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batchhdf2geotiff.py
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#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 19 21:47:21 2018
@author: leonidas
"""
import h5py
import numpy as np
from pyresample import geometry
import os,glob
import xarray as xr
import dask.array as da
from satpy import Scene
import areaSettings
from satpy.utils import debug_on
import argparse
import ntpath
def readhdfDatasets(HDF):
with h5py.File(HDF,'r') as h5_file:
GROUP_DNB_SDR='All_Data/VIIRS-DNB-SDR_All'
radiance = h5_file[GROUP_DNB_SDR]['Radiance'][...]
qf1_viirsdnbsdr = h5_file[GROUP_DNB_SDR]['QF1_VIIRSDNBSDR'][...]
qf2_scan_sdr = h5_file[GROUP_DNB_SDR]['QF2_SCAN_SDR'][...]
GROUP_DNB_SDR_GEO='All_Data/VIIRS-DNB-GEO_All'
lon_data = h5_file[GROUP_DNB_SDR_GEO]['Longitude'][...]
lat_data = h5_file[GROUP_DNB_SDR_GEO]['Latitude'][...]
LunarZenithAngle = h5_file[GROUP_DNB_SDR_GEO]['LunarZenithAngle'][...]
qf2_viirssdrgeo = h5_file[GROUP_DNB_SDR_GEO]['QF2_VIIRSSDRGEO'][...]
qf2_viirssdrgeo_tc = h5_file[GROUP_DNB_SDR_GEO]['QF2_VIIRSSDRGEO_TC'][...]
return radiance, qf1_viirsdnbsdr, qf2_scan_sdr, lon_data, lat_data, LunarZenithAngle, qf2_viirssdrgeo, qf2_viirssdrgeo_tc
def SDR2Geotiff(HDF, output_dir,areaid, radius):
radiance,qf1_viirsdnbsdr,qf2_scan_sdr,lon_data,lat_data,LunarZenithAngle,qf2_viirssdrgeo,qf2_viirssdrgeo_tc = readhdfDatasets(HDF)
HDF = ntpath.basename(HDF)#get filename without path
#QF Flags from https://ncc.nesdis.noaa.gov/documents/documentation/viirs-sdr-dataformat.pdf
#1.VIIRS Fill Values (p.70)
radiance_fillvalues=np.array([-999.3 ,-999.5, -999.8, -999.9 ])
radiance_mask = np.isin(radiance, radiance_fillvalues)
#2.Edge-of-swath pixels
edge_of_swath_mask = np.zeros_like(radiance, dtype='bool')
edge_of_swath_mask[:,0:254]=1
edge_of_swath_mask[:,3810:4064]=1
#3.QF1_VIIRSDNBSDR flags (p.73)
#SDR_Quality_mask = (qf1_viirsdnbsdr & 3)>0
Saturated_Pixel_mask = ((qf1_viirsdnbsdr & 12)>>2)>0
Missing_Data_mask = ((qf1_viirsdnbsdr & 48)>>4)>0
Out_of_Range_mask = ((qf1_viirsdnbsdr & 64)>>6)>0
#4.QF2_VIIRSSDRGEO flags (p.90)
qf2_viirssdrgeo_do0_mask= (qf2_viirssdrgeo & 1)>0
qf2_viirssdrgeo_do1_mask= ((qf2_viirssdrgeo & 2)>>1)>0
qf2_viirssdrgeo_do2_mask= ((qf2_viirssdrgeo & 4)>>2)>0
qf2_viirssdrgeo_do3_mask= ((qf2_viirssdrgeo & 8)>>3)>0
#Combine pixel level flags
viirs_mask=np.logical_or.reduce((
radiance_mask,
edge_of_swath_mask,
#SDR_Quality_mask,
Saturated_Pixel_mask,
Missing_Data_mask,
Out_of_Range_mask,
qf2_viirssdrgeo_do0_mask,
qf2_viirssdrgeo_do1_mask,
qf2_viirssdrgeo_do2_mask,
qf2_viirssdrgeo_do3_mask,
))
fill_value=255.0
radiance[viirs_mask]=fill_value #set fill value for masked pixels in DNB
LunarZenithAngle[viirs_mask]=fill_value #set fill value for masked pixels in DNB
swath_def = geometry.SwathDefinition(
xr.DataArray(da.from_array(lon_data, chunks=4096), dims=('y', 'x')),
xr.DataArray(da.from_array(lat_data, chunks=4096), dims=('y', 'x')))
metadata_dict = {'name': 'dnb', 'area':swath_def}
scn = Scene()
scn['Radiance'] = xr.DataArray(
da.from_array(radiance, chunks=4096),
attrs=metadata_dict,
dims=('y', 'x')) #https://satpy.readthedocs.io/en/latest/dev_guide/xarray_migration.html#id1
scn['LunarZenithAngle'] = xr.DataArray(
da.from_array(LunarZenithAngle, chunks=4096),
attrs=metadata_dict,
dims=('y', 'x'))
scn.load(["Radiance"])
scn.load(["LunarZenithAngle"])
#print(scn)
proj_scn = scn.resample(areaSettings.getarea(areaid),radius_of_influence=radius)
proj_scn.save_datasets(writer='geotiff',base_dir=output_dir ,file_pattern="{}.{}.{}".format(HDF,"{name}","tif"),enhancement_config=False,
dtype=np.float32,fill_value=fill_value)
def batchSDR2Geotiff(input_dir, output_dir,pattern, areaid, debug):
if debug:
debug_on()
curdir=os.getcwd()
os.chdir(input_dir)
#OUTPUT_DIR=os.path.join(input_dir,OUTPUT_DIR_RELATIVE)
output_dir = os.path.abspath(output_dir) #works for abs and relative paths
if not os.path.exists(output_dir):
os.makedirs(output_dir)
hdf_files = glob.glob(os.path.join(input_dir,pattern))
os.chdir(curdir)
for hdf in hdf_files:
SDR2Geotiff(hdf, output_dir, areaid,radius=2000)
def dir_path(string):
string = os.path.abspath(string)
if os.path.isdir(string):
return string
else:
print('Provide a valid directory.')
raise NotADirectoryError(string)
def parse_args():
parser = argparse.ArgumentParser(description='Converts VIIRS SDR DNB hdf dataset to geotiff. Applies Mask for Specific Quality flags.')
parser.add_argument("-i", "--inputdir", help="Directory that contains hdf5 files", required=True, type=dir_path)
parser.add_argument("-o", "--outputdir", help="Directory to export geotiff files",required=True, type=dir_path)
parser.add_argument("-p", "--pattern", help="Regex pattern to match hdf files", default='GMODO-VICMO_npp_d*.h5')
parser.add_argument("-a", "--areaid", help="Area_ID",required=True)
parser.add_argument("-d", "--debug", action='store_true')
args = parser.parse_args()
return args
def main():
args = parse_args()
batchSDR2Geotiff(input_dir=args.inputdir, output_dir=args.outputdir, pattern=args.pattern, areaid=args.areaid, debug=args.debug)
if __name__ == '__main__':
main()
#runfile('/media/leonidas/Hitachi/daily_viirs/2017_packed/batchHDF2Geotiff/batchhdf2geotiff.py', wdir='/media/leonidas/Hitachi/daily_viirs/2017_packed/batchHDF2Geotiff' ,args = '-i /media/leonidas/Hitachi/daily_viirs/2017_packed/SDR_DNB -o /media/leonidas/Hitachi/daily_viirs/2017_packed/SDR_DNB/attiki_cmd_062017 -p GDNBO-SVDNB_npp_d201706*.*h5 -a greek_grid4')