Software Carpentry workshope: Particle tracking (2D and 3D) using Ariane data¶

Imports¶

In [1]:

import netCDF4 as nc
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from matplotlib import animation
from salishsea_tools import (nc_tools)
%matplotlib inline

Download netCDF4? http://netcdf4-python.googlecode.com/svn/trunk/docs/netCDF4-module.html.

Need plt to plot

Need Axes3D to plot in 3d

Need animation to produce an animation

Download salishsea_tools? Is there an easier way to view variables in dataset?

Here, I'm using matplotlib inline, assuming that they will have downloaded FFMpegWriter.

Data¶

In [2]:

data = nc.Dataset('/ocean/imachuca/MEOPAR/Ariane/results/soft_carpentry/ariane_trajectories_qualitative.nc','r');

Relocate data and adjust directory

In [3]:

nc_tools.show_variables(data)

[u'init_x', u'init_y', u'init_z', u'init_t', u'init_age', u'init_transp', u'final_x', u'final_y', u'final_z', u'final_t', u'final_age', u'final_transp', u'traj_lon', u'traj_lat', u'traj_depth', u'traj_time']

In [4]:

lon=data.variables['traj_lon']
lat=data.variables['traj_lat']
dep=data.variables['traj_depth']
x=data.variables['init_x']
y=data.variables['init_y']

In [5]:

lon.shape

Out[5]:

(10, 1)

It is important to know the shape or length for when you reach the animation part. For example, for our animations, we will have 10 frames.

Plotting (2D)¶

In [16]:

fig, ax = plt.subplots(1,1,figsize=(20,10))
ax.scatter(lon[:,:],lat[:,:],color='blue')

ax.set_title('2D')
ax.set_xlabel('Longitude')
ax.set_ylabel('Latitude')

ax.set_xlim([-124.6,-123.0])        
ax.set_ylim([48.25,48.65])

Out[16]:

(48.25, 48.65)

Plotting (3D)¶

In [26]:

fig = plt.figure(figsize=(20,10))
ax = fig.gca(projection='3d')
ax.scatter(lon[:,:],lat[:,:],dep[:,0],color='blue')

ax.set_title('3D')
ax.set_xlabel('Longitude')
ax.set_ylabel('Latitude')
ax.set_zlabel('Depth')

ax.set_xlim([-124.6,-123.0])        
ax.set_ylim([48.25,48.65])
ax.set_zlim([-100,0])

Out[26]:

(-100, 0)

Plotting (3D): Camera Position¶

In [27]:

fig = plt.figure(figsize=(20,10))
ax = fig.gca(projection='3d')
ax.scatter(lon[:,:],lat[:,:],dep[:,:],color='blue')

ax.set_title('3D')
ax.set_xlabel('Longitude')
ax.set_ylabel('Latitude')
ax.set_zlabel('Depth')

ax.set_xlim([-124.6,-123.0])        
ax.set_ylim([48.25,48.65])
ax.set_zlim([-100,0])

ax.view_init(elev=0, azim=-90)

Animation 2D¶

In [28]:

#Empty map
fig, ax = plt.subplots(1,1,figsize=(20,10))

ax.set_title('2D')
ax.set_xlabel('Longitude')
ax.set_ylabel('Latitude')

ax.set_xlim([-124.6,-123.0])        
ax.set_ylim([48.25,48.65])

#Initial image
def init():
    return [fig, ax]

#Animated points
def animate(p):
    ax.scatter(lon[p,:],lat[p,:],color='blue')

#The animation function    
anim = animation.FuncAnimation(fig, animate, init_func=init, frames=10)

#A line that makes it all work
mywriter = animation.FFMpegWriter()

#Save in current folder
anim.save('Software-Carpentry2D.mp4',writer=mywriter)

#Show as a pop-up window
#plt.show()

Animation 3D¶

In [29]:

#Empty map
fig = plt.figure(figsize=(20,10))
ax = fig.gca(projection='3d')

ax.set_title('3D')
ax.set_xlabel('Longitude')
ax.set_ylabel('Latitude')
ax.set_zlabel('Depth')

ax.set_xlim([-124.6,-123.0])        
ax.set_ylim([48.25,48.65])
ax.set_zlim([-100,0])

ax.view_init(elev=0, azim=-90)

#Initial image
def init():
    return [fig, ax]

#Animated points
def animate(p):
    ax.scatter(lon[p,:],lat[p,:],dep[p,:],color='blue')

#The animation function    
anim = animation.FuncAnimation(fig, animate, init_func=init, frames=10)

#A line that makes it all work
mywriter = animation.FFMpegWriter()

#Save in current folder
anim.save('Software-Carpentry3D.mp4',writer=mywriter)

#Show as a pop-up window
#plt.show()

In [ ]: