def setup_class(cls):
TestBase.setup_class()
ctx = cls.local_stack.getAuthenticatedDataStoreCoordinator().getContext()
proj = ctx.insertProject('ABF import', 'ABF import', DateTime())
exp = proj.insertExperiment('ABF experiment', DateTime())
cls.device_info = {u'amplifier.mode': u'I-clamp',
u'amplifier.channels.0.gain': 2.5,
u'amplifier.channels.1.gain': 3.5}
# TODO when we move to beta3
#exp.setEquipmentSetupFromMap(to_map(cls.device_info))
cls.src = ctx.insertSource("recording source", "source-id")
abf_file = 'fixtures/example1.abf'
logging.info("Importing file...")
cls.epoch_group = import_file(abf_file,
exp,
"amplifier",
[cls.src])[0] #single block
reader = AxonIO(filename=abf_file)
cls.block = reader.read()[0] # single block
def read_neo(path):
# Read abf file with neo
reader = AxonIO(filename=path)
block = reader.read()
# Extract analog signals
if len(block[0].segments[0].analogsignals) == 1:
channel1 = np.empty(block[0].segments[0].analogsignals[0].T.shape)
channel1_units = block[0].segments[0].analogsignals[0].units
channel2 = None
channel2_units = None
t = block[0].segments[0].analogsignals[0].times.magnitude
for idx, seg in enumerate(block[0].segments):
channel1[idx] = seg.analogsignals[0].T
#
# return {'file_name': block.file_origin,
# 'recording_date': block.rec_datetime,
# 'time': t,
# 'channel1': channel1,
elif len(block[0].segments[0].analogsignals) == 2:
channel1 = np.empty((len(block[0].segments), block[0].segments[0].analogsignals[0].size))
channel1_units = block[0].segments[0].analogsignals[0].units
channel1_sampling = block[0].segments[0].analogsignals[0].sampling_rate
channel2 = np.empty((len(block[0].segments), block[0].segments[0].analogsignals[1].size))
channel2_units = block[0].segments[0].analogsignals[1].units
channel2_sampling = block[0].segments[0].analogsignals[1].sampling_rate
t = block[0].segments[0].analogsignals[0].times.magnitude
for idx, seg in enumerate(block[0].segments):
channel1[idx] = seg.analogsignals[0].T
channel2[idx] = seg.analogsignals[1].T
#channel1[idx] = seg.analogsignals[0]
#channel2[idx] = seg.analogsignals[1]
channel_1 = AnalogData(
signal=channel1,
time=t,
units=channel1_units,
sampling_rate=channel1_sampling
)
channel_2 = AnalogData(
signal=channel2,
time=t,
units=channel2_units,
sampling_rate=channel2_sampling)
else:
raise Exception('File {0} either has too many channels, or no channels.'.format(path))
return AbfFile(
[channel_1, channel_2],
file_name=block[0].file_origin,
date=block[0].rec_datetime)
from bokeh.io import output_file, show
from bokeh.layouts import widgetbox, row
from bokeh.models import CustomJS, ColumnDataSource, Span
from bokeh.models.widgets import Button, RadioButtonGroup, Select, Slider, RangeSlider
from bokeh.plotting import figure
from bokeh.layouts import layout
import numpy as np
from neo.io import AxonIO
# Set output
output_file("dashboard.html")
# Read data
reader = AxonIO('/home/matt/Downloads/2017_02_23_0110.abf')
block = reader.read()
ch1_data = []
ch2_data = []
for idx, seg in enumerate(block[0].segments):
ch1_data.append(seg.analogsignals[0])
ch2_data.append(seg.analogsignals[1])
ch1_data = np.array(ch1_data).reshape(10,100000)
ch2_data = np.array(ch2_data).reshape(10,100000)
# Plot data
source = ColumnDataSource(data=dict(
x=np.arange(0, len(ch2_data[0])),
y=ch2_data[0],
main=ch2_data[0]
)
)
