def test_download_with_cache():
filename = utils.download(TESTDATA['cmip5_tasmax_2006_nc'], cache=paths.cache)
assert os.path.basename(filename) == 'tasmax_Amon_MPI-ESM-MR_rcp45_r1i1p1_200601-200612.nc'
def reanalyses( start=1948, end=None, variable='slp', dataset='NCEP'):
"""
Fetches the reanalysis data (NCEP, 20CR or ERA_20C) to local file system
:param start: int for start year to fetch source data
:param end: int for end year to fetch source data (if None, current year will be the end)
:param variable: variable name (default='slp'), geopotential height is given as e.g. z700
:param dataset: default='NCEP'
:return list: list of path/files.nc
"""
try:
from datetime import datetime as dt
if end == None:
end = dt.now().year
obs_data = []
if start == None:
if dataset == 'NCEP':
start = 1948
if dataset == '20CR':
start = 1851
logger.info('start / end date set')
except Exception as e:
msg = "get_OBS module failed to get start end dates %s " % e
logger.debug(msg)
raise Exception(msg)
if 'z' in variable:
level = variable.strip('z')
else:
level = None
logger.info('level: %s' % level)
try:
for year in range(start, end + 1):
try:
if dataset == 'NCEP':
if variable == 'slp':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/surface/%s.%s.nc' % (variable, year)
elif 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.%s.nc' % ( year)
elif dataset == '20CRV2':
if variable == 'prmsl':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/monolevel/prmsl.%s.nc' % year
if 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/pressure/hgt.%s.nc' % ( year )
elif dataset == '20CRV2c':
if variable == 'prmsl':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/monolevel/prmsl.%s.nc' % year
if 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/pressure/hgt.%s.nc' % ( year )
else:
logger.error('Dataset %s not known' % dataset)
except Exception as e:
msg = "could not set url: %s " % e
logger.debug(msg)
raise Exception(msg)
try:
obs_data.append(utils.download(url, cache=True))
except:
msg = "wget failed on {0}.".format(url)
logger.debug(msg)
raise Exception(msg)
logger.info('Reanalyses data fetched for %s files' % len(obs_data))
except Exception as e:
msg = "get reanalyses module failed to fetch data %s " % e
logger.debug(msg)
raise Exception(msg)
if level == None:
data = obs_data
else:
logger.info('get level: %s' % level)
data = get_level(obs_data, level=level)
return data
def _handler(self, request, response):
init_process_logger('log.txt')
response.outputs['output_log'].file = 'log.txt'
response.update_status('Start process', 0)
try:
LOGGER.info('reading the arguments')
resources = archiveextract(
resource=rename_complexinputs(request.inputs['resource']))
period = request.inputs['period']
period = period[0].data
indices = [inpt.data for inpt in request.inputs['indices']]
archive_format = request.inputs['archive_format'][0].data
LOGGER.info(
"all arguments read in nr of files in resources: {}".foirmat(
len(resources)))
except Exception as ex:
msg = 'failed to read in the arguments: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
gbif_url = request.inputs['gbif'][0].data
csv_file = download(gbif_url)
LOGGER.info('CSV file fetched sucessfully: %s' % csv_file)
except Exception as ex:
msg = 'failed to fetch GBIF file: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
response.update_status('read in latlon coordinates', 10)
latlon = sdm.latlon_gbifcsv(csv_file)
LOGGER.info('got occurence coordinates %s ' % csv_file)
except Exception as ex:
msg = 'failed to extract the latlon points from file {}: {}'.format(
csv_file, str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
response.update_status('plot map', 20)
occurence_map = map_gbifoccurrences(latlon)
LOGGER.info('GBIF occourence ploted')
except Exception as ex:
msg = 'failed to plot occurence map: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
#################################
# calculate the climate indices
#################################
# get the indices
try:
response.update_status('start calculation of indices', 30)
ncs_indices = sdm.get_indices(resource=resources, indices=indices)
LOGGER.info('indice calculation done')
except Exception as ex:
msg = 'failed to calculate indices: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
# sort indices
indices_dic = sdm.sort_indices(ncs_indices)
LOGGER.info('indice files sorted in dictionary')
except Exception as ex:
msg = 'failed to sort indices: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
indices_dic = {'dummy': []}
ncs_references = []
species_files = []
stat_infos = []
PAmask_pngs = []
response.update_status('Start processing for {} datasets'.format(
len(indices_dic.keys())))
for count, key in enumerate(indices_dic.keys()):
try:
status_nr = 40 + count * 10
response.update_status('Start processing of {}'.format(key),
status_nr)
ncs = indices_dic[key]
LOGGER.info('with {} files'.format(len(ncs)))
try:
response.update_status('generating the PA mask', 20)
PAmask = sdm.get_PAmask(coordinates=latlon, nc=ncs[0])
LOGGER.info('PA mask sucessfully generated')
except Exception as ex:
msg = 'failed to generate the PA mask: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
response.update_status('Ploting PA mask', 25)
PAmask_pngs.extend([map_PAmask(PAmask)])
except Exception as ex:
msg = 'failed to plot the PA mask: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
ncs_reference = sdm.get_reference(ncs_indices=ncs,
period=period)
ncs_references.extend(ncs_reference)
LOGGER.info('reference indice calculated {}'.format(
ncs_references))
except Exception as ex:
msg = 'failed to calculate the reference: {}'.format(
str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
gam_model, predict_gam, gam_info = sdm.get_gam(
ncs_reference, PAmask)
stat_infos.append(gam_info)
response.update_status('GAM sucessfully trained',
status_nr + 5)
except Exception as ex:
msg = 'failed to train GAM for {}: {}'.format(key, str(ex))
LOGGER.debug(msg)
raise Exception(msg)
try:
prediction = sdm.get_prediction(gam_model, ncs)
response.update_status('prediction done', status_nr + 7)
except Exception as ex:
msg = 'failed to predict tree occurence: {}'.format(
str(ex))
LOGGER.exception(msg)
raise Exception(msg)
#
# try:
# response.update_status('land sea mask for predicted data', status_nr + 8)
# from numpy import invert, isnan, nan, broadcast_arrays # , array, zeros, linspace, meshgrid
# mask = invert(isnan(PAmask))
# mask = broadcast_arrays(prediction, mask)[1]
# prediction[mask is False] = nan
# except:
# LOGGER.debug('failed to mask predicted data')
try:
species_files.append(sdm.write_to_file(ncs[0], prediction))
LOGGER.info('Favourability written to file')
except Exception as ex:
msg = 'failed to write species file: {}'.format(str(ex))
LOGGER.debug(msg)
raise Exception(msg)
except Exception as ex:
msg = 'failed to process SDM chain for {} : {}'.format(
key, str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
archive_indices = archive(ncs_indices, format=archive_format)
LOGGER.info('indices added to archive')
except Exception as ex:
msg = 'failed adding indices to archive: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
archive_indices = tempfile.mkstemp(suffix='.tar',
prefix='foobar-',
dir='.')
try:
archive_references = archive(ncs_references, format=archive_format)
LOGGER.info('indices reference added to archive')
except Exception as ex:
msg = 'failed adding reference indices to archive: {}'.format(
str(ex))
LOGGER.exception(msg)
raise Exception(msg)
archive_references = tempfile.mkstemp(suffix='.tar',
prefix='foobar-',
dir='.')
try:
archive_prediction = archive(species_files, format=archive_format)
LOGGER.info('species_files added to archive')
except Exception as ex:
msg = 'failed adding species_files indices to archive: {}'.format(
str(ex))
LOGGER.exception(msg)
raise Exception(msg)
try:
stat_infosconcat = pdfmerge(stat_infos)
LOGGER.debug('pngs {}'.format(PAmask_pngs))
PAmask_png = concat_images(PAmask_pngs, orientation='h')
LOGGER.info('stat infos pdfs and mask pngs merged')
except Exception as ex:
msg = 'failed to concat images: {}'.format(str(ex))
LOGGER.exception(msg)
raise Exception(msg)
_, stat_infosconcat = tempfile.mkstemp(suffix='.pdf',
prefix='foobar-',
dir='.')
_, PAmask_png = tempfile.mkstemp(suffix='.png',
prefix='foobar-',
dir='.')
# self.output_csv.setValue(csv_file)
response.outputs['output_gbif'].file = occurence_map
response.outputs['output_PA'].file = PAmask_png
response.outputs['output_indices'].file = archive_indices
response.outputs['output_reference'].file = archive_references
response.outputs['output_prediction'].file = archive_prediction
response.outputs['output_info'].file = stat_infosconcat
response.update_status('done', 100)
return response
def execute(self):
logger.info('Start process')
init_process_logger('log.txt')
self.output_log.setValue('log.txt')
from datetime import datetime as dt
from flyingpigeon import weatherregimes as wr
from tempfile import mkstemp
################################
# reading in the input arguments
################################
try:
resource = self.getInputValues(identifier='resource')
url_Rdat = self.getInputValues(identifier='Rdat')[0]
url_dat = self.getInputValues(identifier='dat')[0]
url_ref_file = self.getInputValues(
identifier='netCDF') # can be None
season = self.getInputValues(identifier='season')[0]
period = self.getInputValues(identifier='period')[0]
anualcycle = self.getInputValues(identifier='anualcycle')[0]
except Exception as e:
logger.debug('failed to read in the arguments %s ' % e)
try:
start = dt.strptime(period.split('-')[0], '%Y%m%d')
end = dt.strptime(period.split('-')[1], '%Y%m%d')
# kappa = int(self.getInputValues(identifier='kappa')[0])
logger.info('period %s' % str(period))
logger.info('season %s' % str(season))
logger.info('read in the arguments')
logger.info('url_ref_file: %s' % url_ref_file)
logger.info('url_Rdat: %s' % url_Rdat)
logger.info('url_dat: %s' % url_dat)
except Exception as e:
logger.debug('failed to convert arguments %s ' % e)
############################
# fetching trainging data
############################
from flyingpigeon.utils import download, get_time
from os.path import abspath
try:
dat = abspath(download(url_dat))
Rdat = abspath(download(url_Rdat))
logger.info('training data fetched')
except Exception as e:
logger.error('failed to fetch training data %s' % e)
##########################################################
# get the required bbox and time region from resource data
##########################################################
# from flyingpigeon.weatherregimes import get_level
from flyingpigeon.ocgis_module import call
from flyingpigeon.utils import get_variable
time_range = [start, end]
variable = get_variable(resource)
if len(url_ref_file) > 0:
ref_file = download(url_ref_file[0])
model_subset = call(
resource=resource,
variable=variable,
time_range=
time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
regrid_destination=ref_file,
regrid_options='bil')
logger.info('Dataset subset with regridding done: %s ' %
model_subset)
else:
model_subset = call(
resource=resource,
variable=variable,
time_range=
time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
)
logger.info('Dataset time period extracted: %s ' % model_subset)
#######################
# computing anomalies
#######################
cycst = anualcycle.split('-')[0]
cycen = anualcycle.split('-')[0]
reference = [
dt.strptime(cycst, '%Y%m%d'),
dt.strptime(cycen, '%Y%m%d')
]
model_anomal = wr.get_anomalies(model_subset, reference=reference)
#####################
# extracting season
#####################
model_season = wr.get_season(model_anomal, season=season)
#######################
# call the R scripts
#######################
import shlex
import subprocess
from flyingpigeon import config
from os.path import curdir, exists, join
try:
rworkspace = curdir
Rsrc = config.Rsrc_dir()
Rfile = 'weatherregimes_projection.R'
yr1 = start.year
yr2 = end.year
time = get_time(model_season, format='%Y%m%d')
# ip, output_graphics = mkstemp(dir=curdir ,suffix='.pdf')
ip, file_pca = mkstemp(dir=curdir, suffix='.txt')
ip, file_class = mkstemp(dir=curdir, suffix='.Rdat')
ip, output_frec = mkstemp(dir=curdir, suffix='.txt')
args = [
'Rscript',
join(Rsrc, Rfile),
'%s/' % curdir,
'%s/' % Rsrc,
'%s' % model_season,
'%s' % variable,
'%s' % str(time).strip("[]").replace("'", "").replace(" ", ""),
# '%s' % output_graphics,
'%s' % dat,
'%s' % Rdat,
'%s' % file_pca,
'%s' % file_class,
'%s' % output_frec,
'%s' % season,
'%s' % start.year,
'%s' % end.year,
'%s' % 'MODEL'
]
logger.info('Rcall builded')
except Exception as e:
msg = 'failed to build the R command %s' % e
logger.error(msg)
raise Exception(msg)
try:
output, error = subprocess.Popen(
args, stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()
# , shell=True
logger.info('R outlog info:\n %s ' % output)
logger.debug('R outlog errors:\n %s ' % error)
if len(output) > 0:
self.status.set('**** weatherregime in R suceeded', 90)
else:
logger.error('NO! output returned from R call')
except Exception as e:
msg = 'weatherregime in R %s ' % e
logger.error(msg)
raise Exception(msg)
#################
# set the outputs
#################
# self.Routput_graphic.setValue( output_graphics )
self.output_pca.setValue(file_pca)
self.output_classification.setValue(file_class)
self.output_netcdf.setValue(model_season)
self.output_frequency.setValue(output_frec)
def reanalyses(start=1948,
end=None,
variable='slp',
dataset='NCEP',
timres='day',
getlevel=True):
"""
Fetches the reanalysis data (NCEP, 20CR or ERA_20C) to local file system
:param start: int for start year to fetch source data
:param end: int for end year to fetch source data (if None, current year will be the end)
:param variable: variable name (default='slp'), geopotential height is given as e.g. z700
:param dataset: default='NCEP'
:return list: list of path/files.nc
"""
# used for NETCDF convertion
from netCDF4 import Dataset
from os import path, system
from flyingpigeon.ocgis_module import call
from shutil import move
# used for NETCDF convertion
try:
from datetime import datetime as dt
if end is None:
end = dt.now().year
obs_data = []
if start is None:
if dataset == 'NCEP':
start = 1948
if dataset == '20CR':
start = 1851
LOGGER.info('start / end date set')
except:
msg = "get_OBS module failed to get start end dates"
LOGGER.exception(msg)
raise Exception(msg)
if 'z' in variable:
level = variable.strip('z')
else:
level = None
LOGGER.info('level: %s' % level)
try:
for year in range(start, end + 1):
LOGGER.debug('fetching single file for %s year %s ' %
(dataset, year))
try:
if dataset == 'NCEP':
if variable == 'slp':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/surface/%s.%s.nc' % (
variable, year) # noqa
if 'z' in variable:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.%s.nc' % (
year) # noqa
elif dataset == '20CRV2':
if variable == 'prmsl':
if timres == '6h':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/monolevel/prmsl.%s.nc' % year # noqa
else:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/Dailies/monolevel/prmsl.%s.nc' % year # noqa
if 'z' in variable:
if timres == '6h':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/pressure/hgt.%s.nc' % (
year) # noqa
else:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/Dailies/pressure/hgt.%s.nc' % (
year) # noqa
elif dataset == '20CRV2c':
if variable == 'prmsl':
if timres == '6h':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/monolevel/prmsl.%s.nc' % year # noqa
else:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/Dailies/monolevel/prmsl.%s.nc' % year # noqa
if 'z' in variable:
if timres == '6h':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/pressure/hgt.%s.nc' % (
year) # noqa
else:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/Dailies/pressure/hgt.%s.nc' % (
year) # noqa
else:
LOGGER.debug('Dataset %s not known' % dataset)
LOGGER.debug('url: %s' % url)
except:
msg = "could not set url"
LOGGER.exception(msg)
try:
df = utils.download(url, cache=True)
LOGGER.debug('single file fetched %s ' % year)
# convert to NETCDF4_CLASSIC
try:
ds = Dataset(df)
df_time = ds.variables['time']
# Here, need to check not just calendar, but that file is ncdf_classic already...
if (hasattr(df_time, 'calendar')) is False:
p, f = path.split(path.abspath(df))
LOGGER.debug("path = %s , file %s " % (p, f))
# May be an issue if several users are working at the same time
move(df, f)
conv = call(resource=f,
output_format_options={
'data_model': 'NETCDF4_CLASSIC'
},
dir_output=p,
prefix=f.replace('.nc', ''))
obs_data.append(conv)
LOGGER.debug('file %s to NETCDF4_CLASSIC converted' %
conv)
# Cleaning, could be 50gb... for each (!) user
# TODO Check how links work
cmdrm = 'rm -f %s' % (f)
system(cmdrm)
else:
obs_data.append(df)
ds.close()
except:
LOGGER.exception('failed to convert into NETCDF4_CLASSIC')
except:
msg = "download failed on {0}.".format(url)
LOGGER.exception(msg)
LOGGER.info('Reanalyses data fetched for %s files' % len(obs_data))
except:
msg = "get reanalyses module failed to fetch data"
LOGGER.exception(msg)
raise Exception(msg)
if (level is None) or (getlevel == False):
data = obs_data
else:
LOGGER.info('get level: %s' % level)
data = get_level(obs_data, level=level)
return data
def reanalyses(start=1948, end=None, variable='slp', dataset='NCEP'):
"""
Fetches the reanalysis data (NCEP, 20CR or ERA_20C) to local file system
:param start: int for start year to fetch source data
:param end: int for end year to fetch source data (if None, current year will be the end)
:param variable: variable name (default='slp'), geopotential height is given as e.g. z700
:param dataset: default='NCEP'
:return list: list of path/files.nc
"""
try:
from datetime import datetime as dt
if end == None:
end = dt.now().year
obs_data = []
if start == None:
if dataset == 'NCEP':
start = 1948
if dataset == '20CR':
start = 1851
logger.info('start / end date set')
except Exception as e:
msg = "get_OBS module failed to get start end dates %s " % e
logger.debug(msg)
raise Exception(msg)
if 'z' in variable:
level = variable.strip('z')
else:
level = None
logger.info('level: %s' % level)
try:
for year in range(start, end + 1):
try:
if dataset == 'NCEP':
if variable == 'slp':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/surface/%s.%s.nc' % (
variable, year)
elif 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.%s.nc' % (
year)
elif dataset == '20CRV2':
if variable == 'prmsl':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/monolevel/prmsl.%s.nc' % year
if 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/pressure/hgt.%s.nc' % (
year)
elif dataset == '20CRV2c':
if variable == 'prmsl':
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/monolevel/prmsl.%s.nc' % year
if 'z' in variable:
url = 'http://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/pressure/hgt.%s.nc' % (
year)
else:
logger.error('Dataset %s not known' % dataset)
except Exception as e:
msg = "could not set url: %s " % e
logger.debug(msg)
raise Exception(msg)
try:
obs_data.append(utils.download(url, cache=True))
except:
msg = "wget failed on {0}.".format(url)
logger.debug(msg)
raise Exception(msg)
logger.info('Reanalyses data fetched for %s files' % len(obs_data))
except Exception as e:
msg = "get reanalyses module failed to fetch data %s " % e
logger.debug(msg)
raise Exception(msg)
if level == None:
data = obs_data
else:
logger.info('get level: %s' % level)
data = get_level(obs_data, level=level)
return data
def reanalyses(start=1948, end=None, variable='slp', dataset='NCEP'):
"""
Fetches the reanalysis data (NCEP, 20CR or ERA_20C) to local file system
:param start: int for start year to fetch source data
:param end: int for end year to fetch source data (if None, current year will be the end)
:param variable: variable name (default='slp'), geopotential height is given as e.g. z700
:param dataset: default='NCEP'
:return list: list of path/files.nc
"""
# used for NETCDF convertion
from os import path
from flyingpigeon.ocgis_module import call
from shutil import move
# used for NETCDF convertion
try:
from datetime import datetime as dt
if end is None:
end = dt.now().year
obs_data = []
if start is None:
if dataset == 'NCEP':
start = 1948
if dataset == '20CR':
start = 1851
LOGGER.info('start / end date set')
except:
msg = "get_OBS module failed to get start end dates"
LOGGER.exception(msg)
raise Exception(msg)
if 'z' in variable:
level = variable.strip('z')
else:
level = None
LOGGER.info('level: %s' % level)
try:
for year in range(start, end + 1):
LOGGER.debug('fetching single file for %s year %s ' %
(dataset, year))
try:
if dataset == 'NCEP':
if variable == 'slp':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/surface/%s.%s.nc' % (
variable, year) # noqa
if 'z' in variable:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.%s.nc' % (
year) # noqa
elif dataset == '20CRV2':
if variable == 'prmsl':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/monolevel/prmsl.%s.nc' % year # noqa
if 'z' in variable:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2/pressure/hgt.%s.nc' % (
year) # noqa
elif dataset == '20CRV2c':
if variable == 'prmsl':
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/monolevel/prmsl.%s.nc' % year # noqa
if 'z' in variable:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/20thC_ReanV2c/pressure/hgt.%s.nc' % (
year) # noqa
else:
LOGGER.debug('Dataset %s not known' % dataset)
LOGGER.debug('url: %s' % url)
except:
msg = "could not set url"
LOGGER.exception(msg)
try:
df = utils.download(url, cache=True)
LOGGER.debug('single file fetched %s ' % year)
# convert to NETCDF4_CLASSIC
try:
p, f = path.split(path.abspath(df))
LOGGER.debug("path = %s , file %s " % (p, f))
move(df, f)
conv = call(resource=f,
output_format_options={
'data_model': 'NETCDF4_CLASSIC'
},
dir_output=p,
prefix=f.replace('.nc', ''))
obs_data.append(conv)
LOGGER.debug('file %s to NETCDF4_CLASSIC converted' % conv)
except:
LOGGER.exception('failed to convert into NETCDF4_CLASSIC')
except:
msg = "download failed on {0}.".format(url)
LOGGER.exception(msg)
LOGGER.info('Reanalyses data fetched for %s files' % len(obs_data))
except:
msg = "get reanalyses module failed to fetch data"
LOGGER.exception(msg)
raise Exception(msg)
if level is None:
data = obs_data
else:
LOGGER.info('get level: %s' % level)
data = get_level(obs_data, level=level)
return data
from flyingpigeon.utils import download
from ocgis import RequestDataset, OcgOperations
variable = 'slp'
year = 2000
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/surface/%s.%s.nc' % (variable, year)
f = download(url)
rd = RequestDataset(f)
ds = OcgOperations(rd,output_format_options={'data_model': 'NETCDF4_CLASSIC'},prefix='converted_to_NETCDF_CLASSIC' ).execute()
ds = OcgOperations(rd,output_format_options={'data_model': 'NETCDF4_CLASSIC'}, output_format = 'nc', prefix='converted_to_NETCDF_CLASSIC' ).execute()
print ds
def execute(self):
logger.info('Start process')
from datetime import datetime as dt
from flyingpigeon import weatherregimes as wr
from tempfile import mkstemp
################################
# reading in the input arguments
################################
try:
resource = self.getInputValues(identifier='resource')
url_Rdat = self.getInputValues(identifier='Rdat')[0]
url_dat = self.getInputValues(identifier='dat')[0]
url_ref_file = self.getInputValues(identifier='netCDF') # can be None
season = self.getInputValues(identifier='season')[0]
period = self.getInputValues(identifier='period')[0]
anualcycle = self.getInputValues(identifier='anualcycle')[0]
except Exception as e:
logger.debug('failed to read in the arguments %s ' % e)
try:
start = dt.strptime(period.split('-')[0] , '%Y%m%d')
end = dt.strptime(period.split('-')[1] , '%Y%m%d')
# kappa = int(self.getInputValues(identifier='kappa')[0])
logger.info('period %s' % str(period))
logger.info('season %s' % str(season))
logger.info('read in the arguments')
logger.info('url_ref_file: %s' % url_ref_file)
logger.info('url_Rdat: %s' % url_Rdat)
logger.info('url_dat: %s' % url_dat)
except Exception as e:
logger.debug('failed to convert arguments %s ' % e)
############################
# fetching trainging data
############################
from flyingpigeon.utils import download, get_time
from os.path import abspath
try:
dat = abspath(download(url_dat))
Rdat = abspath(download(url_Rdat))
logger.info('training data fetched')
except Exception as e:
logger.error('failed to fetch training data %s' % e)
############################################################
### get the required bbox and time region from resource data
############################################################
# from flyingpigeon.weatherregimes import get_level
from flyingpigeon.ocgis_module import call
from flyingpigeon.utils import get_variable
time_range = [start, end]
variable = get_variable(resource)
if len(url_ref_file) > 0:
ref_file = download(url_ref_file[0])
model_subset = call(resource=resource, variable=variable,
time_range=time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
regrid_destination=ref_file, regrid_options='bil')
logger.info('Dataset subset with regridding done: %s ' % model_subset)
else:
model_subset = call(resource=resource, variable=variable,
time_range=time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
)
logger.info('Dataset time period extracted: %s ' % model_subset)
##############################################
### computing anomalies
##############################################
cycst = anualcycle.split('-')[0]
cycen = anualcycle.split('-')[0]
reference = [dt.strptime(cycst,'%Y%m%d'), dt.strptime(cycen,'%Y%m%d')]
model_anomal = wr.get_anomalies(model_subset, reference=reference)
#####################
### extracting season
#####################
model_season = wr.get_season(model_anomal, season=season)
#######################
### call the R scripts
#######################
import shlex
import subprocess
from flyingpigeon import config
from os.path import curdir, exists, join
try:
rworkspace = curdir
Rsrc = config.Rsrc_dir()
Rfile = 'weatherregimes_projection.R'
yr1 = start.year
yr2 = end.year
time = get_time(model_season, format='%Y%m%d')
#ip, output_graphics = mkstemp(dir=curdir ,suffix='.pdf')
ip, file_pca = mkstemp(dir=curdir ,suffix='.txt')
ip, file_class = mkstemp(dir=curdir ,suffix='.Rdat')
ip, output_frec = mkstemp(dir=curdir ,suffix='.txt')
args = ['Rscript', join(Rsrc,Rfile), '%s/' % curdir,
'%s/' % Rsrc,
'%s' % model_season,
'%s' % variable,
'%s' % str(time).strip("[]").replace("'","").replace(" ",""),
# '%s' % output_graphics,
'%s' % dat,
'%s' % Rdat,
'%s' % file_pca,
'%s' % file_class,
'%s' % output_frec,
'%s' % season,
'%s' % start.year,
'%s' % end.year,
'%s' % 'MODEL']
logger.info('Rcall builded')
except Exception as e:
msg = 'failed to build the R command %s' % e
logger.error(msg)
raise Exception(msg)
try:
output,error = subprocess.Popen(args, stdout = subprocess.PIPE, stderr= subprocess.PIPE).communicate() #, shell=True
logger.info('R outlog info:\n %s ' % output)
logger.debug('R outlog errors:\n %s ' % error)
if len(output) > 0:
self.status.set('**** weatherregime in R suceeded', 90)
else:
logger.error('NO! output returned from R call')
except Exception as e:
msg = 'weatherregime in R %s ' % e
logger.error(msg)
raise Exception(msg)
############################################
### set the outputs
############################################
#self.Routput_graphic.setValue( output_graphics )
self.output_pca.setValue( file_pca )
self.output_classification.setValue( file_class )
self.output_netcdf.setValue( model_season )
self.output_frequency.setValue( output_frec )
def _handler(self, request, response):
init_process_logger('log.txt')
response.outputs['output_log'].file = 'log.txt'
response.update_status('execution started at : {}'.format(dt.now()), 5)
################################
# reading in the input arguments
################################
try:
LOGGER.info('read in the arguments')
# resources = self.getInputValues(identifier='resources')
season = request.inputs['season'][0].data
LOGGER.info('season %s', season)
period = request.inputs['period'][0].data
LOGGER.info('period %s', period)
anualcycle = request.inputs['anualcycle'][0].data
start = dt.strptime(period.split('-')[0], '%Y%m%d')
end = dt.strptime(period.split('-')[1], '%Y%m%d')
LOGGER.debug('start: %s , end: %s ' % (start, end))
resource = archiveextract(resource=rename_complexinputs(request.inputs['resource']))
# resource = archiveextract(resource=[res.file for res in request.inputs['resource']])
url_Rdat = request.inputs['Rdat'][0].data
url_dat = request.inputs['dat'][0].data
url_ref_file = request.inputs['netCDF'][0].data # can be None
# season = self.getInputValues(identifier='season')[0]
# period = self.getInputValues(identifier='period')[0]
# anualcycle = self.getInputValues(identifier='anualcycle')[0]
LOGGER.info('period %s' % str(period))
LOGGER.info('season %s' % str(season))
LOGGER.info('read in the arguments')
LOGGER.info('url_ref_file: %s' % url_ref_file)
LOGGER.info('url_Rdat: %s' % url_Rdat)
LOGGER.info('url_dat: %s' % url_dat)
except Exception as e:
LOGGER.debug('failed to convert arguments %s ' % e)
############################
# fetching trainging data
############################
try:
dat = abspath(download(url_dat))
Rdat = abspath(download(url_Rdat))
LOGGER.info('training data fetched')
except Exception as e:
LOGGER.error('failed to fetch training data %s' % e)
##########################################################
# get the required bbox and time region from resource data
##########################################################
# from flyingpigeon.weatherregimes import get_level
try:
from flyingpigeon.ocgis_module import call
from flyingpigeon.utils import get_variable
time_range = [start, end]
variable = get_variable(resource)
if len(url_ref_file) > 0:
ref_file = download(url_ref_file)
model_subset = call(
resource=resource, variable=variable,
time_range=time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
regrid_destination=ref_file, regrid_options='bil')
LOGGER.info('Dataset subset with regridding done: %s ' % model_subset)
else:
model_subset = call(
resource=resource, variable=variable,
time_range=time_range, # conform_units_to=conform_units_to, geom=bbox, spatial_wrapping='wrap',
)
LOGGER.info('Dataset time period extracted: %s ' % model_subset)
except:
LOGGER.exception('failed to make a data subset ')
#######################
# computing anomalies
#######################
try:
cycst = anualcycle.split('-')[0]
cycen = anualcycle.split('-')[0]
reference = [dt.strptime(cycst, '%Y%m%d'), dt.strptime(cycen, '%Y%m%d')]
model_anomal = wr.get_anomalies(model_subset, reference=reference)
#####################
# extracting season
#####################
model_season = wr.get_season(model_anomal, season=season)
except:
LOGGER.exception('failed to compute anualcycle or seasons')
#######################
# call the R scripts
#######################
import shlex
import subprocess
from flyingpigeon import config
from os.path import curdir, exists, join
try:
rworkspace = curdir
Rsrc = config.Rsrc_dir()
Rfile = 'weatherregimes_projection.R'
yr1 = start.year
yr2 = end.year
time = get_time(model_season, format='%Y%m%d')
# ip, output_graphics = mkstemp(dir=curdir ,suffix='.pdf')
ip, file_pca = mkstemp(dir=curdir, suffix='.txt')
ip, file_class = mkstemp(dir=curdir, suffix='.Rdat')
ip, output_frec = mkstemp(dir=curdir, suffix='.txt')
args = ['Rscript', join(Rsrc, Rfile), '%s/' % curdir,
'%s/' % Rsrc,
'%s' % model_season,
'%s' % variable,
'%s' % str(time).strip("[]").replace("'", "").replace(" ", ""),
# '%s' % output_graphics,
'%s' % dat,
'%s' % Rdat,
'%s' % file_pca,
'%s' % file_class,
'%s' % output_frec,
'%s' % season,
'%s' % start.year,
'%s' % end.year,
'%s' % 'MODEL']
LOGGER.info('Rcall builded')
except Exception as e:
msg = 'failed to build the R command %s' % e
LOGGER.error(msg)
raise Exception(msg)
try:
output, error = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
# , shell=True
LOGGER.info('R outlog info:\n %s ' % output)
LOGGER.debug('R outlog errors:\n %s ' % error)
if len(output) > 0:
response.update_status('**** weatherregime in R suceeded', 90)
else:
LOGGER.error('NO! output returned from R call')
except Exception as e:
msg = 'weatherregime in R %s ' % e
LOGGER.error(msg)
raise Exception(msg)
#################
# set the outputs
#################
response.update_status('Set the process outputs ', 95)
response.outputs['output_pca'].file = file_pca
response.outputs['output_classification'].file = file_class
response.outputs['output_netcdf'].file = model_season
response.outputs['output_frequency'].file = output_frec
response.update_status('done', 100)
return response
from flyingpigeon import utils
from ocgis import RequestDataset, OcgOperations, envs
from ocgis.util.large_array import compute
from datetime import datetime as dt
import uuid
# years = range(1948,2018)
years = range(2010, 2012)
ncs = []
for year in years:
url = 'https://www.esrl.noaa.gov/psd/thredds/fileServer/Datasets/ncep.reanalysis.dailyavgs/pressure/hgt.%s.nc' % (year)
ncs.extend(utils.download(url, cache=True))
level_range = [700, 700]
time_range = [dt.strptime('20100315', '%Y%m%d'), dt.strptime('20111210', '%Y%m%d')]
bbox = [-80, 20, 20, 70]
rd = RequestDataset(ncs)
ops = OcgOperations(rd,
time_range=time_range,
level_range=level_range,
geom=bbox,
output_format='nc',
prefix='ocgis_module_optimisation',
add_auxiliary_files=False)
def test_download_with_cache():
filename = utils.download(TESTDATA["cmip5_tasmax_2006_nc"], cache=True)
assert os.path.basename(filename) == "tasmax_Amon_MPI-ESM-MR_rcp45_r1i1p1_200601-200612.nc"
def execute(self):
init_process_logger('log.txt')
self.output_log.setValue('log.txt')
from os.path import basename
from flyingpigeon import sdm
from flyingpigeon.utils import archive, archiveextract, download
self.status.set('Start process', 0)
try:
logger.info('reading the arguments')
resources_raw = self.getInputValues(identifier='resources')
csv_url = self.getInputValues(identifier='gbif')[0]
period = self.getInputValues(identifier='period')
period = period[0]
indices = self.getInputValues(identifier='input_indices')
archive_format = self.archive_format.getValue()
logger.info('indices %s ' % indices)
logger.debug('csv_url %s' % csv_url)
except Exception as e:
logger.error('failed to read in the arguments %s ' % e)
raise
try:
logger.info('set up the environment')
csv_file = download(csv_url)
resources = archiveextract(resources_raw)
except Exception as e:
logger.error('failed to set up the environment %s ' % e)
raise
try:
self.status.set('read in latlon coordinates', 10)
latlon = sdm.latlon_gbifcsv(csv_file)
logger.info('got occurence coordinates %s ' % csv_file)
except Exception as e:
logger.exception(
'failed to extract the latlon points from file: %s: %s' %
(csv_file, e))
try:
self.status.set('plot map', 20)
from flyingpigeon.visualisation import map_gbifoccurrences
# latlon = sdm.latlon_gbifdic(gbifdic)
occurence_map = map_gbifoccurrences(latlon)
except Exception as e:
logger.exception('failed to plot occurence map %s' % e)
#################################
# calculate the climate indices
#################################
# get the indices
ncs_indices = None
try:
self.status.set(
'start calculation of climate indices for %s' % indices, 30)
ncs_indices = sdm.get_indices(resources=resources, indices=indices)
logger.info('indice calculation done')
except:
msg = 'failed to calculate indices'
logger.exception(msg)
raise Exception(msg)
try:
self.status.set('get domain', 30)
domains = set()
for resource in ncs_indices:
# get_domain works only if metadata are set in a correct way
domains = domains.union([basename(resource).split('_')[1]])
if len(domains) == 1:
domain = list(domains)[0]
logger.debug('Domain %s found in indices files' % domain)
else:
logger.error('Not a single domain in indices files %s' %
domains)
except Exception as e:
logger.exception('failed to get domains %s' % e)
try:
self.status.set('generating the PA mask', 20)
PAmask = sdm.get_PAmask(coordinates=latlon, domain=domain)
logger.info('PA mask sucessfully generated')
except Exception as e:
logger.exception('failed to generate the PA mask: %s' % e)
try:
self.status.set('Ploting PA mask', 25)
from flyingpigeon.visualisation import map_PAmask
PAmask_png = map_PAmask(PAmask)
except Exception as e:
logger.exception('failed to plot the PA mask: %s' % e)
try:
# sort indices
indices_dic = None
indices_dic = sdm.sort_indices(ncs_indices)
logger.info('indice files sorted for %s Datasets' %
len(indices_dic.keys()))
except:
msg = 'failed to sort indices'
logger.exception(msg)
raise Exception(msg)
ncs_references = []
species_files = []
stat_infos = []
for count, key in enumerate(indices_dic.keys()):
try:
staus_nr = 40 + count * 10
self.status.set('Start processing of %s' % key, staus_nr)
ncs = indices_dic[key]
logger.info('with %s files' % len(ncs))
try:
ncs_reference = sdm.get_reference(ncs_indices=ncs,
period=period)
ncs_references.extend(ncs_reference)
logger.info('reference indice calculated %s ' %
ncs_references)
except:
msg = 'failed to calculate the reference'
logger.exception(msg)
raise Exception(msg)
try:
gam_model, predict_gam, gam_info = sdm.get_gam(
ncs_reference, PAmask)
stat_infos.append(gam_info)
self.status.set('GAM sucessfully trained', staus_nr + 5)
except Exception as e:
msg = 'failed to train GAM for %s : %s' % (key, e)
logger.debug(msg)
try:
prediction = sdm.get_prediction(gam_model, ncs)
self.status.set('prediction done', staus_nr + 7)
except Exception as e:
msg = 'failed to predict tree occurence %s' % e
logger.exception(msg)
# raise Exception(msg)
try:
self.status.set('land sea mask for predicted data',
staus_nr + 8)
from numpy import invert, isnan, nan, broadcast_arrays # , array, zeros, linspace, meshgrid
mask = invert(isnan(PAmask))
mask = broadcast_arrays(prediction, mask)[1]
prediction[mask is False] = nan
except Exception as e:
logger.debug('failed to mask predicted data: %s' % e)
try:
species_files.append(sdm.write_to_file(ncs[0], prediction))
logger.info('Favourabillity written to file')
except Exception as e:
msg = 'failed to write species file %s' % e
logger.debug(msg)
# raise Exception(msg)
except Exception as e:
msg = 'failed to calculate reference indices. %s ' % e
logger.exception(msg)
raise Exception(msg)
try:
archive_indices = None
archive_indices = archive(ncs_indices, format=archive_format)
logger.info('indices added to archive')
except:
msg = 'failed adding indices to archive'
logger.exception(msg)
raise Exception(msg)
archive_references = None
try:
archive_references = archive(ncs_references, format=archive_format)
logger.info('indices reference added to archive')
except:
msg = 'failed adding reference indices to archive'
logger.exception(msg)
raise Exception(msg)
archive_predicion = None
try:
archive_predicion = archive(species_files, format=archive_format)
logger.info('species_files added to archive')
except:
msg = 'failed adding species_files indices to archive'
logger.exception(msg)
raise Exception(msg)
try:
from flyingpigeon.visualisation import pdfmerge
stat_infosconcat = pdfmerge(stat_infos)
logger.info('stat infos pdfs merged')
except:
logger.exception('failed to concat images')
_, stat_infosconcat = tempfile.mkstemp(suffix='.pdf',
prefix='foobar-',
dir='.')
# self.output_csv.setValue(csv_file)
self.output_gbif.setValue(occurence_map)
self.output_PA.setValue(PAmask_png)
self.output_indices.setValue(archive_indices)
self.output_reference.setValue(archive_references)
self.output_prediction.setValue(archive_predicion)
self.output_info.setValue(stat_infosconcat)
self.status.set('done', 100)