before photonics west

sandbox/owlAnalysis.py

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+import numpy as np
+import pyabf
+
+import matplotlib.pyplot as plt
+
+import sanpy
+
+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)
+
+    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()
+
+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()
+
+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)
+
+        # 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)
+
+def attemptTwo(abf):
+
+    # sweeps (6,7,8,9,10,11)
+    # path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/data/2022_08_15_0022.abf'
+
+    # abf = pyabf.ABF(path)
+
+    _userList = abf.userList
+    print('userList:', len(_userList), _userList)
+
+    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))
+
+    #print(abf.sweepD)
+    #print('abf.tagTimesSec:', abf.tagTimesSec)
+
+    sweepList = abf.sweepList
+    numSweeps = len(sweepList)
+
+    print('numSweeps:', numSweeps)
+
+    return abf
+
+    for sweep in sweepList:
+        abf.setSweep(sweep)
+        for digitalIdx in range(8):
+            oneSweepD = abf.sweepD(digitalIdx)
+
+    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)
+
+def attemptOne():
+    # 18 sweeps
+    path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_08_15_0022.abf'
+
+    # 1 sweep
+    # path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/2022_09_01_0046.abf'
+
+    path = '/Users/cudmore/Dropbox/data/sanpy-users/porter/data/2022_08_15_0022.abf'
+
+    ba = sanpy.bAnalysis(path)
+    print(ba.fileLoader.getEpochTable(0))
+    print('')
+    print(ba.fileLoader.getEpochTable(1))
+
+    abf = pyabf.ABF(path)
+
+    # _demo_epoch_access(abf)
+    # _demo_sweepD(abf)
+    # _demo_deltaT(abf)
+
+    print('abf.channelList:', abf.channelList)
+
+    #print(abf.sweepD)
+    #print('abf.tagTimesSec:', abf.tagTimesSec)
+
+    sweepList = abf.sweepList
+    numSweeps = len(sweepList)
+
+    print('numSweeps:', numSweeps)
+
+    numDigitialOutputs = 8
+
+    fig, axs = plt.subplots(3, 1, sharex=True)
+
+    print('self._abf.sweepD')
+
+    if 1:
+        sweepD_list = []
+        for sweepIdx, sweep in enumerate(sweepList):
+
+            # if sweepIdx < 4:
+            #     continue
+
+            abf.setSweep(sweep)
+
+            sweepX = abf.sweepX
+            sweepY = abf.sweepY
+            sweepC = abf.sweepC
+
+            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])
+
+            if sweepIdx == 10:
+                oneEpochTable = pyabf.waveform.EpochTable(abf, channel=0)
+                print(oneEpochTable)
+
+            axs[1].plot(sweepX, sweepC)
+            axs[2].plot(sweepX, sweepY)
+
+    # 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)
+
+    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]
+
+                pulseWidth = abf.sweepEpochs.pulseWidths[epochIdx]
+                pulsePeriod = abf.sweepEpochs.pulsePeriods[epochIdx]
+                digitalStates = abf.sweepEpochs.digitalStates[epochIdx]
+
+                # used by pyabf when we access sweepD, getDigitalWaveform
+
+                print(f"sweep:{_sweepIdx} epoch index {epochIdx}: at point {p1} there is a {epochType} to level {epochLevel} pulseWidth:{pulseWidth} pulsePeriod:{pulsePeriod} digitalStates:{digitalStates}")
+
+
+    plt.show()
+
+    return abf
+
+if __name__ == '__main__':
+    print(pyabf.__version__)
+
+    abf = attemptOne()
+    attemptTwo(abf)