cellmap_segmentation_challenge.postprocess#
Functions
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Postprocess a volume in a zarr container with an arbitrary function. |
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Rescale volumes within a zarr container. |
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Resize volumes within a zarr container to a given shape. |
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Threshold a volume in a zarr container. |
- cellmap_segmentation_challenge.postprocess.threshold_volume(input_container: str | UPath, threshold: float | list[float] | dict[str, float] = 0.5, output_path: str | UPath = 'thresholded.zarr', labels: list[str] | None = None)[source]#
Threshold a volume in a zarr container.
- Parameters:
input_container (str | UPath) – The path to the zarr container containing the data for each label.
threshold (float | list[float] | dict[str, float]) – The threshold(s) to apply to each label. If a float, the same threshold is applied to all labels. If a list, the thresholds are applied to the labels in order. If a dict, the thresholds are applied to the labels with the corresponding keys.
output_path (UPath) – The path to the zarr container to write the thresholded data to.
labels (Optional[list[str]], optional) – The labels to threshold in the zarr container. If None, all labels are thresholded. Default is None.
- cellmap_segmentation_challenge.postprocess.process_volume(input_container: str | UPath, process_func: Callable | list[Callable] | dict[str, Callable] | PathLike, output_path: str | UPath, labels: list[str] | None = None)[source]#
Postprocess a volume in a zarr container with an arbitrary function.
- Parameters:
input_container (str | UPath) – The path to the zarr container containing the data for each label.
process_func (Callable | list[Callable] | dict[str, Callable] | os.PathLike) – The function(s) to apply to each label. If a Callable, the same function is applied to all labels. If a list, the functions are applied to the labels in order. If a dict, the functions are applied to the labels with the corresponding keys. If an os.PathLike, the function is loaded from the file at the path (the function should be called process_func in the python file). This last option should take a numpy array as input and return a numpy array as output. This allows for more complex postprocessing functions to be used.
output_path (UPath) – The path to the zarr container to write the thresholded data to.
labels (Optional[list[str]], optional) – The labels to process in the zarr container. If None, all labels are processed. Default is None.
- cellmap_segmentation_challenge.postprocess.rescale_volume(input_container: str | UPath, output_path: str | UPath, output_voxel_size: list[float] | list[list[float]] | dict[str, list[float]], labels: list[str] | None = None)[source]#
Rescale volumes within a zarr container.
- Parameters:
input_container (str | UPath) – The path to the zarr container containing the data for each label.
output_path (UPath) – The path to the zarr container to write the rescaled data to.
output_voxel_size (list[float] | list[list[float]] | dict[str, list[float]]) – The voxel size(s) to rescale the labels to. If a list, the same voxel size is applied to all labels. If a list of lists, the voxel sizes are applied to the labels in order. If a dict, the voxel sizes are applied to the labels with the corresponding keys.
labels (Optional[list[str]], optional) – The labels to rescale in the zarr container. If None, all labels are rescaled. Default is None
- cellmap_segmentation_challenge.postprocess.resize_volume(input_container: str | UPath, output_path: str | UPath, output_shape: list[int] | list[list[int]] | dict[str, list[int]], labels: list[str] | None = None)[source]#
Resize volumes within a zarr container to a given shape.
- Parameters:
input_container (str | UPath) – The path to the zarr container containing the data for each label.
output_path (UPath) – The path to the zarr container to write the resized data to.
output_shape (list[int] | list[list[int]] | dict[str, list[int]]) – The shape(s) to resize the labels to. If a list, the same shape is applied to all labels. If a list of lists, the shapes are applied to the labels in order. If a dict, the shapes are applied to the labels with the corresponding keys.
labels (Optional[list[str]], optional) – The labels to resize in the zarr container. If None, all labels are resized. Default is None