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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 "gdcmSegmentWriter.h"
#include "gdcmAttribute.h"
namespace gdcm
{
SegmentWriter::SegmentWriter()
{
}
SegmentWriter::~SegmentWriter()
{
}
unsigned int SegmentWriter::GetNumberOfSegments() const
{
return (unsigned int)Segments.size();
}
void SegmentWriter::SetNumberOfSegments(const unsigned int size)
{
Segments.resize(size);
}
const SegmentWriter::SegmentVector & SegmentWriter::GetSegments() const
{
return Segments;
}
SegmentWriter::SegmentVector & SegmentWriter::GetSegments()
{
return Segments;
}
SmartPointer< Segment > SegmentWriter::GetSegment(const unsigned int idx /*= 0*/) const
{
assert( idx < Segments.size() );
return Segments[idx];
}
void SegmentWriter::AddSegment(SmartPointer< Segment > segment)
{
Segments.push_back(segment);
}
void SegmentWriter::SetSegments(SegmentVector & segments)
{
Segments = segments;
}
bool SegmentWriter::PrepareWrite()
{
File & file = GetFile();
DataSet & ds = file.GetDataSet();
// Segment Sequence
SmartPointer<SequenceOfItems> segmentsSQ;
if( !ds.FindDataElement( Tag(0x0062, 0x0002) ) )
{
segmentsSQ = new SequenceOfItems;
DataElement detmp( Tag(0x0062, 0x0002) );
detmp.SetVR( VR::SQ );
detmp.SetValue( *segmentsSQ );
detmp.SetVLToUndefined();
ds.Insert( detmp );
}
segmentsSQ = ds.GetDataElement( Tag(0x0062, 0x0002) ).GetValueAsSQ();
segmentsSQ->SetLengthToUndefined();
{
// Fill the Segment Sequence
const unsigned int numberOfSegments = this->GetNumberOfSegments();
assert( numberOfSegments );
const size_t nbItems = segmentsSQ->GetNumberOfItems();
if (nbItems < numberOfSegments)
{
const size_t diff = numberOfSegments - nbItems;
const size_t nbOfItemToMake = (diff > 0?diff:0);
for(unsigned int i = 1; i <= nbOfItemToMake; ++i)
{
Item item;
item.SetVLToUndefined();
segmentsSQ->AddItem(item);
}
}
}
// else Should I remove items?
std::vector< SmartPointer< Segment > >::const_iterator it0 = Segments.begin();
std::vector< SmartPointer< Segment > >::const_iterator it0End = Segments.end();
unsigned int itemNumber = 1;
unsigned long surfaceNumber = 1;
for (; it0 != it0End; it0++)
{
SmartPointer< Segment > segment = *it0;
assert( segment );
Item & segmentItem = segmentsSQ->GetItem(itemNumber);
DataSet & segmentDS = segmentItem.GetNestedDataSet();
// Segment Number (Type 1)
Attribute<0x0062, 0x0004> segmentNumberAt;
unsigned short segmentNumber = segment->GetSegmentNumber();
if (segmentNumber == 0)
segmentNumber = (unsigned short)itemNumber;
segmentNumberAt.SetValue( segmentNumber );
segmentDS.Replace( segmentNumberAt.GetAsDataElement() );
// Segment Label (Type 1)
const char * segmentLabel = segment->GetSegmentLabel();
if ( strcmp(segmentLabel, "") != 0 )
{
gdcmWarningMacro("No segment label specified");
}
Attribute<0x0062, 0x0005> segmentLabelAt;
segmentLabelAt.SetValue( segmentLabel );
segmentDS.Replace( segmentLabelAt.GetAsDataElement() );
// Segment Description (Type 3)
const char * segmentDescription = segment->GetSegmentDescription();
if ( strcmp(segmentDescription, "") != 0 )
{
Attribute<0x0062, 0x0006> segmentDescriptionAt;
segmentDescriptionAt.SetValue( segmentDescription );
segmentDS.Replace( segmentDescriptionAt.GetAsDataElement() );
}
// Segment Algorithm Type (Type 1)
const char * segmentAlgorithmType = Segment::GetALGOTypeString( segment->GetSegmentAlgorithmType() );
if ( segmentAlgorithmType == 0 )
{
gdcmWarningMacro("No segment algorithm type specified");
Attribute<0x0062, 0x0008> segmentAlgorithmTypeAt;
segmentAlgorithmTypeAt.SetValue( "" );
segmentDS.Replace( segmentAlgorithmTypeAt.GetAsDataElement() );
}
else
{
Attribute<0x0062, 0x0008> segmentAlgorithmTypeAt;
segmentAlgorithmTypeAt.SetValue( segmentAlgorithmType );
segmentDS.Replace( segmentAlgorithmTypeAt.GetAsDataElement() );
}
//***** GENERAL ANATOMY MANDATORY MACRO ATTRIBUTES *****//
{
const SegmentHelper::BasicCodedEntry & anatReg = segment->GetAnatomicRegion();
if (anatReg.IsEmpty())
{
gdcmWarningMacro("Anatomic region not specified or incomplete");
}
// Anatomic Region Sequence (0008,2218) Type 1
SmartPointer<SequenceOfItems> anatRegSQ;
const Tag anatRegSQTag(0x0008, 0x2218);
if( !segmentDS.FindDataElement( anatRegSQTag ) )
{
anatRegSQ = new SequenceOfItems;
DataElement detmp( anatRegSQTag );
detmp.SetVR( VR::SQ );
detmp.SetValue( *anatRegSQ );
detmp.SetVLToUndefined();
segmentDS.Insert( detmp );
}
anatRegSQ = segmentDS.GetDataElement( anatRegSQTag ).GetValueAsSQ();
anatRegSQ->SetLengthToUndefined();
// Fill the Anatomic Region Sequence
const size_t nbItems = anatRegSQ->GetNumberOfItems();
if (nbItems < 1) // Only one item is a type 1
{
Item item;
item.SetVLToUndefined();
anatRegSQ->AddItem(item);
}
Item & anatRegItem = anatRegSQ->GetItem(1);
DataSet & anatRegDS = anatRegItem.GetNestedDataSet();
//***** CODE SEQUENCE MACRO ATTRIBUTES *****//
{
// Code Value (Type 1)
Attribute<0x0008, 0x0100> codeValueAt;
codeValueAt.SetValue( anatReg.CV );
anatRegDS.Replace( codeValueAt.GetAsDataElement() );
// Coding Scheme (Type 1)
Attribute<0x0008, 0x0102> codingSchemeAt;
codingSchemeAt.SetValue( anatReg.CSD );
anatRegDS.Replace( codingSchemeAt.GetAsDataElement() );
// Code Meaning (Type 1)
Attribute<0x0008, 0x0104> codeMeaningAt;
codeMeaningAt.SetValue( anatReg.CM );
anatRegDS.Replace( codeMeaningAt.GetAsDataElement() );
}
}
//***** Segmented Property Category Code Sequence *****//
{
const SegmentHelper::BasicCodedEntry & propCat = segment->GetPropertyCategory();
if (propCat.IsEmpty())
{
gdcmWarningMacro("Segmented property category not specified or incomplete");
}
// Segmented Property Category Code Sequence (0062,0003) Type 1
SmartPointer<SequenceOfItems> propCatSQ;
const Tag propCatSQTag(0x0062, 0x0003);
if( !segmentDS.FindDataElement( propCatSQTag ) )
{
propCatSQ = new SequenceOfItems;
DataElement detmp( propCatSQTag );
detmp.SetVR( VR::SQ );
detmp.SetValue( *propCatSQ );
detmp.SetVLToUndefined();
segmentDS.Insert( detmp );
}
propCatSQ = segmentDS.GetDataElement( propCatSQTag ).GetValueAsSQ();
propCatSQ->SetLengthToUndefined();
// Fill the Segmented Property Category Code Sequence
const size_t nbItems = propCatSQ->GetNumberOfItems();
if (nbItems < 1) // Only one item is a type 1
{
Item item;
item.SetVLToUndefined();
propCatSQ->AddItem(item);
}
Item & propCatItem = propCatSQ->GetItem(1);
DataSet & propCatDS = propCatItem.GetNestedDataSet();
//***** CODE SEQUENCE MACRO ATTRIBUTES *****//
{
// Code Value (Type 1)
Attribute<0x0008, 0x0100> codeValueAt;
codeValueAt.SetValue( propCat.CV );
propCatDS.Replace( codeValueAt.GetAsDataElement() );
// Coding Scheme (Type 1)
Attribute<0x0008, 0x0102> codingSchemeAt;
codingSchemeAt.SetValue( propCat.CSD );
propCatDS.Replace( codingSchemeAt.GetAsDataElement() );
// Code Meaning (Type 1)
Attribute<0x0008, 0x0104> codeMeaningAt;
codeMeaningAt.SetValue( propCat.CM );
propCatDS.Replace( codeMeaningAt.GetAsDataElement() );
}
}
//***** Segmented Property Type Code Sequence *****//
{
const SegmentHelper::BasicCodedEntry & propType = segment->GetPropertyType();
if (propType.IsEmpty())
{
gdcmWarningMacro("Segmented property type not specified or incomplete");
}
// Segmented Property Type Code Sequence (0062,000F) Type 1
SmartPointer<SequenceOfItems> propTypeSQ;
const Tag propTypeSQTag(0x0062, 0x000F);
if( !segmentDS.FindDataElement( propTypeSQTag ) )
{
propTypeSQ = new SequenceOfItems;
DataElement detmp( propTypeSQTag );
detmp.SetVR( VR::SQ );
detmp.SetValue( *propTypeSQ );
detmp.SetVLToUndefined();
segmentDS.Insert( detmp );
}
propTypeSQ = segmentDS.GetDataElement( propTypeSQTag ).GetValueAsSQ();
propTypeSQ->SetLengthToUndefined();
// Fill the Segmented Property Type Code Sequence
const size_t nbItems = propTypeSQ->GetNumberOfItems();
if (nbItems < 1) // Only one item is a type 1
{
Item item;
item.SetVLToUndefined();
propTypeSQ->AddItem(item);
}
Item & propTypeItem = propTypeSQ->GetItem(1);
DataSet & propTypeDS = propTypeItem.GetNestedDataSet();
//***** CODE SEQUENCE MACRO ATTRIBUTES *****//
{
// Code Value (Type 1)
Attribute<0x0008, 0x0100> codeValueAt;
codeValueAt.SetValue( propType.CV );
propTypeDS.Replace( codeValueAt.GetAsDataElement() );
// Coding Scheme (Type 1)
Attribute<0x0008, 0x0102> codingSchemeAt;
codingSchemeAt.SetValue( propType.CSD );
propTypeDS.Replace( codingSchemeAt.GetAsDataElement() );
// Code Meaning (Type 1)
Attribute<0x0008, 0x0104> codeMeaningAt;
codeMeaningAt.SetValue( propType.CM );
propTypeDS.Replace( codeMeaningAt.GetAsDataElement() );
}
}
//***** Surface segmentation *****//
const unsigned long surfaceCount = segment->GetSurfaceCount();
if (surfaceCount > 0)
{
// Surface Count
Attribute<0x0066, 0x002A> surfaceCountAt;
surfaceCountAt.SetValue( (unsigned int)surfaceCount );
segmentDS.Replace( surfaceCountAt.GetAsDataElement() );
//***** Referenced Surface Sequence *****//
SmartPointer<SequenceOfItems> segmentsRefSQ;
if( !segmentDS.FindDataElement( Tag(0x0066, 0x002B) ) )
{
segmentsRefSQ = new SequenceOfItems;
DataElement detmp( Tag(0x0066, 0x002B) );
detmp.SetVR( VR::SQ );
detmp.SetValue( *segmentsRefSQ );
detmp.SetVLToUndefined();
segmentDS.Insert( detmp );
}
segmentsRefSQ = segmentDS.GetDataElement( Tag(0x0066, 0x002B) ).GetValueAsSQ();
segmentsRefSQ->SetLengthToUndefined();
// Fill the Segment Surface Generation Algorithm Identification Sequence
const size_t nbItems = segmentsRefSQ->GetNumberOfItems();
if (nbItems < surfaceCount)
{
const size_t diff = surfaceCount - nbItems;
const size_t nbOfItemToMake = (diff > 0?diff:0);
for(unsigned int i = 1; i <= nbOfItemToMake; ++i)
{
Item item;
item.SetVLToUndefined();
segmentsRefSQ->AddItem(item);
}
}
// else Should I remove items?
std::vector< SmartPointer< Surface > > surfaces = segment->GetSurfaces();
std::vector< SmartPointer< Surface > >::const_iterator it = surfaces.begin();
std::vector< SmartPointer< Surface > >::const_iterator itEnd = surfaces.end();
unsigned int itemSurfaceNumber = 1;
for (; it != itEnd; it++)
{
SmartPointer< Surface > surface = *it;
Item & segmentsRefItem = segmentsRefSQ->GetItem( itemSurfaceNumber++ );
DataSet & segmentsRefDS = segmentsRefItem.GetNestedDataSet();
// Referenced Surface Number
Attribute<0x0066, 0x002C> refSurfaceNumberAt;
unsigned long refSurfaceNumber = surface->GetSurfaceNumber();
if (refSurfaceNumber == 0)
{
refSurfaceNumber = surfaceNumber++;
surface->SetSurfaceNumber( refSurfaceNumber );
}
refSurfaceNumberAt.SetValue( (unsigned int)refSurfaceNumber );
segmentsRefDS.Replace( refSurfaceNumberAt.GetAsDataElement() );
//***** Segment Surface Source Instance Sequence *****//
{
// SmartPointer<SequenceOfItems> surfaceSourceSQ;
// if( !segmentsRefDS.FindDataElement( Tag(0x0066, 0x002E) ) )
// {
// surfaceSourceSQ = new SequenceOfItems;
// DataElement detmp( Tag(0x0066, 0x002E) );
// detmp.SetVR( VR::SQ );
// detmp.SetValue( *surfaceSourceSQ );
// detmp.SetVLToUndefined();
// segmentsRefDS.Insert( detmp );
// }
// surfaceSourceSQ = segmentsRefDS.GetDataElement( Tag(0x0066, 0x002E) ).GetValueAsSQ();
// surfaceSourceSQ->SetLengthToUndefined();
//NOTE: If surfaces are derived from image, include 'Image SOP Instance Reference Macro' PS 3.3 Table C.10-3.
// How to know it?
}
}
}
else
{
// Segment Algorithm Name (Type 1)
const char * segmentAlgorithmName = segment->GetSegmentAlgorithmName();
if ( strcmp(segmentAlgorithmName, "") != 0 )
{
gdcmWarningMacro("No segment algorithm name specified");
}
Attribute<0x0062, 0x0009> segmentAlgorithmNameAt;
segmentAlgorithmNameAt.SetValue( segmentAlgorithmName );
segmentDS.Replace( segmentAlgorithmNameAt.GetAsDataElement() );
}
++itemNumber;
}
return true;
}
bool SegmentWriter::Write()
{
if( !PrepareWrite() )
{
return false;
}
assert( Stream );
if( !Writer::Write() )
{
return false;
}
return true;
}
}
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