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ABF: improve support for ABFs with variable sweep lengths #141

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merged 4 commits into from
Sep 17, 2024
Merged

ABF: improve support for ABFs with variable sweep lengths #141

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f6019ae
ABF: improve support for variable sweep lengths
swharden Sep 17, 2024
2274ee1
abf: remove noisy debug message
swharden Sep 17, 2024
35cf7a6
abf: autoformat comments
swharden Sep 17, 2024
f3eeb0b
Merge branch 'main' into 140
swharden Sep 17, 2024
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19 changes: 19 additions & 0 deletions dev/python/2024-09-17 verjinia.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
import sys
import pathlib

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__":
abf = pyabf.ABF(R"C:\Users\swharden\Documents\Temp\24215056.abf")

for abf_path in pathlib.Path(PATH_ABFS).glob("*.abf"):
abf = pyabf.ABF(abf_path)
14 changes: 11 additions & 3 deletions src/pyabf/abf.py
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Expand Up @@ -327,8 +327,8 @@ def _readHeadersV2(self, fb: BufferedReader):
try:
# This is the correct way, but it doesn't seem to work for every ABF.
# I think this is because there is a bug in the string indexer.
#self.userList = self._stringsIndexed.indexedStrings[self._userListSection.nStringIndex[0]]
#self.userList = [float(x) for x in self.userList.split(",")]
# self.userList = self._stringsIndexed.indexedStrings[self._userListSection.nStringIndex[0]]
# self.userList = [float(x) for x in self.userList.split(",")]

# This is weird but it's been in the code for a while and seems to work.
firstBlockStrings = self._stringsSection._stringsRaw[0].split(
Expand All @@ -351,6 +351,14 @@ def _readHeadersV2(self, fb: BufferedReader):
self.sweepCount = self._headerV2.lActualEpisodes
self.channelList = list(range(self.channelCount))

# correct dataPointCount for ABFs with variable length sweeps
# https://github.com/swharden/pyABF/issues/140
# https://github.com/swharden/pyABF/issues/108
if hasattr(self, "_synchArraySection"):
variableDataPointCount = sum(self._synchArraySection.lLength)
if (variableDataPointCount > 0 and variableDataPointCount != self.dataPointCount):
self.dataPointCount = variableDataPointCount

# tags
self.tagComments = self._tagSection.sComment
self.tagTimesSec = self._tagSection.lTagTime
Expand All @@ -376,7 +384,7 @@ def _readHeadersV2(self, fb: BufferedReader):
self._dataGain = [1]*self.channelCount
self._dataOffset = [0]*self.channelCount
for i in range(self.channelCount):
#adcIndex = self._adcSection.nADCSamplingSeq[i]
# adcIndex = self._adcSection.nADCSamplingSeq[i]
# NOTE: ADC sequence is handled inside the ADC section so it doesn't need to be handled here
adcIndex = i
self._dataGain[i] /= self._adcSection.fInstrumentScaleFactor[adcIndex]
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