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Merge branch 'master' of https://github.com/deisseroth-lab/two-photon
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@drinnenb
drinnenb committed Feb 15, 2021
2 parents 66022f0 + 1eba3f4 commit 95e3050
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118 changes: 54 additions & 64 deletions notebooks/check_artefact_removal.ipynb
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16 changes: 10 additions & 6 deletions two-photon/process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,13 +4,13 @@
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --preprocess
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --run_suite2p
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --run_suite2p --prev_recording 20200310M88:regL23-000
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --backup_output
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --backup_output --ETL_depths=30_0_30
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --backup_data
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200310M88:regL23-000 --backup_dir=O:\users\drinnenb\Data2p\ --backup_hdf5
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200325M89:VRmm-000 --backup_dir=O:\users\drinnenb\Data2p\ --preprocess --run_suite2p --backup_output --backup_data --zip_data
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200325M89:playback-000 --backup_dir=O:\users\drinnenb\Data2p\ --preprocess --run_suite2p --prev_recording 202003M89:regL23-000
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200325M89:playback-000 --backup_dir=O:\users\drinnenb\Data2p\ --rip --preprocess --run_suite2p --prev_recording 20200325M89:VRmm-000 --backup_output --backup_data
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200325M89:playback-000 --backup_dir=O:\users\drinnenb\Data2p\ --rip --preprocess --settle_time --backup_output
# python Documents\GitHub\two-photon\two-photon\process.py --input_dir E:\AD --output_dir E:\AD\output --recording 20200325M89:playback-000 --backup_dir=O:\users\drinnenb\Data2p\ --rip --preprocess --settle_time=5 --backup_output

import argparse
from datetime import datetime
Expand Down Expand Up @@ -112,7 +112,7 @@ def get_dirname_hdf5(sess_name, rec_name):
fname_hdf5 = dirname_hdf5 / 'data' / 'data.h5'
if args.preprocess:
preprocess(basename_input, dirname_output, fname_csv, fname_uncorrected_hdf5, fname_hdf5, mdata,
args.artefact_buffer*mdata['period'], args.artefact_shift*mdata['period'], args.channel, stim_channel_name, args.settle_time)
args.artefact_buffer*mdata['period']*1000/mdata['size']['y_px'], args.artefact_shift*mdata['period'], args.channel, stim_channel_name, args.settle_time)
if args.run_suite2p:
data_files = []
for prev_recording in args.prev_recording:
Expand Down Expand Up @@ -143,7 +143,7 @@ def get_dirname_hdf5(sess_name, rec_name):
backup(trial_order_path,dirname_backup / 'trial_order')
# backup_pattern(slm_root, slm_trial_order_pattern, dirname_backup / 'trial_order')

backup_done_file = args.backup_dir / 'backup_done' / f'{session_name}_{recording_name}.backup_done'
backup_done_file = args.backup_dir / 'backup_done' / f'{session_name}_{recording_name}_ETL{args.ETL_depths}.backup_done'
backup_done_file.parent.mkdir(parents=True, exist_ok=True)
logger.info('Creating backup_done file: %s', backup_done_file)
backup_done_file.touch()
Expand Down Expand Up @@ -313,15 +313,19 @@ def parse_args():
default=0,
help='Amount of time at the beginning of an aquisition window to ignore while the hardware is settling.')

group.add_argument('--artefact_buffer', type=float, default=35, help='Time to exclude following calculated artefact')
group.add_argument('--artefact_shift', type=float, default=2, help='Time to shift artefact position from nominal.')
group.add_argument('--artefact_buffer', type=float, default=20, help='Pixel rows to exclude following calculated artefact, will be converted into ms later')
group.add_argument('--artefact_shift', type=float, default=1, help='Pixel rows to shift artefact position from nominal, will be converted into ms later')

group.add_argument('--backup_data', action='store_true', help='Backup all input data (post-ripping)')
group.add_argument('--backup_hdf5',
action='store_true',
help='Backup hdf5 formatted data (with and without artefact removal)')
group.add_argument('--backup_output', action='store_true', help='Backup all output processing')
group.add_argument('--backup_dir', type=pathlib.Path, default='', help='Remote dirname to sync results to.')
group.add_argument('--ETL_depths',
type=str,
help=('ETL depth for each plane in um, separated by _, only used for .backup_done file name '
'e.g. -30_0_30'))

# Temporary argument for testing. If it works, leave it on by default and remove flag.
group.add_argument('--zip_data',
Expand Down

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