This repository was archived by the owner on Feb 26, 2025. It is now read-only.
Nsetm 2196 expand output#44
Open
edasubert wants to merge 66 commits into
Open
Conversation
…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 <michael.gevaert@epfl.ch>
* 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>
…TM-2196-update-create-from-probability-map-probability-map
…ty-map' into parallel
…ty-map' into parallel
mgeplf
reviewed
Aug 4, 2023
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
No description provided.