SBU-BMI · kaczmarj · Dec 26, 2022 · Dec 25, 2022 · Dec 25, 2022 · Dec 25, 2022
diff --git a/Dockerfile b/Dockerfile
@@ -1,5 +1,5 @@
 FROM pytorch/pytorch:1.12.1-cuda11.3-cudnn8-runtime
-WORKDIR /opt/wsi-classification
+WORKDIR /opt/wsinfer
 COPY . .
 RUN apt-get update \
     && apt-get install -y --no-install-recommends gcc git libopenslide0 \
@@ -15,4 +15,5 @@ RUN mkdir -p "$TORCH_HOME" \
     && chmod a+s "$TORCH_HOME"
 WORKDIR /work
 ENTRYPOINT ["wsinfer"]
+CMD ["--help"]
 LABEL maintainer="Jakub Kaczmarzyk <jakub.kaczmarzyk@stonybrookmedicine.edu>"
diff --git a/README.md b/README.md
@@ -7,6 +7,8 @@ Original H&E                        |  Heatmap of Tumor Probability
 🔥 🚀 Blazingly fast pipeline to run patch-based classification models on whole slide images.
 
 ![Continuous Integration](https://github.com/kaczmarj/patch-classification-pipeline/actions/workflows/ci.yml/badge.svg)
+![Supported Python versions](https://img.shields.io/pypi/pyversions/wsinfer)
+![Version on PyPI](https://img.shields.io/pypi/v/wsinfer.svg)
 
 # Table of contents
 
@@ -268,6 +270,8 @@ Define a new model with a YAML configuration file. Please see the example below
 an overview of the specification.
 
 ```yaml
+# The version of the spec. At this time, only "1.0" is valid. (str)
+version: "1.0"
 # Models are referenced by the pair of (architecture, weights), so this pair must be unique.
 # The name of the architecture. We use timm to supply hundreds or network architectures,
 # so the name can be one of those models. If the architecture is not provided in timm,

diff --git a/dockerfiles/tils.dockerfile b/dockerfiles/tils.dockerfile
@@ -2,7 +2,7 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="inceptionv4"

diff --git a/dockerfiles/tumor-brca.dockerfile b/dockerfiles/tumor-brca.dockerfile
@@ -2,7 +2,7 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"

diff --git a/dockerfiles/tumor-luad.dockerfile b/dockerfiles/tumor-luad.dockerfile
@@ -2,7 +2,7 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"

diff --git a/dockerfiles/tumor-paad.dockerfile b/dockerfiles/tumor-paad.dockerfile
@@ -2,7 +2,7 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34_preact"

diff --git a/dockerfiles/tumor-prad.dockerfile b/dockerfiles/tumor-prad.dockerfile
@@ -2,7 +2,7 @@
 #
 # Note about versioning: We should not use the 'latest' tag because it is a moving
 # target. We should prefer using a versioned release of the wsinfer pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.2.1
+FROM kaczmarj/wsinfer:v0.2.1
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"

diff --git a/scripts/build_docker_images.sh b/scripts/build_docker_images.sh
@@ -24,33 +24,33 @@ fi
 version=$1
 
 # Main image.
-docker build -t kaczmarj/patch-classification-pipeline:$version .
+docker build -t kaczmarj/wsinfer:$version .
 
 # TILs
-docker build -t kaczmarj/patch-classification-pipeline:$version-tils - < dockerfiles/tils.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tils - < dockerfiles/tils.dockerfile
 
 # Tumor BRCA
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-brca - < dockerfiles/tumor-brca.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-brca - < dockerfiles/tumor-brca.dockerfile
 
 # Tumor LUAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-luad - < dockerfiles/tumor-luad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-luad - < dockerfiles/tumor-luad.dockerfile
 
 # Tumor PAAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-paad - < dockerfiles/tumor-paad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-paad - < dockerfiles/tumor-paad.dockerfile
 
 # Tumor PRAD
-docker build -t kaczmarj/patch-classification-pipeline:$version-tumor-prad - < dockerfiles/tumor-prad.dockerfile
+docker build -t kaczmarj/wsinfer:$version-tumor-prad - < dockerfiles/tumor-prad.dockerfile
 
 # Push images.
 push_images="${2:-0}"
 if [ $push_images -eq 0 ]; then
     echo "Not pushing images. Pass a 1 to the script to push images."
 else
     echo "Pushing images."
-    docker push kaczmarj/patch-classification-pipeline:$version
-    docker push kaczmarj/patch-classification-pipeline:$version-tils
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-brca
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-luad
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-paad
-    docker push kaczmarj/patch-classification-pipeline:$version-tumor-prad
+    docker push kaczmarj/wsinfer:$version
+    docker push kaczmarj/wsinfer:$version-tils
+    docker push kaczmarj/wsinfer:$version-tumor-brca
+    docker push kaczmarj/wsinfer:$version-tumor-luad
+    docker push kaczmarj/wsinfer:$version-tumor-paad
+    docker push kaczmarj/wsinfer:$version-tumor-prad
 fi
diff --git a/tests/test_all.py b/tests/test_all.py
@@ -62,6 +62,7 @@ def test_cli_list(tmp_path: Path):
     config_root_single.mkdir()
     configs = [
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -73,6 +74,7 @@ def test_cli_list(tmp_path: Path):
             class_names=["tumor"],
         ),
         dict(
+            version="1.0",
             name="foo2",
             architecture="resnet34",
             url="foo",
@@ -412,6 +414,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         dict(name="foo", architecture="resnet34"),
         # Missing url
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             # url="foo",
@@ -424,6 +427,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # missing url_file_name when url is given
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -436,6 +440,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # url and file used together
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             file=__file__,
@@ -449,6 +454,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # nonexistent file
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             file="path/to/fake/file",
@@ -462,6 +468,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # num_classes missing
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -474,6 +481,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # num classes not equal to len of class names
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -486,6 +494,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform missing
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -498,6 +507,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.resize_size missing
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -510,6 +520,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.mean missing
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -522,6 +533,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.std missing
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -534,6 +546,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.resize_size non int
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -546,6 +559,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.resize_size non int
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -560,6 +574,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.mean not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -572,6 +587,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.mean not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -584,6 +600,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.mean not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -596,6 +613,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.std not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -608,6 +626,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.std not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -620,6 +639,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # transform.std not a list of three floats
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -632,6 +652,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid patch_size_pixels -- list
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -644,6 +665,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid patch_size_pixels -- float
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -656,6 +678,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid patch_size_pixels -- negative
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -668,6 +691,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid spacing_um_px -- zero
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -680,6 +704,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid spacing_um_px -- list
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -692,6 +717,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid class_names -- str
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -704,6 +730,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid class_names -- len not equal to num_classes
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -716,6 +743,7 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
         ),
         # invalid class_names -- not list of str
         dict(
+            version="1.0",
             name="foo",
             architecture="resnet34",
             url="foo",
@@ -726,6 +754,33 @@ def test_cli_run_from_config(tiff_image: Path, tmp_path: Path):
             spacing_um_px=0.25,
             class_names=[1],
         ),
+        # unknown key
+        dict(
+            fakekey="foobar",
+            version="1.0",
+            name="foo",
+            architecture="resnet34",
+            url="foo",
+            url_file_name="foo",
+            num_classes=1,
+            transform=dict(resize_size=299, mean=[0.5, 0.5, 0.5], std=[0.5, 0.5, 0.5]),
+            patch_size_pixels=350,
+            spacing_um_px=0.25,
+            class_names=["foo"],
+        ),
+        # version != '1.0'
+        dict(
+            version="2.0",
+            name="foo",
+            architecture="resnet34",
+            url="foo",
+            url_file_name="foo",
+            num_classes=1,
+            transform=dict(resize_size=299, mean=[0.5, 0.5, 0.5], std=[0.5, 0.5, 0.5]),
+            patch_size_pixels=350,
+            spacing_um_px=0.25,
+            class_names=["foo"],
+        ),
     ],
 )
 def test_invalid_modeldefs(modeldef, tmp_path: Path):
@@ -744,6 +799,7 @@ def test_model_registration(tmp_path: Path):
 
     # Test that registering duplicate weights will error.
     d = dict(
+        version="1.0",
         name="foo",
         architecture="resnet34",
         url="foo",
@@ -768,6 +824,7 @@ def test_model_registration(tmp_path: Path):
     path = tmp_path / "configs" / "foobar.yaml"
     path.parent.mkdir()
     d = dict(
+        version="1.0",
         name="foo2",
         architecture="resnet34",
         url="foo",