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Simplification of the pipeline#12

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adjavon wants to merge 14 commits intomasterfrom
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Simplification of the pipeline#12
adjavon wants to merge 14 commits intomasterfrom
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@adjavon adjavon commented Apr 22, 2025

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adjavon and others added 14 commits January 13, 2025 14:02
This should allow a cleaner conversion to new datasets in the future.
Contributes to #7
This makes the training script somewhat more flexible for various datasets in the pipeline.

Works towards #7.
Makes 03_inference more dataset-agnostic.
Details should come from the configuration file.
Voxel size is currently optional, and will be ignored by default.

Addresses part of #7
Specifically, for inference. The spatial order can be set in the data configuration file.

Closes #7
This make sure that it is zyx by default, even if it isn't defined by the data config. This also shows how to define interpolation of optional arguments.
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