In [1]:
import numpy as np
import xarray as xr
import pandas as pd
from salishsea_tools import viz_tools, places, visualisations
from matplotlib import pyplot as plt, dates
from datetime import datetime, timedelta
from calendar import month_name
from scipy.io import loadmat
from tqdm.notebook import tqdm
from salishsea_tools import nc_tools
from dask.diagnostics import ProgressBar
import cmocean
%matplotlib inline
In [2]:
plt.rcParams.update({'font.size': 12, 'axes.titlesize': 'medium'})
SST¶
In [3]:
## Data for original cold and warm years
monthly_array_temp_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['votemper']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
### 2008 original temp
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_slice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
### 2019 original
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_slice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
In [4]:
monthly_array_temp_slice[monthly_array_temp_slice == 0 ] = np.nan
monthly_array_temp_slicemean = \
np.nanmean(np.nanmean(monthly_array_temp_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_temp_slicemean))
(14, 12)
/tmp/ipykernel_3469130/391916811.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_temp_slice, axis = 2),axis = 2)
In [5]:
## Data for Experiments 1 and 2
monthly_array_temp_exp_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['votemper']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
###
## Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.votemper.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_temp_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['votemper']:
data[var].append(ds.votemper.isel(deptht=0, **slc).values)
In [6]:
monthly_array_temp_exp_slice[monthly_array_temp_exp_slice == 0 ] = np.nan
monthly_array_temp_exp_slicemean = \
np.nanmean(np.nanmean(monthly_array_temp_exp_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_temp_exp_slicemean))
(14, 12)
/tmp/ipykernel_3469130/2338418733.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_temp_exp_slice, axis = 2),axis = 2)
In [7]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_temp_slicemean[12,:],color='r',linestyle='-',label='Original WY')
ax.plot(xticks, monthly_array_temp_exp_slicemean[12,:],color='k',linestyle='-.',label='WY with CY nutrients')
ax.set_title('WY SST with CY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,25)
ax.set_ylabel('Degrees C')
Out[7]:
Text(0, 0.5, 'Degrees C')
In [8]:
monthly_array_temp_exp_slicemean[12,:]
Out[8]:
array([ 6.66011314, 5.16426706, 7.25914742, 10.17815932, 14.09488876,
17.59587821, 20.67570395, 20.07901062, 16.81303244, 11.56899786,
8.62051358, 6.7005392 ])
In [9]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_temp_slicemean[1,:],color='b',linestyle='-',label='Original CY')
ax.plot(xticks, monthly_array_temp_exp_slicemean[1,:],color='k',linestyle='-.',label='CY with WY nutrients')
ax.set_title('CY SST with WY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,25)
ax.set_ylabel('Degrees C')
Out[9]:
Text(0, 0.5, 'Degrees C')
In [10]:
monthly_array_temp_exp_slicemean[1,:]
Out[10]:
array([ 6.13830953, 5.82549722, 7.48766262, 9.10256158, 12.68796849,
16.20069323, 18.13362829, 18.18589498, 15.38127229, 11.96611296,
9.38018667, 6.34800222])
In [ ]:
Surface PAR¶
In [11]:
## PAR data for original years
monthly_array_PAR_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['PAR']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
### 2008 original temp
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_slice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
### 2019 original
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_slice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
In [12]:
monthly_array_PAR_slice[monthly_array_PAR_slice == 0 ] = np.nan
monthly_array_PAR_slicemean = \
np.nanmean(np.nanmean(monthly_array_PAR_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_PAR_slicemean))
(14, 12)
/tmp/ipykernel_3469130/2771304440.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_PAR_slice, axis = 2),axis = 2)
In [13]:
# PAR data for experiments 1 and 2
monthly_array_PAR_exp_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['PAR']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
###
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_carp_T.nc') as ds:
q = ds.PAR.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_PAR_exp_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['PAR']:
data[var].append(ds.PAR.isel(deptht=0, **slc).values)
In [14]:
monthly_array_PAR_exp_slice[monthly_array_PAR_exp_slice == 0 ] = np.nan
monthly_array_PAR_exp_slicemean = \
np.nanmean(np.nanmean(monthly_array_PAR_exp_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_PAR_exp_slicemean))
(14, 12)
/tmp/ipykernel_3469130/178454329.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_PAR_exp_slice, axis = 2),axis = 2)
In [15]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_PAR_slicemean[12,:],color='r',linestyle='-',label='Original WY')
ax.plot(xticks, monthly_array_PAR_exp_slicemean[12,:],color='k',linestyle='-.',label='WY with CY nutrients')
ax.set_title('WY PAR with CY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,150)
ax.set_ylabel('m$^{-2}$')
Out[15]:
Text(0, 0.5, 'm$^{-2}$')
In [16]:
monthly_array_PAR_exp_slicemean[12,:]
Out[16]:
array([ 15.32157315, 25.46430715, 53.17412975, 62.44887383,
90.84260541, 103.05034021, 94.88347023, 80.51483052,
51.31051136, 31.57238514, 20.31519746, 8.03565263])
In [17]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_PAR_slicemean[1,:],color='b',linestyle='-',label='Original CY')
ax.plot(xticks, monthly_array_PAR_exp_slicemean[1,:],color='k',linestyle='-.',label='CY with WY Nutrients')
ax.set_title('CY PAR with WY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,150)
ax.set_ylabel('m$^{-2}$')
Out[17]:
Text(0, 0.5, 'm$^{-2}$')
In [18]:
monthly_array_PAR_exp_slicemean[1,:]
Out[18]:
array([ 14.23679829, 25.43165744, 41.19107135, 59.75958975,
85.18338548, 94.02408369, 100.44978733, 80.01338611,
60.86782944, 29.30627043, 13.14189992, 10.14616278])
In [ ]:
Halocline Strength¶
In [19]:
# Halocline Strength data for original years
monthly_array_halocline_depth_orig_SSslice = np.zeros([14,12,50,50])
monthly_array_halocline_strength_orig_SSslice = np.zeros([14,12,50,50])
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask,depth = [mask[var].isel(**slc).values for var in ('e3t_0', 'tmask','gdept_0')]
years, variables = range(2007, 2021), ['halocline','strength']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_orig_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_orig_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_orig_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_orig_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_orig_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_orig_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [20]:
monthly_array_halocline_strength_orig_SSslice[monthly_array_halocline_strength_orig_SSslice == 0 ] = np.nan
monthly_array_halocline_strength_orig_SSslicemean = \
np.nanmean(np.nanmean(monthly_array_halocline_strength_orig_SSslice, axis = 2),axis = 2)
print(np.shape(monthly_array_halocline_strength_orig_SSslicemean))
(14, 12)
/tmp/ipykernel_3469130/1288103633.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_halocline_strength_orig_SSslice, axis = 2),axis = 2)
In [21]:
# Data for Experiments 1 and 2
monthly_array_halocline_depth_SSslice = np.zeros([14,12,50,50])
monthly_array_halocline_strength_SSslice = np.zeros([14,12,50,50])
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask,depth = [mask[var].isel(**slc).values for var in ('e3t_0', 'tmask','gdept_0')]
years, variables = range(2007, 2021), ['halocline','strength']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_grid_T.nc') as ds:
q = ds.vosaline.isel(deptht=0, **slc).values
q2 = q[0,:,:]
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:] = q2 #year2007 is index 0 along 1st dimension
sal=ds.vosaline.isel(**slc).values
#get the gradient in salinity
sal_grad = np.zeros_like(sal)
for i in range(0, (np.shape(sal_grad)[1]-1)):
sal_grad[:,i,:,:] =(sal[:,i,:,:]-sal[:,i+1,:,:])/(depth[:,i,:,:]-depth[:,i+1,:,:])
#print(sal_grad)
loc_max = np.argmax(sal_grad,axis=1)
depths=np.tile(depth,[np.shape(sal)[0],1,1,1])
h1=np.take_along_axis(depths, np.expand_dims(loc_max, axis=1), axis=1)
h2=np.take_along_axis(depths, np.expand_dims(loc_max+1, axis=1), axis=1)
sals=np.tile(sal,[np.shape(sal)[0],1,1,1])
s1=np.take_along_axis(sals, np.expand_dims(loc_max, axis=1), axis=1)
s2=np.take_along_axis(sals, np.expand_dims(loc_max+1, axis=1), axis=1)
#halocline is halfway between the two cells
halocline = 0.5*(h1+h2)
strength = (s2-s1)/(h2-h1)
data['halocline'].append(halocline)
data['strength'].append(strength)
monthly_array_halocline_depth_SSslice[year-2007,month-1,:,:]=halocline
monthly_array_halocline_strength_SSslice[year-2007,month-1,:,:]=strength
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [22]:
monthly_array_halocline_strength_SSslice[monthly_array_halocline_strength_SSslice == 0 ] = np.nan
monthly_array_halocline_strength_SSslicemean = \
np.nanmean(np.nanmean(monthly_array_halocline_strength_SSslice, axis = 2),axis = 2)
print(np.shape(monthly_array_halocline_strength_SSslicemean))
(14, 12)
/tmp/ipykernel_3469130/3661973807.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_halocline_strength_SSslice, axis = 2),axis = 2)
In [23]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_halocline_strength_orig_SSslicemean[12,:],color='r',linestyle='-',label='Original 2019')
ax.plot(xticks, monthly_array_halocline_strength_SSslicemean[12,:],color='k',linestyle='-.',label='2019 with 2008 nutrients')
ax.set_title('WY Halocline with CY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,5)
ax.set_ylabel('g/kg m$^{-1}$')
Out[23]:
Text(0, 0.5, 'g/kg m$^{-1}$')
In [24]:
monthly_array_halocline_strength_SSslicemean[12,:]
Out[24]:
array([0.57723351, 0.32422883, 0.78620486, 1.17592297, 1.92554819,
2.39019519, 2.88495737, 2.02522262, 1.49650757, 0.70498795,
1.51586427, 0.98230242])
In [25]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_halocline_strength_orig_SSslicemean[1,:],color='b',linestyle='-',label='Original CY')
ax.plot(xticks, monthly_array_halocline_strength_SSslicemean[1,:],color='k',linestyle='-.',label='CY with WY Halocline')
ax.set_title('CY Halocline with WY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,5)
ax.set_ylabel('g/kg m$^{-1}$')
Out[25]:
Text(0, 0.5, 'g/kg m$^{-1}$')
In [ ]:
In [26]:
### Depth-averaged Nutrients (0-10m)
In [27]:
### Nitrate data for original cold and warm years
monthly_array_nitrate_orig_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 10),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['nitrate']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [28]:
monthly_array_nitrate_orig_slice[monthly_array_nitrate_orig_slice == 0 ] = np.nan
monthly_array_nitrate_orig_slicemean = \
np.nanmean(np.nanmean(monthly_array_nitrate_orig_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_nitrate_orig_slicemean))
(14, 12)
/tmp/ipykernel_3469130/3312634990.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_nitrate_orig_slice, axis = 2),axis = 2)
In [29]:
### Silicon data for original cold and warm years
monthly_array_silicon_orig_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 10),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['silicon']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
###
## Experimental Year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
In [30]:
monthly_array_silicon_orig_slice[monthly_array_silicon_orig_slice == 0 ] = np.nan
monthly_array_silicon_orig_slicemean = \
np.nanmean(np.nanmean(monthly_array_silicon_orig_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_silicon_orig_slicemean))
(14, 12)
/tmp/ipykernel_3469130/241793216.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_silicon_orig_slice, axis = 2),axis = 2)
In [31]:
### Nitrate data for Experiments 1 and 2
monthly_array_nitrate_depthint_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 10),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['nitrate']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_nitrate_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['nitrate']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [32]:
monthly_array_nitrate_depthint_slice[monthly_array_nitrate_depthint_slice == 0 ] = np.nan
monthly_array_nitrate_depthint_slicemean = \
np.nanmean(np.nanmean(monthly_array_nitrate_depthint_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_nitrate_depthint_slicemean))
(14, 12)
/tmp/ipykernel_3469130/231329215.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_nitrate_depthint_slice, axis = 2),axis = 2)
In [33]:
### Silicon data for Experiments 1 and 2
monthly_array_silicon_depthint_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 10),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['silicon']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data
q2 = q[0,:,:]
monthly_array_silicon_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['silicon']:
data[var].append((ds[var].isel(deptht=slice(None, 10),**slc)*e3t*tmask).sum(axis=1)/((e3t*tmask).sum(axis=1)).data)
# Concatenate months
for var in variables: aggregates[var][year] = np.concatenate(data[var]).mean(axis=0)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [34]:
monthly_array_silicon_depthint_slice[monthly_array_silicon_depthint_slice == 0 ] = np.nan
monthly_array_silicon_depthint_slicemean = \
np.nanmean(np.nanmean(monthly_array_silicon_depthint_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_silicon_depthint_slicemean))
(14, 12)
/tmp/ipykernel_3469130/3737416097.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_silicon_depthint_slice, axis = 2),axis = 2)
In [35]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_nitrate_orig_slicemean[12,:],color='r',linestyle='-',label='Original 2019')
ax.plot(xticks, monthly_array_nitrate_depthint_slicemean[12,:],color='k',linestyle='-.',label='2019 with 2008 N and Si')
ax.set_title('WY Nitrate with CY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=4)
ax.set_ylim(0,30)
ax.set_ylabel('mmol N m$^{-2}$')
Out[35]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [36]:
monthly_array_nitrate_orig_slicemean[12,:]
Out[36]:
array([23.64834195, 22.38691698, 16.99383033, 7.63730902, 4.96273598,
1.56547187, 1.23107567, 1.5230891 , 7.95614177, 16.79074658,
19.52305174, 21.62759183])
In [37]:
monthly_array_nitrate_depthint_slicemean[12,:]
Out[37]:
array([24.47601856, 23.37162061, 17.92793601, 8.21108767, 5.33221614,
1.58238226, 1.21867822, 1.79531768, 8.10286171, 17.52341884,
20.56683092, 23.22281989])
In [38]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_silicon_orig_slicemean[12,:],color='r',linestyle='-',label='Original 2019')
ax.plot(xticks, monthly_array_silicon_depthint_slicemean[12,:],color='k',linestyle='-.',label='2019 with 2008 N and Si')
ax.set_title('WY Silicon with CY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=4)
ax.set_ylim(0,60)
ax.set_ylabel('mmol N m$^{-2}$')
Out[38]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [39]:
monthly_array_silicon_orig_slicemean[12,:]
Out[39]:
array([48.06238141, 49.17238747, 41.59249494, 18.0018168 , 5.46358173,
12.1107789 , 19.87997362, 28.03714477, 36.00806573, 41.96864256,
44.54149611, 47.0336623 ])
In [40]:
monthly_array_silicon_depthint_slicemean[12,:]
Out[40]:
array([50.36258288, 51.49776725, 43.67255925, 19.35702357, 5.51602533,
10.55762737, 16.99747485, 25.10753505, 34.81283984, 42.2860491 ,
45.66187067, 48.57553256])
In [ ]:
In [41]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_nitrate_orig_slicemean[1,:],color='b',linestyle='-',label='Original 2008')
ax.plot(xticks, monthly_array_nitrate_depthint_slicemean[1,:],color='k',linestyle='-.',label='2008 with 2019 N and Si')
ax.set_title('CY Nitrate with WY nutrients',fontsize=18)
ax.legend(frameon=False,loc=4)
ax.set_ylim(0,30)
ax.set_ylabel('mmol N m$^{-2}$')
Out[41]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [42]:
monthly_array_nitrate_depthint_slicemean[1,:]
Out[42]:
array([23.9644255 , 22.29828934, 20.45139818, 8.97187906, 5.34151849,
1.96037127, 1.81394895, 4.30505968, 11.52311063, 16.41310313,
21.46072197, 22.33267238])
In [43]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_silicon_orig_slicemean[1,:],color='b',linestyle='-',label='Original 2008')
ax.plot(xticks, monthly_array_silicon_depthint_slicemean[1,:],color='k',linestyle='-.',label='2008 with 2019 N and Si')
ax.set_title('CY Silicon with WY Nutrients',fontsize=18)
ax.legend(frameon=False,loc=4)
ax.set_ylim(0,60)
ax.set_ylabel('mmol N m$^{-2}$')
Out[43]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [44]:
monthly_array_silicon_depthint_slicemean[1,:]
Out[44]:
array([47.7632301 , 49.11254302, 47.48290684, 23.36581641, 8.2090725 ,
11.07120201, 11.99591242, 12.30988367, 25.86081355, 32.83781192,
41.9107794 , 46.15827035])
In [ ]:
Depth-integrated 0-100 m Diatoms¶
In [45]:
### Diatom data for original years
monthly_array_diatoms_orig_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['diatoms']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
### 2008 using higher temperature threshold
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
### 2019 using higher temperature threshold
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/v201905r/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_orig_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
In [46]:
monthly_array_diatoms_orig_slice[monthly_array_diatoms_orig_slice == 0 ] = np.nan
monthly_array_diatoms_orig_slicemean = \
np.nanmean(np.nanmean(monthly_array_diatoms_orig_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_diatoms_orig_slicemean))
(14, 12)
/tmp/ipykernel_3469130/3403781678.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_diatoms_orig_slice, axis = 2),axis = 2)
In [47]:
#years, months, data
monthly_array_diatoms_depthint_slice = np.zeros([14,12,50,50])
# Load monthly averages
mask = xr.open_dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc')
slc = {'y': slice(450,500), 'x': slice(250,300)}
e3t, tmask = [mask[var].isel(z=slice(None, 27),**slc).values for var in ('e3t_0', 'tmask')]
years, variables = range(2007, 2021), ['diatoms']
# Temporary list dict
data = {}
# Permanent aggregate dict
aggregates = {var: {} for var in variables}
monthlydat = {var: {} for var in variables}
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
# Add experiment year
for year in [2008]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul08_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(1, 7):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jan19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
# Add experiment year
for year in [2019]:
# Initialize lists
for var in variables: data[var] = []
# Load monthly averages
for month in range(7, 13):
datestr = f'{year}{month:02d}'
prefix = f'/data/sallen/results/MEOPAR/Karyn/01jul19_NSi/SalishSea_1m_{datestr}_{datestr}'
# Load grazing variables
with xr.open_dataset(prefix + '_ptrc_T.nc') as ds:
q = np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data
q2 = q[0,:,:]
monthly_array_diatoms_depthint_slice[year-2007,month-1,:,:] = q2 #year2015 is index 0 along 1st dimension
for var in ['diatoms']:
data[var].append(np.ma.masked_where(tmask == 0, ds[var].isel(deptht=slice(None, 27), **slc).values * e3t).sum(axis=1).data)
# # Calculate 5 year mean and anomalies
# for var in variables:
# aggregates[var][‘mean’] = np.concatenate([aggregates[var][year][None, ...] for year in years]).mean(axis=0)
# for year in years: aggregates[var][year] = aggregates[var][year] - aggregates[var][‘mean’]
In [48]:
monthly_array_diatoms_depthint_slice[monthly_array_diatoms_depthint_slice == 0 ] = np.nan
monthly_array_diatoms_depthint_slicemean = \
np.nanmean(np.nanmean(monthly_array_diatoms_depthint_slice, axis = 2),axis = 2)
print(np.shape(monthly_array_diatoms_depthint_slicemean))
(14, 12)
/tmp/ipykernel_3469130/2320522072.py:3: RuntimeWarning: Mean of empty slice np.nanmean(np.nanmean(monthly_array_diatoms_depthint_slice, axis = 2),axis = 2)
In [ ]:
In [49]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_diatoms_orig_slicemean[12,:],color='r',linestyle='-',label='Original 2019')
ax.plot(xticks, monthly_array_diatoms_depthint_slicemean[12,:],color='k',linestyle='-.',label='2019 with 2008 N and Si')
ax.set_title('WY Diatoms (0-100 m) with CY N and Si',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,50)
ax.set_ylabel('mmol N m$^{-2}$')
Out[49]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [50]:
fig, ax = plt.subplots(figsize=(15, 3))
bbox = {'boxstyle': 'round', 'facecolor': 'w', 'alpha': 0.9}
cmap = plt.get_cmap('tab10')
palette = [cmap(0), cmap(0.2), 'k', cmap(0.1), cmap(0.3)]
xticks=['Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov',"Dec"]
ax.plot(xticks, monthly_array_diatoms_orig_slicemean[1,:],color='b',linestyle='-',label='Original 2008')
ax.plot(xticks, monthly_array_diatoms_depthint_slicemean[1,:],color='k',linestyle='-.',label='2008 with 2019 N and Si')
ax.set_title('CY Diatoms (0-100 m) with WY N and Si',fontsize=18)
ax.legend(frameon=False,loc=1)
ax.set_ylim(0,50)
ax.set_ylabel('mmol N m$^{-2}$')
Out[50]:
Text(0, 0.5, 'mmol N m$^{-2}$')
In [ ]: