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.gear/rules | 3 +
.gear/tags/list | 1 +
.gear/vxl.spec | 144 +++++++++++++++++++++++++++++
config/cmake/Modules/FindDCMTK.cmake | 2 +-
core/vil/file_formats/vil_dicom.cxx | 55 ++++++-----
core/vil/file_formats/vil_dicom_stream.cxx | 26 +++---
core/vil/file_formats/vil_dicom_stream.h | 16 ++--
v3p/netlib/CMakeLists.txt | 2 +
8 files changed, 205 insertions(+), 44 deletions(-)
diff --git a/.gear/rules b/.gear/rules
new file mode 100644
index 0000000000..9bd891db25
--- /dev/null
+++ b/.gear/rules
@@ -0,0 +1,3 @@
+tar: v@version@:.
+spec: .gear/vxl.spec
+diff: v@version@:. . name=@name@-@version@-alt.patch
diff --git a/.gear/tags/list b/.gear/tags/list
new file mode 100644
index 0000000000..0af2bb58a3
--- /dev/null
+++ b/.gear/tags/list
@@ -0,0 +1 @@
+ecacd8cb08773d1dc100605e6d634706d34c9fc5 v3.5.0
diff --git a/.gear/vxl.spec b/.gear/vxl.spec
new file mode 100644
index 0000000000..f47aeaf4c5
--- /dev/null
+++ b/.gear/vxl.spec
@@ -0,0 +1,144 @@
+%define _unpackaged_files_terminate_build 1
+
+# documentation build sometimes generates non-identical files
+%def_without docs
+
+# TODO: remove later this fix for documentation
+#%%define _cmake__builddir BUILD
+
+%define openjpeg2_sover 2
+%define ver_maj 3
+%define sover 3.5
+%define libvxl libvxl%ver_maj
+
+Name: libvxl
+Version: 3.5.0
+Release: alt1
+
+Group: System/Libraries
+Summary: C++ Libraries for Computer Vision Research and Implementation
+License: BSD
+Url: https://vxl.github.io/
+
+# https://github.com/vxl/vxl.git
+Source: %name-%version.tar
+Patch1: %name-%version-alt.patch
+
+BuildRequires: gcc-c++ cmake libdcmtk-devel dcmtk libtiff-devel libjpeg-devel libssl-devel rpm-build-ninja
+BuildRequires: libpng-devel libxml2-devel libgeotiff-devel
+%if_with docs
+BuildRequires: doxygen /usr/bin/dot texi2html
+%endif
+
+%define _description \
+VXL (the Vision-something-Libraries) is a collection of C++ libraries designed \
+for computer vision research and implementation. It was created from TargetJr \
+and the IUE with the aim of making a light, fast and consistent system. VXL is \
+written in ANSI/ISO C++ and is designed to be portable over many platforms.
+
+%description
+%_description
+
+%package -n %libvxl
+Summary: Shared libraries for VXL
+Group: System/Libraries
+# dcmtk required, because its contains DICOM tags list
+Requires: dcmtk
+
+%description -n %libvxl
+This package contains shared libraries for VXL.
+%_description
+
+%package devel
+Summary: Headers for VXL
+Group: Development/C++
+
+%description devel
+This package contains development files for VXL.
+%_description
+
+%if_with docs
+%package doc
+Summary: Documentation for VXL
+Group: Documentation
+BuildArch: noarch
+
+%description doc
+This package contains documentation for VXL.
+%_description
+%endif
+
+%prep
+%setup
+%patch1 -p1
+
+%build
+%cmake -GNinja \
+ -DBUILD_SHARED_LIBS:BOOL=ON \
+ -DVXL_INSTALL_LIBRARY_DIR=%_libdir \
+ -DVXL_INSTALL_ARCHIVE_DIR=%_libdir \
+ -DVXL_FORCE_B3P_EXPAT:BOOL=OFF \
+ -DVXL_FORCE_V3P_DCMTK:BOOL=OFF \
+ -DVXL_FORCE_V3P_GEOTIFF:BOOL=OFF \
+ -DVXL_FORCE_V3P_JPEG:BOOL=OFF \
+ -DVXL_FORCE_V3P_PNG:BOOL=OFF \
+ -DVXL_FORCE_V3P_TIFF:BOOL=OFF \
+ -DVXL_FORCE_V3P_ZLIB:BOOL=OFF \
+ -DVXL_USING_NATIVE_ZLIB=ON \
+ -DVXL_USING_NATIVE_JPEG=ON \
+ -DVXL_USING_NATIVE_PNG=ON \
+ -DVXL_USING_NATIVE_TIFF=ON \
+ -DVXL_USING_NATIVE_GEOTIFF=ON \
+ -DBUILD_TESTING:BOOL=OFF \
+ -DVNL_CONFIG_LEGACY_METHODS=ON \
+%if_with docs
+ -DVXL_BUILD_DOCUMENTATION=ON \
+%endif
+ -DVXL_LEGACY_FUTURE_REMOVE:BOOL=OFF \
+ %nil
+
+%ninja_build -C "%_cmake__builddir"
+
+%if_with docs
+%ninja_build -C "%_cmake__builddir" build_doxygen_doc
+%endif
+
+%install
+%ninja_install -C "%_cmake__builddir"
+
+%files -n %libvxl
+%_libdir/lib*.so.%sover
+%_libdir/lib*.so.%sover.*
+%_libdir/libopenjpeg2.so.%openjpeg2_sover.*
+%dir %_datadir/vxl/
+
+%files devel
+%_libdir/lib*.so
+%_includedir/vxl/
+%_datadir/vxl/cmake/
+
+%if_with docs
+%files doc
+%doc %_cmake__builddir/doxy/html
+%endif
+
+%changelog
+* Mon Apr 17 2023 Elizaveta Morozova <morozovaes@altlinux.org> 3.5.0-alt1
+- New version
+- Build using ninja-build
+- Include DCMTK-3.6.4 API update
+
+* Wed Sep 22 2021 Slava Aseev <ptrnine@altlinux.org> 2.0.2-alt4
+- Include missing "limits" std header
+
+* Fri May 14 2021 Aleksei Nikiforov <darktemplar@altlinux.org> 2.0.2-alt3
+- Backported from upstream changes required by new ITK.
+- Fixed build with new cmake macros.
+- Disabled building documentation.
+
+* Tue Jul 16 2019 Aleksei Nikiforov <darktemplar@altlinux.org> 2.0.2-alt2
+- Fixed generated header installation.
+- Enabled deprecated functions.
+
+* Mon Dec 24 2018 Slava Aseev <ptrnine@altlinux.org> 2.0.2-alt1
+- Initial build for ALT
diff --git a/config/cmake/Modules/FindDCMTK.cmake b/config/cmake/Modules/FindDCMTK.cmake
index b70fbfd8e9..1e4e43d861 100644
--- a/config/cmake/Modules/FindDCMTK.cmake
+++ b/config/cmake/Modules/FindDCMTK.cmake
@@ -36,7 +36,7 @@ else()
${dcmtk_SOURCE_DIR}/dcmdata/include ${dcmtk_SOURCE_DIR}/dcmimgle/include)
- set( DCMTK_LIBRARIES dcmtk )
+ set( DCMTK_LIBRARIES dcmdata dcmimgle ofstd )
endif()
diff --git a/core/vil/file_formats/vil_dicom.cxx b/core/vil/file_formats/vil_dicom.cxx
index 5fcdd42287..0650edb080 100644
--- a/core/vil/file_formats/vil_dicom.cxx
+++ b/core/vil/file_formats/vil_dicom.cxx
@@ -27,13 +27,13 @@
# include "vil/vil_pixel_format.h"
# include "vil/vil_exception.h"
-# include <dcfilefo.h>
-# include <dcmetinf.h>
-# include <dcdatset.h>
-# include <dctagkey.h>
-# include <dcdeftag.h>
-# include <dcstack.h>
-# include <diinpxt.h>
+# include <dcmtk/dcmdata/dcfilefo.h>
+# include <dcmtk/dcmdata/dcmetinf.h>
+# include <dcmtk/dcmdata/dcdatset.h>
+# include <dcmtk/dcmdata/dctagkey.h>
+# include <dcmtk/dcmdata/dcdeftag.h>
+# include <dcmtk/dcmdata/dcstack.h>
+# include <dcmtk/dcmimgle/diinpxt.h>
# include "vil_dicom_stream.h"
//
@@ -108,8 +108,9 @@ static void
read_header(DcmObject * dataset, vil_dicom_header_info & i);
static void
-read_pixels_into_buffer(DcmPixelData * pixels,
+read_pixels_into_buffer(DiDocument* doc,
unsigned num_samples,
+ unsigned nplanes,
Uint16 alloc,
Uint16 stored,
Uint16 high,
@@ -119,7 +120,6 @@ read_pixels_into_buffer(DcmPixelData * pixels,
vil_memory_chunk_sptr & out_buf,
vil_pixel_format & out_format);
-
vil_dicom_image::vil_dicom_image(vil_stream * vs)
: pixels_(0)
{@@ -209,12 +209,15 @@ vil_dicom_image::vil_dicom_image(vil_stream * vs)
else
{assert(stack.top()->ident() == EVR_PixelData);
- pixels = static_cast<DcmPixelData *>(stack.top());
}
}
+
+ DiDocument doc(&dset, EXS_Unknown);
+ pixels = doc.getPixelData();
+
unsigned num_samples = ni() * nj() * nplanes();
read_pixels_into_buffer(
- pixels, num_samples, bits_alloc, bits_stored, high_bit, pixel_rep, slope, intercept, pixel_buf, pixel_format);
+ &doc, num_samples, nplanes(), bits_alloc, bits_stored, high_bit, pixel_rep, slope, intercept, pixel_buf, pixel_format);
}
// Create an image resource to manage the pixel buffer
@@ -1035,34 +1038,36 @@ namespace
template <class InT>
void
convert_src_type(InT const *,
- DcmPixelData * pixels,
+ DiDocument *document,
unsigned num_samples,
+ unsigned nplanes,
Uint16 alloc,
Uint16 stored,
Uint16 high,
Uint16 rep,
- DiInputPixel *& pixel_data,
- vil_pixel_format & act_format)
+ DiInputPixel *&pixel_data,
+ vil_pixel_format &act_format)
{+ Uint32 firstFragment = 0;
if (rep == 0 && stored <= 8)
{act_format = VIL_PIXEL_FORMAT_BYTE;
- pixel_data = new DiInputPixelTemplate<InT, Uint8>(pixels, alloc, stored, high, 0, num_samples);
+ pixel_data = new DiInputPixelTemplate<InT,Uint8>( document, alloc, stored, high, 0, num_samples, nplanes, nullptr, firstFragment );
}
else if (rep == 0 && stored <= 16)
{act_format = VIL_PIXEL_FORMAT_UINT_16;
- pixel_data = new DiInputPixelTemplate<InT, Uint16>(pixels, alloc, stored, high, 0, num_samples);
+ pixel_data = new DiInputPixelTemplate<InT,Uint16>( document, alloc, stored, high, 0, num_samples, nplanes, nullptr, firstFragment );
}
else if (rep == 1 && stored <= 8)
{act_format = VIL_PIXEL_FORMAT_SBYTE;
- pixel_data = new DiInputPixelTemplate<InT, Sint8>(pixels, alloc, stored, high, 0, num_samples);
+ pixel_data = new DiInputPixelTemplate<InT,Sint8>( document, alloc, stored, high, 0, num_samples, nplanes, nullptr, firstFragment );
}
else if (rep == 1 && stored <= 16)
{act_format = VIL_PIXEL_FORMAT_INT_16;
- pixel_data = new DiInputPixelTemplate<InT, Sint16>(pixels, alloc, stored, high, 0, num_samples);
+ pixel_data = new DiInputPixelTemplate<InT,Sint16>( document, alloc, stored, high, 0, num_samples, nplanes, nullptr, firstFragment );
}
}
@@ -1095,8 +1100,9 @@ swap_shorts(unsigned short * ip, unsigned short * op, int count)
}
# endif // MIXED_ENDIAN
static void
-read_pixels_into_buffer(DcmPixelData * pixels,
+read_pixels_into_buffer(DiDocument* doc,
unsigned num_samples,
+ unsigned nplanes,
Uint16 alloc,
Uint16 stored,
Uint16 high,
@@ -1106,6 +1112,7 @@ read_pixels_into_buffer(DcmPixelData * pixels,
vil_memory_chunk_sptr & out_buf,
vil_pixel_format & out_format)
{+
// This will be the "true" pixel buffer type after the overlay
// planes are removed and the pixel bits shifted to the lowest bits
// of the bytes.
@@ -1117,14 +1124,14 @@ read_pixels_into_buffer(DcmPixelData * pixels,
// Make sure pixel_data is deleted before this function exits!
//
DiInputPixel * pixel_data = 0;
- if (pixels->getVR() == EVR_OW)
- {- convert_src_type((Uint16 *)0, pixels, num_samples, alloc, stored, high, rep, pixel_data, act_format);
+ if ( doc->getPixelData()->getVR() == EVR_OW ) {+ convert_src_type((Uint16 *) 0, doc, num_samples, nplanes, alloc, stored, high, rep, pixel_data, act_format);
}
else
{- convert_src_type((Uint8 *)0, pixels, num_samples, alloc, stored, high, rep, pixel_data, act_format);
+ convert_src_type((Uint8 *) 0, doc, num_samples, nplanes, alloc, stored, high, rep, pixel_data, act_format);
}
+
# ifdef MIXED_ENDIAN
# ifdef NO_OFFSET
slope = 1;
@@ -1147,7 +1154,7 @@ read_pixels_into_buffer(DcmPixelData * pixels,
}
// The data has been copied and converted. Release the source.
- pixels->clear();
+ doc->getPixelData()->clear();
// Now, the actual buffer is good, or else we need to rescale
//
diff --git a/core/vil/file_formats/vil_dicom_stream.cxx b/core/vil/file_formats/vil_dicom_stream.cxx
index e1f72efc82..87a722aaf3 100644
--- a/core/vil/file_formats/vil_dicom_stream.cxx
+++ b/core/vil/file_formats/vil_dicom_stream.cxx
@@ -4,7 +4,7 @@
# include "vil_dicom_stream.h"
# include "vil/vil_stream.h"
-# include <dcerror.h>
+# include <dcmtk/dcmdata/dcerror.h>
# include <cassert>
# ifdef _MSC_VER
@@ -42,14 +42,14 @@ vil_dicom_stream_producer::status() const
OFBool
-vil_dicom_stream_producer::eos() const
+vil_dicom_stream_producer::eos()
{return vs_->tell() >= vs_->file_size();
}
-Uint32
-vil_dicom_stream_producer::avail() const
+offile_off_t
+vil_dicom_stream_producer::avail()
{vil_streampos n = vs_->file_size() - vs_->tell();
assert(n >= 0);
@@ -57,13 +57,13 @@ vil_dicom_stream_producer::avail() const
// apparently dicom streams only support 32 bit positions
// whereas vil_streams now support 64 bit positions (when
// available)
- assert(n <= (vil_streampos)std::numeric_limits<Uint32>::max());
- return (Uint32)n;
+ assert( n <= (vil_streampos)std::numeric_limits<offile_off_t>::max() );
+ return (offile_off_t)n;
}
-Uint32
-vil_dicom_stream_producer::read(void * buf, Uint32 buflen)
+offile_off_t
+vil_dicom_stream_producer::read( void *buf, offile_off_t buflen )
{vil_streampos n = vs_->read(buf, buflen);
assert(n >= 0);
@@ -71,13 +71,13 @@ vil_dicom_stream_producer::read(void * buf, Uint32 buflen)
// apparently dicom streams only support 32 bit positions
// whereas vil_streams now support 64 bit positions (when
// available)
- assert(n <= (vil_streampos)std::numeric_limits<Uint32>::max());
- return (Uint32)n;
+ assert( n <= (vil_streampos)std::numeric_limits<offile_off_t>::max() );
+ return (offile_off_t)n;
}
-Uint32
-vil_dicom_stream_producer::skip(Uint32 skiplen)
+offile_off_t
+vil_dicom_stream_producer::skip(offile_off_t skiplen)
{vs_->seek(vs_->tell() + skiplen);
return skiplen;
@@ -85,7 +85,7 @@ vil_dicom_stream_producer::skip(Uint32 skiplen)
void
-vil_dicom_stream_producer::putback(Uint32 num)
+vil_dicom_stream_producer::putback(offile_off_t num)
{vs_->seek(vs_->tell() - (long int)num);
}
diff --git a/core/vil/file_formats/vil_dicom_stream.h b/core/vil/file_formats/vil_dicom_stream.h
index 79a639639a..8115184289 100644
--- a/core/vil/file_formats/vil_dicom_stream.h
+++ b/core/vil/file_formats/vil_dicom_stream.h
@@ -4,7 +4,8 @@
// \file
// \author Amitha Perera
-#include <dcistrma.h>
+#include <dcmtk/dcmdata/dcistrma.h>
+#include <dcmtk/dcmimgle/didocu.h>
class vil_stream;
@@ -18,11 +19,11 @@ class vil_dicom_stream_producer
virtual OFBool good() const;
virtual OFCondition status() const;
- virtual OFBool eos() const;
- virtual Uint32 avail() const;
- virtual Uint32 read(void *buf, Uint32 buflen);
- virtual Uint32 skip(Uint32 skiplen);
- virtual void putback(Uint32 num);
+ OFBool eos() override;
+ offile_off_t avail() override;
+ offile_off_t read(void *buf, offile_off_t buflen) override;
+ offile_off_t skip(offile_off_t skiplen) override;
+ void putback(offile_off_t num) override;
private:
vil_stream* vs_;
@@ -43,6 +44,9 @@ class vil_dicom_stream_factory
{return new vil_dicom_stream_factory(*this);
}
+ DcmInputStreamFactoryType ident() const override {+ return DFT_DcmInputFileStreamFactory;
+ }
private:
vil_stream* vs_;
diff --git a/v3p/netlib/CMakeLists.txt b/v3p/netlib/CMakeLists.txt
index 1c3df5db0c..23fc69850a 100644
--- a/v3p/netlib/CMakeLists.txt
+++ b/v3p/netlib/CMakeLists.txt
@@ -13,6 +13,8 @@ vxl_add_library(
DISABLE_MSVC_MP
)
+set_target_properties(${VXL_LIB_PREFIX}netlib PROPERTIES PREFIX "libv3px_")+
if(UNIX)
target_link_libraries( ${VXL_LIB_PREFIX}netlib m )endif()