io_models
InitArgsCellVoyager
¶
Bases: BaseModel
Arguments to be passed from cellvoyager converter init to compute
ATTRIBUTE | DESCRIPTION |
---|---|
image_dir |
Directory where the raw images are found
TYPE:
|
plate_prefix |
part of the image filename needed for finding the right subset of image files
TYPE:
|
well_ID |
part of the image filename needed for finding the right subset of image files
TYPE:
|
image_extension |
part of the image filename needed for finding the right subset of image files
TYPE:
|
include_glob_patterns |
Additional glob patterns to filter the available images with. |
exclude_glob_patterns |
Glob patterns to exclude. |
acquisition |
Acquisition metadata needed for multiplexing |
Source code in fractal_tasks_core/tasks/io_models.py
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InitArgsIllumination
¶
Bases: BaseModel
Dummy model description.
ATTRIBUTE | DESCRIPTION |
---|---|
raw_path |
dummy attribute description.
TYPE:
|
subsets |
dummy attribute description. |
Source code in fractal_tasks_core/tasks/io_models.py
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InitArgsMIP
¶
Bases: BaseModel
Init Args for MIP task.
ATTRIBUTE | DESCRIPTION |
---|---|
origin_url |
Path to the zarr_url with the 3D data
TYPE:
|
method |
Projection method to be used. See
TYPE:
|
overwrite |
If
TYPE:
|
new_plate_name |
Name of the new OME-Zarr HCS plate
TYPE:
|
Source code in fractal_tasks_core/tasks/io_models.py
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InitArgsRegistration
¶
Bases: BaseModel
Registration init args.
Passed from image_based_registration_hcs_init
to
calculate_registration_image_based
.
ATTRIBUTE | DESCRIPTION |
---|---|
reference_zarr_url |
zarr_url for the reference image
TYPE:
|
Source code in fractal_tasks_core/tasks/io_models.py
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InitArgsRegistrationConsensus
¶
Bases: BaseModel
Registration consensus init args.
Provides the list of zarr_urls for all acquisitions for a given well
ATTRIBUTE | DESCRIPTION |
---|---|
zarr_url_list |
List of zarr_urls for all the OME-Zarr images in the well. |
Source code in fractal_tasks_core/tasks/io_models.py
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|
MultiplexingAcquisition
¶
Bases: BaseModel
Input class for Multiplexing Cellvoyager converter
ATTRIBUTE | DESCRIPTION |
---|---|
image_dir |
Path to the folder that contains the Cellvoyager image files for that acquisition and the MeasurementData & MeasurementDetail metadata files.
TYPE:
|
allowed_channels |
A list of
TYPE:
|
Source code in fractal_tasks_core/tasks/io_models.py
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|
NapariWorkflowsInput
¶
Bases: BaseModel
A value of the input_specs
argument in napari_workflows_wrapper
.
ATTRIBUTE | DESCRIPTION |
---|---|
type |
Input type (either
TYPE:
|
label_name |
Label name (for label inputs only). |
channel |
TYPE:
|
Source code in fractal_tasks_core/tasks/io_models.py
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|
channel_is_present()
¶
Check that image inputs have channel
set.
Source code in fractal_tasks_core/tasks/io_models.py
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|
label_name_is_present()
¶
Check that label inputs have label_name
set.
Source code in fractal_tasks_core/tasks/io_models.py
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|
NapariWorkflowsOutput
¶
Bases: BaseModel
A value of the output_specs
argument in napari_workflows_wrapper
.
ATTRIBUTE | DESCRIPTION |
---|---|
type |
Output type (either
TYPE:
|
label_name |
Label name (for label outputs, it is used as the name of
the label; for dataframe outputs, it is used to fill the
TYPE:
|
table_name |
Table name (for dataframe outputs only). |
Source code in fractal_tasks_core/tasks/io_models.py
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|
table_name_only_for_dataframe_type()
¶
Check that table_name is set only for dataframe outputs.
Source code in fractal_tasks_core/tasks/io_models.py
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|