Create renewal movie with tides at Point Atkinson
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from matplotlib import pylab
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import netCDF4 as nc
import numpy as np
from salishsea_tools import tidetools, stormtools
from salishsea_tools import (nc_tools,viz_tools)
from nowcast import figures, analyze
import os
import glob
from matplotlib import animation
import datetime
import types
%matplotlib inline
In [5]:
start = datetime.datetime(2015,12,1)
end = datetime.datetime(2016,1,28)
numdays = (end-start).days
dates = [start + datetime.timedelta(days=num)
for num in range(0, numdays+1)]
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results_home = '/results/SalishSea/nowcast/'
bathy = nc.Dataset('/data/nsoontie/MEOPAR/NEMO-forcing/grid/bathy_meter_SalishSea2.nc')
thalweg = np.loadtxt('/data/nsoontie/MEOPAR/tools/bathymetry/thalweg_working.txt', dtype=int, unpack=True)
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files = analyze.get_filenames(start,end,'1d','grid_T',results_home)
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def combine_files(files, var, jss, iss):
time = np.array([])
var_list = []
for f in files:
G = nc.Dataset(f)
var_tmp = G.variables[var][:]
var_tmp=var_tmp[:,:,jss,iss]
var_list.append(var_tmp)
t = nc_tools.timestamp(G, np.arange(var_tmp.shape[0]))
try:
for ind in range(len(t)):
t[ind] = t[ind].datetime
except TypeError:
t = t.datetime
time = np.append(time, t)
var_ary = np.concatenate(var_list, axis=0)
return var_ary, time
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#load
f = nc.Dataset(files[0])
temp = combine_files(files,'votemper',thalweg[0],thalweg[1])
#f.variables['vosaline'][:,:,thalweg[0],thalweg[1]]
zlevels = f.variables['deptht']
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time = temp[1]
temp=temp[0]
framess = temp.shape[0]
framess
x, z = np.meshgrid(np.arange(thalweg.shape[1]), zlevels)
print(framess)
59
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#Making an initial image i.e. our first ssh reading
def init():
return axl
#The full range of images that will make up the animation
def thalweg_tides(t):
axl.clear()
temp_tzyx = np.ma.masked_values(temp[t, :,:], 0)
cs = [6.9, 7, 7.5, 8, 8.5, 9, 9.8, 9.9, 10.3, 10.5, 11, 11.5, 12, 13, 14,
15, 16, 17, 18, 19]
mesh=axl.contourf(x,-z,temp_tzyx,cs,cmap=cmap,extend='both')
timestamp = time[t]
axl.set_title(timestamp.strftime('%d-%b-%y %H:%M'))
axl.set_xlabel('X Index')
axl.set_ylabel('Depth [m]')
axl.text(50,-400,'Strait of \n Juan de Fuca')
axl.text(670,-430,'Strait of \n Georgia')
#axl.add_patch(patches.Rectangle(
# (450, 0), # (x,y)
# 255, # width
# -350, # height
#fill=False,edgecolor='r',linewidth=2)
#)
return mesh
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#Setting up a blank figure
fig, axl = plt.subplots(1, 1, figsize=(20, 8))
land_colour = 'burlywood'
axl.set_axis_bgcolor(land_colour)
font = {'size' :16}
plt.rc('font', **font)
cmap = plt.get_cmap('jet')
cmap.set_bad(land_colour)
mesh = thalweg_tides(0)
cbar = plt.colorbar(mesh, ax=axl)
cbar.set_ticks([6.9, 7, 7.5, 8, 8.5, 9, 9.8, 9.9, 10.3, 10.5, 11, 11.5, 12, 13, 14,
15, 16, 17, 18, 19])
cbar.set_label('Temperature [deg C]')
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#The animation function
anim = animation.FuncAnimation(fig, thalweg_tides,frames=framess, blit=True, repeat=True)
#A line that makes it all work
mywriter = animation.FFMpegWriter(fps=5)
#Save in current folder
anim.save('ThalwegTemp_Animation.mp4',writer=mywriter,bitrate=-1,dpi=200)
#Show as a pop-up window
#plt.show()
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grid = nc.Dataset('/data/nsoontie/MEOPAR/NEMO-forcing/grid/bathy_meter_SalishSea2.nc')
lats = grid.variables['nav_lat']
lons = grid.variables['nav_lon']
bathy = grid.variables['Bathymetry']
fig, ax = plt.subplots(1, 1, figsize=(10, 8))
viz_tools.set_aspect(ax, coords='map', lats=lats)
cmap = plt.get_cmap('Blues')
cmap.set_bad('SeaGreen')
mesh = ax.pcolormesh(lons[:], lats[:], bathy[:], cmap=cmap)
ax.plot(lons[thalweg[0,:],thalweg[1,:]],lats[thalweg[0,:],thalweg[1,:]],marker='.',color='k')
#iss=450; iee=706
#ax.plot(lons[thalweg[0,iss:iee],thalweg[1,iss:iee]],lats[thalweg[0,iss:iee],thalweg[1,iss:iee]],
# marker='.',color='r')
iss=0; iee=300
ax.plot(lons[thalweg[0,iss:iee],thalweg[1,iss:iee]],lats[thalweg[0,iss:iee],thalweg[1,iss:iee]],
marker='.',color='y')
iss=300; iee=600
ax.plot(lons[thalweg[0,iss:iee],thalweg[1,iss:iee]],lats[thalweg[0,iss:iee],thalweg[1,iss:iee]],
marker='.',color='b')
ax.set_xlim([-126,-122])
ax.set_ylim([47,51])
ax.tick_params(\
axis='x', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
bottom='off', # ticks along the bottom edge are off
top='off', # ticks along the top edge are off
labelbottom='off') # labels along the bottom edge are off
ax.tick_params(\
axis='y', # changes apply to the x-axis
which='both', # both major and minor ticks are affected
left='off', # ticks along the bottom edge are off
right='off', # ticks along the top edge are off
labelleft='off') # labels along the bottom edge are off
/home/nsoontie/anaconda/lib/python2.7/site-packages/matplotlib/axes/_base.py:1057: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal
if aspect == 'normal':
/home/nsoontie/anaconda/lib/python2.7/site-packages/matplotlib/axes/_base.py:1062: UnicodeWarning: Unicode equal comparison failed to convert both arguments to Unicode - interpreting them as being unequal
elif aspect in ('equal', 'auto'):
--------------------------------------------------------------------------- IndexError Traceback (most recent call last) <ipython-input-14-6ac1bd561755> in <module>() 10 cmap.set_bad('SeaGreen') 11 mesh = ax.pcolormesh(lons[:], lats[:], bathy[:], cmap=cmap) ---> 12 ax.plot(lons[thalweg[0,:],thalweg[1,:]],lats[thalweg[0,:],thalweg[1,:]],marker='.',color='k') 13 #iss=450; iee=706 14 #ax.plot(lons[thalweg[0,iss:iee],thalweg[1,iss:iee]],lats[thalweg[0,iss:iee],thalweg[1,iss:iee]], netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable.__getitem__ (netCDF4/_netCDF4.c:30844)() /home/nsoontie/anaconda/lib/python2.7/site-packages/netCDF4/utils.pyc in _StartCountStride(elem, shape, dimensions, grp, datashape, put) 220 # duplicate indices in the sequence) 221 msg = "integer sequences in slices must be sorted and cannot have duplicates" --> 222 raise IndexError(msg) 223 # convert to boolean array. 224 # if unlim, let boolean array be longer than current dimension IndexError: integer sequences in slices must be sorted and cannot have duplicates
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fig.savefig('diff_thalweg.png',dpi=300)
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