def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.first_point is not None:
options.first_point -= 1
if options.scale is not None or options.rotate is not None or options.units is not None or options.first_point is not None:
in_radians = False
if options.units is not None and options.units.lower() in ('um', 'micron', 'microns'):
options.units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(contours, options.scale, options.rotate, in_radians,
options.units, options.first_point, options.show_progress, title = 'Modifying Contours')
if options.weights is not None:
contours = simple_interface.reweight_landmarks(contours, options.weights, options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(
filenames, show_progress=options.show_progress)
if options.reference is not None:
reference = contour_class.from_file(options.reference)
contours = simple_interface.align_contours_to(
contours,
reference,
align_steps=options.alignment_steps,
allow_reflection=options.allow_reflection,
show_progress=options.show_progress)
else:
contours = simple_interface.align_contours(
contours,
options.alignment_steps,
options.allow_reflection,
max_iters=options.max_iterations,
show_progress=options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
intensity_ranges = []
for r in options.intensity_ranges:
try:
low, high = r
except:
low = high = r
intensity_ranges.append([low, high])
if options.weights is None or len(options.weights) == 0:
options.weights = [0.5]
elif len(options.weights) != 1 and len(options.weights) != len(intensity_ranges):
raise optparse.OptionValueError("Either one or %d weights are required; %d sepcified."%(len(intensity_ranges), len(options.weights)))
elif sum(options.weights) > 1:
raise optparse.OptionValueError("The sum of the weights must be <= 1.")
matches = match_files.match_contours_and_images(args, options.match_by_name, options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
filenames = [path.path(contour._filename) for contour in contours]
contours = simple_interface.add_image_landmarks_to_contours(contours, image_names,
intensity_ranges, options.weights, options.image_type, options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.namebase + '.mat' for filename in filenames]
simple_interface.save_contour_data_for_matlab(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
matches = match_files.match_contours_and_images(args,
options.match_by_name,
options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
destination = path.path(options.destination)
destination.makedirs_p()
if options.file_type is not None:
new_names = [
destination / contour.simple_name() + '.' + options.file_type
for contour in contours
]
else:
new_names = [
destination / contour.simple_name() + image.ext
for image, contour in zip(image_names, contours)
]
simple_interface.reorient_images(contours,
image_names,
new_names,
pad_factor=options.pad_factor,
mask=options.mask_background,
show_progress=options.show_progress)
def get_data(data_files):
data_ranges = []
data_names = []
new_data_files = []
row_ranges = []
headers = []
for df in data_files:
if type(df) == list:
df, ranges = df
else:
ranges = None
# read the data file, and don't try to convert column 0 -- the contour names --
# to anything other than a string.
data = datafile.DataFile(df, skip_empty = False, type_dict = {0:str})
header, rows = data.get_header_and_data()
headers.append(header)
if ranges is None:
data_ranges.append(rows)
data_names.append(path.path(df).namebase)
new_data_files.append(df)
if header is None: start = 0
else: start = 1
row_ranges.append(range(1+start, len(data.data)+start))
else:
for low, high, name in ranges:
try:
# recall that low, high give an inclusive, one-indexed range...
data_ranges.append(data.data[low-1:high])
except:
raise ValueError('Cannot get row range (%d, %d) from data file "%s" -- not enough rows?')
data_names.append(name)
new_data_files.append(df)
row_ranges.append(range(low, high+1))
return headers, data_ranges, data_names, new_data_files, row_ranges
def get_data(data_files):
data_ranges = []
data_names = []
new_data_files = []
row_ranges = []
headers = []
for df in data_files:
if type(df) == list:
df, ranges = df
else:
ranges = None
# read the data file, and don't try to convert column 0 -- the contour names --
# to anything other than a string.
data = datafile.DataFile(df, skip_empty = False, type_dict = {0:str})
header, rows = data.get_header_and_data()
headers.append(header)
if ranges is None:
data_ranges.append(rows)
data_names.append(path.path(df).namebase)
new_data_files.append(df)
if header is None: start = 0
else: start = 1
row_ranges.append(list(range(1+start, len(data.data)+start)))
else:
for low, high, name in ranges:
try:
# recall that low, high give an inclusive, one-indexed range...
data_ranges.append(data.data[low-1:high])
except:
raise ValueError('Cannot get row range (%d, %d) from data file "%s" -- not enough rows?')
data_names.append(name)
new_data_files.append(df)
row_ranges.append(list(range(low, high+1)))
return headers, data_ranges, data_names, new_data_files, row_ranges
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(
filenames, show_progress=options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [
destination / filename.namebase + '.mat' for filename in filenames
]
simple_interface.save_contour_data_for_matlab(contours, names,
options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some image files must be specified!')
filenames = [path.path(arg) for arg in args]
contours_groups = simple_interface.extract_contours(
filenames, options.contour_value, options.min_area, options.max_area,
options.show_progress)
contours = []
names = []
destination = path.path(options.destination)
destination.makedirs_p()
for contour_group, image_name in zip(contours_groups, filenames):
num_contours = len(contour_group)
if num_contours == 1:
contours.append(contour_group[0])
# note that with path objects, the '/' operator means 'join path components.'
names.append(destination / image_name.namebase + '.contour')
contour_group[0]._filename = image_name.namebase
else:
width = len(str(num_contours))
for i, contour in enumerate(contour_group):
contours.append(contour)
names.append(destination / image_name.namebase +
'-%.*d.contour' % (width, i + 1))
contour._filename = image_name.namebase + '-%.*d' % (width,
i + 1)
if options.scale is not None:
# if not rescaling, contours are already denominated in pixels, so do nothing.
units = options.units
if units.lower() in ('um', 'micron', 'microns'):
units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(
contours,
scale_factor=options.scale,
units=units,
show_progress=options.show_progress,
title='Rescaling Contours')
if options.resample:
contours = simple_interface.resample_contours(contours,
options.resample_points,
options.smoothing_factor,
options.show_progress)
simple_interface.save_contours(contours, names, options.show_progress)
def read_files(files, data_column):
names = []
data_out = []
for df in files:
names.append(path.path(df).namebase)
data = datafile.DataFile(df, skip_empty=False, type_dict={0: str})
header, rows = data.get_header_and_data()
data_out.append(numpy.array([row[data_column] for row in rows]))
return names, data_out
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.endpoints is None:
endpoints = options.endpoint_method
else:
endpoints = options.endpoints
contours = simple_interface.find_centerlines(contours, options.axis_points, endpoints, options.show_progress)
destination = path.path(options.destination)
if not destination.exists():
destination.makedirs()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(filenames, show_progress = options.show_progress)
if options.reference is not None:
reference = contour_class.from_file(options.reference)
contours = simple_interface.align_contours_to(contours, reference, align_steps=options.alignment_steps,
allow_reflection=options.allow_reflection, show_progress=options.show_progress)
else:
contours = simple_interface.align_contours(contours, options.alignment_steps, options.allow_reflection,
max_iters=options.max_iterations, show_progress = options.show_progress)
destination = path.path(options.destination)
destination.makedirs_p()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
intensity_ranges = []
for r in options.intensity_ranges:
try:
low, high = r
except:
low = high = r
intensity_ranges.append([low, high])
if options.weights is None or len(options.weights) == 0:
options.weights = [0.5]
elif len(options.weights) != 1 and len(
options.weights) != len(intensity_ranges):
raise optparse.OptionValueError(
"Either one or %d weights are required; %d sepcified." %
(len(intensity_ranges), len(options.weights)))
elif sum(options.weights) > 1:
raise optparse.OptionValueError("The sum of the weights must be <= 1.")
matches = match_files.match_contours_and_images(args,
options.match_by_name,
options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
filenames = [path.path(contour._filename) for contour in contours]
contours = simple_interface.add_image_landmarks_to_contours(
contours, image_names, intensity_ranges, options.weights,
options.image_type, options.show_progress)
destination = path.path(options.destination)
if not destination.exists():
destination.makedirs()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour files must be specified!')
filenames = [path.path(arg) for arg in args]
contours = simple_interface.load_contours(
filenames, show_progress=options.show_progress)
if options.first_point is not None:
options.first_point -= 1
if options.scale is not None or options.rotate is not None or options.units is not None or options.first_point is not None:
in_radians = False
if options.units is not None and options.units.lower() in ('um',
'micron',
'microns'):
options.units = u'\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(
contours,
options.scale,
options.rotate,
in_radians,
options.units,
options.first_point,
options.show_progress,
title='Modifying Contours')
if options.weights is not None:
contours = simple_interface.reweight_landmarks(contours,
options.weights,
options.show_progress)
destination = path.path(options.destination)
if not destination.exists():
destination.makedirs()
# note that with path objects, the '/' operator means 'join path components.'
names = [destination / filename.name for filename in filenames]
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some image files must be specified!')
filenames = [path.path(arg) for arg in args]
contours_groups = simple_interface.extract_contours(filenames, options.contour_value,
options.min_area, options.max_area, options.show_progress)
contours = []
names = []
destination = path.path(options.destination)
destination.makedirs_p()
for contour_group, image_name in zip(contours_groups, filenames):
num_contours = len(contour_group)
if num_contours == 1:
contours.append(contour_group[0])
# note that with path objects, the '/' operator means 'join path components.'
names.append(destination / image_name.namebase + '.contour')
contour_group[0]._filename = image_name.namebase
else:
width = len(str(num_contours))
for i, contour in enumerate(contour_group):
contours.append(contour)
names.append(destination / image_name.namebase + '-%.*d.contour'%(width, i+1))
contour._filename = image_name.namebase + '-%.*d'%(width, i+1)
if options.scale is not None:
# if not rescaling, contours are already denominated in pixels, so do nothing.
units = options.units
if units.lower() in ('um', 'micron', 'microns'):
units = '\N{MICRO SIGN}m'
contours = simple_interface.transform_contours(contours, scale_factor=options.scale,
units=units, show_progress=options.show_progress, title='Rescaling Contours')
if options.resample:
contours = simple_interface.resample_contours(contours, options.resample_points, options.smoothing_factor, options.show_progress)
simple_interface.save_contours(contours, names, options.show_progress)
def main(name, arguments):
parser.prog = name
options, args = parser.parse_args(arguments)
args = cli_tools.glob_args(args)
if len(args) == 0:
raise ValueError('Some contour and image files must be specified!')
matches = match_files.match_contours_and_images(args, options.match_by_name, options.show_progress)
contours, image_names, unmatched_contours, unmatched_image_names = matches
destination = path.path(options.destination)
destination.makedirs_p()
if options.file_type is not None:
new_names = [destination / contour.simple_name() + '.' + options.file_type for contour in contours]
else:
new_names = [destination / contour.simple_name() + image.ext for image, contour in zip(image_names, contours)]
simple_interface.reorient_images(contours, image_names, new_names, pad_factor=options.pad_factor,
mask=options.mask_background, show_progress=options.show_progress)
def _get_contours_and_images(filenames, show_progress = True):
contours = []
image_names = []
if show_progress:
filenames = terminal_tools.progress_list(filenames, 'Loading Contours and Images')
for filename in filenames:
filename = path.path(filename)
if not filename.exists():
raise ValueError('File "%s" does not exist.'%filename)
try:
freeimage.read_metadata(filename)
image_names.append(filename)
except IOError as e:
# print e
# print Image.ID
try:
contours.append(contour_class.from_file(filename))
except IOError as e:
# print e
raise ValueError('Could not open file "%s" as an image or a contour.'%filename)
return contours, image_names
def _get_contours_and_images(filenames, show_progress=True):
contours = []
image_names = []
if show_progress:
filenames = terminal_tools.progress_list(
filenames, 'Loading Contours and Images')
for filename in filenames:
filename = path.path(filename)
if not filename.exists():
raise ValueError('File "%s" does not exist.' % filename)
try:
Image.open(filename)
image_names.append(filename)
except IOError, e:
# print e
# print Image.ID
try:
contours.append(contour_class.from_file(filename))
except IOError, e:
# print e
raise ValueError(
'Could not open file "%s" as an image or a contour.' %
filename)
subfont = 12
supfont = 16
xo = numpy.arange(0,240,0.3)
x = numpy.arange(0,241,30)
xti = numpy.arange(0,241,30)
#t = 0.2855
#bins = numpy.arange(0,29.95,t)
brain_regions = ['Lo2','Lo4']
color = ['#9900cc','#00cc66','#808080']
parent_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/gratings/lobula/'
parent_path = path('C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/gratings/lobula/')
header,rows = datafile.DataFile(parent_path/'directories.csv').get_header_and_data()
parent_mdir = parent_dir+'/measurements/'
dir_list = [parent_dir+'/'+row[1] for row in rows]
path_list = [parent_path/row[1] for row in rows]
for br in brain_regions[:]:
out = []
out2 = []
#import gratings ER and RGECO data and separate headers and rows from each dataset
header,rows = datafile.DataFile(parent_mdir+'all_responses-'+br+'-ER210.csv').get_header_and_data()
out = numpy.asarray(rows)
ytmaxer = 0.61
ytier = 0.2
T = numpy.arange(0,5,t)
header_out = ['sample','br','ROI','x','y','epoch']
header_out.extend(list(T))
#print header_out
indices = [[0,50],[50,100],[100,150],[150,200]]
ENUM=[1,2,3,4]
colors = ['#8F02C5','#02C54F','#0F37FF','#F8A51B'] #purple, green, blue, orange
brain_regions = ['M1','M5','M9-M10']
parent_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi1/moving_light_bars/'
parent_path = path('C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi1/moving_light_bars/')
mdir = parent_dir+'/measurements/10s/'
header,rows = datafile.DataFile(parent_path/'10s_directories.csv').get_header_and_data()
dir_list = [parent_dir+'/'+row[1] for row in rows]
path_list = [parent_path/row[1] for row in rows]
for br in brain_regions:
OUT_DFF=[] #RGECO
for directory,p,row in zip(dir_list[:],path_list[:],rows):
print(directory)
if not os.path.exists(directory+'/plots/time'):
import numpy
from celltool.utility.path import path
import celltool.utility.datafile as datafile
import matplotlib.image as mpimg
from PIL import Image
import glob
import os
t = 0.1
bins = numpy.arange(0, 4, t)
"""Sets up some paths..."""
parent_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/flashes/lobula/'
parent_path = path(
'C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/flashes/lobula/')
"""I'll explain this in person, ignore through line 54."""
header, rows = datafile.DataFile(parent_path /
'directories.csv').get_header_and_data()
dir_list = [parent_dir + '/' + row[1] for row in rows]
path_list = [parent_path / row[1] for row in rows]
for directory, p in zip(dir_list[:], path_list[:]):
print(directory)
plot_dir = directory + '/plots/'
print(plot_dir)
image_dir1 = directory + '/RGECO'
print(image_dir1)
"""This IDs and sorts image file names for one channel."""
d.name for d in directory.dirs() if (d / '__init__.py').exists()
]
return plugins
def _monkeypatch_command(plugin_mod, plugin_name):
import celltool.command_line.celltool_commands
celltool.command_line.celltool_commands.celltool_commands.append(
plugin_name)
setattr(celltool.command_line, plugin_name, plugin_mod)
sys.modules['celltool.command_line.' + plugin_name] = plugin_mod
py2exe_plugins = None
if hasattr(sys, "frozen") and sys.frozen == 'console_exe':
py2exe_plugins = path.path(sys.executable).parent.abspath() / 'Plugins'
_plugins = find_plugins(py2exe_plugins)
sys.path.append(py2exe_plugins)
else:
_plugins = find_plugins(path.path(__file__).parent)
celltool_plugins = None
try:
celltool_plugins = os.environ['CELLTOOL_PLUGINS']
_plugins += find_plugins(path.path(celltool_plugins))
sys.path.append(celltool_plugins)
except:
pass
for plugin in _plugins:
plugin_mod = __import__(plugin, globals(), locals())
import os
from celltool.utility.path import path
import celltool.utility.datafile as datafile
stim='/moving_dark_bar/'
"""Copy filenames from raw image files to analysis folders"""
# directory = 'D:/Image_files/Mi9_strongER210+RGECO/'+stim
# parent_dir = path(directory)
# dirs = sorted(os.listdir(parent_dir))
t_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi9_strong/'+stim
target_dir = path(t_dir)
#1) CREATE FILES FROM IMAGE_FILES TO NEW_ER/SCREEN FOLDERS
# for file in dirs[:]:
# targetname=file
# os.mkdir(os.path.join(t_dir,targetname))
# # """2) Create directories.csv file"""
target_list = sorted(os.listdir(target_dir))
header = ['fly','directory']
dir_list = []
for file in target_list:
i=1
if 'fly' in file:
import numpy
from celltool.utility.path import path
import celltool.utility.datafile as datafile
import matplotlib.pyplot as plt
threshold = 1
"""Set up path"""
parent_dir = path('C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi9/moving_dark_bar/')
"""Import list of directories"""
header,rows = datafile.DataFile(parent_dir/'directories.csv').get_header_and_data()
dir_list = [parent_dir/row[1] for row in rows]
#new_dl for indexing samples to fix
# new_dl = []
# indexes=[13,18]
# for i in indexes:
# new_dl.append(dir_list[i])
"""Read stimulus file, count imaging frames, and save output stimulus file for all directories"""
for directory in dir_list[:]: #change list to dir_list or new_dl
print(directory)
"""Import original stimulus file to a numpy array; you'll have to change the name of the file for your particular stimulus"""
stim_file = directory.files('moving*.csv')[0]
header,rows = datafile.DataFile(stim_file).get_header_and_data()
R = numpy.asarray(rows)
"""Set up the output array (just adds another column to the original stimulus array."""
ytmax = 0.61
yti = 0.2
T = numpy.arange(0, 20, t) #(0,5,t) for flashes; (0,31,t) for gratings
header_out = ['sample', 'brain_region', 'ROI', 'x', 'y', 'epoch']
header_out.extend(list(T))
#print header_out
color = '#02C54F'
alphas = [1, 0.6]
brain_regions = ['M1', 'M5', 'M9-M10']
parent_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi1/10s_flashes/'
parent_m_dir = parent_dir + '/measurements/'
parent_path = path('C:/Users/vymak_i7/Desktop/New_ER/Screen/Mi1/10s_flashes/')
header, rows = datafile.DataFile(parent_path /
'directories.csv').get_header_and_data()
dir_list = [parent_dir + '/' + row[1] for row in rows]
path_list = [parent_path / row[1] for row in rows]
for br in brain_regions[:]:
O_DFF = []
for directory, p, row in zip(dir_list[:], path_list[:], rows[:]):
OUT_DFF = []
print(directory)
image_dir = directory + '/binned_images-ER210'
plot_dir = directory + '/plots/'
m_dir = directory + '/measurements/'
if not directory.exists():
return []
plugin_files = [p.namebase for p in directory.files('*.py')]
plugins = [p for p in plugin_files if p not in ('__init__', 'setup')]
plugins += [d.name for d in directory.dirs() if (d / '__init__.py').exists()]
return plugins
def _monkeypatch_command(plugin_mod, plugin_name):
import celltool.command_line.celltool_commands
celltool.command_line.celltool_commands.celltool_commands.append(plugin_name)
setattr(celltool.command_line, plugin_name, plugin_mod)
sys.modules['celltool.command_line.'+plugin_name] = plugin_mod
py2exe_plugins = None
if hasattr(sys,"frozen") and sys.frozen == 'console_exe':
py2exe_plugins = path.path(sys.executable).parent.abspath() / 'Plugins'
_plugins = find_plugins(py2exe_plugins)
sys.path.append(py2exe_plugins)
else:
_plugins = find_plugins(path.path(__file__).parent)
celltool_plugins = None
try:
celltool_plugins = os.environ['CELLTOOL_PLUGINS']
_plugins += find_plugins(path.path(celltool_plugins))
sys.path.append(celltool_plugins)
except:
pass
for plugin in _plugins:
plugin_mod = __import__(plugin, globals(), locals())
import os
import shutil
from celltool.utility.path import path
import celltool.utility.datafile as datafile
stim = '10s_flashes'
"""Set up path"""
directory = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/medulla/' + stim
parent_dir = path(directory)
directories = os.listdir(parent_dir)
t_dir = 'C:/Users/vymak_i7/Desktop/New_ER/Screen/Tm3/medulla/google_drive/'
target_dir = path(t_dir)
dirs = os.listdir(target_dir)
header, rows = datafile.DataFile(parent_dir /
'directories.csv').get_header_and_data()
path_list = [parent_dir / row[1] for row in rows]
##0) to rename files (optional)
# for row in directories[1:19]:
# prev=os.path.join(directory+row,'mask-M3-M4.tif')
# new = os.path.join(directory+row,'mask-M2-M5.tif')
# os.rename(prev,new)
# 1) CREATE DIRECTORIES FOR GOOGLE DRIVE FOLDER
# i=1
# for row in rows[:]:
