From a991af4b3875b1c79672894b59f872254a6aa4ee Mon Sep 17 00:00:00 2001
From: Robert OSFIELD <robert.osfield@gmail.com>
Date: Fri, 22 Aug 2008 16:39:17 +0000
Subject: [PATCH] Introduced initial cut of a dicom loader, which uses ITK to
 do the loading.

---
 CMakeLists.txt                             |   1 +
 src/osgDB/Registry.cpp                     |   3 +
 src/osgPlugins/CMakeLists.txt              |   9 ++
 src/osgPlugins/dicom/CMakeLists.txt        |  14 ++
 src/osgPlugins/dicom/ReaderWriterDICOM.cpp | 175 +++++++++++++++++++++
 5 files changed, 202 insertions(+)
 create mode 100644 src/osgPlugins/dicom/CMakeLists.txt
 create mode 100644 src/osgPlugins/dicom/ReaderWriterDICOM.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 822f28f3f71..f1480784dd5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -225,6 +225,7 @@ FIND_PACKAGE(Performer)
 FIND_PACKAGE(ZLIB)
 FIND_PACKAGE(GDAL)
 FIND_PACKAGE(CURL)
+FIND_PACKAGE(ITK)
 
 SET(wxWidgets_USE_LIBS base core gl net)
 FIND_PACKAGE(wxWidgets)
diff --git a/src/osgDB/Registry.cpp b/src/osgDB/Registry.cpp
index 4f588f72be4..b3ead705348 100644
--- a/src/osgDB/Registry.cpp
+++ b/src/osgDB/Registry.cpp
@@ -211,6 +211,9 @@ Registry::Registry()
     addFileExtensionAlias("ivz",   "gz");
     addFileExtensionAlias("ozg",   "gz");
     
+    addFileExtensionAlias("dcm",   "dicom");
+    addFileExtensionAlias("dic",   "dicom");
+
 #if defined(DARWIN_QUICKTIME)
     addFileExtensionAlias("jpg",  "qt");
     addFileExtensionAlias("jpe",  "qt");
diff --git a/src/osgPlugins/CMakeLists.txt b/src/osgPlugins/CMakeLists.txt
index 9796c94f63d..213bc2a67a2 100644
--- a/src/osgPlugins/CMakeLists.txt
+++ b/src/osgPlugins/CMakeLists.txt
@@ -100,6 +100,15 @@ IF(CURL_FOUND)
     ADD_SUBDIRECTORY(curl)
 ENDIF(CURL_FOUND)
 
+############################################################
+#
+# 3D Image plugins
+#
+IF(ITK_FOUND)
+    ADD_SUBDIRECTORY(dicom)
+ENDIF(ITK_FOUND)
+
+
 ############################################################
 #
 #  3rd party 3d plugins
diff --git a/src/osgPlugins/dicom/CMakeLists.txt b/src/osgPlugins/dicom/CMakeLists.txt
new file mode 100644
index 00000000000..cf92643bcf9
--- /dev/null
+++ b/src/osgPlugins/dicom/CMakeLists.txt
@@ -0,0 +1,14 @@
+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)
+
+#### end var setup  ###
+SETUP_PLUGIN(dicom)
diff --git a/src/osgPlugins/dicom/ReaderWriterDICOM.cpp b/src/osgPlugins/dicom/ReaderWriterDICOM.cpp
new file mode 100644
index 00000000000..4822f82b5d5
--- /dev/null
+++ b/src/osgPlugins/dicom/ReaderWriterDICOM.cpp
@@ -0,0 +1,175 @@
+// Released under the OSGPL license, as part of the OpenSceneGraph distribution.
+//
+// ReaderWriter for sgi's .rgb format.
+// specification can be found at http://local.wasp.uwa.edu.au/~pbourke/dataformats/sgirgb/sgiversion.html
+
+#include <osg/Image>
+#include <osg/Notify>
+
+#include <osg/Geode>
+
+#include <osg/GL>
+
+#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>
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+class ReaderWriterDICOM : public osgDB::ReaderWriter
+{
+    public:
+    
+        ReaderWriterDICOM()
+        {
+            supportsExtension("dic","dicom image format");
+            supportsExtension("dcm","dicom image format");
+            supportsExtension("dicom","dicom image format");
+            supportsExtension("*","dicom image format");
+        }
+        
+        template<typename T>
+        T* readData(std::istream& fin, unsigned int length, unsigned int& numComponents) const
+        {
+            numComponents = length/sizeof(T);
+            T* data = new T[numComponents];
+            fin.read((char*)data, numComponents*sizeof(T));
+            
+            // read over any padding
+            length -= numComponents*sizeof(T);
+            while(fin && length>0) { fin.get(); --length; }
+            
+            return data;
+        }
+
+        template<typename T>
+        void printData(std::ostream& out, T* data, unsigned int numComponents) const
+        {
+            if (sizeof(T)==1)
+            {
+                for(unsigned int i=0; i<numComponents; ++i)
+                {
+                    if (data[i]>32) out<<data[i];
+                    else out<<".";
+                }
+            }
+            else 
+            {                
+                for(unsigned int i=0; i<numComponents; ++i)
+                {
+                    if (i==0) out<<data[i];
+                    else out<<", "<<data[i];
+                }
+            }
+        }
+    
+        virtual const char* className() const { return "DICOM Image Reader/Writer"; }
+        
+        virtual ReadResult readObject(std::istream& fin,const osgDB::ReaderWriter::Options* options =NULL) const
+        {
+            return readImage(fin, options);
+        }
+
+        virtual ReadResult readObject(const std::string& file, const osgDB::ReaderWriter::Options* options =NULL) const
+        {
+            return readImage(file, options);
+        }
+
+        virtual ReadResult readImage(std::istream& fin,const osgDB::ReaderWriter::Options*) const
+        {
+            return 0;
+        }
+
+        virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
+        {
+            std::string ext = osgDB::getLowerCaseFileExtension(file);
+            if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
+
+            std::string fileName = osgDB::findDataFile( file, options );
+            if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
+
+            osg::notify(osg::NOTICE)<<"Reading DICOM file "<<fileName<<std::endl;
+
+            typedef unsigned short PixelType;
+            const unsigned int Dimension = 3;
+            typedef itk::Image< PixelType, Dimension > ImageType;
+
+
+            typedef itk::ImageFileReader< ImageType > ReaderType;
+            ReaderType::Pointer reader = ReaderType::New();
+            reader->SetFileName( fileName.c_str() );
+
+            typedef itk::GDCMImageIO           ImageIOType;
+            ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
+            reader->SetImageIO( gdcmImageIO );
+
+            try
+            {
+                reader->Update();
+            }
+            catch (itk::ExceptionObject & e)
+            {
+                std::cerr << "exception in file reader " << std::endl;
+                std::cerr << e.GetDescription() << std::endl;
+                std::cerr << e.GetLocation() << std::endl;
+                return ReadResult::ERROR_IN_READING_FILE;
+            }
+            
+            ImageType::Pointer inputImage = reader->GetOutput();
+            
+            ImageType::RegionType region = inputImage->GetBufferedRegion();
+            ImageType::SizeType size = region.GetSize();
+            ImageType::IndexType start = region.GetIndex();
+            
+            //inputImage->GetSpacing();
+            //inputImage->GetOrigin();
+            
+            unsigned int width = size[0];
+            unsigned int height = size[1];
+            unsigned int depth = size[2];
+            
+            osg::RefMatrix* matrix = new osg::RefMatrix;
+            
+            osg::notify(osg::NOTICE)<<"width = "<<width<<" height = "<<height<<" depth = "<<depth<<std::endl;
+            for(unsigned int i=0; i<Dimension; ++i)
+            {
+                (*matrix)(i,i) = inputImage->GetSpacing()[i];
+                (*matrix)(3,i) = inputImage->GetOrigin()[i];
+            }
+            
+            osg::Image* image = new osg::Image;
+            image->allocateImage(width, height, depth, GL_LUMINANCE, GL_UNSIGNED_BYTE, 1);
+
+            unsigned char* data = image->data();            
+            typedef itk::ImageRegionConstIterator< ImageType > IteratorType;
+            IteratorType it(inputImage, region);
+            
+            it.GoToBegin();
+            while (!it.IsAtEnd())
+            {
+                *data = it.Get();
+                ++data;
+                ++it;
+            }
+            
+            image->setUserData(matrix);
+
+            return image;
+        }
+
+};
+
+// now register with Registry to instantiate the above
+// reader/writer.
+REGISTER_OSGPLUGIN(dicom, ReaderWriterDICOM)