
+            Thread::sleep(2);
+            //cout << "!_image_shown" << endl;
+        }
+        
+        if(!image1.loadImage(_saved_filenames_synthesis[i])){
+            //couldn't load image
+            cout << "didn't load image" << endl;
+        } 
+        
+            
+        if(image1.loadImage(_saved_filenames_analysis[i])){
+            
+            image1.loadImage(_saved_filenames_analysis[i]);
+            cout << "loaded filenames[i] -  " << _saved_filenames_analysis[i] << endl;
+        
+            image2.setFromPixels(image1.getPixels(),image1.width,image1.height, OF_IMAGE_COLOR);
+          
+            //cout << "_show_image = true;" << endl;
+            _show_image = true;
+            _image_shown = false;
+
+        }
+    }
+*/
+    
 }
 
 
@@ -413,6 +419,7 @@ void ShadowScapesAnalysis::draw()
         {
             //cout << "STATE_DISPLAY_RESULTS...\n" << endl;
 
+            
             if (_frame_cnt > 2)
             {
                 _image_shown = true;
@@ -428,8 +435,7 @@ void ShadowScapesAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                     ofSetColor(255, 255, 255);
-                
+                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
-                    image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
                     image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -439,9 +445,6 @@ void ShadowScapesAnalysis::draw()
             
             // display results of the synthesis
             _RUN_DONE = true;
-            
-            // clear allocated memory...? 
-            
             break;
         }
             
@@ -457,6 +460,17 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
     
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ShadowScapesAnalysis::saving analysis...\n";
+    
     string file_name;
     
     if(_dir == H) {
@@ -471,6 +485,26 @@ void ShadowScapesAnalysis::save_cb(Timer& timer)
         file_name = ofToString(_save_cnt, 2)+"_D_"+ofToString(_line, 2)+"_"+ofToString(_run_cnt,2)+".jpg";
     }
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
         
 }

src/ShadowScapesAnalysis.h

@@ -66,7 +66,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //this is the temporary container to allow us to convert and save out greyscale images
-    ofxCvColorImage         cvConvertorImage;    
-
 };

src/ShapeFromShadingAnalysis.cpp

@@ -15,15 +15,16 @@ using Poco::Thread;
 
 void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 {    
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_shapefromshading", NUMBER_RUNS);
+    
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN ShapeFromShadingAnalysis " << NUM_RUN << endl;
-    //NUM_RUN = 5;
+
+   // NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_shapefromshading", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_shapefromshading", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME ShapeFromShadingAnalysis " << acq_run_time << endl;
     
-
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
     DELTA_T_SAVE = 2*(10*acq_run_time/2); // for 20 seconds, we want this to be around 200 files
@@ -31,7 +32,7 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     
     _frame_cnt_max = acq_run_time*ofGetFrameRate();  // e.g.: 30 frames per second * 20 seconds = 600 frames
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     _frame_cnt = 0;
@@ -40,15 +41,10 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     int anim_time = 5;   // 10 seconds
     _anim_cnt_max = anim_time*ofGetFrameRate();  // e.g.: 30 frames per second = 150 frames
     
+    
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -58,28 +54,9 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    cvConvertorImage.clear();    
-    
     cvColorImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 	cvGrayImage1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
@@ -88,8 +65,6 @@ void ShapeFromShadingAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 
@@ -103,7 +78,7 @@ void ShapeFromShadingAnalysis::acquire()
     _run_cnt++;
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0, _synth_save_cnt = 0;    
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     _animation_cnt1 = 0;
     _animation_cnt2 = 0;
@@ -169,8 +144,8 @@ void ShapeFromShadingAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
                 
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                cvGrayImage2 = cvColorImage2;
                 
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.erode();
@@ -188,23 +163,18 @@ void ShapeFromShadingAnalysis::synthesise()
                 //<---- 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;
+                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.setUseTexture(false);  
                
-                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height, OF_IMAGE_GRAYSCALE);
-                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
                 
-                //_saved_filenames_synthesis.push_back(_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++;
                 
             }
@@ -567,7 +537,7 @@ void ShapeFromShadingAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -592,7 +562,39 @@ void ShapeFromShadingAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
         
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "ShapeFromShadingAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ quad +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+    
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+
 }

src/ShapeFromShadingAnalysis.h

@@ -78,8 +78,4 @@ 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

@@ -15,12 +15,13 @@ using Poco::Thread;
 
 void StrobeAnalysis::setup(int camWidth, int camHeight)
 {
-    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis_NUM_RUN:NUM_RUN_strobe", NUMBER_RUNS);
+    NUM_RUN = RefractiveIndex::XML.getValue("config:analysis:NUM_RUN", NUMBER_RUNS);
     cout << "NUM_RUN StrobeAnalysis " << NUM_RUN << endl;
+
     //NUM_RUN = 5;
     
     int acq_run_time;   // 10 seconds of acquiring per run
-    acq_run_time = RefractiveIndex::XML.getValue("config:analysis_time:acquiretime_strobe", ACQUIRE_TIME);
+    acq_run_time = RefractiveIndex::XML.getValue("config:analysis:acquiretime_strobe", ACQUIRE_TIME);
     cout << "ACQUIRE_TIME StrobeAnalysis " << acq_run_time << endl;
     
     //int acq_run_time = 25;   // 20 seconds of acquiring per run
@@ -34,7 +35,7 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 
     // The British Health and Safety Executive recommend that a net flash rate for a bank of strobe lights does not exceed 5 flashes per second, at which only 5% of photosensitive epileptics are at risk. It also recommends that no strobing effect continue for more than 30 seconds, due to the potential for discomfort and disorientation.
     
-    //create_dir_allocate_images();
+    //create_dir();
     _synth_save_cnt = 0;
     _run_cnt = 0;
     
@@ -44,12 +45,6 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     _show_image = false;
     _image_shown = false;
     
-    image1.clear();
-    image2.clear();
-    image3.clear();  
-    image4.clear();
-    image5.clear();
-    
     //  images use for drawing the synthesized files to the screen ///
     image1.setUseTexture(false);  // the non texture image that is needed to first load the image
     image2.setUseTexture(true);   // the image that needs to get written to the screen which takes the content of image1
@@ -59,28 +54,9 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
     image4.setUseTexture(false);
     image5.setUseTexture(false);
     
-    image1.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image3.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);  
-    image4.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    image5.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h,  OF_IMAGE_COLOR);
-    
    // cout << "RefractiveIndex::_vid_w " << RefractiveIndex::_vid_w << endl;
    // cout << "RefractiveIndex::_vid_h " << RefractiveIndex::_vid_h << endl;
     
-    // clear() apparently fixes the "OF_WARNING: in allocate, reallocating a ofxCvImage" 
-    // that we're getting in OSX/Windows and is maybe crashing Windows
-    // http://forum.openframeworks.cc/index.php?topic=1867.0
-    cvColorImage1.clear();
-	cvGrayImage1.clear();
-    cvGrayDiff1.clear();
-    
-    cvColorImage2.clear();
-	cvGrayImage2.clear();
-    cvGrayDiff2.clear();
-    
-    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);
@@ -89,8 +65,6 @@ void StrobeAnalysis::setup(int camWidth, int camHeight)
 	cvGrayImage2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
     cvGrayDiff2.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
 
-    cvConvertorImage.allocate(RefractiveIndex::_vid_w,RefractiveIndex::_vid_h);
-
 }
 
 
@@ -103,7 +77,7 @@ void StrobeAnalysis::acquire()
     _frame_cnt = 0; _save_cnt = 0; _anim_cnt = 0;  _strobe_cnt = 0, _synth_save_cnt = 0;
     _run_cnt++;
     _RUN_DONE = false;
-    create_dir_allocate_images();
+    create_dir();
     
     // RUN ROUTINE
     //for(int i = 0; i < NUM_RUN; i++) {
@@ -151,8 +125,8 @@ void StrobeAnalysis::synthesise()
                 cvColorImage1.setFromPixels(image1.getPixels(), image1.width, image1.height);
                 cvColorImage2.setFromPixels(image5.getPixels(), image5.width, image5.height);
             
-                cvColorImage1.convertToGrayscalePlanarImage(cvGrayImage1, 1);
+                cvGrayImage1 = cvColorImage1;
-                cvColorImage2.convertToGrayscalePlanarImage(cvGrayImage2, 1);
+                cvGrayImage2 = cvColorImage2;
             
                 cvGrayDiff1.absDiff(cvGrayImage2, cvGrayImage1);
                 cvGrayDiff1.dilate();
@@ -170,26 +144,18 @@ void StrobeAnalysis::synthesise()
                 
                 
                 //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
-                //ofImage image;
+                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.setUseTexture(false);  
                 
-                //image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height,OF_IMAGE_GRAYSCALE);
+                image.setFromPixels(cvGrayDiff1.getPixels(), cvGrayDiff1.width, cvGrayDiff1.height,OF_IMAGE_GRAYSCALE);
-                //image.saveImage(_whole_file_path_synthesis+"/"+file_name);
+                image.saveImage(_whole_file_path_synthesis+"/"+file_name);
                 
-                //_saved_filenames_synthesis.push_back(_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++;
                 
-                
             }
         }
     }
@@ -396,7 +362,7 @@ void StrobeAnalysis::draw()
                 ofEnableAlphaBlending();
                 
                 ofSetColor(255, 255, 255);
-                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_COLOR);
+                image2.setFromPixels(image3.getPixels(),image3.width,image3.height, OF_IMAGE_GRAYSCALE);
                 image2.draw(0,0, ofGetWidth(), ofGetHeight());
                 
                 ofDisableAlphaBlending();
@@ -421,7 +387,39 @@ void StrobeAnalysis::save_cb(Timer& timer)
 {
     _save_cnt++;
     
+    RefractiveIndex::_vidGrabber.grabFrame();  // get a new frame from the camera
+    
+    if (RefractiveIndex::_vidGrabber.isFrameNew())
+    {
+        RefractiveIndex::_pixels = RefractiveIndex::_vidGrabber.getPixelsRef(); //get ofPixels from the camera
+    } else {
+        return;
+    }
+    
+    //cout << "StrobeAnalysis::saving...\n";
+    
     string file_name = ofToString(_save_cnt,2)+"_"+ ofToString(_strobe_on) +"_"+ofToString(_run_cnt,2)+".jpg";
     
-    saveImageAnalysis(file_name);
+    
+    //<---- THE OLD WAY OF SAVING - works on OSX but generates BLACK FRAMES on WINDOWS ---->
+    //ofSaveImage(RefractiveIndex::_pixels, _whole_file_path_analysis+"/"+file_name, OF_IMAGE_QUALITY_BEST);
+    
+    
+    //<---- NEW SAVING - seems to fix WINDOWS saving out BLACK FRAMES PROBLEM ---->
+    unsigned char * somePixels;
+    ofPixels appPix = RefractiveIndex::_pixels;
+    somePixels = new unsigned char [appPix.getWidth()*appPix.getHeight()*3];
+    somePixels = appPix.getPixels();
+
+    ofImage myImage;
+    //myImage.allocate(appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    
+    //*** This needs to be here for OSX of we get a BAD ACCESS ERROR. DOES IT BREAK WINDOWS? ***//
+    myImage.setUseTexture(false);
+    
+    myImage.setFromPixels(somePixels,appPix.getWidth(),appPix.getHeight(), OF_IMAGE_COLOR);
+    myImage.saveImage(ofToDataPath("")+ _whole_file_path_analysis+"/"+file_name);
+    
+    _saved_filenames_analysis.push_back(_whole_file_path_analysis+"/"+file_name);
+
 }

src/StrobeAnalysis.h

@@ -65,7 +65,4 @@ protected:
     
     ofxCvContourFinder      cvContourFinder1;
 
-    //this is the temporary container to allow us to convert and save out greyscale images
-    ofxCvColorImage         cvConvertorImage;    
-
 };

src/rficv/rfiCvContourFinder.cpp

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

src/rficv/rfiCvContourFinder.h

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