https://github.com/insarlab/MintPy
Tip revision: 36a083521b39d9fb557741f9c5d703b7e42448c3 authored by Zhang Yunjun on 16 August 2022, 06:51:05 UTC
wrap up for version 1.4.1 (#829)
wrap up for version 1.4.1 (#829)
Tip revision: 36a0835
add.py
#!/usr/bin/env python3
############################################################
# Program is part of MintPy #
# Copyright (c) 2013, Zhang Yunjun, Heresh Fattahi #
# Author: Zhang Yunjun, Heresh Fattahi, 2013 #
############################################################
import os
import sys
import numpy as np
from mintpy.objects import timeseries
from mintpy.utils import readfile, writefile
from mintpy.utils.arg_utils import create_argument_parser
from mintpy.diff import check_reference
################################################################################
EXAMPLE = """example:
add.py mask_1.h5 mask_2.h5 mask_3.h5 -o mask_all.h5
add.py 081008_100220.unw 100220_110417.unw -o 081008_110417.unw
add.py timeseries_ERA5.h5 inputs/ERA5.h5 -o timeseries.h5
add.py timeseriesRg.h5 inputs/TECsub.h5 -o timeseriesRg_TECsub.h5 --force
"""
def create_parser(subparsers=None):
""" Command line parser """
synopsis = 'Generate the sum of multiple input files.'
epilog = EXAMPLE
name = __name__.split('.')[-1]
parser = create_argument_parser(
name, synopsis=synopsis, description=synopsis, epilog=epilog, subparsers=subparsers)
parser.add_argument('file', nargs='+', help='files (2 or more) to be added')
parser.add_argument('-o', '--output', dest='outfile', help='output file name')
parser.add_argument('--force', action='store_true',
help='Enforce the adding for the shared dates only for time-series files')
return parser
def cmd_line_parse(iargs=None):
parser = create_parser()
inps = parser.parse_args(args=iargs)
if len(inps.file) < 2:
parser.print_usage()
sys.exit('ERROR: At least 2 input files needed!')
# only two input files are supported for time-series type
atr = readfile.read_attribute(inps.file[0])
if atr['FILE_TYPE'] == 'timeseries' and len(inps.file) != 2:
raise ValueError('Only TWO files are supported for time-series, input has {}'.format(len(inps.file)))
return inps
################################################################################
def add_matrix(data1, data2):
"""Sum of 2 input matrix"""
data1 = np.array(data1, dtype=np.float32)
data2 = np.array(data2, dtype=np.float32)
data = data1 + data2
data[np.isnan(data1)] = data2[np.isnan(data1)]
data[np.isnan(data2)] = data1[np.isnan(data2)]
return data
def add_file(fnames, out_file=None, force=False):
"""Generate sum of all input files
Parameters: fnames : list of str, path/name of input files to be added
out_file : str, optional, path/name of output file
Returns: out_file : str, path/name of output file
Example: 'mask_all.h5' = add_file(['mask_1.h5','mask_2.h5','mask_3.h5'], 'mask_all.h5')
"""
# Default output file name
ext = os.path.splitext(fnames[0])[1]
if not out_file:
out_file = os.path.splitext(fnames[0])[0]
for i in range(1, len(fnames)):
out_file += '_plus_' + os.path.splitext(os.path.basename(fnames[i]))[0]
out_file += ext
# read FILE_TYPE
ftypes = [readfile.read_attribute(x)['FILE_TYPE'] for x in fnames]
print(f'input file types: {ftypes}')
if ftypes[0] == 'timeseries':
# check dates shared by two timeseries files
file1, file2 = fnames[0], fnames[1]
atr1 = readfile.read_attribute(file1)
atr2 = readfile.read_attribute(file2)
dateList1 = timeseries(file1).get_date_list()
dateList2 = timeseries(file2).get_date_list()
dateListShared = [i for i in dateList1 if i in dateList2]
dateShared = np.ones((len(dateList1)), dtype=np.bool_)
if dateListShared != dateList1:
print('WARNING: {} does not contain all dates in {}'.format(file2, file1))
if force:
dateListEx = list(set(dateList1) - set(dateListShared))
print('Continue and enforce the differencing for their shared dates only.')
print('\twith following dates are ignored for differencing:\n{}'.format(dateListEx))
dateShared[np.array([dateList1.index(i) for i in dateListEx])] = 0
else:
raise Exception('To enforce the differencing anyway, use --force option.')
# check reference point
ref_date, ref_y, ref_x = check_reference(atr1, atr2)
# read data2 (consider different reference_date/pixel)
print('read from file: {}'.format(file2))
data2 = readfile.read(file2, datasetName=dateListShared)[0]
if ref_y and ref_x:
print('* referencing data from {} to y/x: {}/{}'.format(os.path.basename(file2), ref_y, ref_x))
ref_box = (ref_x, ref_y, ref_x + 1, ref_y + 1)
ref_val = readfile.read(file2, datasetName=dateListShared, box=ref_box)[0]
data2 -= np.tile(ref_val.reshape(-1, 1, 1), (1, data2.shape[1], data2.shape[2]))
if ref_date:
print('* referencing data from {} to date: {}'.format(os.path.basename(file2), ref_date))
ref_ind = dateListShared.index(ref_date)
data2 -= np.tile(data2[ref_ind, :, :], (data2.shape[0], 1, 1))
# read data1
print('read from file: {}'.format(file1))
data = readfile.read(file1)[0]
# apply adding
mask = data == 0.
data[dateShared] += data2
data[mask] = 0. # Do not change zero phase value
del data2
# write file
writefile.write(data, out_file=out_file, metadata=atr1, ref_file=file1)
else:
# get common dataset list
ds_names_list = [readfile.get_dataset_list(x) for x in fnames]
ds_names = list(set.intersection(*map(set, ds_names_list)))
# if all files have one dataset, ignore dataset name variation and take the 1st one as reference
if all(len(x) == 1 for x in ds_names_list):
ds_names = ds_names_list[0]
print('List of common datasets across files: ', ds_names)
if len(ds_names) < 1:
raise ValueError('No common datasets found among files:\n{}'.format(fnames))
# loop over each file
dsDict = {}
for ds_name in ds_names:
print('adding {} ...'.format(ds_name))
data, atr = readfile.read(fnames[0], datasetName=ds_name)
for i, fname in enumerate(fnames[1:]):
# ignore ds_name if input file has single dataset
ds_name2read = None if len(ds_names_list[i+1]) == 1 else ds_name
# read
data2 = readfile.read(fname, datasetName=ds_name2read)[0]
# apply operation
data = add_matrix(data, data2)
dsDict[ds_name] = data
# output
print('use metadata from the 1st file: {}'.format(fnames[0]))
writefile.write(dsDict, out_file=out_file, metadata=atr, ref_file=fnames[0])
return out_file
################################################################################
def main(iargs=None):
inps = cmd_line_parse(iargs)
print('input files to be added: ({})\n{}'.format(len(inps.file), inps.file))
add_file(inps.file, inps.outfile, force=inps.force)
print('Done.')
return
################################################################################
if __name__ == '__main__':
main(sys.argv[1:])