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new package: libvxl

This commit is contained in:
Pooya Moradi 2022-09-30 07:48:41 +08:00 committed by Henrik Grimler
parent 1768d41f31
commit 4d7d8c3c11
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2 changed files with 278 additions and 0 deletions
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261
packages/libvxl/0001-update-to-newer-dcmtk-API.patch Normal file
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@ -0,0 +1,261 @@
From ce3d7e2654bf5bc456a8b2bc89993393cffa9560 Mon Sep 17 00:00:00 2001
From: Slava Aseev <ptrnine@altlinux.org>
Date: Wed, 9 Jan 2019 18:26:57 +0300
Subject: [PATCH] Updated to 3.6.4 DCMTK API
---
config/cmake/Modules/FindDCMTK.cmake | 2 +-
core/vil/file_formats/vil_dicom.cxx | 66 ++++++++++++----------
core/vil/file_formats/vil_dicom_stream.cxx | 26 ++++-----
core/vil/file_formats/vil_dicom_stream.h | 18 ++++--
4 files changed, 63 insertions(+), 49 deletions(-)
diff -uNr a/core/vil/file_formats/vil_dicom.cxx b/core/vil/file_formats/vil_dicom.cxx
--- a/core/vil/file_formats/vil_dicom.cxx 2021-08-02 23:21:08.000000000 +0800
+++ b/core/vil/file_formats/vil_dicom.cxx 2022-09-29 21:27:12.960447500 +0800
@@ -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 @@
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,
@@ -209,12 +210,15 @@
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
@@ -1035,8 +1039,9 @@
template <class InT>
void
convert_src_type(InT const *,
- DcmPixelData * pixels,
+ DiDocument *document,
unsigned num_samples,
+ unsigned nplanes,
Uint16 alloc,
Uint16 stored,
Uint16 high,
@@ -1044,25 +1049,26 @@
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 +1101,9 @@
}
# 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,
@@ -1117,13 +1124,13 @@
// Make sure pixel_data is deleted before this function exits!
//
DiInputPixel * pixel_data = 0;
- if (pixels->getVR() == EVR_OW)
+ if (doc->getPixelData()->getVR() == EVR_OW)
{
- convert_src_type((Uint16 *)0, pixels, num_samples, alloc, stored, high, rep, pixel_data, act_format);
+ 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
@@ -1147,7 +1154,7 @@
}
// 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 -uNr a/core/vil/file_formats/vil_dicom_stream.cxx b/core/vil/file_formats/vil_dicom_stream.cxx
--- a/core/vil/file_formats/vil_dicom_stream.cxx 2021-08-02 23:21:08.000000000 +0800
+++ b/core/vil/file_formats/vil_dicom_stream.cxx 2022-09-29 21:26:54.001356700 +0800
@@ -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 @@
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 @@
// 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 @@
// 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 @@
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 -uNr a/core/vil/file_formats/vil_dicom_stream.h b/core/vil/file_formats/vil_dicom_stream.h
--- a/core/vil/file_formats/vil_dicom_stream.h 2021-08-02 23:21:08.000000000 +0800
+++ b/core/vil/file_formats/vil_dicom_stream.h 2022-09-29 21:20:34.157511200 +0800
@@ -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 @@
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);
+ virtual OFBool eos();
+ virtual offile_off_t avail();
+ virtual offile_off_t read(void *buf, offile_off_t buflen);
+ virtual offile_off_t skip(offile_off_t skiplen);
+ virtual void putback(offile_off_t num);
private:
vil_stream* vs_;
@@ -43,6 +44,11 @@
{
return new vil_dicom_stream_factory(*this);
}
+
+ virtual DcmInputStreamFactoryType ident() const
+ {
+ return DFT_DcmInputFileStreamFactory;
+ }
private:
vil_stream* vs_;

17
packages/libvxl/build.sh Normal file
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@ -0,0 +1,17 @@
TERMUX_PKG_HOMEPAGE="https://vxl.github.io"
TERMUX_PKG_DESCRIPTION="A multi-platform collection of C++ software libraries for Computer Vision and Image Understanding"
TERMUX_PKG_GROUPS="science"
TERMUX_PKG_LICENSE="BSD 3-Clause"
TERMUX_PKG_LICENSE_FILE="core/vxl_copyright.h"
TERMUX_PKG_MAINTAINER="@termux"
TERMUX_PKG_VERSION="3.3.2"
TERMUX_PKG_AUTO_UPDATE=true
TERMUX_PKG_SRCURL="https://github.com/vxl/vxl/archive/refs/tags/v$TERMUX_PKG_VERSION.tar.gz"
TERMUX_PKG_SHA256=95ecde4b02bbe00aec0d656fd2c43373de2a5d41487a68135f0b565254919411
TERMUX_PKG_DEPENDS="libc++, libgeotiff, zlib, libpng, libjpeg-turbo, libexpat, dcmtk"
TERMUX_PKG_EXTRA_CONFIGURE_ARGS="
-DBUILD_SHARED_LIBS=ON
-DVCL_HAS_LFS=NO
-DVXL_HAS_SSE2_HARDWARE_SUPPORT=NO
-DVXL_SSE2_HARDWARE_SUPPORT_POSSIBLE=NO
"