Overhaul package

Author: scaramallion

.coveragerc

@@ -0,0 +1,4 @@
+[run]
+omit =
+    rle/tests/*
+    rle/benchmarks/*

.github/workflows/pytest-builds.yml

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+name: Run pytest
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  pytest:
+    runs-on: ubuntu-latest
+    timeout-minutes: 30
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [3.6, 3.7, 3.8, 3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install setuptools-rust pytest pydicom coverage pytest-cov
+        pip install git+https://github.com/pydicom/pylibjpeg-data
+        pip install -e .
+
+    - name: Test with pytest
+      env:
+        PYTHON_VERSION: ${{ matrix.python-version }}
+      run: |
+        pytest --cov rle

.github/workflows/release-wheels.yml

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+name: Build wheels and deploy to PyPI
+
+on:
+  release:
+    types: [ published ]
+
+jobs:
+  build_wheels:
+    name: Build wheels for ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    env:
+      CIBW_SKIP: "cp35-*"
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.9]
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: true
+
+    # Install rust
+    - uses: actions-rs/toolchain@v1
+      with:
+        toolchain: stable
+
+    # Install Python
+    - uses: actions/setup-python@v2
+      name: Install Python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install requirements
+      run: |
+        pip install -U pip
+        pip install cibuildwheel==1.10.0
+        pip install setuptools-rust
+
+    - name: Build sdist
+      run: |
+         python setup.py sdist
+
+    - name: Build wheels
+      run: |
+        python --version
+        python -m cibuildwheel --output-dir dist
+      env:
+          CIBW_BEFORE_ALL: |
+            curl -sSf https://sh.rustup.rs | sh -s -- --default-toolchain stable -y && rustup target add i686-pc-windows-msvc
+          CIBW_ENVIRONMENT: 'PATH="$PATH:$HOME/.cargo/bin"'
+
+    - uses: actions/upload-artifact@v2
+      with:
+        name: wheels
+        path: ./dist
+
+  # The pypi upload fails with non-linux containers, so grab the uploaded
+  #     artifacts and run using those
+  # See: https://github.com/pypa/gh-action-pypi-publish/discussions/15
+  deploy:
+    name: Upload wheels to PyPI
+    needs:
+    - build_wheels
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Download the wheels
+      uses: actions/download-artifact@v2
+      with:
+        name: wheels
+        path: dist/
+
+    #- name: Publish package to Test PyPi
+    #  uses: pypa/gh-action-pypi-publish@master
+    #  with:
+    #    user: __token__
+    #    password: ${{ secrets.TEST_PYPI_PASSWORD }}
+    #    repository_url: https://test.pypi.org/legacy/
+
+    - name: Publish package to PyPi
+      uses: pypa/gh-action-pypi-publish@master
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_PASSWORD }}

rle/src/rustrle/Cargo.lock renamed to Cargo.lock

@@ -1,15 +1,14 @@
 [package]
-name = "rle"
-version = "0.1.0"
+name = "_rle"
+version = "1.0.0"
 authors = ["scaramallion <[email protected]>"]
 edition = "2018"
 
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
-
-[dependencies]
-pyo3 = { version = "0.13.1", features = ["extension-module"] }
-
 
 [lib]
 name = "_rle"
 crate-type = ["cdylib"]
+
+
+[dependencies]
+pyo3 = { version = "0.13.1", features = ["extension-module"] }

rle/src/rustrle/Cargo.toml renamed to Cargo.toml

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+include Cargo.toml
+include Cargo.lock
+recursive-include src *

MANIFEST.in

@@ -1,2 +1,76 @@
-# pylibjpeg-rle
-Fast RLE decoding plugin for pylibjpeg
+
+## pylibjpeg-rle
+
+A fast DICOM RLE decoding plugin for pylibjpeg, written in Rust with a Python 3.6+ wrapper.
+
+Linux, OSX and Windows are all supported.
+
+### Installation
+#### Installing the current release
+```bash
+pip install pylibjpeg-rle
+```
+#### Installing the development version
+
+Make sure [Python](https://www.python.org/), [Git](https://git-scm.com/) and
+[Rust](https://www.rust-lang.org/) are installed. For Windows, you also need to install
+[Microsoft's C++ Build Tools](https://visualstudio.microsoft.com/thank-you-downloading-visual-studio/?sku=BuildTools&rel=16).
+```bash
+git clone https://github.com/pydicom/pylibjpeg-rle
+cd pylibjpeg-rle
+python -m setup.py develop
+```
+
+### Supported Transfer Syntaxes
+#### Decoding
+| UID                 | Description  |
+| ---                 | ---          |
+| 1.2.840.10008.1.2.5 | RLE Lossless |
+
+### Benchmarks
+#### Decoding
+
+Time per 1000 decodes, pydicom's NumPy RLE handler vs. pylibjpeg-rle
+
+| Dataset                     | Pixels  | Bytes   | NumPy  | pylibjpeg-rle |
+| ---                         | ---     | ---     | ---    | ---           |
+| OBXXXX1A_rle.dcm            | 480,000 | 480,000 | 4.89 s |        0.79 s |
+| OBXXXX1A_rle_2frame.dcm     | 960,000 | 960,000 | 9.89 s |        1.65 s |
+| SC_rgb_rle.dcm              |  10,000 |  30,000 | 0.20 s |        0.15 s |
+| SC_rgb_rle_2frame.dcm       |  20,000 |  60,000 | 0.32 s |        0.18 s |
+| MR_small_RLE.dcm            |   4,096 |   8,192 | 0.35 s |        0.13 s |
+| emri_small_RLE.dcm          |  40,960 |  81,920 | 1.13 s |        0.28 s |
+| SC_rgb_rle_16bit.dcm        |  10,000 |  60,000 | 0.33 s |        0.17 s |
+| SC_rgb_rle_16bit_2frame.dcm |  20,000 | 120,000 | 0.56 s |        0.21 s |
+| rtdose_rle_1frame.dcm       |     100 |     400 | 0.12 s |        0.13 s |
+| rtdose_rle.dcm              |   1,500 |   6,000 | 0.53 s |        0.26 s |
+| SC_rgb_rle_32bit.dcm        |  10,000 | 120,000 | 0.56 s |        0.19 s |
+| SC_rgb_rle_32bit_2frame.dcm |  20,000 | 240,000 | 1.03 s |        0.28 s |
+
+### Usage
+#### With pylibjpeg and pydicom
+
+Because pydicom defaults to the NumPy RLE decoder, you must specify the use
+of pylibjpeg when decompressing:
+*Pixel Data*:
+```python
+from pydicom import dcmread
+from pydicom.data import get_testdata_file
+
+ds = dcmread(get_testdata_file("OBXXXX1A_rle.dcm"))
+ds.decompress("pylibjpeg")
+arr = ds.pixel_array
+```
+
+Alternatively you can use the included functions to decode a given dataset:
+```python
+from rle import pixel_array, generate_frames
+
+# Return the entire Pixel Data as an ndarray
+arr = pixel_array(ds)
+
+# Generator function that only processes 1 frame at a time,
+# may help reduce memory usage when dealing with large Pixel Data
+for arr in generate_frames(ds):
+    print(arr.shape)
+```

README.md

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+[build-system]
+requires = [
+    "setuptools-rust",
+    "wheel"
+]

pyproject.toml

@@ -1,3 +1,4 @@
 """Set package shortcuts."""
 
-from ._version import __version__
+from rle._version import __version__
+from rle.utils import pixel_array, generate_frames, decode_pixel_data