Nsetm 2196 expand output #44
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…TM-2196-update-create-from-probability-map-probability-map
…TM-2196-update-create-from-probability-map-probability-map
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
Likely can be tuned better.
* speed up density creation * :-| --------- Co-authored-by: Mike Gevaert <[email protected]>
* 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 <[email protected]>
…TM-2196-update-create-from-probability-map-probability-map
…ty-map' into parallel
…ty-map' into parallel
mgeplf
reviewed
Aug 4, 2023
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