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fractal_tasks_core/tasks/projection.py

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -13,31 +13,33 @@
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Task for 3D->2D maximum-intensity projection.
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"""
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from __future__ import annotations
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from typing import Any, TYPE_CHECKING
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from typing import Any
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from typing import TYPE_CHECKING
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import dask.array as da
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from ngio import NgffImage
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from ngio.utils import ngio_logger
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from pydantic import validate_call
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from fractal_tasks_core.tasks.io_models import InitArgsMIP
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from fractal_tasks_core.tasks.projection_utils import DaskProjectionMethod
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from ngio.utils import ngio_logger
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if TYPE_CHECKING:
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from ngio.core import Image
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def _compute_new_shape(source_image: Image) -> tuple[int]:
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""" Compute the new shape of the image after the projection.
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The new shape is the same as the original one, except for the z-axis, which is set to 1.
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"""Compute the new shape of the image after the projection.
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The new shape is the same as the original one,
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except for the z-axis, which is set to 1.
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"""
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on_disk_shape = source_image.on_disk_shape
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ngio_logger.info(f"Source {on_disk_shape=}")
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on_disk_z_index = source_image.dataset.on_disk_axes_names.index("z")
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dest_on_disk_shape = list(on_disk_shape)
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dest_on_disk_shape[on_disk_z_index] = 1
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ngio_logger.info(f"Destination {dest_on_disk_shape=}")
@@ -96,8 +98,6 @@ def projection(
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# Process the image
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z_axis_index = orginal_image.find_axis("z")
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assert z_axis_index is not None # This should never happen since we checked for 3D images above
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source_dask = orginal_image.get_array(
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mode="dask", preserve_dimensions=True
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)
@@ -114,7 +114,7 @@ def projection(
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mip_table = new_ngff_image.tables.new(
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roi_table, table_type="roi_table", overwrite=True
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)
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roi_list = []
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for roi in table.rois:
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roi.z_length = roi.z + 1
@@ -143,4 +143,4 @@ def projection(
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run_fractal_task(
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task_function=projection,
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logger_name=ngio_logger.name,
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)
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)

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