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@@ -12,6 +12,107 @@ abspath = os.path.abspath(__file__)
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dname = os.path.dirname(abspath)
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os.chdir(dname)
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+def read_expkeys(
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+ in_file,
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+ ):
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+ """
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+ Read ExpKeys format, which is an internal convention of the Dartmouth PBS van der Meer lab.
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+
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+ Parameters
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+ ----------
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+
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+ in_file: str, optional
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+ Path to ExpKeys file, will have a “.m” format.
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+ """
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+
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+ raw_fields = [
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+ 'species',
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+ 'genetics',
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+ 'subject_id',
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+ 'hemisphere',
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+ 'experimenter',
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+ 'weight',
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+ 'probeDepth',
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+ 'date',
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+ 'target',
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+ 'light_source',
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+ 'wavelength',
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+ 'probeType',
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+ 'probeID',
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+ 'HSID',
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+ 'patch_cord_dia',
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+ 'patch_cord_NA',
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+ 'probe_fiber_dia',
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+ 'probe_fiber_NA',
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+ 'max_power',
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+ 'output_power_calib',
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+ 'dial_values_calib',
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+ 'dial_value',
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+ 'light_power',
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+ 'stim_mode',
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+ 'ISI',
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+ 'short_stim_pulse_width',
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+ 'long_stim_pulse_width',
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+ 'pre_trial_stim_on',
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+ 'trial_stim_on',
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+ 'post_trial_stim_on',
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+ 'long_stim_on',
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+ 'stim_off',
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+ 'pre_baseline_times',
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+ 'pre_stim_times',
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+ 'stim_times',
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+ 'post_baseline_times',
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+ 'post_stim_times',
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+ 'long_stim_times',
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+ 'recording_times',
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+ 'notes',
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+ 'isReferenceRecordedSeparately',
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+ 'hasSpecialStim',
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+ 'LFP_channels',
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+ 'ref_channels',
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+ ]
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+
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+ p1 = re.compile('ExpKeys.(.+?)=')
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+ p2 = ['=(.+?)";', '=(.+?)};', '=(.+?)];', '=(.+?);'] # The order is important
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+ p2 = [re.compile(x) for x in p2]
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+
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+ in_file = os.path.abspath(os.path.expanduser(in_file))
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+
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+ out_dict = {}
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+ with open(in_file, 'r') as f:
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+ for line in f:
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+ m = re.search(p1, line)
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+ if m:
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+ key = m.group(1).strip()
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+ if key in raw_fields:
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+ for iP in range(4):
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+ m = re.search(p2[iP], line)
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+ if m:
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+ if iP == 0: # This is a simple string
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+ value = m.group(1).strip(" \"")
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+ elif iP == 1: # This is a 1-D list
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+ temp = m.group(1).strip()[1:]
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+ value = [x.strip()[1:-1] for x in temp.split(',')]
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+ elif iP == 2: # This can be a nested loop, FML AARRGGGHHHHHHH
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+ temp = m.group(1).strip()[1:]
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+ value = [float(x.strip()) for x in temp.split(',')]
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+ #value = "I don't know man"
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+ else: # iP has to be 3, and this is either a number, or true/false
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+ temp = m.group(1).strip()
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+ if temp == 'true':
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+ value = True
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+ elif temp == 'false':
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+ value = False
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+ else: # definitely a number
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+ value = float(m.group(1).strip())
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+ out_dict[key] = value
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+ break
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+ else:
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+ continue
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+
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+ #print(json.dumps(out_dict))
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+ return out_dict
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+
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try:
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scratch_path = os.environ['MVMNDA_RAWDATA_SCRATCH_PATH']
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@@ -32,13 +133,12 @@ subject = m.groupdict()["subject"]
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# Extract what metadata we can from the source files
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metadata = converter.get_metadata()
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+# Set timezone
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session_start_time = metadata["NWBFile"]["session_start_time"].replace(tzinfo=tz.gettz("US/Eastern"))
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metadata["NWBFile"].update(session_start_time=session_start_time)
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session = (metadata["NWBFile"]["session_start_time"]).strftime("%Y%m%d%H%M%S")
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-#print(session)
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-
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-# Maybe do data of birth rather than age
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+# Maybe do date of birth rather than age
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metadata["Subject"] = dict(
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subject_id=subject,
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sex="F",
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@@ -48,8 +148,12 @@ metadata["Subject"] = dict(
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)
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# No idea why this needs to be done via `.update()`
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metadata["NWBFile"].update(session_id=session)
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-#metadata["session_id"] = session
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-#metadata["NWBFile"] = dict(session_id=session)
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+
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+# Read in Matt's lab “keys” files.
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+
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+
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+
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+
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#print(metadata)
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