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gdcmImageHelper.cxx
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gdcmImageHelper.cxx
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/*=========================================================================
Program: GDCM (Grassroots DICOM). A DICOM library
Copyright (c) 2006-2011 Mathieu Malaterre
All rights reserved.
See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notice for more information.
=========================================================================*/
#include "gdcmImageHelper.h"
#include "gdcmMediaStorage.h"
#include "gdcmFile.h"
#include "gdcmDataSet.h"
#include "gdcmDataElement.h"
#include "gdcmItem.h"
#include "gdcmSequenceOfItems.h"
#include "gdcmGlobal.h"
#include "gdcmDictEntry.h"
#include "gdcmDicts.h"
#include "gdcmAttribute.h"
#include "gdcmImage.h"
#include "gdcmDirectionCosines.h"
#include "gdcmSegmentedPaletteColorLookupTable.h"
#include "gdcmByteValue.h"
#include <cmath> // fabs
/* TODO:
*
* (0028,9145) SQ (Sequence with undefined length #=1) # u/l, 1 PixelValueTransformationSequence
* (fffe,e000) na (Item with undefined length #=3) # u/l, 1 Item
* (0028,1052) DS [0.00000] # 8, 1 RescaleIntercept
* (0028,1053) DS [1.00000] # 8, 1 RescaleSlope
* (0028,1054) LO [US] # 2, 1 RescaleType
* (fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
* (fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
*
* Same goes for window level...
*/
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)
{
if( !ds.FindDataElement( tfgs ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tfgs ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tfgs ).GetValueAsSQ();
if( !(sqi && sqi->GetNumberOfItems() > 0) ) return false;
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// Plane position Sequence
const Tag tpms(0x0020,0x9113);
if( !subds.FindDataElement(tpms) ) return false;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
if( sqi2 && !sqi2->IsEmpty() )
{
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
//
const Tag tps(0x0020,0x0032);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
//assert( bv );
Attribute<0x0020,0x0032> at;
at.SetFromDataElement( de );
//at.Print( std::cout );
ori.push_back( at.GetValue(0) );
ori.push_back( at.GetValue(1) );
ori.push_back( at.GetValue(2) );
return true;
}
return false;
}
static bool GetDirectionCosinesValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &dircos)
{
if( !ds.FindDataElement( tfgs ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tfgs ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tfgs ).GetValueAsSQ();
if( !(sqi && sqi->GetNumberOfItems() > 0) ) return false;
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// Plane position Sequence
const Tag tpms(0x0020,0x9116);
if( !subds.FindDataElement(tpms) ) return false;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
if( !(sqi2 && sqi2->GetNumberOfItems()) ) return false;
assert( sqi2 && sqi2->GetNumberOfItems() );
// Take it from the first item
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
//
const Tag tps(0x0020,0x0037);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
//assert( bv );
Attribute<0x0020,0x0037> at;
at.SetFromDataElement( de );
dircos.push_back( at.GetValue(0) );
dircos.push_back( at.GetValue(1) );
dircos.push_back( at.GetValue(2) );
dircos.push_back( at.GetValue(3) );
dircos.push_back( at.GetValue(4) );
dircos.push_back( at.GetValue(5) );
return true;
}
static bool GetInterceptSlopeValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &intslope)
{
if( !ds.FindDataElement( tfgs ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tfgs ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tfgs ).GetValueAsSQ();
if( !(sqi && sqi->GetNumberOfItems() > 0) ) return false;
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// (0028,9145) SQ (Sequence with undefined length) # u/l,1 Pixel Value Transformation Sequence
const Tag tpms(0x0028,0x9145);
if( !subds.FindDataElement(tpms) ) return false;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
assert( sqi2 );
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
{
// (0028,1052) DS [0] # 2,1 Rescale Intercept
const Tag tps(0x0028,0x1052);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
//assert( bv );
Attribute<0x0028,0x1052> at;
at.SetFromDataElement( de );
//at.Print( std::cout );
intslope.push_back( at.GetValue() );
}
{
// (0028,1053) DS [5.65470085470085] # 16,1 Rescale Slope
const Tag tps(0x0028,0x1053);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
//assert( bv );
Attribute<0x0028,0x1053> at;
at.SetFromDataElement( de );
//at.Print( std::cout );
intslope.push_back( at.GetValue() );
}
assert( intslope.size() == 2 );
return true;
}
static bool ComputeZSpacingFromIPP(const DataSet &ds, double &zspacing)
{
// first we need to get the direction cosines:
const Tag t1(0x5200,0x9229);
const Tag t2(0x5200,0x9230);
std::vector<double> cosines;
// For some reason TOSHIBA-EnhancedCT.dcm is storing the direction cosines in the per-frame section
// and not the shared one... oh well
bool b1 = GetDirectionCosinesValueFromSequence(ds, t1, cosines)
|| GetDirectionCosinesValueFromSequence(ds,t2,cosines);
if(!b1)
{
cosines.resize( 6 );
bool b2 = ImageHelper::GetDirectionCosinesFromDataSet(ds, cosines);
if( b2 )
{
gdcmWarningMacro( "Image Orientation (Patient) cannot be stored here!. Continuing" );
b1 = b2;
}
else
{
gdcmErrorMacro( "Image Orientation (Patient) was not found" );
cosines[0] = 1;
cosines[1] = 0;
cosines[2] = 0;
cosines[3] = 0;
cosines[4] = 1;
cosines[5] = 0;
}
}
assert( b1 && cosines.size() == 6 ); // yeah we really need that
const Tag tfgs(0x5200,0x9230);
if( !ds.FindDataElement( tfgs ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tfgs ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tfgs ).GetValueAsSQ();
if( !sqi ) return false;
assert( sqi );
double normal[3];
DirectionCosines dc( cosines.data() );
dc.Cross( normal );
DirectionCosines::Normalize(normal);
// For each item
SequenceOfItems::SizeType nitems = sqi->GetNumberOfItems();
if( nitems > 1 ) {
std::vector<double> dircos_subds2; dircos_subds2.resize(6);
std::vector<double> distances;
for(SequenceOfItems::SizeType i0 = 1; i0 <= nitems; ++i0)
{
const Item &item = sqi->GetItem(i0);
const DataSet & subds = item.GetNestedDataSet();
// (0020,9113) SQ (Sequence with undefined length #=1) # u/l, 1 PlanePositionSequence
const Tag tpms(0x0020,0x9113);
if( !subds.FindDataElement(tpms) ) return false;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
assert( sqi2 );
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
// Check Image Orientation (Patient)
if( ImageHelper::GetDirectionCosinesFromDataSet(subds2, dircos_subds2) )
{
assert( dircos_subds2 == cosines );
}
// (0020,0032) DS [-82.5\-82.5\1153.75] # 20, 3 ImagePositionPatient
const Tag tps(0x0020,0x0032);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
Attribute<0x0020,0x0032> ipp;
ipp.SetFromDataElement(de);
double dist = 0;
for (int i = 0; i < 3; ++i) dist += normal[i]*ipp[i];
distances.push_back( dist );
}
assert( distances.size() == nitems );
double meanspacing = 0;
double prev = distances[0];
for(unsigned int i = 1; i < nitems; ++i)
{
const double current = distances[i] - prev;
meanspacing += current;
prev = distances[i];
}
bool timeseries = false;
if( nitems > 1 )
{
meanspacing /= (double)(nitems - 1);
if( meanspacing == 0.0 )
{
// Could be a time series. Assume time spacing of 1. for now:
gdcmDebugMacro( "Assuming time series for Z-spacing" );
meanspacing = 1.0;
timeseries = true;
}
}
zspacing = meanspacing;
if( nitems > 1 )
assert( zspacing != 0.0 ); // technically this should not happen
if( !timeseries )
{
// Check spacing is consistent:
const double ZTolerance = 1e-3; // ??? FIXME
prev = distances[0];
for(unsigned int i = 1; i < nitems; ++i)
{
const double current = distances[i] - prev;
if( fabs(current - zspacing) > ZTolerance )
{
// For now simply gives up
gdcmErrorMacro( "This Enhanced Multiframe is not supported for now. Sorry" );
return false;
}
prev = distances[i];
}
}
} else {
// single slice, this is not an error to not find the zspacing in this case.
zspacing = 1.0;
const Tag tfgs0(0x5200,0x9229);
if( !ds.FindDataElement( tfgs0 ) ) return true;
SmartPointer<SequenceOfItems> sqi0 = ds.GetDataElement( tfgs0 ).GetValueAsSQ();
if( !(sqi0 && sqi0->GetNumberOfItems() > 0) ) return true;
// Get first item:
const Item &item = sqi0->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// <entry group="0028" element="9110" vr="SQ" vm="1" name="Pixel Measures Sequence"/>
const Tag tpms(0x0028,0x9110);
if( !subds.FindDataElement(tpms) ) return true;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
assert( sqi2 );
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
// <entry group="0028" element="0030" vr="DS" vm="2" name="Pixel Spacing"/>
const Tag tps(0x0018,0x0088);
if( !subds2.FindDataElement(tps) ) return true;
const DataElement &de = subds2.GetDataElement( tps );
Attribute<0x0018,0x0088> at;
at.SetFromDataElement( de );
zspacing = at.GetValue();
}
return true;
}
// EnhancedMRImageStorage & EnhancedCTImageStorage
static bool GetSpacingValueFromSequence(const DataSet& ds, const Tag& tfgs, std::vector<double> &sp)
{
// (0028,9110) SQ (Sequence with undefined length #=1) # u/l, 1 PixelMeasuresSequence
// (fffe,e000) na (Item with undefined length #=2) # u/l, 1 Item
// (0018,0050) DS [0.5] # 4, 1 SliceThickness
// (0028,0030) DS [0.322\0.322] # 12, 2 PixelSpacing
// <entry group="5200" element="9229" vr="SQ" vm="1" name="Shared Functional Groups Sequence"/>
//const Tag tfgs(0x5200,0x9229);
//const Tag tfgs(0x5200,0x9230);
//assert( ds.FindDataElement( tfgs ) );
if( !ds.FindDataElement( tfgs ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tfgs ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tfgs ).GetValueAsSQ();
if( !(sqi && sqi->GetNumberOfItems() > 0) ) return false;
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// <entry group="0028" element="9110" vr="SQ" vm="1" name="Pixel Measures Sequence"/>
const Tag tpms(0x0028,0x9110);
if( !subds.FindDataElement(tpms) ) return false;
//const SequenceOfItems * sqi2 = subds.GetDataElement( tpms ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi2 = subds.GetDataElement( tpms ).GetValueAsSQ();
assert( sqi2 );
const Item &item2 = sqi2->GetItem(1);
const DataSet & subds2 = item2.GetNestedDataSet();
// <entry group="0028" element="0030" vr="DS" vm="2" name="Pixel Spacing"/>
const Tag tps(0x0028,0x0030);
if( !subds2.FindDataElement(tps) ) return false;
const DataElement &de = subds2.GetDataElement( tps );
//assert( bv );
Attribute<0x0028,0x0030> at;
at.SetFromDataElement( de );
//at.Print( std::cout );
sp.push_back( at.GetValue(1) );
sp.push_back( at.GetValue(0) );
// BUG ! Check for instance:
// gdcmData/BRTUM001.dcm
// Slice Thickness is 5.0 while the Zspacing should be 6.0 !
#if 0
// Do the 3rd dimension zspacing:
// <entry group="0018" element="0050" vr="DS" vm="1" name="Slice Thickness"/>
const Tag tst(0x0018,0x0050);
if( !subds2.FindDataElement(tst) ) return false;
const DataElement &de2 = subds2.GetDataElement( tst );
Attribute<0x0018,0x0050> at2;
at2.SetFromDataElement( de2 );
//at2.Print( std::cout );
sp.push_back( at2.GetValue(0) );
#endif
double zspacing;
bool b = ComputeZSpacingFromIPP(ds, zspacing);
if( !b ) return false;
sp.push_back( zspacing );
return true;
}
static SmartPointer<SequenceOfItems> InsertOrReplaceSQ( DataSet & ds, const Tag &tag )
{
SmartPointer<SequenceOfItems> sqi;
if( !ds.FindDataElement( tag ) )
{
sqi = new SequenceOfItems;
DataElement de( tag );
de.SetVR( VR::SQ );
de.SetValue( *sqi );
assert( de.GetVL().IsUndefined() );
de.SetVLToUndefined();
ds.Insert( de );
}
sqi = ds.GetDataElement( tag ).GetValueAsSQ();
sqi->SetLengthToUndefined();
DataElement de_dup = ds.GetDataElement( tag );
de_dup.SetValue( *sqi );
ds.Replace( de_dup );
return sqi;
}
// UltrasoundMultiframeImageStorage
static bool GetUltraSoundSpacingValueFromSequence(const DataSet& ds, std::vector<double> &sp)
{
/*
(0018,6011) SQ (Sequence with explicit length #=1) # 196, 1 SequenceOfUltrasoundRegions
(fffe,e000) na (Item with explicit length #=15) # 188, 1 Item
(0018,6012) US 1 # 2, 1 RegionSpatialFormat
(0018,6014) US 1 # 2, 1 RegionDataType
(0018,6016) UL 0 # 4, 1 RegionFlags
(0018,6018) UL 0 # 4, 1 RegionLocationMinX0
(0018,601a) UL 0 # 4, 1 RegionLocationMinY0
(0018,601c) UL 479 # 4, 1 RegionLocationMaxX1
(0018,601e) UL 479 # 4, 1 RegionLocationMaxY1
(0018,6020) SL 0 # 4, 1 ReferencePixelX0
(0018,6022) SL 0 # 4, 1 ReferencePixelY0
(0018,6024) US 3 # 2, 1 PhysicalUnitsXDirection
(0018,6026) US 3 # 2, 1 PhysicalUnitsYDirection
(0018,6028) FD 0 # 8, 1 ReferencePixelPhysicalValueX
(0018,602a) FD 0 # 8, 1 ReferencePixelPhysicalValueY
(0018,602c) FD 0.002 # 8, 1 PhysicalDeltaX
(0018,602e) FD 0.002 # 8, 1 PhysicalDeltaY
(fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
*/
const Tag tsqusreg(0x0018,0x6011);
if( !ds.FindDataElement( tsqusreg ) ) return false;
//const SequenceOfItems * sqi = ds.GetDataElement( tsqusreg ).GetSequenceOfItems();
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( tsqusreg ).GetValueAsSQ();
if( !sqi ) return false;
assert( sqi );
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
// (0018,602c) FD 0.002 # 8, 1 PhysicalDeltaX
// (0018,602e) FD 0.002 # 8, 1 PhysicalDeltaY
Attribute<0x0018,0x602c> at1;
Attribute<0x0018,0x602e> at2;
const DataElement &de1 = subds.GetDataElement( at1.GetTag() );
at1.SetFromDataElement( de1 );
assert( at1.GetNumberOfValues() == 1 );
const DataElement &de2 = subds.GetDataElement( at2.GetTag() );
at2.SetFromDataElement( de2 );
assert( at2.GetNumberOfValues() == 1 );
sp.push_back( at1.GetValue() );
sp.push_back( at2.GetValue() );
return true;
}
static void SetUltraSoundSpacingValueFromSequence(DataSet& ds, std::vector<double> const &spacing)
{
/*
(0018,6011) SQ (Sequence with explicit length #=1) # 196, 1 SequenceOfUltrasoundRegions
(fffe,e000) na (Item with explicit length #=15) # 188, 1 Item
(0018,6012) US 1 # 2, 1 RegionSpatialFormat
(0018,6014) US 1 # 2, 1 RegionDataType
(0018,6016) UL 0 # 4, 1 RegionFlags
(0018,6018) UL 0 # 4, 1 RegionLocationMinX0
(0018,601a) UL 0 # 4, 1 RegionLocationMinY0
(0018,601c) UL 479 # 4, 1 RegionLocationMaxX1
(0018,601e) UL 479 # 4, 1 RegionLocationMaxY1
(0018,6020) SL 0 # 4, 1 ReferencePixelX0
(0018,6022) SL 0 # 4, 1 ReferencePixelY0
(0018,6024) US 3 # 2, 1 PhysicalUnitsXDirection
(0018,6026) US 3 # 2, 1 PhysicalUnitsYDirection
(0018,6028) FD 0 # 8, 1 ReferencePixelPhysicalValueX
(0018,602a) FD 0 # 8, 1 ReferencePixelPhysicalValueY
(0018,602c) FD 0.002 # 8, 1 PhysicalDeltaX
(0018,602e) FD 0.002 # 8, 1 PhysicalDeltaY
(fffe,e00d) na (ItemDelimitationItem for re-encoding) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem for re-encod.) # 0, 0 SequenceDelimitationItem
*/
const Tag tsqusreg(0x0018,0x6011);
SmartPointer<SequenceOfItems> sqi = InsertOrReplaceSQ( ds, tsqusreg);
if( !sqi->GetNumberOfItems() )
{
Item item; //( Tag(0xfffe,0xe000) );
sqi->AddItem( item );
}
Item &item1 = sqi->GetItem(1);
item1.SetVLToUndefined();
DataSet &subds = item1.GetNestedDataSet();
// (0018,602c) FD 0.002 # 8, 1 PhysicalDeltaX
// (0018,602e) FD 0.002 # 8, 1 PhysicalDeltaY
Attribute<0x0018,0x602c> at1;
at1.SetValue( spacing[0] );
Attribute<0x0018,0x602e> at2;
at2.SetValue( spacing[1] );
subds.Replace( at1.GetAsDataElement() );
subds.Replace( at2.GetAsDataElement() );
}
/* Enhanced stuff looks like:
(0020,9113) SQ (Sequence with undefined length #=1) # u/l, 1 PlanePositionSequence
(fffe,e000) na (Item with undefined length #=1) # u/l, 1 Item
(0020,0032) DS [73.5100815890831\-129.65028828174\189.777023529388] # 50, 3 ImagePositionPatient
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0020,9116) SQ (Sequence with undefined length #=1) # u/l, 1 PlaneOrientationSequence
(fffe,e000) na (Item with undefined length #=1) # u/l, 1 Item
(0020,0037) DS [0.01604138687252\0.99942564964294\-0.0298495516180\0.0060454937629... # 102, 6 ImageOrientationPatient
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
(0028,9110) SQ (Sequence with undefined length #=1) # u/l, 1 PixelMeasuresSequence
(fffe,e000) na (Item with undefined length #=2) # u/l, 1 Item
(0018,0050) DS [1] # 2, 1 SliceThickness
(0028,0030) DS [0.83333331346511\0.83333331346511] # 34, 2 PixelSpacing
(fffe,e00d) na (ItemDelimitationItem) # 0, 0 ItemDelimitationItem
(fffe,e0dd) na (SequenceDelimitationItem) # 0, 0 SequenceDelimitationItem
*/
std::vector<double> ImageHelper::GetOriginValue(File const & f)
{
std::vector<double> ori;
MediaStorage ms;
ms.SetFromFile(f);
const DataSet& ds = f.GetDataSet();
if( ms == MediaStorage::EnhancedCTImageStorage
|| ms == MediaStorage::EnhancedMRImageStorage
|| ms == MediaStorage::EnhancedMRColorImageStorage
|| ms == MediaStorage::EnhancedPETImageStorage
|| ms == MediaStorage::OphthalmicTomographyImageStorage
|| ms == MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeTrueColorSecondaryCaptureImageStorage
|| ms == MediaStorage::XRay3DAngiographicImageStorage
|| ms == MediaStorage::XRay3DCraniofacialImageStorage
|| ms == MediaStorage::SegmentationStorage
|| ms == MediaStorage::IVOCTForProcessing
|| ms == MediaStorage::IVOCTForPresentation
|| ms == MediaStorage::BreastTomosynthesisImageStorage
|| ms == MediaStorage::BreastProjectionXRayImageStorageForPresentation
|| ms == MediaStorage::BreastProjectionXRayImageStorageForProcessing
|| ms == MediaStorage::LegacyConvertedEnhancedMRImageStorage
|| ms == MediaStorage::LegacyConvertedEnhancedCTImageStorage
|| ms == MediaStorage::LegacyConvertedEnhancedPETImageStorage )
{
const Tag t1(0x5200,0x9229);
const Tag t2(0x5200,0x9230);
if( GetOriginValueFromSequence(ds,t1, ori)
|| GetOriginValueFromSequence(ds, t2, ori) )
{
assert( ori.size() == 3 );
return ori;
}
ori.resize( 3 );
gdcmWarningMacro( "Could not find Origin" );
return ori;
}
if( ms == MediaStorage::NuclearMedicineImageStorage )
{
const Tag t1(0x0054,0x0022);
if( ds.FindDataElement( t1 ) )
{
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( t1 ).GetValueAsSQ();
if( sqi && sqi->GetNumberOfItems() >= 1)
{
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
const Tag timagepositionpatient(0x0020, 0x0032);
assert( subds.FindDataElement( timagepositionpatient ) );
Attribute<0x0020,0x0032> at = {{0,0,0}}; // default value if empty
at.SetFromDataSet( subds );
ori.resize( at.GetNumberOfValues() );
for( unsigned int i = 0; i < at.GetNumberOfValues(); ++i )
{
ori[i] = at.GetValue(i);
}
return ori;
}
}
ori.resize( 3 );
gdcmWarningMacro( "Could not find Origin" );
return ori;
}
ori.resize( 3 );
// else
const Tag timagepositionpatient(0x0020, 0x0032);
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
at.SetFromDataElement( de );
for( unsigned int i = 0; i < at.GetNumberOfValues(); ++i )
{
ori[i] = at.GetValue(i);
}
}
else
{
ori[0] = 0;
ori[1] = 0;
ori[2] = 0;
}
assert( ori.size() == 3 );
return ori;
}
bool ImageHelper::GetDirectionCosinesFromDataSet(DataSet const & ds, std::vector<double> & dircos)
{
// \precondition: this dataset is not a secondary capture !
// else
const Tag timageorientationpatient(0x0020, 0x0037);
if( ds.FindDataElement( timageorientationpatient ) /*&& !ds.GetDataElement( timageorientationpatient ).IsEmpty()*/ )
{
const DataElement& de = ds.GetDataElement( timageorientationpatient );
Attribute<0x0020,0x0037> at = {{1,0,0,0,1,0}}; // default value if empty
at.SetFromDataElement( de );
for( unsigned int i = 0; i < at.GetNumberOfValues(); ++i )
{
dircos[i] = at.GetValue(i);
}
DirectionCosines dc( dircos.data() );
if( !dc.IsValid() )
{
dc.Normalize();
if( dc.IsValid() )
{
gdcmWarningMacro( "DirectionCosines was not normalized. Fixed" );
const double * p = dc;
dircos = std::vector<double>(p, p + 6);
//return dircos;
}
else
{
// PAPYRUS_CR_InvalidIOP.dcm
gdcmWarningMacro( "Could not get DirectionCosines. Will be set to unit vector." );
//dircos[0] = 1;
//dircos[1] = 0;
//dircos[2] = 0;
//dircos[3] = 0;
//dircos[4] = 1;
//dircos[5] = 0;
return false;
}
}
return true;
}
return false;
}
std::vector<double> ImageHelper::GetDirectionCosinesValue(File const & f)
{
std::vector<double> dircos;
MediaStorage ms;
ms.SetFromFile(f);
const DataSet& ds = f.GetDataSet();
if( ms == MediaStorage::EnhancedCTImageStorage
|| ms == MediaStorage::EnhancedMRImageStorage
|| ms == MediaStorage::EnhancedMRColorImageStorage
|| ms == MediaStorage::EnhancedPETImageStorage
|| ms == MediaStorage::MultiframeSingleBitSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeGrayscaleByteSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeGrayscaleWordSecondaryCaptureImageStorage
|| ms == MediaStorage::MultiframeTrueColorSecondaryCaptureImageStorage
|| ms == MediaStorage::XRay3DAngiographicImageStorage
|| ms == MediaStorage::XRay3DCraniofacialImageStorage
|| ms == MediaStorage::SegmentationStorage
|| ms == MediaStorage::IVOCTForPresentation
|| ms == MediaStorage::IVOCTForProcessing
|| ms == MediaStorage::BreastTomosynthesisImageStorage
|| ms == MediaStorage::BreastProjectionXRayImageStorageForPresentation
|| ms == MediaStorage::BreastProjectionXRayImageStorageForProcessing
|| ms == MediaStorage::LegacyConvertedEnhancedMRImageStorage
|| ms == MediaStorage::LegacyConvertedEnhancedCTImageStorage
|| ms == MediaStorage::LegacyConvertedEnhancedPETImageStorage )
{
const Tag t1(0x5200,0x9229);
const Tag t2(0x5200,0x9230);
if( GetDirectionCosinesValueFromSequence(ds,t1, dircos)
|| GetDirectionCosinesValueFromSequence(ds, t2, dircos) )
{
assert( dircos.size() == 6 );
return dircos;
}
else
{
dircos.resize( 6 );
bool b2 = ImageHelper::GetDirectionCosinesFromDataSet(ds, dircos);
if( b2 )
{
gdcmWarningMacro( "Image Orientation (Patient) cannot be stored here!. Continuing" );
}
else
{
gdcmErrorMacro( "Image Orientation (Patient) was not found" );
dircos[0] = 1;
dircos[1] = 0;
dircos[2] = 0;
dircos[3] = 0;
dircos[4] = 1;
dircos[5] = 0;
}
return dircos;
}
}
if( ms == MediaStorage::NuclearMedicineImageStorage )
{
const Tag t1(0x0054,0x0022);
if( ds.FindDataElement( t1 ) )
{
SmartPointer<SequenceOfItems> sqi = ds.GetDataElement( t1 ).GetValueAsSQ();
if( sqi && sqi->GetNumberOfItems() >= 1 )
{
// Get first item:
const Item &item = sqi->GetItem(1);
const DataSet & subds = item.GetNestedDataSet();
dircos.resize( 6 );
bool b2 = ImageHelper::GetDirectionCosinesFromDataSet(subds, dircos);
if( b2 )
{
}
else
{
gdcmErrorMacro( "Image Orientation (Patient) was not found" );
dircos[0] = 1;
dircos[1] = 0;
dircos[2] = 0;
dircos[3] = 0;
dircos[4] = 1;
dircos[5] = 0;
}
return dircos;
}
}
}
dircos.resize( 6 );
if( (ms == MediaStorage::SecondaryCaptureImageStorage && !SecondaryCaptureImagePlaneModule) || !GetDirectionCosinesFromDataSet(ds, dircos) )
{
dircos[0] = 1;
dircos[1] = 0;
dircos[2] = 0;
dircos[3] = 0;
dircos[4] = 1;
dircos[5] = 0;
}
assert( dircos.size() == 6 );
return dircos;
}
void ImageHelper::SetForceRescaleInterceptSlope(bool b)
{
ForceRescaleInterceptSlope = b;
}
bool ImageHelper::GetForceRescaleInterceptSlope()
{
return ForceRescaleInterceptSlope;
}
void ImageHelper::SetPMSRescaleInterceptSlope(bool b)
{
PMSRescaleInterceptSlope = b;
}
bool ImageHelper::GetPMSRescaleInterceptSlope()
{
return PMSRescaleInterceptSlope;
}
void ImageHelper::SetForcePixelSpacing(bool b)
{
ForcePixelSpacing = b;
}
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;
bool intercept = ds.FindDataElement(at1.GetTag());
if( intercept )
{
if( !ds.GetDataElement(at1.GetTag()).IsEmpty() )
{
at1.SetFromDataElement( ds.GetDataElement(at1.GetTag()) );
interceptslope[0] = at1.GetValue();
}
}
Attribute<0x0028,0x1053> at2;
bool slope = ds.FindDataElement(at2.GetTag());
if ( slope )
{
if( !ds.GetDataElement(at2.GetTag()).IsEmpty() )
{
at2.SetFromDataElement( ds.GetDataElement(at2.GetTag()) );
interceptslope[1] = at2.GetValue();
if( interceptslope[1] == 0 )
{
// come' on ! WTF
gdcmDebugMacro( "Cannot have slope == 0. Defaulting to 1.0 instead" );
interceptslope[1] = 1;
}
}
}
return intercept || slope;
}
/// This function returns pixel information about an image from its dataset
/// That includes samples per pixel and bit depth (in that order)
/// Returns a PixelFormat
PixelFormat ImageHelper::GetPixelFormatValue(const File& f)
{
// D 0028|0011 [US] [Columns] [512]
//[10/20/10 9:05:07 AM] Mathieu Malaterre:
PixelFormat pf;
const DataSet& ds = f.GetDataSet();
// D 0028|0100 [US] [Bits Allocated] [16]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0100) );
Attribute<0x0028,0x0100> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsAllocated( at.GetValue() );
}
// D 0028|0101 [US] [Bits Stored] [12]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0101) );
Attribute<0x0028,0x0101> at = { 0 };
at.SetFromDataSet( ds );
pf.SetBitsStored( at.GetValue() );
}
// D 0028|0102 [US] [High Bit] [11]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0102) );
Attribute<0x0028,0x0102> at = { 0 };
at.SetFromDataSet( ds );
pf.SetHighBit( at.GetValue() );
}
// D 0028|0103 [US] [Pixel Representation] [0]
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0103) );
Attribute<0x0028,0x0103> at = { 0 };
at.SetFromDataSet( ds );
pf.SetPixelRepresentation( at.GetValue() );
}
// (0028,0002) US 1 # 2, 1 SamplesPerPixel
{
//if( ds.FindDataElement( Tag(0x0028, 0x0002) ) )
{
//const DataElement& de = ds.GetDataElement( Tag(0x0028, 0x0002) );
Attribute<0x0028,0x0002> at = { 1 };
at.SetFromDataSet( ds );
pf.SetSamplesPerPixel( at.GetValue() );
}
// else pf will default to 1...
}
return pf;
}
/// This function checks tags (0x0028, 0x0010) and (0x0028, 0x0011) for the
/// rows and columns of the image in pixels (as opposed to actual distances).
/// Also checks 0054, 0081 for the number of z slices for a 3D image
/// If that tag is not present, default the z dimension to 1
std::vector<unsigned int> ImageHelper::GetDimensionsValue(const File& f)
{
DataSet const & ds = f.GetDataSet();
MediaStorage ms;
ms.SetFromFile(f);
std::vector<unsigned int> theReturn(3);
#if 0
if( ms == MediaStorage::VLWholeSlideMicroscopyImageStorage )
{
{
Attribute<0x0048,0x0006> at = { 0 };
at.SetFromDataSet( ds );
theReturn[0] = at.GetValue();
}
{
Attribute<0x0048,0x0007> at = { 0 };
at.SetFromDataSet( ds );
theReturn[1] = at.GetValue();
}
theReturn[2] = 1;
}
else
#endif
{
{
Attribute<0x0028,0x0011> at = { 0 }; // Columns
at.SetFromDataSet( ds );
theReturn[0] = at.GetValue();
}
{
Attribute<0x0028,0x0010> at = { 0 }; // Rows
at.SetFromDataSet( ds );
theReturn[1] = at.GetValue();
}
{
Attribute<0x0028,0x0008> at = { 0 };
at.SetFromDataSet( ds );
int numberofframes = at.GetValue();
theReturn[2] = 1;
if( numberofframes > 1 )
{
theReturn[2] = at.GetValue();
}
}
// ACR-NEMA legacy
{
Attribute<0x0028,0x0005> at = { 0 };
if( ds.FindDataElement( at.GetTag() ) )
{
const DataElement &de = ds.GetDataElement( at.GetTag() );
// SIEMENS_MAGNETOM-12-MONO2-Uncompressed.dcm picks VR::SS instead...
if( at.GetVR().Compatible( de.GetVR() ) )
{
at.SetFromDataSet( ds );
int imagedimensions = at.GetValue();
if( imagedimensions == 3 )
{
Attribute<0x0028,0x0012> at2 = { 0 };
at2.SetFromDataSet( ds );
theReturn[2] = at2.GetValue();
}
}
else
{
gdcmWarningMacro( "Sorry cannot read attribute (wrong VR): " << at.GetTag() );
}
}
}
}
return theReturn;
}
void ImageHelper::SetDimensionsValue(File& f, const Pixmap & img)
{
const unsigned int *dims = img.GetDimensions();
MediaStorage ms;
ms.SetFromFile(f);
DataSet& ds = f.GetDataSet();
assert( MediaStorage::IsImage( ms ) );
{
Attribute<0x0028,0x0010> rows;
rows.SetValue( (uint16_t)dims[1] );
ds.Replace( rows.GetAsDataElement() );
Attribute<0x0028,0x0011> columns;
columns.SetValue( (uint16_t)dims[0] );
ds.Replace( columns.GetAsDataElement() );
Attribute<0x0028,0x0008> numframes = { 0 };
numframes.SetValue( dims[2] );
if( img.GetNumberOfDimensions() == 3 && dims[2] >= 1 )
{
if( ms.MediaStorage::GetModalityDimension() > 2 )
ds.Replace( numframes.GetAsDataElement() );
else if( ms.MediaStorage::GetModalityDimension() == 2 && dims[2] == 1 )
ds.Remove( numframes.GetTag() );
else
{
gdcmErrorMacro( "MediaStorage does not allow 3rd dimension. But value is: " << dims[2] );
gdcmAssertAlwaysMacro( "Could not set third dimension" );
}
}
else if( img.GetNumberOfDimensions() == 2 && dims[2] == 1 )
{
// This is a MF instances, need to set Number of Frame to 1 when Required
if (ms.MediaStorage::GetModalityDimension() > 2)
{
// Only include Multi-Frame when required (not Conditional):
if( ms == MediaStorage::XRayAngiographicImageStorage // A.14.3 XA Image IOD Module Table: Multi-frame C.7.6.6 C - Required if pixel data is Multi - frame Cine data
)
{
ds.Remove(numframes.GetTag());
}
else
{
ds.Replace(numframes.GetAsDataElement());
}
}
else if( ms.MediaStorage::GetModalityDimension() == 2 /*&& dims[2] == 1*/ )
ds.Remove( numframes.GetTag() );
}
else // cleanup
ds.Remove( numframes.GetTag() );
}
// cleanup pass: