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run_at_night_cabmi.py
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run_at_night_cabmi.py
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__author__ = 'senis'
# this is a program to run at night and go home leaving the computer to work for me...
import pipeline as pipe
import numpy as np
import imp
import shutil, os
import sys, traceback
from analysis_functions import all_run_SNR, calc_SNR_all_planes, \
online_SNR_single_session, dff_SNR_single_session
from utils_loading import get_all_animals, decode_from_filename
def tonightSNR_uzsh():
folder = '/media/user/Seagate Backup Plus Drive/'
animal = 'IT5'
days = ['190212']
# all_run_SNR(folder, animal, days[0])
for day in days:
folder_path = folder + 'raw/' + animal + '/' + day + '/'
err_file = open(folder_path + "errlog.txt", 'a+') # ERROR HANDLING
vars = imp.load_source('readme', folder_path + 'readme.txt')
try:
calc_SNR_all_planes(folder, animal, day, vars.num_files, vars.num_files_b, 4)
except Exception as e:
tb = sys.exc_info()[2]
err_file.write("\n{}\n".format(folder_path))
err_file.write("{}\n".format(str(e.args)))
traceback.print_tb(tb, file=err_file)
err_file.close()
sys.exit('Error in analyze raw')
try:
shutil.rmtree(folder + 'raw/' + animal + '/' + day + '/separated/')
except OSError as e:
print("Error: %s - %s." % (e.filename, e.strerror))
def tonightAllRun_uzsh():
#folder = "/media/user/Seagate Backup Plus Drive1/"
# sessions = [('PT7', '181211', 1),
# ('IT5', '190129', 1),
# ('PT9', '181219', 0),
# ('PT6', '181128', 1),
# ('IT2', '181001', 1),
# ('PT6', '181126', 0),
# ('PT9', '181128', 2)]
# for a, d, p in sessions[5:]:
# if a == 'PT7':
# planes = [0, p]
# else:
# planes = [p]
# fpath = os.path.join(folder, 'raw', a, d)
# ana = os.path.join(fpath, 'analysis')
# if os.path.exists(ana):
# os.rename(ana, ana+'_old')
# for pl in planes:
# target = os.path.join(fpath, f"bmi__{pl}.hdf5")
# if os.path.exists(target):
# os.rename(os.path.join(fpath, f"bmi__{pl}.hdf5"), os.path.join(fpath, f"bmi__{pl}_old.hdf5"))
# pipe.all_run(folder, a, d, number_planes=planes)
folder = "/media/user/Seagate Backup Plus Drive1/Nuria_data/CaBMI/Layer_project/"
all_run_tonight(folder=folder, animals=['PT19'])
def tonight_dff_SNR_uzsh():
folder = "/media/user/Seagate Backup Plus Drive/Nuria_data/CaBMI/Layer_project/processed/"
out = folder
if not os.path.exists(out):
os.makedirs(out)
err_file = open(os.path.join(out, "errlog.txt"), 'w')
for animal in get_all_animals(folder):
# for animal in ['IT10']:
animal_path = os.path.join(folder, animal)
for day in os.listdir(animal_path):
if day[-5:] == '.hdf5':
_, d = decode_from_filename(day)
elif not day.isnumeric():
continue
else:
d = day
try:
dff_SNR_single_session(folder, animal, d, out)
except Exception as e:
tb = sys.exc_info()[2]
err_file.write(f"\n{animal}, {day}\n")
err_file.write("{}\n".format(str(e.args)))
traceback.print_tb(tb, file=err_file)
print('done', animal, day)
err_file.close()
def tonight():
cut_tonight()
# put_together_tonight(folder = 'G:/Nuria_data/CaBMI/Layer_project/', animals = ('IT5',), toplot=True)
put_together_tonight(folder = 'H:/Nuria_data/CaBMI/Layer_project/', animals = ('PT6','PT9'), toplot=False)
put_together_tonight(folder = 'I:/Nuria_data/CaBMI/Layer_project/', animals = ('IT2', 'PT7'), toplot=False)
# put_together_tonight(folder = 'J:/Nuria_data/CaBMI/Layer_project/', animals = ('IT8',), toplot=False)
# put_together_tonight(folder = 'G:/', animals = ('PT6',), toplot=True)
# folder = 'G:/Nuria_data/CaBMI/Layer_project/'
# animal = 'PT18'
# days = ['190729']
#
# for day in days:
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
#
# cut_tonight()
# analyze_tonight()
# put_together_tonight()
# put_together_tonight(folder = 'G:/Nuria_data/CaBMI/Layer_project/', animals = ['PT13'])
# separate_me_tonight()
#
#analyze_tonight()
#tonight_caiman()
def cut_tonight():
print ('CUTTTTTIIIIIIIIIIIIIIIIIIIING')
# folder = 'J:/Nuria_data/CaBMI/Layer_project/'
# animal = 'PT19'
# days = ['190718']
# lens = [21000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'IT10'
# days = ['190302', '190312', '190314']
# lens = [27000, 18000, 24000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'IT8'
# days = ['190122', '190129']
# lens = [41000, 17000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
folder = 'H:/Nuria_data/CaBMI/Layer_project/'
#
# animal = 'IT3'
# # days = ['181004', '181017', '181018', '181031']
# # lens = [45000, 40000, 40000, 40000]
# days = ['181005']
# lens = [12000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'IT4'
# # days = ['181001', '181003', '181004', '181203']
# # lens = [24000, 27000, 21000, 28000]
# days = ['190108']
# lens = [37000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
animal = 'PT9'
days = [ '181219'] #'181129', '181204',
lens = [28000] # 32000, 27000,
for ind, day in enumerate(days):
print('runing animal: ' + str(animal) + "and day: " + str(day))
pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
#
# folder = 'G:/Nuria_data/CaBMI/Layer_project/'
#
# animal = 'IT5'
# days = ['190128', '190130', '190204']
# lens = [30000, 16000, 37000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'IT6'
# days = ['190121']
# lens = [37000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'PT12'
# days = ['190208']
# lens = [22000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
#
# animal = 'PT13'
# days = ['190121', '190123', '190124']
# lens = [33000, 18000, 17000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'PT18'
# days = ['190723']
# lens = [39000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
#
# folder = 'I:/Nuria_data/CaBMI/Layer_project/'
#
# animal = 'PT7'
# days = ['181130']
# lens = [42000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
#
# animal = 'IT1'
# days = ['181001', '181016']
# lens = [34000, 29000]
#
# for ind, day in enumerate(days):
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day, toplot=False, tocut=True, len_experiment=lens[ind])
def all_run_tonight(folder = 'J:/Nuria_data/CaBMI/Layer_project/', animals = ('IT8', 'IT9', 'IT10')):
#
# animal = 'IT4'
# days = ['181001']
#
# for day in days:
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
raw_folder = os.path.join(folder, 'raw')
processed = os.path.join(folder, 'processed')
ns = "full_{}_{}__data.hdf5"
fails = {}
for animal in animals:
fails[animal] = []
animal_path = os.path.join(raw_folder, animal)
days = []
for d in os.listdir(animal_path):
if d.isalpha():
print(d)
continue
if os.path.exists(os.path.join(processed, animal, ns.format(animal, d))) or os.path.exists(os.path.join(raw_folder, animal, d, 'bmi__1.hdf5')): # TODO: modify for general cases
continue
else:
days.append(d)
print(animal, days)
for day in days:
target = os.path.join(animal_path, day)
if not os.path.exists(target):
print("No target", target)
continue
print('running animal: ' + str(animal) + "and day: " + str(day))
pipe.all_run(folder, animal, day)
# try:
# pipe.all_run(folder, animal, day)
# except Exception as e:
# fails[animal].append((day, e.args))
print(fails)
def put_together_tonight(folder = 'J:/Nuria_data/CaBMI/Layer_project/', animals = ('IT8', 'IT9', 'IT10'), toplot=False):
#
# animal = 'IT4'
# days = ['181001']
#
# for day in days:
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
raw_folder = os.path.join(folder, 'raw')
processed = os.path.join(folder, 'processed')
ns = "full_{}_{}__data.hdf5"
fails = {}
for animal in animals:
fails[animal] = []
animal_path = os.path.join(raw_folder, animal)
days = []
for d in os.listdir(animal_path):
if d.isalpha():
print(d)
continue
if os.path.exists(os.path.join(processed, animal, ns.format(animal, d))):
continue
else:
days.append(d)
print(animal, days)
for day in days:
target = os.path.join(animal_path, day)
if not os.path.exists(target):
print("No target", target)
continue
print('running animal: ' + str(animal) + "and day: " + str(day))
try:
pipe.put_together(folder, animal, day, toplot=toplot)
except Exception as e:
fails[animal].append((day, e.args))
print(fails)
def analyze_tonight():
folder = 'J:/Nuria_data/CaBMI/Layer_project/'
#
# animal = 'IT4'
# days = ['181001']
#
# for day in days:
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
animal = 'IT8'
days = ['190204', '190205', '190206', '190208', '190214', '190215', '190220', '190221',
'190222', '190225', '190227', '190301']
for day in days:
print('runing animal: ' + str(animal) + "and day: " + str(day))
pipe.put_together(folder, animal, day)
# raw_folder = os.path.join(folder, 'raw')
# processed = os.path.join(folder, 'processed')
# ns = "full_{}_{}__data.hdf5"
#
# animal = 'IT1'
# days = ['181102', '181113', '181114', '181115', '181116', '190103']
#
# for day in days:
# target = os.path.join(folder, 'raw', animal, day)
# if not os.path.exists(target):
# print("No target", target)
# continue
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
# animal = 'PT13'
#
# days = ['190121', '190123']
#
# for day in days:
# print('runing animal: ' + str(animal) + "and day: " + str(day))
# pipe.put_together(folder, animal, day)
#
# animal = 'IT2'
# days = ['180928', '181001', '181002', '181003', '181004', '181005', '181015', '181016', '181017', '181018', '181031', '181101',
# '181102', '181113', '181115', '190103', '190104', '190108', '190109', '190110', '190111', '190115', '190116']
# #
#
# for day in days:
# print('runing animal: ' + str(animal) + " and day: " + str(day))
# pipe.put_together(folder, animal, day)
def separate_me_tonight():
folder = 'J:/Nuria_data/CaBMI/Layer_project/'
# animal = 'IT8'
#
# days = ['190121']
#
# for day in days:
# print('runing animal: ' + str(animal) + " and day: " + str(day))
# fbase = [folder + 'raw/' + animal + '/' + day + '/'+ 'baseline_00001.tif']
# ffull = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00001.tif']
# num_files_b, len_base = pipe.separate_planes(folder, animal, day, fbase, 'baseline')
# num_files, len_bmi = pipe.separate_planes(folder, animal, day, ffull, 'bmi')
#
# nam = folder + 'raw/' + animal + '/' + day + '/' + 'readme.txt'
# readme = open(nam, 'w+')
# readme.write("num_files_b = " + str(num_files_b) + '; \n')
# readme.write("num_files = " + str(num_files)+ '; \n')
# readme.write("len_base = " + str(len_base)+ '; \n')
# readme.write("len_bmi = " + str(len_bmi)+ '; \n')
# readme.close()
#
animal = 'IT8'
days = ['190207', '190213']
for day in days:
fbase1 = [folder + 'raw/' + animal + '/' + day + '/'+ 'baseline_00001.tif']
fbase2 = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00000.tif']
ffull = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00001.tif']
num_files_b, len_base = pipe.separate_planes_multiple_baseline(folder, animal, day, fbase1, fbase2)
num_files, len_bmi = pipe.separate_planes(folder, animal, day, ffull, 'bmi')
nam = folder + 'raw/' + animal + '/' + day + '/' + 'readme.txt'
readme = open(nam, 'w+')
readme.write("num_files_b = " + str(num_files_b) + '; \n')
readme.write("num_files = " + str(num_files)+ '; \n')
readme.write("len_base = " + str(len_base)+ '; \n')
readme.write("len_bmi = " + str(len_bmi)+ '; \n')
readme.close()
animal = 'IT9'
days = ['190304', '190308', '190311']
for day in days:
fbase1 = [folder + 'raw/' + animal + '/' + day + '/'+ 'baseline_00001.tif']
fbase2 = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00000.tif']
ffull = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00001.tif']
num_files_b, len_base = pipe.separate_planes_multiple_baseline(folder, animal, day, fbase1, fbase2)
num_files, len_bmi = pipe.separate_planes(folder, animal, day, ffull, 'bmi')
nam = folder + 'raw/' + animal + '/' + day + '/' + 'readme.txt'
readme = open(nam, 'w+')
readme.write("num_files_b = " + str(num_files_b) + '; \n')
readme.write("num_files = " + str(num_files)+ '; \n')
readme.write("len_base = " + str(len_base)+ '; \n')
readme.write("len_bmi = " + str(len_bmi)+ '; \n')
readme.close()
animal = 'IT10'
days = ['190220', '190308']
for day in days:
fbase1 = [folder + 'raw/' + animal + '/' + day + '/'+ 'baseline_00001.tif']
fbase2 = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00000.tif']
ffull = [folder + 'raw/' + animal + '/' + day + '/'+ 'bmi_00001.tif']
num_files_b, len_base = pipe.separate_planes_multiple_baseline(folder, animal, day, fbase1, fbase2)
num_files, len_bmi = pipe.separate_planes(folder, animal, day, ffull, 'bmi')
nam = folder + 'raw/' + animal + '/' + day + '/' + 'readme.txt'
readme = open(nam, 'w+')
readme.write("num_files_b = " + str(num_files_b) + '; \n')
readme.write("num_files = " + str(num_files)+ '; \n')
readme.write("len_base = " + str(len_base)+ '; \n')
readme.write("len_bmi = " + str(len_bmi)+ '; \n')
readme.close()
def tonight_caiman():
folder = 'G:/Nuria_data/CaBMI/Layer_project/'
animal = 'IT1'
days = ['181004', '181005', '181015', '181016', '181017', '181031', '181102', '181113', '181114', '181115', '181116', '190103']
for day in days:
folder_path = folder + 'raw/' + animal + '/' + day + '/'
err_file = open(folder_path + "errlog.txt", 'a+') # ERROR HANDLING
vars = imp.load_source('readme', folder_path + 'readme.txt')
try:
pipe.analyze_raw_planes(folder, animal, day, vars.num_files, vars.num_files_b, 4, False)
except Exception as e:
tb = sys.exc_info()[2]
err_file.write("\n{}\n".format(folder_path))
err_file.write("{}\n".format(str(e.args)))
traceback.print_tb(tb, file=err_file)
err_file.close()
sys.exit('Error in analyze raw')
try:
shutil.rmtree(folder + 'raw/' + animal + '/' + day + '/separated/')
except OSError as e:
print("Error: %s - %s." % (e.filename, e.strerror))
animal = 'IT2'
days = ['190117']
for day in days:
folder_path = folder + 'raw/' + animal + '/' + day + '/'
err_file = open(folder_path + "errlog.txt", 'a+') # ERROR HANDLING
vars = imp.load_source('readme', folder_path + 'readme.txt')
try:
pipe.analyze_raw_planes(folder, animal, day, vars.num_files, vars.num_files_b, 4, False)
except Exception as e:
tb = sys.exc_info()[2]
err_file.write("\n{}\n".format(folder_path))
err_file.write("{}\n".format(str(e.args)))
traceback.print_tb(tb, file=err_file)
err_file.close()
sys.exit('Error in analyze raw')
try:
shutil.rmtree(folder + 'raw/' + animal + '/' + day + '/separated/')
except OSError as e:
print("Error: %s - %s." % (e.filename, e.strerror))
animal = 'PT7'
days = ['181130', '181203', '181204', '181205', '181211', '181212', '181213', '181218', '190114', '190115',
'190116', '190117', '190118']
for day in days:
folder_path = folder + 'raw/' + animal + '/' + day + '/'
err_file = open(folder_path + "errlog.txt", 'a+') # ERROR HANDLING
vars = imp.load_source('readme', folder_path + 'readme.txt')
try:
pipe.analyze_raw_planes(folder, animal, day, vars.num_files, vars.num_files_b, 4, False)
except Exception as e:
tb = sys.exc_info()[2]
err_file.write("\n{}\n".format(folder_path))
err_file.write("{}\n".format(str(e.args)))
traceback.print_tb(tb, file=err_file)
err_file.close()
sys.exit('Error in analyze raw')
try:
shutil.rmtree(folder + 'raw/' + animal + '/' + day + '/separated/')
except OSError as e:
print("Error: %s - %s." % (e.filename, e.strerror))
if __name__ == '__main__':
tonightAllRun_uzsh()