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import numpy as np | ||
import pyabf | ||
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import matplotlib.pyplot as plt | ||
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import sanpy | ||
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def _demo_deltaT(abf): | ||
"""Demonstrate delta duration.""" | ||
import matplotlib.pyplot as plt | ||
# abf = pyabf.ABF(PATH_DATA+"/2018_04_13_0016a_original.abf") | ||
epochTable = pyabf.waveform.EpochTable(abf, 0) | ||
print('epochTable') | ||
print(epochTable) | ||
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fig = plt.figure(figsize=(8, 5)) | ||
ax1 = fig.add_subplot(211) | ||
ax2 = fig.add_subplot(212, sharex=ax1) | ||
# for sweep in abf.sweepList[:20]: | ||
for sweep in abf.sweepList: | ||
abf.setSweep(sweep) | ||
sweepWaveform = epochTable.epochWaveformsBySweep[sweep] | ||
sweepC = sweepWaveform.getWaveform() | ||
ax1.plot(abf.sweepX, abf.sweepY, color='b', lw=.5) | ||
ax2.plot(abf.sweepX, sweepC, color='r', lw=.5) | ||
plt.show() | ||
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def _demo_sweepD(abf): | ||
"""Demonstrate how to access digital outputs.""" | ||
import matplotlib.pyplot as plt | ||
# abf = pyabf.ABF(PATH_DATA+"/17o05026_vc_stim.abf") | ||
epochTable = pyabf.waveform.EpochTable(abf, 0) # channel 0 | ||
for sweep in abf.sweepList: | ||
sweepWaveform = epochTable.epochWaveformsBySweep[sweep] # sweep 0 | ||
for digitalIdx in range(8): | ||
sweepD = sweepWaveform.getDigitalWaveform(digitalIdx) # digital output 4 | ||
print(f'digitalIdx:{digitalIdx} SweepD:{sweepD}') | ||
plt.plot(sweepD) | ||
plt.show() | ||
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def _demo_epoch_access(abf): | ||
"""Demonstrate how to access epoch levels and point indexes.""" | ||
import matplotlib.pyplot as plt | ||
# for fname in glob.glob(PATH_DATA+"/18702001-*.abf"): | ||
if 1: | ||
# abf = pyabf.ABF(fname) | ||
print("\n\n", "#"*20, abf.abfID, "(CH 1)", "#"*20) | ||
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# show waveform info for each sweep | ||
epochTable = pyabf.waveform.EpochTable(abf, 0) | ||
for sweep in abf.sweepList: | ||
sweepWaveform = epochTable.epochWaveformsBySweep[sweep] | ||
print("\n", "#"*5, "Sweep", sweep, "#"*5) | ||
print(sweepWaveform) | ||
print("levels:", sweepWaveform.levels) | ||
print("types:", sweepWaveform.types) | ||
print("p1s:", sweepWaveform.p1s) | ||
print("p2s:", sweepWaveform.p2s) | ||
print("pulsePeriods:", sweepWaveform.pulsePeriods) | ||
print("pulseWidths:", sweepWaveform.pulseWidths) | ||
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def attemptTwo(abf): | ||
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# sweeps (6,7,8,9,10,11) | ||
# path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/data/2022_08_15_0022.abf' | ||
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# abf = pyabf.ABF(path) | ||
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_userList = abf.userList | ||
print('userList:', len(_userList), _userList) | ||
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print('userListEnable:', abf.userListEnable, type(abf.userListEnable)) | ||
print('userListParamToVary:', abf.userListParamToVary, type(abf.userListParamToVary)) | ||
print('userListParamToVaryName:', abf.userListParamToVaryName, type(abf.userListParamToVaryName)) | ||
print('userListRepeat:', abf.userListRepeat, type(abf.userListRepeat)) | ||
print('_userListSection:', abf._userListSection, type(abf._userListSection)) | ||
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#print(abf.sweepD) | ||
#print('abf.tagTimesSec:', abf.tagTimesSec) | ||
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sweepList = abf.sweepList | ||
numSweeps = len(sweepList) | ||
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print('numSweeps:', numSweeps) | ||
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return abf | ||
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for sweep in sweepList: | ||
abf.setSweep(sweep) | ||
for digitalIdx in range(8): | ||
oneSweepD = abf.sweepD(digitalIdx) | ||
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channel = 0 | ||
sweepListSmall = [6,7,8,9,10,11] | ||
for sweep in sweepListSmall: | ||
abf.setSweep(sweep) | ||
print(f'=== sweep {sweep}') | ||
oneEpochTable = pyabf.waveform.EpochTable(abf, channel) | ||
print(oneEpochTable) | ||
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def attemptOne(): | ||
# 18 sweeps | ||
path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_08_15_0022.abf' | ||
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# 1 sweep | ||
# path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_09_01_0046.abf' | ||
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path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/data/2022_08_15_0022.abf' | ||
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ba = sanpy.bAnalysis(path) | ||
print(ba.fileLoader.getEpochTable(0)) | ||
print('') | ||
print(ba.fileLoader.getEpochTable(1)) | ||
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abf = pyabf.ABF(path) | ||
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# _demo_epoch_access(abf) | ||
# _demo_sweepD(abf) | ||
# _demo_deltaT(abf) | ||
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print('abf.channelList:', abf.channelList) | ||
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#print(abf.sweepD) | ||
#print('abf.tagTimesSec:', abf.tagTimesSec) | ||
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sweepList = abf.sweepList | ||
numSweeps = len(sweepList) | ||
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print('numSweeps:', numSweeps) | ||
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numDigitialOutputs = 8 | ||
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fig, axs = plt.subplots(3, 1, sharex=True) | ||
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print('self._abf.sweepD') | ||
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if 1: | ||
sweepD_list = [] | ||
for sweepIdx, sweep in enumerate(sweepList): | ||
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# if sweepIdx < 4: | ||
# continue | ||
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abf.setSweep(sweep) | ||
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sweepX = abf.sweepX | ||
sweepY = abf.sweepY | ||
sweepC = abf.sweepC | ||
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if 1: | ||
for i in range(numDigitialOutputs): | ||
oneSweepD = abf.sweepD(i) # 8 digital per sweep | ||
sweepD_list.append(oneSweepD) | ||
_max = np.max(oneSweepD) | ||
if _max > 0: | ||
equalOne = np.where(oneSweepD == 1) | ||
equalOne = equalOne[0] | ||
print(f'sweep {sweep} digital:{i} len:{len(oneSweepD)} min:{np.min(oneSweepD)} max:{np.max(oneSweepD)} equal1: {len(equalOne)} {equalOne}') | ||
axs[0].plot(sweepX, sweepD_list[-1]) | ||
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if sweepIdx == 10: | ||
oneEpochTable = pyabf.waveform.EpochTable(abf, channel=0) | ||
print(oneEpochTable) | ||
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axs[1].plot(sweepX, sweepC) | ||
axs[2].plot(sweepX, sweepY) | ||
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# use sanpy to generate an epoch table, one table per sweep | ||
if 0: | ||
_numSweeps = len(abf.sweepList) | ||
_epochTableList = [None] * _numSweeps | ||
for _sweepIdx in range(_numSweeps): | ||
abf.setSweep(_sweepIdx) | ||
_epochTableList[_sweepIdx] = sanpy.fileloaders.epochTable( | ||
abf | ||
) | ||
abf.setSweep(0) | ||
for epochTable in _epochTableList: | ||
print(epochTable) | ||
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if 0: | ||
# from the pyabf web documentation | ||
_numSweeps = len(abf.sweepList) | ||
for _sweepIdx in range(_numSweeps): | ||
abf.setSweep(_sweepIdx) | ||
for epochIdx, p1 in enumerate(abf.sweepEpochs.p1s): | ||
epochLevel = abf.sweepEpochs.levels[epochIdx] | ||
epochType = abf.sweepEpochs.types[epochIdx] | ||
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pulseWidth = abf.sweepEpochs.pulseWidths[epochIdx] | ||
pulsePeriod = abf.sweepEpochs.pulsePeriods[epochIdx] | ||
digitalStates = abf.sweepEpochs.digitalStates[epochIdx] | ||
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# used by pyabf when we access sweepD, getDigitalWaveform | ||
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print(f"sweep:{_sweepIdx} epoch index {epochIdx}: at point {p1} there is a {epochType} to level {epochLevel} pulseWidth:{pulseWidth} pulsePeriod:{pulsePeriod} digitalStates:{digitalStates}") | ||
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plt.show() | ||
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return abf | ||
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if __name__ == '__main__': | ||
print(pyabf.__version__) | ||
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abf = attemptOne() | ||
attemptTwo(abf) |
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