def __init__(self):
self.fig = plt.figure(facecolor = 'w', figsize = [12, 6])
self.fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
ax1 = self.fig.add_subplot(2, 1, 1, projection='3d')
ax2 = self.fig.add_subplot(2, 1, 2, projection='3d')
self.track_data = track_data
self.t = np.arange(0,len(track_data['no_ll'][0]['track']))
self.flow = flow[self.t]
self.flow_flash = 0
self.info1 = ax2.text2D(0.90,0.95,'State key',fontsize = 18,transform=ax2.transAxes)
self.info2 = ax2.text2D(0.90,0.90,'------------',fontsize = 18, transform=ax2.transAxes)
self.info2 = ax2.text2D(0.90,0.75,'Blue: rest',fontsize = 18, transform=ax2.transAxes, color = 'blue')
self.info3 = ax2.text2D(0.90,0.60,'Black: swim ', fontsize = 18, transform=ax2.transAxes, color = 'black')
self.info4 = ax2.text2D(0.90,0.45,'Red: lat. line', fontsize = 18, transform=ax2.transAxes, color = 'red')
self.flowtexta1 = ax1.text2D(0.001, 0.65, 'Flow 0 cm/s', fontsize=18, transform=ax1.transAxes)
self.flowtexta2 = ax2.text2D(0.001, 0.65, 'Flow 0 cm/s', fontsize=18, transform=ax2.transAxes)
self.meantext1 = ax1.text2D(0.4, 0, 'X mean = 37.5 +/- 0', fontsize=18, color = 'green', transform=ax1.transAxes)
self.meantext2 = ax2.text2D(0.4, 0, 'X mean = 37.5 +/- 0', fontsize=18, color = 'green', transform=ax2.transAxes)
self.ax1mean = Line3D([37.5, 37.5], [0, 15], [0, 0], color = 'green', linewidth = 2)
ax1.add_line(self.ax1mean)
self.ax2mean = Line3D([37.5, 37.5], [0, 15], [0, 0], color = 'green', linewidth = 2)
ax2.add_line(self.ax2mean)
plot_functions.plot_tank(ax1)
plot_functions.plot_tank(ax2)
self.ax1_lines = []
for animal in self.track_data['no_ll']:
line_dict = {}
line_dict['head'] = Line3D([], [], [], color='blue', marker='o', markeredgecolor='black')
line_dict['tail'] = Line3D([], [], [], color='blue', linewidth=2)
ax1.add_line(line_dict['head'])
ax1.add_line(line_dict['tail'])
self.ax1_lines.append(line_dict)
self.ax2_lines = []
for animal in self.track_data['ll']:
line_dict = {}
line_dict['head'] = Line3D([], [], [], color='blue', marker='o', markeredgecolor='black')
line_dict['tail'] = Line3D([], [], [], color='blue', linewidth=2)
ax2.add_line(line_dict['head'])
ax2.add_line(line_dict['tail'])
self.ax2_lines.append(line_dict)
ax1.set_xlim(0, 68)
ax1.set_ylim(0, 15)
ax1.set_zlim(0, 15)
ax1.set_title('Passive Model')
ax1.set_aspect('equal')
ax2.set_xlim(0, 68)
ax2.set_ylim(0, 15)
ax2.set_zlim(0, 15)
ax2.set_title('Active Lateral Line')
ax2.set_aspect('equal')
ax1.set_xticks([0, 68])
ax1.set_yticks([])
ax1.set_zticks([0, 15])
ax2.set_xticks([0, 68])
ax2.set_yticks([])
ax2.set_zticks([0, 15])
plt.rc('xtick', labelsize=20)
animation.TimedAnimation.__init__(self, self.fig, interval=10, blit=False)
def __init__(self):
fig = plt.figure(facecolor="w", figsize=[12, 6])
# fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
ax1 = plt.subplot2grid((3, 3), (0, 0), colspan=3, projection="3d")
ax2 = plt.subplot2grid((3, 3), (1, 0), colspan=2)
ax3 = plt.subplot2grid((3, 3), (2, 0), colspan=2)
ax4 = plt.subplot2grid((3, 3), (1, 2), rowspan=2)
self.t = np.arange(0, len(frog1["track"]))
self.x = frog1["track"][self.t, 0]
self.y = frog1["track"][self.t, 1]
self.z = frog1["track"][self.t, 2]
self.state = frog1["state"][self.t]
self.x2 = frog1["time"][self.t]
self.y2 = frog1["flow_rate"][self.t]
self.y3 = frog1["lateral_line"][self.t]
ax2.text(0.01, 0.8, str(current) + " cm/s", fontsize=16, transform=ax2.transAxes)
ax2.text(0.01, 0.08, "0 cm/s", fontsize=16, transform=ax2.transAxes)
ax3.text(0.01, 0.8, "threshold", fontsize=16, transform=ax3.transAxes)
ax3.text(0.01, 0.08, "baseline", fontsize=16, transform=ax3.transAxes)
ax1.text2D(0.90, 0.95, "State key", fontsize=16, transform=ax1.transAxes)
ax1.text2D(0.90, 0.90, "------------", fontsize=16, transform=ax1.transAxes)
ax1.text2D(0.90, 0.75, "Blue: rest", fontsize=16, transform=ax1.transAxes)
ax1.text2D(0.90, 0.60, "Black: swim ", fontsize=16, transform=ax1.transAxes)
ax1.text2D(0.90, 0.45, "Red: lat. line.", fontsize=16, transform=ax1.transAxes)
plot_functions.plot_tank(ax1)
plot_functions.plot_flow(current, ax2)
plot_functions.plot_leak(ax3)
plot_functions.plot_flow_field("none", ax4)
self.line1 = Line3D([], [], [], color="black")
self.line1a = Line3D([], [], [], color="red", linewidth=2)
self.line1e = Line3D([], [], [], color="red", marker="o", markeredgecolor="k", markersize=8)
self.line2 = Line2D([], [], color="black")
self.line2e = Line2D([], [], color="red", marker="o", markeredgecolor="k", markersize=8)
self.line3 = Line2D([], [], color="red", linewidth=2)
self.line3e = Line2D([], [], color="red", marker="o", markeredgecolor="k", markersize=8)
self.line4 = Line2D([], [], color="red", marker="o", markeredgewidth=2, markeredgecolor="w", markersize=11)
ax1.add_line(self.line1)
ax1.add_line(self.line1a)
ax1.add_line(self.line1e)
ax2.add_line(self.line2)
ax2.add_line(self.line2e)
ax3.add_line(self.line3)
ax3.add_line(self.line3e)
ax4.add_line(self.line4)
ax1.set_xlim(0, 68)
ax1.set_ylim(0, 15)
ax1.set_zlim(0, 15)
ax1.set_title(FROG1NAME)
ax1.set_aspect("equal")
ax2.set_xlim(0, len(frog1["time"]) * binsize * DOWNSAMPLE_RATE)
ax2.set_ylim(-0.25, 1.05 * current)
ax2.axis("off")
ax3.set_xlim(0, len(frog1["time"]) * binsize * DOWNSAMPLE_RATE)
ax3.set_ylim(-0.05, 1.05)
ax3.axis("off")
ax4.set_title("current field")
ax4.set_aspect("equal")
ax1.set_xticks([0, 68])
ax1.set_yticks([])
ax1.set_zticks([0, 15])
ax2.set_xticks([])
ax2.set_yticks([])
ax3.set_xticks([])
ax3.set_yticks([])
ax4.set_xticks([])
ax4.set_yticks([])
plt.rc("xtick", labelsize=16)
# plt.rc('title', labelsize=18)
plt.tight_layout()
self.axis4 = ax4
animation.TimedAnimation.__init__(self, fig, interval=10, blit=False)
def __init__(self):
fig = plt.figure(facecolor = 'w', figsize = [12, 6])
fig.subplots_adjust(left=0.05, right=0.95, top=0.95, bottom=0.05)
ax1 = fig.add_subplot(2, 1, 1,projection='3d')
ax2 = fig.add_subplot(2, 1, 2,projection='3d')
self.t = np.arange(0,len(frog1['track']))
self.x = frog1['track'][self.t,0]
self.y = frog1['track'][self.t,1]
self.z = frog1['track'][self.t,2]
self.x2 = frog2['track'][self.t,0]
self.y2 = frog2['track'][self.t,1]
self.z2 = frog2['track'][self.t,2]
self.flow = flow[self.t]
self.state1 = frog1['state']
self.state2 = frog2['state']
self.flowtexta1 = ax1.text2D(0.001, 0.65, 'Flow 0 cm/s', fontsize=18, transform=ax1.transAxes)
self.flowtexta2 = ax2.text2D(0.001, 0.65, 'Flow 0 cm/s', fontsize=18, transform=ax2.transAxes)
if REAL_DATA == 0:
self.statetexta1 = ax1.text2D(0.001, 0.50, 'State 0', fontsize=18, transform=ax1.transAxes)
self.statetexta2 = ax2.text2D(0.001, 0.50, 'State 0', fontsize=18, transform=ax2.transAxes)
self.framerate = ax1.text2D(0.90, 0.85, str(DOWNSAMPLE_RATE) + 'x speed', fontsize = 18, transform=ax1.transAxes)
self.info1 = ax2.text2D(0.90,0.95,'State key',fontsize = 18,transform=ax2.transAxes)
self.info2 = ax2.text2D(0.90,0.90,'------------',fontsize = 18, transform=ax2.transAxes)
self.info2 = ax2.text2D(0.90,0.75,'Blue: rest',fontsize = 18, transform=ax2.transAxes, color = 'blue')
self.info3 = ax2.text2D(0.90,0.60,'Black: swim ', fontsize = 18, transform=ax2.transAxes, color = 'black')
self.info4 = ax2.text2D(0.90,0.45,'Red: L.L. orientation.', fontsize = 18, transform=ax2.transAxes, color = 'red')
plot_functions.plot_tank(ax1)
plot_functions.plot_tank(ax2)
#ax1.set_xlabel('x')
#ax1.set_ylabel('y')
#ax1.set_zlabel('z')
#ax2.set_xlabel('x')
#ax2.set_ylabel('y')
#ax2.set_zlabel('z')
self.line1 = Line3D([], [], [], color='black')
self.line1a = Line3D([], [], [], color='green', linewidth=2)
self.line1e = Line3D([], [], [], color='green', marker='o')
self.line2 = Line3D([], [], [], color='black')
self.line2a = Line3D([], [], [], color='red', linewidth=2)
self.line2e = Line3D([], [], [], color='red', marker='o')
ax1.add_line(self.line1)
ax1.add_line(self.line1a)
ax1.add_line(self.line1e)
ax2.add_line(self.line2)
ax2.add_line(self.line2a)
ax2.add_line(self.line2e)
ax1.set_xlim(0, 68)
ax1.set_ylim(0, 15)
ax1.set_zlim(0, 15)
ax1.set_title(FROG1NAME)
ax1.set_aspect('equal')
ax2.set_xlim(0, 68)
ax2.set_ylim(0, 15)
ax2.set_zlim(0, 15)
ax2.set_title('Lateral Line Model')
ax2.set_aspect('equal')
ax1.set_xticks([0, 68])
ax1.set_yticks([])
ax1.set_zticks([0, 15])
ax2.set_xticks([0, 68])
ax2.set_yticks([])
ax2.set_zticks([0, 15])
plt.rc('xtick', labelsize=20)
animation.TimedAnimation.__init__(self, fig, interval=10, blit=False)
orientation[bincount] = orient_angle(np.cos(theta)*np.sin(phi),np.sin(theta)*np.sin(phi)) # record orientation angle
# pack output data
data = {'time': time,
'track': position,
'velocity': velocity,
'orientation': orientation,
'lateral_line': Vll,
'flow_rate': flow_rate,
'state': state_record}
return data
# script to execute example
if __name__ == "__main__":
latline = True
flow = 'JEB'
data = randwalk(300, 0.1, 0, np.array([0.37, 0.075, 0.15]), latline = latline, flow_version = flow)
data = randwalk(300, 0.1, 2, data, latline = latline, flow_version = flow)
import plot_functions
axes = plot_functions.plot_tank()
plot_functions.plot_track3d(data, axes = axes)
plot_functions.plot_xdata(data)
plot_functions.plot_kineticdata(data)
plot_functions.plt.show()
