Add torch reinhard support

.github/workflows/build.yaml

@@ -0,0 +1,44 @@
+name: Build and upload to PyPI
+
+on:
+  push
+
+jobs:
+  build_wheels:
+    name: Build release
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v3
+        with:
+          python-version: '3.x'
+
+      - name: Install deps
+        run: |
+          pip install setuptools wheel
+
+      - name: Build wheels
+        run: python setup.py sdist bdist_wheel
+
+      - uses: actions/upload-artifact@v3
+        with:
+          path: ./dist/*
+
+  upload_pypi:
+    needs: build_wheels
+    runs-on: ubuntu-18.04
+
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: artifact
+          path: dist
+
+      - uses: pypa/gh-action-pypi-publish@v1.5.0
+        with:
+          user: __token__
+          password: ${{ secrets.torchstain_deploy_token }}
+

.github/workflows/tests.yml → .github/workflows/tests_full.yml

@@ -3,14 +3,17 @@ name: tests
 on:
   push:
     branches:
-      - '*'
+      - main
   pull_request:
     branches:
-      - '*'
+      - main
 
 jobs:
   build:
     runs-on: ubuntu-18.04
+
+    if: startsWith(github.ref, 'refs/tags/v') != true
+
     steps:
       - uses: actions/checkout@v1
       - name: Set up Python 3.6
@@ -31,46 +34,14 @@ jobs:
           path: ${{github.workspace}}/dist/torchstain-*.whl
           if-no-files-found: error
 
-  test:
-    needs: build
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: [windows-2019, ubuntu-18.04, macos-11]
-        python-version: [3.6, 3.7, 3.8, 3.9]
-
-    steps:
-      - uses: actions/checkout@v1
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python-version }}
-
-      - name: Download artifact
-        uses: actions/download-artifact@master
-        with:
-          name: "Python wheel"
-
-      - name: Install deps and wheel
-        run: |
-          pip install tensorflow torch
-          pip install --find-links=${{github.workspace}} torchstain
-
-      - name: Install test dependencies
-        run: pip install opencv-python torchvision scikit-image pytest
-
-      - name: Run tests
-        run: |
-          pytest -v tests/test_utils.py
-          pytest -v tests/test_normalizers.py
-
   test-tf:
     needs: build
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ windows-2019, ubuntu-18.04, macos-11 ]
-        python-version: [ 3.7 ]
+        python-version: [ 3.7, 3.8, 3.9 ]
+        tf-version: [2.7.0, 2.8.0, 2.9.0]
 
     steps:
       - uses: actions/checkout@v1
@@ -84,24 +55,30 @@ jobs:
         with:
           name: "Python wheel"
 
-      - name: Install deps and wheel
+      - name: Install dependencies
         run: |
-          pip install tensorflow
-          pip install --find-links=${{github.workspace}} torchstain
+          pip install tensorflow==${{ matrix.tf-version }} protobuf==3.20.* opencv-python-headless scikit-image
+          pip install pytest
 
-      - name: Install test dependencies
-        run: pip install opencv-python scikit-image pytest
+      - name: Install wheel
+        run: pip install --find-links=${{github.workspace}} torchstain
 
       - name: Run tests
-        run: pytest -v tests/test_tf_normalizer.py
+        run: pytest -vs tests/test_tf.py
 
   test-torch:
     needs: build
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: [ windows-2019, ubuntu-18.04, macos-11 ]
-        python-version: [ 3.7 ]
+        python-version: [ 3.6, 3.7, 3.8, 3.9 ]
+        pytorch-version: [1.8.0, 1.9.0, 1.10.0, 1.11.0, 1.12.0]
+        exclude:
+          - python-version: 3.6
+            pytorch-version: 1.11.0
+          - python-version: 3.6
+            pytorch-version: 1.12.0
 
     steps:
       - uses: actions/checkout@v1
@@ -115,13 +92,13 @@ jobs:
         with:
           name: "Python wheel"
 
-      - name: Install deps and wheel wheel
+      - name: Install dependencies
         run: |
-          pip install torch
-          pip install --find-links=${{github.workspace}} torchstain
+          pip install torch==${{ matrix.pytorch-version }} torchvision opencv-python-headless scikit-image
+          pip install pytest
 
-      - name: Install test dependencies
-        run: pip install opencv-python torchvision scikit-image pytest
+      - name: Install wheel
+        run: pip install --find-links=${{github.workspace}} torchstain
 
       - name: Run tests
-        run: pytest -v tests/test_torch_normalizer.py
+        run: pytest -vs tests/test_torch.py

.github/workflows/tests_quick.yml

@@ -0,0 +1,86 @@
+name: tests
+
+on:
+  push:
+    branches-ignore:
+      - main
+  pull_request:
+    branches-ignore:
+      - main
+
+jobs:
+  build:
+    runs-on: ubuntu-18.04
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+
+      - name: Install dependencies
+        run: pip install wheel setuptools
+
+      - name: Build wheel
+        run: python setup.py bdist_wheel
+
+      - name: Upload Python wheel
+        uses: actions/upload-artifact@v2
+        with:
+          name: Python wheel
+          path: ${{github.workspace}}/dist/torchstain-*.whl
+          if-no-files-found: error
+
+  test-tf:
+    needs: build
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Download artifact
+        uses: actions/download-artifact@master
+        with:
+          name: "Python wheel"
+
+      - name: Install dependencies
+        run: |
+          pip install tensorflow protobuf==3.20.* opencv-python-headless scikit-image
+          pip install pytest
+
+      - name: Install wheel
+        run: pip install --find-links=${{github.workspace}} torchstain
+
+      - name: Run tests
+        run: pytest -vs tests/test_tf.py
+
+  test-torch:
+    needs: build
+    runs-on: ubuntu-18.04
+
+    steps:
+      - uses: actions/checkout@v1
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Download artifact
+        uses: actions/download-artifact@master
+        with:
+          name: "Python wheel"
+
+      - name: Install dependencies
+        run: |
+          pip install torch torchvision opencv-python-headless scikit-image
+          pip install pytest
+
+      - name: Install wheel
+        run: pip install --find-links=${{github.workspace}} torchstain
+
+      - name: Run tests
+        run: pytest -vs tests/test_torch.py

README.md

@@ -3,18 +3,22 @@
 [![License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT)
 [![tests](https://github.com/EIDOSLAB/torchstain/workflows/tests/badge.svg)](https://github.com/EIDOSLAB/torchstain/actions)
 [![Pip Downloads](https://img.shields.io/pypi/dm/torchstain?label=pip%20downloads&logo=python)](https://pypi.org/project/torchstain/)
+[![DOI](https://zenodo.org/badge/323590093.svg)](https://zenodo.org/badge/latestdoi/323590093)
 
 GPU-accelerated stain normalization tools for histopathological images. Compatible with PyTorch, TensorFlow, and Numpy.
 Normalization algorithms currently implemented:
 
 - Macenko et al. [\[1\]](#reference) (ported from [numpy implementation](https://github.com/schaugf/HEnorm_python))
+- Reinhard et al. [\[2\]](#reference)
 
 ## Installation
 
 ```bash
 pip install torchstain
 ```
 
+To install a specific backend use either ```torchstain[torch]``` or ```torchstain[tf]```. The numpy backend is included by default in both.
+
 ## Example Usage
 
 ```python
@@ -38,26 +42,62 @@ t_to_transform = T(to_transform)
 norm, H, E = normalizer.normalize(I=t_to_transform, stains=True)
 ```
 
-![alt text](result.png)
+![alt text](data/result.png)
+
+## Implemented algorithms
 
+| Algorithm | numpy | torch | tensorflow |
+|-|-|-|-|
+| Macenko | ✓ | ✓ | ✓ |
+| Reinhard | ✓ | ✓ | ✓ |
 
 ## Backend comparison
 
 Results with 10 runs per size on a Intel(R) Core(TM) i5-8365U CPU @ 1.60GHz
 
-
-|   size | numpy avg. time   | numpy tot. time   | torch avg. time   | torch tot. time   |
-|--------|-------------------|-------------------|-------------------|-------------------|
-|    224x224 | 0.0323s ± 0.0032  | 0.3231s           | 0.0234s ± 0.0384  | 0.2340s           |
-|    448x448 | 0.1228s ± 0.0042  | 1.2280s           | 0.0395s ± 0.0168  | 0.3954s           |
-|    672x672 | 0.2653s ± 0.0106  | 2.6534s           | 0.0753s ± 0.0157  | 0.7527s           |
-|    896x896 | 0.4940s ± 0.0208  | 4.9397s           | 0.1262s ± 0.0159  | 1.2622s           |
-|   1120x1120 | 0.6888s ± 0.0081  | 6.8883s           | 0.2002s ± 0.0141  | 2.0021s           |
-|   1344x1344 | 1.0145s ± 0.0089  | 10.1448s          | 0.2703s ± 0.0136  | 2.7026s           |
-|   1568x1568 | 1.2620s ± 0.0133  | 12.6200s          | 0.3680s ± 0.0128  | 3.6795s           |
-|   1792x1792 | 1.4289s ± 0.0128  | 14.2886s          | 0.5968s ± 0.0160  | 5.9676s           |
-
+|   size | numpy avg. time   | torch avg. time   | tf avg. time     |
+|--------|-------------------|-------------------|------------------|
+|    224 | 0.0182s ± 0.0016  | 0.0180s ± 0.0390  | 0.0048s ± 0.0002 |
+|    448 | 0.0880s ± 0.0224  | 0.0283s ± 0.0172  | 0.0210s ± 0.0025 |
+|    672 | 0.1810s ± 0.0139  | 0.0463s ± 0.0301  | 0.0354s ± 0.0018 |
+|    896 | 0.3013s ± 0.0377  | 0.0820s ± 0.0329  | 0.0713s ± 0.0008 |
+|   1120 | 0.4694s ± 0.0350  | 0.1321s ± 0.0237  | 0.1036s ± 0.0042 |
+|   1344 | 0.6640s ± 0.0553  | 0.1665s ± 0.0026  | 0.1663s ± 0.0021 |
+|   1568 | 1.1935s ± 0.0739  | 0.2590s ± 0.0088  | 0.2531s ± 0.0031 |
+|   1792 | 1.4523s ± 0.0207  | 0.3402s ± 0.0114  | 0.3080s ± 0.0188 |
 
 ## Reference
 
 - [1] Macenko, Marc, et al. "A method for normalizing histology slides for quantitative analysis." 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. IEEE, 2009.
+- [2] Reinhard, Erik, et al. "Color transfer between images." IEEE Computer Graphics and Applications. IEEE, 2001.
+
+## Citing
+
+If you find this software useful for your research, please cite it as: 
+
+```bibtex
+@software{barbano2022torchstain,
+  author       = {Carlo Alberto Barbano and
+                  André Pedersen},
+  title        = {EIDOSLAB/torchstain: v1.2.0-stable},
+  month        = aug,
+  year         = 2022,
+  publisher    = {Zenodo},
+  version      = {v1.2.0-stable},
+  doi          = {10.5281/zenodo.6979540},
+  url          = {https://doi.org/10.5281/zenodo.6979540}
+}
+```
+
+Torchstain was originally developed within the [UNITOPATHO](https://github.com/EIDOSLAB/UNITOPATHO) data collection, which you can cite as:
+
+```bibtex
+@inproceedings{barbano2021unitopatho,
+  title={UniToPatho, a labeled histopathological dataset for colorectal polyps classification and adenoma dysplasia grading},
+  author={Barbano, Carlo Alberto and Perlo, Daniele and Tartaglione, Enzo and Fiandrotti, Attilio and Bertero, Luca and Cassoni, Paola and Grangetto, Marco},
+  booktitle={2021 IEEE International Conference on Image Processing (ICIP)},
+  pages={76--80},
+  year={2021},
+  organization={IEEE}
+}
+```