[Gdcm-hackers] gdcm-git:Grassroots DICOM branch master updated. f35c4876015682222ea10a23d207213eed1673af

[Mathieu M. <ma...@us...>]

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https://sourceforge.net/p/gdcm/gdcm/ci/f35c4876015682222ea10a23d207213eed1673af/

commit f35c4876015682222ea10a23d207213eed1673af
Merge: d19fdba 5adf008
Author: Mathieu Malaterre <mat...@gm...>
Date:   Wed Mar 13 13:06:28 2013 +0100

    Merge branch 'release'


https://sourceforge.net/p/gdcm/gdcm/ci/d19fdba396f0c941cafab4a2d189882ed56c6da8/

commit d19fdba396f0c941cafab4a2d189882ed56c6da8
Author: Mathieu Malaterre <mat...@gm...>
Date:   Wed Mar 13 13:05:26 2013 +0100

    Implement more options in gdcmimg
    
    This commit add support for BitsAllocated,BitsStored and HighBits when needed
    It also allow for specifying PhotometricInterpretation

diff --git a/Applications/Cxx/gdcmimg.cxx b/Applications/Cxx/gdcmimg.cxx
index d760c89..02dd774 100644
--- a/Applications/Cxx/gdcmimg.cxx
+++ b/Applications/Cxx/gdcmimg.cxx
@@ -130,6 +130,8 @@ static void PrintHelp()
   std::cout << "     --sign %s         Pixel sign (0/1)." << std::endl;
   std::cout << "     --spp  %d         Sample Per Pixel (1/3)." << std::endl;
   std::cout << "     --pc [01]         Change planar configuration." << std::endl;
+  std::cout << "     --pi [str]        Change photometric interpretation." << std::endl;
+  std::cout << "     --pf %d,%d,%d     Change pixel format: (BA,BS,HB)." << std::endl;
   std::cout << "  -s --size %d,%d      Size." << std::endl;
   std::cout << "  -C --sop-class-uid   SOP Class UID (name or value)." << std::endl;
   std::cout << "  -T --study-uid       Study UID." << std::endl;
@@ -414,6 +416,10 @@ int main (int argc, char *argv[])
   std::string sopclass;
   std::string lsb_msb;
   int sopclassuid = 0;
+  int pinter = 0;
+  std::string pinterstr;
+  int pformat = 0;
+  std::string pformatstr;
 
   int verbose = 0;
   int warning = 0;
@@ -445,6 +451,8 @@ int main (int argc, char *argv[])
         {"sign", 1, &sign, 1}, //
         {"spp", 1, &spp, 1}, //
         {"pc", 1, &pconf, 1}, //
+        {"pi", 1, &pinter, 1}, //
+        {"pf", 1, &pformat, 1}, //
 
 // General options !
         {"verbose", 0, &verbose, 1},
@@ -541,6 +549,18 @@ int main (int argc, char *argv[])
             assert( strcmp(s, "pc") == 0 );
             pconf = atoi(optarg);
             }
+          else if( option_index == 14 ) /* pinter */
+            {
+            assert( strcmp(s, "pi") == 0 );
+            pinter = 1;
+            pinterstr = optarg;
+            }
+          else if( option_index == 15 ) /* pformat */
+            {
+            assert( strcmp(s, "pf") == 0 );
+            pformat = 1;
+            pformatstr = optarg;
+            }
           //printf (" with arg %s", optarg);
           }
         //printf ("\n");
@@ -754,6 +774,31 @@ int main (int argc, char *argv[])
     {
     if( pixelspp != 3 ) return 1;
     }
+  gdcm::PixelFormat pfref = gdcm::PixelFormat::UINT8;
+  if( pformat )
+    {
+    int ba, bs, hb;
+    int n = sscanf( pformatstr.c_str(), "%d,%d,%d", &ba, &bs, &hb );
+    if( n != 3 ) return 1;
+    pfref.SetBitsAllocated( ba );
+    pfref.SetBitsStored( bs );
+    pfref.SetHighBit( hb );
+    if( spp )
+      pfref.SetSamplesPerPixel( pixelspp );
+    if( sign )
+      pfref.SetPixelRepresentation( pixelsign );
+    }
+  gdcm::PhotometricInterpretation::PIType refpi = gdcm::PhotometricInterpretation::MONOCHROME2;
+  if( pinter )
+    {
+    refpi = gdcm::PhotometricInterpretation::GetPIType( pinterstr.c_str() );
+    if( refpi == gdcm::PhotometricInterpretation::UNKNOW
+      || refpi == gdcm::PhotometricInterpretation::PI_END )
+      {
+      std::cerr << "Invalid PI: " << pinterstr << std::endl;
+      return 1;
+      }
+    }
 
   const char *inputextension = filename.GetExtension();
   const char *outputextension = outfilename.GetExtension();
@@ -784,7 +829,7 @@ int main (int argc, char *argv[])
         }
       raw.SetDimensions( dims );
       gdcm::PixelFormat pf = gdcm::PixelFormat::UINT8;
-      gdcm::PhotometricInterpretation pi = gdcm::PhotometricInterpretation::MONOCHROME2;
+      gdcm::PhotometricInterpretation pi = refpi;
       if( gdcm::System::StrCaseCmp(inputextension,".rgb") == 0 )
         {
         pi = gdcm::PhotometricInterpretation::RGB;
@@ -847,7 +892,7 @@ int main (int argc, char *argv[])
       gdcm::PixelFormat pf = gdcm::PixelFormat::UINT8;
       if( !GetPixelFormat( pf, depth, bpp, sign, pixelsign ) ) return 1;
       rle.SetPixelFormat( pf );
-      gdcm::PhotometricInterpretation pi = gdcm::PhotometricInterpretation::MONOCHROME2;
+      gdcm::PhotometricInterpretation pi = refpi;
       rle.SetPhotometricInterpretation( pi );
 
       if( !Populate( writer, rle, filenames ) ) return 1;
@@ -867,8 +912,22 @@ int main (int argc, char *argv[])
       || gdcm::System::StrCaseCmp(inputextension,".ppm") == 0 )
       {
       gdcm::PNMCodec pnm;
+      // Let's handle the case where user really wants to specify the data:
+      gdcm::PixelFormat pf = gdcm::PixelFormat::UINT8;
+      if( !GetPixelFormat( pf, depth, bpp, sign, pixelsign ) ) return 1;
+
       gdcm::PixmapWriter writer;
       if( !Populate( writer, pnm, filenames ) ) return 1;
+      // populate will guess pixel format and photometric inter from file, need
+      // to override after calling Populate:
+      if( pformat )
+        {
+        writer.GetPixmap().SetPixelFormat( pfref );
+        }
+      if( pinter )
+        {
+        writer.GetPixmap().SetPhotometricInterpretation( refpi );
+        }
       if( !AddUIDs(sopclassuid, sopclass, study_uid, series_uid, writer ) ) return 1;
 
       writer.SetFileName( outfilename );

https://sourceforge.net/p/gdcm/gdcm/ci/cb7333c70877377adefa8aaab49fd0f9f3c26f85/

commit cb7333c70877377adefa8aaab49fd0f9f3c26f85
Author: Mathieu Malaterre <mat...@gm...>
Date:   Wed Mar 13 13:05:11 2013 +0100

    Remove a warning about assert being redefined

diff --git a/Utilities/gdcmcharls/config.h b/Utilities/gdcmcharls/config.h
index ec90c21..ce7b42b 100644
--- a/Utilities/gdcmcharls/config.h
+++ b/Utilities/gdcmcharls/config.h
@@ -9,7 +9,6 @@
 #ifdef NDEBUG
 #  ifndef ASSERT
 #    define ASSERT(t) { }
-#    define assert(t) { }
 #  endif
 #else
 #include <assert.h>

-----------------------------------------------------------------------

Summary of changes:
 Applications/Cxx/gdcmimg.cxx  |   63 +++++++++++++++++++++++++++++++++++++++-
 Utilities/gdcmcharls/config.h |    1 -
 2 files changed, 61 insertions(+), 3 deletions(-)


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