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trajectory_plots.py
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trajectory_plots.py
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import sys
#sys.path.insert(0, '/usr/local/lib/python2.6/dist-packages')
sys.path.append('/home/floris/src/pymovie2')
from matplotlib import rcParams
fig_width = 3.25 # width in inches
fig_height = 3.25 # height in inches
fig_size = (fig_width, fig_height)
fontsize = 8
params = {'backend': 'Agg',
'ps.usedistiller': 'xpdf',
'ps.fonttype' : 3,
'pdf.fonttype' : 3,
'font.family' : 'sans-serif',
'font.serif' : 'Times, Palatino, New Century Schoolbook, Bookman, Computer Modern Roman',
'font.sans-serif' : 'Helvetica, Avant Garde, Computer Modern Sans serif',
'font.cursive' : 'Zapf Chancery',
'font.monospace' : 'Courier, Computer Modern Typewriter',
'font.size' : fontsize,
'text.fontsize': fontsize,
'axes.labelsize': fontsize,
'axes.linewidth': 1.0,
'xtick.major.linewidth': 1,
'xtick.minor.linewidth': 1,
#'xtick.major.size': 6,
#'xtick.minor.size' : 3,
'xtick.labelsize': fontsize,
#'ytick.major.size': 6,
#'ytick.minor.size' : 3,
'ytick.labelsize': fontsize,
'figure.figsize': fig_size,
'figure.dpi' : 72,
'figure.facecolor' : 'white',
'figure.edgecolor' : 'white',
'savefig.dpi' : 300,
'savefig.facecolor' : 'white',
'savefig.edgecolor' : 'white',
'figure.subplot.left': 0.2,
'figure.subplot.right': 0.8,
'figure.subplot.bottom': 0.25,
'figure.subplot.top': 0.9,
'figure.subplot.wspace': 0.0,
'figure.subplot.hspace': 0.0,
'lines.linewidth': 1.0,
'text.usetex': True,
}
rcParams.update(params)
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import matplotlib
import colorline
import flydra_analysis as fa
import sa1_analysis as sa1
import numpy as np
#20101030_C001H001S0019
def flyby_xy_spagetti(dataset, keys=None, show_all_poi=False, filename='flyby_xy_spagetti.pdf', nkeys=300, alpha2=1, color2='gray', show_saccades=True, keys_to_highlight=None, show_deceleration=False):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(-.15,.15)
ax.set_xlim(-.25, .25)
ax.set_autoscale_on(False)
if keys is None:
classified_keys = fa.get_classified_keys(dataset)
keys = classified_keys['straight']
keys = dataset.trajecs.keys()
keys_with_saccades = []
keys_without_saccades = []
for key in keys:
trajec = dataset.trajecs[key]
if len(trajec.sac_ranges) > 0:
keys_with_saccades.append(key)
else:
keys_without_saccades.append(key)
'''
key_to_highlight = None
k = -1
while key_to_highlight is None:
k += 1
trajec = dataset.trajecs[keys[k]]
if len(trajec.saccades) > 0:
key_to_highlight = keys[k]
'''
if keys_to_highlight is None:
keys_to_highlight = ['10_80113']
print keys_to_highlight
if len(keys) > nkeys:
keys = keys[0:nkeys]
keys.extend(keys_to_highlight)
for key in keys:
trajec = dataset.trajecs[key]
if key in keys_to_highlight:
alpha = 1
linewidth = 1
color = 'black'
zorder = 500
ax.plot(trajec.positions[:,0], trajec.positions[:,1], '-', color='black', alpha=1, linewidth=linewidth, zorder=zorder)
frames = np.arange(0,trajec.frames_of_flyby[-1]).tolist()
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1], '-', color='green', alpha=1, linewidth=linewidth, zorder=zorder)
else:
linewidth = 0.5
zorder = 100
frames = np.arange(0,trajec.frames_of_flyby[-1]).tolist()
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1], '-', color=color2, alpha=alpha2, linewidth=linewidth, zorder=zorder)
if show_saccades:
if len(trajec.sac_ranges) > 0:
for sac_range in trajec.sac_ranges:
if sac_range == trajec.last_saccade_range:
color = 'red'
else:
color = 'blue'
if sac_range[0] < trajec.frame_nearest_to_post:
#if 1:
ax.plot(trajec.positions[sac_range,0], trajec.positions[sac_range,1], '-', color=color, alpha=alpha2, linewidth=linewidth, zorder=zorder+1)
#sac = patches.Circle( (trajec.positions[sac_range[0],0], trajec.positions[sac_range[0],1]), radius=0.001, facecolor='red', edgecolor='none', alpha=alpha2, zorder=zorder+1)
#ax.add_artist(sac)
if show_deceleration:
dec = patches.Circle( (trajec.positions[trajec.frame_at_deceleration,0], trajec.positions[trajec.frame_at_deceleration,1]), radius=0.001, facecolor='purple', edgecolor='none', color='purple', linewidth=2, alpha=alpha2, zorder=zorder+1)
ax.add_artist(dec)
post = patches.Circle( (0, 0), radius=0.009565, facecolor='black', edgecolor='none', alpha=1)
ax.add_artist(post)
#ax.text(0,0,'post\ntop view', horizontalalignment='center', verticalalignment='center')
#post = patches.Circle( (0, 0), radius=0.028, facecolor='none', edgecolor='red', alpha=1, linewidth=0.15, linestyle='dashed')
#ax.add_artist(post)
prep_xy_spagetti_for_saving(ax)
fig.savefig(filename, format='pdf')
def landing_xy_spagetti(dataset, keys=None, show_all_poi=False, alpha2=1, color2='gray', show_saccades=True):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(-.15,.15)
ax.set_xlim(-.25, .25)
ax.set_autoscale_on(False)
if keys is None:
#classified_keys = fa.get_classified_keys(dataset)
keys = dataset.trajecs.keys()
#keys_to_highlight = [keys[33]]
# straight: 2_29065, 2_3954, 5_15269
# curve in: 24_68713
# multiple saccades: 1_27887
# hover loop: 10_78813
#keys_to_highlight = ['5_15269', '24_68713', '10_78813', '1_27887']
#keys_to_highlight = ['5_15269']
#keys = keys_to_highlight
keys_to_highlight = []
print keys_to_highlight
for key in keys:
trajec = dataset.trajecs[key]
if key == '24_68713':
flip = -1
else:
flip = 1
initial_frame = fa.get_frame_at_distance(trajec, 0.25)
frames = np.arange(initial_frame, len(trajec.speed)-1).tolist()
#frames = np.arange(initial_frame, trajec.frame_of_landing).tolist()
if key in keys_to_highlight:
alpha = 1
linewidth = 1
color = 'black'
zorder = 500
ax.plot(flip*trajec.positions[frames,0], flip*trajec.positions[frames,1], '-', color=color, alpha=alpha, linewidth=linewidth, zorder=zorder)
else:
linewidth = 0.5
zorder = 100
ax.plot(flip*trajec.positions[frames,0], flip*trajec.positions[frames,1], '-', color=color2, alpha=alpha2, linewidth=linewidth, zorder=zorder)
if show_saccades:
if len(trajec.sac_ranges) > 0:
for sac_range in trajec.sac_ranges:
if sac_range == trajec.last_saccade_range:
color = 'red'
else:
color = 'blue'
if sac_range[-1] in frames and sac_range[-1] < trajec.frame_of_landing:
ax.plot(flip*trajec.positions[sac_range,0], flip*trajec.positions[sac_range,1], '-', color=color, alpha=alpha2, linewidth=linewidth, zorder=zorder+1)
#sac = patches.Circle( (flip*trajec.positions[sac_range[0],0], flip*trajec.positions[sac_range[0],1]), radius=0.001, facecolor='red', edgecolor='none', alpha=alpha2, zorder=zorder+1)
#ax.add_artist(sac)
'''
trajec_to_highlight = dataset.trajecs[key_to_highlight]
d = trajec_to_highlight.frame_at_deceleration
dec = patches.Circle( (trajec_to_highlight.positions[d,0], trajec_to_highlight.positions[d,1]), radius=0.002, facecolor='blue', edgecolor='none', alpha=1, zorder=100)
ax.add_artist(dec)
if len(trajec_to_highlight.saccades) > 0:
for s in trajec_to_highlight.saccades:
#s = trajec_to_highlight.saccades[-1]
sac = patches.Circle( (trajec_to_highlight.positions[s,0], trajec_to_highlight.positions[s,1]), radius=0.002, facecolor='red', edgecolor='none', alpha=1, zorder=100)
ax.add_artist(sac)
'''
post = patches.Circle( (0, 0), radius=0.009565, facecolor='black', edgecolor='none', alpha=1, zorder=1000)
ax.add_artist(post)
#ax.text(0,0,'post\ntop view', horizontalalignment='center', verticalalignment='center')
prep_xy_spagetti_for_saving(ax)
filename = 'landing_xy_spagetti' + '.pdf'
fig.savefig(filename, format='pdf')
def prep_xy_spagetti_for_saving(ax):
rect = patches.Rectangle( [-.25, -.15], .5, .3, facecolor='none', edgecolor='gray', clip_on=False, linewidth=0.2)
ax.add_artist(rect)
'''
offset = 0.00
dxy = 0.05
#xarrow = patches.FancyArrowPatch(posA=(-.25+offset, -.15+offset), posB=(-.25+offset+dxy, -.15+offset), arrowstyle='simple')
#patches.Arrow( -.25+offset, -.15+offset, dxy, 0, color='black', width=0.002)
xarrow = patches.FancyArrowPatch((-.25+offset, -.15+offset), (-.25+offset+dxy, -.15+offset), arrowstyle="-|>", mutation_scale=10, color='gray', shrinkA=0, clip_on=False)
ax.add_patch(xarrow)
yarrow = patches.FancyArrowPatch((-.25+offset, -.15+offset), (-.25+offset, -.15+offset+dxy), arrowstyle="-|>", mutation_scale=10, color='gray', shrinkA=0, clip_on=False)
ax.add_artist(yarrow)
text_offset = -.011
ax.text(-.25+offset+dxy+text_offset, -.15+offset+.005, 'x', verticalalignment='bottom', horizontalalignment='left', color='gray', weight='bold')
ax.text(-.25+offset+.005, -.15+offset+dxy+text_offset, 'y', verticalalignment='bottom', horizontalalignment='left', color='gray', weight='bold')
'''
scale_bar_offset = 0.01
ax.hlines(-0.15+scale_bar_offset, 0.25-scale_bar_offset-.1, 0.25-scale_bar_offset, linewidth=1, color='gray')
ax.text(0.25-scale_bar_offset-.1/2., -0.15+scale_bar_offset+.002, '10cm', horizontalalignment='center', verticalalignment='bottom', color='gray')
ax.set_aspect('equal')
scaling = .5/.75
margin = 0.04
aspect_ratio = 3/5. # height/width
fig_width = 7.204*scaling
plt_width = fig_width - 2*margin*(1-aspect_ratio)
fig_height = plt_width*aspect_ratio + 2*margin
fig = ax.figure
fig.set_size_inches(fig_width,fig_height)
fig.subplots_adjust(bottom=margin, top=1-margin, right=1, left=0)
ax.set_axis_off()
def prep_radial_spagetti_for_saving(ax):
rect = patches.Rectangle( [0, -.15], .25, .3, facecolor='none', edgecolor='gray', clip_on=False, linewidth=0.2)
ax.add_artist(rect)
'''
offset = 0.00
dxy = 0.05
#xarrow = patches.FancyArrowPatch(posA=(-.25+offset, -.15+offset), posB=(-.25+offset+dxy, -.15+offset), arrowstyle='simple')
#patches.Arrow( -.25+offset, -.15+offset, dxy, 0, color='black', width=0.002)
xarrow = patches.FancyArrowPatch((0+offset, -.15+offset), (0+offset+dxy, -.15+offset), arrowstyle="-|>", mutation_scale=10, color='gray', shrinkA=0, clip_on=False)
ax.add_patch(xarrow)
yarrow = patches.FancyArrowPatch((0+offset, -.15+offset), (0+offset, -.15+offset+dxy), arrowstyle="-|>", mutation_scale=10, color='gray', shrinkA=0, clip_on=False)
ax.add_artist(yarrow)
text_offset = -.011
ax.text(0+offset+dxy+text_offset, -.15+offset+.005, 'r', verticalalignment='bottom', horizontalalignment='left', color='gray', weight='bold')
ax.text(0+offset+.002, -.15+offset+dxy+text_offset+.004, 'z', verticalalignment='bottom', horizontalalignment='left', color='gray', weight='bold')
'''
scale_bar_offset = 0.01
ax.hlines(-0.15+scale_bar_offset, 0.25-scale_bar_offset-.1, 0.25-scale_bar_offset, linewidth=1, color='gray')
ax.text(0.25-scale_bar_offset-.1/2., -0.15+scale_bar_offset+.002, '10cm', horizontalalignment='center', verticalalignment='bottom', color='gray')
ax.set_aspect('equal')
scaling = .25/.75
margin = 0.04
aspect_ratio = 3/2.5 # height/width
fig_width = 7.204*scaling
plt_width = fig_width - 2*margin*(aspect_ratio)
fig_height = plt_width*aspect_ratio + 2*margin
fig = ax.figure
fig.set_size_inches(fig_width,fig_height)
fig.subplots_adjust(bottom=margin, top=1-margin, right=1, left=0)
ax.set_axis_off()
def landing_xy_spagetti_types(dataset):
classified_keys = fa.get_classified_keys(dataset)
for key_class in classified_keys.keys():
landing_xy_spagetti(dataset, keys=None, show_all_poi=False, key_class=key_class)
def flyby_xy_spagetti_types(dataset_flyby):
classified_keys_flyby = fa.get_classified_keys(dataset_flyby)
flyby_xy_spagetti(dataset_flyby, keys=classified_keys_flyby['flyby'][100:300], filename='flyby_xy_spagetti_random.pdf')
flyby_xy_spagetti(dataset_flyby, keys=classified_keys_flyby['straight'], filename='flyby_xy_spagetti_straight.pdf')
def flyby_xy_spagetti_nopost(dataset, keys=None, filename='flyby_xy_spagetti_nopost.pdf', alpha2=1, color2='gray', show_saccades=True):
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(-.15,.15)
ax.set_xlim(-.25, .25)
ax.set_autoscale_on(False)
if keys is None:
keys = dataset.trajecs.keys()
keys_to_highlight = ['32_8003']
print keys_to_highlight
for key in keys:
trajec = dataset.trajecs[key]
frames = np.arange(0,trajec.frames_of_flyby[-1]).tolist()
if key in keys_to_highlight:
alpha = 1
linewidth = 1
color = 'black'
zorder = 500
ax.plot(trajec.positions[:,0], trajec.positions[:,1], '-', color='black', alpha=1, linewidth=linewidth, zorder=zorder)
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1], '-', color='blue', alpha=1, linewidth=linewidth, zorder=zorder)
else:
linewidth = 0.5
color = 'black'
zorder = 100
ax.plot(trajec.positions[frames,0], trajec.positions[frames,1], '-', color=color2, alpha=alpha2, linewidth=linewidth, zorder=zorder)
if show_saccades:
if len(trajec.sac_ranges) > 0:
for sac in trajec.sac_ranges:
if sac == trajec.last_saccade_range:
color = 'red'
else:
color = 'blue'
if sac[-1] in frames:
ax.plot(trajec.positions[sac,0], trajec.positions[sac,1], '-', color=color, alpha=alpha2, linewidth=linewidth, zorder=zorder+1)
#sac = patches.Circle( (trajec.positions[sac_range[0],0], trajec.positions[sac_range[0],1]), radius=0.001, facecolor='red', edgecolor='none', alpha=alpha2, zorder=zorder+1)
#ax.add_artist(sac)
post = patches.Circle( (0, 0), radius=0.009565, facecolor='black', edgecolor='none', alpha=1)
#ax.add_artist(post)
#ax.text(0,0,'post\ntop view', horizontalalignment='center', verticalalignment='center')
prep_xy_spagetti_for_saving(ax)
filename = 'nopost_xy_spagetti' + '.pdf'
fig.savefig(filename, format='pdf')
def radial_trajectory_plot(dataset, filename='radial_trajectory_plot.pdf', keys=None, dataset_type='landing', nkeys=None, highlight_trajecs=False, behavior=['landing', 'flyby'], show_saccades=True, alpha2=1, color2='gray'):
radius = 0.009565
fig = plt.figure()
ax = fig.add_subplot(111)
ax.set_ylim(-.15,.15)
ax.set_xlim(0, .25)
ax.set_autoscale_on(False)
if keys is None:
#keys = dataset.trajecs.keys()
keys = fa.get_keys_for_behavior(dataset, behavior=behavior)
if len(keys) > 300:
keys = keys[0:300]
if highlight_trajecs:
if dataset_type == 'landing':
keys_to_highlight = ['5_15269', '24_68713', '10_78813', '1_27887']
elif dataset_type == 'flyby':
keys_to_highlight = ['10_80113']
else:
keys_to_highlight = ['32_8003']
else:
keys_to_highlight = []
if nkeys is not None:
if nkeys < len(keys):
keys = keys[0:nkeys]
for key in keys_to_highlight:
if key not in keys:
keys.append(key)
print keys_to_highlight
for key in keys:
trajec = dataset.trajecs[key]
r = trajec.dist_to_stim_r + radius
if trajec.behavior == 'landing':
initial_frame = fa.get_frame_at_distance(trajec, 0.25)
frames = np.arange(initial_frame, trajec.frame_of_landing).tolist()
else:
#try:
# #frames = trajec.frames_below_post
# frames = np.arange(0,trajec.frame_of_landing).tolist()
#except:
frames = np.arange(0,trajec.frames_of_flyby[-1]).tolist()
if key in keys_to_highlight:
alpha = 1
linewidth = 1
color = 'black'
zorder = 500
#ax.plot(r[:], trajec.positions[:,2], '-', color='black', alpha=1, linewidth=linewidth, zorder=zorder)
ax.plot(r[:], trajec.positions[:,2], '-', color=color, alpha=alpha, linewidth=linewidth, zorder=zorder)
ax.plot(r[frames], trajec.positions[frames,2], '-', color='blue', alpha=alpha, linewidth=linewidth, zorder=zorder)
print 'plotted key to highlight'
else:
linewidth = 0.5
zorder = 100
ax.plot(r[frames], trajec.positions[frames,2], '-', color=color2, alpha=alpha2, linewidth=linewidth, zorder=zorder)
if show_saccades:
if len(trajec.sac_ranges) > 0:
for sac_range in trajec.sac_ranges:
if sac_range == trajec.last_saccade_range:
ax.plot(r[sac_range], trajec.positions[sac_range,2], '-', color='red', alpha=alpha2, linewidth=linewidth, zorder=zorder+1)
elif len(trajec.last_saccade_range) > 0:
if sac_range[0] in frames:
if sac_range[0] < trajec.last_saccade_range[0]:
ax.plot(r[sac_range], trajec.positions[sac_range,2], '-', color='blue', alpha=alpha2, linewidth=linewidth, zorder=zorder+1)
if dataset_type != 'nopost':
post = patches.Rectangle( (0, -0.15), radius, 0.15, facecolor='black', edgecolor='none', alpha=1)
ax.add_artist(post)
prep_radial_spagetti_for_saving(ax)
filename = 'radial_spagetti' + dataset_type + '.pdf'
fig.savefig(filename, format='pdf')