remove unused code; add a test

.github/workflows/pytest_workflow.yml

@@ -0,0 +1,32 @@
+name: Pytest testing
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.10]
+
+    steps:
+    - uses: actions/checkout
+      with:
+        fetch-depth: 2  # Shallow clone last 2 commits
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install pytest
+        python -m pip install .
+
+    - name: Run Pytest
+      run: python -m pytest .
+
+    - name: Run Pytest with Marker
+      run: pytest -m wsi

README.md

@@ -1,4 +1,4 @@
-CLAM
+WSI
 ====
 This is a fork of the repository from [Mahmood lab's CLAM repository](https://github.com/mahmoodlab/CLAM).
 It is made available under the GPLv3 License and is available for non-commercial academic purposes.
@@ -8,7 +8,7 @@ It is made available under the GPLv3 License and is available for non-commercial
 
 The purpose of the fork is to compartimentalize the features related with processing of whole-slide images (WSI) from the CLAM model.
 
-The package has been renamed to `wsi_core` as that was the name of the module related with whole slide image processing.
+The package has been renamed to `wsi`.
 
 
 ## Installation
@@ -17,8 +17,9 @@ While the repository is private, make sure you [exchange SSH keys of the machine
 
 Then simply install with `pip`:
 ```bash
-git clone [email protected]:rendeirolab/CLAM.git
-cd CLAM
+# pip install git+ssh://[email protected]:rendeirolab/wsi.git
+git clone [email protected]:rendeirolab/wsi.git
+cd wsi
 pip install .
 ```
 
@@ -29,12 +30,34 @@ Note that the package uses setuptols-scm for version control and therefore the i
 This package is meant for both interactive use and for use in a pipeline at scale.
 By default actions do not return anything, but instead save the results to disk in files relative to the slide file.
 
+
+```python
+from wsi import WholeSlideImage
+from wsi.utils import Path
+
+# Get example slide image
+slide_file = Path("GTEX-12ZZW-2726.svs")
+if not slide_file.exists():
+    import requests
+    url = f"https://brd.nci.nih.gov/brd/imagedownload/{slide_file.stem}"
+    with open(slide_file, "wb") as handle:
+        req = requests.get(url)
+        handle.write(req.content)
+
+# Instantiate slide object
+slide = WholeSlideImage(slide_file)
+
+# Instantiation can be done with custom attributes
+slide = WholeSlideImage(slide_file, attributes=dict(donor="GTEX-12ZZW"))
+
+
+
 All major functions have sensible defaults but allow for customization.
 Please check the docstring of each function for more information.
 
 ```python
-from wsi_core import WholeSlideImage
-from wsi_core.utils import Path
+from wsi import WholeSlideImage
+from wsi.utils import Path
 
 # Get example slide image
 slide_file = Path("GTEX-12ZZW-2726.svs")
@@ -48,7 +71,7 @@ if not slide_file.exists():
 # Instantiate slide object
 slide = WholeSlideImage(slide_file)
 
-# Instantiate slide object
+# Instantiation can be done with custom attributes
 slide = WholeSlideImage(slide_file, attributes=dict(donor="GTEX-12ZZW"))
 
 # Segment tissue (segmentation mask is stored as polygons in slide.contours_tissue)
@@ -75,15 +98,28 @@ for img in images:
 slide.save_tile_images(output_dir=slide_file.parent / (slide_file.stem + "_tiles"))
 
 # Use in a torch dataloader
-loader = slide.as_data_loader()
+loader = slide.as_data_loader(with_coords=True)
 
-# Extract features
+# Extract features "manually"
 import torch
 from tqdm import tqdm
-model = torch.hub.load("pytorch/vision", "resnet50", pretrained=True) 
-for count, (batch, coords) in tqdm(enumerate(loader), total=len(loader)):
+model = torch.hub.load("pytorch/vision", "resnet18", weights="DEFAULT")
+feats = list()
+coords = list()
+for count, (batch, yx) in tqdm(enumerate(loader), total=len(loader)):
     with torch.no_grad(): 
-        features = model(batch).numpy()
+        f = model(batch).numpy()
+    feats.append(f)
+    coords.append(yx)
+
+feats = np.concatenate(feats, axis=0)
+coords = np.concatenate(coords, axis=0)
+
+# Extract features "automatically"
+feats, coords = slide.inference('resnet18')
+
+# Additional parameters can also be specified
+feats, coords = slide.inference('resnet18', device='cuda', data_loader_kws=dict(batch_size=512))
 ```
 
 ## Reference

pyproject.toml

@@ -1,6 +1,6 @@
 # PIP, using PEP621
 [project]
-name = "wsi_core"
+name = "wsi"
 authors = [
     {name = "Andre Rendeiro", email = "[email protected]"},
 ]
@@ -11,8 +11,9 @@ keywords = [
 ]
 classifiers = [
     "Programming Language :: Python :: 3 :: Only",
-    "Programming Language :: Python :: 3.7",
-    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
     "Development Status :: 3 - Alpha",
     "Typing :: Typed",
     "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
@@ -51,9 +52,9 @@ doc = [
 ]
 
 [project.urls]
-homepage = "https://github.com/rendeirolab/CLAM"
-documentation = "https://github.com/rendeirolab/CLAM/blob/main/README.md"
-repository = "https://github.com/rendeirolab/CLAM"
+homepage = "https://github.com/rendeirolab/wsi"
+documentation = "https://github.com/rendeirolab/wsi/blob/main/README.md"
+repository = "https://github.com/rendeirolab/wsi"
 
 [build-system]
 # requires = ["poetry>=0.12", "setuptools>=45", "wheel", "poetry-dynamic-versioning"]
@@ -62,7 +63,7 @@ requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
-write_to = "wsi_core/_version.py"
+write_to = "wsi/_version.py"
 write_to_template = 'version = __version__ = "{version}"'
 
 [tool.black]
@@ -104,7 +105,7 @@ module = [
     'matplotlib.*',
     'networkx.*',
     #
-    'wsi_core.*'
+    'wsi.*'
 ]
 ignore_missing_imports = true
 
@@ -117,5 +118,5 @@ testpaths = [
 ]
 markers = [
     'slow', # 'marks tests as slow (deselect with "-m 'not slow'")',
-    'serial'
-]
+    "wsi"
+]