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To the ITK code path added support for handling a whole directory of dicom files.

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This commit is contained in:
Robert Osfield 2009-07-03 18:58:01 +00:00
parent 11d7d98e79
commit 1d320d3ca1
1 changed files with 140 additions and 24 deletions
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164
src/osgPlugins/dicom/ReaderWriterDICOM.cpp
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@ -101,6 +101,29 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
virtual const char* className() const { return "DICOM Image Reader/Writer"; }
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;
info()<<"contents = "<<localFile<<std::endl;
if (acceptsExtension(osgDB::getLowerCaseFileExtension(localFile)) &&
osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
{
files.push_back(localFile);
}
}
return !files.empty();
}
virtual ReadResult readObject(std::istream& fin,const osgDB::ReaderWriter::Options* options =NULL) const
{
return readImage(fin, options);
@ -217,10 +240,125 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
std::string ext = osgDB::getLowerCaseFileExtension(file);
if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
std::string fileName = osgDB::findDataFile( file, options );
std::string fileName = file;
if (ext=="dicom")
{
fileName = osgDB::getNameLessExtension(file);
}
fileName = osgDB::findDataFile( fileName, options );
if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
info()<<"Reading DICOM file "<<fileName<<std::endl;
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;
}
typedef std::vector< osg::ref_ptr<osg::Image> > Images;
Images images;
for(Files::iterator itr = files.begin();
itr != files.end();
++itr)
{
ReadResult result = readSingleITKImage(*itr, options);
if (result.success()) images.push_back(result.getImage());
else return result;
}
if (images.empty()) return ReadResult::ERROR_IN_READING_FILE;
if (images.size()==1) return images[0].get();
typedef std::map<float, osg::ref_ptr<osg::Image> > DistanceImageMap;
typedef std::map<osg::Vec3, DistanceImageMap> OrientationDistanceImageMap;
OrientationDistanceImageMap orientationDistanceImageMap;
for(Images::iterator itr = images.begin();
itr != images.end();
++itr)
{
osg::Image* image = itr->get();
osg::RefMatrix* matrix = dynamic_cast<osg::RefMatrix*>(image->getUserData());
if (matrix)
{
osg::Vec3 p0 = osg::Vec3(0.0, 0.0, 0.0) * (*matrix);
osg::Vec3 p1 = osg::Vec3(0.0, 0.0, 1.0) * (*matrix);
osg::Vec3 direction = p1-p0;
direction.normalize();
float distance = p0 * direction;
info()<<" direction="<<direction<<" distance = "<<distance<<std::endl;
orientationDistanceImageMap[direction][distance] = image;
}
}
if (orientationDistanceImageMap.empty()) return ReadResult::ERROR_IN_READING_FILE;
DistanceImageMap& dim = orientationDistanceImageMap.begin()->second;
double totalThickness = dim.rbegin()->first - dim.begin()->first;
int width = 0;
int height = 0;
int depth = 0;
for(DistanceImageMap::iterator itr = dim.begin();
itr != dim.end();
++itr)
{
osg::Image* image = itr->second.get();
if (image->s() > width) width = image->s();
if (image->t() > height) height = image->t();
depth += image->r();
}
osg::ref_ptr<osg::Image> image3D = new osg::Image;
image3D->allocateImage(width, height, depth, GL_LUMINANCE, GL_UNSIGNED_BYTE, 1);
int r = 0;
for(DistanceImageMap::iterator itr = dim.begin();
itr != dim.end();
++itr)
{
osg::Image* image = itr->second.get();
osg::copyImage(image, 0,0,0, image->s(), image->t(), image->r(),
image3D.get(), 0, 0, r,
false);
r += image->r();
}
osg::Image* firstImage = dim.begin()->second.get();
osg::RefMatrix* matrix = dynamic_cast<osg::RefMatrix*>(firstImage->getUserData());
if (matrix)
{
image3D->setUserData(
new osg::RefMatrix(osg::Matrix::scale(1.0,1.0,totalThickness) * (*matrix))
);
}
return image3D.get();
}
virtual ReadResult readSingleITKImage(const std::string& fileName, const osgDB::ReaderWriter::Options* options) const
{
typedef unsigned short PixelType;
const unsigned int Dimension = 3;
@ -354,28 +492,6 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
}
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;
info()<<"contents = "<<localFile<<std::endl;
if (acceptsExtension(osgDB::getLowerCaseFileExtension(localFile)) &&
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