import numpy as np
import netCDF4 as nc
import f90nml
import os
import matplotlib.pyplot as plt
from salishsea_tools import bio_tools as bio
import visualisations
from matplotlib.colors import LinearSegmentedColormap
%matplotlib inline
bathy = nc.Dataset('/data/vdo/MEOPAR/NEMO-forcing/grid/bathymetry_201702.nc')
mesh = nc.Dataset('/data/vdo/MEOPAR/NEMO-forcing/grid/mesh_mask201702.nc')
vmax = 5.0
cmap = LinearSegmentedColormap.from_list('mycmap', [(0 / vmax, 'green'),
(1 / vmax, 'white'),
(1.99 / vmax, 'white'),
(2 / vmax, 'orange'),
(3 / vmax, 'white'),
(3.99 / vmax, 'white'),
(4 / vmax, 'purple'),
(5 / vmax, 'white')]
)
fig, ax = plt.subplots()
mesh1 = ax.pcolormesh(np.random.randint(0,6, size=(20,20)), cmap = cmap)
ticks = [0,1,2,3,4,5]
cbar1 = fig.colorbar(mesh1, ax=ax)
cbar1.set_ticks([0,1,2,3,4,5])
cbar1.set_ticklabels(['0.0 I', '1.0 I', '0.0 N', '1.0 N', '0.0 Si', '1.0 Si'])
ax.set_title('$Example$', fontsize =15)
cbar1.ax.tick_params(labelsize = 12)
def limit_along_thalweg(path, diafile, ptrcfile, phytoplankton):
resDir=path
nampisprod=bio.load_nml_bio(resDir,'nampisprod',
namRefDir='/data/vdo/MEOPAR/NEMO-3.6-code/NEMOGCM/CONFIG/SMELT/EXP00/')
fdia=nc.Dataset(os.path.join(resDir,diafile))
fptc=nc.Dataset(os.path.join(resDir,ptrcfile))
with nc.Dataset('/ocean/eolson/MEOPAR/NEMO-forcing/grid/mesh_mask201702.nc') as m:
tmask=m.variables['tmask'][:,:,:,:]
I=fdia.variables['PAR'][9,:,:,:]
NO= (fptc.variables['nitrate'][19,:,:,:] + fptc.variables['nitrate'][18,:,:,:]) * 0.5
NH= (fptc.variables['ammonium'][19,:,:,:] + fptc.variables['ammonium'][18,:,:,:]) * 0.5
Si= (fptc.variables['silicon'][19,:,:,:] + fptc.variables['silicon'][18,:,:,:]) * 0.5
D,M,N = bio.calc_p_limiters(I,NO,NH,Si,tmask[0,:,:,:],nampisprod)
fig, ax = plt.subplots(2,1,figsize = (14,6))
if phytoplankton == 'dia':
cbar1 = visualisations.contour_thalweg(ax[0], D['limiter'], bathy, mesh,
np.arange(-2, 4.5, 2), cmap = cmap)
cbar2 = visualisations.contour_thalweg(ax[1], D['limval'], bathy, mesh,
np.arange(0,5.1,0.25), cmap = cmap)
ax[0].set_title('Limiting Variable for Diatoms', fontsize = 15)
ax[1].set_title('Rate Limitation Factor for Diatoms', fontsize = 15)
elif phytoplankton == 'meso':
cbar1 = visualisations.contour_thalweg(ax[0], M['limiter'], bathy, mesh,
np.arange(-2,4.5,2), cmap = cmap)
cbar2 = visualisations.contour_thalweg(ax[1], M['limval'], bathy, mesh,
np.arange(0,5.1,0.25), cmap = cmap)
ax[0].set_title('Limiting Variable for $Mesodinium$', fontsize = 15)
ax[1].set_title('Rate Limitation Factor for $Mesodinium$', fontsize = 15)
elif phytoplankton == 'flag':
cbar1 = visualisations.contour_thalweg(ax[0], N['limiter'], bathy, mesh,
np.arange(-2,4.5,2), cmap = cmap)
cbar2 = visualisations.contour_thalweg(ax[1], N['limval'], bathy, mesh,
np.arange(0,5.1,0.25), cmap = cmap)
ax[0].set_title('Limiting Variable for Flagellates', fontsize = 15)
ax[1].set_title('Rate Limitation Factor for Flagellates', fontsize = 15)
cbar1.set_ticks([-1,1,3])
cbar1.set_ticklabels(['I', 'N', 'Si'])
cbar1.ax.tick_params(labelsize=12)
cbar2.set_ticks([0,1,2,3,4,5])
cbar2.set_ticklabels(['0.0 I','1.0 I','0.0 N','1.0 N','0.0 Si','1.0 Si'])
cbar2.ax.tick_params(labelsize=12)
for ax in ax:
ax.set_ylim(35,0)
plt.tight_layout()
limit_along_thalweg('/results/SalishSea/nowcast-green/02jan16',
'SalishSea_2h_20160102_20160111_dia1_T.nc',
'SalishSea_1h_20160102_20160102_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/02jan16',
'SalishSea_2h_20160102_20160111_dia1_T.nc',
'SalishSea_1h_20160102_20160102_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/02jan16',
'SalishSea_2h_20160102_20160111_dia1_T.nc',
'SalishSea_1h_20160102_20160102_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01feb16',
'SalishSea_2h_20160201_20160210_dia1_T.nc',
'SalishSea_1h_20160201_20160201_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01feb16',
'SalishSea_2h_20160201_20160210_dia1_T.nc',
'SalishSea_1h_20160201_20160201_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01feb16',
'SalishSea_2h_20160201_20160210_dia1_T.nc',
'SalishSea_1h_20160201_20160201_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/02mar16',
'SalishSea_2h_20160302_20160311_dia1_T.nc',
'SalishSea_1h_20160302_20160302_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/02mar16',
'SalishSea_2h_20160302_20160311_dia1_T.nc',
'SalishSea_1h_20160302_20160302_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/02mar16',
'SalishSea_2h_20160302_20160311_dia1_T.nc',
'SalishSea_1h_20160302_20160302_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01apr16',
'SalishSea_2h_20160401_20160410_dia1_T.nc',
'SalishSea_1h_20160401_20160401_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01apr16',
'SalishSea_2h_20160401_20160410_dia1_T.nc',
'SalishSea_1h_20160401_20160401_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01apr16',
'SalishSea_2h_20160401_20160410_dia1_T.nc',
'SalishSea_1h_20160401_20160401_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01may16',
'SalishSea_2h_20160501_20160510_dia1_T.nc',
'SalishSea_1h_20160501_20160501_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01may16',
'SalishSea_2h_20160501_20160510_dia1_T.nc',
'SalishSea_1h_20160501_20160501_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01may16',
'SalishSea_2h_20160501_20160510_dia1_T.nc',
'SalishSea_1h_20160501_20160501_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/31may16',
'SalishSea_2h_20160531_20160609_dia1_T.nc',
'SalishSea_1h_20160531_20160531_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/31may16',
'SalishSea_2h_20160531_20160609_dia1_T.nc',
'SalishSea_1h_20160531_20160531_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/31may16',
'SalishSea_2h_20160531_20160609_dia1_T.nc',
'SalishSea_1h_20160531_20160531_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jun16',
'SalishSea_2h_20160630_20160709_dia1_T.nc',
'SalishSea_1h_20160630_20160630_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jun16',
'SalishSea_2h_20160630_20160709_dia1_T.nc',
'SalishSea_1h_20160630_20160630_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jun16',
'SalishSea_2h_20160630_20160709_dia1_T.nc',
'SalishSea_1h_20160630_20160630_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jul16',
'SalishSea_2h_20160730_20160808_dia1_T.nc',
'SalishSea_1h_20160730_20160730_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jul16',
'SalishSea_2h_20160730_20160808_dia1_T.nc',
'SalishSea_1h_20160730_20160730_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/30jul16',
'SalishSea_2h_20160730_20160808_dia1_T.nc',
'SalishSea_1h_20160730_20160730_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/29aug16',
'SalishSea_2h_20160829_20160907_dia1_T.nc',
'SalishSea_1h_20160829_20160829_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/29aug16',
'SalishSea_2h_20160829_20160907_dia1_T.nc',
'SalishSea_1h_20160829_20160829_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/29aug16',
'SalishSea_2h_20160829_20160907_dia1_T.nc',
'SalishSea_1h_20160829_20160829_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/28sep16',
'SalishSea_2h_20160928_20161007_dia1_T.nc',
'SalishSea_1h_20160928_20160928_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/28sep16',
'SalishSea_2h_20160928_20161007_dia1_T.nc',
'SalishSea_1h_20160928_20160928_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/28sep16',
'SalishSea_2h_20160928_20161007_dia1_T.nc',
'SalishSea_1h_20160928_20160928_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/28oct16',
'SalishSea_2h_20161028_20161106_dia1_T.nc',
'SalishSea_1h_20161028_20161028_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/28oct16',
'SalishSea_2h_20161028_20161106_dia1_T.nc',
'SalishSea_1h_20161028_20161028_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/28oct16',
'SalishSea_2h_20161028_20161106_dia1_T.nc',
'SalishSea_1h_20161028_20161028_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/27nov16',
'SalishSea_2h_20161127_20161206_dia1_T.nc',
'SalishSea_1h_20161127_20161127_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/27nov16',
'SalishSea_2h_20161127_20161206_dia1_T.nc',
'SalishSea_1h_20161127_20161127_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/27nov16',
'SalishSea_2h_20161127_20161206_dia1_T.nc',
'SalishSea_1h_20161127_20161127_ptrc_T.nc', 'flag')