Skip to content

Commit

Permalink
after reviewers, fit_kernels as reference for parameters used in resp…
Browse files Browse the repository at this point in the history 
…onse detection
  • Loading branch information
@francescorandi
francescorandi committed Sep 3, 2023
1 parent f11bbee commit 5ca97c7
Showing 1 changed file with 4 additions and 80 deletions.
84 changes: 4 additions & 80 deletions pipelines/fit_kernels_multi_datasets.sh
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,93 +3,17 @@
echo "These scripts expect that you have run identify_stim_neurons.py"

full_array=(
## 0
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210826/pumpprobe_20210826_145453/ # F unc13 A12 mutant
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210826/pumpprobe_20210826_161811/ # F unc13 A12 mutant
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210824/pumpprobe_20210824_104000/ # F
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210824/pumpprobe_20210824_114940/ # F
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210824/pumpprobe_20210824_144628/ # F
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210824/pumpprobe_20210824_161919/ # F
/projects/LEIFER/Sophie/NewRecordings/20210825/pumpprobe_20210825_123600/ # S
## 1
/projects/LEIFER/Sophie/NewRecordings/20210825/pumpprobe_20210825_150349/ # S median
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210827/pumpprobe_20210827_104408/ # F median
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210827/pumpprobe_20210827_115857/ # F median
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210827/pumpprobe_20210827_142226/ # F median
/projects/LEIFER/Sophie/NewRecordings/20210830/pumpprobe_20210830_111646/ # S median
/projects/LEIFER/Sophie/NewRecordings/20210830/pumpprobe_20210830_144155/ # S median
/projects/LEIFER/Sophie/NewRecordings/20210830/pumpprobe_20210830_161543/ # S median
## 2 median
/projects/LEIFER/Sophie/NewRecordings/20210902/pumpprobe_20210902_115146/ # S median
/projects/LEIFER/Sophie/NewRecordings/20210909/pumpprobe_20210909_102637/ # S median
/projects/LEIFER/Sophie/NewRecordings/20210913/pumpprobe_20210913_105324/ # S median
/projects/LEIFER/Sophie/NewRecordings/20210913/pumpprobe_20210913_161934/ # S median
## 2 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210903/pumpprobe_20210903_153005/ # F 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210907/pumpprobe_20210907_110334/ # F 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20210907/pumpprobe_20210907_141336/ # F 30
/projects/LEIFER/Sophie/NewRecordings/20210917/pumpprobe_20210917_104948/ # S 30
## 3 30
/projects/LEIFER/Sophie/NewRecordings/20210917/pumpprobe_20210917_132736/ # S 30
/projects/LEIFER/Sophie/NewRecordings/20210928/pumpprobe_20210928_105933/ # S 30
/projects/LEIFER/Sophie/NewRecordings/20210928/pumpprobe_20210928_134411/ # S 30
/projects/LEIFER/Sophie/NewRecordings/20211008/pumpprobe_20211008_115929/ # S 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211102/pumpprobe_20211102_101248/ # F 30 lambda 5 RID D20 innexins
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211102/pumpprobe_20211102_152524/ # F 30 lambda 5 RID D20 innexins
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211104/pumpprobe_20211104_163944/ # F 30
## 4
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211226_Sophie/pumpprobe_20211216_164305/ # 30 F unc31 mutant
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_101730/ # F 30 unc31 mutant 508.8.9
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_112922/ # F 30 unc31 mutant 508.8.9
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_142740/ # F 30 unc31 mutant 508.8.9
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_153037/ # F 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_165125/ # F 30 unc31 mutant
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220120/pumpprobe_20220120_135951/ # F 30
## 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220120/pumpprobe_20220120_150453/ # F 30 RID
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220120/pumpprobe_20220120_151357/ # F 30
/projects/LEIFER/Sophie/NewRecordings/20211022/pumpprobe_20211022_140822/ # S 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220211/pumpprobe_20220211_094256/ # F 30 RID unc31 mutant 510.9.b
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220211/pumpprobe_20220211_141039/ # F 30 RID unc31 mutant 510.9.b
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220211/pumpprobe_20220211_151211/ # F 30 lambda 5 RID unc31 mutant 510.9.b
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220224/pumpprobe_20220224_140933/ # F 30 lambda 5 RIC inx1 mutant innexins
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220224/pumpprobe_20220224_153744/ # F 30 lambda 5 RIC inx1 mutant innexins
/projects/LEIFER/Sophie/NewRecordings/20220126/pumpprobe_20220126_153426/ # S 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220330/pumpprobe_20220330_110253/ # F 30 lambda 5
## 6
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220330/pumpprobe_20220330_123606/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220330/pumpprobe_20220330_164449/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220331/pumpprobe_20220331_114306/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220331/pumpprobe_20220331_142924/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220331/pumpprobe_20220331_153103/ # F 30 lambda 5
## 7
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220405/pumpprobe_20220405_100245/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220405/pumpprobe_20220405_110704/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220405/pumpprobe_20220405_125435/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220405/pumpprobe_20220405_143326/ # F 30 lambda 5
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220412/pumpprobe_20220412_112143/ # F 30 lambda 5 RID unc31 mutant 510.9.b
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220422/pumpprobe_20220422_104335/ # F 30 lambda 5 AFD unc31 mutant 510.9.b
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211128/pumpprobe_20211128_112504/
...and other folders
)

my_array=(
## 4
#/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20211226_Sophie/pumpprobe_20211216_164305/ # 30 F unc31 mutant
#/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_101730/ # F 30 unc31 mutant 508.8.9
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_112922/ # F 30 unc31 mutant 508.8.9
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_142740/ # F 30 unc31 mutant 508.8.9
#/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_153037/ # F 30
/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220113/pumpprobe_20220113_165125/ # F 30 unc31 mutant
#/projects/LEIFER/francesco/pumpprobe/AKSxneuropal/20220120/pumpprobe_20220120_135951/ # F 30
)

for folder in "${my_array[@]}"
for folder in "${full_array[@]}"
do
echo ""
echo "##################"
echo "processing $folder"
#echo "just updating"
echo ""
python ../scripts/fconnectivity/responses_detect.py $folder --signal:green -y --ampl-min-time:4 --ampl-thresh:1.3 --deriv-min-time:4 --deriv-thresh:0.02 --smooth-mode:sg_causal --smooth-n:13 --smooth-poly:1 --matchless-nan-th:0.5 --matchless-nan-th-added-only
python ../scripts/fconnectivity/responses_detect.py $folder --signal:green -y --ampl-min-time:4 --ampl-thresh:1.3 --deriv-min-time:4 --deriv-thresh:0.02 --smooth-mode:sg_causal --smooth-n:13 --smooth-poly:1 --matchless-nan-th:0.5 --matchless-nan-th-added-only --nan-th:0.05
python ../scripts/fconnectivity/fit_responses_unconstrained_eci.py $folder --signal:green --matchless-nan-th:0.5 --matchless-nan-th-added-only
python ../scripts/fconnectivity/fit_responses_constrained_stim_eci.py $folder --signal:green --skip-if-not-manually-located --matchless-nan-th:0.5 --matchless-nan-th-added-only
done

0 comments on commit 5ca97c7

Please sign in to comment.