def convert_from_ABF_to_HDF5(experiment):
"""
Convierte los ficheros del experimento desde ABF y los graba en un fichero HDF5
:param experiment:
:return:
"""
# Asumimos que el fichero no existe todavia
f = experiment.open_experiment_data(mode='w')
nsig = experiment.abfsensors
datafiles = experiment.datafiles
for dataf in datafiles:
# Leemos los datos del fichero ABF
print('Reading: ', dataf, '...')
data = AxonIO(experiment.dpath + experiment.name + '/' + dataf + '.abf')
bl = data.read_block(lazy=False, cascade=True)
dim = bl.segments[0].analogsignals[0].shape[0]
matrix = np.zeros((len(nsig), dim))
for i, j in enumerate(nsig):
matrix[i][:] = bl.segments[0].analogsignals[j][:].magnitude
# Los guardamos en el almacenamiento del experimento
print('Saving: ', dataf, '...')
experiment.save_raw_data(f, dataf, matrix.T)
del matrix
del bl
datainfo.close_experiment_data(f)
def test_read_protocol(self):
for f in self.files_to_test:
filename = self.get_filename_path(f)
reader = AxonIO(filename=filename)
bl = reader.read_block(lazy=True)
if bl.annotations['abf_version']>=2.:
reader.read_protocol()
def convert_from_ABF_to_HDF5(experiment):
"""
Convierte los ficheros del experimento desde ABF y los graba en un fichero HDF5
:param experiment:
:return:
"""
# Asumimos que el fichero no existe todavia
f = experiment.open_experiment_data(mode='w')
nsig = experiment.abfsensors
datafiles = experiment.datafiles
for dataf in datafiles:
# Leemos los datos del fichero ABF
print('Reading: ', dataf, '...')
data = AxonIO(experiment.dpath + experiment.name + '/' + dataf +
'.abf')
bl = data.read_block(lazy=False)
dim = bl.segments[0].analogsignals[0].shape[0]
matrix = np.zeros((len(nsig), dim))
for i, j in enumerate(nsig):
tmpmat = bl.segments[0].analogsignals[j][:].magnitude
matrix[i][:] = tmpmat.reshape(tmpmat.shape[0])
# Los guardamos en el almacenamiento del experimento
print('Saving: ', dataf, '...')
experiment.save_raw_data(f, dataf, matrix.T)
del matrix
del bl
datainfo.close_experiment_data(f)
def test_read_protocol(self):
for f in self.files_to_test:
filename = self.get_filename_path(f)
reader = AxonIO(filename=filename)
bl = reader.read_block(lazy=True)
if bl.annotations['abf_version'] >= 2.:
reader.read_protocol()
def exp_tracef(Injectcurr=150e-12):
global flnme
global exp_sampdur
global exp_samprate
global exp_samppoints
global exp_trace_injend
global exp_trace_injstart
stim1391 = ['Cell 3 of 181016.abf', 'cell 4 of 61016.abf', 'cell 4 of 111016.abf', 'cell 4 of 131016.abf', 'Cell 4 of 181016.abf', 'cell 5 of 61016.abf', 'Cell 5 of 181016.abf']
# flnme = 'Cell 3 of 10717.abf'
flnme = 'cell 4 of 61016.abf'
exp_tracefile = f'../../Raw_data/Deepanjali_data/WT step input cells/{flnme}'
reader = AxonIO(filename=exp_tracefile)
currno = int(Injectcurr*1e12/25+4)
seg = reader.read_block().segments[currno] # 10 means 150pA current
exp_trace = seg.analogsignals[0]
exp_samprate = float(exp_trace.sampling_rate)
exp_sampdur = float(exp_trace.t_stop) - float(exp_trace.t_start)
exp_samppoints = int(exp_samprate*exp_sampdur)
if flnme in stim1391:
exp_trace_injstart = 139.1e-3
exp_trace_injend = 639.1e-3
else:
exp_trace_injstart = 81.4e-3
exp_trace_injend = 581.4e-3
exp_trace = np.array(exp_trace).flatten()
return exp_trace
def convert_from_ABF_to_HDF5(experiment):
"""
Convierte los ficheros del experimento desde ABF y los graba en un fichero HDF5
:param experiment:
:return:
"""
# Asumimos que el fichero no existe todavia
f = h5py.File(
experiment.dpath + experiment.name + '/' + experiment.name + '.hdf5',
'r+')
nsig = [s for s, _ in experiment.extrasensors]
datafiles = experiment.datafiles
for dataf in datafiles:
# Leemos los datos del fichero ABF
print('Reading: ', dataf, '...')
data = AxonIO(experiment.dpath + experiment.name + '/' + dataf +
'.abf')
bl = data.read_block(lazy=False, cascade=True)
dim = bl.segments[0].analogsignals[0].shape[0]
matrix = np.zeros((len(nsig), dim))
for i, j in enumerate(nsig):
matrix[i][:] = bl.segments[0].analogsignals[j][:].magnitude
# Los guardamos en una carpeta del fichero HDF5 para el fichero dentro de /Raw
print('Saving: ', dataf, '...')
dgroup = f[dataf]
if dataf + '/RawExtra' in f:
del f[dataf + '/RawExtra']
dgroup.create_dataset('RawExtra',
matrix.T.shape,
dtype='f',
data=matrix.T,
compression='gzip')
del matrix
del bl
f[dataf + '/RawExtra'].attrs['Sampling'] = experiment.sampling
f[dataf + '/RawExtra'].attrs['Sensors'] = [
s for _, s in experiment.extrasensors
]
f.flush()
f.close()
def convert_from_ABF_to_HDF5(experiment):
"""
Convierte los ficheros del experimento desde ABF y los graba en un fichero HDF5
:param experiment:
:return:
"""
# Asumimos que el fichero no existe todavia
f = h5py.File(experiment.dpath + experiment.name + "/" + experiment.name + ".hdf5", "r+")
nsig = [s for s, _ in experiment.extrasensors]
datafiles = experiment.datafiles
for dataf in datafiles:
# Leemos los datos del fichero ABF
print("Reading: ", dataf, "...")
data = AxonIO(experiment.dpath + experiment.name + "/" + dataf + ".abf")
bl = data.read_block(lazy=False, cascade=True)
dim = bl.segments[0].analogsignals[0].shape[0]
matrix = np.zeros((len(nsig), dim))
for i, j in enumerate(nsig):
matrix[i][:] = bl.segments[0].analogsignals[j][:].magnitude
# Los guardamos en una carpeta del fichero HDF5 para el fichero dentro de /Raw
print("Saving: ", dataf, "...")
dgroup = f[dataf]
if dataf + "/RawExtra" in f:
del f[dataf + "/RawExtra"]
dgroup.create_dataset("RawExtra", matrix.T.shape, dtype="f", data=matrix.T, compression="gzip")
del matrix
del bl
f[dataf + "/RawExtra"].attrs["Sampling"] = experiment.sampling
f[dataf + "/RawExtra"].attrs["Sensors"] = [s for _, s in experiment.extrasensors]
f.flush()
f.close()
def exp_tracef(currno=10):
global flnme
global exp_trace
global exp_sampdur
global exp_samprate
global exp_samppoints
global exp_trace_injend
global exp_trace_injstart
stim1391 = ['Cell 3 of 181016.abf', 'cell 4 of 61016.abf', 'cell 4 of 111016.abf', 'cell 4 of 131016.abf', 'Cell 4 of 181016.abf', 'cell 5 of 61016.abf', 'Cell 5 of 181016.abf']
exp_tracefile = Exp_tracedir+flnme
reader = AxonIO(filename=exp_tracefile)
seg = reader.read_block().segments[currno] # 10 means 15pA current
exp_trace = seg.analogsignals[0]
exp_samprate = float(exp_trace.sampling_rate)
exp_sampdur = float(exp_trace.t_stop) - float(exp_trace.t_start)
exp_samppoints = int(exp_samprate*exp_sampdur)
if flnme in stim1391:
exp_trace_injstart = 139.1e-3
exp_trace_injend = 639.1e-3
else:
exp_trace_injstart = 81.4e-3
exp_trace_injend = 581.4e-3
exp_trace = np.array(exp_trace).flatten()
def test_annotations(self):
reader = AxonIO(filename=self.get_filename_path('File_axon_2.abf'))
bl = reader.read_block()
ev = bl.segments[0].events[0]
assert 'comments' in ev.annotations
from neo.io import AxonIO
import os
from allensdk.ephys.ephys_extractor import EphysSweepFeatureExtractor
from allensdk.core.cell_types_cache import CellTypesCache
filename = 'Cell 6 of 171117.abf'
seg_no = 17 #0 is -100pA, 4 is 0pA, 20 is 400pA. Now extrapolate
stim_start = 81.4e-3 #in s
stim_stop = 581.4e-3 #in s
Actualstim_start = seg_no * 2 + stim_start
Actualstim_stop = seg_no * 2 + stim_stop
Inputcurr = seg_no * 25 - 100 #in pA
reader = AxonIO(filename='Deepanjali data/WT step input cells/' + filename)
Vtrace = reader.read_block().segments[seg_no].analogsignals[0]
i = np.zeros(int((Vtrace.t_stop - Vtrace.t_start) * Vtrace.sampling_rate))
i[int(stim_start * Vtrace.sampling_rate):int(stim_stop *
Vtrace.sampling_rate)] = Inputcurr
i = np.array(i)
v = np.array([float(V) for V in Vtrace])
t = np.linspace(0, float(Vtrace.t_stop - Vtrace.t_start),
int((Vtrace.t_stop - Vtrace.t_start) * Vtrace.sampling_rate))
t = np.array(t)
sweep_ext = EphysSweepFeatureExtractor(t=t, v=v, i=i, filter=5)
sweep_ext.process_spikes()
sweep_ext.spike_feature_keys() #Lists all the features that can be extracted
sweep_ext.spike_feature("width") #Extracts AP width
import glob
#change directory as needed
flydir = 'C:\\Users\\rancher\\Desktop\\S328_.5stim\\'
from neo.io import AxonIO
abf_name_list = glob.glob(flydir + '*.abf')
for i in abf_name_list:
abf_name = i.replace('.abf','')
abf_name = abf_name.replace(flydir,'')
localfile = flydir + abf_name + '.abf' #change file name as needed
r = AxonIO(localfile)
bl = r.read_block(lazy=False, cascade=True)
# Get info from channels:
l_amp = np.asarray(bl.segments[0].analogsignals[3])*60/np.pi #Left wing from Kinefly
r_amp = np.asarray(bl.segments[0].analogsignals[4])*60/np.pi #Right wing from Kinefly
wbf = np.asarray(bl.segments[0].analogsignals[0])*100. #wing beat frequency from wing beat analyzer
# l_plus_r = np.asarray(bl.segments[0].analogsignals[1])*60/np.pi #from wing beat analyzer
pattern = np.asarray(bl.segments[0].analogsignals[7])
#frames = np.asarray(bl.segments[0].analogsignals[3])
#amp_sum = l_amp + r_amp #use this line if we use Channel 1 l_plus_r from wing beat analyzer again
l_plus_r = l_amp + r_amp
amp_diff = l_amp - r_amp # Note: amp_diff is L-R
fs_axon = 1.0/2000.0 #We know there are 2000 readings per second
def test_annotations(self):
reader = AxonIO(filename=self.get_filename_path('File_axon_2.abf'))
bl = reader.read_block()
ev = bl.segments[0].events[0]
assert 'comments' in ev.annotations
from tkinter.filedialog import askdirectory
Direc = '../../Raw_data/Deepanjali_data/WT step input cells/' #Directory where all the files are stored
CurrAmp = 5 #0 is for -100pA, 1 for -75pA, and so on till 20 which is 400pA. 10 for 150pA
# flist = os.listdir(Direc)
flist = ['cell 4 of 61016.abf']
i = 0
print(os.listdir(Direc))
for filename in flist:
i = i + 1
print(i, end='\r')
try: #Try is used to skip unsupported files that may be there in the folder
reader = AxonIO(filename=Direc + filename)
Samprate = reader.get_signal_sampling_rate()
seg = reader.read_block().segments[CurrAmp]
Tdur = np.array(seg.t_stop - seg.t_start)
plt.plot(np.linspace(0, Tdur, Samprate * Tdur),
seg.analogsignals[0],
label=f'{filename}')
# plt.title('WT 150pA current injection for 0.5s')
# plt.xlim([0,1])
plt.ylim([-75, 50])
plt.xlabel('Time (s)')
plt.ylabel('Membrane potential (mV)')
plt.legend()
mng = plt.get_current_fig_manager()
mng.resize(*mng.window.maxsize())
plt.show()
except:
pass
def binary_to_csv(filename=None):
'''
Writes data for given abf file into a csv format. Two .csv files will be created into csv_data folder
One will be meta_data, one will be time series data.
These sheets are also returned as pandas data frames by this function
'''
if filename is None:
sys.exit('must specify filename and path')
# Set up path to save csv output to
pathtocsv = str.split(filename, '/')
pathtocsv = "/".join(pathtocsv[:-2]) + "/csv_data/"
#Use neo function "AxonIO" to read in the axonb binary file
r = AxonIO(filename=filename)
r = r.read_block()
# for name purposes later on, remove ".abf" extension from filename
filename = splitext(basename(filename))[0]
# Define number of sweeps in this protocol (.abf file)
n_sweeps = len(r.segments)
n_channels = len(r.segments[0].analogsignals)
# Name sweeps
sweep_ids = []
for i in range(0, n_sweeps):
sweep_ids.append('sweep' + str(i + 1))
# List the traits to hold in meta data
meta_traits = ['fs', 'celltype', 'date']
for i in range(0, n_channels):
meta_traits.append('ch' + str(i + 1) + '_units')
# create empty data frame for meta data
meta_data = pd.DataFrame(columns=meta_traits, index=sweep_ids)
# fill meta_data
for i, seg in enumerate(r.segments):
for ch in range(0, n_channels):
meta_data['ch' + str(ch + 1) + '_units'][sweep_ids[i]] = str(
seg.analogsignals[ch].units)[4:]
meta_data['fs'][sweep_ids[i]] = float(
seg.analogsignals[0].sampling_rate)
meta_data['date'][sweep_ids[i]] = filename[-10:]
meta_data['celltype'][sweep_ids[i]] = str.split(
filename,
'_')[0] # example of using string split to get information
# create empty data frame to hold data
data_cols = []
for i in range(0, n_sweeps):
for ch in range(0, n_channels):
data_cols.append('ch' + str(ch + 1) + '_sweep' + str(i + 1))
# Warning about how we are handling time series
import warnings
#warnings.warn('If fs is same for all sweeps, hard coding time series to be the same for all sweeps within an .abf file')
# make sure all sampling rates are the same across segments
if len(meta_data['fs'].unique()) == 1:
time = np.linspace(
0,
len(r.segments[0].analogsignals[0]) /
float(meta_data['fs'].unique()),
len(r.segments[0].analogsignals[0]))
else:
sys.exit(
'sampling rates are different - need to figure out what to do in this case'
)
# initiate the data frame for data
data = pd.DataFrame(index=time, columns=data_cols)
# fill the data frame for data
for s_index, seg in enumerate(r.segments):
for ch_index, ch in enumerate(seg.analogsignals):
data['ch' + str(ch_index + 1) + '_sweep' + str(s_index + 1)] = ch
# Convert the data frames to .csv files
meta_data.to_csv(pathtocsv + 'meta_data_' + str(filename) + '.csv')
data.to_csv(pathtocsv + 'data_' + str(filename) + '.csv')
print('saving data in csv format. Stored in csv_data folder')
# return data frames for further processing
return meta_data, data
def exp_tracef(Injectcurr=150e-12):
global flnme
global exp_sampdur
global exp_samprate
global exp_samppoints
global exp_trace_injend
global exp_trace_injstart
global Vrest
global sm_diam
global sm_len
global Gin
stim1391 = [
'Cell 3 of 181016.abf', 'cell 4 of 61016.abf', 'cell 4 of 111016.abf',
'cell 4 of 131016.abf', 'Cell 4 of 181016.abf', 'cell 5 of 61016.abf',
'Cell 5 of 181016.abf'
]
# flnme = 'Cell 3 of 10717.abf'
flnme = 'cell 4 of 61016.abf'
exp_tracefile = f'../../Raw_data/Deepanjali_data/WT step input cells/{flnme}'
reader = AxonIO(filename=exp_tracefile)
currno = int(Injectcurr * 1e12 / 25 + 4)
seg = reader.read_block().segments[currno] # 10 means 150pA current
exp_trace = seg.analogsignals[0]
exp_samprate = float(exp_trace.sampling_rate)
exp_sampdur = float(exp_trace.t_stop) - float(exp_trace.t_start)
exp_samppoints = int(exp_samprate * exp_sampdur)
if flnme in stim1391:
exp_trace_injstart = 139.1e-3
exp_trace_injend = 639.1e-3
else:
exp_trace_injstart = 81.4e-3
exp_trace_injend = 581.4e-3
exp_trace = np.array(exp_trace).flatten() * 1e-3
Vrest = np.mean(
np.array(
reader.read_block().segments[4].analogsignals[0]).flatten()) * 1e-3
Rinp25 = np.abs(
np.max(
np.array(reader.read_block().segments[5].analogsignals[0]).flatten(
)) * 1e-3 - Vrest) / 25e-12
Rinn25 = np.abs(
np.min(
np.array(reader.read_block().segments[3].analogsignals[0]).flatten(
)) * 1e-3 - Vrest) / 25e-12
Gin = 2 / (Rinp25 + Rinn25)
print(Gin)
t = np.linspace(0, exp_sampdur, int(exp_sampdur * exp_samprate))
Vtracep25 = np.array(
reader.read_block().segments[5].analogsignals[0]).flatten() * 1e-3
Vtracen25 = np.array(
reader.read_block().segments[3].analogsignals[0]).flatten() * 1e-3
str_ind = (np.abs(t - exp_trace_injend + 100e-3)).argmin()
stp_ind = (np.abs(t - exp_trace_injend)).argmin()
Vtracep25_choppped = Vtracep25[:stp_ind]
Vtracen25_choppped = Vtracen25[:stp_ind]
vp63 = np.abs(
np.max(
np.array(reader.read_block().segments[5].analogsignals[0]).flatten(
)) * 1e-3 - Vrest) * 0.63 + Vrest
vn63 = -np.abs(
np.min(
np.array(reader.read_block().segments[3].analogsignals[0]).flatten(
)) * 1e-3 - Vrest) * 0.63 + Vrest
tau = (t[(np.abs(Vtracep25_choppped - vp63)).argmin()] - exp_trace_injstart
+ t[(np.abs(Vtracen25_choppped - vn63)).argmin()] -
exp_trace_injstart) / 2
tauinv = (t[len(Vtracep25_choppped) -
(np.abs(Vtracep25_choppped[stp_ind::-1] - vp63)).argmin()] -
exp_trace_injstart +
t[len(Vtracep25_choppped) -
(np.abs(Vtracep25_choppped[::-1] - vp63)).argmin()] -
exp_trace_injstart) / 2
Cm = (tau + tauinv) * Gin / 2
print(Cm)
sm_len = np.sqrt(Cm / CM / np.pi)
sm_diam = sm_len
return exp_trace
import matplotlib.pyplot as plt
from scipy import signal
import pylab as pl
import numpy as np
'''
Preliminary steps to read in the data.
'''
# I commonly use the variable 'fh' as shorthand for 'file handle'. In
# programming parlance, 'handle' is an abstract reference to a resource (in this
# case, the AxonIO instance that allows you to read from the file).
fh = AxonIO(filename='PVcell3.abf')
# The block is a container for the voltage and current data stored in the file.
block = fh.read_block()
# Some information regarding the experiment has been saved in the file. We need
# to parse this information out for the analysis. A block consists of multiple
# sweeps (i.e., ,trials), known as `segments`. Each segment can contain multiple
# signals, known as `analogsignals`. For this particular data file, the number
# of channels, number of timepoints, sampling rate and sampling period are
# identical across all sweeps.
n_channels = len(block.segments[0].analogsignals)
n_sweeps = len(block.segments)
n_timepoints = len(block.segments[0].analogsignals[0].times)
sampling_rate = int(block.segments[0].analogsignals[0].sampling_rate)
sampling_period = 1.0/sampling_rate
sweep_duration = n_timepoints*sampling_period
message = '''The data contains {n_sweeps} sweeps (i.e., trials) acquired from
datafiles = [(['15514028', '15514029', '15514030',
'15514031', '15514032', '15514033', '15514034', '15514035', '15514036', '15514037', '15514038'], 12, 10000.0)
]
# datafiles = [(['15514027'],
# 12, 10000.0)]
for dataf, nsig, _ in datafiles:
for files in dataf:
print 'Reading: ', files, '...'
data = AxonIO(cinvesdatanew + 'e150514/' + files + '.abf')
bl = data.read_block(lazy=False, cascade=True)
dim = bl.segments[0].analogsignals[0].shape[0]
print dim
matrix = np.zeros((nsig, dim))
# for sig in bl.segments[0].analogsignals:
# i += 1
# #print sig.duration, sig.signal, len(sig.times), i
# print sig.name, sig.units, sig.sampling_rate, sig.dtype, sig.duration, sig.shape
for j in range(nsig):
matrix[j][:] = bl.segments[0].analogsignals[j][:].magnitude
peakdata = {'data': matrix.T}