ADD: docker apps (#30)

* use WSIRUN_ env var prefix for wsi_run cli

* set model and weights for brca model

* add dockerfiles for task-specific docker images

dockerfiles/tils.dockerfile

@@ -0,0 +1,12 @@
+# Tumor-infiltrating lymphocyte detection model.
+#
+# 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 wsi_inference pipeline.
+FROM kaczmarj/patch-classification-pipeline:v0.2.0
+
+# The CLI will use these env vars for model and weights.
+ENV WSIRUN_MODEL="inceptionv4"
+ENV WSIRUN_WEIGHTS="TCGA-TILs-v1"
+
+# Download the weights.
+RUN python -c "from wsi_inference.modellib import models; models.$WSIRUN_MODEL(\"$WSIRUN_WEIGHTS\")"

dockerfiles/tumor-brca.dockerfile

@@ -2,7 +2,11 @@
 #
 # 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 wsi_inference pipeline.
-FROM kaczmarj/patch-classification-pipeline:v0.1.0
-# Download the TCGA-BRCA-v1 weights for resnet34.
-RUN python -c 'from wsi_inference.modellib import models; models.resnet34("TCGA-BRCA-v1")'
-LABEL maintainer="Jakub Kaczmarzyk <[email protected]>"
+FROM kaczmarj/patch-classification-pipeline:v0.2.0
+
+# The CLI will use these env vars for model and weights.
+ENV WSIRUN_MODEL="resnet34"
+ENV WSIRUN_WEIGHTS="TCGA-BRCA-v1"
+
+# Download the weights.
+RUN python -c "from wsi_inference.modellib import models; models.$WSIRUN_MODEL(\"$WSIRUN_WEIGHTS\")"

dockerfiles/tumor-luad.dockerfile

@@ -0,0 +1,12 @@
+# Lung adenocarcinoma detection model.
+#
+# 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 wsi_inference pipeline.
+FROM kaczmarj/patch-classification-pipeline:v0.2.0
+
+# The CLI will use these env vars for model and weights.
+ENV WSIRUN_MODEL="resnet34"
+ENV WSIRUN_WEIGHTS="TCGA-LUAD-v1"
+
+# Download the weights.
+RUN python -c "from wsi_inference.modellib import models; models.$WSIRUN_MODEL(\"$WSIRUN_WEIGHTS\")"

dockerfiles/tumor-paad.dockerfile

@@ -0,0 +1,12 @@
+# Pancreatic adenocarcinoma detection model.
+#
+# 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 wsi_inference pipeline.
+FROM kaczmarj/patch-classification-pipeline:v0.2.0
+
+# The CLI will use these env vars for model and weights.
+ENV WSIRUN_MODEL="resnet34_preact"
+ENV WSIRUN_WEIGHTS="TCGA-PAAD-v1"
+
+# Download the weights.
+RUN python -c "from wsi_inference.modellib import models; models.$WSIRUN_MODEL(\"$WSIRUN_WEIGHTS\")"

dockerfiles/tumor-prad.dockerfile

@@ -0,0 +1,12 @@
+# Prostate adenocarcinoma detection model.
+#
+# 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 wsi_inference pipeline.
+FROM kaczmarj/patch-classification-pipeline:v0.2.0
+
+# The CLI will use these env vars for model and weights.
+ENV WSIRUN_MODEL="resnet34"
+ENV WSIRUN_WEIGHTS="TCGA-PRAD-v1"
+
+# Download the weights.
+RUN python -c "from wsi_inference.modellib import models; models.$WSIRUN_MODEL(\"$WSIRUN_WEIGHTS\")"

wsi_inference/main.py

@@ -85,7 +85,7 @@ def _print_system_info() -> None:
         click.secho("*******************************************", fg="yellow")
 
 
-@click.command()
+@click.command(context_settings=dict(auto_envvar_prefix="WSIRUN"))
 @click.pass_context
 @click.option(
     "--wsi_dir",