def print_tp_stats(
filepath): #FIXME this only works if there is only ONE epoch
#FIXME also need to make all of these things work with NEGATIVE test pulses! (just use the sign on the step)
raw = AxonIO(filepath)
#raw,block,segments,header=load_abf(filepath)
try:
header = raw.read_header()
except FileNotFoundError:
return None
starts, lengths, volts = find_rs_test(header)
#TODO match commands to the proper recording channels (analog signals)
if not volts: #implies that none of the waveforms was on
return None
else:
segments = raw.read_block().segments
sigit = range(len(starts))
Taus, Rss, Rs_ests, Rms = [], [], [], []
for segment in segments:
for analogsignal, i in zip(segment.analogsignals, sigit):
A, Tau, C, Q, Rs, Rs_est, Rm, rest_baseline, pulse_baseline, fit_start_index = compute_test_pulse_statistics(
analogsignal, starts[i], lengths[i], volts[i])
Taus.append(Tau)
Rss.append(Rs)
Rs_ests.append(Rs_est)
Rms.append(Rm)
Taus = ['%3.2f ' % (t * 1000) for t in Taus if t]
Rss = ['%3.2f ' % t for t in Rss if t]
Rs_ests = ['%3.2f ' % t for t in Rs_ests if t]
Rms = ['%3.2f ' % t for t in Rms if t]
print('Taus', Taus)
print('Rses', Rss)
print('Rs_ests', Rs_ests)
print('Rms', Rms)
return Taus, Rss, Rs_ests, Rms
def print_tp_stats(filepath): #FIXME this only works if there is only ONE epoch
#FIXME also need to make all of these things work with NEGATIVE test pulses! (just use the sign on the step)
raw=AxonIO(filepath)
#raw,block,segments,header=load_abf(filepath)
try:
header=raw.read_header()
except FileNotFoundError:
return None
starts,lengths,volts=find_rs_test(header)
#TODO match commands to the proper recording channels (analog signals)
if not volts: #implies that none of the waveforms was on
return None
else:
segments=raw.read_block().segments
sigit=range(len(starts))
Taus,Rss,Rs_ests,Rms=[],[],[],[]
for segment in segments:
for analogsignal,i in zip(segment.analogsignals,sigit):
A,Tau,C,Q,Rs,Rs_est,Rm,rest_baseline,pulse_baseline,fit_start_index=compute_test_pulse_statistics(analogsignal, starts[i], lengths[i], volts[i])
Taus.append(Tau)
Rss.append(Rs)
Rs_ests.append(Rs_est)
Rms.append(Rm)
Taus=['%3.2f '%(t*1000) for t in Taus if t ]
Rss=['%3.2f '%t for t in Rss if t ]
Rs_ests=['%3.2f '%t for t in Rs_ests if t ]
Rms=['%3.2f '%t for t in Rms if t ]
print('Taus',Taus)
print('Rses',Rss)
print('Rs_ests',Rs_ests)
print('Rms',Rms)
return Taus,Rss,Rs_ests,Rms
def importabf(self):
self.abffiletoimport = input('Type (a) to process all files in folder, otherwise type in file number (ex:0012)')
if self.abffiletoimport != 'a':
print ('Searching files:')
self.abffiletoimport = [file for file in self.abffiles if re.search(self.abffiletoimport, file)]
print('Found: ', self.abffiletoimport)
self.foundfile = ''.join(self.abffiletoimport)
print(self.foundfile)
self.fullfilepath = os.path.join(self.fileloc, self.foundfile)
print('Full file path: ', self.fullfilepath)
self.abf = AxonIO(filename=self.fullfilepath)
else:
pass
class filemanage:
def __init__(self):
self.fileloc = None
def directimport(self):
print('IMPORTING DIRECTORIES')
self.homefolder = input('Are the files in the folder /home/pi/ephys/ (y or n)?')
if self.homefolder == 'y':
self.homefolder = '/home/pi/ephys/'
else:
self.homefolder = input('enter the datapath in /folder/subfolder/ format:')
print('Experiments should be stored in subfolder by date in yyyy-mm-dd format.')
self.experdate = input('Enter the experiment date in yyyy-mm-dd format ')
print('Subfolders within home folder:')
print(os.listdir(self.homefolder))
self.fileloc = os.path.join(self.homefolder, self.experdate)
if (os.path.exists(self.fileloc)):
print('Files within experiment date folder')
print(os.listdir(os.path.join(self.homefolder, self.experdate)))
self.fileloclist = os.listdir(os.path.join(self.homefolder, self.experdate))
else:
print('The file does not exist, check the path and date.')
return ()
def findabffile(self):
print('ISOLATING ABF FILES...')
self.abffiles = [extension for extension in self.fileloclist if re.search("\.abf$", extension)]
self.abffiles.sort()
print('*.abf files in folder:')
print(self.abffiles)
def importabf(self):
self.abffiletoimport = input('Type (a) to process all files in folder, otherwise type in file number (ex:0012)')
if self.abffiletoimport != 'a':
print ('Searching files:')
self.abffiletoimport = [file for file in self.abffiles if re.search(self.abffiletoimport, file)]
print('Found: ', self.abffiletoimport)
self.foundfile = ''.join(self.abffiletoimport)
print(self.foundfile)
self.fullfilepath = os.path.join(self.fileloc, self.foundfile)
print('Full file path: ', self.fullfilepath)
self.abf = AxonIO(filename=self.fullfilepath)
else:
pass
def exploreabf(self):
self.numblocks = self.abf.block_count()
self.samplingrate = self.abf.get_signal_sampling_rate()
self.abf.
def get_segments_with_step(filepath):
try:
raw=AxonIO(filepath)
header=raw.read_header()
except FileNotFoundError as e:
print(e)
del(raw)
return None,None,None,None
starts,lengths,volts=find_rs_test(header)
if not volts:
return None,None,None,None
else:
segments=raw.read_block().segments
del(raw)
return segments,starts,lengths,volts
def get_segments_with_step(filepath):
try:
raw = AxonIO(filepath)
header = raw.read_header()
except FileNotFoundError as e:
print(e)
del (raw)
return None, None, None, None
starts, lengths, volts = find_rs_test(header)
if not volts:
return None, None, None, None
else:
segments = raw.read_block().segments
del (raw)
return segments, starts, lengths, volts
def plot_stuff(args):
path, fn = args
print(path)
segments, starts, lengths, volts = get_segments_with_step(path + fn)
if segments:
plot_all_tp_stats(segments, starts, lengths, volts)
else:
try:
segments = AxonIO(path + fn).read_block().segments
except FileNotFoundError as e:
print(e)
return None
def main():
from rig.ipython import embed
test_files=[
'2013_12_13_0045.abf',
'2013_12_13_0046.abf',
'2013_12_13_0047.abf',
'2013_12_13_0048.abf',
'2013_12_13_0049.abf',
'2013_12_13_0050.abf',
'2013_12_13_0051.abf',
'2013_12_13_0052.abf',
'2013_12_13_0053.abf',
'2013_12_13_0054.abf',
]
more=[
'2013_12_13_0055.abf',
'2013_12_13_0056.abf',
'2013_12_13_0057.abf',
'2013_12_13_0058.abf',
'2013_12_13_0059.abf',
'2013_12_13_0060.abf',
'2013_12_13_0061.abf',
'2013_12_13_0062.abf',
'2013_12_13_0063.abf',
'2013_12_13_0064.abf',
'2013_12_13_0065.abf',
'2013_12_13_0066.abf',
'2013_12_13_0067.abf',
'2013_12_13_0068.abf',
]
test_files=[
'/mnt/tstr/db/Dropbox/mlab/chlr project/20140305_0011 Cs.abf',
'/mnt/str/tom/mlab_data/clampex/2014_03_21_0120.abf', #this file is an example of the sampling seq bug
'/mnt/str/tom/mlab_data/clampex/13n29011.abf',
]
#dat_dir='/home/tom/mlab_data/clampex/'
#test_files=np.sort(os.listdir(dat_dir))[-133:]
fig=plt.figure(figsize=(10,10))
for filename in test_files:
#raw=AxonIO(dat_dir+filename)
raw=AxonIO(filename)
header=raw.read_header()
#print(repr(header))
blk=raw.read_block()
waveforms=build_waveform(header)
scale=1
downsample=10
embed()
#break
n_plots=len(waveforms)+len(blk.segments[0].analogsignals)
tmax=0
for s in blk.segments:
c_plot=1
count = 0
for signal in s.analogsignals:
plt.subplot(n_plots,1,c_plot)
c_plot+=1
plt.plot(signal.base[::downsample],'r-',linewidth=.5)
plt.title(signal.name)
plt.xlim(0,len(signal)/(scale*downsample))
plt.ylabel(signal.units)
waveform=waveforms.get(signal.channel_index)
if waveform:
plt.subplot(n_plots,1,c_plot)
c_plot+=1
#plt.plot(waveform[count][::downsample],'k-')
plt.plot(waveform[count],'k-')
plt.title('Command')
#plt.xlim(0,len(signal)/(scale*downsample))
nmax=np.max(waveform)
if nmax > tmax:
tmax = nmax
#plt.ylim(-1.2*tmax,1.2*tmax)
count+=1
plt.savefig('/tmp/test%s.png'%filename[-8:-4])
plt.clf()
def load_abf(filepath):
raw=AxonIO(filename=filepath)
block=raw.read_block(lazy=False,cascade=True)
segments=block.segments
header=raw.read_header()
return raw,block,segments,header
from neo import AxonIO
from scipy import signal
import numpy as np
import quantities as pq
from matplotlib import pyplot as plt
#matplotlib.use('TKAgg')
fname = "/Users/macbookair/Downloads/20180913/18913005.abf"
reader = AxonIO(filename=fname)
#fig = plt.figure()
#ax = fig.add_axes([0.15, 0.1, 0.7, 0.7]) #l,b,w,h
fig, ax = plt.subplots(figsize=(10, 5))
bl = reader.read() # reads the entire blocks
for i in range(0, 10):
#print(bl.readable_objects)
seg = bl[0].segments[i]
#seg = reader.read_segment()
data, units = enumerate(seg.analogsignals)
si = seg.analogsignals[0].sampling_rate
print(seg.analogsignals[0].units)
print(seg.analogsignals[0].sampling_rate)
print(seg.analogsignals[0].t_start)
print(seg.analogsignals[0].t_stop)
print(seg.analogsignals[0].times)
if (i == 0):
t = np.arange(seg.analogsignals[0].t_start,
seg.analogsignals[0].t_stop,
1 / seg.analogsignals[0].sampling_rate)
t = np.asmatrix(t)
t = t.reshape(np.size(t), 1)
def main():
from rig.ipython import embed
test_files = [
'2013_12_13_0045.abf',
'2013_12_13_0046.abf',
'2013_12_13_0047.abf',
'2013_12_13_0048.abf',
'2013_12_13_0049.abf',
'2013_12_13_0050.abf',
'2013_12_13_0051.abf',
'2013_12_13_0052.abf',
'2013_12_13_0053.abf',
'2013_12_13_0054.abf',
]
more = [
'2013_12_13_0055.abf',
'2013_12_13_0056.abf',
'2013_12_13_0057.abf',
'2013_12_13_0058.abf',
'2013_12_13_0059.abf',
'2013_12_13_0060.abf',
'2013_12_13_0061.abf',
'2013_12_13_0062.abf',
'2013_12_13_0063.abf',
'2013_12_13_0064.abf',
'2013_12_13_0065.abf',
'2013_12_13_0066.abf',
'2013_12_13_0067.abf',
'2013_12_13_0068.abf',
]
test_files = [
'/mnt/tstr/db/Dropbox/mlab/chlr project/20140305_0011 Cs.abf',
'/mnt/str/tom/mlab_data/clampex/2014_03_21_0120.abf', #this file is an example of the sampling seq bug
'/mnt/str/tom/mlab_data/clampex/13n29011.abf',
]
#dat_dir='/home/tom/mlab_data/clampex/'
#test_files=np.sort(os.listdir(dat_dir))[-133:]
fig = plt.figure(figsize=(10, 10))
for filename in test_files:
#raw=AxonIO(dat_dir+filename)
raw = AxonIO(filename)
header = raw.read_header()
#print(repr(header))
blk = raw.read_block()
waveforms = build_waveform(header)
scale = 1
downsample = 10
embed()
#break
n_plots = len(waveforms) + len(blk.segments[0].analogsignals)
tmax = 0
for s in blk.segments:
c_plot = 1
count = 0
for signal in s.analogsignals:
plt.subplot(n_plots, 1, c_plot)
c_plot += 1
plt.plot(signal.base[::downsample], 'r-', linewidth=.5)
plt.title(signal.name)
plt.xlim(0, len(signal) / (scale * downsample))
plt.ylabel(signal.units)
waveform = waveforms.get(signal.channel_index)
if waveform:
plt.subplot(n_plots, 1, c_plot)
c_plot += 1
#plt.plot(waveform[count][::downsample],'k-')
plt.plot(waveform[count], 'k-')
plt.title('Command')
#plt.xlim(0,len(signal)/(scale*downsample))
nmax = np.max(waveform)
if nmax > tmax:
tmax = nmax
#plt.ylim(-1.2*tmax,1.2*tmax)
count += 1
plt.savefig('/tmp/test%s.png' % filename[-8:-4])
plt.clf()
def load_abf(filepath):
raw = AxonIO(filename=filepath)
block = raw.read_block(lazy=False, cascade=True)
segments = block.segments
header = raw.read_header()
return raw, block, segments, header
import sys
import os
import numpy as np
from matplotlib import pyplot as plt
import neo
from neo import AxonIO
from cv_bridge import CvBridge, CvBridgeError
from thllib import flylib as flb
import rosbag
fly = flb.NetFly(1525)
abfreader = AxonIO(fly.abfpaths[0])
abffile = abfreader.read()
block = abffile[0]
segment = block.segments[0]
analogsignals = segment.analogsignals
times = np.array(analogsignals[0].times)
signal_idxs = {
'abf_electrode': 0,
'abf_wba_left_amp': 1,
'abf_wba_right_amp': 2,
'abf_sync': 3,
'abf_freq': 4,
'abf_left_hutchen': 5,
'abf_right_hutchen': 6,
'abf_led_pulse': 7,
'abf_kinefly_lmr': 8,
'abf_kinefly_left': 9,
'abf_kinefly_right': 10,
import pyabf
from matplotlib import pyplot as plt
from neo import AxonIO
fname = "/Volumes/Anup_2TB/raw_data/beiquelab/zen/data_anup/20190627/C3/2019_06_27_0152.abf"
abf = pyabf.ABF(fname)
nabf = AxonIO(filename=fname)
fig = plt.figure(figsize=(8, 5))
ax1 = fig.add_subplot(311)
ax1.grid(alpha=.2)
ax1.set_title("Digital Outputs")
ax1.set_ylabel("Digital Outputs")
# plot the digital output of the first sweep
abf.setSweep(sweepNumber=0, channel=0)
# ax1.plot(abf.sweepX, abf.sweepD(0), color='red')
# ax1.plot(abf.sweepX, abf.sweepD(1), color='green')
# ax1.plot(abf.sweepX, abf.sweepD(2), color='blue')
# ax1.plot(abf.sweepX, abf.sweepD(3), color='black')
# ax1.plot(abf.sweepX, abf.sweepD(4), color='red')
# ax1.plot(abf.sweepX, abf.sweepD(5), color='green')
# ax1.plot(abf.sweepX, abf.sweepD(6), color='blue')
# ax1.plot(abf.sweepX, abf.sweepD(7), color='black')
ax1.set_yticks([0, 1])
ax1.set_yticklabels(["OFF", "ON"])
ax1.axes.set_ylim(-.5, 1.5)
from neo import AxonIO
import numpy as np
import re
import os
homefolder = '/home/pi/ephys/2021-02-16/2021_02_16_0009.abf'
# abf = AxonIO(filename=homefolder)
reader = AxonIO(filename=homefolder)
nblocks = reader.block_count()
si = reader.get_signal_sampling_rate()
samplesize = reader.get_signal_size(block_index=0, seg_index=0)
tstart = reader.segment_t_start(block_index=0, seg_index=0)
tstop = reader.segment_t_stop(block_index=0, seg_index=0)
header = reader.header
nchannels = reader.signal_channels_count()
gseg = reader.segment_count(block_index=0)
channelspecs = reader.header["signal_channels"].dtype.names
# bl = reader.read_block(lazy= False)
seg = reader.read_segment(block_index=0, seg_index=1)
print(seg.analogsignals)
protocol = reader.read_protocol()
rawprotocol = reader.read_raw_protocol()
print('numberblocks: ', nblocks)
print('samplerate: ', si)
print('timestart: ', tstart)
print('timestop: ', tstop)
from neo import AxonIO
import numpy as np
from matplotlib import pyplot as plt
import datetime
# fname = "/Volumes/Anup_2TB/raw_data/beiquelab/zen/data_anup/20190627/C3/2019_06_27_0152.abf"
fname = "/Volumes/Anup_2TB/raw_data/beiquelab/o2p/ephys/20200213/C1/20213008.abf"
reader = AxonIO(filename=fname)
print(dir(reader))
# print('block count: ',reader.block_count())
# print('segment count: ',reader.segment_count(0))
# print('signal_channels_count: ',reader.signal_channels_count())
# print('signal sampling rate: ',reader.get_signal_sampling_rate())
# print('segment t_start: ', reader.segment_t_start(block_index=0,seg_index=0))
# print('segment t_start: ',reader.segment_t_stop(block_index=0,seg_index=0))
# print('header: ',reader.header) - implemented
# print('analog_signal_size: ',reader.get_signal_size(block_index=0,seg_index=0))
print(type(reader.get_analogsignal_chunk()))
print('filename', reader.filename)
# print('print_annotations',reader.print_annotations())
print('raw_annotations', reader.raw_annotations)
rawannot = reader.raw_annotations
# print(rawannot.keys())
# print(rawannot["blocks"])
# print(rawannot["blocks"][0].keys())
# doe = rawannot['blocks'][0]["rec_datetime"]
# print(doe.time())
# print(rawannot['blocks'][0]['segments'][0])
# print("protocol",reader.read_protocol())
# protocol_seg=reader.read_protocol()
# print(dir(protocol_seg[0]))