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/************************************************************************
*
* Copyright (C) 2009-2022 IRCAD France
* Copyright (C) 2012-2016 IHU Strasbourg
*
* This file is part of Sight.
*
* Sight is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Sight is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with Sight. If not, see <https://www.gnu.org/licenses/>.
*
***********************************************************************/
#include "io/dicom/helper/StructuredReport.hpp"
#include "io/dicom/container/sr/DicomSRCodeNode.hpp"
#include "io/dicom/container/sr/DicomSRContainerNode.hpp"
#include "io/dicom/container/sr/DicomSRImageNode.hpp"
#include "io/dicom/container/sr/DicomSRNumNode.hpp"
#include "io/dicom/container/sr/DicomSRSCoord3DNode.hpp"
#include "io/dicom/container/sr/DicomSRSCoordNode.hpp"
#include "io/dicom/container/sr/DicomSRTextNode.hpp"
#include "io/dicom/container/sr/DicomSRUIDRefNode.hpp"
#include "io/dicom/helper/DicomDataReader.hxx"
namespace sight::io::dicom
{
namespace helper
{
//------------------------------------------------------------------------------
SPTR(io::dicom::container::sr::DicomSRContainerNode) StructuredReport::readSR(const gdcm::DataSet& dataset)
{
SPTR(io::dicom::container::sr::DicomSRContainerNode) result;
// Value Type - Type 1
const std::string type = io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa040>(dataset);
// Concept Name Code Sequence - Type 1C
const io::dicom::container::DicomCodedAttribute& codedAttribute =
io::dicom::helper::StructuredReport::readCodeSequence<0x0040, 0xa043>(dataset);
if(type == "CONTAINER" && !codedAttribute.isEmpty())
{
result = std::make_shared<io::dicom::container::sr::DicomSRContainerNode>(codedAttribute);
io::dicom::helper::StructuredReport::readSubNodeContainer(dataset, result);
}
return result;
}
//------------------------------------------------------------------------------
void StructuredReport::readSubNodeContainer(
const gdcm::DataSet& dataset,
SPTR(io::dicom::container::sr::DicomSRNode)parent
)
{
// Retrieve the content sequence
if(dataset.FindDataElement(gdcm::Tag(0x0040, 0xa730)))
{
gdcm::SmartPointer<gdcm::SequenceOfItems> sequence =
dataset.GetDataElement(gdcm::Tag(0x0040, 0xa730)).GetValueAsSQ();
for(unsigned int i = 1 ; i <= sequence->GetNumberOfItems() ; ++i)
{
const gdcm::DataSet& itemDataset = sequence->GetItem(i).GetNestedDataSet();
io::dicom::helper::StructuredReport::readSubNode(itemDataset, parent);
}
}
}
//------------------------------------------------------------------------------
void StructuredReport::readSubNode(
const gdcm::DataSet& dataset,
SPTR(io::dicom::container::sr::DicomSRNode)parent
)
{
SPTR(io::dicom::container::sr::DicomSRNode) node;
// Value Type - Type 1
const std::string type = io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa040>(dataset);
// Concept Name Code Sequence - Type 1C
const io::dicom::container::DicomCodedAttribute& codedAttribute =
io::dicom::helper::StructuredReport::readCodeSequence<0x0040, 0xa043>(dataset);
// Relationship Value - Type 1
const std::string relationship = io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa010>(dataset);
if(type == "TEXT")
{
// Text Value - Type 1C
const std::string textValue = io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa160>(dataset);
// Create Text Node
node = std::make_shared<io::dicom::container::sr::DicomSRTextNode>(
codedAttribute,
relationship,
textValue
);
}
else if(type == "NUM")
{
// Retrieve the measured value sequence
if(dataset.FindDataElement(gdcm::Tag(0x0040, 0xa300)))
{
gdcm::SmartPointer<gdcm::SequenceOfItems> sequence =
dataset.GetDataElement(gdcm::Tag(0x0040, 0xa300)).GetValueAsSQ();
if(sequence->GetNumberOfItems() > 0)
{
const gdcm::DataSet& itemDataset = sequence->GetItem(1).GetNestedDataSet();
// Numerical value - Type 1
const double numValue =
io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa30a, double>(itemDataset);
// Measured units code sequence - Type 1
const io::dicom::container::DicomCodedAttribute& measurementUnits =
io::dicom::helper::StructuredReport::readCodeSequence<0x0040, 0x08ea>(itemDataset);
// Create Num Node
node = std::make_shared<io::dicom::container::sr::DicomSRNumNode>(
codedAttribute,
relationship,
numValue,
measurementUnits
);
}
}
}
else if(type == "SCOORD")
{
// Graphic Data - Type 1C
gdcm::Attribute<0x0070, 0x0022> graphicDataAttribute;
graphicDataAttribute.SetFromDataElement(dataset.GetDataElement(gdcm::Tag(0x0070, 0x0022)));
const float* graphicData = graphicDataAttribute.GetValues();
// Graphic Type - Type 1
const std::string graphicType = io::dicom::helper::DicomDataReader::getTagValue<0x0070, 0x0023>(dataset);
if(graphicType == "POINT" && graphicDataAttribute.GetNumberOfValues() == 2)
{
// Create Text Node
std::vector<float> scoordVector(graphicData, graphicData + 2);
node = std::make_shared<io::dicom::container::sr::DicomSRSCoordNode>(
codedAttribute,
relationship,
graphicType,
scoordVector
);
}
else if(graphicType == "POLYLINE" && graphicDataAttribute.GetNumberOfValues() == 4)
{
// Create Text Node
std::vector<float> scoordVector(graphicData, graphicData + 4);
node = std::make_shared<io::dicom::container::sr::DicomSRSCoordNode>(
codedAttribute,
relationship,
graphicType,
scoordVector
);
}
else
{
SIGHT_WARN("Graphic type is not handled or data size doesn't match type. The SR node has been ignored.");
}
}
else if(type == "SCOORD3D")
{
// Referenced Frame of Reference UID - Type 1
const std::string frameOfReferenceUID =
io::dicom::helper::DicomDataReader::getTagValue<0x3006, 0x0024>(dataset);
// Graphic Data - Type 1C
gdcm::Attribute<0x0070, 0x0022> graphicDataAttribute;
graphicDataAttribute.SetFromDataElement(dataset.GetDataElement(gdcm::Tag(0x0070, 0x0022)));
const float* graphicData = graphicDataAttribute.GetValues();
// Graphic Type - Type 1
const std::string graphicType = io::dicom::helper::DicomDataReader::getTagValue<0x0070, 0x0023>(dataset);
if(graphicType == "POINT" && graphicDataAttribute.GetNumberOfValues() == 3)
{
// Create Text Node
std::vector<float> scoordVector(graphicData, graphicData + 3);
node = std::make_shared<io::dicom::container::sr::DicomSRSCoord3DNode>(
codedAttribute,
relationship,
graphicType,
scoordVector,
frameOfReferenceUID
);
}
else if(graphicType == "POLYLINE" && graphicDataAttribute.GetNumberOfValues() == 6)
{
// Create Text Node
std::vector<float> scoordVector(graphicData, graphicData + 6);
node = std::make_shared<io::dicom::container::sr::DicomSRSCoord3DNode>(
codedAttribute,
relationship,
graphicType,
scoordVector,
frameOfReferenceUID
);
}
else
{
SIGHT_WARN("Graphic type is not handled or data size doesn't match type. The SR node has been ignored.");
}
}
else if(type == "IMAGE")
{
// Retrieve the referenced SOP sequence
if(dataset.FindDataElement(gdcm::Tag(0x0008, 0x1199)))
{
gdcm::SmartPointer<gdcm::SequenceOfItems> sequence =
dataset.GetDataElement(gdcm::Tag(0x0008, 0x1199)).GetValueAsSQ();
if(sequence->GetNumberOfItems() > 0)
{
const gdcm::DataSet& itemDataset = sequence->GetItem(1).GetNestedDataSet();
// Referenced SOP Class UID - Type 1
const std::string sopClassUID = io::dicom::helper::DicomDataReader::getTagValue<0x0008, 0x1150>(
itemDataset
);
// Referenced SOP Instance UID - Type 1
const std::string sopInstanceUID =
io::dicom::helper::DicomDataReader::getTagValue<0x0008, 0x1155>(itemDataset);
// Referenced Frame Number - Type 1C
int frameNumber = io::dicom::helper::DicomDataReader::getTagValue<0x0008, 0x1160, int>(itemDataset);
// Create Num Node
node = std::make_shared<io::dicom::container::sr::DicomSRImageNode>(
codedAttribute,
relationship,
sopClassUID,
sopInstanceUID,
frameNumber
);
}
}
}
else if(type == "CODE")
{
const io::dicom::container::DicomCodedAttribute& codedEntry =
io::dicom::helper::StructuredReport::readCodeSequence<0x0040, 0xa168>(dataset);
// Create Code Node
node = std::make_shared<io::dicom::container::sr::DicomSRCodeNode>(codedAttribute, relationship, codedEntry);
}
else if(type == "UIDREF")
{
// UID Value - Type 1C
const std::string uidValue = io::dicom::helper::DicomDataReader::getTagValue<0x0040, 0xa124>(dataset);
// Create UIDRef Node
node = std::make_shared<io::dicom::container::sr::DicomSRUIDRefNode>(codedAttribute, relationship, uidValue);
}
else if(type == "CONTAINER")
{
// Create Container Node
node = std::make_shared<io::dicom::container::sr::DicomSRContainerNode>(codedAttribute, relationship);
}
if(node)
{
// Create children
io::dicom::helper::StructuredReport::readSubNodeContainer(dataset, node);
// Add node to parent
parent->addSubNode(node);
}
}
//------------------------------------------------------------------------------
void StructuredReport::dumpSR(const SPTR(io::dicom::container::sr::DicomSRNode)& root, std::ostream& out)
{
out << "graph SR {" << std::endl;
int index = 0;
StructuredReport::dumpSRNode(root, out, index);
out << "}" << std::endl;
}
//------------------------------------------------------------------------------
void StructuredReport::dumpSRNode(
const SPTR(io::dicom::container::sr::DicomSRNode)& root,
std::ostream& out,
int& index
)
{
// Write node
out << "\t" << index << "[label=\"" << (*root) << "\"][shape=box];" << std::endl;
const int parentIndex = index;
for(const SPTR(io::dicom::container::sr::DicomSRNode) & child : root->getSubNodeContainer())
{
// Write edge
out << "\t" << parentIndex << "--" << (index + 1) << "[label=\""
<< child->getRelationship() << "\"];" << std::endl;
// Write child
StructuredReport::dumpSRNode(child, out, ++index);
}
}
//------------------------------------------------------------------------------
} //namespace helper
} //namespace sight::io::dicom
|
