def plot_odor_plume(config, gm):
fig = plt.figure()
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes(fig)
# get static plume
static_time = 12.
gm_static = gm.get_gaussian_model_at_time_t(static_time)
# set x axis to be huge
gm_static.parameters['mean_0'] = 0
gm_static.parameters['std_0'] = 10000000000000000
#xlim, ylim, resolution, axis=2, axis_slice=0)
odor_image_xy, extent_xy = gm_static.get_array_2d_slice([-.2,1], [-.15,.15], .001, axis=2, axis_slice=.04)
odor_image_xz, extent_xz = gm_static.get_array_2d_slice([-.2,1], [-.15,.15], .001, axis=1, axis_slice=.01)
odor_image_yz, extent_yz = gm_static.get_array_2d_slice([-.15,.15], [-.15,.15], .001, axis=0, axis_slice=0)
ax_xy.imshow(odor_image_xy, extent=extent_xy, origin='lower')
ax_xz.imshow(odor_image_xz, extent=extent_xz, origin='lower')
ax_yz.imshow(odor_image_yz, extent=extent_yz, origin='lower')
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
figure_path = os.path.join(config.path, config.figure_path)
save_figure_path = os.path.join(figure_path, 'odor_traces/')
pdf_name_with_path = os.path.join(save_figure_path, 'odor_plume_model.pdf')
fig.savefig(pdf_name_with_path, format='pdf')
def plot_post_traces(path, config, dataset, keys=None, save=True):
if keys is None:
keys = dataset.trajecs.keys()
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
for key in keys:
trajec = dataset.trajecs[key]
if trajec.post_behavior != 'landing':
if trajec.odor_stimulus != 'none':
if trajec.distance_to_post[-1] < 0.01:
print key
plot_odor_trace_on_ax(path, config, dataset, keys=[key], axis='xy', ax=ax_xy, show_post=config.post)
plot_odor_trace_on_ax(path, config, dataset, keys=[key], axis='xz', ax=ax_xz, show_post=config.post)
plot_odor_trace_on_ax(path, config, dataset, keys=[key], axis='yz', ax=ax_yz, show_post=config.post)
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
if save:
figname = None
figure_path = os.path.join(path, config.figure_path)
save_figure_path = os.path.join(figure_path, 'odor_traces/')
if figname is None:
figname = save_figure_path + 'trajec_ending_near_post' + '.pdf'
else:
figname = os.path.join(save_figure_path, figname)
plt.savefig(figname, format='pdf')
def plot_all_heatmaps(
config, dataset, save_figure_path="", figname=None, keys=None, frames=None, title=None, save=False
):
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
plot_heatmap(
config, dataset, axis="xy", save_figure_path="", figname=None, keys=keys, frames=frames, ax=ax_xy, save=False
)
plot_heatmap(
config, dataset, axis="xz", save_figure_path="", figname=None, keys=keys, frames=frames, ax=ax_xz, save=False
)
plot_heatmap(
config, dataset, axis="yz", save_figure_path="", figname=None, keys=keys, frames=frames, ax=ax_yz, save=False
)
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
if title is not None:
plt.suptitle(title)
if save:
if figname is None:
figname = save_figure_path + "heatmap_" + "all_axes" + ".pdf"
else:
figname = save_figure_path + figname
plt.savefig(figname, format="pdf")
def plot_trace_ends(path, config, dataset, keys=None, show_saccades=False, save=True):
if keys is None:
keys = dataset.trajecs.keys()
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
if config.post:
height = config.post_center[2]-config.ticks['z'][0]
post = patches.Circle(config.post_center[0:2], config.post_radius, color='black')
ax_xy.add_artist(post)
post = patches.Rectangle([config.post_center[0]-1*config.post_radius, config.ticks['z'][0]], config.post_radius*2, height, color='black')
ax_xz.add_artist(post)
post = patches.Rectangle([config.post_center[1]-1*config.post_radius, config.ticks['z'][0]], config.post_radius*2, height, color='black')
ax_yz.add_artist(post)
for key in keys:
trajec = dataset.trajecs[key]
if trajec.post_behavior == 'landing':
color = 'green'
else:
color = 'red'
if np.max(trajec.distance_to_post) > 0.05:
if trajec.positions[-1][2] < 0.0:
ax_xy.plot(trajec.positions[-1][0],trajec.positions[-1][1],'.', color=color, markersize=1, alpha=0.7)
if np.abs(trajec.positions[-1][1]) < 0.03:
ax_xz.plot(trajec.positions[-1][0],trajec.positions[-1][2],'.', color=color, markersize=1, alpha=0.7)
if np.abs(trajec.positions[-1][0]) < 0.05:
ax_yz.plot(trajec.positions[-1][1],trajec.positions[-1][2],'.', color=color, markersize=1, alpha=0.7)
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
if save:
figname = None
figure_path = os.path.join(path, config.figure_path)
save_figure_path = os.path.join(figure_path, 'odor_traces/')
if figname is None:
figname = save_figure_path + 'trajec_ends' + '.pdf'
else:
figname = os.path.join(save_figure_path, figname)
plt.savefig(figname, format='pdf')
def plot_all_heatmaps(config, dataset, save_figure_path='', figname=None, keys=None, frames=None, title=None, save=False):
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
plot_heatmap(config, dataset, axis='xy', save_figure_path='', figname=None, keys=keys, frames=frames, ax=ax_xy, save=False)
plot_heatmap(config, dataset, axis='xz', save_figure_path='', figname=None, keys=keys, frames=frames, ax=ax_xz, save=False)
plot_heatmap(config, dataset, axis='yz', save_figure_path='', figname=None, keys=keys, frames=frames, ax=ax_yz, save=False)
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
if title is not None:
plt.suptitle(title)
if save:
if figname is None:
figname = save_figure_path + 'heatmap_' + 'all_axes' + '.pdf'
else:
figname = save_figure_path + figname
plt.savefig(figname, format='pdf')
def plot_odor_traces(path, config, dataset, keys=None, show_saccades=False, frames_to_show_before_odor='all', frames_to_show_after_odor='all', save=False, odor_multiplier=1, frameranges=None):
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
plot_odor_trace_on_ax(path, config, dataset, keys=keys, axis='xy', show_saccades=show_saccades, frames_to_show_before_odor=frames_to_show_before_odor, frames_to_show_after_odor=frames_to_show_after_odor, ax=ax_xy, odor_multiplier=odor_multiplier, show_post=config.post, frameranges=frameranges)
plot_odor_trace_on_ax(path, config, dataset, keys=keys, axis='xz', show_saccades=show_saccades, frames_to_show_before_odor=frames_to_show_before_odor, frames_to_show_after_odor=frames_to_show_after_odor, ax=ax_xz, odor_multiplier=odor_multiplier, show_post=config.post, frameranges=frameranges)
plot_odor_trace_on_ax(path, config, dataset, keys=keys, axis='yz', show_saccades=show_saccades, frames_to_show_before_odor=frames_to_show_before_odor, frames_to_show_after_odor=frames_to_show_after_odor, ax=ax_yz, odor_multiplier=odor_multiplier, show_post=config.post, frameranges=frameranges)
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
if save:
figname = None
figure_path = os.path.join(path, config.figure_path)
save_figure_path = os.path.join(figure_path, 'odor_traces/')
if figname is None:
figname = save_figure_path + 'odor_trace' + '.pdf'
else:
figname = os.path.join(save_figure_path, figname)
plt.savefig(figname, format='pdf')
def plot_saccade_positions(pp, threshold_odor, path, config, dataset, odor_stimulus, keys=None):
ax_xy, ax_xz, ax_yz = xyz_axis_grid.get_axes()
if odor_stimulus is 'on':
n = 0
for key in keys:
if n > 1000:
break
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:
if len(block) < 5:
continue
first_sac = None
for sac in trajec.saccades:
if trajec.positions[sac[0],0] < -0.1 or trajec.positions[sac[0],0] > 0.9:
continue
if np.abs(trajec.positions[sac[0],1]) > 0.05:
continue
if trajec.positions[sac[0],2] > 0.05 or trajec.positions[sac[0],2] < -0.01:
continue
if sac[0] > block[0]:
if first_sac is None:
first_sac = sac
break
if first_sac is not None:
sac = first_sac
n += 1
f = np.argmax(np.abs(trajec.heading_smooth_diff[sac])) + sac[0]
ax_xy.plot(trajec.positions[f,0], trajec.positions[f,1], '.', color='black')
ax_xz.plot(trajec.positions[f,0], trajec.positions[f,2], '.', color='black')
ax_yz.plot(trajec.positions[f,1], trajec.positions[f,2], '.', color='black')
if odor_stimulus is 'none':
n = 0
for key in keys:
if n > 1000:
break
trajec = dataset.trajecs[key]
for sac in trajec.saccades:
if trajec.positions[sac[0],0] < -0.1 or trajec.positions[sac[0],0] > 0.9:
continue
if np.abs(trajec.positions[sac[0],1]) > 0.05:
continue
if trajec.positions[sac[0],2] > 0.05 or trajec.positions[sac[0],2] < -0.01:
continue
n += 1
f = np.argmax(np.abs(trajec.heading_smooth_diff[sac])) + sac[0]
ax_xy.plot(trajec.positions[f,0], trajec.positions[f,1], '.', color='black')
ax_xz.plot(trajec.positions[f,0], trajec.positions[f,2], '.', color='black')
ax_yz.plot(trajec.positions[f,1], trajec.positions[f,2], '.', color='black')
xyz_axis_grid.set_spines_and_labels(ax_xy, ax_xz, ax_yz)
pp.savefig()
plt.close('all')
