def pre_process(self, *args, **kwargs):
wrf_config = self.get_config(**kwargs)
wrf_home = wrf_config.get('wrf_home')
nfs_metgrid_dir = os.path.join(wrf_config.get('nfs_dir'), 'metgrid')
logging.info('Running em_real...')
em_real_dir = utils.get_em_real_dir(wrf_home)
logging.info('Cleaning up files')
utils.delete_files_with_prefix(em_real_dir, 'met_em*')
utils.delete_files_with_prefix(em_real_dir, 'rsl*')
# Linking met_em.*
# logging.info('Creating met_em.d* symlinks')
logging.info('Copying met_em.d.zip file')
utils.copy_files_with_prefix(nfs_metgrid_dir, 'metgrid.zip',
em_real_dir)
logging.info('Unzipping met_em.d.zip')
ZipFile(os.path.join(em_real_dir, 'metgrid.zip'),
'r',
compression=zipfile.ZIP_DEFLATED).extractall(path=em_real_dir)
logging.info('Cleaning up met_em.d.zip')
os.remove(os.path.join(em_real_dir, 'metgrid.zip'))
def create_daily_gif(start, output_dir, output_filename, output_prefix):
tmp_dir = tempfile.mkdtemp(prefix='tmp_jaxa_daily')
utils.copy_files_with_prefix(
output_dir, output_prefix + '_' + start.strftime('%Y-%m-%d') + '*.png',
tmp_dir)
logging.info('Writing gif ' + output_filename)
gif_list = [os.path.join(tmp_dir, i) for i in sorted(os.listdir(tmp_dir))]
if len(gif_list) > 0:
ext_utils.create_gif(gif_list, os.path.join(output_dir,
output_filename))
else:
logging.info('No images found to create the gif')
logging.info('Cleaning up ' + tmp_dir)
shutil.rmtree(tmp_dir)
def create_rf_plots_wrf(nc_f, plots_output_dir, plots_output_base_dir, lon_min=None, lat_min=None, lon_max=None,
lat_max=None, filter_threshold=0.05, run_prefix='WRF'):
if not all([lon_min, lat_min, lon_max, lat_max]):
lon_min, lat_min, lon_max, lat_max = constants.SRI_LANKA_EXTENT
variables = ext_utils.extract_variables(nc_f, 'RAINC, RAINNC', lat_min, lat_max, lon_min, lon_max)
lats = variables['XLAT']
lons = variables['XLONG']
# cell size is calc based on the mean between the lat and lon points
cz = np.round(np.mean(np.append(lons[1:len(lons)] - lons[0: len(lons) - 1], lats[1:len(lats)]
- lats[0: len(lats) - 1])), 3)
clevs = [0, 1, 2.5, 5, 7.5, 10, 15, 20, 30, 40, 50, 70, 100, 150, 200, 250, 300, 400, 500, 600, 750]
cmap = cm.s3pcpn
basemap = Basemap(projection='merc', llcrnrlon=lon_min, llcrnrlat=lat_min, urcrnrlon=lon_max,
urcrnrlat=lat_max, resolution='h')
data = variables['RAINC'] + variables['RAINNC']
logging.info('Filtering with the threshold %f' % filter_threshold)
data[data < filter_threshold] = 0.0
variables['PRECIP'] = data
prefix = 'wrf_plots'
with TemporaryDirectory(prefix=prefix) as temp_dir:
t0 = dt.datetime.strptime(variables['Times'][0], '%Y-%m-%d_%H:%M:%S')
t1 = dt.datetime.strptime(variables['Times'][1], '%Y-%m-%d_%H:%M:%S')
step = (t1 - t0).total_seconds() / 3600.0
inst_precip = ext_utils.get_two_element_average(variables['PRECIP'])
cum_precip = ext_utils.get_two_element_average(variables['PRECIP'], return_diff=False)
for i in range(1, len(variables['Times'])):
time = variables['Times'][i]
ts = dt.datetime.strptime(time, '%Y-%m-%d_%H:%M:%S')
lk_ts = utils.datetime_utc_to_lk(ts, shift_mins=30)
logging.info('processing %s', time)
# instantaneous precipitation (hourly)
inst_file = os.path.join(temp_dir, 'wrf_inst_' + lk_ts.strftime('%Y-%m-%d_%H:%M:%S'))
ext_utils.create_asc_file(np.flip(inst_precip[i - 1], 0), lats, lons, inst_file + '.asc', cell_size=cz)
title = {
'label': 'Hourly rf for %s LK' % lk_ts.strftime('%Y-%m-%d_%H:%M:%S'),
'fontsize': 30
}
ext_utils.create_contour_plot(inst_precip[i - 1], inst_file + '.png', lat_min, lon_min, lat_max, lon_max,
title, clevs=clevs, cmap=cmap, basemap=basemap)
if (i * step) % 24 == 0:
t = 'Daily rf from %s LK to %s LK' % (
(lk_ts - dt.timedelta(hours=24)).strftime('%Y-%m-%d_%H:%M:%S'), lk_ts.strftime('%Y-%m-%d_%H:%M:%S'))
d = int(i * step / 24) - 1
logging.info('Creating images for D%d' % d)
cum_file = os.path.join(temp_dir, 'wrf_cum_%dd' % d)
if i * step / 24 > 1:
cum_precip_24h = cum_precip[i - 1] - cum_precip[i - 1 - int(24 / step)]
else:
cum_precip_24h = cum_precip[i - 1]
ext_utils.create_asc_file(np.flip(cum_precip_24h, 0), lats, lons, cum_file + '.asc', cell_size=cz)
ext_utils.create_contour_plot(cum_precip_24h, cum_file + '.png', lat_min, lon_min, lat_max, lon_max, t,
clevs=clevs, cmap=cmap, basemap=basemap)
gif_file = os.path.join(temp_dir, 'wrf_inst_%dd' % d)
images = [os.path.join(temp_dir, 'wrf_inst_' + j.strftime('%Y-%m-%d_%H:%M:%S') + '.png') for j in
np.arange(lk_ts - dt.timedelta(hours=24 - step), lk_ts + dt.timedelta(hours=step),
dt.timedelta(hours=step)).astype(dt.datetime)]
ext_utils.create_gif(images, gif_file + '.gif')
logging.info('Creating the zips')
utils.create_zip_with_prefix(temp_dir, '*.png', os.path.join(temp_dir, 'pngs.zip'))
utils.create_zip_with_prefix(temp_dir, '*.asc', os.path.join(temp_dir, 'ascs.zip'))
logging.info('Cleaning up instantaneous pngs and ascs - wrf_inst_*')
utils.delete_files_with_prefix(temp_dir, 'wrf_inst_*.png')
utils.delete_files_with_prefix(temp_dir, 'wrf_inst_*.asc')
logging.info('Copying pngs to ' + plots_output_dir)
utils.move_files_with_prefix(temp_dir, '*.png', plots_output_dir)
logging.info('Copying ascs to ' + plots_output_dir)
utils.move_files_with_prefix(temp_dir, '*.asc', plots_output_dir)
logging.info('Copying gifs to ' + plots_output_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', plots_output_dir)
logging.info('Copying zips to ' + plots_output_dir)
utils.copy_files_with_prefix(temp_dir, '*.zip', plots_output_dir)
plots_latest_dir = os.path.join(plots_output_base_dir, 'latest', run_prefix, os.path.basename(plots_output_dir))
# <nfs>/latest/wrf0 .. 3
utils.create_dir_if_not_exists(plots_latest_dir)
# todo: this needs to be adjusted to handle the multiple runs
logging.info('Copying gifs to ' + plots_latest_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', plots_latest_dir)
def run_em_real(wrf_config):
logging.info('Running em_real...')
wrf_home = wrf_config.get('wrf_home')
em_real_dir = utils.get_em_real_dir(wrf_home)
procs = wrf_config.get('procs')
run_id = wrf_config.get('run_id')
output_dir = utils.create_dir_if_not_exists(
os.path.join(wrf_config.get('nfs_dir'), 'results', run_id, 'wrf'))
archive_dir = utils.create_dir_if_not_exists(
os.path.join(wrf_config.get('archive_dir'), 'results', run_id, 'wrf'))
logging.info('Backup the output dir')
utils.backup_dir(output_dir)
logs_dir = utils.create_dir_if_not_exists(os.path.join(output_dir, 'logs'))
logging.info('Copying metgrid.zip')
metgrid_dir = os.path.join(wrf_config.get('nfs_dir'), 'metgrid')
if wrf_config.is_set('wps_run_id'):
logging.info('wps_run_id is set. Copying metgrid from ' +
wrf_config.get('wps_run_id'))
utils.copy_files_with_prefix(
metgrid_dir,
wrf_config.get('wps_run_id') + '_metgrid.zip', em_real_dir)
metgrid_zip = os.path.join(
em_real_dir,
wrf_config.get('wps_run_id') + '_metgrid.zip')
else:
utils.copy_files_with_prefix(metgrid_dir,
wrf_config.get('run_id') + '_metgrid.zip',
em_real_dir)
metgrid_zip = os.path.join(em_real_dir,
wrf_config.get('run_id') + '_metgrid.zip')
logging.info('Extracting metgrid.zip')
ZipFile(metgrid_zip, 'r',
compression=ZIP_DEFLATED).extractall(path=em_real_dir)
# logs destination: nfs/logs/xxxx/rsl*
try:
try:
logging.info('Starting real.exe')
utils.run_subprocess(
'mpirun --allow-run-as-root -np %d ./real.exe' % procs,
cwd=em_real_dir)
finally:
logging.info('Moving Real log files...')
utils.create_zip_with_prefix(em_real_dir,
'rsl*',
os.path.join(em_real_dir,
'real_rsl.zip'),
clean_up=True)
utils.move_files_with_prefix(em_real_dir, 'real_rsl.zip', logs_dir)
try:
logging.info('Starting wrf.exe')
utils.run_subprocess(
'mpirun --allow-run-as-root -np %d ./wrf.exe' % procs,
cwd=em_real_dir)
finally:
logging.info('Moving WRF log files...')
utils.create_zip_with_prefix(em_real_dir,
'rsl*',
os.path.join(em_real_dir,
'wrf_rsl.zip'),
clean_up=True)
utils.move_files_with_prefix(em_real_dir, 'wrf_rsl.zip', logs_dir)
finally:
logging.info('Moving namelist input file')
utils.move_files_with_prefix(em_real_dir, 'namelist.input', output_dir)
logging.info('WRF em_real: DONE! Moving data to the output dir')
logging.info('Extracting rf from domain3')
d03_nc = glob.glob(os.path.join(em_real_dir, 'wrfout_d03_*'))[0]
ncks_query = 'ncks -v %s %s %s' % ('RAINC,RAINNC,XLAT,XLONG,Times', d03_nc,
d03_nc + '_rf')
utils.run_subprocess(ncks_query)
logging.info('Extracting rf from domain1')
d01_nc = glob.glob(os.path.join(em_real_dir, 'wrfout_d01_*'))[0]
ncks_query = 'ncks -v %s %s %s' % ('RAINC,RAINNC,XLAT,XLONG,Times', d01_nc,
d01_nc + '_rf')
utils.run_subprocess(ncks_query)
logging.info('Moving data to the output dir')
utils.move_files_with_prefix(em_real_dir, 'wrfout_d03*_rf', output_dir)
utils.move_files_with_prefix(em_real_dir, 'wrfout_d01*_rf', output_dir)
logging.info('Moving data to the archive dir')
utils.move_files_with_prefix(em_real_dir, 'wrfout_*', archive_dir)
logging.info('Cleaning up files')
utils.delete_files_with_prefix(em_real_dir, 'met_em*')
utils.delete_files_with_prefix(em_real_dir, 'rsl*')
os.remove(metgrid_zip)
def process(self, *args, **kwargs):
config = self.get_config(**kwargs)
logging.info('wrf conifg: ' + config.to_json_string())
start_date = config.get('start_date')
d03_dir = config.get('wrf_output_dir')
d03_sl = os.path.join(d03_dir, 'wrfout_d01_' + start_date + ':00_SL')
# create a temp work dir & get a local copy of the d03.._SL
temp_dir = utils.create_dir_if_not_exists(
os.path.join(config.get('wrf_home'), 'temp_d01'))
shutil.copy2(d03_sl, temp_dir)
d03_sl = os.path.join(temp_dir, os.path.basename(d03_sl))
lat_min = -3.06107
lon_min = 71.2166
lat_max = 18.1895
lon_max = 90.3315
variables = ext_utils.extract_variables(d03_sl, 'RAINC, RAINNC',
lat_min, lat_max, lon_min,
lon_max)
lats = variables['XLAT']
lons = variables['XLONG']
# cell size is calc based on the mean between the lat and lon points
cz = np.round(
np.mean(
np.append(lons[1:len(lons)] - lons[0:len(lons) - 1],
lats[1:len(lats)] - lats[0:len(lats) - 1])), 3)
# clevs = 10 * np.array([0.1, 0.5, 1, 2, 3, 5, 10, 15, 20, 25, 30])
# clevs_cum = 10 * np.array([0.1, 0.5, 1, 2, 3, 5, 10, 15, 20, 25, 30, 50, 75, 100])
# norm = colors.BoundaryNorm(boundaries=clevs, ncolors=256)
# norm_cum = colors.BoundaryNorm(boundaries=clevs_cum, ncolors=256)
# cmap = plt.get_cmap('jet')
clevs = [
0, 1, 2.5, 5, 7.5, 10, 15, 20, 30, 40, 50, 70, 100, 150, 200, 250,
300, 400, 500, 600, 750
]
clevs_cum = clevs
norm = None
cmap = cm.s3pcpn
basemap = Basemap(projection='merc',
llcrnrlon=lon_min,
llcrnrlat=lat_min,
urcrnrlon=lon_max,
urcrnrlat=lat_max,
resolution='h')
filter_threshold = 0.05
data = variables['RAINC'] + variables['RAINNC']
logging.info('Filtering with the threshold %f' % filter_threshold)
data[data < filter_threshold] = 0.0
variables['PRECIP'] = data
for i in range(1, len(variables['Times'])):
time = variables['Times'][i]
ts = dt.datetime.strptime(time, '%Y-%m-%d_%H:%M:%S')
lk_ts = utils.datetime_utc_to_lk(ts)
logging.info('processing %s', time)
# instantaneous precipitation (hourly)
inst_precip = variables['PRECIP'][i] - variables['PRECIP'][i - 1]
inst_file = os.path.join(temp_dir, 'wrf_inst_' + time)
title = {
'label':
'3Hourly rf for %s LK\n%s UTC' %
(lk_ts.strftime('%Y-%m-%d_%H:%M:%S'), time),
'fontsize':
30
}
ext_utils.create_contour_plot(inst_precip,
inst_file + '.png',
lat_min,
lon_min,
lat_max,
lon_max,
title,
clevs=clevs,
cmap=cmap,
basemap=basemap,
norm=norm)
if i % 8 == 0:
d = int(i / 8) - 1
logging.info('Creating gif for D%d' % d)
gif_file = os.path.join(temp_dir, 'wrf_inst_D01_%dd' % d)
images = [
os.path.join(
temp_dir,
'wrf_inst_' + i.strftime('%Y-%m-%d_%H:%M:%S') + '.png')
for i in np.arange(ts - dt.timedelta(hours=24 - 3), ts +
dt.timedelta(
hours=3), dt.timedelta(
hours=3)).astype(dt.datetime)
]
ext_utils.create_gif(images, gif_file + '.gif')
# move all the data in the tmp dir to the nfs
logging.info('Copying gifs to ' + d03_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', d03_dir)
d03_latest_dir = os.path.join(config.get('nfs_dir'), 'latest',
os.path.basename(config.get('wrf_home')))
# <nfs>/latest/wrf0 .. 3
utils.create_dir_if_not_exists(d03_latest_dir)
# todo: this needs to be adjusted to handle the multiple runs
logging.info('Copying gifs to ' + d03_latest_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', d03_latest_dir)
logging.info('Cleaning up the dir ' + temp_dir)
shutil.rmtree(temp_dir)
def process(self, *args, **kwargs):
config = self.get_config(**kwargs)
logging.info('wrf conifg: ' + config.to_json_string())
start_date = config.get('start_date')
d03_dir = config.get('wrf_output_dir')
d03_sl = os.path.join(d03_dir, 'wrfout_d03_' + start_date + ':00_SL')
# create a temp work dir & get a local copy of the d03.._SL
temp_dir = utils.create_dir_if_not_exists(
os.path.join(config.get('wrf_home'), 'temp'))
shutil.copy2(d03_sl, temp_dir)
d03_sl = os.path.join(temp_dir, os.path.basename(d03_sl))
lat_min = 5.722969
lon_min = 79.52146
lat_max = 10.06425
lon_max = 82.18992
variables = ext_utils.extract_variables(d03_sl, 'RAINC, RAINNC',
lat_min, lat_max, lon_min,
lon_max)
lats = variables['XLAT']
lons = variables['XLONG']
# cell size is calc based on the mean between the lat and lon points
cz = np.round(
np.mean(
np.append(lons[1:len(lons)] - lons[0:len(lons) - 1],
lats[1:len(lats)] - lats[0:len(lats) - 1])), 3)
# clevs = 10 * np.array([0.1, 0.5, 1, 2, 3, 5, 10, 15, 20, 25, 30])
# clevs_cum = 10 * np.array([0.1, 0.5, 1, 2, 3, 5, 10, 15, 20, 25, 30, 50, 75, 100])
# norm = colors.BoundaryNorm(boundaries=clevs, ncolors=256)
# norm_cum = colors.BoundaryNorm(boundaries=clevs_cum, ncolors=256)
# cmap = plt.get_cmap('jet')
clevs = [
0, 1, 2.5, 5, 7.5, 10, 15, 20, 30, 40, 50, 70, 100, 150, 200, 250,
300, 400, 500, 600, 750
]
clevs_cum = clevs
norm = None
norm_cum = None
cmap = cm.s3pcpn
basemap = Basemap(projection='merc',
llcrnrlon=lon_min,
llcrnrlat=lat_min,
urcrnrlon=lon_max,
urcrnrlat=lat_max,
resolution='h')
filter_threshold = 0.05
data = variables['RAINC'] + variables['RAINNC']
logging.info('Filtering with the threshold %f' % filter_threshold)
data[data < filter_threshold] = 0.0
variables['PRECIP'] = data
pngs = []
ascs = []
for i in range(1, len(variables['Times'])):
time = variables['Times'][i]
ts = dt.datetime.strptime(time, '%Y-%m-%d_%H:%M:%S')
lk_ts = utils.datetime_utc_to_lk(ts)
logging.info('processing %s', time)
# instantaneous precipitation (hourly)
inst_precip = variables['PRECIP'][i] - variables['PRECIP'][i - 1]
inst_file = os.path.join(temp_dir, 'wrf_inst_' + time)
title = {
'label':
'Hourly rf for %s LK\n%s UTC' %
(lk_ts.strftime('%Y-%m-%d_%H:%M:%S'), time),
'fontsize':
30
}
ext_utils.create_asc_file(np.flip(inst_precip, 0),
lats,
lons,
inst_file + '.asc',
cell_size=cz)
ascs.append(inst_file + '.asc')
ext_utils.create_contour_plot(inst_precip,
inst_file + '.png',
lat_min,
lon_min,
lat_max,
lon_max,
title,
clevs=clevs,
cmap=cmap,
basemap=basemap,
norm=norm)
pngs.append(inst_file + '.png')
if i % 24 == 0:
t = 'Daily rf from %s LK to %s LK' % (
(lk_ts -
dt.timedelta(hours=24)).strftime('%Y-%m-%d_%H:%M:%S'),
lk_ts.strftime('%Y-%m-%d_%H:%M:%S'))
d = int(i / 24) - 1
logging.info('Creating images for D%d' % d)
cum_file = os.path.join(temp_dir, 'wrf_cum_%dd' % d)
ext_utils.create_asc_file(np.flip(variables['PRECIP'][i], 0),
lats,
lons,
cum_file + '.asc',
cell_size=cz)
ascs.append(cum_file + '.asc')
ext_utils.create_contour_plot(variables['PRECIP'][i] -
variables['PRECIP'][i - 24],
cum_file + '.png',
lat_min,
lon_min,
lat_max,
lon_max,
t,
clevs=clevs,
cmap=cmap,
basemap=basemap,
norm=norm_cum)
pngs.append(inst_file + '.png')
gif_file = os.path.join(temp_dir, 'wrf_inst_%dd' % d)
images = [
os.path.join(
temp_dir,
'wrf_inst_' + i.strftime('%Y-%m-%d_%H:%M:%S') + '.png')
for i in np.arange(ts - dt.timedelta(hours=23), ts +
dt.timedelta(
hours=1), dt.timedelta(
hours=1)).astype(dt.datetime)
]
ext_utils.create_gif(images, gif_file + '.gif')
logging.info('Creating the zips')
utils.create_zip_with_prefix(temp_dir, '*.png',
os.path.join(temp_dir, 'pngs.zip'))
utils.create_zip_with_prefix(temp_dir, '*.asc',
os.path.join(temp_dir, 'ascs.zip'))
# utils.create_zipfile(pngs, os.path.join(temp_dir, 'pngs.zip'))
# utils.create_zipfile(ascs, os.path.join(temp_dir, 'ascs.zip'))
logging.info('Cleaning up instantaneous pngs and ascs - wrf_inst_*')
utils.delete_files_with_prefix(temp_dir, 'wrf_inst_*.png')
utils.delete_files_with_prefix(temp_dir, 'wrf_inst_*.asc')
logging.info('Copying pngs to ' + d03_dir)
utils.move_files_with_prefix(temp_dir, '*.png', d03_dir)
logging.info('Copying ascs to ' + d03_dir)
utils.move_files_with_prefix(temp_dir, '*.asc', d03_dir)
logging.info('Copying gifs to ' + d03_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', d03_dir)
logging.info('Copying zips to ' + d03_dir)
utils.copy_files_with_prefix(temp_dir, '*.zip', d03_dir)
d03_latest_dir = os.path.join(config.get('nfs_dir'), 'latest',
os.path.basename(config.get('wrf_home')))
# <nfs>/latest/wrf0 .. 3
utils.create_dir_if_not_exists(d03_latest_dir)
# todo: this needs to be adjusted to handle the multiple runs
logging.info('Copying gifs to ' + d03_latest_dir)
utils.copy_files_with_prefix(temp_dir, '*.gif', d03_latest_dir)
logging.info('Cleaning up temp dir')
shutil.rmtree(temp_dir)
