#! /usr/bin/env python3
#
# Copyright 2019 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.
#
# ISOFIT: Imaging Spectrometer Optimal FITting
# Author: David R Thompson, david.r.thompson@jpl.nasa.gov
#
import scipy as s
from spectral.io import envi
[docs]def remap(inputfile, labels, outputfile, flag, chunksize):
"""."""
ref_file = inputfile
lbl_file = labels
out_file = outputfile
nchunk = chunksize
ref_img = envi.open(ref_file+'.hdr', ref_file)
ref_meta = ref_img.metadata
ref_mm = ref_img.open_memmap(interleave='source', writable=False)
ref = s.array(ref_mm[:, :])
lbl_img = envi.open(lbl_file+'.hdr', lbl_file)
lbl_meta = lbl_img.metadata
labels = lbl_img.read_band(0)
nl = int(lbl_meta['lines'])
ns = int(lbl_meta['samples'])
nb = int(ref_meta['bands'])
out_meta = dict([(k, v) for k, v in ref_meta.items()])
out_meta["samples"] = ns
out_meta["bands"] = nb
out_meta["lines"] = nl
out_meta['data type'] = ref_meta['data type']
out_meta["interleave"] = "bil"
out_img = envi.create_image(out_file+'.hdr', metadata=out_meta,
ext='', force=True)
out_mm = out_img.open_memmap(interleave='source', writable=True)
# Iterate through image "chunks," restoring as we go
for lstart in s.arange(0, nl, nchunk):
print(lstart)
del out_mm
out_mm = out_img.open_memmap(interleave='source', writable=True)
# Which labels will we extract? ignore zero index
lend = min(lstart+nchunk, nl)
lbl = labels[lstart:lend, :]
out = flag * s.ones((lbl.shape[0], nb, lbl.shape[1]))
for row in range(lbl.shape[0]):
for col in range(lbl.shape[1]):
out[row, :, col] = s.squeeze(ref[int(lbl[row, col]), :])
out_mm[lstart:lend, :, :] = out