#! /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: Evan Greenberg, evan.greenberg@jpl.nasa.gov
import click
import numpy as np
from spectral.io import envi
from isofit.core.common import envi_header
[docs]
def reconstruct_subs(input_subs_path, output_path, lbl_working_path):
"""Helper function to take the flat array that the superpixel
algorithms work with and turn them into images at the full resolution
of the input/output file. They will have the full array-resolution,
but appear as coarser pixel-resolution images.\n
args:
input_subs_path: Input subs file path.
output_path: Output reconstructed file path.
lbl_working_path: File path to label file for reconstruction.
returns:
None
"""
# Load the input data
subs_input = envi.open(envi_header(input_subs_path))
subs_input_ar = np.squeeze(subs_input.open_memmap(interleave="bip"))
lbl = envi.open(envi_header(lbl_working_path))
lbl_ar = np.squeeze(lbl.open_memmap(interleave="bip"))
# Make the reconstructed file
sub_full = np.zeros((lbl_ar.shape[0], lbl_ar.shape[1], subs_input_ar.shape[1]))
labels = [0] + list(np.unique(lbl_ar))
for label, lbl_val in zip(labels, subs_input_ar):
row, col = np.where(lbl_ar == label)
sub_full[row, col, :] = lbl_val
# Construct header and init file
output_metadata = subs_input.metadata
output_metadata["samples"] = sub_full.shape[1]
output_metadata["lines"] = sub_full.shape[0]
output_metadata["interleave"] = "bil"
out = envi.create_image(
envi_header(output_path),
ext="",
metadata=output_metadata,
force=True,
)
del out
# Write file
output = envi.open(envi_header(output_path)).open_memmap(
interleave="source", writable=True
)
output[...] = np.swapaxes(sub_full, 1, 2)
del output
# Input arguments
@click.command(
name="reconstruct_subs", help=reconstruct_subs.__doc__, no_args_is_help=True
)
@click.argument("input_subs_path")
@click.argument("output_path")
@click.argument("lbl_working_path")
[docs]
def cli(**kwargs):
reconstruct_subs(**kwargs)
click.echo("Done")