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[NeuralynxRawIO] Generalize header processing #1566

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Merged
zm711 merged 11 commits into from
Jul 2, 2025
Merged

[NeuralynxRawIO] Generalize header processing #1566

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ac3b3d4
Extracting check and conversions from read_properties.
Sep 21, 2024
5d983c1
Remove argument for setApplicationAndVersion.
Sep 21, 2024
ed74132
Make acquisition type a proper IntEnum which is defined in ncssection…
Sep 21, 2024
692fb43
Add example comments.
Sep 24, 2024
a911d33
Change base classes to avoid duplication.
Sep 24, 2024
0b79e84
Remove unused method.
Sep 24, 2024
fac5fbe
Replace ‘def’ and ‘peg’ header types with ‘inProps’
Sep 24, 2024
9bccef3
Add comment to explain contents of dictionary more fully.
Sep 24, 2024
24f0a9f
First condense of header patterns.
Sep 24, 2024
6192359
Second condense of header patterns.
Sep 24, 2024
c450970
condense and filename regex moved out
Sep 24, 2024
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20 changes: 17 additions & 3 deletions neo/rawio/neuralynxrawio/ncssections.py
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Original file line number Diff line number Diff line change
Expand Up @@ -37,6 +37,19 @@
import math
import numpy as np

from enum import IntEnum, auto


class AcqType(IntEnum):
PRE4 = auto()
BML = auto()
DIGITALLYNX = auto()
DIGITALLYNXSX = auto()
CHEETAH64 = auto()
RAWDATAFILE = auto()
CHEETAH560 = auto()
ATLAS = auto()
UNKNOWN = auto()

class NcsSections:
"""
Expand Down Expand Up @@ -250,7 +263,7 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None, strict_gap_mode=Tru
acqType = nlxHdr.type_of_recording()
freq = nlxHdr["sampling_rate"]

if acqType == "PRE4":
if acqType == AcqType.PRE4:
# Old Neuralynx style with truncated whole microseconds for actual sampling. This
# restriction arose from the sampling being based on a master 1 MHz clock.
microsPerSampUsed = math.floor(NcsSectionsFactory.get_micros_per_samp_for_freq(freq))
Expand All @@ -266,7 +279,8 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None, strict_gap_mode=Tru
ncsSects.sampFreqUsed = sampFreqUsed
ncsSects.microsPerSampUsed = microsPerSampUsed

elif acqType in ["DIGITALLYNX", "DIGITALLYNXSX", "CHEETAH64", "CHEETAH560", "RAWDATAFILE"]:
elif acqType in [AcqType.DIGITALLYNX, AcqType.DIGITALLYNXSX, AcqType.CHEETAH64,
AcqType.CHEETAH560, AcqType.RAWDATAFILE]:
# digital lynx style with fractional frequency and micros per samp determined from block times
if gapTolerance is None:
if strict_gap_mode:
Expand All @@ -293,7 +307,7 @@ def build_for_ncs_file(ncsMemMap, nlxHdr, gapTolerance=None, strict_gap_mode=Tru
ncsSects.sampFreqUsed = sampFreqUsed
ncsSects.microsPerSampUsed = NcsSectionsFactory.get_micros_per_samp_for_freq(sampFreqUsed)

elif acqType == "BML" or acqType == "ATLAS":
elif acqType == AcqType.BML or acqType == AcqType.ATLAS:
# BML & ATLAS style with fractional frequency and micros per samp
if strict_gap_mode:
# this is the old behavior, maybe we could put 0.9 sample interval no ?
Expand Down
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