Merge pull request #738 from fstur/cellpose_normalization

Cellpose normalization

Author: jluethi

.pre-commit-config.yaml

@@ -17,6 +17,7 @@ repos:
     rev: 3.9.2
     hooks:
     -   id: flake8
+        args: ["--ignore=E203,W503"]
 -   repo: https://github.com/PyCQA/bandit
     rev: '1.7.4'
     hooks:

CHANGELOG.md

@@ -1,9 +1,15 @@
 **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository.
 
-# 1.0.3 (unreleased)
+# Unreleased
 
-* Support JSON-Schema generation for `Enum` task arguments (\#749).
-* Make JSON-Schema generation tools more flexible, to simplify testing (\#749).
+* Tasks:
+    * Refactor Cellpose Task inputs: Combine Channel inputs & channel normalization parameters (\#738).
+    * Refactor Cellpose Task inputs: Group advanced Cellpose parameters into the `CellposeModelParams` model that's provided via `advanced_cellpose_model_params` (\#738).
+    * Refactor Cellpose Task inputs: Support independent normalization of 2 input channels in the Cellpose task (\#738).
+    * Rename `task.cellpose_transforms` into `tasks.cellpose_utils` (\#738).
+* Development:
+    * Support JSON-Schema generation for `Enum` task arguments (\#749).
+    * Make JSON-Schema generation tools more flexible, to simplify testing (\#749).
 * Update documentation (\#751).
 
 * Documentation:
@@ -14,7 +20,7 @@
 
 # 1.0.2
 
-* Fix bug in plate metadata in MIP task (in the copy_ome_zarr_hcs_plate init function) (\#736).
+* Fix bug in plate metadata in MIP task (in the `copy_ome_zarr_hcs_plate` init function) (\#736).
 
 # 1.0.1
 

fractal_tasks_core/__FRACTAL_MANIFEST__.json

@@ -109,7 +109,9 @@ class ChannelInputModel(BaseModel):
 
     Attributes:
         wavelength_id: Unique ID for the channel wavelength, e.g. `A01_C01`.
-        label: Name of the channel.
+            Can only be specified if label is not set.
+        label: Name of the channel. Can only be specified if wavelength_id is
+            not set.
     """
 
     wavelength_id: Optional[str] = None

fractal_tasks_core/channels.py

@@ -64,9 +64,24 @@
     ),
     (
         "fractal_tasks_core",
-        "tasks/cellpose_transforms.py",
+        "tasks/cellpose_utils.py",
         "CellposeCustomNormalizer",
     ),
+    (
+        "fractal_tasks_core",
+        "tasks/cellpose_utils.py",
+        "CellposeChannel1InputModel",
+    ),
+    (
+        "fractal_tasks_core",
+        "tasks/cellpose_utils.py",
+        "CellposeChannel2InputModel",
+    ),
+    (
+        "fractal_tasks_core",
+        "tasks/cellpose_utils.py",
+        "CellposeModelParams",
+    ),
     (
         "fractal_tasks_core",
         "tasks/io_models.py",