def __init__(self, app, options=None):
# Start pyferret
pyferret.start(journal=False, unmapped=True, quiet=True, verify=False)
master_pid = os.getpid()
print('---------> gunicorn master pid: ', master_pid)
instance_WMS_Client = Template(template_WMS_client())
instance_NW_Package = Template(template_nw_package())
with open(tmpdir + '/index.html', 'wb') as f:
f.write(instance_WMS_Client.render(gunicornPID=master_pid,
mapWidth=mapWidth, mapHeight=mapHeight,
mapCenter=mapCenter, mapZoom=mapZoom, port=port))
with open(tmpdir + '/package.json', 'wb') as f:
f.write(instance_NW_Package.render())
# Copy icon
path = os.path.dirname(os.path.realpath(__file__))
shutil.copy(path + "/icon.png", tmpdir)
# Launch NW.js
proc = subprocess.Popen(['nw', tmpdir])
print('Client nw process: ', proc.pid)
self.options = options or {}
self.application = app
super(StandaloneApplication, self).__init__()
def __init__(self, app, options=None):
# Start pyferret
pyferret.start(journal=False, unmapped=True, quiet=True, verify=False)
master_pid = os.getpid()
print('---------> gunicorn master pid: ', master_pid)
if not serverOnly: # nw will be launched
listSynchroMapsToSet = list(itertools.permutations(range(1,nbMaps+1), 2))
instance_WMS_Client = Template(template_WMS_client())
instance_NW_Package = Template(template_nw_package())
with open(tmpdir + '/index.html', 'wb') as f:
f.write(instance_WMS_Client.render(cmdArray=cmdArray, gunicornPID=master_pid,
listSynchroMapsToSet=listSynchroMapsToSet,
mapWidth=mapWidth, mapHeight=mapHeight,
mapCenter=mapCenter, mapZoom=mapZoom, port=port))
with open(tmpdir + '/package.json', 'wb') as f:
f.write(instance_NW_Package.render(nbMaps=nbMaps,
mapWidth=mapWidth, mapHeight=mapHeight))
# Launch NW.js
proc = subprocess.Popen(['nw', tmpdir])
print('Client nw process: ', proc.pid)
self.options = options or {}
self.application = app
super(StandaloneApplication, self).__init__()
def __init__(self, shell):
"""
Parameters
----------
shell : IPython shell
"""
super(ferretMagics, self).__init__(shell)
try:
pyferret.start(memsize=(_DEFAULT_MEMSIZE/8.0), verify=False, journal=False, unmapped=True, quiet=True)
except ExceptionPexpect:
raise ferretMagicError('pyferret cannot be started')
self._shell = shell
self._shell.ferret_locked = False
def __init__(self, shell):
"""
Parameters
----------
shell : IPython shell
"""
super(ferretMagics, self).__init__(shell)
try:
pyferret.start(memsize=(_DEFAULT_MEMSIZE/8.0), verify=False, journal=False, unmapped=True, quiet=True)
except ExceptionPexpect:
raise ferretMagicError('pyferret cannot be started')
self._shell = shell
self._shell.ferret_locked = False
def __init__(self, app, options=None):
# Start pyferret
pyferret.start(journal=False,
unmapped=True,
quiet=True,
verify=False,
memsize=50)
master_pid = os.getpid()
print('---------> gunicorn master pid: ', master_pid)
self.options = options or {}
self.application = app
super(StandaloneApplication, self).__init__()
def app3z(nc_file='', var_name='tmn', k=1, l=1, outDir=''):
# init_ferret
import pyferret as pf
pf.start(quiet=True, unmapped=True)
pf.run('set memory/size=500')
pf.run('cancel mode logo')
pf.run('cancel mode journal')
temp1 = 'use "%s"' % nc_file
print(temp1)
pf.run(temp1)
temp1 = 'show data'
print(temp1)
pf.run(temp1)
#temp1 = 'shade %s[k=%d,l=%d]\ngo land'%(var_name, k, l)
temp1 = 'shade %s[l=%d]' % (var_name, l)
print(temp1)
pf.run(temp1)
temp1 = 'go land'
print(temp1)
pf.run(temp1)
t1 = outDir.find('static')
outDir1 = outDir[t1:]
figFile1 = '%s/plot.png' % outDir1
print(figFile1)
figFile0 = '%s/plot.png' % outDir
temp1 = 'frame/file="%s"' % figFile0
print(temp1)
pf.run(temp1)
mess = 'Plot var %s of file:\n%s' % (nc_file, var_name)
figFile = 'http://ec2-13-56-153-11.us-west-1.compute.amazonaws.com:5003/%s' % figFile1
return mess, figFile, None
import os
import pyferret
pyferret.start(quiet=True)
import shutil
import iris_sample_data
fname = 'A1B_north_america.nc'
srcpath = os.path.join(iris_sample_data.path, fname)
ncpath = os.path.join('/tmp', fname)
shutil.copy(srcpath, ncpath)
ds = pyferret.FerDSet(ncpath)
assert (ds['height'].unit == 'm')
assert (ds['air_temperature'].data.shape == (49, 37, 1, 240, 1, 1))
os.remove(ncpath)
print('ran pyferret test')
def regrid_once_primitive(var, ref_var, axis,
verbose=False, prerun=None, transform='@ave'):
''' A generic function that regrids a variable without the dependence of
geodat.nc.Variable
Args:
var (dict) : arguments for num2fer
Required keys: data,coords,dimunits
ref_var (dict) : arguments for num2fer.
This supplies the grid for regridding
Required keys: coords,dimunits
axis (str) : the axis for regridding e.g. 'X'/'Y'/'XY'/"YX"
verbose (bool) : whether to print progress (default: False)
prerun (a list of str) : commands to be run at the start (default: None)
transform (str): "@ave" (Conserve area average),
"@lin" (Linear interpolation),...see Ferret doc
Returns:
dict
'''
if not PYFERRET_INSTALLED:
raise _IMPORT_PYFERRET_ERROR
pyferret.start(quiet=True, journal=verbose,
verify=False, server=True)
# commands to run before regridding
if prerun is not None:
if type(prerun) is str:
pyferret.run(prerun)
elif type(prerun) is list:
for s in prerun:
if type(s) is str:
pyferret.run(prerun)
else:
raise Exception("prerun has to be either a string or "+\
"a list of string")
else:
raise Exception("prerun has to be either a string or a list of "+\
"string")
assert isinstance(axis, str)
axis = axis.upper()
# Make sure axis is a string denoting X or Y axis
#if axis not in ['X', 'Y', 'XY', 'YX']:
# raise Exception("Currently axis can only be X/Y/XY")
# Construct the source data read by pyferret.putdata
source_fer = num2fer(**var)
source_fer["name"] = "source"
# Fill in unnecessary input for Ferret
if "data" not in ref_var:
ref_var['data'] = numpy.zeros((1,)*len(ref_var['coords']))
# Construct the destination data read by pyferret.putdata
dest_fer = num2fer(**ref_var)
dest_fer["name"] = "dest"
if verbose:
print source_fer
print dest_fer
pyferret.putdata(source_fer, axis_pos=source_fer['axis_pos'])
if verbose:
print "Put source variable"
pyferret.run('show grid source')
pyferret.putdata(dest_fer, axis_pos=dest_fer['axis_pos'])
if verbose:
print "Put destination variable"
pyferret.run('show grid dest')
pyfer_command = 'let result = source[g'+axis.lower()+'=dest'+transform+']'
pyferret.run(pyfer_command)
if verbose:
print "Regridded in FERRET"
pyferret.run('show grid result')
# Get results
result_ref = pyferret.getdata('result')
if verbose: print "Get data from FERRET"
# Convert from ferret data structure to geodat.nc.Variable
tmp_result = fer2num(result_ref)
if 'varname' in var:
tmp_result['varname'] = var['varname']
tmp_caxes = [geodat.units.assign_caxis(dimunit)
for dimunit in tmp_result['dimunits']]
var_caxes = [geodat.units.assign_caxis(dimunit)
for dimunit in var['dimunits']]
# Preserve dimension order (Ferret reverts the order)
neworder = [tmp_caxes.index(cax)
for cax in var_caxes]
# Change the dimension order of the result to match with the input
tmp_result['coords'] = [tmp_result['coords'][iax] for iax in neworder]
tmp_result['dimunits'] = [tmp_result['dimunits'][iax] for iax in neworder]
if 'dimnames' in tmp_result:
tmp_result['dimnames'] = [tmp_result['dimnames'][iax]
for iax in neworder]
tmp_result['data'] = tmp_result['data'].transpose(neworder).astype(
var['data'].dtype)
# Return the input var with the data and dimensions replaced by
# the regridded ones
var.update(tmp_result)
result = var
status = pyferret.stop()
if verbose:
if status:
print "PyFerret stopped."
else:
print "PyFerret failed to stop."
return result
#=========================================
# Dependencies
#=================================================================
# Initialize access to PyFerret.
# Understanding the following lines of code is not part of the course.
# Acknowlegements:
# -> Pyferret: NOAA, https://ferret.pmel.noaa.gov/Ferret/
# -> ferretmagic: Patrick Brockmann, https://pypi.org/project/ferretmagic/
# -> These exact lines for running PyFerret on the Bowdoin HPC Grid: DJ Merrill
#=================================================================
import sys
sys.path.append('/mnt/local/pyferret/lib/python3.6/site-packages')
import pyferret
pyferret.addenv(FER_DIR='/mnt/local/pyferret', FER_DAT='/mnt/local/FerretDatasets')
pyferret.start(journal=False, quiet=True, unmapped=True)
import numpy as np
import pandas as pd
import datetime
#==========================================
# This is a very simple function for the
# purposes of testing.
#==========================================
def add_one(x):
y = x + 1
return y
#==========================================
# Function to load glider data from mission
# NetCDF files
def app3(nc_file='', var_name=None, k=1, l=1, outDir=''):
# checkNc
import checkNc2
dict1 = {}
dict1['fileName'] = nc_file
dict1['source'] = 'online'
dict1['message'] = ''
ok1 = checkNc2.checkNc(nc_file, dict1, allowOverwrite=0)
mes1 = dict1['message']
mes1 += '\n\n' + dict1['check']
print(ok1)
print('dict1.key:')
for kk in dict1.keys():
print(kk)
varList = dict1['varList']
var_name1 = None
if var_name is None:
for v in varList:
d2 = dict1['varDict'][v]['dim2']
if (len(d2) > 1) and (len(d2) < 5):
if (d2[-1] == 'lon') and (d2[-2] == 'lat'):
var_name1 = v
nD = len(d2)
else:
var_name1 = var_name
try:
d2 = dict1['varDict'][var_name]['dim2']
nD = len(d2)
except:
text1 = 'Variable %s does not exist in the file.' % var_name
print(text1)
mes1 += '\n%s' % text1
if var_name1 is None:
mes1 += '\n\n## Cannot figure out which variable to plot.##'
# plotting
k = int(k)
l = int(l)
# use_ferret
if 1:
# init_ferret
import pyferret as pf
pf.start(quiet=True, unmapped=True)
pf.run('set memory/size=1000')
pf.run('cancel mode logo')
pf.run('cancel mode journal')
temp1 = 'use "%s"' % nc_file
print(temp1)
pf.run(temp1)
temp1 = 'show data'
print(temp1)
pf.run(temp1)
if nD == 2:
temp1 = 'shade %s' % (var_name1)
elif nD == 3:
temp1 = 'shade %s[l=%d]' % (var_name1, l)
elif nD == 4:
temp1 = 'shade %s[k=%d, l=%d]' % (var_name1, k, l)
print(temp1)
pf.run(temp1)
temp1 = 'go land'
print(temp1)
pf.run(temp1)
t1 = outDir.find('static')
outDir1 = outDir[t1:]
figFile1 = '%s/plot.png' % outDir1
print(figFile1)
figFile0 = '%s/plot.png' % outDir
temp1 = 'frame/file="%s"' % figFile0
print(temp1)
pf.run(temp1)
if 0: # use basemap
from netCDF4 import Dataset
import matplotlib as mpl
mpl.use('Agg') # for interactive. Work on svm3
import matplotlib.pylab as Mat
from mpl_toolkits.basemap import Basemap
mpl.rcParams['image.cmap'] = 'jet'
nc = Dataset(nc_file)
ncVar = nc.variables[var_name1]
dims1 = ncVar.dimensions
print(dims1)
print(ncVar.shape)
if 0:
if len(dims1) == 3:
data1 = ncVar[k - 1, ::-1, :]
elif len(dims1) == 4:
data1 = ncVar[k - 1, l - 1, ::-1, :]
elif len(dims1) == 2:
data1 = ncVar[::-1, :]
if 1:
if len(dims1) == 3:
data1 = ncVar[k - 1, :, :]
elif len(dims1) == 4:
data1 = ncVar[k - 1, l - 1, :, :]
elif len(dims1) == 2:
data1 = ncVar[:, :]
lon2 = nc.variables[dims1[-1]][:]
lat2 = nc.variables[dims1[-2]][:]
m = Basemap(lon2[0],
lat2[0],
lon2[-1],
lat2[-1],
resolution='c',
suppress_ticks=False)
#m.pcolor(lon2, lat2, pattern1[i, ::-1, :], vmin=min2, vmax=max2, shading='flat')
#data1 = data1[::-1, :]
m.pcolor(lon2, lat2, data1)
m.drawcoastlines(color=(.7, .7, .7))
m.colorbar()
#Mat.title('EOF %d'%(i+1))
figFile0 = '%s/plot.png' % outDir
Mat.savefig(figFile0, dpi=100)
#figFile = 'http://localhost:5003/%s'%figFile0
#figFile = 'http://ec2-13-56-67-192.us-west-1.compute.amazonaws.com:8080/%s'%figFile0
# for ec20
t1 = outDir.find('static')
outDir1 = outDir[t1:]
figFile1 = '%s/plot.png' % outDir1
print(figFile1)
figFile = 'http://ec2-13-56-153-11.us-west-1.compute.amazonaws.com:5003/%s' % figFile1
return mes1, figFile, None
