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/06jan17',
'SalishSea_2h_20170106_20170115_dia1_T.nc',
'SalishSea_1h_20170106_20170106_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/06jan17',
'SalishSea_2h_20170106_20170115_dia1_T.nc',
'SalishSea_1h_20170106_20170106_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/06jan17',
'SalishSea_2h_20170106_20170115_dia1_T.nc',
'SalishSea_1h_20170106_20170106_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/05feb17',
'SalishSea_2h_20170205_20170214_dia1_T.nc',
'SalishSea_1h_20170205_20170205_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/05feb17',
'SalishSea_2h_20170205_20170214_dia1_T.nc',
'SalishSea_1h_20170205_20170205_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/05feb17',
'SalishSea_2h_20170205_20170214_dia1_T.nc',
'SalishSea_1h_20170205_20170205_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/07mar17',
'SalishSea_2h_20170307_20170316_dia1_T.nc',
'SalishSea_1h_20170307_20170307_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/07mar17',
'SalishSea_2h_20170307_20170316_dia1_T.nc',
'SalishSea_1h_20170307_20170307_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/07mar17',
'SalishSea_2h_20170307_20170316_dia1_T.nc',
'SalishSea_1h_20170307_20170307_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/06apr17',
'SalishSea_2h_20170406_20170415_dia1_T.nc',
'SalishSea_1h_20170406_20170406_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/06apr17',
'SalishSea_2h_20170406_20170415_dia1_T.nc',
'SalishSea_1h_20170406_20170406_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/06apr17',
'SalishSea_2h_20170406_20170415_dia1_T.nc',
'SalishSea_1h_20170406_20170406_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/06may17',
'SalishSea_2h_20170506_20170515_dia1_T.nc',
'SalishSea_1h_20170506_20170506_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/06may17',
'SalishSea_2h_20170506_20170515_dia1_T.nc',
'SalishSea_1h_20170506_20170506_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/06may17',
'SalishSea_2h_20170506_20170515_dia1_T.nc',
'SalishSea_1h_20170506_20170506_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jun17',
'SalishSea_2h_20170605_20170614_dia1_T.nc',
'SalishSea_1h_20170605_20170605_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jun17',
'SalishSea_2h_20170605_20170614_dia1_T.nc',
'SalishSea_1h_20170605_20170605_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jun17',
'SalishSea_2h_20170605_20170614_dia1_T.nc',
'SalishSea_1h_20170605_20170605_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jul17',
'SalishSea_2h_20170705_20170714_dia1_T.nc',
'SalishSea_1h_20170705_20170705_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jul17',
'SalishSea_2h_20170705_20170714_dia1_T.nc',
'SalishSea_1h_20170705_20170705_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/05jul17',
'SalishSea_2h_20170705_20170714_dia1_T.nc',
'SalishSea_1h_20170705_20170705_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01aug17',
'SalishSea_2h_20170801_20170801_dia1_T.nc',
'SalishSea_1h_20170801_20170801_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01aug17',
'SalishSea_2h_20170801_20170801_dia1_T.nc',
'SalishSea_1h_20170801_20170801_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01aug17',
'SalishSea_2h_20170801_20170801_dia1_T.nc',
'SalishSea_1h_20170801_20170801_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01sep17',
'SalishSea_2h_20170901_20170901_dia1_T.nc',
'SalishSea_1h_20170901_20170901_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01sep17',
'SalishSea_2h_20170901_20170901_dia1_T.nc',
'SalishSea_1h_20170901_20170901_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01sep17',
'SalishSea_2h_20170901_20170901_dia1_T.nc',
'SalishSea_1h_20170901_20170901_ptrc_T.nc', 'flag')
limit_along_thalweg('/results/SalishSea/nowcast-green/01oct17',
'SalishSea_2h_20171001_20171001_dia1_T.nc',
'SalishSea_1h_20171004_20171004_ptrc_T.nc', 'dia')
limit_along_thalweg('/results/SalishSea/nowcast-green/01oct17',
'SalishSea_2h_20171001_20171001_dia1_T.nc',
'SalishSea_1h_20171004_20171004_ptrc_T.nc', 'meso')
limit_along_thalweg('/results/SalishSea/nowcast-green/01oct17',
'SalishSea_2h_20171001_20171001_dia1_T.nc',
'SalishSea_1h_20171004_20171004_ptrc_T.nc', 'flag')