Add model and ground_truth tarball examples

grand_challenge_forge/forge.py

@@ -156,6 +156,8 @@ def generate_example_algorithm(
         output_path=algorithm_path,
         context={
             "image_tag": f"example-algorithm-{context['phase']['slug']}",
+            "tarball_dirname": "model",
+            "tarball_extraction_dir": "/opt/ml/model/",
             "_no_gpus": context.get("_no_gpus", False),
         },
     )
@@ -196,6 +198,8 @@ def generate_example_evaluation(
         output_path=evaluation_path,
         context={
             "image_tag": f"example-evaluation-{context['phase']['slug']}",
+            "tarball_dirname": "ground_truth",
+            "tarball_extraction_dir": "/opt/ml/input/data/ground_truth/",
             "_no_gpus": context.get("_no_gpus", False),
         },
     )
@@ -293,6 +297,8 @@ def generate_algorithm_template(
         output_path=template_path,
         context={
             "image_tag": algorithm_slug,
+            "tarball_dirname": "model",
+            "tarball_extraction_dir": "/opt/ml/model/",
             "_no_gpus": context.get("_no_gpus", False),
         },
     )

grand_challenge_forge/partials/algorithm-template/inference.py.j2

@@ -32,7 +32,6 @@ import numpy
 
 INPUT_PATH = Path("/input")
 OUTPUT_PATH = Path("/output")
-RESOURCE_PATH = Path("resources")
 
 {% if "__should_fail" in algorithm -%} 1/0 {%- endif %}
 
@@ -59,7 +58,16 @@ def run():
     # Process the inputs: any way you'd like
     _show_torch_cuda_info()
 
-    with open(RESOURCE_PATH / "some_resource.txt", "r") as f:
+    # Some additional resources might be required, place these in one of two locations.
+
+    # First location: part of the Docker-container image: resources/
+    resource_dir = Path("/opt/app/resources")
+    with open(resource_dir / "some_resource.txt", "r") as f:
+        print(f.read())
+
+    # Second location: part of the model tarball
+    model_dir = Path("/opt/ml/model")
+    with open(model_dir / "a_tarball_subdirectory" / "some_tarball_resource.txt", "r") as f:
         print(f.read())
 
     # TODO: add your custom inference here

grand_challenge_forge/partials/algorithm-template/model/README.md

@@ -0,0 +1,5 @@
+You can upload your method's model separately from the container image as a tarball (.tar.gz). Alternatively, you can include it in the container-image build by adding it to the `resources/`.
+
+A tarball is easier to update than the entire container image.
+
+If provided, the tarball will be extracted to `/opt/ml/model/` at runtime.

grand_challenge_forge/partials/algorithm-template/model/a_tarball_subdirectory/some_tarball_resource.txt

@@ -0,0 +1,3 @@
+# Inside a_tarball_subdirectory/some_tarball_resource.txt
+This might be some resource you would require to do a forward pass.
+For instance: some weights for your model.

grand_challenge_forge/partials/algorithm-template/resources/README.md

@@ -0,0 +1 @@
+With the instructions in the Dockerfile, the contents of this `resources/` directory will be included in the Docker image when build.

grand_challenge_forge/partials/docker-bash-scripts/do_save.sh.j2

@@ -30,8 +30,23 @@ formatted_build_info=$(echo $build_timestamp | sed -E 's/(.*)T(.*)\..*Z/\1_\2/'
 # Set the output filename with timestamp and build information
 output_filename="${SCRIPT_DIR}/${DOCKER_IMAGE_TAG}_${formatted_build_info}.tar.gz"
 
-# Save the Docker container and gzip it
-echo "Saving the container as ${output_filename}. This can take a while."
+# Save the Docker-container image and gzip it
+echo "==+=="
+echo "Saving the container image as ${output_filename}. This can take a while."
+
+echo ""
+
 docker save "$DOCKER_IMAGE_TAG" | gzip -c > "$output_filename"
+echo "Container image saved as ${output_filename}"
+echo "==+=="
+
+# Create the tarbal
+echo "==+=="
+output_tarball_name="${SCRIPT_DIR}/{{ tarball_dirname }}.tar.gz"
+echo "Creating the optional tarball as ${output_tarball_name}. This can take a while."
+
+echo ""
 
-echo "Container saved as ${output_filename}"
+tar -czf $output_tarball_name -C "${SCRIPT_DIR}/{{ tarball_dirname }}" .
+echo "(Optional) Uploadable tarball was created as ${output_tarball_name}"
+echo "==+=="

grand_challenge_forge/partials/example-algorithm/inference.py.j2

@@ -59,7 +59,16 @@ def run():
     # Process the inputs: any way you'd like
     _show_torch_cuda_info()
 
-    with open(RESOURCE_PATH / "some_resource.txt", "r") as f:
+    # Some additional resources might be required, place these in one of two locations.
+
+    # First location: part of the Docker-container image: resources/
+    resource_dir = Path("/opt/app/resources")
+    with open(resource_dir / "some_resource.txt", "r") as f:
+        print(f.read())
+
+    # Second location: part of the model tarball
+    model_dir = Path("/opt/ml/model")
+    with open(model_dir / "a_tarball_subdirectory" / "some_tarball_resource.txt", "r") as f:
         print(f.read())
 
     # For now, let us make bogus predictions

grand_challenge_forge/partials/example-algorithm/model/README.md

@@ -0,0 +1,5 @@
+You can upload your method's model separately from the container image as a tarball (.tar.gz). Alternatively, you can include it in the container-image build by adding it to the `resources/`.
+
+A tarball is easier to update than the entire container image.
+
+If provided, the tarball will be extracted to `/opt/ml/model/` at runtime.

grand_challenge_forge/partials/example-algorithm/model/a_tarball_subdirectory/some_tarball_resource.txt

@@ -0,0 +1,3 @@
+# Inside a_tarball_subdirectory/some_tarball_resource.txt
+This might be some resource you would require to do a forward pass.
+For instance: some weights for your model.

grand_challenge_forge/partials/example-algorithm/resources/README.md

@@ -0,0 +1 @@
+With the instructions in the Dockerfile, the contents of this `resources/` directory will be included in the Docker image when build.

grand_challenge_forge/partials/example-evaluation-method/Dockerfile

@@ -9,7 +9,7 @@ USER user
 WORKDIR /opt/app
 
 COPY --chown=user:user requirements.txt /opt/app/
-COPY --chown=user:user ground_truth /opt/app/ground_truth
+COPY --chown=user:user resources /opt/app/resources
 
 # You can add any Python dependencies to requirements.txt
 RUN python -m pip install \

grand_challenge_forge/partials/example-evaluation-method/evaluate.py.j2

@@ -43,9 +43,6 @@ from helpers import run_prediction_processing, tree
 
 INPUT_DIRECTORY = Path("/input")
 OUTPUT_DIRECTORY = Path("/output")
-GROUND_TRUTH_DIRECTORY = Path("ground_truth")
-
-
 
 {% if "__should_fail" in phase -%} 1/0 {%- endif %}
 
@@ -104,9 +101,21 @@ def process(job):
     {%- endfor %}
 
     # Fourthly, load your ground truth
-    # Include it in your evaluation container by placing it in ground_truth/
-    with open(GROUND_TRUTH_DIRECTORY / "some_resource.txt", "r") as f:
-        report += f.read()
+    # Include it in your evaluation-method container by placing it one of two locations:
+
+    # First location: part of the Docker-container image: resources/
+    resource_dir = Path("/opt/app/resources")
+    with open(resource_dir / "some_resource.txt", "r") as f:
+        truth = f.read()
+    report += truth
+
+
+    # Second location: part of the ground-truth tarball
+    ground_truth_dir = Path("/opt/ml/input/data/ground_truth")
+    with open(ground_truth_dir / "a_tarball_subdirectory" / "some_tarball_resource.txt", "r") as f:
+        truth = f.read()
+    report += truth
+
     print(report)
 
     # TODO: compare the results to your ground truth and compute some metrics

grand_challenge_forge/partials/example-evaluation-method/ground_truth/README.md

@@ -0,0 +1,5 @@
+You can upload your method's ground truth separately from the container image as a tarball (.tar.gz). Alternatively, you can include it in the container-image build by adding it to the `resources/`.
+
+A tarball is easier to update than the entire container image.
+
+If provided, the tarball will be extracted to `/opt/ml/input/data/ground_truth/` at runtime.

grand_challenge_forge/partials/example-evaluation-method/ground_truth/a_tarball_subdirectory/some_tarball_resource.txt

@@ -0,0 +1,3 @@
+# Inside a_tarball_subdirectory/some_tarball_resource.txt
+This might be some resource you would require to evaluate a submission.
+For instance: some ground truth for each image for your model.

grand_challenge_forge/partials/example-evaluation-method/resources/README.md

@@ -0,0 +1 @@
+With the instructions in the Dockerfile, the contents of this `resources/` directory will be included in the Docker image when build.

grand_challenge_forge/partials/example-evaluation-method/ground_truth/some_resource.txt → grand_challenge_forge/partials/example-evaluation-method/resources/some_resource.txt

@@ -1,3 +1,3 @@
-# Inside ground_truth/some_resource.txt
+# Inside resources/some_resource.txt
 This might be some resource you would require to evaluate a submission.
 For instance: some ground truth for each image for your model.