Merge branch 'dicomNet' into 'master'

Basic Functionality - UI, DCMDB, DCMNet

See merge request cpt_bioeng/drt!11

reg23Topograms/itkDTRrecon/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8.8)
+cmake_minimum_required(VERSION 2.8.12)
 
 SET(LIB_NAME itkDTRrecon)
 
@@ -10,7 +10,6 @@ find_package(VTK REQUIRED)
 INCLUDE_DIRECTORIES(${VTK_INCLUDE_DIRS})
 
 FIND_PACKAGE(GDCM REQUIRED)
-include(${GDCM_USE_FILE})
 INCLUDE_DIRECTORIES(${GDCM_INCLUDE_DIRS})
 
 SET(SRCS
@@ -34,7 +33,7 @@ SET(LINK_LIBS
     ${LIB_NAME}
     ${VTK_LIBRARIES}
     ${ITK_LIBRARIES}
-    ${GDCM_LIBRARIES}
+    gdcmMSFF
 )
 
 TARGET_LINK_LIBRARIES(
@@ -45,3 +44,7 @@ TARGET_LINK_LIBRARIES(
 target_include_directories (${LIB_NAME}
     PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}
 )
+
+
+set(EXTRA_LIBS ${EXTRA_LIBS} itkDTRrecon)
+set(EXTRA_LIBS ${EXTRA_LIBS} PARENT_SCOPE)

reg23Topograms/itkDTRrecon/itkImageProcessor.cpp

@@ -22,6 +22,7 @@ gfattori 08.11.2021
 #include "itkMatrix.h"
 #include "itkGDCMSeriesFileNames.h"
 #include "itkOrientImageFilter.h"
+#include <gdcmIPPSorter.h>
 
 #include <string>
 
@@ -369,8 +370,108 @@ void itkImageProcessor::SetCustom_2Dsize(int nX1, int nY1,int nX2,int nY2)
     //TODO UPDATE TO FOLLOW
 }
 
+int itkImageProcessor::load3DSerieFromFiles( std::vector<std::string> v_fnames){
 
-int itkImageProcessor::load3DSerie(const char * pcDirName)
+    tPatOrientation m_PatOrientation
+            = tPatOrientation::NotDefined;
+
+    /* Since are not sure DB indexer to sort images,
+     * we run the IPP sorter here. */
+    using IppSorterType = gdcm::IPPSorter;
+    IppSorterType ZSorter;
+
+    ZSorter.SetComputeZSpacing( true );
+    ZSorter.SetZSpacingTolerance( 1e-3 );
+    bool b = ZSorter.Sort(v_fnames);
+    if( !b )
+    {
+        std::cerr << "itkImageProcessor::load3DSerieFromFiles :: Failed to sort files based on IPP." << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    /* Some debugging output */
+    //std::cout << "Sorting succeeded:" << std::endl;
+    //ZSorter.Print( std::cout );
+    //std::cout << "Found z-spacing:" << std::endl;
+    //std::cout << ZSorter.GetZSpacing() << std::endl;
+
+    const std::vector<std::string> & v_sortedFnames =
+            ZSorter.GetFilenames();
+
+    try
+    {
+
+        using ImageIOType = itk::GDCMImageIO;
+        ImageIOType::Pointer dicomIO = ImageIOType::New();
+
+        ImageSeriesReaderType3D::Pointer
+                imageSeriesReader3D = ImageSeriesReaderType3D::New();
+
+        imageSeriesReader3D->SetImageIO(dicomIO);
+        imageSeriesReader3D->SetFileNames(v_sortedFnames);
+        //imageSeriesReader3D->SetNumberOfWorkUnits(8);
+        imageSeriesReader3D->ForceOrthogonalDirectionOff(); // properly read CTs with gantry tilt
+        //imageSeriesReader3D->SetSpacingWarningRelThreshold();
+
+        imageSeriesReader3D->Update();
+
+        if(v_fnames.size()>0){
+
+            gdcm::Reader R;
+            R.SetFileName(v_sortedFnames.at(0).c_str());
+            if(!R.Read())
+            {
+                cerr<<"ERROR: cannot read file: "<<v_sortedFnames.at(0).c_str()<<endl;
+                return -1;
+            }
+            const gdcm::File &file = R.GetFile();
+            const gdcm::DataSet &ds = file.GetDataSet();
+
+            char* sTmpString = new char [255];
+            strcpy( sTmpString,gGetStringValueFromTag( gdcm::Tag(0x0018,0x5100), ds));
+            *std::remove(sTmpString, sTmpString + strlen(sTmpString), ' ') = 0;
+
+            if(!strcmp(sTmpString,ImageOrientationStrings[eImageOrientationType::HFS])){
+                m_PatOrientation = eImageOrientationType::HFS;
+            } else if(!strcmp(sTmpString,ImageOrientationStrings[eImageOrientationType::FFS])){
+                m_PatOrientation = eImageOrientationType::FFS;
+            } else {
+                m_PatOrientation =  eImageOrientationType::NotDefined;
+            }
+
+            delete []  (sTmpString);
+        } else {
+            return -1;
+        }
+
+
+        CastFilterType3D::Pointer caster3D =
+                CastFilterType3D::New();
+
+        caster3D->SetInput(imageSeriesReader3D->GetOutput());
+        caster3D->Update();
+
+        m_VolumeSourceDupli->SetInputImage(caster3D->GetOutput());
+        m_VolumeSourceDupli->Update();
+
+        caster3D = NULL;
+
+
+    }
+    catch (itk::ExceptionObject & ex)
+    {
+        std::cout << ex << std::endl;
+        return EXIT_FAILURE;
+    }
+
+    InternalImageType::Pointer m_InputImage =
+            m_VolumeSourceDupli->GetOutput();
+    return
+            this->fill3DVolumeMeta(m_InputImage, m_PatOrientation);
+
+}
+
+int itkImageProcessor::load3DSerieFromFolder(const char * pcDirName)
 {
 
     using NamesGeneratorType = itk::GDCMSeriesFileNames;
@@ -402,7 +503,7 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
         else
         {
             std::cout << "No DICOMs in: " << pcDirName << std::endl;
-            return EXIT_SUCCESS;
+            return EXIT_FAILURE;
         }
 
         while (seriesItr != seriesEnd)
@@ -467,7 +568,7 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
                     m_PatOrientation =  eImageOrientationType::NotDefined;
                 }
 
-                free (sTmpString);
+                delete []  (sTmpString);
             } else {
                 return -1;
             }
@@ -493,9 +594,17 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
         return EXIT_FAILURE;
     }
 
-
     InternalImageType::Pointer m_InputImage =
             m_VolumeSourceDupli->GetOutput();
+    return
+            this->fill3DVolumeMeta(m_InputImage, m_PatOrientation);
+
+}
+
+/** Fill Meta after 3D volume load */
+int itkImageProcessor::fill3DVolumeMeta(
+        InternalImageType::Pointer m_InputImage,
+        tPatOrientation m_PatOrientation){
 
 
     if(m_CTMetaInfo != NULL){
@@ -597,9 +706,9 @@ int itkImageProcessor::load3DSerie(const char * pcDirName)
     image3DIn =
             m_3DInputChangeInformationToZero->GetOutput();
 
-
     return EXIT_SUCCESS;
 
+
 }
 
 const std::vector <double>  itkImageProcessor::GetRTImportOffset()

reg23Topograms/itkDTRrecon/itkImageProcessor.h

@@ -72,7 +72,9 @@ public:
     itkTypeMacro(itkImageProcessor, Object);
 
     /** Input data load methods*/
-    int load3DSerie(const char* );
+    int load3DSerieFromFolder(const char* );
+    int load3DSerieFromFiles( std::vector<std::string> );
+
     int load2D(const char *);
 
     void loadRTPlanInfo(double, double, double, double, double ,double);
@@ -167,6 +169,9 @@ private:
     itkImageProcessor(const Self&); //purposely not implemented
     void operator=(const Self&); //purposely not implemented
 
+    /** Fill Meta after 3D volume load */
+    int fill3DVolumeMeta(InternalImageType::Pointer,
+                          tPatOrientation);
 
     /** Image types */
     using ImageType2D = itk::Image<PixelType3D, Dimension>;

reg23Topograms/itkDTRrecon/vtkContourTopogramProjectionFilter.cxx

@@ -148,6 +148,8 @@ int vtkContourTopogramProjectionFilter::RequestData(
         pp2[1] -= dProjectionLPSOffset [1];
         pp2[2] -= dProjectionLPSOffset [2];
 
+//        std::cout << ii << " " << pp2[0] << " " << pp2[1] << " " << pp2[2] << std::endl;
+
         PrjPoints->InsertPoint(ii,pp2);
      }