def get_or_create(self, uri, reprocess=False, *args, **kwargs):
# ingest file to db
ds, created = super(DatasetManager,
self).get_or_create(uri, *args, **kwargs)
# set Dataset entry_title
ds.entry_title = 'SAR NRCS'
ds.save()
# Unless reprocess==True, we may not need to do the following... (see
# managers.py in sar doppler processor)
#visExists = ... # check if visualization(s) already created
#if visExists and not reprocess:
# warnings.warn('NO VISUALISATIONS CREATED - update managers.py')
# return ds, created
n = Nansat(nansat_filename(uri))
n.reproject_GCPs()
n.resize(pixelsize=500)
lon, lat = n.get_corners()
lat_max = min(lat.max(), 85)
d = Domain(
NSR(3857), '-lle %f %f %f %f -ts %d %d' %
(lon.min(), lat.min(), lon.max(), lat_max, n.shape()[1],
n.shape()[0]))
# Get all NRCS bands
s0bands = []
pp = []
for key, value in n.bands().iteritems():
try:
if value['standard_name'] == standard_name:
s0bands.append(key)
pp.append(value['polarization'])
except KeyError:
continue
''' Create data products
'''
mm = self.__module__.split('.')
module = '%s.%s' % (mm[0], mm[1])
mp = media_path(module, n.fileName)
# ppath = product_path(module, n.fileName)
# Create png's for each band
num_products = 0
for band in s0bands:
print 'Visualize', band
s0_tmp = n[band]
n_tmp = Nansat(domain=n, array=s0_tmp)
n_tmp.reproject_GCPs()
n_tmp.reproject(d)
s0 = n_tmp[1]
n_tmp = None
mask = np.ones(s0.shape, np.uint8)
mask[np.isnan(s0) + (s0 <= 0)] = 0
s0 = np.log10(s0) * 10.
meta = n.bands()[band]
product_filename = '%s_%s.png' % (meta['short_name'],
meta['polarization'])
nansatFigure(s0, mask, polarization_clims[meta['polarization']][0],
polarization_clims[meta['polarization']][1], mp,
product_filename)
# Get DatasetParameter
param = Parameter.objects.get(short_name=meta['short_name'])
dsp, created = DatasetParameter.objects.get_or_create(
dataset=ds, parameter=param)
# Create Visualization
geom, created = GeographicLocation.objects.get_or_create(
geometry=WKTReader().read(n.get_border_wkt()))
vv, created = Visualization.objects.get_or_create(
uri='file://localhost%s/%s' % (mp, product_filename),
title='%s %s polarization' %
(param.standard_name, meta['polarization']),
geographic_location=geom)
# Create VisualizationParameter
vp, created = VisualizationParameter.objects.get_or_create(
visualization=vv, ds_parameter=dsp)
return ds, True
def process(self, uri, *args, **kwargs):
""" Create data products
"""
ds, created = self.get_or_create(uri, *args, **kwargs)
fn = nansat_filename(uri)
swath_data = {}
# Read subswaths
for i in range(self.N_SUBSWATHS):
swath_data[i] = Doppler(fn, subswath=i)
# Get module name
mm = self.__module__.split('.')
module = '%s.%s' % (mm[0], mm[1])
# Set media path (where images will be stored)
mp = media_path(module, swath_data[i].filename)
# Set product path (where netcdf products will be stored)
ppath = product_path(module, swath_data[i].filename)
# Loop subswaths, process each of them and create figures for display with leaflet
for i in range(self.N_SUBSWATHS):
is_corrupted = False
# Check if the file is corrupted
try:
inci = swath_data[i]['incidence_angle']
# TODO: What kind of exception ?
except:
is_corrupted = True
continue
# Add Doppler anomaly
swath_data[i].add_band(array=swath_data[i].anomaly(), parameters={
'wkv':
'anomaly_of_surface_backwards_doppler_centroid_frequency_shift_of_radar_wave'
})
# Get band number of DC freq, then DC polarisation
band_number = swath_data[i]._get_band_number({
'standard_name': 'surface_backwards_doppler_centroid_frequency_shift_of_radar_wave',
})
pol = swath_data[i].get_metadata(bandID=band_number, key='polarization')
# Calculate total geophysical Doppler shift
fdg = swath_data[i].geophysical_doppler_shift()
swath_data[i].add_band(
array=fdg,
parameters={
'wkv': 'surface_backwards_doppler_frequency_shift_of_radar_wave_due_to_surface_velocity'
})
# Set filename of exported netcdf
fn = os.path.join(ppath,
os.path.basename(swath_data[i].filename).split('.')[0]
+ 'subswath%d.nc' % i)
# Set filename of original gsar file in metadata
swath_data[i].set_metadata(key='Originating file',
value=swath_data[i].filename)
# Export data to netcdf
print('Exporting %s (subswath %d)' % (swath_data[i].filename, i))
swath_data[i].export(filename=fn)
# Add netcdf uri to DatasetURIs
ncuri = os.path.join('file://localhost', fn)
new_uri, created = DatasetURI.objects.get_or_create(uri=ncuri,
dataset=ds)
# Reproject to leaflet projection
xlon, xlat = swath_data[i].get_corners()
d = Domain(NSR(3857),
'-lle %f %f %f %f -tr 1000 1000'
% (xlon.min(), xlat.min(), xlon.max(), xlat.max()))
swath_data[i].reproject(d, eResampleAlg=1, tps=True)
# Check if the reprojection failed
try:
inci = swath_data[i]['incidence_angle']
except:
is_corrupted = True
warnings.warn('Could not read incidence angles - reprojection failed')
continue
# Create visualizations of the following bands (short_names)
ingest_creates = ['valid_doppler',
'valid_land_doppler',
'valid_sea_doppler',
'dca',
'fdg']
for band in ingest_creates:
filename = '%s_subswath_%d.png' % (band, i)
# check uniqueness of parameter
param = Parameter.objects.get(short_name=band)
fig = swath_data[i].write_figure(
os.path.join(mp, filename),
bands=band,
mask_array=swath_data[i]['swathmask'],
mask_lut={0: [128, 128, 128]},
transparency=[128, 128, 128])
if type(fig) == Figure:
print 'Created figure of subswath %d, band %s' % (i, band)
else:
warnings.warn('Figure NOT CREATED')
# Get or create DatasetParameter
dsp, created = DatasetParameter.objects.get_or_create(dataset=ds,
parameter=param)
# Create GeographicLocation for the visualization object
geom, created = GeographicLocation.objects.get_or_create(
geometry=WKTReader().read(swath_data[i].get_border_wkt()))
# Create Visualization
vv, created = Visualization.objects.get_or_create(
uri='file://localhost%s/%s' % (mp, filename),
title='%s (swath %d)' % (param.standard_name, i + 1),
geographic_location=geom
)
# Create VisualizationParameter
vp, created = VisualizationParameter.objects.get_or_create(
visualization=vv,
ds_parameter=dsp
)
# TODO: consider merged figures like Jeong-Won has added in the development branch
return ds, not is_corrupted
def get_or_create(self, uri, reprocess=False, *args, **kwargs):
# ingest file to db
ds, created = super(DatasetManager,
self).get_or_create(uri, *args, **kwargs)
fn = nansat_filename(uri)
n = Nansat(fn)
# Reproject to leaflet projection
xlon, xlat = n.get_corners()
d = Domain(
NSR(3857), '-lle %f %f %f %f -tr 1000 1000' %
(xlon.min(), xlat.min(), xlon.max(), xlat.max()))
n.reproject(d)
# Get band numbers of required bands according to standard names
speedBandNum = n._get_band_number({'standard_name': 'wind_speed'})
dirBandNum = n._get_band_number(
{'standard_name': 'wind_from_direction'})
# Get numpy arrays of the bands
speed = n[speedBandNum]
dir = n[dirBandNum]
## It probably wont work with nansatmap...
#nmap = Nansatmap(n, resolution='l')
#nmap.pcolormesh(speed, vmax=18)
#nmap.quiver(-speed*np.sin(dir), speed*np.cos(dir), step=10, scale=300,
# width=0.002)
# Set paths - this code should be inherited but I think there is an
# issue in generalising the first line that defines the current module
mm = self.__module__.split('.')
module = '%s.%s' % (mm[0], mm[1])
mp = media_path(module, n.fileName)
ppath = product_path(module, n.fileName)
filename = os.path.basename(n.fileName).split('.')[0] + '.' + \
os.path.basename(n.fileName).split('.')[1] + '.png'
# check uniqueness of parameter
param1 = Parameter.objects.get(standard_name=n.get_metadata(
bandID=speedBandNum, key='standard_name'))
param2 = Parameter.objects.get(standard_name=n.get_metadata(
bandID=dirBandNum, key='standard_name'))
n.write_figure(os.path.join(mp, filename),
bands=speedBandNum,
mask_array=n['swathmask'],
mask_lut={0: [128, 128, 128]},
transparency=[128, 128, 128])
# Get DatasetParameter
dsp1, created = DatasetParameter.objects.get_or_create(
dataset=ds, parameter=param1)
# Create Visualization
geom, created = GeographicLocation.objects.get_or_create(
geometry=WKTReader().read(n.get_border_wkt()))
vv, created = Visualization.objects.get_or_create(
uri='file://localhost%s/%s' % (mp, filename),
title='%s' % (param1.standard_name),
geographic_location=geom)
# Create VisualizationParameter
vp, created = VisualizationParameter.objects.get_or_create(
visualization=vv, ds_parameter=dsp1)
return ds, True
def update_geophysical_doppler(dopplerFile, t0, t1, swath, sensor='ASAR',
platform='ENVISAT'):
dop2correct = Doppler(dopplerFile)
bandnum = dop2correct._get_band_number({
'standard_name':
'surface_backwards_doppler_centroid_frequency_shift_of_radar_wave'
})
polarization = dop2correct.get_metadata(bandID=bandnum, key='polarization')
lon,lat = dop2correct.get_geolocation_grids()
indmidaz = lat.shape[0]/2
indmidra = lat.shape[1]/2
if lat[indmidaz,indmidra]>lat[0,indmidra]:
use_pass = '******'
else:
use_pass = '******'
# Get datasets
DS = Dataset.objects.filter(source__platform__short_name=platform,
source__instrument__short_name=sensor)
dopDS = DS.filter(
parameters__short_name = 'dca',
time_coverage_start__gte = t0,
time_coverage_start__lt = t1
)
swath_files = []
for dd in dopDS:
try:
fn = dd.dataseturi_set.get(
uri__endswith='subswath%s.nc' %swath).uri
except DatasetURI.DoesNotExist:
continue
n = Doppler(fn)
try:
dca = n.anomaly(pol=polarization)
except OptionError: # wrong polarization..
continue
lon,lat=n.get_geolocation_grids()
indmidaz = lat.shape[0]/2
indmidra = lat.shape[1]/2
if lat[indmidaz,indmidra]>lat[0,indmidra]:
orbit_pass = '******'
else:
orbit_pass = '******'
if use_pass==orbit_pass:
swath_files.append(fn)
valid_land = np.array([])
valid = np.array([])
for ff in swath_files:
n = Nansat(ff)
view_bandnum = n._get_band_number({
'standard_name': 'sensor_view_angle'
})
std_bandnum = n._get_band_number({
'standard_name': \
'standard_deviation_of_surface_backwards_doppler_centroid_frequency_shift_of_radar_wave',
})
pol = n.get_metadata(bandID=std_bandnum, key='polarization')
# For checking when antenna pattern changes
if valid.shape==(0,):
valid = n['valid_doppler']
dca0 = n['dca']
dca0[n['valid_doppler']==0] = np.nan
dca0[n['valid_sea_doppler']==1] = dca0[n['valid_sea_doppler']==1] - \
n['fww'][n['valid_sea_doppler']==1]
view_angle0 = n[view_bandnum]
else:
validn = n['valid_doppler']
dca0n = n['dca']
dca0n[n['valid_doppler']==0] = np.nan
dca0n[n['valid_sea_doppler']==1] = dca0n[n['valid_sea_doppler']==1] - \
n['fww'][n['valid_sea_doppler']==1]
view_angle0n = n[view_bandnum]
if not validn.shape==valid.shape:
if validn.shape[1] > valid.shape[1]:
valid = np.resize(valid, (valid.shape[0], validn.shape[1]))
dca0 = np.resize(dca0, (dca0.shape[0], dca0n.shape[1]))
view_angle0 = np.resize(view_angle0,
(view_angle0.shape[0], view_angle0n.shape[1]))
else:
validn = np.resize(validn, (validn.shape[0],
valid.shape[1]))
dca0n = np.resize(dca0n, (dca0n.shape[0], dca0.shape[1]))
view_angle0n = np.resize(view_angle0n,
(view_angle0n.shape[0], view_angle0.shape[1]))
valid = np.concatenate((valid, validn))
dca0 = np.concatenate((dca0, dca0n))
view_angle0 = np.concatenate((view_angle0, view_angle0n))
if valid_land.shape==(0,):
valid_land = n['valid_land_doppler'][n['valid_land_doppler'].any(axis=1)]
dca = n['dca'][n['valid_land_doppler'].any(axis=1)]
view_angle = n[view_bandnum][n['valid_land_doppler'].any(axis=1)]
std_dca = n[std_bandnum][n['valid_land_doppler'].any(axis=1)]
else:
vn = n['valid_land_doppler'][n['valid_land_doppler'].any(axis=1)]
dcan = n['dca'][n['valid_land_doppler'].any(axis=1)]
view_angle_n = n[view_bandnum][n['valid_land_doppler'].any(axis=1)]
std_dca_n = n[std_bandnum][n['valid_land_doppler'].any(axis=1)]
if not vn.shape==valid_land.shape:
# Resize arrays - just for visual inspection. Actual interpolation
# is view angle vs doppler anomaly
if vn.shape[1] > valid_land.shape[1]:
valid_land = np.resize(valid_land, (valid_land.shape[0],
vn.shape[1]))
dca = np.resize(dca, (dca.shape[0],
vn.shape[1]))
view_angle = np.resize(view_angle, (view_angle.shape[0],
vn.shape[1]))
std_dca = np.resize(std_dca, (std_dca.shape[0],
vn.shape[1]))
if vn.shape[1] < valid_land.shape[1]:
vn = np.resize(vn, (vn.shape[0], valid_land.shape[1]))
dcan = np.resize(dcan, (dcan.shape[0], valid_land.shape[1]))
view_angle_n = np.resize(view_angle_n, (view_angle_n.shape[0], valid_land.shape[1]))
std_dca_n = np.resize(std_dca_n, (std_dca_n.shape[0], valid_land.shape[1]))
valid_land = np.concatenate((valid_land, vn))
dca = np.concatenate((dca, dcan))
view_angle = np.concatenate((view_angle, view_angle_n))
std_dca = np.concatenate((std_dca, std_dca_n))
view_angle0 = view_angle0.flatten()
dca0 = dca0.flatten()
view_angle0 = np.delete(view_angle0, np.where(np.isnan(dca0)))
dca0 = np.delete(dca0, np.where(np.isnan(dca0)))
ind = np.argsort(view_angle0)
view_angle0 = view_angle0[ind]
dca0 = dca0[ind]
# Set dca, view_angle and std_dca to nan where not land
dca[valid_land==0] = np.nan
std_dca[valid_land==0] = np.nan
view_angle[valid_land==0] = np.nan
dca = dca.flatten()
std_dca = std_dca.flatten()
view_angle = view_angle.flatten()
dca = np.delete(dca, np.where(np.isnan(dca)))
std_dca = np.delete(std_dca, np.where(np.isnan(std_dca)))
view_angle = np.delete(view_angle, np.where(np.isnan(view_angle)))
ind = np.argsort(view_angle)
view_angle = view_angle[ind]
dca = dca[ind]
std_dca = std_dca[ind]
freqLims = [-200,200]
# Show this in presentation:
plt.subplot(2,1,1)
count, anglebins, dcabins, im = plt.hist2d(view_angle0, dca0, 100, cmin=1,
range=[[np.min(view_angle), np.max(view_angle)], freqLims])
plt.colorbar()
plt.title('Wind Doppler subtracted')
plt.subplot(2,1,2)
count, anglebins, dcabins, im = plt.hist2d(view_angle, dca, 100, cmin=1,
range=[[np.min(view_angle), np.max(view_angle)], freqLims])
plt.colorbar()
plt.title('Doppler over land')
#plt.show()
plt.close()
countLims = 200
#{
# 0: 600,
# 1: 250,
# 2: 500,
# 3: 140,
# 4: 130,
#}
dcabins_grid, anglebins_grid = np.meshgrid(dcabins[:-1], anglebins[:-1])
anglebins_vec = anglebins_grid[count>countLims]
dcabins_vec = dcabins_grid[count>countLims]
#anglebins_vec = anglebins_grid[count>countLims[swath]]
#dcabins_vec = dcabins_grid[count>countLims[swath]]
va4interp = []
rb4interp = []
std_rb4interp = []
for i in range(len(anglebins)-1):
if i==0:
ind0 = 0
else:
ind0 = np.where(view_angle>anglebins[i])[0][0]
ind1 = np.where(view_angle<=anglebins[i+1])[0][-1]
va4interp.append(np.mean(view_angle[ind0:ind1]))
rb4interp.append(np.median(dca[ind0:ind1]))
std_rb4interp.append(np.std(dca[ind0:ind1]))
va4interp = np.array(va4interp)
rb4interp = np.array(rb4interp)
std_rb4interp = np.array(std_rb4interp)
van = dop2correct['sensor_view']
rbfull = van.copy()
rbfull[:,:] = np.nan
# Is there a more efficient method than looping?
import time
start_time = time.time()
for ii in range(len(anglebins)-1):
vaii0 = anglebins[ii]
vaii1 = anglebins[ii+1]
rbfull[(van>=vaii0) & (van<=vaii1)] = \
np.median(dca[(view_angle>=vaii0) & (view_angle<=vaii1)])
#print("--- %s seconds ---" % (time.time() - start_time))
plt.plot(np.mean(van, axis=0), np.mean(rbfull, axis=0), '.')
#plt.plot(anglebins_vec, dcabins_vec, '.')
#plt.show()
plt.close()
#guess = [.1,.1,.1,.1,.1,.1]
#[a,b,c,d,e,f], params_cov = optimize.curve_fit(rb_model_func,
# va4interp, rb4interp, guess)
# #anglebins_vec, dcabins_vec, guess)
#n = Doppler(swath_files[0])
#van = np.mean(dop2correct['sensor_view'], axis=0)
#plt.plot(van, rb_model_func(van,a,b,c,d,e,f), 'r--')
#plt.plot(anglebins_vec, dcabins_vec, '.')
#plt.show()
#ww = 1./std_rb4interp
#ww[np.isinf(ww)] = 0
#rbinterp = UnivariateSpline(
# va4interp,
# rb4interp,
# w = ww,
# k = 5
# )
#van = dop2correct['sensor_view']
#y = rbinterp(van.flatten())
#rbfull = y.reshape(van.shape)
#plt.plot(np.mean(van, axis=0), np.mean(rbfull, axis=0), 'r--')
#plt.plot(anglebins_vec, dcabins_vec, '.')
#plt.show()
band_name = 'fdg_corrected'
fdg = dop2correct.anomaly() - rbfull
#plt.imshow(fdg, vmin=-60, vmax=60)
#plt.colorbar()
#plt.show()
dop2correct.add_band(array=fdg,
parameters={
'wkv':'surface_backwards_doppler_frequency_shift_of_radar_wave_due_to_surface_velocity',
'name': band_name
}
)
current = -(np.pi*(fdg - dop2correct['fww']) / 112 /
np.sin(dop2correct['incidence_angle']*np.pi/180))
dop2correct.add_band(array=current,
parameters={'name': 'current', 'units': 'm/s', 'minmax': '-2 2'}
)
land = np.array([])
# add land data for accuracy calculation
if land.shape==(0,):
land = dop2correct['valid_land_doppler'][dop2correct['valid_land_doppler'].any(axis=1)]
land_fdg = fdg[dop2correct['valid_land_doppler'].any(axis=1)]
else:
landn = dop2correct['valid_land_doppler'][dop2correct['valid_land_doppler'].any(axis=1)]
land_fdgn = fdg[dop2correct['valid_land_doppler'].any(axis=1)]
if not landn.shape==land.shape:
if landn.shape[1] > land.shape[1]:
land = np.resize(land, (land.shape[0], landn.shape[1]))
land_fdg = np.resize(land_fdg, (land_fdg.shape[0],
land_fdgn.shape[1]))
if landn.shape[1] < land.shape[1]:
landn = np.resize(landn, (landn.shape[0], land.shape[1]))
land_fdgn = np.resize(land_fdgn, (land_fdgn.shape[0],
land.shape[1]))
land = np.concatenate((land, landn))
land_fdg = np.concatenate((land_fdg, land_fdgn))
module = 'sar_doppler'
DS = Dataset.objects.get(dataseturi__uri__contains=dop2correct.fileName)
#fn = '/mnt/10.11.12.232/sat_downloads_asar/level-0/2010-01/gsar_rvl/' \
# + dop2correct.fileName.split('/')[-2]+'.gsar'
mp = media_path(module, nansat_filename( DS.dataseturi_set.get(
uri__endswith='gsar').uri))
ppath = product_path(module, nansat_filename( DS.dataseturi_set.get(
uri__endswith='gsar').uri))
# See managers.py -- this must be generalized!
pngfilename = '%s_subswath_%d.png'%(band_name, swath)
ncfilename = '%s_subswath_%d.nc'%(band_name, swath)
# Export to new netcdf with fdg as the only band
expFile = os.path.join(ppath, ncfilename)
print 'Exporting file: %s\n\n' %expFile
dop2correct.export(expFile, bands=[dop2correct._get_band_number(band_name)])
ncuri = os.path.join('file://localhost', expFile)
new_uri, created = DatasetURI.objects.get_or_create(uri=ncuri,
dataset=DS)
# Reproject to leaflet projection
xlon, xlat = dop2correct.get_corners()
dom = Domain(NSR(3857),
'-lle %f %f %f %f -tr 1000 1000' % (
xlon.min(), xlat.min(), xlon.max(), xlat.max()))
dop2correct.reproject(dom, eResampleAlg=1, tps=True)
# Update figure
dop2correct.write_figure(os.path.join(mp, pngfilename),
clim = [-60,60],
bands=band_name,
mask_array=dop2correct['swathmask'],
mask_lut={0:[128,128,128]}, transparency=[128,128,128])
print("--- %s seconds ---" % (time.time() - start_time))
land_fdg[land==0] = np.nan
print('Standard deviation over land: %.2f' %np.nanstd(land_fdg))