Merge branch 'main' into development

Author: carloalbertobarbano

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,28 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior. Ideally a gist but a simple code example is also fine.
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Logs**
+If applicable, add sufficient logs to assist in debugging the problem.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. Ubuntu, Windows, macOS]
+ - Version [e.g. 20.04, 10, Catalina]
+ 

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/workflows/build.yaml

@@ -15,8 +15,7 @@ jobs:
           python-version: '3.x'
 
       - name: Install deps
-        run: |
-          pip install setuptools wheel
+        run: pip install setuptools wheel
 
       - name: Build wheels
         run: python setup.py sdist bdist_wheel
@@ -37,8 +36,8 @@ jobs:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.5.0
+      - uses: pypa/gh-action-pypi-publish@release/v1.12
         with:
           user: __token__
           password: ${{ secrets.torchstain_deploy_token }}
-      
+      

.github/workflows/tests_full.yml

@@ -39,7 +39,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ windows-2019, ubuntu-20.04, macos-11 ]
+        os: [ windows-2019, ubuntu-20.04, macos-12 ]
         python-version: [ 3.7, 3.8, 3.9 ]
         tf-version: [2.7.0, 2.8.0, 2.9.0]
 
@@ -51,17 +51,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Download artifact
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v3
         with:
           name: "Python wheel"
 
       - name: Install dependencies
-        run: |
-          pip install tensorflow==${{ matrix.tf-version }} protobuf==3.20.* opencv-python-headless scikit-image
-          pip install pytest
+        run: pip install tensorflow==${{ matrix.tf-version }} protobuf==3.20.* opencv-python-headless scikit-image pytest
 
       - name: Install wheel
-        run: pip install --find-links=${{github.workspace}} torchstain
+        run: pip install --find-links=${{github.workspace}} torchstain-*
+        shell: bash
 
       - name: Run tests
         run: pytest -vs tests/test_tf.py
@@ -71,7 +70,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ windows-2019, ubuntu-20.04, macos-11 ]
+        os: [ windows-2019, ubuntu-20.04, macos-12 ]
         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, 1.13.0]
         exclude:
@@ -90,17 +89,16 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Download artifact
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v3
         with:
           name: "Python wheel"
 
       - name: Install dependencies
-        run: |
-          pip install torch==${{ matrix.pytorch-version }} torchvision opencv-python-headless scikit-image
-          pip install pytest
+        run: pip install torch==${{ matrix.pytorch-version }} torchvision opencv-python-headless scikit-image pytest
 
       - name: Install wheel
-        run: pip install --find-links=${{github.workspace}} torchstain
+        run: pip install --find-links=${{github.workspace}} torchstain-*
+        shell: bash
 
       - name: Run tests
         run: pytest -vs tests/test_torch.py

.github/workflows/tests_quick.yml

@@ -43,24 +43,23 @@ jobs:
           python-version: 3.8
 
       - name: Download artifact
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v3
         with:
           name: "Python wheel"
 
       - name: Install dependencies
-        run: |
-          pip install tensorflow protobuf==3.20.* opencv-python-headless scikit-image
-          pip install pytest
+        run: pip install tensorflow protobuf==3.20.* opencv-python-headless scikit-image pytest
 
       - name: Install wheel
-        run: pip install --find-links=${{github.workspace}} torchstain
+        run: pip install --find-links=${{github.workspace}} torchstain-*
+        shell: bash
 
       - name: Run tests
         run: pytest -vs tests/test_tf.py
 
   test-torch:
     needs: build
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
 
     steps:
       - uses: actions/checkout@v1
@@ -70,17 +69,16 @@ jobs:
           python-version: 3.8
 
       - name: Download artifact
-        uses: actions/download-artifact@master
+        uses: actions/download-artifact@v3
         with:
           name: "Python wheel"
 
       - name: Install dependencies
-        run: |
-          pip install torch torchvision opencv-python-headless scikit-image
-          pip install pytest
+        run: pip install torch torchvision opencv-python-headless scikit-image pytest
 
       - name: Install wheel
-        run: pip install --find-links=${{github.workspace}} torchstain
+        run: pip install --find-links=${{github.workspace}} torchstain-*
+        shell: bash
 
       - name: Run tests
         run: pytest -vs tests/test_torch.py

README.md

@@ -3,7 +3,7 @@
 [![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)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7692014.svg)](https://doi.org/10.5281/zenodo.7692014)
 
 GPU-accelerated stain normalization tools for histopathological images. Compatible with PyTorch, TensorFlow, and Numpy.
 Normalization algorithms currently implemented:
@@ -38,8 +38,8 @@ T = transforms.Compose([
     transforms.Lambda(lambda x: x*255)
 ])
 
-torch_normalizer = torchstain.normalizers.MacenkoNormalizer(backend='torch')
-torch_normalizer.fit(T(target))
+normalizer = torchstain.normalizers.MacenkoNormalizer(backend='torch')
+normalizer.fit(T(target))
 
 t_to_transform = T(to_transform)
 norm, H, E = normalizer.normalize(I=t_to_transform, stains=True)

apps/example_aug.py

@@ -0,0 +1,96 @@
+import cv2
+import matplotlib.pyplot as plt
+import torchstain
+import torch
+from torchvision import transforms
+import time
+import os
+
+
+size = 1024
+dir_path = os.path.dirname(os.path.abspath(__file__))
+target = cv2.resize(cv2.cvtColor(cv2.imread(dir_path + "/../data/target.png"), cv2.COLOR_BGR2RGB), (size, size))
+to_transform = cv2.resize(cv2.cvtColor(cv2.imread(dir_path + "/../data/source.png"), cv2.COLOR_BGR2RGB), (size, size))
+
+T = transforms.Compose([
+    transforms.ToTensor(),
+    transforms.Lambda(lambda x: x*255)
+])
+
+t_to_transform = T(to_transform)
+
+# setup augmentors for the different backends
+augmentor = torchstain.augmentors.MacenkoAugmentor(backend='numpy')
+augmentor.fit(to_transform)
+
+tf_augmentor = torchstain.augmentors.MacenkoAugmentor(backend='tensorflow')
+tf_augmentor.fit(t_to_transform)
+
+torch_augmentor = torchstain.augmentors.MacenkoAugmentor(backend='torch')
+torch_augmentor.fit(t_to_transform)
+
+
+print("NUMPY" + "-"*20)
+
+plt.figure()
+plt.suptitle('numpy augmentor')
+plt.subplot(4, 4, 1)
+plt.title('Original')
+plt.axis('off')
+plt.imshow(to_transform)
+
+for i in range(16):
+    # generate augmented sample
+    result = augmentor.augment()
+
+    plt.subplot(4, 4, i + 1)
+    if i == 1:
+        plt.title('Augmented ->')
+    plt.axis('off')
+    plt.imshow(result)
+
+plt.show()
+
+
+print("TensorFlow (TF)" + "-"*20)
+
+plt.figure()
+plt.suptitle('tf augmentor')
+plt.subplot(4, 4, 1)
+plt.title('Original')
+plt.axis('off')
+plt.imshow(to_transform)
+
+for i in range(16):
+    # generate augmented sample
+    result = tf_augmentor.augment()
+
+    plt.subplot(4, 4, i + 1)
+    if i == 1:
+        plt.title('Augmented ->')
+    plt.axis('off')
+    plt.imshow(result)
+
+plt.show()
+
+
+print("Torch" + "-"*20)
+
+plt.figure()
+plt.suptitle('torch augmentor')
+plt.subplot(4, 4, 1)
+plt.title('Original')
+plt.axis('off')
+plt.imshow(to_transform)
+
+for i in range(16):
+    # generate augmented sample
+    result = torch_augmentor.augment()
+
+    plt.subplot(4, 4, i + 1)
+    if i == 1:
+        plt.title('Augmented ->')
+    plt.axis('off')
+    plt.imshow(result)
+
+plt.show()

example.py apps/example_norm.pyexample.py renamed to apps/example_norm.py

@@ -4,10 +4,12 @@
 import torch
 from torchvision import transforms
 import time
+import os
 
 size = 1024
-target = cv2.resize(cv2.cvtColor(cv2.imread("./data/target.png"), cv2.COLOR_BGR2RGB), (size, size))
-to_transform = cv2.resize(cv2.cvtColor(cv2.imread("./data/source.png"), cv2.COLOR_BGR2RGB), (size, size))
+dir_path = os.path.dirname(os.path.abspath(__file__))
+target = cv2.resize(cv2.cvtColor(cv2.imread(dir_path + "/../data/target.png"), cv2.COLOR_BGR2RGB), (size, size))
+to_transform = cv2.resize(cv2.cvtColor(cv2.imread(dir_path + "/../data/source.png"), cv2.COLOR_BGR2RGB), (size, size))
 
 normalizer = torchstain.normalizers.MacenkoNormalizer(backend='numpy')
 normalizer.fit(target)

torchstain/__init__.py

@@ -1,3 +1,3 @@
 __version__ = '1.3.0'
 
-from torchstain.base import normalizers
+from torchstain.base import augmentors, normalizers

torchstain/base/__init__.py

@@ -1 +1 @@
-from torchstain.base import normalizers
+from torchstain.base import augmentors, normalizers