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ghg_process.py
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#! /usr/bin/env python
#
# Copyright 2023 California Institute of Technology
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
# Authors: Philip G. Brodrick, [email protected]
import argparse
import subprocess
import target_generation
import parallel_mf
import local_surface_control_simple
import scale
import logging
from spectral.io import envi
import numpy as np
import os
from utils import envi_header, ReadAbstractDataSet
from osgeo import gdal
import pdb
def main(input_args=None):
parser = argparse.ArgumentParser(description="Robust MF")
parser.add_argument('radiance_file', type=str, metavar='INPUT', help='path to input image')
parser.add_argument('obs_file', type=str, help='path to observation image')
parser.add_argument('loc_file', type=str, help='path to location image')
parser.add_argument('glt_file', type=str, help='path to glt image')
parser.add_argument('l1b_bandmask_file', type=str, help='path to l1b bandmask image')
parser.add_argument('l2a_mask_file', type=str, help='path to l2a mask image')
parser.add_argument('output_base', type=str, help='output basepath for output image')
parser.add_argument('--state_subs', type=str, default=None, help='state file from OE retrieval')
parser.add_argument('--overwrite', action='store_true', help='state file from OE retrieval')
parser.add_argument('--ace_filter', action='store_true', help='use an ACE filter during matched filter')
parser.add_argument('--loglevel', type=str, default='INFO', help='logging verbosity')
parser.add_argument('--logfile', type=str, default=None, help='output file to write log to')
parser.add_argument('--mask_flares', type=int, default=1, help='mask flares in output')
parser.add_argument('--co2', action='store_true', help='flag to indicate whether to run co2')
args = parser.parse_args(input_args)
irr_file = '/beegfs/scratch/brodrick/src/isofit/data/kurudz_0.1nm.dat'
radiance_file = args.radiance_file
radiance_file_hdr = envi_header(radiance_file)
if radiance_file[-3:] == '.nc':
radiance_file_hdr = radiance_file
obs_file = args.obs_file
obs_file_hdr = envi_header(obs_file)
loc_file = args.loc_file
loc_file_hdr = envi_header(loc_file)
logging.basicConfig(format='%(levelname)s:%(asctime)s ||| %(message)s', level=args.loglevel,
filename=args.logfile, datefmt='%Y-%m-%d,%H:%M:%S')
# Target
co2_target_file = f'{args.output_base}_co2_target'
ch4_target_file = f'{args.output_base}_ch4_target'
# MF
co2_mf_file = f'{args.output_base}_co2_mf'
ch4_mf_file = f'{args.output_base}_ch4_mf'
# Flares
flare_file = f'{args.output_base}_flares.json'
# MF - ORT
co2_mf_ort_file = f'{args.output_base}_co2_mf_ort'
ch4_mf_ort_file = f'{args.output_base}_ch4_mf_ort'
# MF - Refined
co2_mf_refined_file = f'{args.output_base}_co2_mf_refined'
ch4_mf_refined_file = f'{args.output_base}_ch4_mf_refined'
# MF - Refined - ORT
co2_mf_refined_ort_file = f'{args.output_base}_co2_mf_refined_ort'
ch4_mf_refined_ort_file = f'{args.output_base}_ch4_mf_refined_ort'
# MF - Refined - ORT - Scaled
co2_mf_refined_scaled_ort_file = f'{args.output_base}_co2_mf_refined_scaled_ort.tif'
ch4_mf_refined_scaled_ort_file = f'{args.output_base}_ch4_mf_refined_scaled_ort.tif' ### CHANGE THIS NAME TO ch4_mf_refined_scaled_ort.tif
# MF - ORT - Scaled Color
ch4_mf_scaled_color_ort_file = f'{args.output_base}_ch4_mf_scaled_color_ort.tif'
co2_mf_scaled_color_ort_file = f'{args.output_base}_co2_mf_scaled_color_ort.tif'
# MF - Refined - ORT - Scaled Color
ch4_mf_refined_scaled_color_ort_file = f'{args.output_base}_ch4_mf_refined_scaled_color_ort.tif'
co2_mf_refined_scaled_color_ort_file = f'{args.output_base}_co2_mf_refined_scaled_color_ort.tif'
co2_mf_refined_kmz_file = f'{args.output_base}_co2_mf_refined.kmz'
ch4_mf_refined_kmz_file = f'{args.output_base}_ch4_mf_refined.kmz'
co2_mf_refined_color_kmz_file = f'{args.output_base}_co2_mf_refined_color.kmz'
ch4_mf_refined_color_kmz_file = f'{args.output_base}_ch4_mf_refined_color.kmz'
co2_mf_kmz_file = f'{args.output_base}_co2_mf.kmz'
ch4_mf_kmz_file = f'{args.output_base}_ch4_mf.kmz'
co2_mf_color_kmz_file = f'{args.output_base}_co2_mf_color.kmz'
ch4_mf_color_kmz_file = f'{args.output_base}_ch4_mf_color.kmz'
path = os.environ['PATH']
path = path.replace('\Library\\bin;',':')
os.environ['PATH'] = path
if os.path.isfile(ch4_mf_file):
dat = gdal.Open(ch4_mf_file).ReadAsArray()
if np.all(dat == -9999):
subprocess.call(f'rm {args.output_base}_ch4*',shell=True)
if (os.path.isfile(co2_target_file) is False and args.co2) or args.overwrite or os.path.isfile(ch4_target_file) is False:
#sza = envi.open(obs_file_hdr).open_memmap(interleave='bip')[...,4]
sza = ReadAbstractDataSet(args.obs_file, netcdf_key = 'obs', envi_interleave = 'bip')[...,4]
mean_sza = np.mean(sza[sza != -9999])
if args.loc_file[-3:] == '.nc':
elevation = ReadAbstractDataSet(args.radiance_file, netcdf_group = 'location', netcdf_key = 'elev', envi_interleave = 'bip')
else:
elevation = envi.open(loc_file_hdr).open_memmap(interleave='bip')[...,2]
mean_elevation = np.mean(elevation[elevation != -9999]) / 1000.
mean_elevation = min(max(0, mean_elevation),3)
if args.state_subs is not None:
if args.state_subs[-3:] == '.nc':
h2o = ReadAbstractDataSet(args.l2a_mask_file, netcdf_key = 'mask')[:,:,6]
else:
state_ds = envi.open(envi_header(args.state_subs))
band_names = state_ds.metadata['band names']
h2o = state_ds.open_memmap(interleave='bip')[...,band_names.index('H2OSTR')]
mean_h2o = np.mean(h2o[h2o != -9999])
else:
# Just guess something...
exit()
mean_h2o = 1.3
if (os.path.isfile(co2_target_file) is False or args.overwrite) and args.co2:
target_generation.main(['--co2', '-z', str(mean_sza), '-s', '100', '-g', str(mean_elevation), '-w', str(mean_h2o), '--output', co2_target_file, '--hdr', radiance_file_hdr])
if os.path.isfile(ch4_target_file) is False or args.overwrite:
target_generation.main(['--ch4', '-z', str(mean_sza), '-s', '100', '-g', str(mean_elevation), '-w', str(mean_h2o), '--output', ch4_target_file, '--hdr', radiance_file_hdr])
if (os.path.isfile(co2_mf_file) is False or args.overwrite) and args.co2:
subargs = [args.radiance_file, co2_target_file, co2_mf_file, '--n_mc', '1', '--l1b_bandmask_file', args.l1b_bandmask_file, '--l2a_mask_file', args.l2a_mask_file, '--wavelength_range', '1900', '2350', '--fixed_alpha', '0.0000000001', '--mask_clouds_water']
if args.ace_filter:
subargs.append('--use_ace_filter')
parallel_mf.main(subargs)
if os.path.isfile(ch4_mf_file) is False or args.overwrite:
logging.info('starting parallel mf')
subargs = [args.radiance_file, ch4_target_file, ch4_mf_file, '--n_mc', '1', '--l1b_bandmask_file', args.l1b_bandmask_file, '--l2a_mask_file', args.l2a_mask_file, '--wavelength_range', '500', '2450', '--fixed_alpha', '0.0000000001', '--mask_clouds_water', '--flare_outfile', flare_file]
if args.mask_flares == 1:
subargs.append('--mask_flares')
if args.ace_filter:
subargs.append('--use_ace_filter')
parallel_mf.main(subargs)
#if (os.path.isfile(co2_mf_refined_file) is False or args.overwrite) and args.co2:
# local_surface_control_simple.main([co2_mf_file, args.radiance_file, args.l1b_bandmask_file, co2_mf_refined_file, '--type', 'co2'])
#if os.path.isfile(ch4_mf_refined_file) is False or args.overwrite:
# local_surface_control_simple.main([ch4_mf_file, args.radiance_file, args.l1b_bandmask_file, ch4_mf_refined_file, '--type', 'ch4'])
#if (os.path.isfile(co2_mf_refined_ort_file) is False or args.overwrite) and args.co2:
# subprocess.call(f'python apply_glt.py {args.glt_file} {co2_mf_refined_file} {co2_mf_refined_ort_file}',shell=True)
#if os.path.isfile(ch4_mf_refined_ort_file) is False or args.overwrite:
# subprocess.call(f'python apply_glt.py {args.glt_file} {ch4_mf_refined_file} {ch4_mf_refined_ort_file}',shell=True)
# 20241003 gshen: skip this code path for now so it doesn't crap out
#if False:
# if (os.path.isfile(co2_mf_ort_file) is False or args.overwrite) and args.co2:
# subprocess.call(f'python apply_glt.py {args.glt_file} {co2_mf_file} {co2_mf_ort_file}',shell=True)
# if os.path.isfile(ch4_mf_ort_file) is False or args.overwrite:
# subprocess.call(f'python apply_glt.py {args.glt_file} {ch4_mf_file} {ch4_mf_ort_file}',shell=True)
#if os.path.isfile(ch4_mf_refined_scaled_ort_file) is False or args.overwrite:
# scale.main([ch4_mf_refined_ort_file, ch4_mf_refined_scaled_ort_file, '1', '500'])
#if (os.path.isfile(co2_mf_refined_scaled_ort_file) is False or args.overwrite) and args.co2:
# scale.main([co2_mf_refined_ort_file, co2_mf_refined_scaled_ort_file, '180', '11000'])
#if os.path.isfile(ch4_mf_refined_scaled_color_ort_file) is False or args.overwrite:
# scale.main([ch4_mf_refined_ort_file, ch4_mf_refined_scaled_color_ort_file, '1', '1000', '--cmap', 'plasma'])
#if (os.path.isfile(co2_mf_refined_scaled_color_ort_file) is False or args.overwrite) and args.co2:
# scale.main([co2_mf_refined_ort_file, co2_mf_refined_scaled_color_ort_file, '1', '100000', '--cmap', 'YlOrRd'])
# 20240905 gshen: skip this code path for now so it runs to completion
if False:
if os.path.isfile(ch4_mf_scaled_color_ort_file) is False or args.overwrite:
scale.main([ch4_mf_ort_file, ch4_mf_scaled_color_ort_file, '1', '1000', '--cmap', 'plasma'])
if (os.path.isfile(co2_mf_scaled_color_ort_file) is False or args.overwrite) and args.co2:
scale.main([co2_mf_ort_file, co2_mf_scaled_color_ort_file, '1', '100000', '--cmap', 'YlOrRd'])
#if os.path.isfile(ch4_mf_refined_kmz_file) is False or args.overwrite:
# hr_temp = f'{ch4_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {ch4_mf_refined_scaled_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {ch4_mf_refined_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
#if (os.path.isfile(co2_mf_refined_kmz_file) is False or args.overwrite) and args.co2:
# hr_temp = f'{co2_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {co2_mf_refined_scaled_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {co2_mf_refined_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
#if os.path.isfile(ch4_mf_refined_color_kmz_file) is False or args.overwrite:
# hr_temp = f'{ch4_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {ch4_mf_refined_scaled_color_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {ch4_mf_refined_color_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
#if os.path.isfile(co2_mf_refined_color_kmz_file) is False or args.overwrite:
# hr_temp = f'{co2_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {co2_mf_refined_scaled_color_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {co2_mf_refined_color_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
#if os.path.isfile(ch4_mf_color_kmz_file) is False or args.overwrite:
# hr_temp = f'{ch4_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {ch4_mf_scaled_color_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {ch4_mf_color_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
#if os.path.isfile(co2_mf_color_kmz_file) is False or args.overwrite:
# hr_temp = f'{co2_mf_refined_ort_file}_hrtemp'
# subprocess.call(f'gdalwarp -tr 0.00025 -0.00025 {co2_mf_scaled_color_ort_file} {hr_temp} -dstnodata 0',shell=True)
# subprocess.call(f'gdal_translate {hr_temp} {co2_mf_color_kmz_file} -a_nodata 0 -of KMLSUPEROVERLAY -co format=PNG',shell=True)
# subprocess.call(f'rm {hr_temp}',shell=True)
rdn_kmz = args.radiance_file.replace('.img','.kmz')
dst_rdn_kmz = f'{args.output_base}_rdn_rgb.kmz'
if os.path.isfile(rdn_kmz) and os.path.isfile(dst_rdn_kmz) is False:
subprocess.call(f'cp {rdn_kmz} {dst_rdn_kmz}',shell=True)
if __name__ == '__main__':
main()