def plot_odor_heading_book(pp, threshold_odor, path, config, dataset, keys=None): fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111) saccades_odor = {'saccade_angles': [], 'heading_prior': []} saccades_control = {'saccade_angles': [], 'heading_prior': []} for key in keys: trajec = dataset.trajecs[key] frames_in_odor = np.where(trajec.odor > threshold_odor)[0] odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5, return_longest_only=False) for block in odor_blocks: #middle_of_block = int(np.mean(block)) if len(block) < 5: continue # find next saccade first_sac = None #second_sac = None #third_sac = None for sac in trajec.saccades: if trajec.positions[sac[0],0] < -0.15 or trajec.positions[sac[0],0] > 0.9: continue if np.abs(trajec.positions[sac[0],1]) > 0.08: continue if np.abs(trajec.positions[sac[0],2]) > 0.08: continue if sac[0] > block[0]: if first_sac is None: first_sac = sac break #elif second_sac is None: # if trajec.odor[sac[0]] < threshold_odor: # second_sac = sac #elif third_sac is None: # if trajec.odor[sac[0]] < threshold_odor: # third_sac = sac # break if first_sac is not None: next_sac = first_sac angle_of_saccade = tac.get_angle_of_saccade(trajec, next_sac) heading_prior_to_saccade = trajec.heading_smooth[next_sac[0]] # flip heading if heading_prior_to_saccade < 0: heading_prior_to_saccade += np.pi else: heading_prior_to_saccade -= np.pi saccade_angles_after_odor.append(angle_of_saccade) heading_at_saccade_initiation.append(heading_prior_to_saccade) heading_after_saccade.append(heading_prior_to_saccade + angle_of_saccade) speed_at_saccade.append(trajec.speed[next_sac[0]]) saccade_angles_after_odor = np.array(saccade_angles_after_odor) heading_at_saccade_initiation = np.array(heading_at_saccade_initiation) heading_after_saccade = np.array(heading_after_saccade) speed_at_saccade = np.array(speed_at_saccade) ax.plot(heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, '.', markersize=4) #fpl.scatter(ax, heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, color=speed_at_saccade, radius=1) #ax.plot(heading_at_saccade_initiation*180./np.pi, heading_after_saccade*180./np.pi, '.') xticks = [-180, -90, 0, 90, 180] yticks = [-180, -90, 0, 90, 180] fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks, yticks=yticks) ax.set_xlabel('Heading before saccade') ax.set_ylabel('Angle of saccade') title_text = 'Odor: ' + trajec.odor_stimulus.title() ax.set_title(title_text) ax.text(0,-180, 'Upwind', horizontalalignment='center', verticalalignment='top') ax.text(90,-180, 'Starboard', horizontalalignment='center', verticalalignment='top') ax.text(-90,-180, 'Port', horizontalalignment='center', verticalalignment='top') ax.text(-180,90, 'Starboard', horizontalalignment='left', verticalalignment='center', rotation='vertical') ax.text(-180,-90, 'Port', horizontalalignment='left', verticalalignment='center', rotation='vertical') pp.savefig() plt.close('all') # angle of saccade histogram if 0: fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111) fpl.histogram_stack(ax, [np.array(time_to_saccade_cast)], bins=40, bin_width_ratio=0.9, colors=['red'], edgecolor='none', normed=True) ax.set_xlabel('Angle of Saccade') ax.set_ylabel('Occurences, normalized') #xticks = [-180, -90, 0, 90, 180] fpl.adjust_spines(ax, ['left', 'bottom']) ax.set_title(title_text) pp.savefig() plt.close('all')
def plot_odor_heading_book(pp, threshold_odor, path, config, dataset, keys=None): fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111) saccade_angles_after_odor = [] heading_at_saccade_initiation = [] heading_after_saccade = [] for key in keys: trajec = dataset.trajecs[key] frames_in_odor = np.where(trajec.odor > threshold_odor)[0] odor_blocks = hf.find_continuous_blocks(frames_in_odor, 5, return_longest_only=False) for block in odor_blocks: middle_of_block = int(np.mean(block)) # find next saccade first_sac = None second_sac = None for sac in trajec.saccades: if sac[0] > middle_of_block: if first_sac is None: first_sac = sac elif second_sac is None: if trajec.odor[sac[0]] < threshold_odor: second_sac = sac break if first_sac is not None: next_sac = first_sac angle_of_saccade = tac.get_angle_of_saccade(trajec, next_sac) heading_prior_to_saccade = trajec.heading_smooth[next_sac[0]] # flip heading if heading_prior_to_saccade < 0: heading_prior_to_saccade += np.pi else: heading_prior_to_saccade -= np.pi # flip saccade angle if angle_of_saccade < 0: angle_of_saccade += np.pi else: angle_of_saccade -= np.pi saccade_angles_after_odor.append(angle_of_saccade) heading_at_saccade_initiation.append(heading_prior_to_saccade) heading_after_saccade.append(heading_prior_to_saccade + angle_of_saccade) saccade_angles_after_odor = np.array(saccade_angles_after_odor) heading_at_saccade_initiation = np.array(heading_at_saccade_initiation) heading_after_saccade = np.array(heading_after_saccade) ax.plot(heading_at_saccade_initiation*180./np.pi, saccade_angles_after_odor*180./np.pi, '.') #ax.plot(heading_at_saccade_initiation*180./np.pi, heading_after_saccade*180./np.pi, '.') xticks = [-180, -90, 0, 90, 180] yticks = [-180, -90, 0, 90, 180] fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks, yticks=yticks) ax.set_xlabel('Heading before saccade') ax.set_ylabel('Angle of saccade') title_text = 'Odor: ' + trajec.odor_stimulus.title() ax.set_title(title_text) ax.text(0,-180, 'Upwind', horizontalalignment='center', verticalalignment='top') ax.text(90,-180, 'Starboard', horizontalalignment='center', verticalalignment='top') ax.text(-90,-180, 'Port', horizontalalignment='center', verticalalignment='top') ax.text(-180,90, 'Starboard', horizontalalignment='left', verticalalignment='center', rotation='vertical') ax.text(-180,-90, 'Port', horizontalalignment='left', verticalalignment='center', rotation='vertical') pp.savefig() plt.close('all') # angle of saccade histogram fig = plt.figure() ax = fig.add_subplot(111) fpl.histogram_stack(ax, [saccade_angles_after_odor*180./np.pi], bins=20, bin_width_ratio=0.9, colors=['red'], edgecolor='none', normed=True) ax.set_xlabel('Angle of Saccade') ax.set_ylabel('Occurences, normalized') xticks = [-180, -90, 0, 90, 180] fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks) ax.set_title(title_text) pp.savefig() plt.close('all')
def plot_landing_histogram(config, dataset, save_figure_path=''): keys = get_keys(dataset) print 'number of keys: ', len(keys) if len(keys) < 1: print 'No data' return threshold_distance_min = 0.05 keys_tmp = dataset.trajecs.keys() keys = [] keys_not_near_post = [] for key in keys_tmp: trajec = dataset.trajecs[key] if trajec.distance_to_post_min < threshold_distance_min: keys.append(key) else: keys_not_near_post.append(key) timestamps_not_landings = [] timestamps_landings = [] timestamps_not_near_post = [] for i, key in enumerate(keys): trajec = dataset.trajecs[key] if 'landing' in trajec.post_behavior: timestamps_landings.append( trajec.timestamp_local_float ) else: timestamps_not_landings.append( trajec.timestamp_local_float ) for key in keys_not_near_post: trajec = dataset.trajecs[key] timestamps_not_near_post.append(trajec.timestamp_local_float) # shift so time continuous for i, t in enumerate(timestamps_not_landings): if t > 12: timestamps_not_landings[i] = t-24 for i, t in enumerate(timestamps_landings): if t > 12: timestamps_landings[i] = t-24 for i, t in enumerate(timestamps_not_near_post): if t > 12: timestamps_not_near_post[i] = t-24 timestamps_not_landings = np.array(timestamps_not_landings) timestamps_landings = np.array(timestamps_landings) timestamps_not_near_post = np.array(timestamps_not_near_post) fig = plt.figure(figsize=(4,4)) ax = fig.add_subplot(111) nbins = 36 # note: if show_smoothed=True with default butter filter, nbins needs to be > ~15 bins1 = np.linspace(-12,-0.21,int(nbins/2.),endpoint=True) bins2 = np.linspace(-.21,12,int(nbins/2.),endpoint=True) #bins = [16.05-24, 17.05-24, 18.05-24, 19.05-24, 20.05-24, 21.05-24, 22.05-24, 23.05-24, 0.05, 1.05, 2.05, 3.05, 4.05, 5.05, 6.05, 7.05, 8.05, 9.05, 10.05] bins = np.arange(16.05-24,10.05, 0.5) data = [timestamps_landings, timestamps_not_landings, timestamps_not_near_post] if save_figure_path == '': save_figure_path = os.path.join(config.path, config.figure_path, 'activity/') colors = ['black', 'green'] fpl.histogram_stack(ax, data, bins=bins, bin_width_ratio=0.8, colors=['green', 'black', 'gray'], edgecolor='none', normed=True) #fpl.histogram(ax, data, bins=bins, bin_width_ratio=0.8, colors=colors, edgecolor='none', bar_alpha=1, curve_fill_alpha=0.4, curve_line_alpha=0, curve_butter_filter=[3,0.3], return_vals=False, show_smoothed=False, normed=True, normed_occurences=False, bootstrap_std=False, exponential_histogram=False) if 'on' in config.odor_stimulus.keys(): odor_on = config.odor_stimulus['on'] if type(odor_on[0]) is not list: ax.fill_between(np.array(odor_on), -10, 10, color='red', alpha=0.25, zorder=-10, edgecolor='none') else: for vals in odor_on: odor_start = vals[0] odor_end = vals[-1] if odor_start > 12: odor_start -= 24 if odor_end > 12: odor_end -= 24 print 'odor on for time ranges: ' print odor_start, odor_end ax.fill_between(np.array([odor_start, odor_end]), -10, 10, color='red', alpha=0.25, zorder=-10, edgecolor='none') #xticks = [0,6,12,18,24] xticks = [-12,-6,0,6,12] fpl.adjust_spines(ax, ['left', 'bottom'], xticks=xticks) ax.set_xlabel('Time of day, hours') ax.set_ylabel('Occurences, normalized') ax.set_title('Landings: green -- Nonlandings: black') fig.set_size_inches(4,4) if save_figure_path == '': save_figure_path = os.path.join(config.path, config.figure_path, 'activity/') figname = save_figure_path + 'landing_histogram' + '.pdf' fig.savefig(figname, format='pdf')