Merge branch 'experimental' into topic-qt5

Author: shakes76

apps/milxImageApp/milxImageApp.cxx

@@ -27,7 +27,7 @@ using namespace TCLAP;
 typedef std::vector< std::string >::iterator stringiterator;
 
 //Supported operations
-enum operations {none = 0, info, convert, labelinfo, rescale, invert, relabel, smooth, bilateral, median, gradmag, laplacian, distancemap, threshold, Otsu, crop, mask, resample, match, checker, add, diff, mean, merge, cast, flip};
+enum operations {none = 0, info, convert, labelinfo, rescale, invert, relabel, smooth, bilateral, median, gradmag, laplacian, distancemap, threshold, Otsu, crop, mask, resample, match, checker, add, diff, mean, merge, cast, flip, subsample};
 
 //Image stuff
 typedef unsigned char charPixelType;
@@ -106,6 +106,7 @@ int main(int argc, char *argv[])
   ValueArg<size_t> OtsuArg("", "Otsu", "Otsu multiple threshold with the number of bins to use.", false, 128, "Otsu");
   ValueArg<size_t> paddingArg("", "padding", "Number of pixels to pad in the operation in question (such as crop).", false, 1, "Padding");
   ValueArg<size_t> flipArg("f", "flip", "Flip the image about origin at axis indicated (0: x-axis, 1:y-axis, 2:z-axis).", false, 0, "Flip");
+  ValueArg<size_t> subsampleArg("x", "subsample", "Downsample the image by the factor indicated (same in all dimensions).", false, 0, "Subsample");
   ///Switches
   ///XOR Switches
   SwitchArg infoArg("", "info", "Report the image information(s).", false);
@@ -171,6 +172,7 @@ int main(int argc, char *argv[])
   xorlist.push_back(&meanArg);
   xorlist.push_back(&castArg);
   xorlist.push_back(&flipArg);
+  xorlist.push_back(&subsampleArg);
   //~ xorlist.push_back(&mseArg);
 #if (ITK_REVIEW || ITK_VERSION_MAJOR > 3) //Review only members
   xorlist.push_back(&labelInfoArg);
@@ -206,6 +208,7 @@ int main(int argc, char *argv[])
   size_t OtsuValue = OtsuArg.getValue(); //number of bins
   size_t paddingValue = paddingArg.getValue(); //number of bins
   size_t flipAxis = flipArg.getValue(); //number of bins
+  size_t subsampleFactor = subsampleArg.getValue(); //downsample by
 
   std::string maskName;
   if(cropArg.isSet())
@@ -260,7 +263,7 @@ int main(int argc, char *argv[])
   }
   if( smoothArg.isSet() || bilateralArg.isSet() || medianArg.isSet() || gradMagArg.isSet() || laplacianArg.isSet() || distancemapArg.isSet() || cropArg.isSet() || maskArg.isSet()
      || resampleArg.isSet() || matchArg.isSet() || checkerArg.isSet() || thresholdArg.isSet() || OtsuArg.isSet() || rescaleArg.isSet() || invertArg.isSet() || relabelArg.isSet() || addArg.isSet()
-     || diffArg.isSet() || meanArg.isSet() || mergeArg.isSet() || castArg.isSet() || flipArg.isSet() )
+     || diffArg.isSet() || meanArg.isSet() || mergeArg.isSet() || castArg.isSet() || flipArg.isSet() || subsampleArg.isSet() )
   {
     ///Check if output argument given and only doing one image
     if(filenames.size() == 1 && (addArg.isSet() || diffArg.isSet() || meanArg.isSet() || mergeArg.isSet()))
@@ -343,6 +346,8 @@ int main(int argc, char *argv[])
       operation = cast;
     if(flipArg.isSet())
       operation = flip;
+    if(subsampleArg.isSet())
+      operation = subsample;
   }
   if(aboveArg.isSet() || belowArg.isSet())
   {
@@ -402,6 +407,15 @@ int main(int argc, char *argv[])
       exit(EXIT_FAILURE);
     }
   }
+  if(subsampleArg.isSet())
+  {
+    if(subsampleFactor < 2)
+    {
+      milx::PrintError("Argument Error: Incorrect value provided for subsampling.");
+      milx::PrintError("Re-run with value correctly set.");
+      exit(EXIT_FAILURE);
+    }
+  }
   if(thresholdArg.isSet() || rescaleArg.isSet())
   {
     if( (!aboveArg.isSet() || !belowArg.isSet()) && rescaleArg.isSet() )
@@ -764,6 +778,10 @@ int main(int argc, char *argv[])
           milx::Image<charImageType>::FlipCollection(labelledCollection, false, false, true, true);
         break;
 
+      case subsample:
+        milx::Image<charImageType>::SubsampleCollection(labelledCollection, subsampleFactor);
+        break;
+
       case none: //--------------------------------
         break;
 
@@ -985,6 +1003,10 @@ int main(int argc, char *argv[])
           milx::Image<floatImageType>::FlipCollection(collection, false, false, true, true);
         break;
 
+      case subsample:
+        milx::Image<floatImageType>::SubsampleCollection(collection, subsampleFactor);
+        break;
+
       case none: //--------------------------------
         break;
 

include/milxImage.h

@@ -769,6 +769,11 @@ class SMILI_EXPORT Image : public ImageBase
   template<typename TOutImage>
   static std::vector< typename itk::SmartPointer<TOutImage> > OtsuMultipleThresholdCollection(const std::vector< typename itk::SmartPointer<TImage> > &images, const int bins, const int noOfLabels);
 
+  /*!
+  \fn Image::SubsampleCollection(std::vector< typename itk::SmartPointer<TImage> > &images, unsigned factor = 2)
+  \brief Batch process images by downsampling each image by factor provided.
+  */
+  static void SubsampleCollection(std::vector< typename itk::SmartPointer<TImage> > &images, unsigned factor = 2);
 #if (ITK_REVIEW || ITK_VERSION_MAJOR > 3)
   /*!
   	\fn Image::MaskAndCropCollection(std::vector< typename itk::SmartPointer<TImage> > &images, itk::SmartPointer<TMaskImage> maskImage, const size_t pixelPadding = 1)
@@ -3373,6 +3378,22 @@ std::vector< typename itk::SmartPointer<TOutImage> > Image<TImage>::OtsuMultiple
   return collection;
 }
 
+template<class TImage>
+void Image<TImage>::SubsampleCollection(std::vector< typename itk::SmartPointer<TImage> > &images, unsigned factor)
+{
+  const size_t n = images.size();
+
+  typename TImage::SizeType factors;
+  factors[0] = factor;
+  factors[1] = factor;
+  factors[2] = factor;
+
+  for (size_t j = 0; j < n; j++)
+  {
+    images[j] = SubsampleImage(images[j], factors);
+  }
+}
+
 #if (ITK_REVIEW || ITK_VERSION_MAJOR > 3)
 template<class TImage>
 template<class TMaskImage>