import os
import sys
import shutil
import argparse
import requests
import warnings
warnings.filterwarnings("ignore")
import numpy as np
from glob import glob
from SIAC.get_MCD43 import get_mcd43
from datetime import datetime
from SIAC.create_logger import create_logger
from SIAC.s2_preprocessing import s2_pre_processing
from SIAC.the_aerosol import solve_aerosol
from SIAC.the_correction import atmospheric_correction
from SIAC.downloaders import downloader
from SIAC.multi_process import parmap
from os.path import expanduser
home = expanduser("~")
file_path = os.path.dirname(os.path.realpath(__file__))
[docs]def SIAC_S2(s2_t, send_back = False, mcd43 = home + '/MCD43/', vrt_dir = home + '/MCD43_VRT/', aoi = None,
global_dem = None, cams_dir = None, jasmin = False):
'''
if not os.path.exists(file_path + '/emus/'):
os.mkdir(file_path + '/emus/')
if len(glob(file_path + '/emus/' + 'isotropic_MSI_emulators_*_x?p_S2?.pkl')) < 12:
url = 'http://www2.geog.ucl.ac.uk/~ucfafyi/emus/'
req = requests.get(url)
to_down = []
for line in req.text.split():
if 'MSI' in line:
fname = line.split('"')[1].split('<')[0]
if 'MSI' in fname:
to_down.append([fname, url])
f = lambda fname_url: downloader(fname_url[0], fname_url[1], file_path + '/emus/')
parmap(f, to_down)
'''
rets = s2_pre_processing(s2_t, cams_dir, global_dem)
aero_atmos = []
for ret in rets:
ret += (mcd43, vrt_dir, aoi, global_dem, cams_dir, jasmin)
aero_atmo = do_correction(*ret)
if send_back:
aero_atmos.append(aero_atmo)
if send_back:
return aero_atmos
def do_correction(sun_ang_name, view_ang_names, toa_refs, cloud_name, \
cloud_mask, aot, tcwv, metafile, mcd43 = home + '/MCD43/', \
vrt_dir = home + '/MCD43_VRT/', aoi=None, \
global_dem = None, cams_dir = None, jasmin = False):
if jasmin:
if global_dem is None:
global_dem = '/work/scratch-pw/marcyin/DEM/global_dem.vrt'
if cams_dir is None:
cams_dir = '/work/scratch-pw/marcyin/CAMS/'
os.environ['jasmin_memory_limit'] = '6.4e+10'
else:
if global_dem is None:
global_dem = '/vsicurl/http://www2.geog.ucl.ac.uk/~ucfafyi/eles/global_dem.vrt'
if cams_dir is None:
cams_dir = '/vsicurl/http://www2.geog.ucl.ac.uk/~ucfafyi/cams/'
if os.path.realpath(mcd43) in os.path.realpath(home + '/MCD43/'):
if not os.path.exists(home + '/MCD43/'):
os.mkdir(home + '/MCD43/')
if os.path.realpath(vrt_dir) in os.path.realpath(home + '/MCD43_VRT/'):
if not os.path.exists(home + '/MCD43_VRT/'):
os.mkdir(home + '/MCD43_VRT/')
base = os.path.dirname(toa_refs[0])
base = toa_refs[0].replace('B01.jp2', '')
with open(metafile) as f:
for i in f.readlines():
if 'SENSING_TIME' in i:
sensing_time = i.split('</')[0].split('>')[-1]
obs_time = datetime.strptime(sensing_time, u'%Y-%m-%dT%H:%M:%S.%fZ')
if 'TILE_ID' in i:
sat = i.split('</')[0].split('>')[-1].split('_')[0]
tile = i.split('</')[0].split('>')[-1]
log_file = os.path.dirname(metafile) + '/SIAC_S2.log'
logger = create_logger(log_file)
logger.info('Starting atmospheric corretion for %s'%tile)
if not np.all(cloud_mask):
# handlers = logger.handlers[:]
# for handler in handlers:
# handler.close()
# logger.removeHandler(handler)
#if not jasmin:
vrt_dir = get_mcd43(toa_refs[0], obs_time, mcd43_dir = mcd43, vrt_dir = vrt_dir, logger = logger, jasmin = jasmin)
#logger = create_logger(log_file)
else:
logger.info('No clean pixel in this scene and no MCD43 is downloaded.')
sensor_sat = 'MSI', sat
band_index = [1,2,3,7,11,12]
band_wv = [469, 555, 645, 859, 1640, 2130]
toa_bands = (np.array(toa_refs)[band_index,]).tolist()
view_angles = (np.array(view_ang_names)[band_index,]).tolist()
sun_angles = sun_ang_name
#logger.info('First pass AOT and TCWV: %.02f, %.02f'%(aot.mean(), tcwv.mean()))
#logger.info('Running SIAC for tile: %s on %s'%(tile, obs_time.strftime('%Y-%M-%d')))
aero = solve_aerosol(sensor_sat,toa_bands,band_wv, band_index,view_angles,\
sun_angles,obs_time,cloud_mask, gamma=10., spec_m_dir= \
file_path+'/spectral_mapping/', emus_dir=file_path+'/emus/',\
mcd43_dir=vrt_dir, aoi=aoi, log_file = log_file, global_dem = global_dem, cams_dir = cams_dir, \
prior_scale = [1., 0.1, 46.698, 1., 1., 1.])
aero._solving()
toa_bands = toa_refs
view_angles = view_ang_names
aot = base + 'aot.tif'
tcwv = base + 'tcwv.tif'
tco3 = base + 'tco3.tif'
aot_unc = base + 'aot_unc.tif'
tcwv_unc = base + 'tcwv_unc.tif'
tco3_unc = base + 'tco3_unc.tif'
rgb = [toa_bands[3], toa_bands[2], toa_bands[1]]
band_index = [0,1,2,3,4,5,6,7,8,9,10,11,12]
atmo = atmospheric_correction(sensor_sat,toa_bands, band_index,view_angles,\
sun_angles, aot = aot, cloud_mask = cloud_mask,\
tcwv = tcwv, tco3 = tco3, aot_unc = aot_unc, \
tcwv_unc = tcwv_unc, tco3_unc = tco3_unc, rgb = \
rgb, emus_dir=file_path+'/emus/', log_file = log_file, global_dem = global_dem, cams_dir = cams_dir)
atmo._doing_correction()
if not np.all(cloud_mask):
# if jasmin:
shutil.rmtree(vrt_dir)
return aero, atmo
def exe():
parser = argparse.ArgumentParser(description='Sentinel 2 Atmospheric Correction Excutable')
parser.add_argument('-f', "--file_path", help='Sentinel 2 file path', required=True)
parser.add_argument("-m", "--MCD43_file_dir", help="Directory where you store MCD43A1.006 data", default = home + '/MCD43/')
parser.add_argument("-v", "--vrt_dir", help="Where MCD43 vrt stored.", default = home + '/MCD43_VRT/')
parser.add_argument("-a", "--aoi", help="Area of Interest.", default = None)
args = parser.parse_args()
SIAC_S2(s2_t=args.file_path, mcd43=args.MCD43_file_dir, vrt_dir=args.vrt_dir, aoi=args.aoi)
if __name__ == '__main__':
exe()