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- # -*- coding: utf-8 -*-
- """
- Code for generating the first data figure in the manuscript.
- 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.
- """
- # This loads the Neo and odML libraries shipped with this code. For production
- # use, please use the newest releases of odML and Neo.
- import load_local_neo_odml_elephant
- import os
- import numpy as np
- from scipy import stats
- import quantities as pq
- import matplotlib.pyplot as plt
- from matplotlib import gridspec, ticker
- from reachgraspio import reachgraspio
- import odml.tools
- from neo import utils as neo_utils
- import odml_utils
- # =============================================================================
- # Define data and metadata directories
- # =============================================================================
- def get_monkey_datafile(monkey):
- if monkey == "Lilou":
- return "l101210-001" # ns2 (behavior) and ns5 present
- elif monkey == "Nikos2":
- return "i140703-001" # ns2 and ns6 present
- else:
- return ""
- # Enter your dataset directory here
- datasetdir = "../datasets/"
- trialtype_colors = {
- 'SGHF': 'MediumBlue', 'SGLF': 'Turquoise',
- 'PGHF': 'DarkGreen', 'PGLF': 'YellowGreen',
- 'LFSG': 'Orange', 'LFPG': 'Yellow',
- 'HFSG': 'DarkRed', 'HFPG': 'OrangeRed',
- 'SGSG': 'SteelBlue', 'PGPG': 'LimeGreen',
- 'NONE': 'k', 'PG': 'k', 'SG': 'k', 'LF': 'k', 'HF': 'k'}
- event_colors = {
- 'TS-ON': 'Gray', # 'TS-OFF': 'Gray',
- 'WS-ON': 'Gray', # 'WS-OFF': 'Gray',
- 'CUE-ON': 'Gray',
- 'CUE-OFF': 'Gray',
- 'GO-ON': 'Gray', # 'GO-OFF': 'Gray',
- # 'GO/RW-OFF': 'Gray',
- 'SR': 'Gray', # 'SR-REP': 'Gray',
- 'RW-ON': 'Gray', # 'RW-OFF': 'Gray',
- 'STOP': 'Gray'}
- # =============================================================================
- # Plot helper functions
- # =============================================================================
- def force_aspect(ax, aspect=1):
- ax.set_aspect(abs(
- (ax.get_xlim()[1] - ax.get_xlim()[0]) /
- (ax.get_ylim()[1] - ax.get_ylim()[0])) / aspect)
- def get_arraygrid(blackrock_elid_list, chosen_el, rej_el=None):
- if rej_el is None:
- rej_el = []
- array_grid = np.zeros((10, 10))
- for m in range(10):
- for n in range(10):
- idx = (9 - m) * 10 + n
- bl_id = blackrock_elid_list[idx]
- if bl_id == -1:
- array_grid[m, n] = 0.7
- elif bl_id == chosen_el:
- array_grid[m, n] = -0.7
- elif bl_id in rej_el:
- array_grid[m, n] = -0.35
- else:
- array_grid[m, n] = 0
- return np.ma.array(array_grid, mask=np.isnan(array_grid))
- # =============================================================================
- # Load data and metadata for a monkey
- # =============================================================================
- # CHANGE this parameter to load data of the different monkeys
- # monkey = 'Nikos2'
- monkey = 'Lilou'
- nsx_none = {'Lilou': None, 'Nikos2': None}
- nsx_lfp = {'Lilou': 2, 'Nikos2': 2}
- nsx_raw = {'Lilou': 5, 'Nikos2': 6}
- chosen_el = {'Lilou': 71, 'Nikos2': 63}
- chosen_units = {'Lilou': range(1, 5), 'Nikos2': range(1, 5)}
- datafile = get_monkey_datafile(monkey)
- session = reachgraspio.ReachGraspIO(
- filename=os.path.join(datasetdir, datafile),
- odml_directory=datasetdir)
- bl = session.read_block(lazy=True, load_waveforms=False)
- seg = bl.segments[0]
- # Displaying loaded data structure as string output
- print("\nBlock")
- print('Attributes ', bl.__dict__.keys())
- print('Annotations', bl.annotations)
- print("\nSegment")
- print('Attributes ', seg.__dict__.keys())
- print('Annotations', seg.annotations)
- print("\nEvents")
- for x in seg.events:
- print('\tEvent with name', x.name)
- print('\t\tAttributes ', x.__dict__.keys())
- print('\t\tAnnotation keys', x.annotations.keys())
- print('\t\tArray annotation keys', x.array_annotations.keys())
- print('\t\ttimes', x.times[:20])
- for anno_key in ['trial_id', 'trial_timestamp_id', 'trial_event_labels',
- 'trial_reject_IFC']:
- if anno_key in x.array_annotations:
- print('\t\t'+anno_key, x.array_annotations[anno_key][:20])
- print("\nGroup")
- for x in bl.groups:
- print('\tGroup with name', x.name)
- print('\t\tAttributes ', x.__dict__.keys())
- print('\t\tAnnotations', x.annotations)
- print("\nSpikeTrains")
- for x in seg.spiketrains:
- print('\tSpiketrain with name', x.name)
- print('\t\tAttributes ', x.__dict__.keys())
- print('\t\tAnnotations', x.annotations)
- print('\t\tArray annotations', x.array_annotations)
- print('\t\tchannel_id', x.annotations['channel_id'])
- print('\t\tunit_id', x.annotations['unit_id'])
- print("\nAnalogSignals")
- for x in seg.analogsignals:
- print('\tAnalogSignal with name', x.name)
- print('\t\tAttributes ', x.__dict__.keys())
- print('\t\tAnnotations', x.annotations)
- print('\t\tArray annotations', x.array_annotations)
- print('\t\tchannel_id', x.array_annotations['channel_ids'])
- # get start and stop events of trials
- start_events = neo_utils.get_events(seg, properties={'name': 'TrialEvents'})[0]
- start_event_mask = np.logical_and(start_events.array_annotations['trial_event_labels'] == 'TS-ON',
- start_events.array_annotations['performance_in_trial'] == 255)
- start_events = start_events[start_event_mask]
- stop_events = neo_utils.get_events( seg, properties={'name': 'TrialEvents'})[0]
- stop_event_mask = np.logical_and(stop_events.array_annotations['trial_event_labels'] == 'STOP',
- stop_events.array_annotations['performance_in_trial' == 255])
- stop_events = stop_events[stop_event_mask]
- # insert epochs between 10ms before TS to 50ms after RW corresponding to trails
- neo_utils.add_epoch(
- seg,
- start_events[0],
- stop_events[0],
- pre=-250 * pq.ms,
- post=500 * pq.ms,
- trial_status='complete_trials',
- trial_type=start_events[0].annotations['belongs_to_trialtype'],
- trial_performance=start_events[0].annotations['performance_in_trial'])
- # access single epoch of this data_segment
- epochs = neo_utils.get_epochs(seg,
- properties={'trial_status': 'complete_trials'})
- assert len(epochs) == 1
- # cut segments according to inserted 'complete_trials' epochs and reset trial
- # times
- cut_segments = neo_utils.cut_segment_by_epoch(
- seg, epochs[0], reset_time=True)
- # =============================================================================
- # Define data for overview plots
- # =============================================================================
- trial_index = {'Lilou': 0, 'Nikos2': 6}
- trial_seg = cut_segments[trial_index[monkey]]
- blackrock_elid_list = bl.annotations['avail_electrode_ids']
- # get 'TrialEvents'
- event = trial_seg.events[2]
- start = event.annotations['trial_event_labels'].index('TS-ON')
- trialx_trty = event.annotations['belongs_to_trialtype'][start]
- trialx_trtimeid = event.annotations['trial_timestamp_id'][start]
- trialx_color = trialtype_colors[trialx_trty]
- # find trial index for next trial with opposite force type (for ax5b plot)
- if 'LF' in trialx_trty:
- trialz_trty = trialx_trty.replace('LF', 'HF')
- else:
- trialz_trty = trialx_trty.replace('HF', 'LF')
- for i, tr in enumerate(cut_segments):
- eventz = tr.events[2]
- nextft = eventz.annotations['trial_event_labels'].index('TS-ON')
- if eventz.annotations['belongs_to_trialtype'][nextft] == trialz_trty:
- trialz_trtimeid = eventz.annotations['trial_timestamp_id'][nextft]
- trialz_color = trialtype_colors[trialz_trty]
- trialz_seg = tr
- break
- # =============================================================================
- # Define figure and subplot axis for first data overview
- # =============================================================================
- fig = plt.figure()
- fig.set_size_inches(6.5, 10.) # (w, h) in inches
- gs = gridspec.GridSpec(
- nrows=5,
- ncols=4,
- left=0.05,
- bottom=0.07,
- right=0.9,
- top=0.975,
- wspace=0.3,
- hspace=0.5,
- width_ratios=None,
- height_ratios=[1, 3, 3, 6, 3])
- ax1 = plt.subplot(gs[0, :]) # top row / odml data
- # second row
- ax2a = plt.subplot(gs[1, 0]) # electrode overview plot
- ax2b = plt.subplot(gs[1, 1]) # waveforms unit 1
- ax2c = plt.subplot(gs[1, 2]) # waveforms unit 2
- ax2d = plt.subplot(gs[1, 3]) # waveforms unit 3
- ax3 = plt.subplot(gs[2, :]) # third row / spiketrains
- ax4 = plt.subplot(gs[3, :], sharex=ax3) # fourth row / raw signal
- ax5a = plt.subplot(gs[4, 0:3]) # fifth row / behavioral signals
- ax5b = plt.subplot(gs[4, 3])
- fontdict_titles = {'fontsize': 'small', 'fontweight': 'bold'}
- fontdict_axis = {'fontsize': 'x-small'}
- wf_time_unit = pq.ms
- wf_signal_unit = pq.microvolt
- plotting_time_unit = pq.s
- raw_signal_unit = wf_signal_unit
- behav_signal_unit = pq.V
- # =============================================================================
- # PLOT TRIAL SEQUENCE OF SUBSESSION
- # =============================================================================
- # load complete metadata collection
- odmldoc = odml.tools.xmlparser.load(datasetdir + datafile + '.odml')
- # get total trial number
- trno_tot = odml_utils.get_TrialCount(odmldoc)
- trno_ctr = odml_utils.get_TrialCount(odmldoc, performance_code=255)
- trno_ertr = trno_tot - trno_ctr
- # get trial id of chosen trial (and next trial with opposite force)
- trtimeids = odml_utils.get_TrialIDs(odmldoc, idtype='TrialTimestampID')
- trids = odml_utils.get_TrialIDs(odmldoc)
- trialx_trid = trids[trtimeids.index(trialx_trtimeid)]
- trialz_trid = trids[trtimeids.index(trialz_trtimeid)]
- # get all trial ids for grip error trials
- trids_pc191 = odml_utils.get_trialids_pc(odmldoc, 191)
- # get all trial ids for correct trials
- trids_pc255 = odml_utils.get_trialids_pc(odmldoc, 255)
- # get occurring trial types
- octrty = odml_utils.get_OccurringTrialTypes(odmldoc, code=False)
- # Subplot 1: Trial sequence
- boxes, labels = [], []
- for tt in octrty:
- # Plot trial ids of current trial type into trial sequence bar plot
- left = odml_utils.get_trialids_trty(odmldoc, tt)
- height = np.ones_like(left)
- width = 1.
- if tt in ['NONE', 'PG', 'SG', 'LF', 'HF']:
- color = 'w'
- else:
- color = trialtype_colors[tt]
- B = ax1.bar(
- x=left, height=height, width=width, color=color, linewidth=0.001, align='edge')
- # Mark trials of current trial type (left) if a grip error occurred
- x = [i for i in list(set(left) & set(trids_pc191))]
- y = np.ones_like(x) * 2.0
- ax1.scatter(x, y, s=5, color='k', marker='*')
- # Mark trials of current trial type (left) if any other error occurred
- x = [i for i in list(
- set(left) - set(trids_pc255) - set(trids_pc191))]
- y = np.ones_like(x) * 2.0
- ax1.scatter(x, y, s=5, color='gray', marker='*')
- # Collect information for trial type legend
- if tt not in ['PG', 'SG', 'LF', 'HF']:
- boxes.append(B[0])
- if tt == 'NONE':
- # use errors for providing total trial number
- labels.append('total: # %i' % trno_tot)
- # add another box and label for error numbers
- boxes.append(B[0])
- labels.append('* errors: # %i' % trno_ertr)
- else:
- # trial type trial numbers
- labels.append(tt + ': # %i' % len(left))
- # mark chosen trial
- x = [trialx_trid]
- y = np.ones_like(x) * 2.0
- ax1.scatter(x, y, s=5, marker='D', color='Red', edgecolors='Red')
- # mark next trial with opposite force
- x = [trialz_trid]
- y = np.ones_like(x) * 2.0
- ax1.scatter(x, y, s=5, marker='D', color='orange', edgecolors='orange')
- # Generate trial type legend; bbox: (left, bottom, width, height)
- leg = ax1.legend(
- boxes, labels, bbox_to_anchor=(0., 1., 0.5, 0.1), loc=3, handlelength=1.1,
- ncol=len(labels), borderaxespad=0., handletextpad=0.4,
- prop={'size': 'xx-small'})
- leg.draw_frame(False)
- # adjust x and y axis
- xticks = [i for i in range(1, 101, 10)] + [100]
- ax1.set_xticks(xticks)
- ax1.set_xticklabels([str(int(t)) for t in xticks], size='xx-small')
- ax1.set_xlabel('trial ID', size='x-small')
- ax1.set_xlim(1.-width/2., 100.+width/2.)
- ax1.yaxis.set_visible(False)
- ax1.set_ylim(0, 3)
- ax1.spines['top'].set_visible(False)
- ax1.spines['left'].set_visible(False)
- ax1.spines['right'].set_visible(False)
- ax1.tick_params(direction='out', top='off')
- ax1.set_title('sequence of the first 100 trials', fontdict_titles, y=2)
- ax1.set_aspect('equal')
- # =============================================================================
- # PLOT ELECTRODE POSITION of chosen electrode
- # =============================================================================
- arraygrid = get_arraygrid(blackrock_elid_list, chosen_el[monkey])
- cmap = plt.cm.RdGy
- ax2a.pcolormesh(
- np.flipud(arraygrid), vmin=-1, vmax=1, lw=1, cmap=cmap, edgecolors='k',
- shading='faceted')
- force_aspect(ax2a, aspect=1)
- ax2a.tick_params(
- bottom='off', top='off', left='off', right='off',
- labelbottom='off', labeltop='off', labelleft='off', labelright='off')
- ax2a.set_title('electrode pos.', fontdict_titles)
- # =============================================================================
- # PLOT WAVEFORMS of units of the chosen electrode
- # =============================================================================
- unit_ax_translator = {1: ax2b, 2: ax2c, 3: ax2d}
- unit_type = {1: '', 2: '', 3: ''}
- wf_lim = []
- # plotting waveform for all spiketrains available
- for spiketrain in trial_seg.spiketrains:
- unit_id = spiketrain.annotations['unit_id']
- # get unit type
- if spiketrain.annotations['sua']:
- unit_type[unit_id] = 'SUA'
- elif spiketrain.annotations['mua']:
- unit_type[unit_id] = 'MUA'
- else:
- pass
- # get correct ax
- ax = unit_ax_translator[unit_id]
- # get wf sampling time before threshold crossing
- left_sweep = spiketrain.left_sweep
- # plot waveforms in subplots according to unit id
- for st_id, st in enumerate(spiketrain):
- wf = spiketrain.waveforms[st_id]
- wf_lim.append((np.min(wf), np.max(wf)))
- wf_color = str(
- (st / spiketrain.t_stop).rescale('dimensionless').magnitude)
- times = range(len(wf[0])) * spiketrain.units - left_sweep
- ax.plot(
- times.rescale(wf_time_unit), wf[0].rescale(wf_signal_unit),
- color=wf_color)
- ax.set_xlim(
- times.rescale(wf_time_unit)[0], times.rescale(wf_time_unit)[-1])
- # adding xlabels and titles
- for unit_id, ax in unit_ax_translator.items():
- ax.set_title('unit %i (%s)' % (unit_id, unit_type[unit_id]),
- fontdict_titles)
- ax.tick_params(direction='in', length=3, labelsize='xx-small',
- labelleft='off', labelright='off')
- ax.set_xlabel(wf_time_unit.dimensionality.latex, fontdict_axis)
- xticklocator = ticker.MaxNLocator(nbins=5)
- ax.xaxis.set_major_locator(xticklocator)
- ax.set_ylim(np.min(wf_lim), np.max(wf_lim))
- force_aspect(ax, aspect=1)
- # adding ylabel
- ax2d.tick_params(labelsize='xx-small', labelright='on')
- ax2d.set_ylabel(wf_signal_unit.dimensionality.latex, fontdict_axis)
- ax2d.yaxis.set_label_position("right")
- # =============================================================================
- # PLOT SPIKETRAINS of units of chosen electrode
- # =============================================================================
- plotted_unit_ids = []
- # plotting all available spiketrains
- for st in trial_seg.spiketrains:
- unit_id = st.annotations['unit_id']
- plotted_unit_ids.append(unit_id)
- ax3.plot(st.times.rescale(plotting_time_unit),
- np.zeros(len(st.times)) + unit_id,
- 'k|')
- # setting layout of spiktrain plot
- ax3.set_ylim(min(plotted_unit_ids) - 0.5, max(plotted_unit_ids) + 0.5)
- ax3.set_ylabel(r'unit ID', fontdict_axis)
- ax3.yaxis.set_major_locator(ticker.MultipleLocator(base=1))
- ax3.yaxis.set_label_position("right")
- ax3.tick_params(axis='y', direction='in', length=3, labelsize='xx-small',
- labelleft='off', labelright='on')
- ax3.invert_yaxis()
- ax3.set_title('spiketrains', fontdict_titles)
- # =============================================================================
- # PLOT "raw" SIGNAL of chosen trial of chosen electrode
- # =============================================================================
- # get "raw" data from chosen electrode
- assert len(trial_seg.analogsignals) == 1
- el_sig = trial_seg.analogsignals[0]
- # plotting raw signal trace
- ax4.plot(el_sig.times.rescale(plotting_time_unit),
- el_sig.squeeze().rescale(raw_signal_unit),
- color='k')
- # setting layout of raw signal plot
- ax4.set_ylabel(raw_signal_unit.units.dimensionality.latex, fontdict_axis)
- ax4.yaxis.set_label_position("right")
- ax4.tick_params(axis='y', direction='in', length=3, labelsize='xx-small',
- labelleft='off', labelright='on')
- ax4.set_title('"raw" signal', fontdict_titles)
- ax4.set_xlim(trial_seg.t_start.rescale(plotting_time_unit),
- trial_seg.t_stop.rescale(plotting_time_unit))
- ax4.xaxis.set_major_locator(ticker.MultipleLocator(base=1))
- # =============================================================================
- # PLOT EVENTS across ax3 and ax4 and add time bar
- # =============================================================================
- # find trial relevant events
- startidx = event.annotations['trial_event_labels'].index('TS-ON')
- stopidx = event.annotations['trial_event_labels'][startidx:].index('STOP') + \
- startidx + 1
- for ax in [ax3, ax4]:
- xticks = []
- xticklabels = []
- for ev_id, ev in enumerate(event[startidx:stopidx]):
- ev_labels = event.annotations['trial_event_labels'][startidx:stopidx]
- if ev_labels[ev_id] in event_colors.keys():
- ev_color = event_colors[ev_labels[ev_id]]
- ax.axvline(
- ev.rescale(plotting_time_unit), color=ev_color, zorder=0.5)
- xticks.append(ev.rescale(plotting_time_unit))
- if ev_labels[ev_id] == 'CUE-OFF':
- xticklabels.append('-OFF')
- elif ev_labels[ev_id] == 'GO-ON':
- xticklabels.append('GO')
- else:
- xticklabels.append(ev_labels[ev_id])
- ax.set_xticks(xticks)
- ax.set_xticklabels(xticklabels)
- ax.tick_params(axis='x', direction='out', length=3, labelsize='xx-small',
- labeltop='off', top='off')
- timebar_ypos = ax4.get_ylim()[0] + np.diff(ax4.get_ylim())[0] / 10
- timebar_labeloffset = np.diff(ax4.get_ylim())[0] * 0.01
- timebar_xmin = xticks[-2] + ((xticks[-1] - xticks[-2]) / 2 - 0.25 * pq.s)
- timebar_xmax = timebar_xmin + 0.5 * pq.s
- ax4.plot([timebar_xmin, timebar_xmax], [timebar_ypos, timebar_ypos], '-',
- linewidth=3, color='k')
- ax4.text(timebar_xmin + 0.25 * pq.s, timebar_ypos + timebar_labeloffset,
- '500 ms', ha='center', va='bottom', size='xx-small', color='k')
- # =============================================================================
- # PLOT BEHAVIORAL SIGNALS of chosen trial
- # =============================================================================
- # get behavioral signals
- ainp_signals = [nsig for nsig in trial_seg.analogsignals if
- nsig.annotations['channel_id'] > 96]
- ainp_trialz = [nsig for nsig in trialz_seg.analogsignals if
- nsig.annotations['channel_id'] == 141][0]
- # find out what signal to use
- trialx_sec = odmldoc['Recording']['TaskSettings']['Trial_%03i' % trialx_trid]
- # get correct channel id
- trialx_chids = [143]
- FSRi = trialx_sec['AnalogEvents'].properties['UsedForceSensor'].values[0]
- FSRinfosec = odmldoc['Setup']['Apparatus']['TargetObject']['FSRSensor']
- if 'SG' in trialx_trty:
- sgchids = FSRinfosec.properties['SGChannelIDs'].values
- trialx_chids.append(min(sgchids) if FSRi == 1 else max(sgchids))
- else:
- pgchids = FSRinfosec.properties['PGChannelIDs'].values
- trialx_chids.append(min(pgchids) if FSRi == 1 else max(pgchids))
- # define time epoch
- startidx = event.annotations['trial_event_labels'].index('SR')
- stopidx = event.annotations['trial_event_labels'].index('OBB')
- sr = event[startidx].rescale(plotting_time_unit)
- stop = event[stopidx].rescale(plotting_time_unit) + 0.050 * pq.s
- startidx = event.annotations['trial_event_labels'].index('FSRplat-ON')
- stopidx = event.annotations['trial_event_labels'].index('FSRplat-OFF')
- fplon = event[startidx].rescale(plotting_time_unit)
- fploff = event[stopidx].rescale(plotting_time_unit)
- # define time epoch trialz
- startidx = eventz.annotations['trial_event_labels'].index('FSRplat-ON')
- stopidx = eventz.annotations['trial_event_labels'].index('FSRplat-OFF')
- fplon_trz = eventz[startidx].rescale(plotting_time_unit)
- fploff_trz = eventz[stopidx].rescale(plotting_time_unit)
- # plotting grip force and object displacement
- ai_legend = []
- ai_legend_txt = []
- for ainp in ainp_signals:
- if ainp.annotations['channel_id'] in trialx_chids:
- ainp_times = ainp.times.rescale(plotting_time_unit)
- mask = (ainp_times > sr) & (ainp_times < stop)
- ainp_ampli = stats.zscore(ainp.magnitude[mask])
- if ainp.annotations['channel_id'] != 143:
- color = 'gray'
- ai_legend_txt.append('grip force')
- else:
- color = 'k'
- ai_legend_txt.append('object disp.')
- ai_legend.append(
- ax5a.plot(ainp_times[mask], ainp_ampli, color=color)[0])
- # get force load of this trial for next plot
- elif ainp.annotations['channel_id'] == 141:
- ainp_times = ainp.times.rescale(plotting_time_unit)
- mask = (ainp_times > fplon) & (ainp_times < fploff)
- force_av_01 = np.mean(ainp.rescale(behav_signal_unit).magnitude[mask])
- # setting layout of grip force and object displacement plot
- ax5a.set_title('grip force and object displacement', fontdict_titles)
- ax5a.yaxis.set_label_position("left")
- ax5a.tick_params(direction='in', length=3, labelsize='xx-small',
- labelleft='off', labelright='on')
- ax5a.set_ylabel('zscore', fontdict_axis)
- ax5a.legend(
- ai_legend, ai_legend_txt,
- bbox_to_anchor=(0.65, .85, 0.25, 0.1), loc=2, handlelength=1.1,
- ncol=len(labels), borderaxespad=0., handletextpad=0.4,
- prop={'size': 'xx-small'})
- # plotting load/pull force of LF and HF trial
- force_times = ainp_trialz.times.rescale(plotting_time_unit)
- mask = (force_times > fplon_trz) & (force_times < fploff_trz)
- force_av_02 = np.mean(ainp_trialz.rescale(behav_signal_unit).magnitude[mask])
- bar_width = [0.4, 0.4]
- color = [trialx_color, trialz_color]
- ax5b.bar([0, 0.6], [force_av_01, force_av_02], bar_width, color=color)
- ax5b.set_title('load/pull force', fontdict_titles)
- ax5b.set_ylabel(behav_signal_unit.units.dimensionality.latex, fontdict_axis)
- ax5b.set_xticks([0, 0.6])
- ax5b.set_xticklabels([trialx_trty, trialz_trty], fontdict_axis)
- ax5b.yaxis.set_label_position("right")
- ax5b.tick_params(direction='in', length=3, labelsize='xx-small',
- labelleft='off', labelright='on')
- # =============================================================================
- # PLOT EVENTS across ax5a and add time bar
- # =============================================================================
- # find trial relevant events
- startidx = event.annotations['trial_event_labels'].index('SR')
- stopidx = event.annotations['trial_event_labels'].index('OBB')
- xticks = []
- xticklabels = []
- for ev_id, ev in enumerate(event[startidx:stopidx]):
- ev_labels = event.annotations['trial_event_labels'][startidx:stopidx + 1]
- if ev_labels[ev_id] in ['RW-ON']:
- ax5a.axvline(ev.rescale(plotting_time_unit), color='k', zorder=0.5)
- xticks.append(ev.rescale(plotting_time_unit))
- xticklabels.append(ev_labels[ev_id])
- elif ev_labels[ev_id] in ['OT', 'OR', 'DO', 'OBB', 'FSRplat-ON',
- 'FSRplat-OFF', 'HEplat-ON']:
- ev_color = 'k'
- xticks.append(ev.rescale(plotting_time_unit))
- xticklabels.append(ev_labels[ev_id])
- ax5a.axvline(
- ev.rescale(plotting_time_unit), color='k', ls='-.', zorder=0.5)
- elif ev_labels[ev_id] == 'HEplat-OFF':
- ev_color = 'k'
- ax5a.axvline(
- ev.rescale(plotting_time_unit), color='k', ls='-.', zorder=0.5)
- ax5a.set_xticks(xticks)
- ax5a.set_xticklabels(xticklabels, fontdict_axis, rotation=90)
- ax5a.tick_params(axis='x', direction='out', length=3, labelsize='xx-small',
- labeltop='off', top='off')
- ax5a.set_ylim([-2.0, 2.0])
- timebar_ypos = ax5a.get_ylim()[0] + np.diff(ax5a.get_ylim())[0] / 10
- timebar_labeloffset = np.diff(ax5a.get_ylim())[0] * 0.02
- timebar_xmax = xticks[xticklabels.index('RW-ON')] - 0.1 * pq.s
- timebar_xmin = timebar_xmax - 0.25 * pq.s
- ax5a.plot([timebar_xmin, timebar_xmax], [timebar_ypos, timebar_ypos], '-',
- linewidth=3, color='k')
- ax5a.text(timebar_xmin + 0.125 * pq.s, timebar_ypos + timebar_labeloffset,
- '250 ms', ha='center', va='bottom', size='xx-small', color='k')
- # add time window of ax5a to ax4
- ax4.axvspan(ax5a.get_xlim()[0], ax5a.get_xlim()[1], facecolor=[0.9, 0.9, 0.9],
- zorder=-0.1, ec=None)
- # =============================================================================
- # SAVE FIGURE
- # =============================================================================
- fname = 'data_overview_1_%s' % monkey
- for file_format in ['eps', 'png', 'pdf']:
- fig.savefig(fname + '.%s' % file_format, dpi=400, format=file_format)
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