ENH: A new program called "BRAINSConstellationLandmarksTransform" is added

BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.cxx

@@ -0,0 +1,73 @@
+/*
+ * Author: Ali Ghayoor
+ * at Psychiatry Imaging Lab,
+ * University of Iowa Health Care 2013
+ */
+
+/*
+ This program program uses the input transform to propagate
+ reference landmarks to the target landmark file.
+*/
+
+#include "itkPoint.h"
+#include "itkTransformFileReader.h"
+#include "itkCompositeTransform.h"
+#include "Slicer3LandmarkIO.h"
+
+#include "BRAINSConstellationLandmarksTransformCLP.h"
+
+
+int main( int argc, char *argv[] )
+{
+  PARSE_ARGS;
+
+  if( inputLandmarksFile == ""
+     || inputTransformFile == ""
+     || outputLandmarksFile == "")
+    {
+    std::cerr << "Input and output file names should be given by commandline. " << std::endl;
+    std::cerr << "Usage:\n"
+              << "~/BRAINSConstellationLandmarksTransform\n"
+              << "--inputLandmarksFile (-i)\n"
+              << "--inputTransformFile (-t)\n"
+              << "--outputLandmarksFile (-o)"
+              << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  const unsigned int Dimension = 3;
+
+  typedef itk::Point<double,Dimension> PointType;
+  typedef std::map< std::string, PointType > LandmarksMapType;
+
+  LandmarksMapType origLandmarks = ReadSlicer3toITKLmk( inputLandmarksFile );
+  LandmarksMapType transformedLandmarks;
+
+  typedef itk::TransformFileReader ReaderType;
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName( inputTransformFile );
+  reader->Update();
+
+  ReaderType::TransformListType *transformList = reader->GetTransformList();
+
+  typedef itk::CompositeTransform<double, Dimension> CompositeTransformType;
+
+  CompositeTransformType::Pointer inputCompTrans =
+  dynamic_cast<CompositeTransformType *>( transformList->front().GetPointer() );
+  if( inputCompTrans.IsNull() )
+    {
+    std::cerr << "The input transform should be a composite transform." << std::endl;
+    return EXIT_FAILURE;
+    }
+
+  LandmarksMapType::const_iterator it = origLandmarks.begin();
+  for(; it!=origLandmarks.end(); it++)
+    {
+    transformedLandmarks[it->first] = inputCompTrans->TransformPoint( it->second );
+    }
+
+  WriteITKtoSlicer3Lmk( outputLandmarksFile, transformedLandmarks );
+  std::cout << "The transformed landmarks file is written." << std::endl;
+
+  return EXIT_SUCCESS;
+}

BRAINSConstellationDetector/src/BRAINSConstellationLandmarksTransform.xml

@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="utf-8"?>
+<executable>
+  <category>Utilities.BRAINS</category>
+  <title>Landmarks Transformation</title>
+  <description>
+  This program converts the original landmark file to the target landmark file using the input transform.
+  </description>
+  <version>1.0</version>
+  <documentation-url> </documentation-url>
+  <license> </license>
+  <contributor>Ali Ghayoor</contributor>
+<acknowledgements>
+</acknowledgements>
+
+  <parameters>
+    <label>IO</label>
+    <description>Input/output parameters</description>
+
+    <file fileExtensions=".fcsv">
+      <name>inputLandmarksFile</name>
+      <flag>i</flag>
+      <longflag>inputLandmarksFile</longflag>
+      <label>Input landmarks file</label>
+      <channel>input</channel>
+      <description>Input landmarks file (.fcsv)</description>
+    </file>
+
+    <transform fileExtensions=".h5,.hdf5">
+      <name>inputTransformFile</name>
+      <flag>t</flag>
+      <longflag>inputTransformFile</longflag>
+      <label>Input transform file</label>
+      <channel>input</channel>
+      <description>input composite transform file (.h5,.hdf5)</description>
+    </transform>
+
+    <file fileExtensions=".fcsv">
+      <name>outputLandmarksFile</name>
+      <flag>o</flag>
+      <longflag>outputLandmarksFile</longflag>
+      <label>Output landmarks file</label>
+      <channel>output</channel>
+      <description>Output landmarks file (.fcsv)</description>
+    </file>
+
+  </parameters>
+
+</executable>

BRAINSConstellationDetector/src/CMakeLists.txt

@@ -26,6 +26,7 @@ set(ALL_PROGS_LIST
   landmarksConstellationAligner
   landmarksConstellationWeights
   BinaryMaskEditorBasedOnLandmarks
+  BRAINSConstellationLandmarksTransform
   )
 foreach(prog ${ALL_PROGS_LIST})
   StandardBRAINSBuildMacro(NAME ${prog} TARGET_LIBRARIES landmarksConstellationCOMMONLIB )

DWIConvert/SiemensDWIConverter.h

@@ -289,19 +289,19 @@ class SiemensDWIConverter : public DWIConverter
   void DeMosaic()
     {
       // de-mosaic
-      this->m_Rows /= this->m_MMosaic;
-      this->m_Cols /= this->m_NMosaic;
+      this->m_Cols /= this->m_MMosaic;
+      this->m_Rows /= this->m_NMosaic;
 
       // center the volume since the image position patient given in the
       // dicom header was useless
-      this->m_Origin[0] = -(this->m_Rows * (this->m_NRRDSpaceDirection[0][0])
-                         + this->m_Cols * (this->m_NRRDSpaceDirection[0][1])
+      this->m_Origin[0] = -(this->m_Cols * (this->m_NRRDSpaceDirection[0][0])
+                         + this->m_Rows * (this->m_NRRDSpaceDirection[0][1])
                          + this->m_SlicesPerVolume * (this->m_NRRDSpaceDirection[0][2]) ) / 2.0;
-      this->m_Origin[1] = -(this->m_Rows * (this->m_NRRDSpaceDirection[1][0])
-                         + this->m_Cols * (this->m_NRRDSpaceDirection[1][1])
+      this->m_Origin[1] = -(this->m_Cols * (this->m_NRRDSpaceDirection[1][0])
+                         + this->m_Rows * (this->m_NRRDSpaceDirection[1][1])
                          + this->m_SlicesPerVolume * (this->m_NRRDSpaceDirection[1][2]) ) / 2.0;
-      this->m_Origin[2] = -(this->m_Rows * (this->m_NRRDSpaceDirection[2][0])
-                         + this->m_Cols * (this->m_NRRDSpaceDirection[2][1])
+      this->m_Origin[2] = -(this->m_Cols * (this->m_NRRDSpaceDirection[2][0])
+                         + this->m_Rows * (this->m_NRRDSpaceDirection[2][1])
                          + this->m_SlicesPerVolume * (this->m_NRRDSpaceDirection[2][2]) ) / 2.0;
 
       VolumeType::Pointer img = this->m_Volume;