use wsinfer version 0.3.3 (#63)

SBU-BMI · Jan 10, 2023 · 1cc6f6a · 1cc6f6a
1 parent 25da8fe
commit 1cc6f6a
Show file tree

Hide file tree

Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/dockerfiles/tils.dockerfile b/dockerfiles/tils.dockerfile
@@ -2,13 +2,13 @@
 #
 # 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/wsinfer:0.3.2
+FROM kaczmarj/wsinfer:0.3.3
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="inceptionv4nobn"
 ENV WSINFER_WEIGHTS="TCGA-TILs-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
+RUN python -c "from wsinfer import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/
diff --git a/dockerfiles/tumor-brca.dockerfile b/dockerfiles/tumor-brca.dockerfile
@@ -2,13 +2,13 @@
 #
 # 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/wsinfer:0.3.2
+FROM kaczmarj/wsinfer:0.3.3
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-BRCA-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
+RUN python -c "from wsinfer import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/
diff --git a/dockerfiles/tumor-luad.dockerfile b/dockerfiles/tumor-luad.dockerfile
@@ -2,13 +2,13 @@
 #
 # 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/wsinfer:0.3.2
+FROM kaczmarj/wsinfer:0.3.3
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-LUAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
+RUN python -c "from wsinfer import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/
diff --git a/dockerfiles/tumor-paad.dockerfile b/dockerfiles/tumor-paad.dockerfile
@@ -2,13 +2,13 @@
 #
 # 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/wsinfer:0.3.2
+FROM kaczmarj/wsinfer:0.3.3
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="preactresnet34"
 ENV WSINFER_WEIGHTS="TCGA-PAAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
+RUN python -c "from wsinfer import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/
diff --git a/dockerfiles/tumor-prad.dockerfile b/dockerfiles/tumor-prad.dockerfile
@@ -2,13 +2,13 @@
 #
 # 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/wsinfer:0.3.2
+FROM kaczmarj/wsinfer:0.3.3
 
 # The CLI will use these env vars for model and weights.
 ENV WSINFER_MODEL="resnet34"
 ENV WSINFER_WEIGHTS="TCGA-PRAD-v1"
 
 # Download the weights.
-RUN python -c "from wsinfer.modellib.models import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
+RUN python -c "from wsinfer import get_model_weights; get_model_weights(architecture=\"$WSINFER_MODEL\", name=\"$WSINFER_WEIGHTS\").load_model()" \
     # Downloaded models are mode 0600. Make them readable by all users.
     && chmod -R +r $TORCH_HOME/hub/checkpoints/