Nsetm 2196 synapse class #43
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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 <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
Codecov Report
@@ Coverage Diff @@
## main #43 +/- ##
=======================================
Coverage ? 97.76%
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Files ? 22
Lines ? 1385
Branches ? 0
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Hits ? 1354
Misses ? 31
Partials ? 0
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mgeplf
reviewed
Aug 4, 2023
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I think the existing synapses were inhibitory, no?
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I switched it around several times, you are more likely to be correct than me 😊
| @@ -49,7 +59,7 @@ def _check_probability_map_consistency( | |||
| """ | |||
| check_probability_map_sanity(probability_map) | |||
|
|
|||
| _, df_molecular_types = zip(*probability_map.index) | |||
| _, df_molecular_types, _ = zip(*probability_map.index) | |||
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similar here: probability_map.index.get_level_values('molecular_types')?
|
@mgeplf I think we should merge this one to make the densities usable |
mgeplf
approved these changes
Aug 23, 2023
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