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scaramallionscaramallion
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Add skeletons
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‎docs/release_notes/v1.0.0.rst‎

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‎rle/__init__.py‎

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"""Set package shortcuts."""
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from ._version import __version__

‎rle/_rle.pyx‎

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# cython: language_level=3
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# distutils: language=c++
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cdef extern from "decode.hpp":
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pass
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#cdef string Decode(
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# char *inArray,
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# char *outArray,
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# int inLength,
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# int outLength,
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#)

‎rle/_version.py‎

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"""Version information based on PEP396 and 440."""
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import re
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__version__ = '1.0.0.dev0'
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VERSION_PATTERN = r"""
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v?
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(?:
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(?:(?P<epoch>[0-9]+)!)? # epoch
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(?P<release>[0-9]+(?:\.[0-9]+)*) # release segment
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(?P<pre> # pre-release
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[-_\.]?
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(?P<pre_l>(a|b|c|rc|alpha|beta|pre|preview))
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[-_\.]?
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(?P<pre_n>[0-9]+)?
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)?
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(?P<post> # post release
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(?:-(?P<post_n1>[0-9]+))
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|
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(?:
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[-_\.]?
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(?P<post_l>post|rev|r)
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[-_\.]?
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(?P<post_n2>[0-9]+)?
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)
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)?
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(?P<dev> # dev release
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[-_\.]?
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(?P<dev_l>dev)
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[-_\.]?
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(?P<dev_n>[0-9]+)?
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)?
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)
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(?:\+(?P<local>[a-z0-9]+(?:[-_\.][a-z0-9]+)*))? # local version
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"""
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def is_canonical(version):
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"""Return True if `version` is a PEP440 conformant version."""
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match = re.match(
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(
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r'^([1-9]\d*!)?(0|[1-9]\d*)'
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r'(\.(0|[1-9]\d*))'
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r'*((a|b|rc)(0|[1-9]\d*))'
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r'?(\.post(0|[1-9]\d*))'
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r'?(\.dev(0|[1-9]\d*))?$'
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),
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version
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)
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return match is not None
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assert is_canonical(__version__)

‎rle/src/decode.cpp‎

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// Includes
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#include "std/stdio.hpp"
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#include "std/string.hpp"
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#include <sstream>
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#include "decode.hpp"
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std::string Decode(char *inArray, char *outArray, int inLength, int outLength)
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{
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/*
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Parameters
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----------
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char *inArray
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Pointer to the first element of a byte array containing the RLE
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data to be decompressed.
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char *outArray
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Pointer to the first element of a numpy.ndarray where the decompressed
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RLE data should be written.
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int inLength
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Length of the input array
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int outLength
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Expected length of the output array
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*/
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//
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};
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int decode_segment(const char *segment, unsigned int expected_length) {
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/*
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Parameters
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----------
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char *segment
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The RLE encoded segment to be decoded
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int length
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Length of the segment
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*/
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// Output
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std::stringstream out;
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// Current position
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unsigned int pos = 0;
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// Length of the output
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unsigned int output_length = 0;
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unsigned char header_byte;
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// Can only copy or extend by at most 128 bytes per loop
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// TODO:
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// Need proper output location
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// Need to fix up pointers, etc
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// Need to make sure we don't go past the end of the input
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while (output_length < expected_length) {
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header_byte = segment[pos] + 1;
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pos += 1;
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if (header_byte > 129) {
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// Extend by copying the next byte (-N + 1) times, however since
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// we are using uint8 this will be (256 - N + 1) times
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// memset(ptr out, int value, int nr of bytes to set to `value`)
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extend_len = 258 - header_byte;
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memset(out, segment[pos], extend_len);
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output_length += extend_len;
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pos += 1;
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} else if (header_byte < 129) {
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// Extend by literally copying the next (N + 1) bytes
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// memcopy(ptr out, ptr src, int nr of bytes to copy)
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memcopy(out, segment[pos], header_byte)
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//result.extend(segment[pos:pos + header_byte])
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output_length += header_byte;
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pos += header_byte;
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}
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}
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if (output_length != expected_length) {
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return -1;
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}
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return out;
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};

‎rle/src/decode.hpp‎

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#include <iostream>
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#include <string>
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#ifndef DECODE_HPP
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#define DECODE_HPP
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// Prototypes
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// Decode an RLE encoded frame `inArray` to `outArray`
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//extern std::string decode_frame(
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// char *inArray,
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// char *outArray,
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// int inLength,
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// int outLength,
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//);
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// Decode an RLE encoded segment
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//extern decode_segment();
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// Parse the RLE header
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extern int decode_segment(const char *segment, int length);
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#endif

‎rle/utils.py‎

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‎setup.py‎

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import os
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import sys
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from pathlib import Path
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import platform
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import setuptools
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from setuptools import setup, find_packages
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from setuptools.extension import Extension
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import subprocess
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from distutils.command.build import build as build_orig
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import distutils.sysconfig
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RLE_SRC = os.path.join('rle', 'src', 'rle')
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# Workaround for needing cython and numpy
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# Solution from: https://stackoverflow.com/a/54128391/12606901
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class build(build_orig):
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def finalize_options(self):
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super().finalize_options()
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__builtins__.__NUMPY_SETUP__ = False
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import numpy
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for ext in self.distribution.ext_modules:
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if ext in extensions:
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ext.include_dirs.append(numpy.get_include())
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def get_mscv_args():
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"""Return a list of compiler args for MSVC++'s compiler."""
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flags = [
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'/GS', # Buffer security check
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'/W3', # Warning level
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'/wd"4335"', # Ignore warning 4335
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'/Zc:wchar_t', # Use windows char type
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'/Zc:inline', # Remove unreferenced function or data (...)
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'/Zc:forScope',
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'/Od', # Disable optimisation
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'/Oy-', # (x86 only) don't omit frame pointer
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'/openmp-', # Disable #pragma omp directive
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'/FC', # Display full path of source code files
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'/fp:precise', # Floating-point behaviour
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'/Gd', # (x86 only) use __cdecl calling convention
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'/GF-', # Disable string pooling
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'/GR', # Enable run-time type info
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'/RTC1', # Enable run-time error checking
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'/MT', # Create multithreading executable
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# /D defines constants and macros
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'/D_UNICODE',
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'/DUNICODE',
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]
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# Set the architecture based on system architecture and Python
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is_x64 = platform.architecture()[0] == '64bit'
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if is_x64 and sys.maxsize > 2**32:
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flags.append('/DWIN64=1')
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else:
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# Architecture is 32-bit, or Python is 32-bit
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flags.append('/DWIN32=1')
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return flags
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def get_source_files():
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"""Return a list of paths to the source files to be compiled."""
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source_files = [
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'rle/_libjpeg.pyx',
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os.path.join(RLE_SRC, 'decode.cpp'),
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]
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#for fname in Path(RLE_SRC).glob('*/*'):
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# if '.cpp' in str(fname):
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# source_files.append(str(fname))
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return source_files
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# Compiler and linker arguments
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extra_compile_args = []
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extra_link_args = []
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if platform.system() == 'Windows':
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os.environ['LIB'] = os.path.abspath(
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os.path.join(sys.executable, '../', 'libs')
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)
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extra_compile_args = get_mscv_args()
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extensions = [
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Extension(
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'_rle',
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get_source_files(),
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language='c++',
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include_dirs=[
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RLE_SRC,
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distutils.sysconfig.get_python_inc(),
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# Numpy includes get added by the `build` subclass
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],
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extra_compile_args=extra_compile_args,
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extra_link_args=extra_link_args,
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)
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]
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VERSION_FILE = os.path.join('rle', '_version.py')
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with open(VERSION_FILE) as fp:
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exec(fp.read())
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with open('README.md', 'r') as fp:
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long_description = fp.read()
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setup(
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name = 'pylibjpeg-rle',
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description = (
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"A Python wrapper for libjpeg, with a focus on use as a plugin for "
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"for pylibjpeg"
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),
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long_description = long_description,
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long_description_content_type = 'text/markdown',
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version = __version__,
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author = "scaramallion",
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author_email = "[email protected]",
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url = "https://github.com/pydicom/pylibjpeg-rle",
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license = "MIT",
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keywords = (
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"dicom pydicom python medicalimaging radiotherapy oncology imaging "
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"radiology nuclearmedicine rle pylibjpeg"
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),
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classifiers = [
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"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
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"Intended Audience :: Developers",
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"Intended Audience :: Healthcare Industry",
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"Intended Audience :: Science/Research",
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"Development Status :: 3 - Alpha",
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#"Development Status :: 4 - Beta",
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#"Development Status :: 5 - Production/Stable",
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"Natural Language :: English",
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"Programming Language :: C++",
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"Programming Language :: Python :: 3.6",
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"Programming Language :: Python :: 3.7",
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"Programming Language :: Python :: 3.8",
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"Operating System :: MacOS :: MacOS X",
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"Operating System :: POSIX :: Linux",
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"Operating System :: Microsoft :: Windows",
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"Topic :: Scientific/Engineering :: Medical Science Apps.",
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"Topic :: Software Development :: Libraries",
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],
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packages = find_packages(),
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package_data = {'': ['*.txt', '*.cpp', '*.h', '*.hpp', '*.pyx']},
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include_package_data = True,
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zip_safe = False,
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python_requires = ">=3.6",
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setup_requires = ['setuptools>=18.0', 'cython', 'numpy>=1.16.0'],
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install_requires = ["numpy>=1.16.0"],
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cmdclass = {'build': build},
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ext_modules = extensions,
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# Plugin registrations
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entry_points={
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'pylibjpeg.pixel_data_decoders': [
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"1.2.840.10008.1.2.5 = rle:decode_pixel_data",
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],
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},
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)

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