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Nsetm 2196 synapse class #43

Merged
merged 66 commits into from
Aug 23, 2023
Merged

Nsetm 2196 synapse class #43

merged 66 commits into from
Aug 23, 2023

Commits on Jun 20, 2023

  1. pytest posargs

    @edasubert
    edasubert committed Jun 20, 2023
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  2. extract densities adjustments

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    edasubert committed Jun 20, 2023
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Commits on Jun 21, 2023

  1. properly config tools

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    edasubert committed Jun 21, 2023
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  2. lint

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    edasubert committed Jun 21, 2023
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Commits on Jun 23, 2023

  1. new probability_map

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    edasubert committed Jun 23, 2023
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Commits on Jun 29, 2023

  1. use regions

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    edasubert committed Jun 29, 2023
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Commits on Jun 30, 2023

  1. remove "with_region"

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    edasubert committed Jun 30, 2023
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  2. revert test to be closer to original

    @edasubert
    edasubert committed Jun 30, 2023
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  3. remove lamp5 synthesis

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    edasubert committed Jun 30, 2023
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  4. Merge branch 'NSETM-2196-update-create-from-probability-map' into NSE… 

    …TM-2196-update-create-from-probability-map-probability-map
    @edasubert
    edasubert committed Jun 30, 2023
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  5. add lamp5

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    edasubert committed Jun 30, 2023
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  6. Merge branch 'NSETM-2196-update-create-from-probability-map' into NSE… 

    …TM-2196-update-create-from-probability-map-probability-map
    @edasubert
    edasubert committed Jun 30, 2023
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  7. approx_lamp5

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    edasubert committed Jun 30, 2023
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Commits on Jul 4, 2023

  1. switch to region map

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    edasubert committed Jul 4, 2023
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Commits on Jul 10, 2023

  1. fixes to probability map

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    edasubert committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. add vip to probability map

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    edasubert committed Jul 11, 2023
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  2. lint

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    edasubert committed Jul 11, 2023
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  3. mypy issue

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    edasubert committed Jul 11, 2023
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Commits on Jul 12, 2023

  1. cleanup

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    edasubert committed Jul 12, 2023
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  2. restore a file for a test

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    edasubert committed Jul 12, 2023
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Commits on Jul 14, 2023

  1. speed up density creation

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    mgeplf committed Jul 14, 2023
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  2. Stop using as many config files 

    new command line:
    OUTPUT=output/create-from-probability-map
    DATA=../data
    atlas-densities  \
     mtype-densities -vv create-from-probability-map                              \
        --hierarchy-path=$DATA/1.json                                             \
        --annotation-path=$DATA/ccfv2/annotation_25.nrrd                          \
        --probability-map probability_map.csv                                     \
        --marker gad67 $DATA/create-from-probability-map/gad67.nrrd               \
        --marker sst $DATA/create-from-probability-map/sst.nrrd                   \
        --marker vip $DATA/create-from-probability-map/vip.nrrd                   \
        --marker approx_lamp5 $DATA/create-from-probability-map/approx_lamp5.nrrd \
        --marker pv $DATA/create-from-probability-map/pv.nrrd                     \
        --output-dir=$OUTPUT

Thus `--metadata-path` and `--mtypes-config-path` aren't used any more
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    mgeplf committed Jul 14, 2023
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  3. logger

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    edasubert committed Jul 14, 2023
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  4. lint

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    edasubert committed Jul 14, 2023
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  5. try parallelizing w/ joblib. 

    Likely can be tuned better.
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    mgeplf committed Jul 14, 2023
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Commits on Jul 17, 2023

  1. speed up density creation (#37) 

    * speed up density creation

* :-|

---------

Co-authored-by: Mike Gevaert <michael.gevaert@epfl.ch>
    @edasubert @mgeplf
    edasubert and mgeplf authored Jul 17, 2023
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  2. Stop using as many config files (#38) 

    * speed up density creation

* Stop using as many config files

new command line:
    OUTPUT=output/create-from-probability-map
    DATA=../data
    atlas-densities  \
     mtype-densities -vv create-from-probability-map                              \
        --hierarchy-path=$DATA/1.json                                             \
        --annotation-path=$DATA/ccfv2/annotation_25.nrrd                          \
        --probability-map probability_map.csv                                     \
        --marker gad67 $DATA/create-from-probability-map/gad67.nrrd               \
        --marker sst $DATA/create-from-probability-map/sst.nrrd                   \
        --marker vip $DATA/create-from-probability-map/vip.nrrd                   \
        --marker approx_lamp5 $DATA/create-from-probability-map/approx_lamp5.nrrd \
        --marker pv $DATA/create-from-probability-map/pv.nrrd                     \
        --output-dir=$OUTPUT

Thus `--metadata-path` and `--mtypes-config-path` aren't used any more

* :-|

* tests

* values should not change

* unique region acronyms

* :-|

---------

Co-authored-by: Mike Gevaert <michael.gevaert@epfl.ch>
    @edasubert @mgeplf
    edasubert and mgeplf authored Jul 17, 2023
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  3. Merge branch 'NSETM-2196-update-create-from-probability-map' into NSE… 

    …TM-2196-update-create-from-probability-map-probability-map
    @edasubert
    edasubert committed Jul 17, 2023
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  4. logger

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    edasubert committed Jul 17, 2023
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  5. remove logger

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    edasubert committed Jul 17, 2023
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  6. Merge branch 'NSETM-2196-update-create-from-probability-map-probabili… 

    …ty-map' into parallel
    @edasubert
    edasubert committed Jul 17, 2023
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  7. merge

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    edasubert committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. parallel

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    edasubert committed Jul 18, 2023
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  2. requirements

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    edasubert committed Jul 18, 2023
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Commits on Jul 19, 2023

  1. multiple probability maps

    @edasubert
    edasubert committed Jul 19, 2023
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  2. undo shrink

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    edasubert committed Jul 19, 2023
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  3. no more 3.7

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    edasubert committed Jul 19, 2023
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  4. no more 3.7 - second try

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    edasubert committed Jul 19, 2023
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  5. no more 3.7 - 3rd try

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    edasubert committed Jul 19, 2023
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  6. remove joblib name

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    edasubert committed Jul 19, 2023
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  7. remove comment

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    edasubert committed Jul 19, 2023
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  8. Merge branch 'NSETM-2196-update-create-from-probability-map-probabili… 

    …ty-map' into parallel
    @edasubert
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  9. Merge branch 'parallel' into NSETM-2196-multiple-probability-maps

    @edasubert
    edasubert committed Jul 19, 2023
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  10. clean tests

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    edasubert committed Jul 19, 2023
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  11. restore metadata

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    edasubert committed Jul 19, 2023
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Commits on Jul 20, 2023

  1. restore metadata

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  2. Merge branch 'NSETM-2196-update-create-from-probability-map-probabili… 

    …ty-map' into parallel
    @edasubert
    edasubert committed Jul 20, 2023
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  3. Merge branch 'parallel' into NSETM-2196-multiple-probability-maps

    @edasubert
    edasubert committed Jul 20, 2023
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  4. restore 3.8

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    edasubert committed Jul 20, 2023
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Commits on Jul 21, 2023

  1. metype, | separator

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    edasubert committed Jul 21, 2023
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  2. save after

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    edasubert committed Jul 21, 2023
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  3. tests and logs

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    edasubert committed Jul 21, 2023
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Commits on Jul 24, 2023

  1. Merge remote-tracking branch 'origin/main' into NSETM-2196-update-output

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    edasubert committed Jul 24, 2023
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  2. Merge branch 'main' into NSETM-2196-update-output

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    edasubert committed Jul 24, 2023
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  3. docs

    @edasubert
    edasubert committed Jul 24, 2023
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  4. revert utils

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    edasubert committed Jul 24, 2023
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  5. test

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    edasubert committed Jul 24, 2023
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  6. :-|

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    edasubert committed Jul 24, 2023
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Commits on Jul 27, 2023

  1. synapse class

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    edasubert committed Jul 27, 2023
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  2. Merge branch 'main' into NSETM-2196-synapse-class

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    edasubert committed Jul 27, 2023
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  3. lint

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    edasubert committed Jul 27, 2023
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Commits on Jul 31, 2023

  1. update timestamp

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    edasubert committed Jul 31, 2023
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  2. include synapse class in metadata

    @edasubert
    edasubert committed Jul 31, 2023
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  3. remove all option

    @edasubert
    edasubert committed Jul 31, 2023
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  4. revert suffix to synapse_class

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    edasubert committed Jul 31, 2023
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Commits on Aug 7, 2023

  1. review

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    edasubert committed Aug 7, 2023
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