Prepare docker images

.github/workflows/package.yml

@@ -1,6 +1,6 @@
 name: Package
 
-on:   
+on:
   repository_dispatch:
     types: [docker]
   workflow_dispatch:
@@ -16,18 +16,18 @@ jobs:
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
       - name: Login to DockerHub
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v1
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_TOKEN }}
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1 
+        uses: docker/login-action@v1
         with:
           registry: ghcr.io
           username: ${{ github.repository_owner }}
           password: ${{ secrets.GITHUB_TOKEN }}
 
-      - name: Build and Push Base
+      - name: Build and Push Base Image
         uses: docker/build-push-action@v2
         with:
           context: .
@@ -36,7 +36,27 @@ jobs:
           tags: |
             platipy/platipy:latest
             ghcr.io/pyplati/platipy:latest
-      - name: Build and Push Cardiac Docker Image
+      - name: Build and Push Service Image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: service.Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: |
+            platipy/platipy:service
+            ghcr.io/pyplati/platipy:service
+      - name: Build and Push Dev Image
+        uses: docker/build-push-action@v2
+        with:
+          context: .
+          file: service.Dockerfile
+          platforms: linux/amd64
+          push: true
+          tags: |
+            platipy/platipy:dev
+            ghcr.io/pyplati/platipy:dev
+      - name: Build and Push Cardiac Image
         uses: docker/build-push-action@v2
         with:
           context: services/cardiac
@@ -45,7 +65,7 @@ jobs:
           tags: |
             platipy/platipy:cardiac
             ghcr.io/pyplati/platipy:cardiac
-      - name: Build and Push Bronchus Docker Image
+      - name: Build and Push Bronchus Image
         uses: docker/build-push-action@v2
         with:
           context: services/bronchus
@@ -54,8 +74,8 @@ jobs:
           tags: |
             platipy/platipy:bronchus
             ghcr.io/pyplati/platipy:bronchus
-    
-      - name: Build and Push Pinnacle Docker Image
+
+      - name: Build and Push Pinnacle Image
         uses: docker/build-push-action@v2
         with:
           context: services/pinnacle
@@ -65,7 +85,7 @@ jobs:
             platipy/platipy:pinnacle
             ghcr.io/pyplati/platipy:pinnacle
 
-      - name: Build and Push MRI Dixon Docker Image
+      - name: Build and Push MRI Dixon Image
         uses: docker/build-push-action@v2
         with:
           context: services/mridixon
@@ -75,7 +95,7 @@ jobs:
             platipy/platipy:mridixon
             ghcr.io/pyplati/platipy:mridixon
 
-      - name: Build and Push Radiomics Docker Image
+      - name: Build and Push Radiomics Image
         uses: docker/build-push-action@v2
         with:
           context: services/radiomics
@@ -95,7 +115,7 @@ jobs:
             platipy/platipy:dirqa
             ghcr.io/pyplati/platipy:dirqa
 
-      - name: Build and Push nnUNet Docker Image
+      - name: Build and Push nnUNet Image
         uses: docker/build-push-action@v2
         with:
           context: services/nnunet

Dockerfile

@@ -1,14 +1,15 @@
 FROM ubuntu:20.04
 
-RUN apt-get update; DEBIAN_FRONTEND="noninteractive" apt-get install -y redis-server git python3-pip libgl1-mesa-glx libsm6 libxext6 libxrender-dev libglib2.0-0 pandoc curl
+RUN apt-get update; DEBIAN_FRONTEND="noninteractive" apt-get install -y python3-pip libgl1-mesa-glx libsm6 libxext6 libxrender-dev libglib2.0-0 curl
 
 RUN ln -s /usr/bin/python3 /usr/bin/python
-RUN pip install --upgrade pip
+# RUN pip install --upgrade pip
 
 COPY poetry.lock /platipy/poetry.lock
 COPY pyproject.toml /platipy/pyproject.toml
 
 RUN curl -sSL https://install.python-poetry.org | python -  --version 1.2.0rc1
-RUN echo 'export PATH="/root/.local/bin:$PATH"' >> ~/.bashrc 
+RUN echo 'export PATH="/root/.local/bin:$PATH"' >> ~/.bashrc
+RUN echo "/usr/lib/python3.8/site-packages" >> /usr/local/lib/python3.8/dist-packages/site-packages.pth
+
 RUN /root/.local/bin/poetry config virtualenvs.create false
-RUN env -C /platipy /root/.local/bin/poetry install --without dev,docs

dev.Dockerfile

@@ -0,0 +1,5 @@
+FROM platipy/platipy
+
+RUN apt-get update; DEBIAN_FRONTEND="noninteractive" apt-get install -y redis-server git libgl1-mesa-glx libsm6 libxext6 libxrender-dev libglib2.0-0 pandoc curl
+
+RUN env -C /platipy /root/.local/bin/poetry install --with dev,docs --all-extras

docker-compose.yml

@@ -2,7 +2,7 @@ version: '3'
 
 services:
   platipy:
-    image: platipy/platipy
+    image: platipy/platipy:dev
     ports:
       - "8001:8000"
       - "7777:7777"
@@ -14,6 +14,8 @@ services:
     entrypoint: /bin/sh -c "while sleep 1000; do :; done"
     environment:
       PYTHONPATH: "/platipy"
+      REDIS_HOST: redis
+      REDIS_PORT: 6379
     deploy:
       resources:
         limits:

platipy/backend/__init__.py

@@ -19,11 +19,10 @@
 from flask_sqlalchemy import SQLAlchemy
 from flask_restful import Api
 from celery import Celery
+from loguru import logger
 
 from platipy.backend.application import FlaskApp
 
-import logging
-logger = logging.getLogger(__name__)
 
 env_work = os.getcwd()
 if "WORK" in os.environ:
@@ -38,9 +37,7 @@
 app.config["SECRET_KEY"] = uuid.uuid4().hex
 
 # Configure SQL Alchemy
-app.config["SQLALCHEMY_DATABASE_URI"] = "sqlite:///{0}/{1}.db".format(
-    env_work, os.path.basename(os.getcwd())
-)
+app.config["SQLALCHEMY_DATABASE_URI"] = f"sqlite:///{env_work}/{os.path.basename(os.getcwd())}.db"
 app.config["SQLALCHEMY_TRACK_MODIFICATIONS"] = False
 db = SQLAlchemy(app)
 

platipy/backend/tasks.py

@@ -93,7 +93,7 @@ def clean_up_task(task):
                     )
 
     logger.info(
-        "Clean Up Task Complete: Removed {0} DataObjects", num_data_objs_removed
+        "Clean Up Task Complete: Removed %s DataObjects", num_data_objs_removed
     )
 
 

platipy/dicom/io/rtstruct_to_nifti.py

@@ -132,7 +132,7 @@ def transform_point_set_from_dicom_struct(dicom_image, dicom_struct, spacing_ove
 
     for struct_index, struct_name in enumerate(struct_name_sequence):
         image_blank = np.zeros(dicom_image.GetSize()[::-1], dtype=np.uint8)
-        logger.debug("Converting structure {0} with name: {1}".format(struct_index, struct_name))
+        logger.debug("Converting structure %d with name: %s", struct_index, struct_name)
 
         if not hasattr(struct_point_sequence[struct_index], "ContourSequence"):
             logger.debug("No contour sequence found for this structure, skipping.")

platipy/imaging/label/iar.py

@@ -114,7 +114,7 @@ def run_iar(
     g_val_list = []
     logger.info("  Calculating surface distance maps: ")
     for test_id in remaining_id_list:
-        logger.info("    {0}".format(test_id))
+        logger.info("    %s", test_id)
         #   2. Calculate the distance from the surface to the consensus surface
 
         test_volume = atlas_set[test_id][label][reference_structure]
@@ -174,7 +174,7 @@ def run_iar(
             g_val_std = np.std(g_val_list_test, axis=0)
 
             if np.any(g_val_std == 0):
-                logger.info("    Std Dev zero count: {0}".format(np.sum(g_val_std == 0)))
+                logger.info("    Std Dev zero count: %d", np.sum(g_val_std == 0))
                 g_val_std[g_val_std == 0] = g_val_std.mean()
 
             z_score_vals_array = (g_vals - g_val_mean) / g_val_std
@@ -188,25 +188,25 @@ def run_iar(
                 logger.info(g_val_mad)
 
             if np.any(g_val_mad == 0):
-                logger.info("    MAD zero count: {0}".format(np.sum(g_val_mad == 0)))
+                logger.info("    MAD zero count: %d", np.sum(g_val_mad == 0))
                 g_val_mad[g_val_mad == 0] = np.median(g_val_mad)
 
             z_score_vals_array = (g_vals - g_val_median) / g_val_mad
 
         else:
             logger.error(" Error!")
             logger.error(" z_score must be one of: MAD, STD")
-            sys.exit()
+            raise ValueError("z_score must be one of: MAD, STD")
 
         z_score_vals = np.ravel(z_score_vals_array)
 
-        logger.debug("      [{0}] Statistics of mZ-scores".format(test_id))
-        logger.debug("        Min(Z)    = {0:.2f}".format(z_score_vals.min()))
-        logger.debug("        Q1(Z)     = {0:.2f}".format(np.percentile(z_score_vals, 25)))
-        logger.debug("        Mean(Z)   = {0:.2f}".format(z_score_vals.mean()))
-        logger.debug("        Median(Z) = {0:.2f}".format(np.percentile(z_score_vals, 50)))
-        logger.debug("        Q3(Z)     = {0:.2f}".format(np.percentile(z_score_vals, 75)))
-        logger.debug("        Max(Z)    = {0:.2f}\n".format(z_score_vals.max()))
+        logger.debug("      [%s] Statistics of mZ-scores", test_id)
+        logger.debug("        Min(Z)    = %.2f", z_score_vals.min())
+        logger.debug("        Q1(Z)     = %.2f", np.percentile(z_score_vals, 25))
+        logger.debug("        Mean(Z)   = %.2f", z_score_vals.mean())
+        logger.debug("        Median(Z) = %.2f", np.percentile(z_score_vals, 50))
+        logger.debug("        Q3(Z)     = %.2f", np.percentile(z_score_vals, 75))
+        logger.debug("        Max(Z)    = %.2f\n", z_score_vals.max())
 
         # Calculate excess area from Gaussian: the Q-metric
         bins = np.linspace(-15, 15, 501)
@@ -249,34 +249,34 @@ def run_iar(
         sys.exit()
 
     logger.info("  Analysing results")
-    logger.info("   Outlier limit: {0:06.3f}".format(outlier_limit))
+    logger.info("   Outlier limit: %6.3f}", outlier_limit)
     keep_id_list = []
 
     logger.info(
-        "{0},{1},{2},{3:.4g}\n".format(
+        "%s,%s,%s,%.4g}\n",
             iteration,
             " ".join(remaining_id_list),
             " ".join(["{0:.4g}".format(i) for i in list(q_results.values())]),
             outlier_limit,
-        )
+
     )
 
     for idx, result in q_results.items():
 
         accept = result <= outlier_limit
 
         logger.info(
-            "      {0}: Q = {1:06.3f} [{2}]".format(
+            "      %s: Q = %6.3f [%s]",
                 idx, result, {True: "KEEP", False: "REMOVE"}[accept]
-            )
+
         )
 
         if accept:
             keep_id_list.append(idx)
 
     if len(keep_id_list) < len(remaining_id_list):
-        logger.info("\n  Step {0} Complete".format(iteration))
-        logger.info("  Num. Removed = {0} --\n".format(len(remaining_id_list) - len(keep_id_list)))
+        logger.info("\n  Step %d Complete", iteration)
+        logger.info("  Num. Removed = %d --\n", len(remaining_id_list) - len(keep_id_list))
 
         iteration += 1
         atlas_set_new = {i: atlas_set[i] for i in keep_id_list}
@@ -298,6 +298,6 @@ def run_iar(
             label=label,
         )
 
-    logger.info("  End point reached. Keeping:\n   {0}".format(keep_id_list))
+    logger.info("  End point reached. Keeping:\n   %s", keep_id_list)
 
     return atlas_set