Merge pull request #142 from swharden/138

ABF.getOnlySweep()

dev/python/2024-10-15 single sweep.py

@@ -0,0 +1,29 @@
+import sys
+import pathlib
+import matplotlib.pyplot as plt
+import numpy as np
+
+try:
+    PATH_HERE = pathlib.Path(__file__).parent
+    PATH_ABFS = PATH_HERE.joinpath("../../data/abfs/").resolve()
+    PATH_SRC = PATH_HERE.joinpath("../../src/").resolve()
+    print(PATH_SRC)
+    sys.path.insert(0, str(PATH_SRC))
+    import pyabf
+except:
+    raise EnvironmentError()
+1
+
+if __name__ == "__main__":
+    abfPath = pathlib.Path(PATH_ABFS).joinpath("14o08011_ic_pair.abf")
+
+    abf = pyabf.ABF(abfPath, loadData=False)
+    channelA = abf.getOnlySweep(sweepIndex=0, channelIndex=0)
+    channelB = abf.getOnlySweep(sweepIndex=0, channelIndex=1)
+
+    print(np.mean(channelA))
+    print(np.mean(channelB))
+
+    plt.plot(channelA)
+    plt.plot(channelB)
+    plt.show()

src/pyabf/abf.py

@@ -688,6 +688,48 @@ def setSweep(self,
             epochTable = None
             self.sweepEpochs = None
 
+    def getOnlySweep(self, sweepIndex: int, channelIndex: int = 0, startTime: float = None, endTime: float = None):
+        """
+        Get values for a sweep by reading directly from the ABF file instead of loading all sweeps into memory.
+        This method is useful for ABF files which are too large to be loaded into memory.
+
+        ### Parameters
+        * `sweepIndex` - The sweep number (starting at zero). Note that all channels for this sweep will be returned.
+        * `startTime` - Data returned will begin at this time within the sweep (in seconds)
+        * `endTime` - Data returned will end at this time within the sweep (in seconds)
+        """
+
+        startTime = startTime if startTime else 0
+        startTime = max(0, startTime)
+
+        endTime = endTime if endTime else self.sweepLengthSec
+        endTime = min(endTime, self.sweepLengthSec)
+
+        bytesPerSample = int(self.dataPointByteSize)
+        bytesPerSecond = int(self.dataPointByteSize * self.sampleRate)
+        samplesPerSweep = int(self.dataPointCount / self.sweepCount)
+        bytesPerSweep = samplesPerSweep * bytesPerSample
+        sweepFirstByte = self.dataByteStart + bytesPerSweep * sweepIndex
+        startTime = startTime if startTime else 0
+        sweepFirstByte += int(startTime * bytesPerSecond)
+        endTime = endTime if endTime else self.sweepLengthSec
+        samplesPerSweep = int((endTime - startTime) * self.sampleRate)
+        samplesTotal = self.channelCount*samplesPerSweep
+
+        with open(self.abfFilePath, 'rb') as fb:
+            fb.seek(sweepFirstByte)
+            raw = np.fromfile(fb, dtype=self._dtype, count=samplesTotal)
+            nRows = self.channelCount
+            nCols = samplesPerSweep
+            raw = np.reshape(raw, (nCols, nRows))
+            raw = np.transpose(raw)
+            data = raw[channelIndex]
+            data = data.astype(np.float32)
+            if self._dtype == np.int16:
+                data *= self._dataGain[channelIndex]
+                data += self._dataOffset[channelIndex]
+            return data
+
     def _getAdcNameAndUnits(self, adcIndex: int) -> Tuple[str, str]:
         if (adcIndex < len(self.adcNames)):
             return [self.adcNames[adcIndex], self.adcUnits[adcIndex]]

tests/test_api.py

@@ -184,3 +184,12 @@ def test_headerText(abfPath):
     html = abf.headerHTML
     assert isinstance(html, str)
     assert len(html)
+
+
+def test_readOneSweep():
+    abfPath = "data/abfs/14o08011_ic_pair.abf"
+    abf = pyabf.ABF(abfPath, loadData=False)
+    channelA = abf.getOnlySweep(sweepIndex=0, channelIndex=0)
+    channelB = abf.getOnlySweep(sweepIndex=0, channelIndex=1)
+    assert np.mean(channelA) == pytest.approx(-58.870506, 5)
+    assert np.mean(channelB) == pytest.approx(-52.948666, 5)