added triangular mesh and scaling for z axis.

example/RefractiveIndex.cpp

@@ -42,6 +42,9 @@ ofxXmlSettings   RefractiveIndex::XML;
 
 void RefractiveIndex::setup()
 {
+    camDist=1000;
+
+    //camera.setOrientation(ofVec3f(1,-1,1));
     bool save_config = false;
     
     cout << "Loading configuration..." << endl;
@@ -110,7 +113,6 @@ void RefractiveIndex::setup()
 	    
     _analysisVector.push_back(new RelaxRateAnalysis());
 	
-	
     _analysisVector.push_back(new IResponseAnalysis());
     
     _analysisVector.push_back(new ShapeFromShadingAnalysis());
@@ -133,8 +135,6 @@ void RefractiveIndex::setup()
     _currentAnalysis = NULL;
     _state = ISTATE_UNDEF;
   
-     fbo.allocate(_vid_w,_vid_h);
-    _meshRotation=0;
     
 }
 
@@ -151,6 +151,16 @@ void RefractiveIndex::start_analysis()
     _analysisAdapator = new AnalysisAdaptor(_currentAnalysis);
     _currentAnalysis->setup(_vid_w, _vid_h);
     _analysisAdapator->start();    
+    
+    
+    //allocate fbo for HD
+    fbo.allocate(1920,1080);
+
+//    fbo.allocate( _currentAnalysis->_mesh_size_multiplier *_vid_w,_currentAnalysis->_mesh_size_multiplier * _vid_h);
+    camera.setPosition(fbo.getWidth()/2, fbo.getHeight()/2,_currentAnalysis->_mesh_size_multiplier *500);
+    _meshRotation=0;
+    
+    
 }
 
 void RefractiveIndex::stop_analysis()
@@ -217,26 +227,42 @@ void RefractiveIndex::draw()
     if(_currentAnalysis){
         _currentAnalysis->draw();
        
-        if(_currentAnalysis->meshIsComplete){
-            fbo.begin();
     
+        if(_currentAnalysis->meshIsComplete){
+            
+            fbo.begin();
+            glShadeModel(GL_SMOOTH);  
+            ofClear(0,0,0);
+            
+            camera.begin();
             ofSetColor(0, 0, 0);
-            ofRect(0, 0, fbo.getWidth(), fbo.getHeight());
+            //this is a hack, I don't know how to colour the fbo with black pixels so I'm drawing a massive black rectangle in the  background
             ofPushMatrix();
-            ofTranslate(fbo.getWidth()/2, fbo.getHeight()/2);
+            ofTranslate(0, 0,-500);
-            ofRotateY(_meshRotation );
+            ofRect(-fbo.getWidth(), -fbo.getHeight(), fbo.getWidth()*3, fbo.getHeight()*3);
-            ofTranslate(-fbo.getWidth()/2, -fbo.getHeight()/2);
+            
-            _meshRotation+=0.5;
+            
+            ofPopMatrix();
+            ofSetColor(255);
+            
+            float xDiff= (fbo.getWidth()- (_currentAnalysis->_mesh_size_multiplier *_vid_w))/2;
+            float yDiff= (fbo.getHeight()- (_currentAnalysis->_mesh_size_multiplier *_vid_h))/2;
+
+            
+            ofTranslate(xDiff,yDiff,-_currentAnalysis->zPlaneAverage );
             _currentAnalysis->aMesh.draw();
-             fbo.end();
+            
+            camera.end();
+            fbo.end();
+            
             ofPixels pixels;
             fbo.readToPixels(pixels);
           
-
             ofSaveImage(pixels,_currentAnalysis->meshFileName, OF_IMAGE_QUALITY_BEST);
-            //saving jpgs doesn't work maybe because of of_image_quality
+            //saving jpgs doesn't work - pngs only!
 
         }
+       
     }
 }
 

example/RefractiveIndex.h

@@ -10,6 +10,8 @@
 
 #include "ofxOpenCv.h"
 #include "ofxXmlSettings.h"
+#include "ofxOpenCv.h"
+
 
 #define MODE_DRAWING        0xEEFF
 #define MODE_ANALYSING      0xFFEE
@@ -55,7 +57,8 @@ protected:
     vector<AbstractAnalysis*>   _analysisVector;    
     
     float                         _meshRotation;
-    
+    float                           camDist;
+    ofEasyCam                     cam;
 public:    
     // acquisition
     static ofPixels         _pixels;    
@@ -70,8 +73,8 @@ public:
     // this should be in xml
     static string           _location;
     static ofxXmlSettings   XML;  // made this static so we can access RUN_NUM in the analyses 
-    
+    ofCamera    camera;
+    ofPixels    keepOnScreen;
     ofFbo fbo;
-    
+    ofLight light;
-    
 };

src/AbstractAnalysis.cpp

@@ -8,6 +8,8 @@
 void AbstractAnalysis::setup(int camWidth, int camHeight) {
     
     meshIsComplete=false;
+    imageForContourAvailable=false;
+    
     _cam_w = camWidth; _cam_h = camHeight;
     if(RefractiveIndex::_mode == MODE_DRAWING) {
         ofFileDialogResult r = ofSystemLoadDialog("choooose da folda", true);

src/AbstractAnalysis.h

@@ -62,9 +62,19 @@ public:
     // event
     ofEvent<string> _synthesize_cb;    
     bool    meshIsComplete;
+    bool    imageForContourAvailable;
     ofMesh  aMesh;
     string  meshFileName;
+    //difference between our image size and the size of the fbo
+    float   widthScaleFactor;
+    float   heightScaleFactor;
+    ofImage  contourImage;
+    ofPixels meshPix;
+    ofPixels publicColorImage;
+    float    zPlaneAverage;
     
+    //added Tom 1/5/12 defines the stretch we make to the mesh to make it fit HD proportions
+    float           _mesh_size_multiplier;
     
 protected:    
     int             _cam_w, _cam_h;          

src/IResponseAnalysis.cpp

@@ -29,6 +29,8 @@ void IResponseAnalysis::setup(int camWidth, int camHeight)
     meshIsComplete=false;
     _gotFirstImage=false;
     
+    _mesh_size_multiplier=4;
+    
 
     //int acq_run_time = 20;   // 20 seconds of acquiring per run
     
@@ -175,24 +177,18 @@ void IResponseAnalysis::synthesise()
                     else{
                         imagePixels1[i]=0;
                     }
-                    if(imagePixels2[i]-backgroundPixels[i]>0){
-                        imagePixels2[i]-=backgroundPixels[i];
-                    }
-                    else{
-                        imagePixels2[i]=0;
-                    }
                   
                 }
+               
                 //update the images with their new background subtracted selves
                 image1.setFromPixels(imagePixels1);
-                image5.setFromPixels(imagePixels2);
-                //subtract background end///////////////
 
                 
                 //flag the main app that we aren't read yet
                 meshIsComplete=false;
                 //make a mesh - this mesh will be drawn in the main app
-                setMeshFromPixels(make3DZmap(image1, image5, _background), image1,image5, aMesh);
+                setMeshFromPixels(_returnDepthsAtEachPixel(image1, image1, _background), image1,image1, aMesh);
+                 //meshPix=make3DZmap(image1, image5, _background);
                 //with jpgs this was refusing to save out
                 meshFileName = _whole_file_path_synthesis+"/"+ofToString(_synth_save_cnt, 2)+"_IResponseSynthesis_"+ofToString(_run_cnt,2)+".png";
                 _saved_filenames_synthesis.push_back(meshFileName);
@@ -200,6 +196,7 @@ void IResponseAnalysis::synthesise()
                 //flag that we are finished  
                 meshIsComplete=true;
                 _synth_save_cnt++;
+                
             }
         }
     }
@@ -417,65 +414,139 @@ void IResponseAnalysis::save_cb(Timer& timer)
     saveImageAnalysis(file_name);
 }
 
-void IResponseAnalysis::setMeshFromPixels(ofPixels somePixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
+void IResponseAnalysis::setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh){
     int x=0;
     int y=0;
     
     //get rid of all previous vectors and colours
     mesh.clear();
+    mesh.setMode(OF_PRIMITIVE_TRIANGLES);
     
-   //unsigned char * thesePixels =currentSecondImage.getPixels();
+    ofColor meshColour=ofColor(255,0,0);
     
-    for(int i=0;i<somePixels.size();i+=3){
+    int chooseColour=1  ;
-        mesh.addVertex(ofVec3f(x,y,- somePixels.getColor(x, y).getBrightness()   ));
-        // add colour from current second image of two - this is a hang over from when i was comparing two images 
-        mesh.addColor(  currentSecondImage.getColor(x, y)   );
-        x++;
-        if(x>=somePixels.getWidth()){
-            x=0;
-            y++;
-        }
     
+    //the average z position of the matrix - used later to centre the mesh on the z axis when drawing
+    float zPlaneAverage=0;
+    
+    for(int i=0;i<sPixels.size();i++){
+        zPlaneAverage+=sPixels[i];
     }
+    if (sPixels.size()!=0) {
+        zPlaneAverage/=sPixels.size();
+        //cout<<zPlaneAverage<<" zPlaneAverage "<<endl;
+    }
+
+    else{
+        cout<<"DEPTH FLOAT ARRAY IS EMPTY";
+    }
+         
+    if(chooseColour==1){
+            for(int i=0;i<sPixels.size();i++){
+                mesh.addColor(  currentSecondImage.getColor(x, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- sPixels[ (currentSecondImage.getWidth()*(y+1))+x    ]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1 ]  ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x+1, y+1)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- sPixels[(currentSecondImage.getWidth()*(y+1))+x+1]   ));
+              
+                mesh.addColor(  currentSecondImage.getColor(x, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x ]  ));
+                
+                mesh.addColor(  currentSecondImage.getColor(x+1, y)   );
+                mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- sPixels[(currentSecondImage.getWidth()*(y))+x +1 ]));
+
+                x++;
+                if(x>=currentSecondImage.getWidth()-1){
+                    x=0;
+                    y++;
+                    //something is going badly wrong with my maths for me to need this HELP TODO fix this - why am I running over the end of the vector?
+                    if(y>=479){
+                        break;
+                    }
+                }
+             }
+    }
+    /*else{
+           for(int i=0;i<somePixels.getWidth()*(somePixels.getHeight()-1);i++){      
+               
+        
+               ofVec3f U;
+               ofVec3f V;
+                              //tri 1
+               U =ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness() ).operator-  ( ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- somePixels.getColor(x, y).getBrightness()  ) );
+               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ));
+               
+               ofVec3f normal;
+               float mult=5.2;
+               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x, y+1).getBrightness() )  ));
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*x,_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
+               
+               mesh.addNormal(normal);
+               
+               //tri 2
+               U =ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- somePixels.getColor(x, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
+               V =ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,- somePixels.getColor(x+1, y).getBrightness()   ).operator-(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- somePixels.getColor(x+1, y+1).getBrightness() )  );
+               
+               normal = ofVec3f( (U.y*V.z)-(U.z-V.y)   , (U.z*V.x)-(U.x*V.z)    , (U.x*V.y)-(U.y*V.x)  );
+               
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*(y+1),- mult*(1+somePixels.getColor(x+1, y+1).getBrightness())   ));
+                 //       mesh.addColor( ofColor(255,10,10)   );
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x),_mesh_size_multiplier*y,- mult*(1+somePixels.getColor(x, y).getBrightness() )  ));
+
+                 mesh.addColor(meshColour);
+                 mesh.addVertex(ofVec3f(_mesh_size_multiplier*(x+1),_mesh_size_multiplier*y,-mult*(1+ somePixels.getColor(x+1, y).getBrightness())   ));
+               
+               mesh.addNormal(normal);
+
+                x++;
+                if(x>=somePixels.getWidth()-1){
+                    x=0;
+                    y++;
+                    if(y>=479){
+                       break;
+                   }
+                }
+             }*/
+         
+     // add colour from current second image of two - this is a hang over from when i was comparing two image
+        
+
 }
-ofPixels IResponseAnalysis::make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
+vector<float> IResponseAnalysis::_returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImag){
     
     ofPixels imagePixels1 = image1.getPixelsRef();
     ofPixels imagePixels2 = image2.getPixelsRef();
     ofPixels backgroundPixels = backgroundImag.getPixelsRef();
-    
+    vector<float> differences;
     
     ofPixels difference;
     //this unsigned char should be unnecessary - I would have thought - can't you just address the pixel locations in ofPixels directly? 
     unsigned char * thesePixels = new unsigned char[ imagePixels1.getWidth()*imagePixels1.getHeight()*3];
-    
+    for(int i=0;i<imagePixels1.size();i++){
+        thesePixels[i]=0;
+    }
     int x=0;
     int y=0;
     
     int chooseComparison=1;
-    //previous versiom which compared two images -now deprecated
-    if(chooseComparison==0){
-    //for each pixel...
-        for(int i=0;i<imagePixels1.size();i+=3){
     
-            ofColor colourImage1 = imagePixels1.getColor(x, y);
-            ofColor colourImage2 = imagePixels2.getColor(x, y);
-        
-            //the brightness difference at this pixel address for both images
-            int thisDiff=abs(colourImage1.getBrightness()-colourImage2.getBrightness());
-        
-            thesePixels[i]=thisDiff;
-            thesePixels[i+1]=thisDiff;
-            thesePixels[i+2]=thisDiff;
-            x++;
-            if(x>=imagePixels1.getWidth()){
-                x=0;
-                y++;
-            
-            }
-        
-        }
-    }
     //the current version compares how bright this pixel is with how bright it would be following inverse square fall off from centre
     if(chooseComparison==1){
         //for each pixel...
@@ -483,14 +554,15 @@ ofPixels IResponseAnalysis::make3DZmap(ofImage &image1, ofImage &image2, ofImage
         for(int i=0;i<imagePixels1.size();i+=3){
             
             ofColor colourImage1 = imagePixels1.getColor(x, y);
-            ofColor colourImage2 = imagePixels2.getColor(x, y);
+            //ofColor colourImage2 = imagePixels2.getColor(x, y);
             
             float _distanceToCentre=ofDist(imagePixels1.getWidth()/2, imagePixels1.getHeight()/2, x, y);
             float _presumedBrightness=ofMap( sqrt(_maxPossibleDistanceToCentre)-sqrt(_distanceToCentre), 0,  sqrt(_maxPossibleDistanceToCentre), 0, 255);
             //float _presumedBrightness=255;
             int thisDiff=abs(colourImage1.getBrightness()-_presumedBrightness);
             //cout<<thisDiff<< " thisDiff "<<endl;
-
+            float multiplier=2.0;
+            differences.push_back(multiplier* thisDiff);
             thesePixels[i]=thisDiff;
             thesePixels[i+1]=thisDiff;
             thesePixels[i+2]=thisDiff;
@@ -505,7 +577,8 @@ ofPixels IResponseAnalysis::make3DZmap(ofImage &image1, ofImage &image2, ofImage
     }
     
     difference.setFromPixels(thesePixels,imagePixels1.getWidth(),imagePixels1.getHeight(), 3);
-    return difference;
+    return differences;
     
 }
 
+

src/IResponseAnalysis.h

@@ -63,9 +63,10 @@ protected:
     ofxCvColorImage         cvConvertorImage;
     
     //mesh making function
-    void setMeshFromPixels(ofPixels somePixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
+    void setMeshFromPixels(vector<float> sPixels, ofImage currentFirstImage, ofImage currentSecondImage, ofMesh & mesh);
     //returns ofPixels but these pixels actually hold depth data.
-    ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    //ofPixels make3DZmap(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
+    vector<float> _returnDepthsAtEachPixel(ofImage &image1, ofImage &image2, ofImage &backgroundImage);
     bool _gotFirstImage;
     ofImage _background;
 };