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Grassroots DiCoM i.e. GDCM based DICOM image reader is added.

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look4pritam 2015-04-20 17:57:57 +05:30 committed by Maksim Shabunin
parent 627e2b15b3
commit 6f22f49c02
7 changed files with 327 additions and 0 deletions
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8
CMakeLists.txt
View File

@ -191,6 +191,7 @@ OCV_OPTION(WITH_OPENGL "Include OpenGL support" OFF
OCV_OPTION(WITH_OPENNI "Include OpenNI support" OFF IF (NOT ANDROID AND NOT IOS AND NOT WINRT) )
OCV_OPTION(WITH_OPENNI2 "Include OpenNI2 support" OFF IF (NOT ANDROID AND NOT IOS AND NOT WINRT) )
OCV_OPTION(WITH_PNG "Include PNG support" ON)
OCV_OPTION(WITH_GDCM "Include DICOM support" OFF)
OCV_OPTION(WITH_PVAPI "Include Prosilica GigE support" OFF IF (NOT ANDROID AND NOT IOS AND NOT WINRT) )
OCV_OPTION(WITH_GIGEAPI "Include Smartek GigE support" OFF IF (NOT ANDROID AND NOT IOS AND NOT WINRT) )
OCV_OPTION(WITH_QT "Build with Qt Backend support" OFF IF (NOT ANDROID AND NOT IOS AND NOT WINRT) )
@ -1008,6 +1009,7 @@ if(WITH_PNG)
else()
status(" PNG:" "NO")
endif()
if(WITH_TIFF)
if(TIFF_VERSION_STRING AND TIFF_FOUND)
status(" TIFF:" "${TIFF_LIBRARY} (ver ${TIFF_VERSION} - ${TIFF_VERSION_STRING})")
@ -1034,6 +1036,12 @@ else()
status(" GDAL:" "NO")
endif()
if(WITH_GDCM)
status(" GDCM:" GDCM_FOUND THEN "YES (ver ${GDCM_VERSION})" ELSE "NO")
else()
status(" GDCM:" "NO")
endif()
# ========================== VIDEO IO ==========================
status("")
status(" Video I/O:")

12
cmake/OpenCVFindLibsGrfmt.cmake
View File

@ -212,3 +212,15 @@ if(WITH_GDAL)
ocv_include_directories(${GDAL_INCLUDE_DIR})
endif()
endif()
if (WITH_GDCM)
find_package(GDCM)
if(NOT GDCM_FOUND)
set(HAVE_GDCM NO)
ocv_clear_vars(GDCM_VERSION GDCM_LIBRARIES)
else()
set(HAVE_GDCM YES)
# include(${GDCM_USE_FILE})
set(GDCM_LIBRARIES gdcmMSFF) # GDCM does not set this variable for some reason
endif()
endif()

3
cmake/templates/cvconfig.h.in
View File

@ -111,6 +111,9 @@
/* libpng/png.h needs to be included */
#cmakedefine HAVE_LIBPNG_PNG_H
/* GDCM DICOM codec */
#cmakedefine HAVE_GDCM
/* V4L/V4L2 capturing support via libv4l */
#cmakedefine HAVE_LIBV4L

11
modules/imgcodecs/CMakeLists.txt
View File

@ -35,6 +35,11 @@ if(HAVE_PNG)
list(APPEND GRFMT_LIBS ${PNG_LIBRARIES})
endif()
if(HAVE_GDCM)
ocv_include_directories(${GDCM_INCLUDE_DIRS})
list(APPEND GRFMT_LIBS ${GDCM_LIBRARIES})
endif()
if(HAVE_TIFF)
ocv_include_directories(${TIFF_INCLUDE_DIR})
list(APPEND GRFMT_LIBS ${TIFF_LIBRARIES})
@ -57,6 +62,12 @@ endif()
file(GLOB grfmt_hdrs ${CMAKE_CURRENT_LIST_DIR}/src/grfmt*.hpp)
file(GLOB grfmt_srcs ${CMAKE_CURRENT_LIST_DIR}/src/grfmt*.cpp)
if(HAVE_GDCM)
list(APPEND grfmt_hdrs ${CMAKE_CURRENT_LIST_DIR}/src/gdcm_dicom.hpp)
list(APPEND grfmt_srcs ${CMAKE_CURRENT_LIST_DIR}/src/gdcm_dicom.cpp)
endif()
list(APPEND grfmt_hdrs ${CMAKE_CURRENT_LIST_DIR}/src/bitstrm.hpp)
list(APPEND grfmt_srcs ${CMAKE_CURRENT_LIST_DIR}/src/bitstrm.cpp)
list(APPEND grfmt_hdrs ${CMAKE_CURRENT_LIST_DIR}/src/rgbe.hpp)

216
modules/imgcodecs/src/gdcm_dicom.cpp Normal file
View File

@ -0,0 +1,216 @@
/*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, install,
// copy or use the software.
//
//
// License Agreement
// For Open Source Computer Vision Library
//
// Copyright (C) 2000-2008, Intel Corporation, all rights reserved.
// Copyright (C) 2009, Willow Garage Inc., all rights reserved.
// Third party copyrights are property of their respective owners.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// * Redistribution's of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// * Redistribution's in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// * The name of the copyright holders may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// This software is provided by the copyright holders and contributors "as is" and
// any express or implied warranties, including, but not limited to, the implied
// warranties of merchantability and fitness for a particular purpose are disclaimed.
// In no event shall the Intel Corporation or contributors be liable for any direct,
// indirect, incidental, special, exemplary, or consequential damages
// (including, but not limited to, procurement of substitute goods or services;
// loss of use, data, or profits; or business interruption) however caused
// and on any theory of liability, whether in contract, strict liability,
// or tort (including negligence or otherwise) arising in any way out of
// the use of this software, even if advised of the possibility of such damage.
//
//M*/
#include "precomp.hpp"
#include "gdcm_dicom.hpp"
#include <gdcmImageReader.h>
namespace cv
{
/************************ DICOM decoder *****************************/
DICOMDecoder::DICOMDecoder()
{
/// DICOM preable is 128 bytes (can have any vale, defaults to x00) + 4 bytes magic number (DICM)
m_signature = "";
for(int iSize=0; iSize<128; iSize++)
{
m_signature = m_signature + "\xFF";
}
m_signature = m_signature + "\x44\x49\x43\x4D";
m_buf_supported = false;
}
DICOMDecoder::~DICOMDecoder()
{
}
bool DICOMDecoder::checkSignature( const String& signature ) const
{
size_t len = signatureLength();
bool bOK = signature.size() >= len;
for(int iIndex = 128; iIndex < len; iIndex++)
{
if(signature[iIndex] == m_signature[iIndex])
{
continue;
}
else
{
bOK = false;
break;
}
}
return(bOK);
}
void DICOMDecoder::close()
{
}
ImageDecoder DICOMDecoder::newDecoder() const
{
return makePtr<DICOMDecoder>();
}
bool DICOMDecoder::readHeader()
{
gdcm::ImageReader csImageReader;
csImageReader.SetFileName(m_filename.c_str());
if(!csImageReader.Read())
{
return(false);
}
bool bOK = true;
const gdcm::Image &csImage = csImageReader.GetImage();
if( ( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME1 )
|| ( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::MONOCHROME2 )
)
{
gdcm::PixelFormat ePixelFormat = csImage.GetPixelFormat();
if( ePixelFormat == gdcm::PixelFormat::INT8)
{
m_type = CV_8SC1;
}
else if( ePixelFormat == gdcm::PixelFormat::UINT8)
{
m_type = CV_8UC1;
}
else if( ePixelFormat == gdcm::PixelFormat::INT16)
{
m_type = CV_16SC1;
}
else if( ePixelFormat == gdcm::PixelFormat::UINT16)
{
m_type = CV_16UC1;
}
else if( ePixelFormat == gdcm::PixelFormat::INT32)
{
m_type = CV_32SC1;
}
else if( ePixelFormat == gdcm::PixelFormat::FLOAT32)
{
m_type = CV_32FC1;
}
else if( ePixelFormat == gdcm::PixelFormat::FLOAT64)
{
m_type = CV_64FC1;
}
else if( ePixelFormat == gdcm::PixelFormat::INT12)
{
bOK = false;
}
else if( ePixelFormat == gdcm::PixelFormat::UINT12)
{
bOK = false;
}
else if( ePixelFormat == gdcm::PixelFormat::UINT32)
{
bOK = false;
}
else if( ePixelFormat == gdcm::PixelFormat::SINGLEBIT)
{
bOK = false;
}
else
{
bOK = false;
}
}
else if( csImage.GetPhotometricInterpretation() == gdcm::PhotometricInterpretation::RGB )
{
gdcm::PixelFormat ePixelFormat = csImage.GetPixelFormat();
if( ePixelFormat == gdcm::PixelFormat::UINT8)
{
m_type = CV_8UC3;
}
else
{
bOK = false;
}
}
else
{
bOK = false;
}
if(bOK)
{
const unsigned int *piDimension = csImage.GetDimensions();
m_width = piDimension[0];
m_height = piDimension[1];
if( ( m_width <=0 ) || ( m_height <=0 ) )
{
bOK = false;
}
}
return(bOK);
}
bool DICOMDecoder::readData( Mat& csImage )
{
csImage.create(m_width,m_height,m_type);
gdcm::ImageReader csImageReader;
csImageReader.SetFileName(m_filename.c_str());
if(!csImageReader.Read())
{
return(false);
}
bool bOK = true;
const gdcm::Image &csGDCMImage = csImageReader.GetImage();
bOK = csGDCMImage.GetBuffer((char*)csImage.ptr());
return(bOK);
}
}

71
modules/imgcodecs/src/gdcm_dicom.hpp Normal file
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@ -0,0 +1,71 @@
/*M///////////////////////////////////////////////////////////////////////////////////////
//
// IMPORTANT: READ BEFORE DOWNLOADING, COPYING, INSTALLING OR USING.
//
// By downloading, copying, installing or using the software you agree to this license.
// If you do not agree to this license, do not download, install,
// copy or use the software.
//
//
// License Agreement
// For Open Source Computer Vision Library
//
// Copyright (C) 2000-2008, Intel Corporation, all rights reserved.
// Copyright (C) 2009, Willow Garage Inc., all rights reserved.
// Third party copyrights are property of their respective owners.
//
// Redistribution and use in source and binary forms, with or without modification,
// are permitted provided that the following conditions are met:
//
// * Redistribution's of source code must retain the above copyright notice,
// this list of conditions and the following disclaimer.
//
// * Redistribution's in binary form must reproduce the above copyright notice,
// this list of conditions and the following disclaimer in the documentation
// and/or other materials provided with the distribution.
//
// * The name of the copyright holders may not be used to endorse or promote products
// derived from this software without specific prior written permission.
//
// This software is provided by the copyright holders and contributors "as is" and
// any express or implied warranties, including, but not limited to, the implied
// warranties of merchantability and fitness for a particular purpose are disclaimed.
// In no event shall the Intel Corporation or contributors be liable for any direct,
// indirect, incidental, special, exemplary, or consequential damages
// (including, but not limited to, procurement of substitute goods or services;
// loss of use, data, or profits; or business interruption) however caused
// and on any theory of liability, whether in contract, strict liability,
// or tort (including negligence or otherwise) arising in any way out of
// the use of this software, even if advised of the possibility of such damage.
//
//M*/
#ifndef _GDCM_DICOM_H_
#define _GDCM_DICOM_H_
#include "grfmt_base.hpp"
namespace cv
{
// DICOM image reader using GDCM
class DICOMDecoder : public BaseImageDecoder
{
public:
DICOMDecoder();
~DICOMDecoder();
bool readData( Mat& img );
bool readHeader();
void close();
ImageDecoder newDecoder() const;
virtual bool checkSignature( const String& signature ) const;
protected:
};
}
#endif/*_GDCM_DICOM_H_*/

6
modules/imgcodecs/src/loadsave.cpp
View File

@ -45,6 +45,9 @@
#include "precomp.hpp"
#include "grfmts.hpp"
#ifdef HAVE_GDCM
#include "gdcm_dicom.hpp"
#endif
#undef min
#undef max
#include <iostream>
@ -93,6 +96,9 @@ struct ImageCodecInitializer
decoders.push_back( makePtr<PngDecoder>() );
encoders.push_back( makePtr<PngEncoder>() );
#endif
#ifdef HAVE_GDCM
decoders.push_back( makePtr<DICOMDecoder>() );
#endif
#ifdef HAVE_JASPER
decoders.push_back( makePtr<Jpeg2KDecoder>() );
encoders.push_back( makePtr<Jpeg2KEncoder>() );