Image Plane Module for SecondaryCaptureImageStorage

Create an extension for SecondaryCaptureImageStorage as if Image Plane Module would be optional. This will allow reading IPP/IOP/PixelSpacing for SecondaryCaptureImageStorage for some particular dataset. Make this feature opt-in per the discussion: * #158 This extension does not implement Basic Pixel Spacing Calibration Macro Attributes since the original target dataset to support is as follow: $ dcmdump 000198cd-cd88-4760-97d1-21bbea047fff.dcm | grep Spacin (0018,0088) DS [1] # 2, 1 SpacingBetweenSlices (0028,0030) DS [.33\.33] # 8, 2 PixelSpacing > If Pixel Spacing Calibration Type (0028,0A02) and Imager Pixel Spacing > (0018,1164) and Nominal Scanned Pixel Spacing (0018,2010) are absent, > then it cannot be determined whether or not correction or calibration > have been performed. References: * https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_C.8.6.2.html#table_C.8-25 * https://dicom.nema.org/medical/dicom/current/output/chtml/part03/sect_10.7.html#table_10-10 Co-authored-by: Matt McCormick <[email protected]> Co-authored-by: Mihail Isakov <[email protected]> Co-authored-by: Steve Pieper <[email protected]>
malaterre · Mar 25, 2024 · 0609129 · 0609129
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commit 0609129
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diff --git a/Applications/Cxx/gdcminfo.cxx b/Applications/Cxx/gdcminfo.cxx
@@ -350,6 +350,7 @@ static void PrintHelp()
   std::cout << "     --force-rescale    force rescale." << std::endl;
   std::cout << "     --force-spacing    force spacing." << std::endl;
   std::cout << "     --mosaic           dump image information of MOSAIC." << std::endl;
+  std::cout << "     --scipm            Include Image Plane Module for Secondary Capture Image." << std::endl;
 
   std::cout << "General Options:" << std::endl;
   std::cout << "  -V --verbose   more verbose (warning+error)." << std::endl;
@@ -626,6 +627,7 @@ int main(int argc, char *argv[])
   std::string xmlpath;
   int forcerescale = 0;
   int forcespacing = 0;
+  int scipm = 0;
 
   int resourcespath = 0;
   int verbose = 0;
@@ -647,6 +649,7 @@ int main(int argc, char *argv[])
         {"force-rescale", 0, &forcerescale, 1},
         {"force-spacing", 0, &forcespacing, 1},
         {"mosaic", 0, &mosaic, 1},
+        {"scipm", 0, &scipm, 1},
 
         {"verbose", 0, &verbose, 1},
         {"warning", 0, &warning, 1},
@@ -769,6 +772,7 @@ int main(int argc, char *argv[])
 
   gdcm::ImageHelper::SetForceRescaleInterceptSlope(forcerescale ? true : false);
   gdcm::ImageHelper::SetForcePixelSpacing(forcespacing ? true : false);
+  gdcm::ImageHelper::SetSecondaryCaptureImagePlaneModule(scipm ? true : false);
 
   if( filename.empty() )
     {

diff --git a/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx b/Source/MediaStorageAndFileFormat/gdcmImageHelper.cxx
@@ -48,6 +48,7 @@ namespace gdcm
 bool ImageHelper::ForceRescaleInterceptSlope = false;
 bool ImageHelper::PMSRescaleInterceptSlope = true;
 bool ImageHelper::ForcePixelSpacing = false;
+bool ImageHelper::SecondaryCaptureImagePlaneModule = false;
 
 static bool GetOriginValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &ori)
 {
@@ -578,7 +579,7 @@ std::vector<double> ImageHelper::GetOriginValue(File const & f)
 
   // else
   const Tag timagepositionpatient(0x0020, 0x0032);
-  if( ms != MediaStorage::SecondaryCaptureImageStorage && ds.FindDataElement( timagepositionpatient ) )
+  if( (ms != MediaStorage::SecondaryCaptureImageStorage || SecondaryCaptureImagePlaneModule) && ds.FindDataElement( timagepositionpatient ) )
     {
     const DataElement& de = ds.GetDataElement( timagepositionpatient );
     Attribute<0x0020,0x0032> at = {{0,0,0}}; // default value if empty
@@ -730,7 +731,7 @@ std::vector<double> ImageHelper::GetDirectionCosinesValue(File const & f)
     }
 
   dircos.resize( 6 );
-  if( ms == MediaStorage::SecondaryCaptureImageStorage || !GetDirectionCosinesFromDataSet(ds, dircos) )
+  if( (ms == MediaStorage::SecondaryCaptureImageStorage && !SecondaryCaptureImagePlaneModule) || !GetDirectionCosinesFromDataSet(ds, dircos) )
     {
     dircos[0] = 1;
     dircos[1] = 0;
@@ -774,6 +775,16 @@ bool ImageHelper::GetForcePixelSpacing()
   return ForcePixelSpacing;
 }
 
+void ImageHelper::SetSecondaryCaptureImagePlaneModule(bool b)
+{
+  SecondaryCaptureImagePlaneModule = b;
+}
+
+bool ImageHelper::GetSecondaryCaptureImagePlaneModule()
+{
+  return SecondaryCaptureImagePlaneModule;
+}
+
 bool GetRescaleInterceptSlopeValueFromDataSet(const DataSet& ds, std::vector<double> & interceptslope)
 {
   Attribute<0x0028,0x1052> at1;
@@ -1264,6 +1275,14 @@ Tag ImageHelper::GetSpacingTagFromMediaStorage(MediaStorage const &ms)
     t = Tag(0x3002,0x0011); // ImagePlanePixelSpacing
     break;
   case MediaStorage::SecondaryCaptureImageStorage:
+    if( ImageHelper::SecondaryCaptureImagePlaneModule ) {
+      // Make SecondaryCaptureImagePlaneModule act as ForcePixelSpacing
+      // This is different from Basic Pixel Spacing Calibration Macro Attributes
+      t = Tag(0x0028,0x0030);
+    } else {
+      t = Tag(0x0018,0x2010);
+    }
+    break;
   case MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage:
   case MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage:
   case MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage:

diff --git a/Source/MediaStorageAndFileFormat/gdcmImageHelper.h b/Source/MediaStorageAndFileFormat/gdcmImageHelper.h
@@ -85,6 +85,13 @@ class GDCM_EXPORT ImageHelper
   static void SetForcePixelSpacing(bool);
   static bool GetForcePixelSpacing();
 
+  /// Opt into Image Plane Module for Secondary Capture Image Storage
+  /// Enable reading Image Position Patient (IPP), Image Orientation Patient
+  /// (IOP) and Pixel Spacing (0028,0030)
+  /// This is a custom extension for some existing dataset (academic)
+  static void SetSecondaryCaptureImagePlaneModule(bool);
+  static bool GetSecondaryCaptureImagePlaneModule();
+
   /// This function checks tags (0x0028, 0x0010) and (0x0028, 0x0011) for the
   /// rows and columns of the image in pixels (as opposed to actual distances).
   /// The output is {col , row}
@@ -156,6 +163,7 @@ class GDCM_EXPORT ImageHelper
   static bool ForceRescaleInterceptSlope;
   static bool PMSRescaleInterceptSlope;
   static bool ForcePixelSpacing;
+  static bool SecondaryCaptureImagePlaneModule;
 };
 
 } // end namespace gdcm