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Added optional usage of DCMTK in the dicom plugin

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This commit is contained in:
Robert Osfield
2008-09-15 19:59:12 +00:00
parent c7b66322be
commit d07f3d5662
6 changed files with 477 additions and 60 deletions
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247
src/osgPlugins/dicom/ReaderWriterDICOM.cpp
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@@ -5,23 +5,32 @@
#include <osg/Image>
#include <osg/Notify>
#include <osg/Geode>
#include <osg/GL>
#include <osg/io_utils>
#include <osgDB/FileNameUtils>
#include <osgDB/FileUtils>
#include <osgDB/Registry>
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkImage.h>
#include <itkImageRegionConstIterator.h>
#include <itkMetaDataDictionary.h>
#include <itkMetaDataObject.h>
#include <itkGDCMImageIO.h>
#ifdef USE_DCMTK
#define HAVE_CONFIG_H
#include <dcmtk/config/osconfig.h>
#include <dcmtk/dcmdata/dcfilefo.h>
#include <dcmtk/dcmdata/dcdeftag.h>
#include <dcmtk/dcmimgle/dcmimage.h>
#endif
#ifdef USE_ITK
#include <itkImageFileReader.h>
#include <itkImageFileWriter.h>
#include <itkImage.h>
#include <itkImageRegionConstIterator.h>
#include <itkMetaDataDictionary.h>
#include <itkMetaDataObject.h>
#include <itkGDCMImageIO.h>
#endif
#include <stdio.h>
#include <stdlib.h>
@@ -91,6 +100,8 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
return 0;
}
#ifdef USE_ITK
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
{
std::string ext = osgDB::getLowerCaseFileExtension(file);
@@ -167,6 +178,224 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
return image;
}
#endif
#ifdef USE_DCMTK
typedef std::vector<std::string> Files;
bool getDicomFilesInDirectory(const std::string& path, Files& files) const
{
osgDB::DirectoryContents contents = osgDB::getDirectoryContents(path);
std::sort(contents.begin(), contents.end());
for(osgDB::DirectoryContents::iterator itr = contents.begin();
itr != contents.end();
++itr)
{
std::string localFile = path + "/" + *itr;
std::cout<<"contents = "<<localFile<<std::endl;
if (osgDB::getLowerCaseFileExtension(localFile)=="dcm" &&
osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
{
files.push_back(localFile);
}
}
return !files.empty();
}
virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
{
osg::notify(osg::NOTICE)<<"Reading DICOM file "<<file<<" using DCMTK"<<std::endl;
std::string ext = osgDB::getLowerCaseFileExtension(file);
if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
std::string fileName = file;
if (ext=="dicom")
{
fileName = osgDB::getNameLessExtension(file);
}
fileName = osgDB::findDataFile( fileName, options );
if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
Files files;
osgDB::FileType fileType = osgDB::fileType(fileName);
if (fileType==osgDB::DIRECTORY)
{
getDicomFilesInDirectory(fileName, files);
}
else
{
#if 1
files.push_back(fileName);
#else
if (!getDicomFilesInDirectory(osgDB::getFilePath(fileName), files))
{
files.push_back(fileName);
}
#endif
}
if (files.empty())
{
return ReadResult::FILE_NOT_FOUND;
}
osg::ref_ptr<osg::RefMatrix> matrix = new osg::RefMatrix;
osg::ref_ptr<osg::Image> image;
unsigned int imageNum = 0;
EP_Representation pixelRep;
unsigned int numPlanes = 0;
GLenum pixelFormat = 0;
GLenum dataType = 0;
unsigned int pixelSize = 0;
for(Files::iterator itr = files.begin();
itr != files.end();
++itr)
{
std::auto_ptr<DicomImage> dcmImage(new DicomImage((*itr).c_str()));
if (dcmImage.get())
{
if (dcmImage->getStatus()==EIS_Normal)
{
// get the pixel data
const DiPixel* pixelData = dcmImage->getInterData();
if(!pixelData) return ReadResult::ERROR_IN_READING_FILE;
if (!image)
{
// read dicom file format to extra spacing info
DcmFileFormat fileformat;
OFCondition status = fileformat.loadFile((*itr).c_str());
if(!status.good()) return ReadResult::ERROR_IN_READING_FILE;
// get the dimension of the dicom image
OFString spacingString;
if(fileformat.getDataset()->findAndGetOFString(DCM_PixelSpacing, spacingString).good())
{
float xy_spacing = atof(spacingString.c_str());
(*matrix)(0,0) = xy_spacing;
(*matrix)(1,1) = xy_spacing * dcmImage->getWidthHeightRatio();
}
// Get slice thickness
if(fileformat.getDataset()->findAndGetOFString(DCM_SliceThickness, spacingString).good())
{
(*matrix)(2,2) = atof(spacingString.c_str());
}
osg::notify(osg::NOTICE)<<"dicomImage->getWidth() = "<<dcmImage->getWidth()<<std::endl;
osg::notify(osg::NOTICE)<<"dicomImage->getHeight() = "<<dcmImage->getHeight()<<std::endl;
osg::notify(osg::NOTICE)<<"dicomImage->getFrameCount() = "<<dcmImage->getFrameCount()<<std::endl;
osg::notify(osg::NOTICE)<<"pixelData->getCount() = "<<pixelData->getCount()<<std::endl;
osg::notify(osg::NOTICE)<<"pixelFormat = ";
dataType = GL_UNSIGNED_BYTE;
unsigned int pixelSize = 0;
pixelRep = pixelData->getRepresentation();
switch(pixelRep)
{
case(EPR_Uint8):
dataType = GL_UNSIGNED_BYTE;
pixelSize = 1;
osg::notify(osg::NOTICE)<<"unsigned char"<<std::endl;
break;
case(EPR_Sint8):
dataType = GL_BYTE;
pixelSize = 1;
osg::notify(osg::NOTICE)<<"char"<<std::endl;
break;
case(EPR_Uint16):
dataType = GL_UNSIGNED_SHORT;
pixelSize = 2;
osg::notify(osg::NOTICE)<<"unsigned short"<<std::endl;
break;
case(EPR_Sint16):
dataType = GL_SHORT;
pixelSize = 2;
osg::notify(osg::NOTICE)<<"short"<<std::endl;
break;
case(EPR_Uint32):
dataType = GL_UNSIGNED_INT;
pixelSize = 4;
osg::notify(osg::NOTICE)<<"unsigned int"<<std::endl;
break;
case(EPR_Sint32):
osg::notify(osg::NOTICE)<<"int"<<std::endl;
dataType = GL_INT;
pixelSize = 4;
break;
default:
osg::notify(osg::NOTICE)<<"unidentified"<<std::endl;
dataType = 0;
break;
}
pixelFormat = GL_INTENSITY;
numPlanes = pixelData->getPlanes();
switch(numPlanes)
{
case(1):
pixelFormat = GL_LUMINANCE;
break;
case(2):
pixelFormat = GL_LUMINANCE_ALPHA;
pixelSize *= 2;
break;
case(3):
pixelFormat = GL_RGB;
pixelSize *= 3;
break;
case(4):
pixelFormat = GL_RGBA;
pixelSize *= 4;
break;
}
image = new osg::Image;
image->setFileName(fileName.c_str());
image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), files.size() * dcmImage->getFrameCount(),
pixelFormat, dataType);
}
if (pixelData->getPlanes()==numPlanes &&
pixelData->getRepresentation()==pixelRep &&
dcmImage->getWidth()==image->s() &&
dcmImage->getHeight()==image->t())
{
int numFramesToCopy = std::min(static_cast<unsigned int>(image->r()-imageNum),
static_cast<unsigned int>(dcmImage->getFrameCount()));
unsigned int numPixels = dcmImage->getWidth() * dcmImage->getHeight() * numFramesToCopy;
unsigned int dataSize = numPixels * pixelSize;
memcpy(image->data(imageNum), pixelData->getData(), dataSize);
imageNum += numFramesToCopy;
}
}
else
{
osg::notify(osg::NOTICE)<<"Error in reading dicom file "<<fileName.c_str()<<", error = "<<DicomImage::getString(dcmImage->getStatus())<<std::endl;
}
}
}
if (!image)
{
return ReadResult::ERROR_IN_READING_FILE;
}
osg::notify(osg::NOTICE)<<"Spacing = "<<*matrix<<std::endl;
return image.get();
}
#endif
};