Added optional usage of DCMTK in the dicom plugin

CMakeLists.txt

@@ -289,6 +289,7 @@ FIND_PACKAGE(ZLIB)
 FIND_PACKAGE(GDAL)
 FIND_PACKAGE(CURL)
 FIND_PACKAGE(ITK)
+FIND_PACKAGE(OurDCMTK)
 
 SET(wxWidgets_USE_LIBS base core gl net)
 FIND_PACKAGE(wxWidgets)

CMakeModules/FindOurDCMTK.cmake

@@ -0,0 +1,159 @@
+# - find DCMTK libraries
+#
+
+#  DCMTK_INCLUDE_DIR   - Directories to include to use DCMTK
+#  DCMTK_LIBRARIES     - Files to link against to use DCMTK
+#  DCMTK_FOUND         - If false, don't try to use DCMTK
+#  DCMTK_DIR           - (optional) Source directory for DCMTK
+#
+# DCMTK_DIR can be used to make it simpler to find the various include
+# directories and compiled libraries if you've just compiled it in the
+# source tree. Just set it to the root of the tree where you extracted
+# the source.
+#
+# Written for VXL by Amitha Perera.
+# 
+
+FIND_PATH( DCMTK_config_INCLUDE_DIR osconfig.h
+    ${DCMTK_DIR}/config/include 
+    ${DCMTK_DIR}/include
+    /usr/local/include/dcmtk/config
+    /usr/include/dcmtk/config
+)
+
+FIND_PATH( DCMTK_ofstd_INCLUDE_DIR ofstdinc.h
+    ${DCMTK_DIR}/ofstd/include 
+    ${DCMTK_DIR}/include/ofstd
+    /usr/local/include/dcmtk/ofstd
+    /usr/include/dcmtk/ofstd
+)
+
+FIND_LIBRARY( DCMTK_ofstd_LIBRARY ofstd
+    ${DCMTK_DIR}/ofstd/libsrc
+    ${DCMTK_DIR}/ofstd/libsrc/Release
+    ${DCMTK_DIR}/ofstd/libsrc/Debug
+    ${DCMTK_DIR}/ofstd/Release
+    ${DCMTK_DIR}/ofstd/Debug
+    ${DCMTK_DIR}/lib
+    /usr/local/lib64
+    /usr/lib64
+    /usr/local/lib
+    /usr/lib
+)
+
+
+FIND_PATH( DCMTK_dcmdata_INCLUDE_DIR dctypes.h
+    ${DCMTK_DIR}/dcmdata/include
+    ${DCMTK_DIR}/include/dcmdata
+    /usr/local/include/dcmtk/dcmdata
+    /usr/include/dcmtk/dcmdata
+)
+
+FIND_LIBRARY( DCMTK_dcmdata_LIBRARY dcmdata
+    ${DCMTK_DIR}/dcmdata/libsrc
+    ${DCMTK_DIR}/dcmdata/libsrc/Release
+    ${DCMTK_DIR}/dcmdata/libsrc/Debug
+    ${DCMTK_DIR}/dcmdata/Release
+    ${DCMTK_DIR}/dcmdata/Debug
+    ${DCMTK_DIR}/lib
+    /usr/local/lib64
+    /usr/lib64
+    /usr/local/lib
+    /usr/lib
+)
+
+
+FIND_PATH( DCMTK_dcmimgle_INCLUDE_DIR dcmimage.h
+    ${DCMTK_DIR}/dcmimgle/include
+    ${DCMTK_DIR}/include/dcmimgle
+    /usr/local/include/dcmtk/dcmimgle
+    /usr/include/dcmtk/dcmimgle
+)
+
+FIND_LIBRARY( DCMTK_dcmimgle_LIBRARY dcmimgle
+    ${DCMTK_DIR}/dcmimgle/libsrc
+    ${DCMTK_DIR}/dcmimgle/libsrc/Release
+    ${DCMTK_DIR}/dcmimgle/libsrc/Debug
+    ${DCMTK_DIR}/dcmimgle/Release
+    ${DCMTK_DIR}/dcmimgle/Debug
+    ${DCMTK_DIR}/lib
+    /usr/local/lib64
+    /usr/lib64
+    /usr/local/lib
+    /usr/lib
+)
+
+FIND_LIBRARY(DCMTK_imagedb_LIBRARY imagedb 
+    ${DCMTK_DIR}/imagectn/libsrc/Release
+    ${DCMTK_DIR}/imagectn/libsrc/
+    ${DCMTK_DIR}/imagectn/libsrc/Debug
+    /usr/local/lib64
+    /usr/lib64
+    /usr/local/lib
+    /usr/lib
+)
+
+FIND_LIBRARY(DCMTK_dcmnet_LIBRARY dcmnet 
+    ${DCMTK_DIR}/dcmnet/libsrc/Release
+    ${DCMTK_DIR}/dcmnet/libsrc/Debug
+    ${DCMTK_DIR}/dcmnet/libsrc/
+    /usr/local/lib64
+    /usr/lib64
+    /usr/local/lib
+    /usr/lib
+)
+
+
+IF( DCMTK_config_INCLUDE_DIR 
+    AND DCMTK_ofstd_INCLUDE_DIR 
+    AND DCMTK_ofstd_LIBRARY
+    AND DCMTK_dcmdata_INCLUDE_DIR
+    AND DCMTK_dcmdata_LIBRARY
+    AND DCMTK_dcmimgle_INCLUDE_DIR
+    AND DCMTK_dcmimgle_LIBRARY )
+
+  SET( DCMTK_FOUND "YES" )
+  SET( DCMTK_INCLUDE_DIR
+    ${DCMTK_config_INCLUDE_DIR}
+    ${DCMTK_ofstd_INCLUDE_DIR}
+    ${DCMTK_dcmdata_INCLUDE_DIR}
+    ${DCMTK_dcmimgle_INCLUDE_DIR}
+  )
+
+  SET( DCMTK_LIBRARIES
+    ${DCMTK_dcmimgle_LIBRARY}
+    ${DCMTK_dcmdata_LIBRARY}
+    ${DCMTK_ofstd_LIBRARY}
+    ${DCMTK_config_LIBRARY}
+  )
+
+  IF(DCMTK_imagedb_LIBRARY)
+   SET( DCMTK_LIBRARIES
+   ${DCMTK_LIBRARIES}
+   ${DCMTK_imagedb_LIBRARY}
+   )
+  ENDIF(DCMTK_imagedb_LIBRARY)
+
+  IF(DCMTK_dcmnet_LIBRARY)
+   SET( DCMTK_LIBRARIES
+   ${DCMTK_LIBRARIES}
+   ${DCMTK_dcmnet_LIBRARY}
+   )
+  ENDIF(DCMTK_dcmnet_LIBRARY)
+
+  IF( WIN32 )
+    SET( DCMTK_LIBRARIES ${DCMTK_LIBRARIES} netapi32 )
+  ENDIF( WIN32 )
+
+ENDIF( DCMTK_config_INCLUDE_DIR 
+    AND DCMTK_ofstd_INCLUDE_DIR 
+    AND DCMTK_ofstd_LIBRARY
+    AND DCMTK_dcmdata_INCLUDE_DIR
+    AND DCMTK_dcmdata_LIBRARY
+    AND DCMTK_dcmimgle_INCLUDE_DIR
+    AND DCMTK_dcmimgle_LIBRARY )
+
+IF( NOT DCMTK_FOUND )
+  SET( DCMTK_DIR "" CACHE PATH "Root of DCMTK source tree (optional)." )
+  MARK_AS_ADVANCED( DCMTK_DIR )
+ENDIF( NOT DCMTK_FOUND )

examples/osgvolume/osgvolume.cpp

@@ -437,6 +437,7 @@ osg::Image* createTexture3D(ImageList& imageList, ProcessRow& processRow,
         osg::Image* image = itr->get();
         GLenum pixelFormat = image->getPixelFormat();
         if (pixelFormat==GL_ALPHA || 
+            pixelFormat==GL_INTENSITY || 
             pixelFormat==GL_LUMINANCE || 
             pixelFormat==GL_LUMINANCE_ALPHA || 
             pixelFormat==GL_RGB || 
@@ -519,6 +520,7 @@ osg::Image* createTexture3D(ImageList& imageList, ProcessRow& processRow,
         GLenum pixelFormat = image->getPixelFormat();
         if (pixelFormat==GL_ALPHA || 
             pixelFormat==GL_LUMINANCE || 
+            pixelFormat==GL_INTENSITY || 
             pixelFormat==GL_LUMINANCE_ALPHA || 
             pixelFormat==GL_RGB || 
             pixelFormat==GL_RGBA)
@@ -1849,54 +1851,59 @@ int main( int argc, char **argv )
         if (!arguments.isOption(pos))
         {
             std::string filename = arguments[pos];
-            
+            if (osgDB::getLowerCaseFileExtension(filename)=="dicom")
-            osgDB::FileType fileType = osgDB::fileType(filename);
-            if (fileType == osgDB::FILE_NOT_FOUND)
             {
-                filename = osgDB::findDataFile(filename);
-                fileType = osgDB::fileType(filename);
-            }
-            
-            if (fileType == osgDB::DIRECTORY)
-            {
-                osgDB::DirectoryContents contents = osgDB::getDirectoryContents(filename);
-                
-                std::sort(contents.begin(), contents.end());
-                
-                ImageList imageList;
-                for(osgDB::DirectoryContents::iterator itr = contents.begin();
-                    itr != contents.end();
-                    ++itr)
-                {
-                    std::string localFile = filename + "/" + *itr;
-                    std::cout<<"contents = "<<localFile<<std::endl;
-                    if (osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
-                    {
-                        // not an option so assume string is a filename.
-                        osg::Image *image = osgDB::readImageFile(localFile);
-                        if(image)
-                        {
-                            imageList.push_back(image);
-                        }
-                    }
-                }
-
-                // pack the textures into a single texture.
-                ProcessRow processRow;
-                image_3d = createTexture3D(imageList, processRow, numComponentsDesired, s_maximumTextureSize, t_maximumTextureSize, r_maximumTextureSize, resizeToPowerOfTwo);
-
-            }
-            else if (fileType == osgDB::REGULAR_FILE)
-            {
-                // not an option so assume string is a filename.
                 image_3d = osgDB::readImageFile( filename );
             }
             else
             {
-                osg::notify(osg::NOTICE)<<"Error: could not find file: "<<filename<<std::endl;
+                osgDB::FileType fileType = osgDB::fileType(filename);
-                return 1;
+                if (fileType == osgDB::FILE_NOT_FOUND)
-            }
+                {
+                    filename = osgDB::findDataFile(filename);
+                    fileType = osgDB::fileType(filename);
+                }
 
+                if (fileType == osgDB::DIRECTORY)
+                {
+                    osgDB::DirectoryContents contents = osgDB::getDirectoryContents(filename);
+
+                    std::sort(contents.begin(), contents.end());
+
+                    ImageList imageList;
+                    for(osgDB::DirectoryContents::iterator itr = contents.begin();
+                        itr != contents.end();
+                        ++itr)
+                    {
+                        std::string localFile = filename + "/" + *itr;
+                        std::cout<<"contents = "<<localFile<<std::endl;
+                        if (osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
+                        {
+                            // not an option so assume string is a filename.
+                            osg::Image *image = osgDB::readImageFile(localFile);
+                            if(image)
+                            {
+                                imageList.push_back(image);
+                            }
+                        }
+                    }
+
+                    // pack the textures into a single texture.
+                    ProcessRow processRow;
+                    image_3d = createTexture3D(imageList, processRow, numComponentsDesired, s_maximumTextureSize, t_maximumTextureSize, r_maximumTextureSize, resizeToPowerOfTwo);
+
+                }
+                else if (fileType == osgDB::REGULAR_FILE)
+                {
+                    // not an option so assume string is a filename.
+                    image_3d = osgDB::readImageFile( filename );
+                }
+                else
+                {
+                    osg::notify(osg::NOTICE)<<"Error: could not find file: "<<filename<<std::endl;
+                    return 1;
+                }
+            }            
         }
     }
     

src/osgPlugins/CMakeLists.txt

@@ -104,9 +104,9 @@ ENDIF(CURL_FOUND)
 #
 # 3D Image plugins
 #
-IF(ITK_FOUND)
+IF   (ITK_FOUND OR DCMTK_FOUND)
     ADD_SUBDIRECTORY(dicom)
-ENDIF(ITK_FOUND)
+ENDIF(ITK_FOUND OR DCMTK_FOUND)
 
 
 ############################################################

src/osgPlugins/dicom/CMakeLists.txt

@@ -1,14 +1,35 @@
-INCLUDE(${ITK_USE_FILE})
+IF  (DCMTK_FOUND)
 
-INCLUDE_DIRECTORIES( ITK_INCLUDE_DIRS )
+    INCLUDE_DIRECTORIES( DCMTK_INCLUDE_DIRS )
 
-SET(TARGET_SRC ReaderWriterDICOM.cpp )
+    SET(TARGET_SRC ReaderWriterDICOM.cpp )
 
-LINK_DIRECTORIES(${ITK_LIBRARY_DIRS})
+    LINK_LIBRARIES(${DCMTK_LIBRARIES})
 
-# LINK_LIBRARIES(${ITK_LIBRARIES})
+    ADD_DEFINITIONS(-DUSE_DCMTK)
+
+ELSE(DCMTK_FOUND)
+
+    IF (ITK_FOUND)
+
+    INCLUDE(${ITK_USE_FILE})
+
+    INCLUDE_DIRECTORIES( ITK_INCLUDE_DIRS )
+
+    SET(TARGET_SRC ReaderWriterDICOM.cpp )
+
+    LINK_DIRECTORIES(${ITK_LIBRARY_DIRS})
+
+    # LINK_LIBRARIES(${ITK_LIBRARIES})
+
+    LINK_LIBRARIES(ITKCommon ITKIO)
+
+    ADD_DEFINITIONS(-DUSE_ITK)
+
+    ENDIF(ITK_FOUND)
+
+ENDIF(DCMTK_FOUND)
 
-LINK_LIBRARIES(ITKCommon ITKIO)
 
 #### end var setup  ###
 SETUP_PLUGIN(dicom)

src/osgPlugins/dicom/ReaderWriterDICOM.cpp

@@ -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
 
 };