def run(exptfilename):
foldname = []
filenames = []
foldname, filenames = re.read_exptlist(exptfilename,
lines_per_expt=3,
fileline=1)
for i in range(len(foldname)):
# do matlab stuff to save cropping rectangles
print('hope you saved a cropping rectangle for ' + foldname[i])
for i in range(len(foldname)):
matlab_options = "options.green_only = 0; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; "
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames[i]) + ",options); exit" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids = [str(x) for x in filenames[i]]
rpt.process_data(animalid,
date,
expt_ids,
nchannels=1,
delete_raw=True,
result_base=result_fold,
raw_base=raw_fold)
def run(exptfilename):
foldname = []
filenames = []
foldname, filenames = re.read_exptlist(exptfilename,
lines_per_expt=3,
fileline=1)
# for i in range(len(foldname)):
# # do matlab stuff to save cropping rectangles
# print('now saving a cropping rectangle for ' + foldname[i])
for i in range(len(foldname)):
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids = [str(x) for x in filenames[i]]
subfold = '_'.join(expt_ids)
thisfold = suite2p_fold + animalid + '/' + date + '/' + subfold + '/'
save_meanImg(thisfold)
matlab_cmd = '"' + "s2p_output_to_opto_corrected_rois('" + thisfold + "','datafold','" + matfile_fold + "'); exit;" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
def run(exptfilename,
diameter=15,
sbx_fold='/home/mossing/modulation/2P/',
suite2p_fold='/home/mossing/data1/suite2P/',
fast_disk='/home/mossing/data_ssd/suite2P/bin/',
matfile_fold='/home/mossing/modulation/matfiles/'):
raw_fold = suite2p_fold + 'raw/'
result_fold = suite2p_fold + 'results/'
foldname = []
filenames = []
foldname, filenames = re.read_exptlist(exptfilename,
lines_per_expt=3,
fileline=1)
for i in range(len(foldname)):
# do matlab stuff to save cropping rectangles
print('hope you saved a cropping rectangle for ' + foldname[i])
for i in range(len(foldname)):
try:
#shutil.rmtree(fast_disk+'suite2p')
os.system('rm -rf ' + fast_disk + 'suite2p')
print('fast disk contents deleted')
except:
print('fast disk location empty')
matlab_options = "options.green_only = 0; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; options.matfile_foldbase = '" + matfile_fold + "';"
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames[i]) + ",options); exit; " + '"' # exit
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids = [str(x) for x in filenames[i]]
rpt.process_data(animalid,
date,
expt_ids,
nchannels=1,
delete_raw=True,
result_base=result_fold,
raw_base=raw_fold,
diameter=diameter,
fast_disk=fast_disk)
try:
#shutil.rmtree(fast_disk+'suite2p')
os.system('rm -rf ' + fast_disk + 'suite2p')
print('fast disk contents deleted')
except:
print('fast disk location empty')
def run(exptfilename):
foldname = []
filenames = []
foldname,filenames = re.read_exptlist(exptfilename,lines_per_expt=3,fileline=1)
for i in range(len(foldname)):
# do matlab stuff to save cropping rectangles
print('now saving a cropping rectangle for ' + foldname[i])
thisfold = matfile_fold+foldname[i]
if not os.path.exists(thisfold):
os.makedirs(thisfold)
matlab_cmd = '"' + "save_and_transfer_crop_remote('" + thisfold + "','" + sbx_fold + "',true); exit;" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
import sys
import os
sys.path.insert(0, '/home/mossing/code/adesnal')
import run_pipeline_tiffs as rpt
import read_exptlist as re
suite2p_fold = '/home/mossing/data1/suite2P/'
sbx_fold = '/home/mossing/modulation/2P/'
raw_fold = suite2p_fold + 'raw/'
result_fold = suite2p_fold + 'results/'
foldname = []
filenames = []
foldname, filenames = re.read_exptlist('exptlist_191118.txt',
lines_per_expt=4,
fileline=(1, 2)) # 190709
for i in range(len(foldname)):
matlab_options = "options.green_only = 1; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; "
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames[i]) + ",options); exit" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids = [str(x) for x in filenames[i]]
import os
sys.path.insert(0, '/home/mossing/code/adesnal')
import run_pipeline_tiffs as rpt
import read_exptlist as re
suite2p_fold = '/home/mossing/data1/suite2P/'
sbx_fold = '/home/mossing/modulation/2P/'
raw_fold = suite2p_fold + 'raw/'
result_fold = suite2p_fold + 'results/'
foldname = []
filenames = []
foldname, filenames = re.read_exptlist('exptlist_190623.txt',
lines_per_expt=4,
fileline=2)
for i in range(len(foldname)):
matlab_options = "options.green_only = 0; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; "
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames[i]) + ",options); exit" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids = [str(x) for x in filenames[i]]
def run(exptfilename,
diameter=15,
sbx_fold='/home/mossing/modulation/2P/',
suite2p_fold='/home/mossing/data1/suite2P/',
fast_disk='/home/mossing/data_ssd/suite2P/bin',
matfile_fold='/home/mossing/modulation/matfiles/'):
raw_fold = suite2p_fold + 'raw/'
result_fold = suite2p_fold + 'results/'
foldname = []
filenames = []
foldname, filenames_1ch = re.read_exptlist(
exptfilename, lines_per_expt=4,
fileline=(1, 2)) # should this be (1,2) ?
_, filenames_2ch = re.read_exptlist(exptfilename,
lines_per_expt=4,
fileline=2)
for i in range(len(foldname)):
fileparts = foldname[i].split('/')
date = fileparts[0]
animalid = fileparts[1]
expt_ids_1ch = [str(x) for x in filenames_1ch[i]]
expt_ids_2ch = [str(x) for x in filenames_2ch[i]]
try:
shutil.rmtree(fast_disk + '/suite2p')
os.system('rm -rf ' + fast_disk + '/suite2p')
print('fast disk contents deleted')
except:
print('fast disk location empty')
matlab_options = "options.green_only = 1; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; options.matfile_foldbase = '" + matfile_fold + "';"
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames_1ch[i]) + ",options); exit" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
try:
shutil.rmtree(fast_disk + '/suite2p')
os.system('rm -rf ' + fast_disk + '/suite2p')
print('fast disk contents deleted')
except:
print('fast disk location empty')
rpt.process_data(animalid,
date,
expt_ids_1ch,
delete_raw=delete_raw,
raw_base=raw_fold,
result_base=result_fold,
diameter=diameter,
nchannels=1,
fast_disk=fast_disk)
matlab_options = "addpath(genpath('~/adesnal')); options.green_only = 0; options.targetfold = '" + raw_fold + "'; options.data_foldbase = '" + sbx_fold + "'; options.matfile_foldbase = '" + matfile_fold + "';"
matlab_cmd = '"' + matlab_options + "gen_2channel_tiffs('" + foldname[
i] + "'," + str(filenames_2ch[i]) + ",options); exit" + '"'
print(matlab_cmd)
os.system('matlab -r ' + matlab_cmd)
rpt.add_2ch_data(animalid,
date,
expt_ids_1ch,
expt_ids_2ch,
raw_base=raw_fold,
result_base=result_fold,
delete_raw=delete_raw,
diameter=diameter,
fast_disk=fast_disk)
try:
shutil.rmtree(fast_disk + '/suite2p')
os.system('rm -rf ' + fast_disk + '/suite2p')
print('fast disk contents deleted')
except:
print('fast disk location empty')
