# coding=utf-8 ''' Reach-to-grasp IO module This module provides an IO to load data recorded in the context of the reach- to-grasp experiments conducted by Thomas Brochier and Alexa Riehle at the Institute de Neurosciences de la Timone. The IO is based on the BlackrockIO of the Neo library, which is used in the background to load the primary data, and utilized the odML library to load metadata information. Specifically, this IO annotates the Neo object returned by BlackrockIO with semantic information, e.g., interpretation of digital event codes, and key-value pairs found in the corresponding odML file are attached to relevant Neo objects as annotations. Authors: Julia Sprenger, Lyuba Zehl, Michael Denker Copyright (c) 2017, Institute of Neuroscience and Medicine (INM-6), Forschungszentrum Juelich, Germany All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the names of the copyright holders nor the names of the contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ''' import glob import os import re import warnings import numpy as np import odml import odml.tools import quantities as pq import neo from neo.io.blackrockio import BlackrockIO from neo.io.proxyobjects import SpikeTrainProxy, AnalogSignalProxy class ReachGraspIO(BlackrockIO): """ Derived class from Neo's BlackrockIO to load recordings obtained from the reach-to-grasp experiments. Args: filename (string): File name (without extension) of the set of Blackrock files to associate with. Any .nsX or .nev, .sif, or .ccf extensions are ignored when parsing this parameter. Note: unless the parameter nev_override is given, this IO will load the nev file containing the most recent spike sorted data of all nev files found in the same directory as filename. The spike sorting version is attached to filename by a postfix '-XX', where XX is the version, e.g., l101010-001-02 for spike sorting version 2 of file l101010-001. If an odML file is specified, the version must be listed in the odML entries at "/PreProcessing/OfflineSpikeSorting/Sortings" and relates to the section "/PreProcessing/OfflineSpikeSorting/Sorting-XX". If no odML is present, no information on the spike sorting (e.g., if a unit is SUA or MUA) is provided by this IO. odml_directory (string): Alternative directory where the odML file is stored. If None, the directory is assumed to be the same as the .nev and .nsX data files. Default: None. nsx_override (string): File name of the .nsX files (without extension). If None, filename is used. Default: None. nev_override (string): File name of the .nev file (without extension). If None, the current spike-sorted version filename is used (see parameter filename above). Default: None. nsx_to_load (int, list, 'max', 'all' (=None)) default None: IDs of nsX file from which to load data, e.g., if set to 5 only data from the ns5 file are loaded. If 'all', then all nsX will be loaded. Contrary to previsous version of the IO (<0.7), nsx_to_load must be set at the init before parse_header(). sif_override (string): DEPRECATED File name of the .sif file (without extension). If None, filename is used. Default: None. ccf_override (string): DEPRECATED File name of the .ccf file (without extension). If None, filename is used. Default: None. odml_override (string): File name of the .odml file (without extension). If None, filename is used. Default: None. verbose (boolean): If True, the class will output additional diagnostic information on stdout. Default: False Returns: - Attributes: condition_str (dict): Dictionary containing a list of string codes reflecting the trial types that occur in recordings in a certain condition code (dictionary keys). For example, for condition 1 (all grip first conditions), condition_str[1] contains the list ['SGHF', 'SGLF', 'PGHF', 'PGLF']. Possible conditions: 0:[] No trials, or condition not conclusive from file 4 types (two_cues_task): 1: all grip-first trial types with two different cues 2: all force-first trial types with two different cues 2 types (two_cues_task): 11: grip-first, but only LF types 12: grip-first, but only HF types 13: grip-first, but only SG types 14: grip-first, but only PG types 2 types (two_cues_task): 21: force-first, but only LF types 22: force-first, but only HF types 23: force-first, but only SG types 24: force-first, but only PG types 1 type (two_cues_task): 131: grip-first, but only SGLF type 132: grip-first, but only SGHF type 141: grip-first, but only PGLF type 142: grip-first, but only PGHF type 213: force-first, but only LFSG type 214: force-first, but only LFPG type 223: force-first, but only HFSG type 224: force-first, but only HFPG type 1 type (one_cue_task): 133: SGSG, only grip info, force unknown 144: PGPG, only grip info, force unknown 211: LFLF, only force info, grip unknown 222: HFHF, only force info, grip unknown event_labels_str (dict): Provides a text label for each digital event code returned as events by the parent BlackrockIO. For example, event_labels_str['65296'] contains the string 'TS-ON'. event_labels_codes (dict): Reverse of `event_labels_str`: Provides a list of event codes related to a specific text label for a trial event. For example, event_labels_codes['TS-ON'] contains the list ['65296']. In addition to the detailed codes, for convenience the meta codes 'CUE/GO', 'RW-ON', and 'SR' summarizing a set of digital events are defined for easier access. trial_const_sequence_str (dict): Dictionary contains the ordering of selected constant trial events for correct trials, e.g., as TS is the first trial event in a correct trial, trial_const_sequence_codes['TS'] is 0. trial_const_sequence_codes (dict): Reverse of trial_const_sequence_str: Dictionary contains the ordering of selected constant trial events for correct trials, e.g., trial_const_sequence_codes[0] is 'TS'. performance_str (dict): Text strings to help interpret the performance code of a trial. For example, correct trials have a performance code of 255, and thus performance_str[255] == 'correct_trial' performance_codes (dict): Reverse of performance_const_sequence_str. Returns the performance code of a given text string indicating trial performance. For example, performance_str['correct_trial'] == 255 """ # Create a dictionary of conditions (i.e., the trial types presented in a # given recording session) condition_str = { 0: [], 1: ['SGHF', 'SGLF', 'PGHF', 'PGLF'], 2: ['HFSG', 'HFPG', 'LFSG', 'LFPG'], 11: ['SGLF', 'PGLF'], 12: ['SGHF', 'PGHF'], 13: ['SGHF', 'SGLF'], 14: ['PGHF', 'PGLF'], 21: ['LFSG', 'LFPG'], 22: ['HFSG', 'HFPG'], 23: ['HFSG', 'LFSG'], 24: ['HFPG', 'LFPG'], 131: ['SGLF'], 132: ['SGHF'], 133: ['SGSG'], 141: ['PGLF'], 142: ['PGHF'], 144: ['PGPG'], 211: ['LFLF'], 213: ['LFSG'], 214: ['LFPG'], 222: ['HFHF'], 223: ['HFSG'], 224: ['HFPG']} ########################################################################### # event labels, the corresponding first 8 digits of their binary # representation and their meaning # # R L T T L L L L # w E a r E E E E # P D S S D D D D in # u c w t b t t b mo- # l r l r nk- # label:| ^ ^ ^ ^ ^ ^ ^ ^ | status of devices: | trial event label:| ey # 65280 < 0 0 0 0 0 0 0 0 > TS-OFF > TS-OFF/STOP > L,T # 65296 < 0 0 0 1 0 0 0 0 > TS-ON > TS-ON > all # 65312 < 0 0 1 0 0 0 0 0 > TaSw > STOP > all # 65344 < 0 1 0 0 0 0 0 0 > LEDc (+TS-OFF) > WS-ON/CUE-OFF > L,T # 65349 < 0 1 0 0 0 1 0 1 > LEDc|rt|rb (+TS-OFF) > PG-ON (CUE/GO-ON) > L,T # 65350 < 0 1 0 0 0 1 1 0 > LEDc|tl|tr (+TS-OFF) > HF-ON (CUE/GO-ON) > L,T # 65353 < 0 1 0 0 1 0 0 1 > LEDc|bl|br (+TS-OFF) > LF-ON (CUE/GO-ON) > L,T # 65354 < 0 1 0 0 1 0 1 0 > LEDc|lb|lt (+TS-OFF) > SG-ON (CUE/GO-ON) > L,T # 65359 < 0 1 0 0 1 1 1 1 > LEDall > ERROR-FLASH-ON > L,T # 65360 < 0 1 0 1 0 0 0 0 > LEDc (+TS-ON) > WS-ON/CUE-OFF > N # 65365 < 0 1 0 1 0 1 0 1 > LEDc|rt|rb (+TS-ON) > PG-ON (CUE/GO-ON) > N # 65366 < 0 1 0 1 0 1 1 0 > LEDc|tl|tr (+TS-ON) > HF-ON (CUE/GO-ON) > N # 65369 < 0 1 0 1 1 0 0 1 > LEDc|bl|br (+TS-ON) > LF-ON (CUE/GO-ON) > N # 65370 < 0 1 0 1 1 0 1 0 > LEDc|lb|lt (+TS-ON) > SG-ON (CUE/GO-ON) > N # 65376 < 0 1 1 0 0 0 0 0 > LEDc+TaSw > GO-OFF/RW-OFF > all # 65381 < 0 1 1 0 0 1 0 1 > TaSw (+LEDc|rt|rb) > SR (+PG) > all # 65382 < 0 1 1 0 0 1 1 0 > TaSw (+LEDc|tl|tr) > SR (+HF) > all # 65383 < 0 1 1 0 0 1 1 1 > TaSw (+LEDc|rt|rb|tl) > SR (+PGHF/HFPG) > # 65385 < 0 1 1 0 1 0 0 1 > TaSw (+LEDc|bl|br) > SR (+LF) > all # 65386 < 0 1 1 0 1 0 1 0 > TaSw (+LEDc|lb|lt) > SR (+SG) > all # 65387 < 0 1 1 0 1 0 1 1 > TaSw (+LEDc|lb|lt|br) > SR (+SGLF/LGSG) > # 65389 < 0 1 1 0 1 1 0 1 > TaSw (+LEDc|rt|rb|bl) > SR (+PGLF/LFPG) > # 65390 < 0 1 1 0 1 1 1 0 > TaSw (+LEDc|lb|lt|tr) > SR (+SGHF/HFSG) > # 65391 < 0 1 1 0 1 1 1 1 > LEDall (+TaSw) > ERROR-FLASH-ON > L,T # 65440 < 1 0 1 0 0 0 0 0 > RwPu (+TaSw) > RW-ON (noLEDs) > N # 65504 < 1 1 1 0 0 0 0 0 > RwPu (+LEDc) > RW-ON (-CONF) > L,T # 65509 < 1 1 1 0 0 1 0 1 > RwPu (+LEDcr) > RW-ON (+CONF-PG) > all # 65510 < 1 1 1 0 0 1 1 0 > RwPu (+LEDct) > RW-ON (+CONF-HF) > N? # 65513 < 1 1 1 0 1 0 0 1 > RwPu (+LEDcb) > RW-ON (+CONF-LF) > N? # 65514 < 1 1 1 0 1 0 1 0 > RwPu (+LEDcl) > RW-ON (+CONF-SG) > all # ^ ^ ^ ^ ^ ^ ^ ^ # label binary code # # ABBREVIATIONS: # c (central), l (left), t (top), b (bottom), r (right), # HF (high force, LEDt), LF (low force, LEDb), SG (side grip, LEDl), # PG (precision grip, LEDr), RwPu (reward pump), TaSw (table switch), # TS (trial start), SR (switch release), WS (warning signal), RW (reward), # L (Lilou), T (Tanya t+a), N (Nikos n+i) ########################################################################### # Create dictionaries for event labels event_labels_str = { '65280': 'TS-OFF/STOP', '65296': 'TS-ON', '65312': 'STOP', '65344': 'WS-ON/CUE-OFF', '65349': 'PG-ON', '65350': 'HF-ON', '65353': 'LF-ON', '65354': 'SG-ON', '65359': 'ERROR-FLASH-ON', '65360': 'WS-ON/CUE-OFF', '65365': 'PG-ON', '65366': 'HF-ON', '65369': 'LF-ON', '65370': 'SG-ON', '65376': 'GO/RW-OFF', '65381': 'SR (+PG)', '65382': 'SR (+HF)', '65383': 'SR (+PGHF/HFPG)', '65385': 'SR (+LF)', '65386': 'SR (+SG)', '65387': 'SR (+SGLF/LFSG)', '65389': 'SR (+PGLF/LFPG)', '65390': 'SR (+SGHF/HFSG)', '65391': 'ERROR-FLASH-ON', '65440': 'RW-ON (noLEDs)', '65504': 'RW-ON (-CONF)', '65509': 'RW-ON (+CONF-PG)', '65510': 'RW-ON (+CONF-HF)', '65513': 'RW-ON (+CONF-LF)', '65514': 'RW-ON (+CONF-SG)'} event_labels_codes = dict([(k, []) for k in np.unique(list(event_labels_str.values()))]) for k in list(event_labels_codes): for l, v in event_labels_str.items(): if v == k: event_labels_codes[k].append(l) # additional summaries event_labels_codes['CUE/GO'] = \ event_labels_codes['SG-ON'] + \ event_labels_codes['PG-ON'] + \ event_labels_codes['LF-ON'] + \ event_labels_codes['HF-ON'] event_labels_codes['RW-ON'] = \ event_labels_codes['RW-ON (+CONF-PG)'] + \ event_labels_codes['RW-ON (+CONF-HF)'] + \ event_labels_codes['RW-ON (+CONF-LF)'] + \ event_labels_codes['RW-ON (+CONF-SG)'] + \ event_labels_codes['RW-ON (-CONF)'] + \ event_labels_codes['RW-ON (noLEDs)'] event_labels_codes['SR'] = \ event_labels_codes['SR (+PG)'] + \ event_labels_codes['SR (+HF)'] + \ event_labels_codes['SR (+LF)'] + \ event_labels_codes['SR (+SG)'] + \ event_labels_codes['SR (+PGHF/HFPG)'] + \ event_labels_codes['SR (+SGHF/HFSG)'] + \ event_labels_codes['SR (+PGLF/LFPG)'] + \ event_labels_codes['SR (+SGLF/LFSG)'] del k, l, v # Create dictionaries for constant trial sequences (in all monkeys) # (bit position (value) set if trial event (key) occurred) trial_const_sequence_codes = { 'TS-ON': 0, 'WS-ON': 1, 'CUE-ON': 2, 'CUE-OFF': 3, 'GO-ON': 4, 'SR': 5, 'RW-ON': 6, 'STOP': 7} trial_const_sequence_str = dict((v, k) for k, v in trial_const_sequence_codes.items()) # Create dictionaries for trial performances # (resulting decimal number from binary number created from trial_sequence) performance_codes = { 'incomplete_trial': 0, 'error 0 def __set_bit(self, flag, pos): """ Returns the given flag with an additional bit set at the given position. for flag. If flag is an array, an array will be returned. """ return flag | (1 << pos) def __add_rejection_to_event(self, event): """ Given an event with annotation trial_id, adds information on whether to reject the trial or not. """ if self.odmldoc: # Get rejection bands sec = self.odmldoc['PreProcessing'] bands = sec.properties['LFPBands'].values for band in bands: sec = self.odmldoc['PreProcessing'][band] if type(sec.properties['RejTrials'].values) != []: rej_trials = [int(_) for _ in sec.properties['RejTrials'].values] rej_index = np.in1d(event.array_annotations['trial_id'], rej_trials) elif sec.properties['RejTrials'].values == []: rej_index = np.zeros((len(event.array_annotations['trial_id'])), dtype=bool) else: raise ValueError( "Invalid entry %s in odML for rejected trials in LFP band %s." % (sec.properties['RejTrials'].values, band)) event.array_annotate(**{str('trial_reject_' + band): list(rej_index)}) def __extract_task_condition(self, trialtypes): """ Extracts task condition from trialtypes. """ occurring_trtys = np.unique(trialtypes).tolist() # reduce occurring_trtys to actual trialtypes # (remove all not identifiable trialtypes (incomplete/error trial)) if 'NONE' in occurring_trtys: occurring_trtys.remove('NONE') # (remove all trialtypes where only the CUE was detected (error trial)) if 'SG' in occurring_trtys: occurring_trtys.remove('SG') if 'PG' in occurring_trtys: occurring_trtys.remove('PG') if 'LF' in occurring_trtys: occurring_trtys.remove('LF') if 'HF' in occurring_trtys: occurring_trtys.remove('HF') # first set to unidentified task condition task_condition = 0 if len(occurring_trtys) > 0: for cnd, trtys in self.condition_str.items(): if set(trtys) == set(occurring_trtys): # replace with detected task condition task_condition = cnd return task_condition def __extract_analog_events_from_odml(self, t_start, t_stop): event_name = [] event_time = [] trial_id = [] trial_timestamp_id = [] performance_code = [] trial_type = [] # Look for all Trial Sections sec = self.odmldoc['Recording']['TaskSettings'] ff = lambda x: x.name.startswith('Trial_') tr_secs = sec.itersections(filter_func=ff) for trial_sec in tr_secs: for signalname in ['GripForceSignals', 'DisplacementSignal']: for analog_events in trial_sec['AnalogEvents'][signalname].properties: # skip invalid values if analog_events.values == []: # this was used as default time continue time = analog_events.values * pq.CompoundUnit(analog_events.unit) time = time.rescale('ms') if time >= t_start and time < t_stop: event_name.append(analog_events.name) event_time.append(time) trial_id.extend(trial_sec.properties['TrialID'].values) trial_timestamp_id.extend(trial_sec.properties['TrialTimestampID'].values) performance_code.extend(trial_sec.properties['PerformanceCode'].values) trial_type.extend(trial_sec.properties['TrialType'].values) # Create event object with analog events analog_events = neo.Event( times=pq.Quantity(event_time, 'ms').flatten(), labels=np.array(event_name), name='AnalogTrialEvents', description='Events extracted from analog signals') performance_str = [] for pit in performance_code: if pit in self.performance_codes: performance_str.append(self.performance_codes[pit]) else: performance_str.append('unknown') analog_events.array_annotate( trial_id=trial_id, trial_timestamp_id=trial_timestamp_id, performance_in_trial=performance_code, performance_in_trial_str=performance_str, belongs_to_trialtype=trial_type, trial_event_labels=event_name) return analog_events def __annotate_dig_trial_events(self, events): """ Modifies events of digital input port to trial events of the reach-to-grasp project. """ # Modifiy name and description events.name = "DigitalTrialEvents" events.description = "Trial " + events.description.lower() events_rescaled = events.rescale(pq.CompoundUnit('1/30000*s')) # Extract beginning of first complete trial tson_label = self.event_labels_codes['TS-ON'][0] if tson_label in events_rescaled.labels: first_TSon_idx = list(events_rescaled.labels).index(tson_label) else: first_TSon_idx = len(events_rescaled.labels) # Extract end of last complete trial stop_label = self.event_labels_codes['STOP'][0] if stop_label in events_rescaled.labels: last_WSoff_idx = len(events_rescaled.labels) - list(events_rescaled.labels[::-1]).index(stop_label) - 1 else: last_WSoff_idx = -1 # Annotate events with modified labels, trial ids, and trial types trial_event_labels = [] trial_ID = [] trial_timestamp_ID = [] trialtypes = {-1: 'NONE'} trialsequence = {-1: 0} for i, l in enumerate(events_rescaled.labels): if i < first_TSon_idx or i > last_WSoff_idx: trial_event_labels.append('NONE') trial_ID.append(-1) trial_timestamp_ID.append(-1) else: # interpretation of TS-ON if self.event_labels_str[l] == 'TS-ON': if i > 0: prev_ev = events_rescaled.labels[i - 1] if self.event_labels_str[prev_ev] in ['STOP', 'TS-OFF/STOP']: timestamp_id = int(round(events_rescaled.times[i].item())) trial_timestamp_ID.append(timestamp_id) trial_event_labels.append('TS-ON') trialsequence[timestamp_id] = self.__set_bit( 0, self.trial_const_sequence_codes['TS-ON']) else: timestamp_id = trial_timestamp_ID[-1] trial_timestamp_ID.append(timestamp_id) trial_event_labels.append('TS-ON-ERROR') else: timestamp_id = int(events_rescaled.times[i].item()) trial_timestamp_ID.append(timestamp_id) trial_event_labels.append('TS-ON') trialsequence[timestamp_id] = self.__set_bit( 0, self.trial_const_sequence_codes['TS-ON']) # Identify trial ID if odML exists ID = -1 if self.odmldoc: sec = self.odmldoc['Recording']['TaskSettings'] ff = lambda x: x.name.startswith('Trial_') tr_secs = sec.itersections(filter_func=ff) for trial_sec in tr_secs: if trial_sec.properties['TrialTimestampID'].values[0] == timestamp_id: ID = trial_sec.properties['TrialID'].values[0] trial_ID.append(ID) # interpretation of GO/RW-OFF elif self.event_labels_str[l] == 'GO/RW-OFF': trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) trial_event_labels.append('GO/RW-OFF') # interpretation of ERROR-FLASH-ON elif l in self.event_labels_codes['ERROR-FLASH-ON']: trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) trial_event_labels.append('ERROR-FLASH-ON') # Error-Flash hides too early activation of SR # SR is set to 1 here to match perf codes between monkeys trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['SR']) # TS-OFF/STOP elif self.event_labels_str[l] == 'TS-OFF/STOP': trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prev_ev = events_rescaled.labels[i - 1] if self.event_labels_str[prev_ev] == 'TS-ON': trial_event_labels.append('TS-OFF') elif prev_ev in self.event_labels_codes['ERROR-FLASH-ON']: trial_event_labels.append('STOP') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['STOP']) else: trial_event_labels.append('STOP') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['STOP']) # interpretation of WS-ON/CUE-OFF elif self.event_labels_str[l] == 'WS-ON/CUE-OFF': trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prev_ev = events_rescaled.labels[i - 1] if self.event_labels_str[prev_ev] in ['TS-ON', 'TS-OFF/STOP']: trial_event_labels.append('WS-ON') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['WS-ON']) elif (prev_ev in self.event_labels_codes['CUE/GO'] or prev_ev in self.event_labels_codes['GO/RW-OFF']): trial_event_labels.append('CUE-OFF') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['CUE-OFF']) else: raise ValueError("Unknown trial event sequence.") # interpretation of CUE and GO events and trialtype detection elif l in self.event_labels_codes['CUE/GO']: trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prprev_ev = events_rescaled.labels[i - 2] if self.event_labels_str[prprev_ev] in ['TS-ON', 'TS-OFF/STOP']: trial_event_labels.append('CUE-ON') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['CUE-ON']) trialtypes[timestamp_id] = self.event_labels_str[l][:2] elif prprev_ev in self.event_labels_codes['CUE/GO']: trial_event_labels.append('GO-ON') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['GO-ON']) trialtypes[timestamp_id] += self.event_labels_str[l][:2] else: raise ValueError("Unknown trial event sequence.") # interpretation of WS-OFF elif self.event_labels_str[l] == 'STOP': trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prev_ev = self.event_labels_str[events_rescaled.labels[i - 1]] if prev_ev == 'ERROR-FLASH-ON': trial_event_labels.append('ERROR-FLASH-OFF') else: trial_event_labels.append('STOP') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['STOP']) # interpretation of SR events elif l in self.event_labels_codes['SR']: trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prev_ev = events_rescaled.labels[i - 1] if prev_ev in self.event_labels_codes['SR']: trial_event_labels.append('SR-REP') elif prev_ev in self.event_labels_codes['RW-ON']: trial_event_labels.append('RW-OFF') else: trial_event_labels.append('SR') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['SR']) # interpretation of RW events_rescaled elif l in self.event_labels_codes['RW-ON']: trial_timestamp_ID.append(timestamp_id) trial_ID.append(ID) prev_ev = events_rescaled.labels[i - 1] if prev_ev in self.event_labels_codes['RW-ON']: trial_event_labels.append('RW-ON-REP') else: trial_event_labels.append('RW-ON') trialsequence[timestamp_id] = self.__set_bit( trialsequence[timestamp_id], self.trial_const_sequence_codes['RW-ON']) else: raise ValueError("Unknown event label.") # add modified trial_event_labels to annotations events.array_annotate(trial_event_labels=trial_event_labels) # add trial timestamp IDs events.array_annotate(trial_timestamp_id=trial_timestamp_ID) # add trial IDs events.array_annotate(trial_id=trial_ID) # add modified belongs_to_trialtype to annotations for tid in trial_timestamp_ID: if tid not in list(trialtypes): trialtypes[tid] = 'NONE' belongs_to_trialtype = [trialtypes[tid] for tid in trial_timestamp_ID] events.array_annotate(belongs_to_trialtype=belongs_to_trialtype) # add modified trial_performance_codes to annotations performance_in_trial = [trialsequence[tid] for tid in trial_timestamp_ID] performance_in_trial_str = [] for pit in performance_in_trial: if pit in self.performance_str: performance_in_trial_str.append(self.performance_str[pit]) else: performance_in_trial_str.append('unknown') events.array_annotate(performance_in_trial=performance_in_trial) events.array_annotate(performance_in_trial_str=performance_in_trial_str) def __create_unit_groups(self, block, view_dict=None): unit_dict = {} for seg in block.segments: for st in seg.spiketrains: chid = st.annotations['channel_id'] unit_id = st.annotations['unit_id'] if chid not in unit_dict: unit_dict[chid] = {} if unit_id not in unit_dict[chid]: group = neo.Group(name='Unit {} on channel {}'.format(unit_id, chid), description='Group for neuronal data related to unit {} on ' 'channel {}'.format(unit_id, chid), group_type='unit', allowed_types=[neo.SpikeTrain, SpikeTrainProxy, neo.AnalogSignal, AnalogSignalProxy, neo.ChannelView], channel_id=chid, unit_id=unit_id) block.groups.append(group) unit_dict[chid][unit_id] = group unit_dict[chid][unit_id].add(st) # if views are already created, link them to unit groups if view_dict: for chid, channel_dict in unit_dict.items(): if chid in view_dict: for unit_id, group in channel_dict.items(): group.add(view_dict[chid]) def __create_channel_views(self, block): view_dict = {} for seg in block.segments: for anasig in seg.analogsignals: for chidx, chid in enumerate(anasig.array_annotations['channel_ids']): if chid not in view_dict: view = neo.ChannelView(anasig, [chidx], name='Channel {} of {}'.format(chid, anasig.name), channel_id=chid) view_dict[chid] = view return view_dict def __annotate_units_with_odml(self, groups): """ Annotates units with metadata from odml file. """ units = [g for g in groups if 'group_type' in g.annotations and g.annotations['group_type'] == 'unit'] if not self._load_spikesorting_info: return for un in units: an_dict = dict( sua=False, mua=False, noise=False) try: sec = self.odmldoc['UtahArray']['Array'][ 'Electrode_%03d' % un.annotations['channel_id']][ 'OfflineSpikeSorting'] except KeyError: return suaids = sec.properties['SUAIDs'].values if sec.properties['MUAID'].values: muaid = sec.properties['MUAID'].values[0] else: muaid = None noiseids = sec.properties['NoiseIDs'].values if un.annotations['unit_id'] in suaids: an_dict['sua'] = True elif un.annotations['unit_id'] in noiseids: an_dict['noise'] = True elif un.annotations['unit_id'] == muaid: an_dict['mua'] = True else: raise ValueError( "Unit %i is not registered for channel %i in odML file." % (un.annotations['unit_id'], un.annotations['channel_id'])) if ('Unit_%02i' % un.annotations['unit_id']) in sec.sections: unit_sec = sec['Unit_%02i' % un.annotations['unit_id']] if an_dict['sua']: an_dict['SNR'] = unit_sec.properties['SNR'].values[0] # TODO: Add units here an_dict['spike_duration'] = unit_sec.properties['SpikeDuration'].values[0] an_dict['spike_amplitude'] = unit_sec.properties['SpikeAmplitude'].values[0] an_dict['spike_count'] = unit_sec.properties['SpikeCount'].values[0] # Annotate Unit and all children for convenience un.annotate(**an_dict) for st in un.spiketrains: st.annotate(**an_dict) def __annotate_analogsignals_with_odml(self, asig): """ Annotates analogsignals with metadata from odml file. """ if self.odmldoc: chids = np.asarray(asig.array_annotations['channel_ids'], dtype=int) neural_chids = [chid in self.avail_electrode_ids for chid in chids] if not any(neural_chids): asig.annotate(neural_signal=False) elif all(neural_chids): asig.annotate(neural_signal=True) # Annotate filter settings from odML nchan = asig.shape[-1] if 'nsx' in asig.annotations: nsx = asig.annotations['nsx'] else: nsx = asig.array_annotations['nsx'][0] filter = 'Filter_ns%i' % nsx sec = self.odmldoc['Cerebus']['NeuralSignalProcessor']['NeuralSignals'][filter] props = sec.properties hi_pass_freq = np.full((nchan), pq.Quantity(props['HighPassFreq'].values[0], props['HighPassFreq'].unit)) lo_pass_freq = np.full((nchan), pq.Quantity(props['LowPassFreq'].values[0], props['LowPassFreq'].unit)) hi_pass_order = np.zeros_like(hi_pass_freq) lo_pass_order = np.zeros_like(lo_pass_freq) filter_type = np.empty((nchan), np.str) for chidx in range(nchan): filter = 'Filter_ns%i' % nsx sec = self.odmldoc['Cerebus']['NeuralSignalProcessor']['NeuralSignals'][filter] hi_pass_freq[chidx] = pq.Quantity( sec.properties['HighPassFreq'].values[0], sec.properties['HighPassFreq'].unit) lo_pass_freq[chidx] = pq.Quantity( sec.properties['LowPassFreq'].values[0], sec.properties['LowPassFreq'].unit) hi_pass_order[chidx] = sec.properties['HighPassOrder'].values[0] lo_pass_order[chidx] = sec.properties['LowPassOrder'].values[0] filter_type[chidx] = sec.properties['Type'].values[0] asig.array_annotations.update(dict( hi_pass_freq=hi_pass_freq, lo_pass_freq=lo_pass_freq, hi_pass_order=hi_pass_order, lo_pass_order=lo_pass_order, filter_type=filter_type )) self.__annotate_electrode_rejections(asig) def __annotate_electrode_rejections(self, obj): # Get rejection bands sec = self.odmldoc['PreProcessing'] bands = sec.properties['LFPBands'].values if hasattr(bands, '__iter__'): for band in bands: sec = self.odmldoc['PreProcessing'][band] rej_els = np.asarray(sec.properties['RejElectrodes'].values, dtype=int) if 'channel_id' in obj.annotations: rejection_value = bool(obj.annotations['channel_id'] in rej_els) obj.annotations['electrode_reject_' + band] = rejection_value elif hasattr(obj, 'array_annotations') and 'channel_ids' in obj.array_annotations: rej = np.isin(obj.array_annotations['channel_ids'], rej_els) obj.array_annotations.update({str('electrode_reject_' + band): rej}) else: warnings.warn( 'Could not annotate {} with electrode rejection information.'.format(obj)) def __convert_chids_and_coordinates(self, channel_ids): nchan = len(channel_ids) ca_ids = np.full(nchan, fill_value=None) # use negative infinity for invalid coordinates as None is incompatible with pq.mm coordinates_x = np.full(nchan, fill_value=-np.inf) * pq.mm coordinates_y = np.full(nchan, fill_value=-np.inf) * pq.mm for i, channel_id in enumerate(channel_ids): if channel_id not in self.connector_aligned_map: continue ca_ids[i] = self.connector_aligned_map[channel_id] coordinates_x[i] = np.mod(ca_ids[i] - 1, 10) * 0.4 * pq.mm coordinates_y[i] = int((ca_ids[i] - 1) / 10) * 0.4 * pq.mm return ca_ids, coordinates_x, coordinates_y def __annotate_channel_infos(self, block): if self.odmldoc: # updating array annotations of neuronal analogsignals for seg in block.segments: for obj in seg.analogsignals: if 'neural_signal' in obj.annotations and obj.annotations[ 'neural_signal'] and 'channel_ids' in obj.array_annotations: chids = np.asarray(obj.array_annotations['channel_ids'], dtype=int) ca_ids, *coordinates = self.__convert_chids_and_coordinates(chids) obj.array_annotations.update(dict(connector_aligned_ids=ca_ids, coordinates_x=coordinates[0], coordinates_y=coordinates[1])) # updating annotations of groups and spiketrains sts = [] for seg in block.segments: sts.extend(seg.spiketrains) for obj in sts + block.groups: if 'channel_id' in obj.annotations: chid = obj.annotations['channel_id'] ca_id, *coordinates = self.__convert_chids_and_coordinates([chid]) obj.annotate(connector_aligned_id=ca_id[0], coordinate_x=coordinates[0][0], coordinate_y=coordinates[1][0]) def __annotate_block_with_odml(self, bl): """ Annotates block with metadata from odml file. """ sec = self.odmldoc['Project'] bl.annotate( project_name=sec.properties['Name'].values, project_type=sec.properties['Type'].values, project_subtype=sec.properties['Subtype'].values) sec = self.odmldoc['Project']['TaskDesigns'] bl.annotate(taskdesigns=[v for v in sec.properties['UsedDesign'].values]) sec = self.odmldoc['Subject'] bl.annotate( subject_name=sec.properties['GivenName'].values, subject_gender=sec.properties['Gender'].values, subject_activehand=sec.properties['ActiveHand'].values, subject_birthday=str( sec.properties['Birthday'].values)) # datetime is not a valid annotation dtype sec = self.odmldoc['Setup'] bl.annotate(setup_location=sec.properties['Location'].values) sec = self.odmldoc['UtahArray'] bl.annotate(array_serialnum=sec.properties['SerialNo'].values) sec = self.odmldoc['UtahArray']['Connector'] bl.annotate(connector_type=sec.properties['Style'].values) sec = self.odmldoc['UtahArray']['Array'] bl.annotate(arraygrids_tot_num=sec.properties['GridCount'].values) sec = self.odmldoc['UtahArray']['Array']['Grid_01'] bl.annotate( electrodes_tot_num=sec.properties['ElectrodeCount'].values, electrodes_pitch=pq.Quantity( sec.properties['ElectrodePitch'].values, units=sec.properties['ElectrodePitch'].unit), arraygrid_row_num=sec.properties['GridRows'].values, arraygrid_col_num=sec.properties['GridColumns'].values) bl.annotate(avail_electrode_ids=self.avail_electrode_ids) def __correct_filter_shifts(self, asig): if self.odmldoc and asig.annotations['neural_signal']: # assert all signals are originating from same nsx file if 'nsx' in asig.array_annotations and \ len(np.unique(asig.array_annotations['nsx'])) > 1: raise ValueError('Multiple nsx file origins (%s) in single AnalogSignal' ''.format(asig.array_annotations['nsx'])) if 'nsx' in asig.annotations: nsx = asig.annotations['nsx'] else: nsx = asig.array_annotations['nsx'][0] # Get and correct for shifts filter_name = 'Filter_ns%i' % nsx # use nsx of 1st signal sec = self.odmldoc['Cerebus']['NeuralSignalProcessor']['NeuralSignals'][filter_name] shift = pq.Quantity( sec.properties['EstimatedShift'].values[0], sec.properties['EstimatedShift'].unit) asig.t_start = asig.t_start - shift # Annotate shift asig.annotate(filter_shift_correction=shift) def __merge_digital_analog_events(self, events): """ Merge the two event arrays AnalogTrialEvents and DigitalTrialEvents into one common event array TrialEvents. """ event_name = [] event_time = None trial_id = [] trial_timestamp_id = [] performance_code = [] performance_str = [] trial_type = [] for event in events: if event.name in ['AnalogTrialEvents', 'DigitalTrialEvents']: # Extract event times if event_time is None: event_time = event.times.magnitude.flatten() event_units = event.times.units else: event_time = np.concatenate(( event_time, event.times.rescale(event_units).magnitude.flatten())) # Transfer annotations trial_id.extend( event.array_annotations['trial_id']) trial_timestamp_id.extend( event.array_annotations['trial_timestamp_id']) performance_code.extend( event.array_annotations['performance_in_trial']) performance_str.extend( event.array_annotations['performance_in_trial_str']) trial_type.extend( event.array_annotations['belongs_to_trialtype']) event_name.extend( event.array_annotations['trial_event_labels']) # Sort time stamps and save sort order sort_idx = np.argsort(event_time) event_time = event_time[sort_idx] # Create event object with analog events merged_event = neo.Event( times=pq.Quantity(event_time, units=event_units), labels=np.array([event_name[_] for _ in sort_idx]), name='TrialEvents', description='All trial events (digital and analog)') merged_event.array_annotate( trial_id=[trial_id[_] for _ in sort_idx], trial_timestamp_id=[trial_timestamp_id[_] for _ in sort_idx], performance_in_trial=[performance_code[_] for _ in sort_idx], performance_in_trial_str=[performance_str[_] for _ in sort_idx], belongs_to_trialtype=[trial_type[_] for _ in sort_idx], trial_event_labels=[event_name[_] for _ in sort_idx]) return merged_event def read_block( self, index=None, block_index=0, name=None, description=None, nsx_to_load='none', n_starts=None, n_stops=None, channels=range(1, 97), units='none', load_waveforms=False, load_events=False, scaling='raw', correct_filter_shifts=True, lazy=False, cascade=True, **kwargs): """ Reads file contents as a Neo Block. The Block contains one Segment for each entry in zip(n_starts, n_stops). If these parameters are not specified, the default is to store all data in one Segment. The Block contains one ChannelIndex per channel. Args: index (None, int): DEPRECATED If not None, index of block is set to user input. block_index (int): Index of block to load. name (None, str): If None, name is set to default, otherwise it is set to user input. description (None, str): If None, description is set to default, otherwise it is set to user input. nsx_to_load (int, list, str): DEPRECATED ID(s) of nsx file(s) from which to load data, e.g., if set to 5 only data from the ns5 file are loaded. If 'none' or empty list, no nsx files and therefore no analog signals are loaded. If 'all', data from all available nsx are loaded. n_starts (None, Quantity, list): DEPRECATED Start times for data in each segment. Number of entries must be equal to length of n_stops. If None, intrinsic recording start times of files set are used. n_stops (None, Quantity, list): DEPRECATED Stop times for data in each segment. Number of entries must be equal to length of n_starts. If None, intrinsic recording stop times of files set are used. channels (int, list, str): DEPRECATED Channel id(s) from which to load data. If 'none' or empty list, no channels and therefore no analog signal or spiketrains are loaded. If 'all', all available channels are loaded. By default, all neural channels (1-96) are loaded. units (int, list, str, dict): DEPRECATED ID(s) of unit(s) to load. If 'none' or empty list, no units and therefore no spiketrains are loaded. If 'all', all available units are loaded. If dict, the above can be specified individually for each channel (keys), e.g. {1: 5, 2: 'all'} loads unit 5 from channel 1 and all units from channel 2. load_waveforms (boolean): Control SpikeTrains.waveforms is None or not. Default: False load_events (boolean): DEPRECATED If True, all recorded events are loaded. scaling (str): DEPRECATED Determines whether time series of individual electrodes/channels are returned as AnalogSignals containing raw integer samples ('raw'), or scaled to arrays of floats representing voltage ('voltage'). Note that for file specification 2.1 and lower, the option 'voltage' requires a nev file to be present. correct_filter_shifts (bool): If True, shifts of the online-filtered neural signals (e.g., ns2, channels 1-128) are corrected by time-shifting the signal by a heuristically determined estimate stored in the metadata, in the property EstimatedShift, under the path /Cerebus/NeuralSignalProcessor/NeuralSignals/Filter_nsX/ lazy (bool): If True, only the shape of the data is loaded. cascade (bool or "lazy"): DEPRECATED If True, only the block without children is returned. kwargs: Additional keyword arguments are forwarded to the BlackrockIO. Returns: Block (neo.segment.Block): Block linking to all loaded Neo objects. Block annotations: avail_file_set (list of str): List of file extensions of the files found to be associated to the project, and which are used in loading the data, e.g., ccf, odml, nev, ns2,... avail_nsx (list of int): List of integers specifying the .nsX files available, e.g., [2, 5] indicates that an ns2 and and ns5 file are available. avail_nev (bool): True if a .nev file is available. avail_ccf (bool): True if a .ccf file is available. avail_sif (bool): True if a .sif file is available. nb_segments (int): Number of segments created after merging recording times specified by user with the intrinsic ones of the file set. project_name (str): Identifier for the project/experiment. project_type (str): Identifier for the type of project/experiment. project_subtype (str): Identifier of the subtype of the project/experiment. taskdesigns (list of str): List of strings identifying the task designed presented during the recording. The standard task reach-to-grasp is denoted by the string "TwoCues". conditions (list of int): List of condition codes (each code describing the set of trial types presented to the subject during a segment of the recording) present during the recording. For a mapping of condition codes to trial types, see the condition_str attribute of the ReachGraspIO class. subject_name (str): Name of the recorded subject. subject_gender (bool): 'male' or 'female'. subject_birthday (datetime): Birthday of the recorded subject. subject_activehand (str): Handedness of the subject. setup_location (str): Physical location of the recording setup. avail_electrode_ids (list of int): List of length 100 of electrode channel IDs (Blackrock IDs) ordered corresponding to the connector-aligned linear electrode IDs. The connector-aligned IDs start at 1 in the bottom left corner, and increase from left to right, and from bottom to top assuming the array is placed in front of the observer pins facing down, connector extruding to the right: 91 92 ... 99 100 \ 81 82 ... 89 90 \ ... ... --- Connector Wires 11 12 ... 19 20 / 1 2 ... 9 10 / Thus, avail_electrode_ids[k-1] is the Blackrock channel ID corresponding to connector- aligned ID k. Unconnected/unavailable channels are marked by -1. arraygrids_tot_num (int): Number of Utah arrays (not necessarily all connected). electrodes_tot_num (int): Number of electrodes of the Utah array (not necessarily all connected). electrodes_pitch (float): Distance in micrometers between neighboring electrodes in one row/column. array_serial_num (str): Serial number of the recording array. array_grid_col_num, array_grid_row_num (int): Number of columns / rows of the array. connector_type (str): Type of connector used for recording. rec_pauses (bool): True if the session contains a recording pause (i.e., multiple segments). Segment annotations: condition (int): Condition code (describing the set of trial types presented to the subject) of this segment. For a mapping of condition codes to trial types, see the condition_str attribute of the ReachGraspIO class. ChannelIndex annotations: connector_aligned_id (int): Connector-aligned channel ID from which the spikes were loaded. This is a channel ID between 1 and 100 that is related to the location of an electrode on the Utah array and thus common across different arrays (independent of the Blackrock channel ID). The ID considers a top-view of the array with the connector wires extruding to the right. Electrodes are then numbered from bottom left to top right: 91 92 ... 99 100 \ 81 82 ... 89 90 \ ... ... --- Connector Wires 11 12 ... 19 20 / 1 2 ... 9 10 / Note: The Blackrock IDs are given in the 'channel_ids' property of the ChannelIndex object. waveform_size (Quantitiy): Length of time used to save spike waveforms (in units of 1/30000 s). nev_hi_freq_corner (Quantitiy), nev_lo_freq_corner (Quantitiy), nev_hi_freq_order (int), nev_lo_freq_order (int), nev_hi_freq_type (str), nev_lo_freq_type (str), nev_hi_threshold, nev_lo_threshold, nev_energy_threshold (Quantity): Indicates parameters of spike detection. nev_dig_factor (int): Digitization factor in microvolts of the nev file, used to convert raw samples to volt. connector_ID, connector_pinID (int): ID of connector and pin on the connector where the channel was recorded from. nb_sorted_units (int): Number of sorted units on this channel (noise, mua and sua). electrode_reject_XXX (bool): For different filter ranges XXX (as defined in the odML file), if this variable is True it indicates whether the spikes were recorded on an electrode that should be rejected based on preprocessing analysis for removing electrodes due to noise/artefacts in the respective frequency range. Unit annotations: coordinates (Quantity): Contains the x and y coordinate of the electrode in mm (spacing: 0.4mm). The coordinates use the same representation as the connector_aligned_id with the origin located at the bottom left electrode. Thus, e.g., connector aligned ID 14 is at coordinates: (1.2 mm, 0.4 mm) unit_id (int): ID of the unit. channel_id (int): Channel ID (Blackrock ID) from which the unit was loaded (equiv. to the single list entry in the attribute channel_ids of ChannelIndex parent). connector_aligned_id (int): Connector-aligned channel ID from which the unit was loaded. This is a channel ID between 1 and 100 that is related to the location of an electrode on the Utah array and thus common across different arrays (independent of the Blackrock channel ID). The ID considers a top-view of the array with the connector wires extruding to the right. Electrodes are then numbered from bottom left to top right: 91 92 ... 99 100 \ 81 82 ... 89 90 \ ... ... --- Connector Wires 11 12 ... 19 20 / 1 2 ... 9 10 / electrode_reject_XXX (bool): For different filter ranges XXX (as defined in the odML file), if this variable is True it indicates whether the spikes were recorded on an electrode that should be rejected based on preprocessing analysis for removing electrodes due to noise/artefacts in the respective frequency range. noise, mua, sua (bool): True, if the unit is classified as a noise unit, i.e., not considered neural activity (noise), a multi-unit (mua), or a single unit (sua). SNR (float): Signal to noise ratio of SUA/MUA waveforms. A higher value indicates that the unit could be better distinguished in the spike detection and spike sorting procedure. spike_duration (float): Approximate duration of the spikes of SUAs/MUAs in microseconds. spike_amplitude (float): Maximum amplitude of the spike waveform. spike_count (int): Number of spikes sorted into this unit. AnalogSignal annotations: nsx (int): nsX file the signal was loaded from, e.g., 5 indicates the .ns5 file. channel_id (int): Channel ID (Blackrock ID) from which the signal was loaded. connector_aligned_id (int): Connector-aligned channel ID from which the signal was loaded. This is a channel ID between 1 and 100 that is related to the location of an electrode on the Utah array and thus common across different arrays (independent of the Blackrock channel ID). The ID considers a top-view of the array with the connector wires extruding to the right. Electrodes are then numbered from bottom left to top right: 91 92 ... 99 100 \ 81 82 ... 89 90 \ ... ... --- Connector Wires 11 12 ... 19 20 / 1 2 ... 9 10 / electrode_reject_XXX (bool): For different filter ranges XXX (as defined in the odML file), if this variable is True it indicates whether the spikes were recorded on an electrode that should be rejected based on preprocessing analysis for removing electrodes due to noise/artefacts in the respective frequency range. filter_shift_correction (Quantity): If the parameter correct_filter_shift is True, and a shift estimate was found in the odML, this annotation indicates the amount of time by which the signal was shifted. I.e., adding this number to t_start will result in the uncorrected, originally recorded time axis. Spiketrain annotations: unit_id (int): ID of the unit from which the spikes were recorded. channel_id (int): Channel ID (Blackrock ID) from which the spikes were loaded. connector_aligned_id (int): Connector-aligned channel ID from which the spikes were loaded. This is a channel ID between 1 and 100 that is related to the location of an electrode on the Utah array and thus common across different arrays (independent of the Blackrock channel ID). The ID considers a top-view of the array with the connector wires extruding to the right. Electrodes are then numbered from bottom left to top right: 91 92 ... 99 100 \ 81 82 ... 89 90 \ ... ... --- Connector Wires 11 12 ... 19 20 / 1 2 ... 9 10 / electrode_reject_XXX (bool): For different filter ranges XXX (as defined in the odML file), if this variable is True it indicates whether the spikes were recorded on an electrode that should be rejected based on preprocessing analysis for removing electrodes due to noise/artefacts in the respective frequency range. noise, mua, sua (bool): True, if the unit is classified as a noise unit, i.e., not considered neural activity (noise), a multi-unit (mua), or a single unit (sua). SNR (float): Signal to noise ratio of SUA/MUA waveforms. A higher value indicates that the unit could be better distinguished in the spike detection and spike sorting procedure. spike_duration (float): Approximate duration of the spikes of SUAs/MUAs in microseconds. spike_amplitude (float): Maximum amplitude of the spike waveform. spike_count (int): Number of spikes sorted into this unit. Event annotations: The resulting Block contains three Event objects with the following names: 'DigitalTrialEvents' contains all digitally recorded events returned by BlackrockIO, annotated with semantic labels in accordance with the reach-to-grasp experiment (e.g., 'TS-ON'). 'AnalogTrialEvents' contains events extracted from the analog behavioral signals during preprocessing and stored in the odML (e.g., 'OT'). 'TrialEvents' contains all events of DigitalTrialEvents and AnalogTrialEvents merged into a single Neo object. Each annotation is a list containing one entry per time point stored in the event. trial_event_labels (list of str): Name identifying the name of the event, e.g., 'TS-ON'. trial_id (list of int): Trial ID the event belongs to. trial_timestamp_id (list of int): Timestamp-based trial ID (equivalent to the time of TS- ON of a trial) the event belongs to. belongs_to_trialtype (str): String identifying the trial type (e.g., SGHF) the trial belongs to. performance_in_trial (list of int): Performance code of the trial that the event belongs to. Compare to the performance_codes and performance_str attributes of ReachGraspIO class. trial_reject_XXX: For different filter ranges XXX (defined in the odML file), if True this variable indicates whether the trial was rejected based on preprocessing analysis. """ if not name: name = 'Reachgrasp Recording Data Block' if not description: description = "Block of reach-to-grasp project data from Blackrock file set." if index is not None: warnings.warn('`index` is deprecated and will be replaced by `block_index`.') if nsx_to_load != 'none': warnings.warn('`nsx_to_load` is deprecated for `read_block`. ' 'Specify `nsx_to_load when initializing the IO or use lazy loading.') if n_starts is not None: warnings.warn('`n_starts` is deprecated. Use lazy loading instead.') if n_stops is not None: warnings.warn('`n_stops` is deprecated. Use lazy loading instead.') if channels != range(1, 97): warnings.warn('`channels` is deprecated. Use lazy loading instead.') if units != 'none': warnings.warn('`units` is deprecated. Use lazy loading instead.') if load_events is not False: warnings.warn('`load_events` is deprecated. Use lazy loading instead.') if scaling != 'raw': warnings.warn('`scaling` is deprecated.') if cascade is not True: warnings.warn('`cascade` is deprecated. Use lazy loading instead.') # Load neo block bl = BlackrockIO.read_block( self, block_index=block_index, load_waveforms=load_waveforms, lazy=lazy, **kwargs) if name is not None: bl.name = name if description is not None: bl.description = description bl.annotate(conditions=[]) for seg in bl.segments: if 'condition' in list(seg.annotations): bl.annotations['conditions'].append(seg.annotations['condition']) ch_dict = self.__create_channel_views(bl) self.__create_unit_groups(bl, ch_dict) if self.odmldoc: self.__annotate_block_with_odml(bl) self.__annotate_channel_infos(bl) self.__annotate_units_with_odml(bl.groups) return bl def read_segment( self, block_index=0, seg_index=0, name=None, description=None, index=None, nsx_to_load='none', channels=range(1, 97), units='none', load_waveforms=False, load_events=False, scaling='raw', correct_filter_shifts=True, lazy=False, cascade=True, **kwargs): """ Reads file contents as a Neo Block. The Block contains one Segment for each entry in zip(n_starts, n_stops). If these parameters are not specified, the default is to store all data in one Segment. The Block contains one ChannelIndex per channel. Args: n_start (Quantity): DEPRECATED Start time of maximum time range of signals contained in this segment. Deprecated, use lazy loading instead. n_stop (Quantity): DEPRECATED Stop time of maximum time range of signals contained in this segment. Deprecated, use lazy loading instead. name (None, string): If None, name is set to default, otherwise it is set to user input. description (None, string): If None, description is set to default, otherwise it is set to user input. index (None, int): DEPRECATED If not None, index of segment is set to user index. Deprecated, use `seg_index` instead. nsx_to_load (int, list, str): ID(s) of nsx file(s) from which to load data, e.g., if set to 5 only data from the ns5 file are loaded. If 'none' or empty list, no nsx files and therefore no analog signals are loaded. If 'all', data from all available nsx are loaded. channels (int, list, str): DEPRECATED Channel id(s) from which to load data. If 'none' or empty list, no channels and therefore no analog signal or spiketrains are loaded. If 'all', all available channels are loaded. By default, all neural channels (1-96) are loaded. units (int, list, str, dict): DEPRECATED ID(s) of unit(s) to load. If 'none' or empty list, no units and therefore no spiketrains are loaded. If 'all', all available units are loaded. If dict, the above can be specified individually for each channel (keys), e.g. {1: 5, 2: 'all'} loads unit 5 from channel 1 and all units from channel 2. load_waveforms (boolean): If True, waveforms are attached to all loaded spiketrains. load_events (boolean): DEPRECATED If True, all recorded events are loaded. scaling (str): DEPRECATED Determines whether time series of individual electrodes/channels are returned as AnalogSignals containing raw integer samples ('raw'), or scaled to arrays of floats representing voltage ('voltage'). Note that for file specification 2.1 and lower, the option 'voltage' requires a nev file to be present. correct_filter_shifts (bool): If True, shifts of the online-filtered neural signals (e.g., ns2, channels 1-128) are corrected by time-shifting the signal by a heuristically determined estimate stored in the metadata, in the property EstimatedShift, under the path /Cerebus/NeuralSignalProcessor/NeuralSignals/Filter_nsX/ lazy (boolean): If True, only the shape of the data is loaded. cascade (boolean): DEPRECATED If True, only the segment without children is returned. kwargs: Additional keyword arguments are forwarded to the BlackrockIO. Returns: Segment (neo.segment.Segment): Segment linking to all loaded Neo objects. See documentation of read_block() for a full list of annotations per Neo object. """ if index is not None: warnings.warn('`index` is deprecated and will be replaced by `segment_index`.') if nsx_to_load != 'none': warnings.warn('`nsx_to_load` is deprecated for `read_block`. ' 'Specify `nsx_to_load when initializing the IO or use lazy loading.') if channels != range(1, 97): warnings.warn('`channels` is deprecated. Use lazy loading instead.') if units != 'none': warnings.warn('`units` is deprecated. Use lazy loading instead.') if load_events is not False: warnings.warn('`load_events` is deprecated. Use lazy loading instead.') if scaling != 'raw': warnings.warn('`scaling` is deprecated.') if cascade is not True: warnings.warn('`cascade` is deprecated. Use lazy loading instead.') # Load neo block seg = BlackrockIO.read_segment( self, block_index=block_index, seg_index=seg_index, load_waveforms=load_waveforms, lazy=lazy, **kwargs) if name is not None: seg.name = name if description is not None: seg.description = description # load data of all events and epochs for ev_idx, event in enumerate(seg.events): if hasattr(event, 'load'): seg.events[ev_idx] = event.load() seg.events[ev_idx].segment = seg for ep_idx, epoch in enumerate(seg.epochs): if hasattr(epoch, 'load'): seg.epochs[ep_idx] = epoch.load() seg.epochs[ep_idx].segment = seg for asig in seg.analogsignals: self.__annotate_analogsignals_with_odml(asig) if correct_filter_shifts: self.__correct_filter_shifts(asig) for st in seg.spiketrains: self.__annotate_electrode_rejections(st) for ev in seg.events: # Modify digital trial events to include semantic event information if ev.name == 'digital_input_port': self.__annotate_dig_trial_events(ev) self.__add_rejection_to_event(ev) cnd = self.__extract_task_condition(ev.array_annotations['belongs_to_trialtype']) seg.annotate(condition=cnd) # If digital trial events exist, extract analog events from odML # and create one common event array if len(seg.events) > 0 and self.odmldoc: analog_event = self.__extract_analog_events_from_odml(seg.t_start, seg.t_stop) self.__add_rejection_to_event(analog_event) seg.events.append(analog_event) merged_event = self.__merge_digital_analog_events(seg.events) self.__add_rejection_to_event(merged_event) seg.events.append(merged_event) return seg if __name__ == '__main__': pass