import ome zarr utils
Pydantic models for the import_ome_zarr task.
| CLASS | DESCRIPTION |
|---|---|
AdvancedOptions |
Advanced options for importing an OME-Zarr. |
GridRoiTable |
Configuration for building a |
Classes¶
AdvancedOptions
pydantic-model
¶
Bases: BaseModel
Advanced options for importing an OME-Zarr.
Fields:
-
update_omero_metadata(bool) -
add_image_roi_table(bool) -
grid_roi_table(GridRoiTable | None) -
table_backend(AVAILABLE_TABLE_BACKENDS) -
overwrite(bool)
Source code in fractal_tasks_core/_import_ome_zarr_utils.py
Attributes¶
add_image_roi_table = False
pydantic-field
¶
Whether to add an image_ROI_table table to each image, with a single ROI
covering the whole image.
grid_roi_table = None
pydantic-field
¶
If set, add a grid_ROI_table table to each image, with the image split
into a rectangular grid of ROIs of the given shape. If None, no
grid_ROI_table is created.
overwrite = False
pydantic-field
¶
Whether new ROI tables (added when add_image_roi_table=True and/or
grid_roi_table is not None) can overwrite existing ones.
table_backend = 'csv'
pydantic-field
¶
Table backend to use for the new ROI tables. Defaults to "csv".
update_omero_metadata = False
pydantic-field
¶
Whether to update Omero-channels metadata with channel labels and wavelength ids to make them compatible with some downstream Fractal tasks.
GridRoiTable
pydantic-model
¶
Bases: BaseModel
Configuration for building a grid_ROI_table.
Fields:
Source code in fractal_tasks_core/_import_ome_zarr_utils.py
Attributes¶
grid_x_shape = 2
pydantic-field
¶
Number of ROIs along the X axis. The image is split into a grid_y_shape by
grid_x_shape grid of ROIs (e.g. the default 2 by 2 produces 4 ROIs).
grid_y_shape = 2
pydantic-field
¶
Number of ROIs along the Y axis. The image is split into a grid_y_shape by
grid_x_shape grid of ROIs (e.g. the default 2 by 2 produces 4 ROIs).