Add illumination correction to the manifest

Add illumination correction to the manifest

Author: tcompa

fractal_tasks_core/__init__.py

@@ -1,4 +1,4 @@
-__VERSION__ = "0.1.1"
+__VERSION__ = "0.1.3"
 
 __FRACTAL_MANIFEST__ = [
     {
@@ -40,7 +40,7 @@
         "resource_type": "core task",
         "input_type": "zarr",
         "output_type": "zarr",
-        "module": f"{__name__}.replicate_zarr_structure:replicate_zarr_structure",
+        "module": f"{__name__}.replicate_zarr_structure:replicate_zarr_structure",  # noqa: E501
         "default_args": {
             "executor": "cpu",
             "project_to_2D": True,
@@ -52,7 +52,7 @@
         "resource_type": "core task",
         "input_type": "zarr",
         "output_type": "zarr",
-        "module": f"{__name__}.maximum_intensity_projection:maximum_intensity_projection",
+        "module": f"{__name__}.maximum_intensity_projection:maximum_intensity_projection",  # noqa: E501
         "default_args": {"executor": "cpu", "parallelization_level": "well"},
     },
     {
@@ -72,7 +72,7 @@
         "resource_type": "core task",
         "input_type": "zarr",
         "output_type": "zarr",
-        "module": f"{__name__}.image_labeling_whole_well:image_labeling_whole_well",
+        "module": f"{__name__}.image_labeling_whole_well:image_labeling_whole_well",  # noqa: E501
         "default_args": {
             "labeling_channel": "A01_C01",
             "executor": "cpu",  # FIXME: put gpu
@@ -93,4 +93,18 @@
             "parallelization_level": "well",
         },
     },
+    {
+        "name": "Illumination correction",
+        "resource_type": "core task",
+        "input_type": "zarr",
+        "output_type": "zarr",
+        "module": f"{__name__}.illumination_correction:illumination_correction",  # noqa: E501
+        "default_args": {
+            "overwrite": False,
+            "dict_corr": None,
+            "background": 100,
+            "executor": "cpu",
+            "parallelization_level": "well",
+        },
+    },
 ]

fractal_tasks_core/illumination_correction.py

@@ -265,6 +265,10 @@ def illumination_correction(
 
 
 if __name__ == "__main__":
+
+    # FIXME
+    raise NotImplementedError("TODO: CLI argument parsing is not up to date")
+
     from argparse import ArgumentParser
 
     parser = ArgumentParser(prog="illumination_correction.py")

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-tasks-core"
-version = "0.1.1"
+version = "0.1.3"
 description = ""
 authors = [
     "Jacopo Nespolo <[email protected]>",
@@ -47,7 +47,7 @@ build-backend = "poetry.core.masonry.api"
 
 
 [tool.bumpver]
-current_version = "0.1.1"
+current_version = "0.1.3"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true