Merge pull request #4647 from hjmjohnson/update-gdcm

Update gdcm

Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt

@@ -17,7 +17,7 @@ endif()
 #----------------------------------------------------------------------------
 
 project(GDCM
-  VERSION 3.0.23
+  VERSION 3.0.24
   LANGUAGES CXX C
 )
 ## NOTE: the "DESCRIPTION" feature of project() was introduced in cmake 3.10.0
@@ -564,6 +564,7 @@ if(APPLE)
   if(GDCM_USE_COREFOUNDATION_LIBRARY)
     find_library(COREFOUNDATION_LIBRARY CoreFoundation )
   endif()
+  mark_as_advanced(COREFOUNDATION_LIBRARY)
 endif()
 
 #-----------------------------------------------------------------------------

Modules/ThirdParty/GDCM/src/gdcm/Source/DataDictionary/gdcmPrivateDefaultDicts.cxx

@@ -7416,11 +7416,11 @@ static const DICT_ENTRY DICOMV3DataDict [] = {
   /* end of dups */
   {0x2005,0x0032,"Philips MR Imaging DD 002",VR::SQ,VM::VM1,"Protocol Data Sequence",false },
   {0x2005,0x0034,"Philips MR Imaging DD 002",VR::LT,VM::VM1,"?SeriesTransactionUID?",false },
-  {0x2005,0x0037,"Philips MR Imaging DD 002",VR::PN,VM::VM1,"Protocol Data Name",false },
-  {0x2005,0x0038,"Philips MR Imaging DD 002",VR::PN,VM::VM1,"?MRApplicationName",false },
-  {0x2005,0x0039,"Philips MR Imaging DD 002",VR::PN,VM::VM1,"Protocol Data Type",false },
-  {0x2005,0x0040,"Philips MR Imaging DD 002",VR::PN,VM::VM1,"?MRVersionStr",false },
-  {0x2005,0x0041,"Philips MR Imaging DD 002",VR::PN,VM::VM1,"?MRCommentStr",false },
+  {0x2005,0x0037,"Philips MR Imaging DD 002",VR::LO,VM::VM1,"Protocol Data Name",false },
+  {0x2005,0x0038,"Philips MR Imaging DD 002",VR::LO,VM::VM1,"?MRApplicationName",false },
+  {0x2005,0x0039,"Philips MR Imaging DD 002",VR::LO,VM::VM1,"Protocol Data Type",false },
+  {0x2005,0x0040,"Philips MR Imaging DD 002",VR::LO,VM::VM1,"?MRVersionStr",false },
+  {0x2005,0x0041,"Philips MR Imaging DD 002",VR::LO,VM::VM1,"?MRCommentStr",false },
   {0x2005,0x0043,"Philips MR Imaging DD 002",VR::SL,VM::VM1,"Protocol Data Block Length (non-padded)",false },
   {0x2005,0x0044,"Philips MR Imaging DD 002",VR::OW,VM::VM1,"Protocol Data Block",false },
   {0x2005,0x0047,"Philips MR Imaging DD 002",VR::CS,VM::VM1,"Protocol Data Boolean",false },

Modules/ThirdParty/GDCM/src/gdcm/Source/DataStructureAndEncodingDefinition/gdcmDataSet.h

@@ -209,13 +209,9 @@ class GDCM_EXPORT DataSet
 
   // DUMB: this only search within the level of the current DataSet
   bool FindDataElement(const Tag &t) const {
-    const DataElement r(t);
-    //ConstIterator it = DES.find(r);
-    if( DES.find(r) != DES.end() )
-      {
-      return true;
-      }
-    return false;
+    const auto it = GetDataElement(t);
+    // Return if tag is found
+    return it != GetDEEnd();
     }
 
   // WARNING:

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx

@@ -48,6 +48,7 @@ namespace gdcm
 bool ImageHelper::ForceRescaleInterceptSlope = false;
 bool ImageHelper::PMSRescaleInterceptSlope = true;
 bool ImageHelper::ForcePixelSpacing = false;
+// By default, this is off, if you want behavior documented in DICOM CP 2330, turn it on
 bool ImageHelper::SecondaryCaptureImagePlaneModule = false;
 
 static bool GetOriginValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &ori)
@@ -1279,8 +1280,7 @@ Tag ImageHelper::GetSpacingTagFromMediaStorage(MediaStorage const &ms)
       // Make SecondaryCaptureImagePlaneModule act as ForcePixelSpacing
       // This is different from Basic Pixel Spacing Calibration Macro Attributes
       //
-      // Per the note: https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_A.8.html#sect_A.8.1.3
-      gdcmWarningMacro( "FIXME: Multiple tags can identify Secondary Capture spacing. This function should not be used for Secondary Capture data." );
+      gdcmDebugMacro( "FIXME: Multiple tags can identify Secondary Capture spacing. This function should not be used for Secondary Capture data." );
       t = Tag(0x0028,0x0030);
     } else {
       t = Tag(0x0018,0x2010);
@@ -1375,6 +1375,13 @@ Warning - Dicom dataset contains attributes not present in standard DICOM IOD -
   case MediaStorage::UltrasoundMultiFrameImageStorageRetired:
   // SC:
   case MediaStorage::SecondaryCaptureImageStorage:
+    // (0018,0088) DS [3]                                      #   2, 1 SpacingBetweenSlices
+    if( ImageHelper::SecondaryCaptureImagePlaneModule ) {
+    t = Tag(0x0018,0x0088);
+    } else {
+    t = Tag(0xffff,0xffff);
+    }
+    break;
   case MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage:
   case MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage:
   case MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage:
@@ -1993,7 +2000,7 @@ void ImageHelper::SetOriginValue(DataSet & ds, const Image & image)
   ms.SetFromDataSet(ds);
   assert( MediaStorage::IsImage( ms ) );
 
-  if( ms == MediaStorage::SecondaryCaptureImageStorage )
+  if( ms == MediaStorage::SecondaryCaptureImageStorage && !ImageHelper::SecondaryCaptureImagePlaneModule )
     {
     // https://sourceforge.net/p/gdcm/bugs/322/
     // default behavior is simply to pass
@@ -2007,6 +2014,7 @@ void ImageHelper::SetOriginValue(DataSet & ds, const Image & image)
    && ms != MediaStorage::PETImageStorage
    //&& ms != MediaStorage::ComputedRadiographyImageStorage
    && ms != MediaStorage::SegmentationStorage
+   && ms != MediaStorage::SecondaryCaptureImageStorage /* CP 2330 */
    && ms != MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage
    && ms != MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage
    && ms != MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage
@@ -2144,7 +2152,7 @@ void ImageHelper::SetDirectionCosinesValue(DataSet & ds, const std::vector<doubl
   ms.SetFromDataSet(ds);
   assert( MediaStorage::IsImage( ms ) );
 
-  if( ms == MediaStorage::SecondaryCaptureImageStorage )
+  if( ms == MediaStorage::SecondaryCaptureImageStorage && !ImageHelper::SecondaryCaptureImagePlaneModule )
     {
     // https://sourceforge.net/p/gdcm/bugs/322/
     // default behavior is simply to pass
@@ -2157,6 +2165,7 @@ void ImageHelper::SetDirectionCosinesValue(DataSet & ds, const std::vector<doubl
    && ms != MediaStorage::RTDoseStorage
    && ms != MediaStorage::PETImageStorage
    //&& ms != MediaStorage::ComputedRadiographyImageStorage
+   && ms != MediaStorage::SecondaryCaptureImageStorage /* CP 2330 */
    && ms != MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage
    && ms != MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage
    && ms != MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageHelper.h

@@ -129,6 +129,7 @@ class GDCM_EXPORT ImageHelper
 
   /// Set/Get Spacing from/to a File
   static std::vector<double> GetSpacingValue(File const & f);
+  /// \warning You need to call SetSpacingValue after SetOriginValue / SetDirectionCosinesValue
   static void SetSpacingValue(DataSet & ds, const std::vector<double> & spacing);
 
   /// DO NOT USE

Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmSplitMosaicFilter.cxx

@@ -271,7 +271,7 @@ bool SplitMosaicFilter::ComputeMOSAICSliceNormal( double slicenormalvector[3], b
     }
     else if( fabs(-1. - snv_dot) < 1e-6 )
     {
-      gdcmWarningMacro("SliceNormalVector is opposite direction");
+      gdcmDebugMacro("SliceNormalVector is opposite direction");
       inverted = true;
     }
     else
@@ -298,6 +298,10 @@ bool SplitMosaicFilter::ComputeMOSAICImagePositionPatient( double ret[3],
   DataSet& ds = GetFile().GetDataSet();
   DirectionCosines dc( dircos );
   dc.Normalize();
+  double z[3]={};
+  dc.Cross (z);
+  DirectionCosines::Normalize(z);
+
   const double *dircos_normalized = dc;
   const double *x = dircos_normalized;
   const double *y = dircos_normalized + 3;
@@ -315,9 +319,8 @@ bool SplitMosaicFilter::ComputeMOSAICImagePositionPatient( double ret[3],
       if( size ) {
         // two cases:
         if( size == mosaic_dims[2] ) {
-          // all mosaic have there own slice position, simply need to pick the right one
-          // Handle inverted case:
-          size_t index = inverted ? size - 1 : 0;
+          // all mosaic have there own slice position, always pick the first one for computation:
+          size_t index = 0;
           MrProtocol::Slice & slice = sa.Slices[index];
           MrProtocol::Vector3 & p = slice.Position;
           double pos[3];
@@ -327,12 +330,13 @@ bool SplitMosaicFilter::ComputeMOSAICImagePositionPatient( double ret[3],
           for(int i = 0; i < 3; ++i ) {
             ipp_csa[i] = pos[i] - mosaic_dims[0] / 2. * pixelspacing[0] * x[i] - mosaic_dims[1] / 2. * pixelspacing[1] * y[i];
           }
+          int mult = mosaic_dims[2] % 2;
+          if( inverted ) {
+            ipp_csa[2] = ipp_csa[2] + mult * pixelspacing[2];
+          }
           hasIppCsa = true;
         } else if( size == 1 /*&& mosaic_dims[2] % 2 == 0*/) {
           // there is a single SliceArray but multiple mosaics, assume this is exactly the center one
-          double z[3]={};
-          dc.Cross(z);
-          DirectionCosines::Normalize(z);
           size_t index = 0;
           MrProtocol::Slice & slice = sa.Slices[index];
           MrProtocol::Vector3 & p = slice.Position;
@@ -359,6 +363,12 @@ bool SplitMosaicFilter::ComputeMOSAICImagePositionPatient( double ret[3],
       ipp_dcm[i] = ipp[i] + (image_dims[0]  - mosaic_dims[0]) / 2. * pixelspacing[0] * x[i] +
         (image_dims[1]  - mosaic_dims[1]) / 2. * pixelspacing[1] * y[i] ;
     }
+    // When SNV inverted, first slice is actually the last one:
+    if( inverted ) {
+      for(int i = 0; i < 3; ++i ) {
+        ipp_dcm[i] = ipp_dcm[i] - z[i] * pixelspacing[2] * (mosaic_dims[2] - 1);
+      }
+    }
   }
   if(hasIppCsa ) {
     double diff[3];