import netCDF4 as nc
import datetime as dt
import subprocess
import matplotlib.pyplot as plt
import cmocean
import numpy as np
from salishsea_tools import viz_tools
plt.style.use('/ocean/vdo/MEOPAR/biomodelevalpaper/bioModelEvalPaper.mplstyle')
from IPython.core.display import display, HTML
display(HTML("<style>.container { width:90% !important; }</style>"))
%matplotlib inline
from IPython.display import HTML
HTML('''<script>
code_show=true;
function code_toggle() {
if (code_show){
$('div.input').hide();
} else {
$('div.input').show();
}
code_show = !code_show
}
$( document ).ready(code_toggle);
</script>
<form action="javascript:code_toggle()"><input type="submit" value="Click here to toggle on/off the raw code."></form>''')
t0=dt.datetime(2014,9,12)
fformat1='%d%b%y/'
fformat2='SalishSea_1d_%Y%m%d_%Y%m%d_ptrc_T.nc'
flist=list()
for idt0 in [t0+dt.timedelta(days=ii*1) for ii in range(0,1230)]:
fformat1='%d%b%y/'
fformat2='SalishSea_1d_%Y%m%d_%Y%m%d_ptrc_T.nc'
iff=idt0.strftime(fformat1).lower()+idt0.strftime(fformat2)
flist.append(iff)
%time subprocess.call('ncrcat -v silicon -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/silicon.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
CPU times: user 32 ms, sys: 0 ns, total: 32 ms Wall time: 13min 27s
0
t0=dt.datetime(2014,9,12)
fformat1='%d%b%y/'
fformat2='SalishSea_1d_%Y%m%d_%Y%m%d_ptrc_T.nc'
flist=list()
for idt0 in [t0+dt.timedelta(days=ii*1) for ii in range(0,1230)]:
fformat1='%d%b%y/'
fformat2='SalishSea_1d_%Y%m%d_%Y%m%d_ptrc_T.nc'
iff=idt0.strftime(fformat1).lower()+idt0.strftime(fformat2)
flist.append(iff)
%time subprocess.call('ncrcat -v biodenic_silicon -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/biogemic_silicon.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
%time subprocess.call('ncrcat -v ammonium -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/ammonium.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
%time subprocess.call('ncrcat -v nitrate -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/nitrate.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
%time subprocess.call('ncrcat -v particulate_organic_nitrogen -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/pon.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
%time subprocess.call('ncrcat -v dissolved_organic_nitrogen -d y,673,673 -d x,156,156 '+' '.join(flist)+' /data/vdo/MEOPAR/don.nc',shell=True,cwd="/results/SalishSea/nowcast-green")
CPU times: user 4 ms, sys: 0 ns, total: 4 ms Wall time: 23.2 ms CPU times: user 32 ms, sys: 4 ms, total: 36 ms Wall time: 14min 24s CPU times: user 24 ms, sys: 8 ms, total: 32 ms Wall time: 14min CPU times: user 24 ms, sys: 8 ms, total: 32 ms Wall time: 14min 42s CPU times: user 20 ms, sys: 20 ms, total: 40 ms Wall time: 14min 42s
0
bathy = nc.Dataset('/data/vdo/MEOPAR/NEMO-forcing/grid/bathymetry_201702.nc')
mesh = nc.Dataset('/data/vdo/MEOPAR/NEMO-forcing/grid/mesh_mask201702.nc')
fig, ax = plt.subplots(figsize = (12,8))
b = ax.pcolormesh(bathy.variables['Bathymetry'][:], cmap = cmocean.cm.deep)
c = fig.colorbar(b, ax=ax)
c.set_label('depth (m)')
viz_tools.set_aspect(ax)
ax.plot(156, 673, 'r*', label = 'Northern Strait')
ax.plot(257, 450, 'y*', label = 'Central Strait')
ax.plot(73, 329, '*', color = 'black', label = 'Juan de Fuca')
ax.legend()
ax.set_ylim(300, 800)
ax.set_title('Stations');
f = nc.Dataset('/data/vdo/MEOPAR/silicon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(f.variables['time_counter'][:], f.variables['time_counter'].units),
f.variables['deptht'][:36], f.variables['silicon'][:,:36,0,0].T,
vmin = 30, vmax = 80, cmap = cmocean.cm.dense)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Silicon')
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
f = nc.Dataset('/data/vdo/MEOPAR/central_silicon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(f.variables['time_counter'][:], f.variables['time_counter'].units),
f.variables['deptht'][:36],
np.ma.masked_array(f.variables['silicon'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 30, vmax = 80, cmap = cmocean.cm.dense)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Silicon')
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
f = nc.Dataset('/data/vdo/MEOPAR/jdf_silicon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(f.variables['time_counter'][:], f.variables['time_counter'].units),
f.variables['deptht'][:36],
np.ma.masked_array(f.variables['silicon'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 30, vmax = 80, cmap = cmocean.cm.dense)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Silicon')
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/biogenic_silicon2.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
h.variables['biogenic_silicon'][:,:36,0,0].T,
vmin = 0, vmax = 10, cmap = cmocean.cm.speed)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Biogenic Silicon');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_biogenic_silicon2.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['biogenic_silicon'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 10, cmap = cmocean.cm.speed)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Biogenic Silicon');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_biogenic_silicon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['biogenic_silicon'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 10, cmap = cmocean.cm.speed)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Biogenic Silicon');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
g = nc.Dataset('/data/vdo/MEOPAR/ammonium.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(g.variables['time_counter'][:], g.variables['time_counter'].units),
g.variables['deptht'][:36], g.variables['ammonium'][:,:36,0,0].T,
vmin = 0, vmax = 4, cmap = cmocean.cm.turbid)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Ammonium');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
g = nc.Dataset('/data/vdo/MEOPAR/dentral_ammonium.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(g.variables['time_counter'][:], g.variables['time_counter'].units),
g.variables['deptht'][:36],
np.ma.masked_array(g.variables['ammonium'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 4, cmap = cmocean.cm.turbid)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Ammonium');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
g = nc.Dataset('/data/vdo/MEOPAR/jdf_ammonium.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(g.variables['time_counter'][:], g.variables['time_counter'].units),
g.variables['deptht'][:36],
np.ma.masked_array(g.variables['ammonium'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 4, cmap = cmocean.cm.turbid)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Ammonium');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/nitrate.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['nitrate'][:,:36,0,0].T,
vmin = 20, vmax = 40, cmap = cmocean.cm.matter)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Nitrate');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_nitrate.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['nitrate'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 20, vmax = 40, cmap = cmocean.cm.matter)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Nitrate');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_nitrate.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['nitrate'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 20, vmax = 40, cmap = cmocean.cm.matter)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Nitrate');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/pon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['particulate_organic_nitrogen'][:,:36,0,0].T,
vmin = 0, vmax = 2, cmap = cmocean.cm.tempo)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, PON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_pon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['particulate_organic_nitrogen'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 2, cmap = cmocean.cm.tempo)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, PON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_pon.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['particulate_organic_nitrogen'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 2, cmap = cmocean.cm.tempo)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, PON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/don.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['dissolved_organic_nitrogen'][:,:36,0,0].T,
vmin = 0, vmax = 7, cmap = cmocean.cm.amp)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, DON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_don.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['dissolved_organic_nitrogen'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 7, cmap = cmocean.cm.amp)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, DON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_don.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['dissolved_organic_nitrogen'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 7, cmap = cmocean.cm.amp)
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, DON');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/northern_meso.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['mesozooplankton'][:,:36,0,0].T,
vmin = 0, vmax = 3, cmap = 'Greens')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Mesozooplankton');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_meso.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['mesozooplankton'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 3, cmap = 'Greens')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Mesozooplankton');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_meso.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['mesozooplankton'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 3, cmap = 'Greens')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Mesozooplankton');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/northern_ciliates.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['ciliates'][:,:36,0,0].T,
vmin = 0, vmax = 2, cmap = 'Blues')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Ciliates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_ciliates.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['ciliates'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 2, cmap = 'Blues')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Ciliates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_ciliates.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['ciliates'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 2, cmap = 'Blues')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Ciliates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/northern_diatoms.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['diatoms'][:,:36,0,0].T,
vmin = 0, vmax = 10, cmap = 'Oranges')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Diatoms');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_diatoms.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['diatoms'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 10, cmap = 'Oranges')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Diatoms');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_diatoms.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['diatoms'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 10, cmap = 'Oranges')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Diatoms');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/northern_flag.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36], h.variables['flagellates'][:,:36,0,0].T,
vmin = 0, vmax = 5, cmap = 'Purples')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Northern Strait, Flagellates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/central_flag.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['flagellates'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,450,257][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 5, cmap = 'Purples')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Central Strait, Flagellates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');
h = nc.Dataset('/data/vdo/MEOPAR/jdf_flag.nc')
fig, ax = plt.subplots(figsize = (25,5))
s = ax.pcolormesh(nc.num2date(h.variables['time_counter'][:], h.variables['time_counter'].units),
h.variables['deptht'][:36],
np.ma.masked_array(h.variables['flagellates'][:,:36,0,0].T,
mask = (1-mesh.variables['tmask'][0,:36,329,73][:,np.newaxis])
*np.ones((36, 1230))),
vmin = 0, vmax = 10, cmap = 'Purples')
c = fig.colorbar(s, ax=ax)
c.set_label('mmol m-3')
ax.set_title('Juan de Fuca, Flagellates');
ax.invert_yaxis()
ax.set_ylabel('Depth (m)')
ax.set_xlabel('Date');