Merge pull request #1 from jluethi/drop_t_dimension

Drop t dimension Task

Author: jluethi

.DS_Store

@@ -0,0 +1,111 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+.DS_Store
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
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+
+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
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+# mypy
+.mypy_cache/
+
+# ruff
+.ruff_cache/
+
+# IDE settings
+.vscode/
+.idea/

.gitignore

@@ -0,0 +1,17 @@
+"""Dev script to test the Drop T dimension task."""
+from fractal_helper_tasks.drop_t_dimension import drop_t_dimension
+
+input_paths = [
+    "/Users/joel/Desktop/dyn_CHX_pos1_mmIntOrg_121z_0-2um_640-1000ms-200g_561-1000ms-200g__488-1000ms-200g_405-100ms-200g_11.zarr"
+]
+output_path = ""
+component = "0"
+
+drop_t_dimension(
+    input_paths=input_paths,
+    output_path=output_path,
+    component=component,
+    metadata={},
+    suffix="no_T",
+    overwrite_input=False,
+)

examples/run_drop_t_dimension.py

@@ -131,6 +131,60 @@
         "mem": 1000
       },
       "docs_info": "Workaround task to manually change the hard-coded metadata components\nA fractal workflow sets them to the mip.zarr components after running the\nmaximum intensity projection task. This resets them to the 3D components."
+    },
+    {
+      "name": "Drop T dimension",
+      "executable": "drop_t_dimension.py",
+      "input_type": "zarr",
+      "output_type": "zarr",
+      "meta": {
+        "parallelization_level": "image",
+        "cpus_per_task": 2,
+        "mem": 8000
+      },
+      "docs_info": "Drops singleton t dimension.",
+      "args_schema": {
+        "title": "DropTDimension",
+        "type": "object",
+        "properties": {
+          "input_paths": {
+            "title": "Input Paths",
+            "type": "array",
+            "items": {
+              "type": "string"
+            },
+            "description": "This parameter is not used by this task. This task only supports a single input path. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "output_path": {
+            "title": "Output Path",
+            "type": "string",
+            "description": "Path were the output of this task is stored. Example: `\"/some/path/\"` => puts the new OME-Zarr file in that folder. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "component": {
+            "title": "Component",
+            "type": "string",
+            "description": "Path to the OME-Zarr image in the OME-Zarr plate that is processed. Component is typically changed by the `copy_ome_zarr` task before, to point to a new mip Zarr file. Example: `\"some_plate_mip.zarr/B/03/0\"`. (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "metadata": {
+            "title": "Metadata",
+            "type": "object",
+            "description": "Dictionary containing metadata about the OME-Zarr. This task requires the key `copy_ome_zarr` to be present in the metadata (as defined in `copy_ome_zarr` task). (standard argument for Fractal tasks, managed by Fractal server)."
+          },
+          "suffix": {
+            "title": "Suffix",
+            "default": "no_T",
+            "type": "string",
+            "description": "Suffix to be used for the new Zarr image. If overwrite_input is True, this file is only temporary."
+          }
+        },
+        "required": [
+          "input_paths",
+          "output_path",
+          "component",
+          "metadata"
+        ],
+        "additionalProperties": false
+      }
     }
   ],
   "has_args_schemas": true,