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Convert PS-OCT MAT files to OME-Zarr #19

Merged
merged 55 commits into from
Nov 21, 2024
Merged

Convert PS-OCT MAT files to OME-Zarr #19

merged 55 commits into from
Nov 21, 2024

Commits on Apr 22, 2024

  1. WIP: conversion form OCT's mat files to zarr

    @balbasty
    balbasty committed Apr 22, 2024
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Commits on Aug 13, 2024

  1. WIP

    @balbasty
    balbasty committed Aug 13, 2024
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  2. Merge branch 'main' into oct_mat_to_zarr

    @balbasty
    balbasty committed Aug 13, 2024
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  3. WIp

    @balbasty
    balbasty committed Aug 13, 2024
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  4. WIP

    @balbasty
    balbasty committed Aug 13, 2024
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  5. WIP

    @balbasty
    balbasty committed Aug 13, 2024
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  6. FIX: units

    @balbasty
    balbasty committed Aug 13, 2024
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  7. FIX: units

    @balbasty
    balbasty committed Aug 13, 2024
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Commits on Aug 14, 2024

  1. WIP

    @balbasty
    balbasty committed Aug 14, 2024
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  2. WIP

    @balbasty
    balbasty committed Aug 14, 2024
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  3. WIP

    @balbasty
    balbasty committed Aug 14, 2024
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  4. WIP

    @balbasty
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  5. WIP

    @balbasty
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Commits on Oct 30, 2024

  1. Raise exception when input is not a ndarray

    @calvinchai
    calvinchai committed Oct 30, 2024
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  2. Raise exception when input does not have enough dimension

    @calvinchai
    calvinchai committed Oct 30, 2024
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  3. Fix error message

    @calvinchai
    calvinchai committed Oct 30, 2024
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  4. Add an argument "key" to use in .mat file data

    @calvinchai
    calvinchai committed Oct 30, 2024
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  5. Fix the error when output file is not given

    @calvinchai
    calvinchai committed Oct 30, 2024
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  6. Fix the error when output file is not given

    @calvinchai
    calvinchai committed Oct 30, 2024
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  7. Add argument key's doc

    @calvinchai
    calvinchai committed Oct 30, 2024
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  8. Add capability to handle multiple input files and stack them

    @calvinchai
    calvinchai committed Oct 30, 2024
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  9. Cleanup

    @calvinchai
    calvinchai committed Oct 30, 2024
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  10. Fix typo

    @calvinchai
    calvinchai committed Oct 30, 2024
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  11. Raise exception when the key is not found in the input file. Ensure a… 

    …ll input files using the same key.
    @calvinchai
    calvinchai committed Oct 30, 2024
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Commits on Nov 13, 2024

  1. Merge branch 'main' into oct_mat_to_zarr

    @calvinchai
    calvinchai committed Nov 13, 2024
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  2. Move PSOCT conversion script into modalities

    @calvinchai
    calvinchai committed Nov 13, 2024
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  3. Update OCT process naming

    @calvinchai
    calvinchai committed Nov 13, 2024
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Commits on Nov 14, 2024

  1. docs/style

    @calvinchai
    calvinchai committed Nov 14, 2024
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  2. style

    @calvinchai
    calvinchai committed Nov 14, 2024
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  3. refactor: generate_pyramid from oct pipeline

    @calvinchai
    calvinchai committed Nov 14, 2024
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  4. fix: wrong shape was used for nii header in zarr, no effect

    @calvinchai
    calvinchai committed Nov 14, 2024
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  5. refactor: nifti-zarr header

    @calvinchai
    calvinchai committed Nov 14, 2024
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  6. fix: nifti unit

    @calvinchai
    calvinchai committed Nov 14, 2024
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Commits on Nov 15, 2024

  1. WIP

    @calvinchai
    calvinchai committed Nov 15, 2024
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  2. Seperate OCT pipeline to multi_slice.py and single_volume.py

    @calvinchai
    calvinchai committed Nov 15, 2024
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  3. Seperate OCT pipeline to multi_slice.py and single_volume.py

    @calvinchai
    calvinchai committed Nov 15, 2024
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  4. feat: generate pyramid without pooling specific axis

    @calvinchai
    calvinchai committed Nov 15, 2024
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  5. refactor: write_ome_metadata

    @calvinchai
    calvinchai committed Nov 15, 2024
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Commits on Nov 18, 2024

  1. refactor: move unused function

    @calvinchai
    calvinchai committed Nov 18, 2024
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  2. refactor: cleanup

    @calvinchai
    calvinchai committed Nov 18, 2024
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  3. docs

    @calvinchai
    calvinchai committed Nov 18, 2024
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  4. fix: shape was concated to the list

    @calvinchai
    calvinchai committed Nov 18, 2024
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Commits on Nov 19, 2024

  1. docs: add annotations and fix lint error

    @calvinchai
    calvinchai committed Nov 19, 2024
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  2. fix: add dependency for psoct pipeline

    @calvinchai
    calvinchai committed Nov 19, 2024
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  3. fix: add dependency for psoct pipeline

    @calvinchai
    calvinchai committed Nov 19, 2024
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  4. feat: add multislice for psoct

    @calvinchai
    calvinchai committed Nov 19, 2024
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  5. docs

    @calvinchai
    calvinchai committed Nov 19, 2024
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  6. feat: lazy load input instead of loading all at the beginning

    @calvinchai
    calvinchai committed Nov 19, 2024
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  7. Update linc_convert/modalities/psoct/__init__.py 

    Co-authored-by: Kabilar Gunalan <[email protected]>
    @calvinchai @kabilar
    calvinchai and kabilar authored Nov 19, 2024
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  8. Update linc_convert/modalities/psoct/cli.py 

    Co-authored-by: Kabilar Gunalan <[email protected]>
    @calvinchai @kabilar
    calvinchai and kabilar authored Nov 19, 2024
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Commits on Nov 21, 2024

  1. Merge branch 'main' into oct_mat_to_zarr

    @balbasty
    balbasty committed Nov 21, 2024
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  2. Merge branch 'main' into oct_mat_to_zarr

    @balbasty
    balbasty committed Nov 21, 2024
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  3. MNT(pyproject) make psoct dep optional

    @balbasty
    balbasty committed Nov 21, 2024
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  4. FIX: wrap optional imports in try/catch

    @balbasty
    balbasty committed Nov 21, 2024
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  5. style fixes by ruff

    @balbasty @github-actions
    balbasty authored and github-actions[bot] committed Nov 21, 2024
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