Pre-release fixes and updates (#3)

Author: scaramallion

.codecov.yml

@@ -0,0 +1,24 @@
+comment:
+  layout: "diff, files"
+  behavior: default
+  require_changes: false  # if true: only post the comment if coverage changes
+  require_base: yes        # [yes :: must have a base report to post]
+  require_head: yes       # [yes :: must have a head report to post]
+  branches:               # branch names that can post comment
+    - "master"
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 0.1%
+    patch:
+      default:
+        target: auto
+        threshold: 0.1%
+
+ignore:
+  - "rle/tests"
+  - "rle/src"
+  - "rle/benchmarks"

.github/workflows/pytest-builds.yml

@@ -8,15 +8,18 @@ on:
 
 jobs:
   pytest:
-    runs-on: ubuntu-latest
-    timeout-minutes: 30
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 10
     strategy:
       fail-fast: false
       matrix:
         python-version: [3.6, 3.7, 3.8, 3.9]
+        os: [ubuntu-latest, windows-latest, macos-latest]
 
     steps:
     - uses: actions/checkout@v2
+      with:
+        fetch-depth: 2
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
@@ -39,3 +42,11 @@ jobs:
         PYTHON_VERSION: ${{ matrix.python-version }}
       run: |
         pytest --cov rle
+
+    - name: Send coverage results
+      if: ${{ success() && matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9' }}
+      run: |
+        bash <(curl --connect-timeout 10 --retry 10 --retry-max-time \
+        0 https://codecov.io/bash) || (sleep 30 && bash <(curl \
+        --connect-timeout 10 --retry 10 --retry-max-time \
+        0 https://codecov.io/bash))

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020 scaramallion
+Copyright (c) 2020-2021 scaramallion
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,7 +1,7 @@
 
 ## pylibjpeg-rle
 
-A fast DICOM RLE decoding plugin for pylibjpeg, written in Rust with a Python 3.6+ wrapper.
+A fast DICOM ([PackBits](https://en.wikipedia.org/wiki/PackBits)) RLE plugin for [pylibjpeg](https://github.com/pydicom/pylibjpeg) RLE decoding plugin for pylibjpeg, written in Rust with a Python 3.6+ wrapper.
 
 Linux, OSX and Windows are all supported.
 
@@ -22,10 +22,10 @@ python -m setup.py develop
 ```
 
 ### Supported Transfer Syntaxes
-#### Decoding
-| UID                 | Description  |
-| ---                 | ---          |
-| 1.2.840.10008.1.2.5 | RLE Lossless |
+
+| UID                 | Description  | Decoding | Encoding |
+| ---                 | ---          | ---      | ---      |
+| 1.2.840.10008.1.2.5 | RLE Lossless | Yes      | No       |
 
 ### Benchmarks
 #### Decoding
@@ -48,10 +48,11 @@ Time per 1000 decodes, pydicom's NumPy RLE handler vs. pylibjpeg-rle
 | SC_rgb_rle_32bit_2frame.dcm |  20,000 | 240,000 | 1.03 s |        0.28 s |
 
 ### Usage
-#### With pylibjpeg and pydicom
+#### Decoding
+##### With pylibjpeg
 
 Because pydicom defaults to the NumPy RLE decoder, you must specify the use
-of pylibjpeg when decompressing:
+of pylibjpeg when decompressing (**note: requires pydicom v2.2+**):
 *Pixel Data*:
 ```python
 from pydicom import dcmread
@@ -62,6 +63,7 @@ ds.decompress("pylibjpeg")
 arr = ds.pixel_array
 ```
 
+#### Standalone with pydicom
 Alternatively you can use the included functions to decode a given dataset:
 ```python
 from rle import pixel_array, generate_frames

docs/release_notes/v1.0.0.rst

@@ -0,0 +1,11 @@
+.. _v1.0.0:
+
+1.0.0
+=====
+
+Enhancements
+............
+
+* Initial release
+* Added support for decoding *RLE Lossless* encoded *Pixel Data*
+* Added support for use of a plugin with pylibjpeg

rle/_version.py

@@ -3,7 +3,7 @@
 import re
 
 
-__version__ = '1.0.0.dev0'
+__version__ = '1.0.0'
 
 
 VERSION_PATTERN = r"""

rle/tests/test_handler.py

@@ -4,6 +4,7 @@
 
 try:
     from pydicom import dcmread
+    from pydicom.encaps import generate_pixel_data_frame
     from pydicom.uid import RLELossless
     HAVE_PYDICOM = True
 except ImportError:
@@ -29,27 +30,12 @@ def test_u8_1s_1f(self):
         assert 800 == ds.Columns
         assert 1 == getattr(ds, 'NumberOfFrames', 1)
 
-        arr = decode_pixel_data(ds.PixelData, ds)
+        frame = next(generate_pixel_data_frame(ds.PixelData))
+        arr = decode_pixel_data(frame, ds)
         assert (480000, ) == arr.shape
         assert arr.flags.writeable
         assert 'uint8' == arr.dtype
 
-    def test_u8_1s_2f(self):
-        """Test plugin decoder for 8 bit, 1 sample, 2 frame data."""
-        ds = INDEX["OBXXXX1A_rle_2frame.dcm"]['ds']
-        assert ds.file_meta.TransferSyntaxUID == RLELossless
-        assert 8 == ds.BitsAllocated
-        assert 1 == ds.SamplesPerPixel
-        assert 0 == ds.PixelRepresentation
-        assert 600 == ds.Rows
-        assert 800 == ds.Columns
-        assert 2 == getattr(ds, 'NumberOfFrames', 1)
-
-        arr = decode_pixel_data(ds.PixelData, ds)
-        assert (960000, ) == arr.shape
-        assert arr.flags.writeable
-        assert 'uint8' == arr.dtype
-
     def test_u32_3s_1f(self):
         """Test plugin decoder for 32 bit, 3 sample, 1 frame data."""
         ds = INDEX["SC_rgb_rle_32bit.dcm"]['ds']
@@ -61,23 +47,8 @@ def test_u32_3s_1f(self):
         assert 100 == ds.Columns
         assert 1 == getattr(ds, 'NumberOfFrames', 1)
 
-        arr = decode_pixel_data(ds.PixelData, ds)
+        frame = next(generate_pixel_data_frame(ds.PixelData))
+        arr = decode_pixel_data(frame, ds)
         assert (120000, ) == arr.shape
         assert arr.flags.writeable
         assert 'uint8' == arr.dtype
-
-    def test_u32_3s_2f(self):
-        """Test plugin decoder for 32 bit, 3 sample, 2 frame data."""
-        ds = INDEX["SC_rgb_rle_32bit_2frame.dcm"]['ds']
-        assert ds.file_meta.TransferSyntaxUID == RLELossless
-        assert 32 == ds.BitsAllocated
-        assert 3 == ds.SamplesPerPixel
-        assert 0 == ds.PixelRepresentation
-        assert 100 == ds.Rows
-        assert 100 == ds.Columns
-        assert 2 == getattr(ds, 'NumberOfFrames', 1)
-
-        arr = decode_pixel_data(ds.PixelData, ds)
-        assert (240000, ) == arr.shape
-        assert arr.flags.writeable
-        assert 'uint8' == arr.dtype

rle/utils.py

@@ -14,43 +14,26 @@ def decode_pixel_data(stream: bytes, ds: "Dataset") -> "np.ndarray":
     Parameters
     ----------
     stream : bytes
-        The contents of the dataset's *Pixel Data*.
+        The image frame to be decoded.
     ds : pydicom.dataset.Dataset
         A :class:`~pydicom.dataset.Dataset` containing the group ``0x0028``
         elements corresponding to the *Pixel Data*.
 
     Returns
     -------
     numpy.ndarray
-        A 1D array of ``numpy.uint8`` containing the decoded image data,
+        A 1D array of ``numpy.uint8`` containing the decoded frame data,
         with big-endian encoding and planar configuration 1.
 
     Raises
     ------
     ValueError
         If the decoding failed.
     """
-    from pydicom.encaps import generate_pixel_data_frame
-    from pydicom.pixel_data_handlers.util import get_expected_length
-    from pydicom.uid import RLELossless
-
-    nr_frames = getattr(ds, "NumberOfFrames", 1)
-    r, c = ds.Rows, ds.Columns
-    bpp = ds.BitsAllocated
-
-    expected_len = get_expected_length(ds, 'bytes')
-    frame_len = expected_len // getattr(ds, "NumberOfFrames", 1)
-    # Empty destination array for our decoded pixel data
-    arr = np.empty(expected_len, dtype='uint8')
-
-    generate_frames = generate_pixel_data_frame(ds.PixelData, nr_frames)
-    generate_offsets = range(0, expected_len, frame_len)
-    for frame, offset in zip(generate_frames, generate_offsets):
-        arr[offset:offset + frame_len] = np.frombuffer(
-            decode_frame(frame, r * c, bpp), dtype='uint8'
-        )
-
-    return arr
+    return np.frombuffer(
+        decode_frame(stream, ds.Rows * ds.Columns, ds.BitsAllocated),
+        dtype='uint8'
+    )
 
 
 def generate_frames(

src/lib.rs

@@ -1,7 +1,3 @@
-// https://pyo3.rs/v0.13.2/conversions/tables.html
-// bytes -> &[u8] or Vec<u8>
-// bytearray -> Vec<u8>
-// list[T] -> Vec<T>
 
 use std::error::Error;
 use std::convert::TryFrom;
@@ -105,7 +101,8 @@ fn _decode_frame(
     px_per_sample
         The number of pixels per sample (rows x columns), maximum (2^32 - 1).
     bits_per_px
-        The number of bits per pixel, should be a multiple of 8 and no larger than 64.
+        The number of bits per pixel, should be a multiple of 8 and no larger
+        than 64.
     */
 
     // Pre-define our errors for neatness