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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 grid_ROI_table.

Classes

AdvancedOptions pydantic-model

Bases: BaseModel

Advanced options for importing an OME-Zarr.

Fields:

Source code in fractal_tasks_core/_import_ome_zarr_utils.py
class AdvancedOptions(BaseModel):
    """Advanced options for importing an OME-Zarr."""

    update_omero_metadata: bool = False
    """
    Whether to update Omero-channels metadata with channel labels and
    wavelength ids to make them compatible with some downstream Fractal tasks.
    """

    add_image_roi_table: bool = False
    """
    Whether to add an `image_ROI_table` table to each image, with a single ROI
    covering the whole image.
    """

    grid_roi_table: GridRoiTable | None = None
    """
    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.
    """

    table_backend: AVAILABLE_TABLE_BACKENDS = "csv"
    """
    Table backend to use for the new ROI tables. Defaults to "csv".
    """

    overwrite: bool = False
    """
    Whether new ROI tables (added when `add_image_roi_table=True` and/or
    `grid_roi_table` is not `None`) can overwrite existing ones.
    """

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
class GridRoiTable(BaseModel):
    """Configuration for building a `grid_ROI_table`."""

    grid_y_shape: int = 2
    """
    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).
    """

    grid_x_shape: int = 2
    """
    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).
    """

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).