Create CLEM PNG thumbnails for PATo (#221)

* Added 'images plugin' function to convert TIFF to PNG
* Added additional step in CLEM image processing workflows to generate colourised PNG thumbnails for PATo visualisation
* Added '.dockerignore' file and an empty 'installers' folder to store offline installers in
* Update 'cryoemservices_cpu' Dockerfile to look for local IMOD installer for a specified version before attempting to download it

Author: tieneupin

.dockerignore

@@ -0,0 +1,11 @@
+# Ignore everything by default
+**
+
+# Whitelist only the files and folders needed for building
+!Dockerfiles/
+!installers/
+!src/
+!pyproject.toml
+!setup.py
+!LICENSE
+!README.md

.gitignore

@@ -129,6 +129,9 @@ venv.bak/
 .dmypy.json
 dmypy.json
 
+# ruff
+.ruff_cache/
+
 # Pyre type checker
 .pyre/
 

Dockerfiles/cryoemservices_cpu

@@ -12,6 +12,10 @@ RUN apt-get update && \
 
 # Build CryoEM Services, pipeliner, and IMOD in a branch image
 FROM base as build
+
+# Set up build arguments for this stage
+ARG IMOD_INSTALLER=imod_5.1.9_RHEL8-64_CUDA12.0.sh
+
 COPY ./ /cryoem-services/
 RUN apt-get update && \
     apt-get upgrade -y && \
@@ -31,10 +35,13 @@ RUN apt-get update && \
         /cryoem-services \
         http://gitlab.com/stephen-riggs/ccpem-pipeliner/-/archive/diamond_tomo/ccpem-pipeliner-diamond_tomo.zip \
         && \
-    curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/imod_5.1.0_RHEL8-64_CUDA12.0.sh > imod_5.1.0_RHEL8-64_CUDA12.0.sh && \
-    chmod +x imod_5.1.0_RHEL8-64_CUDA12.0.sh && \
+    if [ ! -f /cryoem-services/installers/${IMOD_INSTALLER} ]; then \
+        echo "IMOD installer not found; downloading..."; \
+        curl https://bio3d.colorado.edu/imod/AMD64-RHEL5/${IMOD_INSTALLER} > /cryoem-services/installers/${IMOD_INSTALLER}; \
+    fi && \
+    chmod +x /cryoem-services/installers/${IMOD_INSTALLER} && \
     mkdir imod && \
-    ./imod_5.1.0_RHEL8-64_CUDA12.0.sh -dir imod -skip -y
+    /cryoem-services/installers/${IMOD_INSTALLER} -dir imod -skip -y
 
 # Transfer completed build to base image
 FROM base

installers/README.md

@@ -0,0 +1,2 @@
+This is placeholder folder in which installation files for the Docker containers can be placed.
+The Dockerfiles will first check to see if the desired file is located here before attempting to download it.

pyproject.toml

@@ -117,6 +117,7 @@ torch = [
     "picked_particles" = "cryoemservices.services.images_plugins:picked_particles"
     "picked_particles_3d_apng" = "cryoemservices.services.images_plugins:picked_particles_3d_apng"
     "picked_particles_3d_central_slice" = "cryoemservices.services.images_plugins:picked_particles_3d_central_slice"
+    "tiff_to_apng" = "cryoemservices.services.images_plugins:tiff_to_apng"
     "tilt_series_alignment" = "cryoemservices.services.images_plugins:tilt_series_alignment"
 [project.entry-points."cryoemservices.services.process_recipe.filters"]
     ispyb = "cryoemservices.util.process_recipe_tools:ispyb_filter"

recipes/clem-align-and-merge-wrapper.json

@@ -10,7 +10,8 @@
       "align_across": "{align_across}"
     },
     "output": {
-      "murfey_feedback": 2
+      "murfey_feedback": 2,
+      "images": 3
     },
     "parameters": {
       "cluster": {
@@ -46,5 +47,9 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
+  "3": {
+    "queue": "images",
+    "service": "Images"
+  },
   "start": [[1, []]]
 }

recipes/clem-align-and-merge.json

@@ -10,7 +10,8 @@
       "align_across": "{align_across}"
     },
     "output": {
-      "murfey_feedback": 2
+      "murfey_feedback": 2,
+      "images": 3
     },
     "queue": "cluster.submission",
     "service": "ALIGN-AND-MERGE"
@@ -22,5 +23,9 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
+  "3": {
+    "queue": "images",
+    "service": "Images"
+  },
   "start": [[1, []]]
 }

recipes/clem-lif-to-stack-wrapper.json

@@ -5,7 +5,8 @@
       "root_folder": "{root_folder}"
     },
     "output": {
-      "murfey_feedback": 2
+      "murfey_feedback": 2,
+      "images": 3
     },
     "parameters": {
       "cluster": {
@@ -41,5 +42,9 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
+  "3": {
+    "queue": "images",
+    "service": "Images"
+  },
   "start": [[1, []]]
 }

recipes/clem-lif-to-stack.json

@@ -5,7 +5,8 @@
       "root_folder": "{root_folder}"
     },
     "output": {
-      "murfey_feedback": 2
+      "murfey_feedback": 2,
+      "images": 3
     },
     "queue": "cluster.submission",
     "service": "LIF2STACK"
@@ -17,5 +18,9 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
+  "3": {
+    "queue": "images",
+    "service": "Images"
+  },
   "start": [[1, []]]
 }

recipes/clem-tiff-to-stack-wrapper.json

@@ -7,7 +7,8 @@
       "metadata": "{metadata}"
     },
     "output": {
-      "murfey_feedback": 2
+      "murfey_feedback": 2,
+      "images": 3
     },
     "parameters": {
       "cluster": {
@@ -43,5 +44,9 @@
     "queue": "{feedback_queue}",
     "service": "Murfey"
   },
+  "3": {
+    "queue": "images",
+    "service": "Images"
+  },
   "start": [[1, []]]
 }