Merge pull request #8 from pelkmanslab/7_itk_fixes

Pin itk dependencies

.github/workflows/build_and_test.yml

@@ -16,11 +16,11 @@ jobs:
   tests:
     strategy:
       matrix:
-        os: [ubuntu-22.04, macos-latest]
-        python-version: ["3.10", "3.11", "3.12"]
-        exclude:
-          - os: macos-latest
-            python-version: '3.10'
+        os: [ubuntu-22.04] #, macos-latest
+        python-version: ["3.10"] #, "3.11", "3.12"
+        # exclude:
+        #   - os: macos-latest
+        #     python-version: '3.10'
     name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}"
     runs-on: ${{ matrix.os }}
     timeout-minutes: 10

pyproject.toml

@@ -25,11 +25,12 @@ authors = [
 ]
 
 # Required Python version and dependencies
-requires-python = ">=3.10"
+requires-python = ">=3.10,<3.11" # relax Python upwards versions once itk is unpinned
 dependencies = [
     "fractal-tasks-core == 1.4.0", 
-    "itk", 
-    "itk-elastix", 
+    "itk==5.3.0", 
+    "itk-elastix==0.17.1", 
+    "numpy<2",
     "h5py", 
     "ngio == 0.1.4", 
     "scikit-image",

src/abbott/__FRACTAL_MANIFEST__.json

@@ -9,11 +9,42 @@
         "Multiplexing"
       ],
       "docs_info": "### Purpose\n- **Computes image-based registration** transformations for acquisitions in **HCS** OME-Zarr datasets using the elastix library.\n- Needs Elastix profiles to configure the registration.\n- Processes images grouped by well, under the assumption that each well contains one image per acquisition.\n- Calculates transformations for **specified regions of interest (ROIs)** and stores the results in a registration subfolder per OME-Zarr image.\n- Typically used as the first task in a workflow, followed by `Apply Registration (elastix)`.\n\n### Limitations\n- Supports only HCS OME-Zarr datasets, leveraging their acquisition metadata and well-based image grouping.\n- Assumes each well contains a single image per acquisition.\n",
+      "executable_non_parallel": "fractal_tasks/init_registration_hcs.py",
       "executable_parallel": "fractal_tasks/compute_registration_elastix.py",
       "meta_parallel": {
         "cpus_per_task": 4,
         "mem": 16000
       },
+      "args_schema_non_parallel": {
+        "additionalProperties": false,
+        "properties": {
+          "zarr_urls": {
+            "items": {
+              "type": "string"
+            },
+            "title": "Zarr Urls",
+            "type": "array",
+            "description": "List of paths or urls to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "zarr_dir": {
+            "title": "Zarr Dir",
+            "type": "string",
+            "description": "path of the directory where the new OME-Zarrs will be created. Not used by this task. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "reference_acquisition": {
+            "default": 0,
+            "title": "Reference Acquisition",
+            "type": "integer",
+            "description": "Which acquisition to register against. Needs to match the acquisition metadata in the OME-Zarr image."
+          }
+        },
+        "required": [
+          "zarr_urls",
+          "zarr_dir"
+        ],
+        "type": "object",
+        "title": "InitRegistrationHcs"
+      },
       "args_schema_parallel": {
         "$defs": {
           "InitArgsRegistration": {

src/abbott/dev/task_list.py

@@ -1,10 +1,11 @@
 """Contains the list of tasks available to fractal."""
 
-from fractal_tasks_core.dev.task_models import ParallelTask
+from fractal_tasks_core.dev.task_models import CompoundTask, ParallelTask
 
 TASK_LIST = [
-    ParallelTask(
+    CompoundTask(
         name="Compute Registration (elastix)",
+        executable_init="fractal_tasks/init_registration_hcs.py",
         executable="fractal_tasks/compute_registration_elastix.py",
         meta={"cpus_per_task": 4, "mem": 16000},
         category="Registration",