Merge branch 'mci3d_changes'

core/image/MultiChannelImage3DT.h

@@ -4,6 +4,7 @@
 #include <core/image/MultiChannelImageAccess3D.h>
 #include <core/image/ImageT.h>
 #include <core/image/MultiChannelImageT.h>
+#include <core/image/Histogram.h>
 
 #include <vector>
 #include <fstream>
@@ -139,9 +140,6 @@ public:
   /** convert to ice image */
   void convertToGrey( NICE::Image & img, int z, uint channel = 0, bool normalize = true ) const;
 
-	/** convert to ice image template */
-  void convertToGrey( NICE::ImageT<P> & img, int z, uint channel = 0, bool normalize = false ) const;
-	
   /** convert to ice colorimage */
   void convertToColor( NICE::ColorImage & img, int z, const int chan1 = 0, const int chan2 = 1, const int chan3 = 2 ) const;
 
@@ -157,8 +155,13 @@ public:
   /** calculate image statistics */
   void statistics( P & min, P & max, uint channel = 0 ) const;
 
-  /** correct inhomogeneous illuminations (shading) between the image slices **/
+  /** correct inhomogeneous illuminations between the image slices
+   *  ! Deprecated, use 'equalizeHistogram' instead !
+   */
   void correctShading( uint channel = 0 ) const;
+
+  /** do a histogram equalization */
+  void equalizeHistogram( uint channel = 0 ) const;
   
   /** dump all data to RAW format: xsize, ysize, numChannels, <data> */
   void store( std::string filename ) const;

core/image/MultiChannelImage3DT.tcc

@@ -37,17 +37,10 @@ P & MultiChannelImage3DT<P>::operator() (int x, int y, int z, uint channel)
 }
 
 template<class P>
-MultiChannelImageT<P> MultiChannelImage3DT<P>::operator[] (uint c)
-{
-  // This was our first idea ... but it creates a real copy
-  // ImageT<P> tmp ( data[c], xsize, ysize, xsize*sizeof(P), GrayColorImageCommonImplementation::noAlignment );
-  // This is the correct version. The funny thing about this is that shallowCopy
-  // is not an enum parameter, but an instance of ShallowCopyMode, which is a class.
-  // This fancy trick was done in older to prevent automatic conversion between enum types
-  // as done implicitly by C++.
-  
+MultiChannelImageT<P> MultiChannelImage3DT<P>::operator[] (uint z)
+{
   MultiChannelImageT<P> img;
-  for( int z = 0; z < zsize; z++ )
+  for( int c = 0; c < numChannels; c++ )
   {
     P * datatmp = data[c];
     ImageT<P> tmp ( &datatmp[z*(xsize*ysize)], xsize, ysize, xsize*sizeof(P), GrayColorImageCommonImplementation::shallowCopy );
@@ -352,6 +345,7 @@ void MultiChannelImage3DT<P>::correctShading( uint channel ) const
 {
   assert( channel < numChannels );
   
+  // some sort of correction trick hardly understandable :-)
   std::vector<double> meanVals;
   for( int z = 0; z < zsize; z++ )
   {
@@ -365,10 +359,12 @@ void MultiChannelImage3DT<P>::correctShading( uint channel ) const
     }
     sumVal /= (xsize*ysize);
     meanVals.push_back( sumVal );
+
   }
 
   P newMax = std::numeric_limits<P>::min();
-  short int maxVal = 255;
+
+  const short int maxVal = 255;
   for ( int z = 0; z < zsize; z++ )
   {
     for ( int y = 0; y < ysize; y++ )
@@ -391,90 +387,76 @@ void MultiChannelImage3DT<P>::correctShading( uint channel ) const
 }
 
 template<class P>
-Image MultiChannelImage3DT<P>::getChannel( int z, uint channel ) const
+void MultiChannelImage3DT<P>::equalizeHistogram( uint channel ) const
 {
-  assert( channel < numChannels );
+  assert(channel < numChannels );
 
-  NICE::Image img;
-  convertToGrey( img, z, channel, true );
+  for( int z = 0; z < zsize; z++ )
+  {
+    NICE::Image img = getChannel(z, channel );
+    NICE::Histogram hist(img,0,255,256);
 
-  return img;
+    NICE::IntVector *histVec = NULL;
+    histVec = hist.cumulative();
+    for ( int i = 0; i < (int)histVec->size(); i++)
+    {
+      histVec->set(i, histVec->get(i) * 255 / (double)histVec->get(histVec->size()-1));
+    }
+
+    for ( int y = 0; y < ysize; y++ )
+    {
+      for ( int x = 0; x < xsize; x++ )
+      {
+        data [channel][x + y*xsize + z*xsize*ysize] = histVec->get( img.getPixel(x,y) );
+      }
+    }
+
+    delete histVec;
+  }
 }
 
 template<class P>
-ImageT<P> MultiChannelImage3DT<P>::getChannelT( int z, uint channel ) const
+Image MultiChannelImage3DT<P>::getChannel( int z, uint channel ) const
 {
   assert( channel < numChannels );
 
-  NICE::ImageT<P> img;
-  convertToGrey( img, z, channel, false );
-  
-  P min, max;
-  statistics ( min, max, channel );
-  fprintf (stderr, "MultiChannelImage3DT<>::showChannel: max %f min %f\n", (double)max, (double)min );
+  NICE::Image img;
+  convertToGrey( img, z, channel, true );
 
   return img;
 }
 
-/** convert to ice image */
 template<class P>
-void MultiChannelImage3DT<P>::convertToGrey( NICE::Image & img, int z, uint channel,  bool normalize ) const
+ImageT<P> MultiChannelImage3DT<P>::getChannelT( int z, uint channel ) const
 {
   assert( channel < numChannels );
 
-  P min, max;
+  //  P min, max;
+  //  statistics ( min, max, channel );
+  //  fprintf (stderr, "MultiChannelImage3DT<>::showChannel: max %f min %f\n", (double)max, (double)min );
 
-  if ( normalize ) {
-    statistics( min, max, channel );
-    fprintf( stderr, "MultiChannelImage3DT<>::showChannel: max %f min %f\n", ( double )max, ( double )min );
-  }
+  NICE::ImageT<P> img(xsize,ysize);
 
-  bool skip_assignment = false;
-
-  img.resize( xsize, ysize );
-
-  if ( normalize )
-    if ( max - min < std::numeric_limits<double>::min() )
+  long k = 0;
+  for ( int y = 0; y < ysize; y++ )
+    for( int x = 0; x < xsize; x++, k++ )
     {
-      img.set( max );
-      skip_assignment = true;
-      fprintf( stderr, "MultiChannelImage3DT::showChannel: image is uniform! (%f)\n", ( double )max );
+      img.setPixel( x, y, data[channel][z*xsize*ysize + k] );
     }
 
-
-  if ( ! skip_assignment )
-  {
-    long k = 0;
-
-    for ( int y = 0 ; y < ysize; y++ )
-    {
-      for ( int x = 0 ; x < xsize ; x++, k++ )
-      {
-        if ( normalize )
-        {
-          img.setPixel( x, y, ( int )(( data[channel][z*xsize*ysize + k] - min ) * 255 / ( max - min ) ) );
-        }
-        else
-        {
-          img.setPixel( x, y, ( int )( data[channel][z*xsize*ysize + k] ) );
-        }
-      }
-    }
-  }
+  return img;
 }
 
-/** convert to ice image template */
+/** convert to ice image */
 template<class P>
-void MultiChannelImage3DT<P>::convertToGrey( NICE::ImageT<P> & img, int z, uint channel,  bool normalize ) const
+void MultiChannelImage3DT<P>::convertToGrey( NICE::Image & img, int z, uint channel,  bool normalize ) const
 {
   assert( channel < numChannels );
 
   P min, max;
 
-  if ( normalize ) {
+  if ( normalize )
     statistics( min, max, channel );
-    fprintf( stderr, "MultiChannelImage3DT<>::showChannel: max %f min %f\n", ( double )max, ( double )min );
-  }
 
   bool skip_assignment = false;
 
@@ -483,9 +465,10 @@ void MultiChannelImage3DT<P>::convertToGrey( NICE::ImageT<P> & img, int z, uint
   if ( normalize )
     if ( max - min < std::numeric_limits<double>::min() )
     {
+      fprintf( stderr, "MultiChannelImage3DT<>::showChannel: max %f min %f\n", ( double )max, ( double )min );
       img.set( max );
       skip_assignment = true;
-      fprintf( stderr, "MultiChannelImage3DT::showChannel: image is uniform! (%f)\n", ( double )max );
+      fprintf( stderr, "MultiChannelImage3DT<>::showChannel: image is uniform! (%f)\n", ( double )max );
     }
 
 

core/image/ippwrapper.h

@@ -203,7 +203,7 @@
   typedef struct ipcvMorphGrayState_32f IppiMorphGrayState_32f;
 
   struct OptFlowPyrLK;
-  typedef struct IppiOptFlowPyrLK;
+  typedef struct OptFlowPyrLK IppiOptFlowPyrLK;
   typedef IppiOptFlowPyrLK IppiOptFlowPyrLK_8u_C1R;
   typedef IppiOptFlowPyrLK IppiOptFlowPyrLK_16u_C1R;
   typedef IppiOptFlowPyrLK IppiOptFlowPyrLK_32f_C1R;