# David R Thompson, Adam Erickson, Jay Fahlen
from isofit.core.isofit import Isofit
from isofit.utils import surface_model
# Build the surface model
surface_model("configs/surface.json")
# Run retrievals
model1 = Isofit("configs/joint_isofit_with_prof_WATER_nogrid.json").run(
debug=True)
wave_fit = pd.DataFrame(index = [x for x in range(radiance.bands)])
wave_fit[0] =np.round(radiance.wavelengths/1000,5)
wave_fit[1] = np.round(radiance.fwhm/1000,5)
wave_fit.to_csv(wavelength_file, sep = '\t',header=False)
# Create decorrelated surface model
windows= [[380.0, 1300.0], [1500, 1780.0], [1975.0, 2450.0]]
surface_data_path = "%s/isotest/data/surface/surface_20210215_emit" % home
surface_file = "%s/data/surface_emit.mat" % cal_dir
surface_config = "%s/configs/surface.json" % cal_dir
surface_config_gen_decorr(surface_data_path,
windows,
wavelength_file,
surface_file,
surface_config)
surface_model(surface_config)
# Create modtran template file
engine = 'sRTMnet'
template_file = '%s/configs/radtran_template.json' % cal_dir
modtran_template_create(obs_mean.astype(np.float64),
loc_mean.astype(np.float64),
doy,
template_file)
# Create forward model configs
rtm_config,surface_config,instrument_config =fw_configs(iso_base,
cal_dir,
template_file,
wavelength_file,
surface_file,
def main():
parser = argparse.ArgumentParser()
parser.add_argument('rdn_file', type=str,
help='Radiance')
parser.add_argument('obs_file', type=str,
help='Observables')
parser.add_argument('loc_file', type=str,
help='Location')
parser.add_argument('output_dir', type=str,
help='Output directory')
parser.add_argument('temp_dir', type=str,
help='Temp directory')
parser.add_argument('config', type=str,
help='ISOFIT config files')
args = parser.parse_args()
base_name = os.path.basename(args.rdn_file)[:38]
date = base_name[4:12]
# Load ISOFIT config file
with open(args.config,'r') as file:
configs = yaml.load(file, Loader=yaml.FullLoader)
for key in configs['surface']:
get_surface_spectra(args.temp_dir + key,
configs['surface'][key])
surface_config = "%s/surface_config.json" % args.temp_dir
surface_file = '%s/surface.mat'% args.temp_dir
wavelength_file = gen_wavelength_file(args.rdn_file,
args.temp_dir)
surface_config_gen(configs['windows'],
surface_config,
configs['prior'])
surface_model(surface_config)
apply_oe = ['python']
apply_oe.append('%s/isofit/utils/apply_oe.py' % configs['base'])
apply_oe.append(args.rdn_file)
apply_oe.append(args.loc_file)
apply_oe.append(args.obs_file)
apply_oe.append(args.output_dir)
apply_oe.append('NA-%s' % date)
apply_oe += ['--surface_path', surface_file]
apply_oe += ['--n_cores',str(configs['n_cores'])]
apply_oe += ['--empirical_line',str(configs['empirical_line'])]
apply_oe += ['--presolve',str(configs['presolve'])]
apply_oe += ['--ray_temp_dir',args.temp_dir]
apply_oe += ['--log_file','%s/%s_logfile' % (args.temp_dir,base_name)]
apply_oe += ['--emulator_base',configs['emulator']]
if configs['radiance_factors']:
rad_factors = "%s/radiance_factors.txt" % args.temp_dir
download_file(rad_factors,configs['radiance_factors'])
apply_oe += ['--rdn_factors_path',rad_factors]
apply = subprocess.Popen(apply_oe)
apply.wait()
# David R Thompson, Adam Erickson
from isofit.core.isofit import Isofit
from isofit.utils import surface_model
# Build the surface model
surface_model("configs/ang20171108t184227_surface.json")
# Run retrievals
model1 = Isofit("configs/ang20171108t173546_darklot.json")
model1.run()
model2 = Isofit("configs/ang20171108t173546_horse.json")
model2.run()
model3 = Isofit("configs/ang20171108t184227_astrored.json")
model3.run()
model4 = Isofit("configs/ang20171108t184227_astrogreen.json")
model4.run()
model5 = Isofit("configs/ang20171108t184227_beckmanlawn.json")
model5.run()
model6 = Isofit("configs/ang20171108t184227_beckmanlawn-oversmoothed.json")
model6.run()
model7 = Isofit("configs/ang20171108t184227_beckmanlawn-undersmoothed.json")
model7.run()
# David R Thompson, Adam Erickson
from isofit.core.isofit import Isofit
from isofit.utils import surface_model
# Build the surface model
surface_model("configs/prm20151026t173213_surface_coastal.json")
# Run retrievals
model1 = Isofit("configs/prm20151026t173213_D8W_6s.json")
model1.run()
model2 = Isofit("configs/prm20151026t173213_D8p5W_6s.json")
model2.run()
model3 = Isofit("configs/prm20151026t173213_D9W_6s.json")
model3.run()
model4 = Isofit("configs/prm20151026t173213_D9p5W_6s.json")
model4.run()
def reflectance(self):
'''Run ISOFIT reflectance inversion
'''
# Check for input files
if not (self.exists(self.rdn_file) & self.exists(self.loc_file) & self.exists(self.obs_file)):
print('Radiance data not found, generating radiance datasets')
self.radiance()
rfl_tmp = self.tmp_dir + '%s_isofit/' % self.base_name
if not os.path.isdir(rfl_tmp):
os.mkdir(rfl_tmp)
else:
shutil.rmtree(rfl_tmp)
os.mkdir(rfl_tmp)
for key in self.isofit['surface']:
get_surface_spectra(rfl_tmp + key,
self.isofit['surface'][key])
surface_config = "%s/surface_config.json" % rfl_tmp
surface_file = '%s/surface_filtered.mat'% rfl_tmp
wavelength_file = gen_wavelength_file(self.rdn_file,
rfl_tmp)
surface_config_gen(rfl_tmp,
self.isofit['surface_type'],
self.isofit['windows'],
wavelength_file,
surface_file,
surface_config)
surface_model(surface_config)
apply_oe = ['python']
apply_oe.append('%s/isofit/utils/apply_oe.py' % self.isofit['base'])
apply_oe.append(self.rdn_file)
apply_oe.append(self.loc_file)
apply_oe.append(self.obs_file)
apply_oe.append(rfl_tmp)
if self.sensor in ['prisma','desis']:
apply_oe.append('NA-%s' % self.date)
apply_oe += ['--surface_path', surface_file]
apply_oe += ['--n_cores',str(cpu_count())]
apply_oe += ['--empirical_line',str(self.isofit['empirical_line'])]
apply_oe += ['--presolve',str(self.isofit['presolve'])]
apply_oe += ['--ray_temp_dir',rfl_tmp]
apply_oe += ['--log_file','%s/%s_logfile' % (rfl_tmp,self.base_name)]
apply_oe += ['--emulator_base',self.isofit['emulator']]
if self.rdn_cfg['radiance_factors']:
rad_factors = "%s/radiance_factors.txt" % rfl_tmp
download_file(rad_factors,self.rdn_cfg['radiance_factors'])
apply_oe += ['--rdn_factors_path',rad_factors]
apply = subprocess.Popen(apply_oe)
apply.wait()
if not os.path.isdir(os.path.dirname(self.rfl_file)):
os.mkdir(os.path.dirname(self.rfl_file))
# Mask windows and rename ISOFIT output files
rfl = glob.glob('%s/output/*_rfl_prj_rfl' % rfl_tmp)[0]
uncert = glob.glob('%s/output/*_uncert_prj_uncert'% rfl_tmp)[0]
for new,old in [(self.rfl_file,rfl),(self.unc_file,uncert)]:
hy_obj = ht.HyTools()
hy_obj.read_file(old,'envi')
mask = []
for wave in hy_obj.wavelengths:
window = False
for start,end in self.isofit['windows']:
if (wave>start) and (wave<end):
window |= True
mask.append(window)
header_dict = hy_obj.get_header()
writer = ht.io.WriteENVI(new, header_dict)
for band_num in range(hy_obj.bands):
band = hy_obj.get_band(band_num)
if not mask[band_num]:
band = np.zeros(band.shape)
writer.write_band(band,band_num)
shutil.rmtree(rfl_tmp)
