diff --git a/.github/workflows/ci_pip.yml b/.github/workflows/ci_pip.yml index f6e59e2d1..aec2bb940 100644 --- a/.github/workflows/ci_pip.yml +++ b/.github/workflows/ci_pip.yml @@ -15,10 +15,8 @@ jobs: strategy: matrix: os: [ubuntu-22.04, macos-latest] - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] exclude: - - os: macos-latest - python-version: '3.9' - os: macos-latest python-version: '3.10' name: "Core, Python ${{ matrix.python-version }}, ${{ matrix.os }}" @@ -50,10 +48,8 @@ jobs: strategy: matrix: os: [ubuntu-latest, macos-latest] - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] exclude: - - os: macos-latest - python-version: '3.9' - os: macos-latest python-version: '3.10' name: "Tasks, Python ${{ matrix.python-version }}, ${{ matrix.os }}" diff --git a/.github/workflows/ci_poetry.yml b/.github/workflows/ci_poetry.yml index 1b2f27bff..8d9ef4626 100644 --- a/.github/workflows/ci_poetry.yml +++ b/.github/workflows/ci_poetry.yml @@ -15,7 +15,7 @@ jobs: strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v4 @@ -60,7 +60,7 @@ jobs: strategy: matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] steps: - uses: actions/checkout@v4 @@ -131,7 +131,7 @@ jobs: python-version: "3.10" - name: Install dependencies - run: poetry install --only dev + run: poetry install --with dev -E fractal-tasks - name: Download data uses: actions/download-artifact@v4 diff --git a/CHANGELOG.md b/CHANGELOG.md index 38a2e93bb..15a54b8b2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,7 +1,15 @@ **Note**: Numbers like (\#123) point to closed Pull Requests on the fractal-tasks-core repository. + # Unreleased +* Tasks: + * Refactor projection task to use ngio +* Dependencies: + * Add `ngio==0.1.4` to the dependencies + * Require `python >=3.10,<3.13` +* CI: + * Remove Python 3.9 from the CI matrix * Tests: * Use locked version of `coverage` in GitHub action (\#882). * Bump `coverage` version from 6.5 to 7.6 (\#882). @@ -13,6 +21,7 @@ * Support providing `docs_info=file:task_info/description.md` (\#876). * Deprecate `check_manifest.py` module, in favor of additional GitHub action steps (\#876). + # 1.3.3 * Add new metadata (authors, category, modality, tags) to manifest models and to tasks (\#855). diff --git a/docs/development.md b/docs/development.md index 2d7e6f15a..60d7980c4 100644 --- a/docs/development.md +++ b/docs/development.md @@ -36,7 +36,7 @@ poetry run pytest --ignore tests/tasks The tests files are in the `tests` folder of the repository. Its structure reflects the `fractal_tasks_core` structure, with tests for the core library in the main folder and tests for `tasks` and `dev` subpckages in their own subfolders. -Tests are also run through GitHub Actions, with Python 3.9, 3.10 and 3.11. Note that within GitHub actions we run tests for both the `poetry`-installed and `pip`-installed versions of the code, which may e.g. have different versions of some dependencies (since `pip install` does not rely on the `poetry.lock` lockfile). +Tests are also run through GitHub Actions, with Python 3.10, 3.11 and 3.12. Note that within GitHub actions we run tests for both the `poetry`-installed and `pip`-installed versions of the code, which may e.g. have different versions of some dependencies (since `pip install` does not rely on the `poetry.lock` lockfile). ## Documentation diff --git a/fractal_tasks_core/__FRACTAL_MANIFEST__.json b/fractal_tasks_core/__FRACTAL_MANIFEST__.json index e73ef4a28..270edd868 100644 --- a/fractal_tasks_core/__FRACTAL_MANIFEST__.json +++ b/fractal_tasks_core/__FRACTAL_MANIFEST__.json @@ -653,12 +653,17 @@ "overwrite": { "title": "Overwrite", "type": "boolean" + }, + "new_plate_name": { + "title": "New Plate Name", + "type": "string" } }, "required": [ "origin_url", "method", - "overwrite" + "overwrite", + "new_plate_name" ], "title": "InitArgsMIP", "type": "object" diff --git a/fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py b/fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py index 203c61f93..4ec5e8111 100644 --- a/fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py +++ b/fractal_tasks_core/tasks/copy_ome_zarr_hcs_plate.py @@ -244,7 +244,10 @@ def copy_ome_zarr_hcs_plate( parallelization_item = dict( zarr_url=new_zarr_url, init_args=dict( - origin_url=zarr_url, method=method.value, overwrite=overwrite + origin_url=zarr_url, + method=method.value, + overwrite=overwrite, + new_plate_name=f"{new_plate_name}.zarr", ), ) InitArgsMIP(**parallelization_item["init_args"]) diff --git a/fractal_tasks_core/tasks/io_models.py b/fractal_tasks_core/tasks/io_models.py index 6e0fe0ae8..c061afc89 100644 --- a/fractal_tasks_core/tasks/io_models.py +++ b/fractal_tasks_core/tasks/io_models.py @@ -86,11 +86,13 @@ class InitArgsMIP(BaseModel): origin_url: Path to the zarr_url with the 3D data method: Projection method to be used. See `DaskProjectionMethod` overwrite: If `True`, overwrite the task output. + new_plate_name: Name of the new OME-Zarr HCS plate """ origin_url: str method: str overwrite: bool + new_plate_name: str class MultiplexingAcquisition(BaseModel): diff --git a/fractal_tasks_core/tasks/projection.py b/fractal_tasks_core/tasks/projection.py index 23ce26268..03ab6ae13 100644 --- a/fractal_tasks_core/tasks/projection.py +++ b/fractal_tasks_core/tasks/projection.py @@ -12,30 +12,39 @@ """ Task for 3D->2D maximum-intensity projection. """ +from __future__ import annotations + import logging from typing import Any -import anndata as ad import dask.array as da -import zarr +from ngio import NgffImage +from ngio.core import Image from pydantic import validate_call -from zarr.errors import ContainsArrayError - -from fractal_tasks_core.ngff import load_NgffImageMeta -from fractal_tasks_core.pyramids import build_pyramid -from fractal_tasks_core.roi import ( - convert_ROIs_from_3D_to_2D, -) -from fractal_tasks_core.tables import write_table -from fractal_tasks_core.tables.v1 import get_tables_list_v1 + from fractal_tasks_core.tasks.io_models import InitArgsMIP from fractal_tasks_core.tasks.projection_utils import DaskProjectionMethod -from fractal_tasks_core.zarr_utils import OverwriteNotAllowedError - logger = logging.getLogger(__name__) +def _compute_new_shape(source_image: Image) -> tuple[int]: + """Compute the new shape of the image after the projection. + + The new shape is the same as the original one, + except for the z-axis, which is set to 1. + """ + on_disk_shape = source_image.on_disk_shape + logger.info(f"Source {on_disk_shape=}") + + on_disk_z_index = source_image.dataset.on_disk_axes_names.index("z") + + dest_on_disk_shape = list(on_disk_shape) + dest_on_disk_shape[on_disk_z_index] = 1 + logger.info(f"Destination {dest_on_disk_shape=}") + return tuple(dest_on_disk_shape) + + @validate_call def projection( *, @@ -60,116 +69,60 @@ def projection( logger.info(f"{method=}") # Read image metadata - ngff_image = load_NgffImageMeta(init_args.origin_url) - # Currently not using the validation models due to wavelength_id issue - # See #681 for discussion - # new_attrs = ngff_image.model_dump(exclude_none=True) - # Current way to get the necessary metadata for MIP - group = zarr.open_group(init_args.origin_url, mode="r") - new_attrs = group.attrs.asdict() - - # Create the zarr image with correct - new_image_group = zarr.group(zarr_url) - new_image_group.attrs.put(new_attrs) - - # Load 0-th level - data_czyx = da.from_zarr(init_args.origin_url + "/0") - num_channels = data_czyx.shape[0] - chunksize_y = data_czyx.chunksize[-2] - chunksize_x = data_czyx.chunksize[-1] - logger.info(f"{num_channels=}") - logger.info(f"{chunksize_y=}") - logger.info(f"{chunksize_x=}") - - # Loop over channels - accumulate_chl = [] - for ind_ch in range(num_channels): - # Perform MIP for each channel of level 0 - project_yx = da.stack( - [method.apply(data_czyx[ind_ch], axis=0)], axis=0 - ) - accumulate_chl.append(project_yx) - accumulated_array = da.stack(accumulate_chl, axis=0) - - # Write to disk (triggering execution) - try: - accumulated_array.to_zarr( - f"{zarr_url}/0", - overwrite=init_args.overwrite, - dimension_separator="/", - write_empty_chunks=False, - ) - except ContainsArrayError as e: - error_msg = ( - f"Cannot write array to zarr group at '{zarr_url}/0', " - f"with {init_args.overwrite=} (original error: {str(e)}).\n" - "Hint: try setting overwrite=True." + original_ngff_image = NgffImage(init_args.origin_url) + orginal_image = original_ngff_image.get_image() + + if orginal_image.is_2d or orginal_image.is_2d_time_series: + raise ValueError( + "The input image is 2D, " + "projection is only supported for 3D images." ) - logger.error(error_msg) - raise OverwriteNotAllowedError(error_msg) - # Starting from on-disk highest-resolution data, build and write to disk a - # pyramid of coarser levels - build_pyramid( - zarrurl=zarr_url, + # Compute the new shape and pixel size + dest_on_disk_shape = _compute_new_shape(orginal_image) + + dest_pixel_size = orginal_image.pixel_size + dest_pixel_size.z = 1.0 + logger.info(f"New shape: {dest_on_disk_shape=}") + + # Create the new empty image + new_ngff_image = original_ngff_image.derive_new_image( + store=zarr_url, + name="MIP", + on_disk_shape=dest_on_disk_shape, + pixel_sizes=dest_pixel_size, overwrite=init_args.overwrite, - num_levels=ngff_image.num_levels, - coarsening_xy=ngff_image.coarsening_xy, - chunksize=(1, 1, chunksize_y, chunksize_x), + copy_labels=False, + copy_tables=True, ) + logger.info(f"New Projection image created - {new_ngff_image=}") + new_image = new_ngff_image.get_image() - # Copy over any tables from the original zarr - # Generate the list of tables: - tables = get_tables_list_v1(init_args.origin_url) - roi_tables = get_tables_list_v1(init_args.origin_url, table_type="ROIs") - non_roi_tables = [table for table in tables if table not in roi_tables] - - for table in roi_tables: - logger.info( - f"Reading {table} from " - f"{init_args.origin_url=}, convert it to 2D, and " - "write it back to the new zarr file." - ) - new_ROI_table = ad.read_zarr(f"{init_args.origin_url}/tables/{table}") - old_ROI_table_attrs = zarr.open_group( - f"{init_args.origin_url}/tables/{table}" - ).attrs.asdict() - - # Convert 3D ROIs to 2D - pxl_sizes_zyx = ngff_image.get_pixel_sizes_zyx(level=0) - new_ROI_table = convert_ROIs_from_3D_to_2D( - new_ROI_table, pixel_size_z=pxl_sizes_zyx[0] - ) - # Write new table - write_table( - new_image_group, - table, - new_ROI_table, - table_attrs=old_ROI_table_attrs, - overwrite=init_args.overwrite, - ) + # Process the image + z_axis_index = orginal_image.find_axis("z") + source_dask = orginal_image.get_array( + mode="dask", preserve_dimensions=True + ) - for table in non_roi_tables: - logger.info( - f"Reading {table} from " - f"{init_args.origin_url=}, and " - "write it back to the new zarr file." - ) - new_non_ROI_table = ad.read_zarr( - f"{init_args.origin_url}/tables/{table}" - ) - old_non_ROI_table_attrs = zarr.open_group( - f"{init_args.origin_url}/tables/{table}" - ).attrs.asdict() - - # Write new table - write_table( - new_image_group, - table, - new_non_ROI_table, - table_attrs=old_non_ROI_table_attrs, - overwrite=init_args.overwrite, - ) + dest_dask = method.apply(dask_array=source_dask, axis=z_axis_index) + dest_dask = da.expand_dims(dest_dask, axis=z_axis_index) + new_image.set_array(dest_dask) + new_image.consolidate() + # Ends + + # Copy over the tables + for roi_table_name in new_ngff_image.tables.list(table_type="roi_table"): + table = new_ngff_image.tables.get_table(roi_table_name) + + roi_list = [] + for roi in table.rois: + roi.z = 0.0 + roi.z_length = 1.0 + roi_list.append(roi) + + table.set_rois(roi_list, overwrite=True) + table.consolidate() + logger.info(f"Table {roi_table_name} Projection done") # Generate image_list_updates image_list_update_dict = dict( @@ -177,6 +130,7 @@ def projection( dict( zarr_url=zarr_url, origin=init_args.origin_url, + attributes=dict(plate=init_args.new_plate_name), types=dict(is_3D=False), ) ] diff --git a/poetry.lock b/poetry.lock index ad74a9299..493eda05f 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,14 +1,137 @@ # This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand. +[[package]] +name = "aiohappyeyeballs" +version = "2.4.4" +description = "Happy Eyeballs for asyncio" +optional = false +python-versions = ">=3.8" +files = [ + {file = 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"sphinx-issues"] @@ -6421,13 +6956,13 @@ jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"] [[package]] name = "zipp" -version = "3.20.2" +version = "3.21.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, - {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, + {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, + {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] @@ -6443,5 +6978,5 @@ fractal-tasks = ["Pillow", "cellpose", "image_registration", "imageio-ffmpeg", " [metadata] lock-version = "2.0" -python-versions = "^3.9" -content-hash = "3847d5031efb2f749ca68ad00e60f2adbd725cf9111f8d7f18acc2654cb3cd8b" +python-versions = ">=3.10,<3.13" +content-hash = "b0eaeb17bef01cf8e6966e181b086284412dea28661fed8a2a29e3e1e6b5fa6f" diff --git a/pyproject.toml b/pyproject.toml index 73a0c6b72..48843ba15 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,7 +9,7 @@ authors = [ "Jacopo Nespolo ", ] readme = "README.md" -packages = [{include = "fractal_tasks_core"}] +packages = [{ include = "fractal_tasks_core" }] license = "BSD-3-Clause" homepage = "https://github.com/fractal-analytics-platform/fractal-tasks-core" repository = "https://github.com/fractal-analytics-platform/fractal-tasks-core" @@ -23,7 +23,7 @@ documentation = "https://fractal-analytics-platform.github.io/fractal-tasks-core [tool.poetry.dependencies] # Required dependencies -python = "^3.9" +python = ">=3.10,<3.13" dask = ">=2023.1.0" fsspec = "!=2023.9.0" zarr = ">=2.13.6,<3" @@ -34,6 +34,7 @@ pydantic = ">2,<=2.8.2" docstring-parser = "^0.15" anndata = ">=0.8.0,<0.11.0" filelock = "3.13.*" +ngio = "0.1.4" # Optional dependencies (used in extras) Pillow = { version = ">=9.1.1", optional = true } @@ -49,7 +50,20 @@ torch = { version = "<=3.0.0", optional = true } image_registration = { version = ">=0.2.9", optional = true } [tool.poetry.extras] -fractal-tasks = ["Pillow", "imageio-ffmpeg", "scikit-image", "llvmlite", "napari-segment-blobs-and-things-with-membranes", "napari-workflows", "stackview", "napari-skimage-regionprops", "napari-tools-menu", "cellpose", "torch", "image_registration"] +fractal-tasks = [ + "Pillow", + "imageio-ffmpeg", + "scikit-image", + "llvmlite", + "napari-segment-blobs-and-things-with-membranes", + "napari-workflows", + "stackview", + "napari-skimage-regionprops", + "napari-tools-menu", + "cellpose", + "torch", + "image_registration", +] [tool.poetry.group.dev] optional = true @@ -63,7 +77,7 @@ coverage = {extras = ["toml"], version = ">=7.6,<7.7"} jsonschema = "^4.16.0" mypy = "^1.3.0" requests = ">=2.28.0" -napari-skimage-regionprops-mock = { file="tests/data/napari_workflows/mock_package/dist/napari_skimage_regionprops_mock-9.9.9-py3-none-any.whl" } +napari-skimage-regionprops-mock = { file = "tests/data/napari_workflows/mock_package/dist/napari_skimage_regionprops_mock-9.9.9-py3-none-any.whl" } pooch = "1.8.0" [tool.poetry.group.docs] @@ -98,15 +112,9 @@ tag = true push = true [tool.bumpver.file_patterns] -"pyproject.toml" = [ - 'version = "{version}"$', -] -"fractal_tasks_core/__init__.py" = [ - '__VERSION__ = "{version}"$' -] +"pyproject.toml" = ['version = "{version}"$'] +"fractal_tasks_core/__init__.py" = ['__VERSION__ = "{version}"$'] [tool.deptry] -exclude = [ - 'tests', 'examples', 'docs' -] +exclude = ['tests', 'examples', 'docs'] diff --git a/tests/tasks/test_workflows.py b/tests/tasks/test_workflows.py index 1e2ac6302..2ae0602d9 100644 --- a/tests/tasks/test_workflows.py +++ b/tests/tasks/test_workflows.py @@ -20,6 +20,7 @@ import pytest import zarr from devtools import debug +from ngio.utils import NgioFileExistsError from ._validation import check_file_number from ._validation import validate_schema @@ -362,6 +363,7 @@ def test_MIP( "types": { "is_3D": False, }, + "attributes": {"plate": "plate_mip.zarr"}, } debug(expected_image_list_updates) assert image_list_updates[0] == expected_image_list_updates @@ -373,15 +375,13 @@ def test_MIP( init_args=image["init_args"], ) - # Re-run with overwrite=False - with pytest.raises(OverwriteNotAllowedError): + with pytest.raises(NgioFileExistsError): for image in parallelization_list: image["init_args"]["overwrite"] = False projection( zarr_url=image["zarr_url"], init_args=image["init_args"], ) - # OME-NGFF JSON validation image_zarr = Path(parallelization_list[0]["zarr_url"]) debug(image_zarr) @@ -442,6 +442,7 @@ def test_projection_methods( "origin_url": zarr_urls[0], "method": method, "overwrite": True, + "new_plate_name": f"plate_{method}.zarr", }, } ]