#!/usr/bin/env python
# coding: utf-8

# In[1]:


import numpy as np
import matplotlib.pyplot as plt
import netCDF4 as nc 
import datetime as dt
import os
import glob
import cmocean
from salishsea_tools import viz_tools, places, visualisations

get_ipython().run_line_magic('matplotlib', 'inline')


# In[2]:


x=np.arange(0,10)
print('x:',x)
y=x[4:8]
print('y:',y)
print('last element:', x[-1])
print('all of x:',x[:])


# In[3]:


places.PLACES['S3']


# ### Load a file from the 201812 hindcast

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f=nc.Dataset('/results/SalishSea/nowcast-green.201812/01apr15/SalishSea_1h_20150401_20150401_ptrc_T.nc')


# In[5]:


print(f.variables.keys())


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fe3t=nc.Dataset('/results/SalishSea/nowcast-green.201812/01apr15/SalishSea_1h_20150401_20150401_carp_T.nc')


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print(fe3t.variables.keys())


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fe3t.variables['time_centered']


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# return times as datetime objects:
torig=dt.datetime.strptime(f.variables['time_centered'].time_origin,'%Y-%m-%d %H:%M:%S')


# In[10]:


torig


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f.variables['time_centered'][:]


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times=np.array([torig+dt.timedelta(seconds=ii) for ii in \
               f.variables['time_centered'][:]])


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times


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# load model mesh
with nc.Dataset('/data/eolson/results/MEOPAR/NEMO-forcing-new/grid/mesh_mask201702.nc') as fm:
    print(fm.variables.keys())
    tmask=fm.variables['tmask'][:,:,:,:]
    navlon=fm.variables['nav_lon'][:,:]
    navlat=fm.variables['nav_lat'][:,:]


# ### Dept Profile

# In[17]:


fig,ax=plt.subplots(1,2,figsize=(6,6))
fig.subplots_adjust(wspace=.5) # space the axes out more
il=12
# use location 'S3'
ij,ii=places.PLACES['S3']['NEMO grid ji']
ax[0].plot(np.ma.masked_where(tmask[0,:,ij,ii]==0,
                             f.variables['microzooplankton'][il,:,ij,ii]),
          f.variables['deptht'][:],'b-x',label='microzo')
ax[0].plot(np.ma.masked_where(tmask[0,:,ij,ii]==0,f.variables['diatoms'][il,:,ij,ii]),f.variables['deptht'][:],'g-x',label='diatoms')
ax[0].set_ylim(300,0)
ax[0].legend()
ax[0].set_xlabel('Concentration ($\mu$M)')
ax[0].set_ylabel('Depth (m)')
ax[1].plot(np.ma.masked_where(tmask[0,:,ij,ii]==0,f.variables['nitrate'][il,:,ij,ii]),f.variables['deptht'][:],'-x',color='orange',label='NO$_3$')
ax[1].plot(np.ma.masked_where(tmask[0,:,ij,ii]==0,f.variables['silicon'][il,:,ij,ii]),f.variables['deptht'][:],'-x',color='r',label='dissolved Si')
ax[1].set_ylim(300,0)
ax[1].set_ylabel('Depth (m)')
ax[1].legend()
ax[1].set_xlabel('Concentration ($\mu$M)')


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