Merge pull request #122 from pnewstein/master

allow more adc channels than dac channels

src/README.rst

@@ -29,7 +29,7 @@ Access ABF sweep data:
 
   import pyabf
   abf = pyabf.ABF("demo.abf")
-  abf.setSweep(sweepNumber: 3, channel: 0)
+  abf.setSweep(sweepNumber=3, channel=0)
   print(abf.sweepY) # displays sweep data (ADC)
   print(abf.sweepX) # displays sweep times (seconds)
   print(abf.sweepC) # displays command waveform (DAC)

src/pyabf/__init__.py

@@ -5,7 +5,7 @@
 Documentation and code examples, and more can be found at:
     https://github.com/swharden/pyABF
 """
-__version__ = '2.3.2'
+__version__ = '2.3.3'
 
 import sys
 import os

src/pyabf/abf.py

@@ -32,7 +32,7 @@
 import numpy as np
 from pathlib import PureWindowsPath
 import hashlib
-from typing import Union, List
+from typing import Union, List, Tuple
 
 
 class ABF:
@@ -604,18 +604,19 @@ def setSweep(self,
             with open(self.abfFilePath, 'rb') as fb:
                 self._loadAndScaleData(fb)
 
+        adcName, adcUnits = self._getAdcNameAndUnits(channel)
+        dacName, dacUnits = self._getDacNameAndUnits(channel)
+
         # sweep information
         self.sweepNumber = sweepNumber
         self.sweepChannel = channel
-        self.sweepUnitsY = self.adcUnits[channel]
-        self.sweepUnitsC = self.dacUnits[channel]
+        self.sweepUnitsY = adcUnits
+        self.sweepUnitsC = dacUnits
         self.sweepUnitsX = "sec"
 
         # standard labels
-        self.sweepLabelY = "{} ({})".format(
-            self.adcNames[channel], self.adcUnits[channel])
-        self.sweepLabelC = "{} ({})".format(
-            self.dacNames[channel], self.dacUnits[channel])
+        self.sweepLabelY = f"{adcName} ({adcUnits})"
+        self.sweepLabelC = f"{dacName} ({dacUnits})"
         self.sweepLabelX = "Time (seconds)"
         self.sweepLabelD = "Digital Output (V)"
 
@@ -673,8 +674,24 @@ def setSweep(self,
             assert (self.sweepPointCount == len(self.sweepY))
 
         # prepare the stimulus waveform table for this sweep/channel
-        epochTable = pyabf.waveform.EpochTable(self, channel)
-        self.sweepEpochs = epochTable.epochWaveformsBySweep[sweepNumber]
+        if (channel < len(self.holdingCommand)):
+            epochTable = pyabf.waveform.EpochTable(self, channel)
+            self.sweepEpochs = epochTable.epochWaveformsBySweep[sweepNumber]
+        else:
+            epochTable = None
+            self.sweepEpochs = None
+
+    def _getAdcNameAndUnits(self, adcIndex: int) -> Tuple[str, str]:
+        if (adcIndex < len(self.adcNames)):
+            return [self.adcNames[adcIndex], self.adcUnits[adcIndex]]
+        else:
+            return [None, None]
+
+    def _getDacNameAndUnits(self, dacIndex: int) -> Tuple[str, str]:
+        if (dacIndex < len(self.dacNames)):
+            return [self.dacNames[dacIndex], self.dacUnits[dacIndex]]
+        else:
+            return [None, None]
 
     @property
     def sweepC(self):
@@ -713,6 +730,8 @@ def sweepC(self, sweepData=None):
     def sweepD(self, digOutNumber=0):
         """Generate a waveform for the given digital output."""
         assert isinstance(self, pyabf.ABF)
+        if (self.sweepChannel >= len(self.holdingCommand)):
+            return None
         epochTable = pyabf.waveform.EpochTable(self, self.sweepChannel)
         sweepWaveform = epochTable.epochWaveformsBySweep[self.sweepNumber]
         sweepD = sweepWaveform.getDigitalWaveform(digOutNumber)

src/setup.py

@@ -14,7 +14,7 @@
 # standard pypi stuff
 setup(
     name='pyabf',
-    version='2.3.2',
+    version='2.3.3',
     author='Scott W Harden',
     author_email='SWHarden@gmail.com',
     python_requires='>=3.6',

tests/test_api.py

@@ -117,15 +117,25 @@ def test_ABF_properties(abfPath):
             abf.setSweep(sweep, channel)
             assert isinstance(abf.sweepChannel, int)
             assert isinstance(abf.sweepNumber, int)
-            assert isinstance(abf.sweepLabelC, str)
+
+            # time units are manually defined
+            assert isinstance(abf.sweepUnitsX, str)
+            assert abf.sweepUnitsX == "sec"
+
+            # labels are pyabf inventions and will always be present
             assert isinstance(abf.sweepLabelX, str)
             assert isinstance(abf.sweepLabelY, str)
-            assert isinstance(abf.sweepUnitsC, str)
-            assert isinstance(abf.sweepUnitsX, str)
-            assert isinstance(abf.sweepUnitsY, str)
+            assert isinstance(abf.sweepLabelC, str)
+
+            # ADC labels are likely available for every channel
+            if (abf.sweepLabelY is not None):
+                assert isinstance(abf.sweepUnitsY, str)
 
-            sweepD = abf.sweepD(0)  # digital output generation
-            assert isinstance(sweepD, np.ndarray)
+            # DAC labels are likely available for every channel
+            # but may not if there are more ADCs than DACs
+            if (abf.sweepUnitsC is not None):
+                assert isinstance(abf.sweepUnitsC, str)
+                assert isinstance(abf.sweepD(0), np.ndarray)
 
 
 def test_uuid_isExpectedValue():

tests/test_sweepHashes.py

@@ -2643,3 +2643,20 @@
 knownAbfSweepValues["user-list-durations.abf SW1 CH1"] = "51612, -35.00000000, -35.00000000, 39.15184402"
 knownAbfSweepValues["user-list-durations.abf SW2 CH0"] = "51612, -44.68749619, -49.68749619, 211.29635620"
 knownAbfSweepValues["user-list-durations.abf SW2 CH1"] = "51612, -35.00000000, -35.00000000, 35.34297180"
+
+knownAbfSweepValues["test_0001.abf SW0 CH0"] = "12896, -0.24414062, -0.24414062, 0.01767103"
+knownAbfSweepValues["test_0001.abf SW0 CH1"] = "12896, -0.36621094, -0.33569336, 0.01851589"
+knownAbfSweepValues["test_0001.abf SW0 CH2"] = "12896, 0.18310547, 0.15258789, 0.01685126"
+knownAbfSweepValues["test_0001.abf SW0 CH3"] = "12896, -0.18310547, -0.15258789, 0.01687169"
+knownAbfSweepValues["test_0001.abf SW0 CH4"] = "12896, -0.15258789, -0.15258789, 0.01728301"
+knownAbfSweepValues["test_0001.abf SW0 CH5"] = "12896, -0.00610352, -0.00610352, 0.00167757"
+knownAbfSweepValues["test_0001.abf SW0 CH6"] = "12896, -0.06103516, -0.03051758, 0.01647715"
+knownAbfSweepValues["test_0001.abf SW0 CH7"] = "12896, -0.00274658, -0.00274658, 0.00016622"
+knownAbfSweepValues["test_0001.abf SW0 CH8"] = "12896, -0.00274658, -0.00274658, 0.00016532"
+knownAbfSweepValues["test_0001.abf SW0 CH9"] = "12896, -0.00213623, -0.00244141, 0.00017623"
+knownAbfSweepValues["test_0001.abf SW0 CH10"] = "12896, -0.00305176, -0.00305176, 0.00016586"
+knownAbfSweepValues["test_0001.abf SW0 CH11"] = "12896, 0.00213623, 0.00213623, 0.00016889"
+knownAbfSweepValues["test_0001.abf SW0 CH12"] = "12896, -0.00122070, -0.00122070, 0.00017642"
+knownAbfSweepValues["test_0001.abf SW0 CH13"] = "12896, 0.00152588, 0.00183105, 0.00016845"
+knownAbfSweepValues["test_0001.abf SW0 CH14"] = "12896, -0.21362305, -0.18310547, 0.01735568"
+knownAbfSweepValues["test_0001.abf SW0 CH15"] = "12896, 0.00000000, 0.00000000, 0.00191588"

tests/test_values.py

@@ -101,6 +101,7 @@
 FIRSTVALUES['sine sweep magnitude 20'] = [0.00000]
 FIRSTVALUES['user-list-durations'] = [-69.68749, -35.00000]
 FIRSTVALUES['vc_drug_memtest'] = [-7.20215]
+FIRSTVALUES["test_0001"] = [-0.24414062, -0.36621094, 0.18310547, -0.18310547, -0.15258789, -0.0061035156, -0.061035156, -0.002746582, -0.002746582, -0.0021362305, -0.0030517578, 0.0021362305, -0.0012207031, 0.0015258789, -0.21362305, 0.0]
 
 
 @pytest.mark.parametrize("abfPath", glob.glob("data/abfs/*.abf"))