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Adding metadata in export2netcdf)
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@frodedinessen
frodedinessen committed Apr 9, 2024
1 parent aee9497 commit 6cbd3b9
Showing 1 changed file with 102 additions and 139 deletions.
241 changes: 102 additions & 139 deletions sarwind/sarwind.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@
from sarwind.cmod5n import cmod5n_inverse
from matplotlib import pyplot as plt
from matplotlib import cm
import logging
import uuid
import netCDF4


class TimeDiffError(Exception):
pass

Expand Down Expand Up @@ -48,7 +48,7 @@ def __init__(self, sar_image, wind, pixelsize=500, resample_alg=1, *args, **kwar
raise ValueError('Input parameter for SAR and wind direction must be of type string')

super(SARWind, self).__init__(sar_image, *args, **kwargs)

print(wind)
print(sar_image)
self.set_metadata('wind_filename', wind)
Expand Down Expand Up @@ -307,6 +307,99 @@ def export(self, *args, **kwargs):

super(SARWind, self).export(bands=self.get_bands_to_export(bands), *args, **kwargs)

def export2netcdf(self, history_message='', filename='', bands=None):
if not filename:
raise ValueError('Please provide a netcdf filename!')

# Export data to netcdf
self.export(filename=filename, bands=bands)

# Get metadata
metadata = self.get_metadata()

# Updata history
try:
history = metadata['history']
except ValueError:
history = ''

if not history_message:
history_message = '%s: %s, SARWind.export2netcdf(%s)' % \
(datetime.now(tz=pytz.UTC).isoformat(), history, filename.split('/')[-1])
else:
history_message = '%s: %s, %s' % \
(datetime.now(tz=pytz.UTC).isoformat(), history, history_message)

metadata['history'] = history_message

# Get and set dataset id
if 'id' not in metadata.keys():
metadata['id'] = str(uuid.uuid4())

# Set global metadata
sar_filename = metadata['sar_filename'].split('/')[-1]
metadata['title'] = 'Surface wind derived from %s' % sar_filename
metadata['title_no'] = 'Overflate vind utledet fra %s' % sar_filename
metadata['creator_role'] = 'Technical contact'
metadata['creator_type'] = 'person'
metadata['creator_name'] = 'Morten Wergeland Hansen'
metadata['creator_email'] = '[email protected]'
metadata['creator_institution'] = 'Norwegian Meteorological Institute (MET Norway)'
metadata['contributor_name'] = 'Frode Dinessen'
metadata['contributor_role'] = 'Metadata author'
metadata['contributor_email'] = '[email protected]'
metadata['contributor_institution'] = 'Norwegian Meteorological Institute (MET Norway)'
metadata['project'] = 'MET Norway core services (METNCS)'
metadata['institution'] = 'Norwegian Meteorological Institute (MET NOrway)'
metadata['publisher_type'] = 'institution'
metadata['publisher_name'] = 'Norwegian Meteorological Institute'
metadata['publisher_url'] = 'https://www.met.no/'
metadata['publisher_email'] = '[email protected]'
metadata['references'] = 'https://www.researchgate.net/publication/'\
'288260682_CMOD5_An_improved_geophysical_model_function_for_ERS_C-band_scatterometry '\
'(Scientific publication)'
metadata['doi'] = '10.1029/2006JC003743'
metadata['dataset_production_status'] = 'Complete'
metadata['summary'] = 'Derived wind information based on the SENTINEL-1 C-band synthetic' \
' aperture radar mission'
metadata['summary_no'] = 'Beregnet vindstyrkt og vindretning utledet fra SENTINEL-1 '\
'C-band Synthetic Aperture Radar (SAR) mission'
metadata['platform'] = 'Sentinel-1%s' % sar_filename[2]
metadata['platform_vocabulary'] = 'https://vocab.met.no/mmd/Platform/Sentinel-1A'
metadata['instrument'] = 'SAR-C'
metadata['instrument_vocabulary'] = 'https://vocab.met.no/mmd/Instrument/SAR-C'
metadata['Conventions'] = 'CF-1.10,ACDD-1.3'
metadata['keywords'] = 'GCMDSK:Earth Science > Oceans > RADAR backscatter > Wind'
metadata['keywords'] = 'GCMDSK:Earth Science > Oceans > RADAR backscatter > '\
'Wind, GCMDSK:Earth Science > Spectral/Engineering > RADAR > RADAR imagery,'\
'GCMDLOC:Geographic Region > Northern Hemisphere, GCMDLOC:Vertical Location > '\
'Sea Surface, GCMDPROV: Government Agencies-non-US > Norway > NO/MET > '\
'Norwegian Meteorological Institute'
metadata['keywords_vocabulary'] = 'GCMDSK:GCMD Science Keywords:'\
'https://gcmd.earthdata.nasa.gov/kms/concepts/concept_scheme/sciencekeywords,'\
'GCMDPROV:GCMD Providers:https://gcmd.earthdata.nasa.gov/kms/concepts/'\
'concept_scheme/providers,'\
'GCMDLOC:GCMD Locations:https://gcmd.earthdata.nasa.gov/kms/concepts/'\
'concept_scheme/locations'

# Get image boundary
lon, lat = self.get_border()
boundary = 'POLYGON (('
for la, lo in list(zip(lat, lon)):
boundary += '%.2f %.2f, '%(la, lo)
boundary = boundary[:-2]+'))'
# Set bounds as (lat,lon) following ACDD convention and EPSG:4326
metadata['geospatial_bounds'] = boundary
metadata['geospatial_bounds_crs'] = 'EPSG:4326'

metadata['sar_wind_resource'] = \
"https://github.com/metno/met-sar-vind"

# Set metadata from dict
ncid = netCDF4.Dataset(filename, 'r+')
ncid.setncatts(metadata)
ncid.close()

def plot(self, filename=None, numVectorsX=16, show=True,
clim=[0, 20], maskWindAbove=35,
windspeedBand='windspeed', winddirBand='winddirection',
Expand All @@ -316,9 +409,9 @@ def plot(self, filename=None, numVectorsX=16, show=True,
palette = cm.get_cmap('jet')
# sar_windspeed, palette = self._get_masked_windspeed(landmask,
# icemask, windspeedBand=windspeedBand)
except:
raise ValueError('SAR wind has not been calculated,'
'execute calculate_wind(wind_direction) before plotting.')
except ValueError:
print('SAR wind has not been calculated,'
'execute calculate_wind(wind_direction) before plotting.')
sar_windspeed[sar_windspeed > maskWindAbove] = np.nan

winddirReductionFactor = int(np.round(self.vrt.dataset.RasterXSize/numVectorsX))
Expand All @@ -330,7 +423,8 @@ def plot(self, filename=None, numVectorsX=16, show=True,
try: # scaling of wind vector length, if model wind is available
model_windspeed = self['model_windspeed']
model_windspeed = model_windspeed[Y, X]
except:
except ValueError:
print('Model wind not available.')
model_windspeed = 8*np.ones(X.shape)

Ux = np.sin(np.radians(winddir_relative_up[Y, X]))*model_windspeed
Expand All @@ -356,8 +450,8 @@ def plot(self, filename=None, numVectorsX=16, show=True,
dpi = 100.0

fig = plt.figure()
fig.set_size_inches((figSize[1]/dpi, (figSize[0]/dpi)*\
(1+legendFraction + legendPadFraction)))
fig.set_size_inches((figSize[1]/dpi, (figSize[0]/dpi)* \
(1 + legendFraction + legendPadFraction)))
ax = fig.add_axes([0, 0, 1, 1+legendFraction])
ax.set_axis_off()
plt.imshow(sar_windspeed, cmap=palette, interpolation='nearest')
Expand All @@ -376,134 +470,3 @@ def plot(self, filename=None, numVectorsX=16, show=True,
if show:
plt.show()
return fig


def export2netcdf(self, history_message='', filename='', bands=None):

if not filename:
raise ValueError('Please provide a netcdf filename!')

fn = filename
log_message = 'Exporting merged subswaths to %s' % fn

date_created = datetime.now(tz=pytz.UTC)

# Get metadata
metadata = self.get_metadata()

# Updata history
try:
history = metadata['history']
except ValueError:
history = ''
history = ''
if not history_message:
history_message = '%s: %s, SARWind.export2netcdf(%s)' % \
(datetime.now(tz=pytz.UTC).isoformat(), history,filename.split('/')[-1])
else:
history_message = '%s: %s, %s' % \
(datetime.now(tz=pytz.UTC).isoformat(), history, history_message)

metadata['history'] = history_message

# Get and set dataset id
if 'id' not in metadata.keys():
metadata['id'] = str(uuid.uuid4())

# Set global metadata
sar_filename = metadata['sar_filename'].split('/')[-1]
metadata['title'] = 'Surface wind derived from %s' % sar_filename
metadata['title_no'] = 'Overflate vind utledet fra %s' % sar_filename
metadata['creator_role'] = 'Technical contact'
metadata['creator_type'] = 'person'
metadata['creator_name'] = 'Morten Wergeland Hansen'
metadata['creator_email'] = '[email protected]'
metadata['creator_institution'] = 'Norwegian Meteorological Institute (MET Norway)'
metadata['contributor_name'] = 'Frode Dinessen'
metadata['contributor_role'] = 'Metadata author'
metadata['contributor_email'] = '[email protected]'
metadata['contributor_institution'] = 'Norwegian Meteorological Institute (MET Norway)'
metadata['project'] = 'MET Norway core services (METNCS)'
metadata['institution'] = 'Norwegian Meteorological Institute (MET NOrway)'
metadata['publisher_type'] = 'institution'
metadata['publisher_name'] = 'Norwegian Meteorological Institute'
metadata['publisher_url'] = 'https://www.met.no/'
metadata['publisher_email'] = '[email protected]'

metadata['references'] = 'https://www.researchgate.net/publication/288260682_CMOD5_An_improved_geophysical_model_function_for_ERS_C-band_scatterometry (Scientific publication)'
metadata['doi'] = '10.1029/2006JC003743'
metadata['dataset_production_status'] = 'Complete'
metadata['summary'] = 'Derived wind information based on the SENTINEL-1 C-band synthetic aperture radar mission'
metadata['summary_no'] = 'Beregnet vindstyrkt og vindretning utledet fra SENTINEL-1 C-band Synthetic Aperture Radar (SAR) mission'
metadata['platform'] = 'Sentinel-1%s' % sar_filename[2]
metadata['platform_vocabulary'] = 'https://vocab.met.no/mmd/Platform/Sentinel-1A'
metadata['instrument'] = 'SAR-C'
metadata['instrument_vocabulary'] = 'https://vocab.met.no/mmd/Instrument/SAR-C'
metadata['Conventions'] = 'CF-1.10,ACDD-1.3'
metadata['keywords'] = 'GCMDSK:Earth Science > Oceans > RADAR backscatter > Wind'
metadata['keywords'] = 'GCMDSK:Earth Science > Oceans > RADAR backscatter > Wind, GCMDSK:Earth Science > Spectral/Engineering > RADAR > RADAR imagery,' \
'GCMDLOC:Geographic Region > Northern Hemisphere, GCMDLOC:Vertical Location > Sea Surface, ' \
'GCMDPROV: Government Agencies-non-US > Norway > NO/MET > Norwegian Meteorological Institute'
metadata['keywords_vocabulary'] = 'GCMDSK:GCMD Science Keywords:https://gcmd.earthdata.nasa.gov/kms/concepts/concept_scheme/sciencekeywords,' \
'GCMDPROV:GCMD Providers:https://gcmd.earthdata.nasa.gov/kms/concepts/concept_scheme/providers,' \
'GCMDLOC:GCMD Locations:https://gcmd.earthdata.nasa.gov/kms/concepts/concept_scheme/locations'


# Get image boundary
lon,lat= self.get_border()
boundary = 'POLYGON (('
for la, lo in list(zip(lat,lon)):
boundary += '%.2f %.2f, '%(la,lo)
boundary = boundary[:-2]+'))'
# Set bounds as (lat,lon) following ACDD convention and EPSG:4326
metadata['geospatial_bounds'] = boundary
metadata['geospatial_bounds_crs'] = 'EPSG:4326'

metadata['sar_wind_resource'] = \
"https://github.com/metno/met-sar-vind"

# Set metadata from dict
for key, val in metadata.items():
self.set_metadata(key=key, value=val)

# If all_bands=True, everything is exported. This is
# useful when not all the bands in the list above have
# been created
if not bands:
# Bands to be exported
bands = [self.get_band_number("model_windspeed"),
self.get_band_number("windspeed"),
self.get_band_number("U"),
self.get_band_number("V")
]

# Export data to netcdf
logging.debug(log_message)
self.export(filename=fn, bands=bands)

# # Nansat has filename metadata, which is wrong, and adds GCPs as variables.
# # Just remove everything.
# nc = netCDF4.Dataset(fn, 'a')
# if 'filename' in nc.ncattrs():
# nc.delncattr('filename')
# tmp = nc.variables.pop("GCPX")
# tmp = nc.variables.pop("GCPY")
# tmp = nc.variables.pop("GCPZ")
# tmp = nc.variables.pop("GCPPixel")
# tmp = nc.variables.pop("GCPLine")
# nc.close()

# # Add netcdf uri to DatasetURIs
# ncuri = 'file://localhost' + fn

# locked = True
# while locked:
# try:
# new_uri, created = DatasetURI.objects.get_or_create(uri=ncuri, dataset=ds)
# except OperationalError as oe:
# locked = True
# else:
# locked = False
# connection.close()

# return new_uri, created

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