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Fixing time stamps for the Multiscope pilot data #838

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3b70417
use cell_roi_id when no cell_specimen_id
matchings Oct 19, 2021
7f488c2
use cell_roi_ids for all dfs
matchings Oct 19, 2021
9f35907
revise metrics_mask plotting
matchings Oct 19, 2021
be88e5f
multi session dfs for learning project mouse
matchings Oct 19, 2021
5614866
change directory
matchings Oct 21, 2021
cd82874
fix cache usage
matchings Oct 21, 2021
3452244
load from lims not s3
matchings Oct 21, 2021
6a705e8
use session number
matchings Oct 21, 2021
ee01ee0
typo
matchings Oct 21, 2021
d16d4e0
load from lims
matchings Oct 21, 2021
b54e6f9
change default loading behavior to include dev data
matchings Oct 21, 2021
0dc377a
use learning project cache dir
matchings Oct 21, 2021
8fcde97
get learning proj experiments
matchings Oct 21, 2021
6ce84b1
set default env
matchings Oct 21, 2021
d8eec01
update for slurm
matchings Oct 21, 2021
93ab523
fix import
matchings Oct 21, 2021
ddf2063
add env
matchings Oct 21, 2021
afa6d8b
typo
matchings Oct 21, 2021
3313e1c
dont filter out expts we want
matchings Oct 21, 2021
5ddb7da
hack
matchings Oct 22, 2021
4710ec9
filter session types
matchings Oct 22, 2021
449624f
fix metadata_string
matchings Oct 22, 2021
d6c97b3
fix metadata_string again
matchings Oct 22, 2021
451c5a8
standardize filename for saving
matchings Oct 22, 2021
bf35b70
use csids
matchings Oct 22, 2021
863886e
change omission response window
matchings Oct 22, 2021
e427231
process omissions
matchings Oct 22, 2021
d874db3
longer walltime
matchings Oct 22, 2021
be03955
fix pop avgs plot
matchings Oct 22, 2021
9920a6b
Merge branch 'master' into learning_mFISH
matchings Feb 11, 2022
f3cc693
prep to produce QC plots
matchings Feb 11, 2022
a74b677
Merge branch 'mg_paper_figures' into learning_mFISH
matchings Feb 12, 2022
1641f9d
updates for container qc plots
matchings Feb 12, 2022
e229b28
stdout
matchings Feb 12, 2022
bc32c3b
typo
matchings Feb 12, 2022
bbca5d2
typo
matchings Feb 14, 2022
314ef28
use new directories
matchings Feb 14, 2022
ac2886d
filename with container id not expt
matchings Feb 15, 2022
81af976
dont reload expts table all the time
matchings Feb 15, 2022
fdc0a85
update cluster scripts for learning project data
matchings Feb 15, 2022
ffaae4c
typo
matchings Feb 15, 2022
3548113
test
matchings Feb 15, 2022
f2c5d2d
require expts table to be passed
matchings Feb 15, 2022
82384ef
cleanup
matchings Feb 16, 2022
f2e7076
generate expt_table if not provided
matchings Feb 16, 2022
de3ea4d
use session type instead of session number
matchings Feb 16, 2022
63fd5e9
minor updates
matchings Feb 17, 2022
db552ec
save plots to 'all' folder
matchings Feb 17, 2022
596f04a
expt plots for max projection and segmentation
matchings Feb 17, 2022
fda3203
typo
matchings Feb 17, 2022
5ce5dd8
missing import
matchings Feb 17, 2022
6700fbe
change save_dir
matchings Feb 17, 2022
b004cb4
test qc plots
matchings Feb 22, 2022
367ece4
run container plots again
matchings Mar 30, 2022
a5bd1a6
multi session dfs
matchings Mar 30, 2022
81bfddf
save stim response dfs
matchings Mar 30, 2022
6dd2f56
use mouse id instead of session id
matchings Mar 30, 2022
734e257
path mixup
matchings Mar 30, 2022
6d32d53
minor change
matchings Mar 30, 2022
8987768
slashes
matchings Apr 6, 2022
40919a0
updates to make multi session df
matchings Apr 27, 2022
ff9d026
dont filter omissions in mdf
matchings Apr 28, 2022
46ba321
add ability to include invalid ROIs in dataset and stim response df
matchings Apr 28, 2022
6a2c1cf
multi session df needs frame rate column
matchings Apr 29, 2022
cebac7c
adding option to provide hue_order to pop avgs plot
matchings Apr 29, 2022
a581ed8
document get_multi_session_df
matchings Jun 7, 2022
45aa5d4
run QC for MSN an TTN
matchings Jun 9, 2022
18f7366
run create multi session df
matchings Jun 10, 2022
b003b0b
typo in script
matchings Jun 11, 2022
963bf8a
exclude invalid ROIs by default
matchings Jun 11, 2022
c0ec976
document and update key plotting functions
matchings Jun 11, 2022
80e9de2
document mean response df and align argument names with stim_response_df
matchings Jun 11, 2022
4edd917
update plot title
matchings Jun 14, 2022
ad8ecbe
add stim response df notebook
matchings Jun 14, 2022
5aa3524
put notebooks in correct location
matchings Jun 14, 2022
d61c141
update stim response df loading in single cell plots
matchings Jun 20, 2022
2e2123f
dont invert masks in plot cell zoom
matchings Jun 20, 2022
3dc5636
more updates to stim response df plotting
matchings Jun 20, 2022
f6f1f28
update cell zoom fig
matchings Jun 20, 2022
d9bcc44
add alpha to cell zoom plot
matchings Jun 20, 2022
5e2c919
revise QC plotting to save per expt in addn to per container
matchings Jun 20, 2022
8fea656
use correct plot directory
matchings Jun 20, 2022
badd167
typo
matchings Jun 21, 2022
846f1fd
run just for suite2p mouse
matchings Jun 21, 2022
c72298b
exlude acq date from container QC
matchings Jun 22, 2022
952e655
print statements to debug saving
matchings Jun 30, 2022
f241b67
dont need to load cache when getting dataset
matchings Jun 30, 2022
99f7918
dont re-load dataset when getting metadata_string
matchings Jun 30, 2022
57114d8
run the rest of the QC plots
matchings Jun 30, 2022
3f2e6fa
more QC plots
matchings Jun 30, 2022
d281484
add corrected fluor to dff trace plots
matchings Jun 30, 2022
9128b58
use avg instead of mask in overlays
matchings Jun 30, 2022
96eac4b
plot traces and masks
matchings Jun 30, 2022
fded1d8
plots for golden mouse
matchings Jun 30, 2022
a9f5792
use doug's figrid tool for experiment summary
matchings Jun 30, 2022
666ba53
reorder QC plots
matchings Jun 30, 2022
58475aa
plots for golden mouse
matchings Jun 30, 2022
bf6f687
include experiment summary figure
matchings Jun 30, 2022
7bf36f7
run for gold, silver and bronze
matchings Jun 30, 2022
b0336bb
ditto
matchings Jun 30, 2022
6457aad
try exp summary again
matchings Jul 1, 2022
08a7d63
clean up paths
matchings Jul 1, 2022
c02e04a
QC plots for LAMF dev mouse
matchings Jul 1, 2022
19938d7
run save all container plots
matchings Jul 14, 2022
d800a02
add sesion type color map
matchings Jul 20, 2022
eea7df6
include omFISH 210 mice for processing
matchings Sep 12, 2022
216f672
lint
matchings Sep 12, 2022
313a6b1
lint
matchings Sep 12, 2022
5ac96a5
weird
matchings Sep 12, 2022
20c4a3d
load expts table from file
matchings Sep 25, 2022
d42acf0
debug
matchings Sep 25, 2022
2766f9b
debug
matchings Sep 25, 2022
d54441b
mouse_id as int
matchings Sep 25, 2022
de3673c
set index properly
matchings Sep 25, 2022
f6ea71b
updates to loading.get_data_dict()
matchings Oct 6, 2022
ed8862f
typo
matchings Oct 6, 2022
70d30b9
change default sdf window
matchings Oct 6, 2022
807b129
update conda
matchings Oct 6, 2022
c6fffd0
use correct conda env
matchings Oct 6, 2022
435addd
cleanup
matchings Oct 6, 2022
5e9c369
remove try except
matchings Oct 6, 2022
91ae9ea
try using container instead of project code
matchings Oct 6, 2022
635af73
backslashes
matchings Oct 6, 2022
788ea75
typo
matchings Oct 7, 2022
dde3cd4
print statements
matchings Oct 7, 2022
4d6d6a9
try enforcing types
matchings Oct 7, 2022
8918a49
update file saving
matchings Oct 7, 2022
4e0bdb1
function to get matched cells
matchings Oct 7, 2022
7eef9da
add single cell plots for matched cells
matchings Oct 7, 2022
2c47ea4
update mdf file name
matchings Oct 7, 2022
94ac4e8
typo
matchings Oct 7, 2022
cce4f95
edit file saving
matchings Oct 7, 2022
bc5f462
stupid mistake
matchings Oct 7, 2022
037f397
prints
matchings Oct 7, 2022
2b2e3fc
dont use extended stim presentations
matchings Oct 7, 2022
d67897c
LAMF only
matchings Oct 7, 2022
187ee65
single cell plots
matchings Oct 7, 2022
d21b2f2
fix paths
matchings Oct 7, 2022
75b9527
imports
matchings Oct 7, 2022
59ad51d
more imports
matchings Oct 7, 2022
3788a53
erros
matchings Oct 7, 2022
69d2ae5
load expts from file
matchings Oct 7, 2022
ecfdbd1
need cache
matchings Oct 7, 2022
38845be
cache
matchings Oct 7, 2022
e37fb92
read cells table from file
matchings Oct 7, 2022
9874d9e
create data dictionary
matchings Oct 7, 2022
e43dd0f
print statements
matchings Oct 7, 2022
ac3a5a4
set index
matchings Oct 7, 2022
14b5c91
create data_dict before looping
matchings Oct 7, 2022
fa9882c
ophys_container not expt_container
matchings Oct 7, 2022
076cf4c
typo
matchings Oct 7, 2022
d7d0e9c
wrong directory
matchings Oct 7, 2022
6ca2a85
update cell zoom panel
matchings Oct 7, 2022
861693c
function to get simple genotype
matchings Oct 7, 2022
6bfbf4b
update matched cell plots
matchings Oct 7, 2022
96303d6
fix cell zoom
matchings Oct 7, 2022
155acf5
last change
matchings Oct 7, 2022
98a6add
load expts from file
matchings Oct 9, 2022
195f6ed
multi session df for omFISH mice
matchings Oct 9, 2022
d8db7fa
multi session df LAMF development mice
matchings Oct 9, 2022
9109177
functions to simplify genotype and label dox mice
matchings Oct 10, 2022
fa5c544
multi session df with images
matchings Oct 10, 2022
ef533d5
update single cell plots
matchings Oct 10, 2022
d9e8ff8
typo
matchings Oct 10, 2022
34675a3
ophys container id not expt
matchings Oct 10, 2022
7b3985d
add new matched cell plot with mdfs
matchings Oct 10, 2022
9044ea6
container qc plots
matchings Oct 10, 2022
053c16f
multi session df matched cell figs
matchings Oct 10, 2022
a7e1e94
import
matchings Oct 10, 2022
76a7dd7
minor
matchings Oct 10, 2022
ce2bf3c
add cell list to tuning curve heatmap
matchings Oct 10, 2022
bd52f08
wrong conda
matchings Oct 10, 2022
1c02bdd
load expts from file
matchings Oct 10, 2022
73c32ba
error
matchings Oct 10, 2022
2aeea0f
run plots for omFISH
matchings Oct 10, 2022
b8245dd
minor changes to plots and such
matchings Oct 14, 2022
abacb91
paths
matchings Nov 9, 2022
1572013
use BehaviorOphysExperimentDev
matchings Apr 25, 2023
e8f1800
multi_session_df attempt
matchings Apr 25, 2023
f284870
typo
matchings Apr 25, 2023
2bab867
remove skip eye tracking arg
matchings Apr 25, 2023
6ea921b
try original dataset object
matchings Apr 25, 2023
35b8fa0
always save mdf
matchings Apr 26, 2023
890dac0
fixed time stamps
jkim0731 Sep 11, 2023
9a96e0b
Merge branch 'learning_mFISH' of https://github.com/AllenInstitute/vi…
jkim0731 Sep 11, 2023
abffe25
switch directories
matchings Nov 29, 2023
80ce0a8
remove container_id from multi session df creation
matchings Feb 21, 2024
f346e4f
remove container_id from run script
matchings Feb 21, 2024
a3aebbe
Auto stash before merge of "finalize_fig_2" and "origin/finalize_fig_2"
matchings Feb 27, 2024
f9f6b2f
update convert for LAMF
matchings Jun 18, 2024
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set default env
  • Loading branch information
matchings committed Oct 21, 2021
commit 6ce84b17df6179c2bcdb0a21921d744e9b44b3f7
Original file line number Diff line number Diff line change
@@ -10,7 +10,7 @@


parser = argparse.ArgumentParser(description='run container qc plot generation functions on the cluster')
parser.add_argument('--env', type=str, default='', metavar='name of conda environment to use')
parser.add_argument('--env', type=str, default='visual_behavior_sdk', metavar='name of conda environment to use')
parser.add_argument('--scriptname', type=str, default='save_all_container_plots.py', metavar='name of script to run (must be in same folder)')
parser.add_argument("--plots", type=str, default=None, metavar='plot name to generate')