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ENH: Serialize+parallelize 4D apply() into 3D+t and add 'low memory' loading #215

Merged
merged 24 commits into from
Aug 10, 2024
Merged

ENH: Serialize+parallelize 4D apply() into 3D+t and add 'low memory' loading #215

merged 24 commits into from
Aug 10, 2024

Commits on Jul 23, 2024

  1. wip: initiate implementation

    @oesteban
    oesteban committed Jul 23, 2024
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Commits on Jul 24, 2024

  1. enh: draft implementation of serialize 4d

    Julien Marabotto authored and Julien Marabotto committed Jul 24, 2024
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Commits on Jul 25, 2024

  1. fix: passes more tests, more suggestions in progress

    Julien Marabotto authored and Julien Marabotto committed Jul 25, 2024
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  2. fix: pass tests

    Julien Marabotto authored and Julien Marabotto committed Jul 25, 2024
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  3. fix: pass tests, serialization implemented

    Julien Marabotto authored and Julien Marabotto committed Jul 25, 2024
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Commits on Jul 29, 2024

  1. wip: initiate implementation

    @oesteban
    oesteban committed Jul 29, 2024
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  2. Merge remote-tracking branch 'jmarabotto/patch/oesteban-pr' into enh/… 

    …reenable-parallelization-apply-214
    @oesteban
    oesteban committed Jul 29, 2024
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Commits on Jul 30, 2024

  1. enh: integrating @jmarabotto's code

    @oesteban
    oesteban committed Jul 30, 2024
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  2. fix: ensure output dtype when resampling

    @oesteban
    oesteban committed Jul 30, 2024
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  3. fix: resolve some failing tests

    @oesteban
    oesteban committed Jul 30, 2024
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Commits on Jul 31, 2024

  1. fix: ensure __len__ is defined for all transforms``

    @oesteban
    oesteban committed Jul 31, 2024
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  2. fix: clarify what is a 3D transform chain and a 4D transform 

    3D transform chains resulting of composing several transformations
(e.g., affine and deformation fields in spatial normalization) should
not be split into its components.

This is in contrast to lists of 3D transforms such as head-motion
correcting affines, where each applies to one timepoint.
These should be considered 4D and in some future they may integrate
slice timing correction in them.
    @oesteban
    oesteban committed Jul 31, 2024
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  3. maint: reorganize tests around the spun-off apply

    @oesteban
    oesteban committed Jul 31, 2024
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  4. sty: format changed files

    @oesteban
    oesteban committed Jul 31, 2024
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  5. Merge remote-tracking branch 'upstream/master' into enh/reenable-para… 

    …llelization-apply-214
    @oesteban
    oesteban committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. enh: expand test coverage

    @oesteban
    oesteban committed Aug 1, 2024
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  2. enh: prepare code for easy parallelization with a process pool executor 

    Resolves: #214.
    @oesteban
    oesteban committed Aug 1, 2024
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  3. enh: create process pool

    @oesteban
    oesteban committed Aug 1, 2024
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  4. Merge pull request #220 from nipy/enh/reenable-parallelization-apply-… 

    …214-parallel

ENH: Parallelize serialized 3D+t transforms
    @oesteban
    oesteban authored Aug 1, 2024
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  5. enh: expand test coverage

    @oesteban
    oesteban committed Aug 1, 2024
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Commits on Aug 2, 2024

  1. sty: add type annotations

    @oesteban
    oesteban committed Aug 2, 2024
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  2. enh: implement a memory limitation mechanism in loading data 

    Resolves: #218.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
    @oesteban @effigies
    oesteban and effigies committed Aug 2, 2024
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  3. Merge pull request #221 from nipy/enh/reenable-parallelization-apply-… 

    …214-dtypes

ENH: Implement a memory limitation mechanism in loading data
    @oesteban
    oesteban authored Aug 2, 2024
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Commits on Aug 6, 2024

  1. enh: port from process pool into asyncio concurrent 

    Co-authored-by: Chris Markiewicz <effigies@gmail.com>
    @oesteban @effigies
    oesteban and effigies committed Aug 6, 2024
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