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Merge pull request #7 from jluethi/update_to_fractal_v2
Update to fractal v2
2 parents b634753 + 1c059c7 commit 9f82f4d

13 files changed

+286
-536
lines changed

‎pyproject.toml

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# Project metadata (see https://peps.python.org/pep-0621)
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[project]
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name = "fractal-helper-tasks"
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version = "0.0.1"
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version = "0.1.0a5"
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description = "Collection of Fractal helper tasks"
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readme = "README.md"
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license = { text = "BSD-3-Clause" }
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]
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# Required Python version and dependencies
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requires-python = ">=3.8"
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requires-python = ">=3.9"
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dependencies = [
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"fractal-tasks-core==0.14.2"
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"fractal-tasks-core==1.0.0"
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]
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# Optional dependencies (e.g. for `pip install -e ".[dev]"`, see
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]
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extend-ignore = [
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"D401", # First line should be in imperative mood (remove to opt in)
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"C408", # Unnecessary `dict` call
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]
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[tool.ruff.per-file-ignores]
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"tests/*.py" = ["D", "S"]
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"setup.py" = ["D"]
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[tool.deptry]
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exclude = [
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'tests', 'examples'
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]

‎src/fractal_helper_tasks/__FRACTAL_MANIFEST__.json

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{
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"manifest_version": "1",
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"manifest_version": "2",
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"task_list": [
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{
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"name": "Convert 2D segmentation to 3D",
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"executable": "convert_2D_segmentation_to_3D.py",
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"input_type": "zarr",
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"output_type": "zarr",
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"args_schema": {
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"title": "Convert2dSegmentationTo3d",
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"name": "Drop T Dimension",
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"output_types": {
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"has_t": false
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},
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"executable_non_parallel": "drop_t_dimension.py",
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"meta_non_parallel": {
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"cpus_per_task": 2,
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"mem": 8000
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},
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"args_schema_non_parallel": {
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"title": "DropTDimension",
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"type": "object",
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"properties": {
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"input_paths": {
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"title": "Input Paths",
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"description": "List of paths to the input files (Fractal managed)"
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},
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"output_path": {
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"title": "Output Path",
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"description": "Path to the output file (Fractal managed)"
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"zarr_url": {
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"title": "Zarr Url",
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"type": "string",
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"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server)."
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},
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"component": {
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"title": "Component",
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"description": "Component name, e.g. \"plate_name.zarr/B/03/0\" (Fractal managed)"
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"suffix": {
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"title": "Suffix",
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"default": "no_T",
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"type": "string",
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"description": "Suffix to be used for the new Zarr image. If overwrite_input is True, this file is only temporary."
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},
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"metadata": {
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"title": "Metadata",
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"description": "Metadata dictionary (Fractal managed)"
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"overwrite_input": {
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"title": "Overwrite Input",
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"default": false,
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"type": "boolean",
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"description": "Whether"
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}
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},
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"required": [
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"zarr_url"
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],
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"additionalProperties": false
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},
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"docs_info": "## drop_t_dimension\nDrops singleton t dimension.\n"
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},
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{
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"name": "Convert 2D segmentation to 3D",
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"input_types": {
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"is_3D": false
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},
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"executable_parallel": "convert_2D_segmentation_to_3D.py",
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"meta_parallel": {
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"cpus_per_task": 2,
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"mem": 8000
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},
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"args_schema_parallel": {
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"title": "Convert2dSegmentationTo3d",
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"type": "object",
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"properties": {
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"zarr_url": {
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"title": "Zarr Url",
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"type": "string",
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"description": "Path or url to the individual OME-Zarr image to be processed. (standard argument for Fractal tasks, managed by Fractal server)."
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},
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"label_name": {
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"title": "Label Name",
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"type": "string",
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"description": "Name of the label to copy from 2D OME-Zarr to 3D OME-Zarr"
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},
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"level": {
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"title": "Level",
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"default": 0,
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"type": "integer",
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"description": "Level of the 2D OME-Zarr label to copy from"
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},
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"ROI_tables_to_copy": {
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"title": "Roi Tables To Copy",
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"type": "array",
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"items": {},
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"description": "Optionally overwriting the names of the ROI tables in the 3D OME-Zarr"
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},
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"level": {
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"title": "Level",
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"default": 0,
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"type": "integer",
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"description": "Level of the 2D OME-Zarr label to copy from"
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"plate_suffix": {
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"title": "Plate Suffix",
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"default": "_mip",
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"type": "string",
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"description": "Suffix of the 2D OME-Zarr that needs to be removed to generate the path to the 3D OME-Zarr. If the 2D OME-Zarr is \"/path/to/my_plate_mip.zarr/B/03/0\" and the 3D OME-Zarr is located in \"/path/to/my_plate.zarr/B/03/0\", the correct suffix is \"_mip\"."
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},
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"suffix": {
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"title": "Suffix",
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"default": "mip",
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"image_suffix_2D_to_remove": {
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"title": "Image Suffix 2D To Remove",
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"type": "string",
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"description": "Suffix of the 2D OME-Zarr to copy from"
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"description": "If the image name between 2D & 3D don't match, this is the suffix that should be removed from the 2D image. If the 2D image is in \"/path/to/my_plate_mip.zarr/B/03/ 0_registered\" and the 3D image is in \"/path/to/my_plate.zarr/ B/03/0\", the value should be \"_registered\""
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},
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"image_suffix_3D_to_add": {
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"title": "Image Suffix 3D To Add",
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"type": "string",
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"description": "If the image name between 2D & 3D don't match, this is the suffix that should be added to the 3D image. If the 2D image is in \"/path/to/my_plate_mip.zarr/B/03/0\" and the 3D image is in \"/path/to/my_plate.zarr/B/03/0_illum_corr\", the value should be \"_illum_corr\"."
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},
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"overwrite": {
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"title": "Overwrite",
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}
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},
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"required": [
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"input_paths",
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"output_path",
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"component",
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"metadata",
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"zarr_url",
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"label_name"
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],
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"additionalProperties": false
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},
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"meta": {
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"parallelization_level": "image",
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"cpus_per_task": 2,
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"mem": 8000
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},
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"docs_info": "This task loads the 2D segmentation, replicates it along the Z slice and\nstores it back into the 3D OME-Zarr image.\n\nThis is a temporary workaround task, as long as we store 2D data in\na separate OME-Zarr file from the 3D data. Also, some assumptions are made\non the metadata structure, generalization to be tested."
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},
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{
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"name": "Convert Metadata Components 2D to 3D",
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"executable": "convert_metadata_components_2D_to_3D.py",
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"input_type": "zarr",
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"output_type": "zarr",
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"args_schema": {
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"title": "ConvertMetadataComponents2dTo3d",
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"type": "object",
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"properties": {
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"input_paths": {
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"title": "Input Paths",
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"description": "List of paths to the input files (Fractal managed)"
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},
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"output_path": {
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"title": "Output Path",
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"description": "Path to the output file (Fractal managed)"
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},
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"metadata": {
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"title": "Metadata",
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"description": "Metadata dictionary (Fractal managed)"
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},
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"from_2d_to_3d": {
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"title": "From 2D To 3D",
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"default": true,
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"type": "boolean",
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"description": "If True, removes the suffix. If False, adds the suffix to the metadata"
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},
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"suffix": {
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"title": "Suffix",
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"default": "mip",
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"type": "string",
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"description": "Suffix of the 2D OME-Zarr"
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}
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},
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"required": [
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"input_paths",
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"output_path",
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"metadata"
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],
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"additionalProperties": false
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},
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"meta": {
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"cpus_per_task": 1,
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"mem": 1000
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},
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"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."
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},
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{
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"name": "Drop T dimension",
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"executable": "drop_t_dimension.py",
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"input_type": "zarr",
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"output_type": "zarr",
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"meta": {
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"parallelization_level": "image",
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"cpus_per_task": 2,
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"mem": 8000
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},
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"docs_info": "Drops singleton t dimension.",
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"args_schema": {
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"title": "DropTDimension",
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"type": "object",
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"properties": {
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"input_paths": {
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"title": "Input Paths",
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"type": "array",
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"items": {
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"type": "string"
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},
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"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)."
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},
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"output_path": {
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"title": "Output Path",
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"type": "string",
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"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)."
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},
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"component": {
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"title": "Component",
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"type": "string",
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"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)."
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},
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"metadata": {
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"title": "Metadata",
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"type": "object",
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"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)."
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},
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"suffix": {
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"title": "Suffix",
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"default": "no_T",
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"type": "string",
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"description": "Suffix to be used for the new Zarr image. If overwrite_input is True, this file is only temporary."
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}
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},
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"required": [
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"input_paths",
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"output_path",
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"component",
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"metadata"
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],
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"additionalProperties": false
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}
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"docs_info": "## convert_2D_segmentation_to_3D\nConvert 2D segmentation to 3D segmentation.\n\nThis task loads the 2D segmentation, replicates it along the Z slice and\nstores it back into the 3D OME-Zarr image.\n\nThis is a temporary workaround task, as long as we store 2D data in\na separate OME-Zarr file from the 3D data. If the 2D & 3D OME-Zarr images\nhave different suffixes in their name, use `image_suffix_2D_to_remove` &\n`image_suffix_3D_to_add`. If their base names are different, this task\ndoes not support processing them at the moment.\n"
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}
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],
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"has_args_schemas": true,

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