#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Copyright (c) 2020-2022 INRAE Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. """ """Pre-process one Sentinel-2 image""" import logging import argparse import otbApplication from decloud.core import system, tile_io import decloud.preprocessing.constants as constants system.basic_logging_init() def fconc(il, suffix, tilesize, out_tile_dir, pixel_type=otbApplication.ImagePixelType_int16): """ Performs the concatenation of bands + tiling + compression :param il: input images list :param suffix: suffix :param tilesize: tile size :param out_tile_dir: Output repository :param pixel_type: otb pixel type """ logging.info("Concatenate + Tile + Compress GeoTiff for files: %s", "".join(il)) out_fn = system.basename(il[0]) out_fn = out_fn[:out_fn.rfind("_")] out_fn = os.path.join(out_tile_dir, out_fn + "_" + suffix) out_fn += ".tif?&gdal:co:COMPRESS=DEFLATE" out_fn += "&streaming:type=tiled&streaming:sizemode=height&streaming:sizevalue={}".format(4 * tilesize) out_fn += "&gdal:co:TILED=YES&gdal:co:BLOCKXSIZE={ts}&gdal:co:BLOCKYSIZE={ts}".format(ts=tilesize) if system.is_complete(out_fn): logging.info("File %s already existing. Skipping.", system.remove_ext_filename(out_fn)) return logging.info("Output: %s Tile size: %s", out_fn, tilesize) conc = otbApplication.Registry.CreateApplication("ConcatenateImages") conc.SetParameterStringList("il", il) conc.SetParameterString("out", out_fn) conc.SetParameterOutputImagePixelType("out", pixel_type) conc.ExecuteAndWriteOutput() system.declare_complete(out_fn) def main(args): """Main""" # Arguments parser = argparse.ArgumentParser(description="S2 to tiled geotiff", usage="The input (\"--in_image parameter\") can be a .zip file, or a directory " "containing the product. " "The \"--out_s2_dir\" parameter is for the root directory for all " "Sentinel-2 tiles sub-folders, that will be automatically created if they " "don't exist. No need to create the tiles folders like \"T31TEJ\"... just " "provide the root directory that will host all the tiles using the " "\"--out_s2_dir\" parameter (e.g. \"--out_s2_dir /path/to/S2_PREPARE/\"). " "When the output files already exist, they are skipped.") parser.add_argument("--in_image", required=True, help="Input Sentinel-2 image (dir or .zip file)") parser.add_argument("--out_s2_dir", required=True, help="Directory for processed Sentinel-2 images") parser.add_argument("--tilesize", type=int, default=constants.PATCHSIZE_REF) params = parser.parse_args(args) is_zip = params.in_image.lower().endswith(".zip") if is_zip: logging.info("Input type is a .zip archive") files = system.list_files_in_zip(params.in_image) else: logging.info("Input type is a directory") files = system.get_files(params.in_image, ".tif") edg_mask = None cld_mask = None channels_10m = [] channels_20m = [] for file in files: if is_zip: file = system.to_vsizip(params.in_image, file) if "EDG_R1" in file: edg_mask = file if "CLM_R1" in file: cld_mask = file if any(bn in file for bn in ["FRE_B2.", "FRE_B3.", "FRE_B4.", "FRE_B8."]): channels_10m.append(file) if any(bn in file for bn in ["FRE_B5.", "FRE_B6.", "FRE_B7.", "FRE_B8A.", "FRE_B11.", "FRE_B12."]): channels_20m.append(file) channels_10m.sort() channels_20m.sort() assert edg_mask is not None assert cld_mask is not None assert len(channels_10m) == 4 assert len(channels_20m) == 6 # Tile name first_ch_fn = channels_10m[0] tile_name_matches = constants.SENTINEL_TILE.search(first_ch_fn) if tile_name_matches is None: logging.fatal("ERROR: unable to detect tile name! (from file %s)", first_ch_fn) system.terminate() tile_name = tile_name_matches[0] logging.info("Tile name is %s", tile_name) # Product name product_name = system.basename(params.in_image) if is_zip: product_name = product_name[:product_name.rfind(".")] if not product_name.startswith("SENTINEL2"): logging.fatal( "ERROR: Wrong product name: %s (Matched from input path: %s)", product_name, params.in_image) system.terminate() logging.info("Product name is %s", product_name) # Out directory out_tile_dir = os.path.join(params.out_s2_dir, tile_name, product_name) logging.info("Create or use the following output directory: %s", out_tile_dir) system.mkdir(out_tile_dir) # Concatenate + Tile + Compress fconc(channels_10m, "10m", int(1.0 * params.tilesize), out_tile_dir) fconc(channels_20m, "20m", int(0.5 * params.tilesize), out_tile_dir) fconc([edg_mask], "R1", int(1.0 * params.tilesize), out_tile_dir, otbApplication.ImagePixelType_uint8) fconc([cld_mask], "R1", int(1.0 * params.tilesize), out_tile_dir, otbApplication.ImagePixelType_uint8) # Generate ancillary files tile_io.create_s2_image_from_dir(s2_product_dir=out_tile_dir, ref_patchsize=constants.PATCHSIZE_REF, patchsize_10m=256, with_cld_mask=True, with_20m_bands=True) if __name__ == "__main__": system.run_and_terminate(main)