Merge pull request #6813 from mshabunin:gdcm-cmake-search

CMakeLists.txt

@@ -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:")

cmake/OpenCVFindLibsGrfmt.cmake

@@ -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()

cmake/templates/cvconfig.h.in

@@ -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
 

modules/imgcodecs/CMakeLists.txt

@@ -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 +62,7 @@ endif()
 
 file(GLOB grfmt_hdrs ${CMAKE_CURRENT_LIST_DIR}/src/grfmt*.hpp)
 file(GLOB grfmt_srcs ${CMAKE_CURRENT_LIST_DIR}/src/grfmt*.cpp)
+
 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)

modules/imgcodecs/src/grfmt_gdcm.cpp

@@ -0,0 +1,197 @@
+/*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 "grfmt_gdcm.hpp"
+
+#ifdef HAVE_GDCM
+
+//#define DBG(...) printf(__VA_ARGS__)
+#define DBG(...)
+
+#include <gdcmImageReader.h>
+
+static const size_t preamble_skip = 128;
+static const size_t magic_len = 4;
+
+inline cv::String getMagic()
+{
+    return cv::String("\x44\x49\x43\x4D", 4);
+}
+
+namespace cv
+{
+
+/************************ DICOM decoder *****************************/
+
+DICOMDecoder::DICOMDecoder()
+{
+    // DICOM preamble is 128 bytes (can have any value, defaults to 0) + 4 bytes magic number (DICM)
+    m_signature = String(preamble_skip, (char)'\x0') + getMagic();
+    m_buf_supported = false;
+}
+
+bool DICOMDecoder::checkSignature( const String& signature ) const
+{
+    if (signature.size() >= preamble_skip + magic_len)
+    {
+        if (signature.substr(preamble_skip, magic_len) == getMagic())
+        {
+            return true;
+        }
+    }
+    DBG("GDCM | Signature does not match\n");
+    return false;
+}
+
+ImageDecoder DICOMDecoder::newDecoder() const
+{
+    return makePtr<DICOMDecoder>();
+}
+
+bool  DICOMDecoder::readHeader()
+{
+    gdcm::ImageReader csImageReader;
+    csImageReader.SetFileName(m_filename.c_str());
+    if(!csImageReader.Read())
+    {
+        DBG("GDCM | Failed to open DICOM file\n");
+        return(false);
+    }
+
+    const gdcm::Image &csImage = csImageReader.GetImage();
+    bool bOK = true;
+    switch (csImage.GetPhotometricInterpretation().GetType())
+    {
+        case gdcm::PhotometricInterpretation::MONOCHROME1:
+        case gdcm::PhotometricInterpretation::MONOCHROME2:
+        {
+            switch (csImage.GetPixelFormat().GetScalarType())
+            {
+                case gdcm::PixelFormat::INT8: m_type = CV_8SC1; break;
+                case gdcm::PixelFormat::UINT8: m_type = CV_8UC1; break;
+                case gdcm::PixelFormat::INT16: m_type = CV_16SC1; break;
+                case gdcm::PixelFormat::UINT16: m_type = CV_16UC1; break;
+                case gdcm::PixelFormat::INT32: m_type = CV_32SC1; break;
+                case gdcm::PixelFormat::FLOAT32: m_type = CV_32FC1; break;
+                case gdcm::PixelFormat::FLOAT64: m_type = CV_64FC1; break;
+                default: bOK = false; DBG("GDCM | Monochrome scalar type not supported\n"); break;
+            }
+            break;
+        }
+
+        case gdcm::PhotometricInterpretation::RGB:
+        {
+            switch (csImage.GetPixelFormat().GetScalarType())
+            {
+                case gdcm::PixelFormat::UINT8: m_type = CV_8UC3; break;
+                default: bOK = false; DBG("GDCM | RGB scalar type not supported\n"); break;
+            }
+            break;
+        }
+
+        default:
+        {
+            bOK = false;
+            DBG("GDCM | PI not supported: %s\n", csImage.GetPhotometricInterpretation().GetString());
+            break;
+        }
+    }
+
+    if(bOK)
+    {
+        unsigned int ndim = csImage.GetNumberOfDimensions();
+        if (ndim != 2)
+        {
+            DBG("GDCM | Invalid dimensions number: %d\n", ndim);
+            bOK = false;
+        }
+    }
+    if (bOK)
+    {
+        const unsigned int *piDimension = csImage.GetDimensions();
+        m_height = piDimension[0];
+        m_width = piDimension[1];
+        if( ( m_width <=0 )  || ( m_height <=0 ) )
+        {
+            DBG("GDCM | Invalid dimensions: %d x %d\n", piDimension[0], piDimension[1]);
+            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())
+    {
+        DBG("GDCM | Failed to Read\n");
+        return false;
+    }
+
+    const gdcm::Image &img = csImageReader.GetImage();
+
+    unsigned long len = img.GetBufferLength();
+    if (len > csImage.elemSize() * csImage.total())
+    {
+        DBG("GDCM | Buffer is bigger than Mat: %ld > %ld * %ld\n", len, csImage.elemSize(), csImage.total());
+        return false;
+    }
+
+    if (!img.GetBuffer((char*)csImage.ptr()))
+    {
+        DBG("GDCM | Failed to GetBuffer\n");
+        return false;
+    }
+    DBG("GDCM | Read OK\n");
+    return true;
+}
+
+}
+
+#endif // HAVE_GDCM

modules/imgcodecs/src/grfmt_gdcm.hpp

@@ -0,0 +1,70 @@
+/*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 "cvconfig.h"
+
+#ifdef HAVE_GDCM
+
+#include "grfmt_base.hpp"
+
+namespace cv
+{
+
+// DICOM image reader using GDCM
+class DICOMDecoder : public BaseImageDecoder
+{
+public:
+    DICOMDecoder();
+    bool  readData( Mat& img );
+    bool  readHeader();
+    ImageDecoder newDecoder() const;
+    virtual bool checkSignature( const String& signature ) const;
+};
+
+}
+
+#endif // HAVE_GDCM
+
+#endif/*_GDCM_DICOM_H_*/

modules/imgcodecs/src/grfmts.hpp

@@ -54,5 +54,6 @@
 #include "grfmt_webp.hpp"
 #include "grfmt_hdr.hpp"
 #include "grfmt_gdal.hpp"
+#include "grfmt_gdcm.hpp"
 
 #endif/*_GRFMTS_H_*/

modules/imgcodecs/src/loadsave.cpp

@@ -93,6 +93,9 @@ 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>() );