[Gdcm-hackers] gdcm-git:Grassroots DICOM branch release updated. 4c9220ed971f01a9df1396dadfedd74c90b9faab

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

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- Log -----------------------------------------------------------------
https://sourceforge.net/p/gdcm/gdcm/ci/4c9220ed971f01a9df1396dadfedd74c90b9faab/

commit 4c9220ed971f01a9df1396dadfedd74c90b9faab
Merge: 5e1a5a658 c6a84d0c2
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 16:21:39 2020 +0100

    Merge branch 'release-2-8' into release


https://sourceforge.net/p/gdcm/gdcm/ci/c6a84d0c2f8704e8c2620d936332c3f8652cfb87/

commit c6a84d0c2f8704e8c2620d936332c3f8652cfb87
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 16:05:12 2020 +0100

    VR:OB when in encapsulated format

diff --git a/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx b/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
index 57f602633..9f0810f22 100644
--- a/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx
@@ -610,7 +610,10 @@ bool PixmapWriter::PrepareWrite( MediaStorage const & ref_ms )
       case 12:
       case 16:
       case 32:
-        depixdata.SetVR( VR::OW );
+        if( depixdata.GetSequenceOfFragments() )
+          depixdata.SetVR( VR::OB );
+        else
+          depixdata.SetVR( VR::OW );
         break;
       default:
         assert( 0 && "should not happen" );

https://sourceforge.net/p/gdcm/gdcm/ci/5e1a5a65831d4d793e7bcfc7a54c8d5358c90f75/

commit 5e1a5a65831d4d793e7bcfc7a54c8d5358c90f75
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 15:17:38 2020 +0100

    Revert "Better handling of encapsulated Pixel Data"
    
    This reverts commit e429ef9a830adecff14304e14002f856457482da.

diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
index f17f512f3..45301ac5e 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
@@ -15,7 +15,6 @@
 #define GDCMDATASET_TXX
 
 #include "gdcmByteValue.h"
-#include "gdcmSequenceOfFragments.h"
 #include "gdcmPrivateTag.h"
 #include "gdcmParseException.h"
 
@@ -434,24 +433,11 @@ namespace gdcm_ns
         gdcmAssertAlwaysMacro( pd.GetTag() == Tag(0x7fe0,0x0010) );
         gdcmAssertAlwaysMacro( pd.GetVR() == VR::OB );
         gdcmAssertAlwaysMacro( pd.IsUndefinedLength() );
-        const VL fraglen = locallength - l - 12;
-#if 1
-        Fragment frag;
-        frag.SetVL( fraglen );
-        frag.template ReadValue<TSwap>(is);
-        SmartPointer<SequenceOfFragments> sqf = new SequenceOfFragments;
-        sqf->AddFragment(frag);
-        pd.SetValue( *sqf );
-        InsertDataElement( pd );
-        length = locallength = l;
-        gdcmWarningMacro( "Item length is wrong" );
-        throw Exception( "Changed Length" );
-#else
-        pd.SetVL( fraglen );
+        const VL pdlen = locallength - l - 12;
+        pd.SetVL( pdlen );
         pd.template ReadValue<TSwap>(is, true);
         InsertDataElement( pd );
         length = locallength = l;
-#endif
         }
       else
         {

https://sourceforge.net/p/gdcm/gdcm/ci/e429ef9a830adecff14304e14002f856457482da/

commit e429ef9a830adecff14304e14002f856457482da
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 15:02:54 2020 +0100

    Better handling of encapsulated Pixel Data
    
    When VL is undefined try to load the Pixel Data as Encapsulated, craft an empty Basic Offset Table

diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
index 45301ac5e..f17f512f3 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
@@ -15,6 +15,7 @@
 #define GDCMDATASET_TXX
 
 #include "gdcmByteValue.h"
+#include "gdcmSequenceOfFragments.h"
 #include "gdcmPrivateTag.h"
 #include "gdcmParseException.h"
 
@@ -433,11 +434,24 @@ namespace gdcm_ns
         gdcmAssertAlwaysMacro( pd.GetTag() == Tag(0x7fe0,0x0010) );
         gdcmAssertAlwaysMacro( pd.GetVR() == VR::OB );
         gdcmAssertAlwaysMacro( pd.IsUndefinedLength() );
-        const VL pdlen = locallength - l - 12;
-        pd.SetVL( pdlen );
+        const VL fraglen = locallength - l - 12;
+#if 1
+        Fragment frag;
+        frag.SetVL( fraglen );
+        frag.template ReadValue<TSwap>(is);
+        SmartPointer<SequenceOfFragments> sqf = new SequenceOfFragments;
+        sqf->AddFragment(frag);
+        pd.SetValue( *sqf );
+        InsertDataElement( pd );
+        length = locallength = l;
+        gdcmWarningMacro( "Item length is wrong" );
+        throw Exception( "Changed Length" );
+#else
+        pd.SetVL( fraglen );
         pd.template ReadValue<TSwap>(is, true);
         InsertDataElement( pd );
         length = locallength = l;
+#endif
         }
       else
         {

https://sourceforge.net/p/gdcm/gdcm/ci/081616400886d3b6e516c91632e139f487b69e7d/

commit 081616400886d3b6e516c91632e139f487b69e7d
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 15:17:18 2020 +0100

    Update code location

diff --git a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
index 4acdcc69d..45301ac5e 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx
@@ -421,7 +421,9 @@ namespace gdcm_ns
         }
       else if( /*pe.GetLastElement().GetTag() == Tag(0xffd8,0xffe0) &&*/ de.GetTag() == Tag(0x7fe0,0x0010) && de.IsUndefinedLength() )
         {
+        // Bug_Siemens_PrivateIconNoItem.dcm
         // PET-GE-dicomwrite-PixelDataSQUN.dcm
+        // PET-GE-dicomwrite-PixelDataSQUNv2.dcm
         // some bozo crafted an undefined length Pixel Data but is actually
         // defined length. Since inside SQ/Item it should be possible to
         // compute the proper length

https://sourceforge.net/p/gdcm/gdcm/ci/b1b806cdf19e74c8b0548af4eb74d3d53db46b1c/

commit b1b806cdf19e74c8b0548af4eb74d3d53db46b1c
Author: Mathieu Malaterre <mat...@gm...>
Date:   Fri Mar 20 15:02:02 2020 +0100

    Remvoe extra assert()
    
    The whole point of this code path is to recompute invalid Sequence Length

diff --git a/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx b/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
index f92a5c1e8..0d28e74d2 100644
--- a/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
+++ b/Source/DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx
@@ -339,7 +339,6 @@ std::istream &ExplicitDataElement::ReadValue(std::istream &is, bool readvalues)
 #ifdef GDCM_SUPPORT_BROKEN_IMPLEMENTATION
   if( SequenceOfItems *sqi = dynamic_cast<SequenceOfItems*>(&GetValue()) )
     {
-    assert( ValueField->GetLength() == ValueLengthField );
     // Recompute the total length:
     if( !ValueLengthField.IsUndefined() )
       {

https://sourceforge.net/p/gdcm/gdcm/ci/7e3be76f17521d4124eb97ca0cddcda5f4c623bb/

commit 7e3be76f17521d4124eb97ca0cddcda5f4c623bb
Author: Mathieu Malaterre <mat...@gm...>
Date:   Thu Oct 24 08:54:09 2019 +0200

    Handle the case where Slope is negative

diff --git a/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx b/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx
index b03accd30..0db715e78 100644
--- a/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx
+++ b/Source/MediaStorageAndFileFormat/gdcmRescaler.cxx
@@ -129,8 +129,11 @@ static inline PixelFormat::ScalarType ComputeBestFit(const PixelFormat &pf, doub
   PixelFormat::ScalarType st = PixelFormat::UNKNOWN;
   assert( slope == (int)slope && intercept == (int)intercept);
 
-  const double min = slope * (double)pf.GetMin() + intercept;
-  const double max = slope * (double)pf.GetMax() + intercept;
+  assert( pf.GetMin() <= pf.GetMax() );
+  const double pfmin = slope >= 0 ? pf.GetMin() : pf.GetMax();
+  const double pfmax = slope >= 0 ? pf.GetMax() : pf.GetMin();
+  const double min = slope * pfmin + intercept;
+  const double max = slope * pfmax + intercept;
   assert( min <= max );
   assert( min == (int64_t)min && max == (int64_t)max );
   if( min >= 0 ) // unsigned
@@ -402,8 +405,14 @@ static PixelFormat ComputeInverseBestFitFromMinMax(/*const PixelFormat &pf,*/ do
   PixelFormat st = PixelFormat::UNKNOWN;
   //assert( slope == (int)slope && intercept == (int)intercept);
 
+  assert( _min <= _max );
   double dmin = (_min - intercept ) / slope;
   double dmax = (_max - intercept ) / slope;
+  if( slope < 0 )
+    {
+    dmin = (_max - intercept ) / slope;
+    dmax = (_min - intercept ) / slope;
+    }
   assert( dmin <= dmax );
   assert( dmax <= std::numeric_limits<int64_t>::max() );
   assert( dmin >= std::numeric_limits<int64_t>::min() );

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

Summary of changes:
 Source/DataStructureAndEncodingDefinition/gdcmDataSet.txx            | 2 ++
 .../DataStructureAndEncodingDefinition/gdcmExplicitDataElement.txx   | 1 -
 Source/MediaStorageAndFileFormat/gdcmPixmapWriter.cxx                | 5 ++++-
 3 files changed, 6 insertions(+), 2 deletions(-)


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