Coverage for enpt/cli.py: 89%

1#!/usr/bin/env python

2# -*- coding: utf-8 -*-

4# EnPT, EnMAP Processing Tool - A Python package for pre-processing of EnMAP Level-1B data

7# (GFZ Potsdam, danschef@gfz-potsdam.de), Niklas Bohn (GFZ Potsdam, nbohn@gfz-potsdam.de),

8# Stephane Guillaso (GFZ Potsdam, stephane.guillaso@gfz-potsdam.de)

10# This software was developed within the context of the EnMAP project supported

11# by the DLR Space Administration with funds of the German Federal Ministry of

12# Economic Affairs and Energy (on the basis of a decision by the German Bundestag:

13# 50 EE 1529) and contributions from DLR, GFZ and OHB System AG.

14#

15# This program is free software: you can redistribute it and/or modify it under

16# the terms of the GNU General Public License as published by the Free Software

17# Foundation, either version 3 of the License, or (at your option) any later

18# version. Please note the following exception: `EnPT` depends on tqdm, which

19# is distributed under the Mozilla Public Licence (MPL) v2.0 except for the files

20# "tqdm/_tqdm.py", "setup.py", "README.rst", "MANIFEST.in" and ".gitignore".

21# Details can be found here: https://github.com/tqdm/tqdm/blob/master/LICENCE.

22#

23# This program is distributed in the hope that it will be useful, but WITHOUT

24# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS

25# FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more

26# details.

27#

28# You should have received a copy of the GNU Lesser General Public License along

29# with this program. If not, see <https://www.gnu.org/licenses/>.

31"""EnPT console argument parser."""

33import argparse

34import sys

36from enpt import __version__

37from enpt.options.config import EnPTConfig

38from enpt.execution.controller import EnPT_Controller

40__author__ = 'Daniel Scheffler'

43def get_enpt_argparser():

44 """Return argument parser for the 'enpt' program."""

46 ##########################################################

47 # CONFIGURE MAIN PARSER FOR THE EnPT PREPROCESSING CHAIN #

48 ##########################################################

50 parser = argparse.ArgumentParser(

51 prog='enpt',

52 description='=' * 70 + '\n' + 'EnMAP Processing Tool console argument parser. ',

53 epilog="use '>>> enpt -h' for detailed documentation and usage hints.")

55 add = parser.add_argument

56 add('--version', action='version', version=__version__)

58 # NOTE: don't define any defaults here for parameters that are passed to EnPTConfig!

59 # -> otherwise, we cannot distinguish between explicity given parameters and default values

60 # => see docs in parsedArgs_to_user_opts() for explanation

61 add('-jc', '--json_config', nargs='?', type=str,

62 help='file path of a JSON file containing options. See here for an example: '

63 'https://git.gfz-potsdam.de/EnMAP/GFZ_Tools_EnMAP_BOX/'

64 'EnPT/blob/main/enpt/options/options_default.json')

65 add('--CPUs', type=int, default=None,

66 help='number of CPU cores to be used for processing (default: "None" -> use all available)')

67 add('-im', '--path_l1b_enmap_image', type=str, default=None,

68 help='input path of the EnMAP L1B image to be processed '

69 '(zip-archive or root directory; must be given if not contained in --json-config.)')

70 add('-imgap', '--path_l1b_enmap_image_gapfill', type=str, default=None,

71 help='input path of an adjacent EnMAP L1B image to be used for gap-filling (zip-archive or root directory)')

72 add('-dem', '--path_dem', type=str, default=None,

73 help='input path of digital elevation model in map or sensor geometry; GDAL compatible file format '

74 '(must cover the EnMAP L1B data completely if given in map geometry or must have the same pixel '

75 'dimensions like the EnMAP L1B data if given in sensor geometry)')

76 add('-dummyfmt', '--is_dummy_dataformat', type=_str2bool, default=False, nargs='?', const=True,

77 help='Set to true in case of the preliminary, GFZ-internal dataformat as used for the Alpine test dataset. '

78 '(default: False. Note: This will be removed in future.)')

79 add('-ele', '--average_elevation', type=int, default=0,

80 help='average elevation in meters above sea level; may be provided if no DEM is available; '

81 'ignored if DEM is given')

82 add('-od', '--output_dir', type=str, default=None,

83 help='output directory where processed data and log files are saved')

84 add('-of', '--output_format', type=str, default='GTiff',

85 help="file format of all raster output files ('GTiff': GeoTIFF, 'ENVI': ENVI BSQ; default: 'ENVI')")

86 add('-ointlv', '--output_interleave', type=str, default='pixel',

87 help="raster data interleaving type ('band', 'line', 'pixel'; default: 'pixel')")

88 add('-ond', '--output_nodata_value', type=int, default=-32768,

89 help="output no-data/background value (should be within the integer 16-bit range)")

90 add('-wd', '--working_dir', type=str, default=None,

91 help='directory to be used for temporary files')

92 add('-nla', '--n_lines_to_append', type=int, default=None,

93 help='number of lines to be added to the main image [if None, use the whole imgap]. Requires --imgap to be set')

94 add('-dbb', '--drop_bad_bands', type=_str2bool, default=True,

95 help='if set to True (default), the water absorption bands between 1358 and 1453 nm as well as between 1814 '

96 'and 1961 nm are excluded from processing and will not be contained in the L2A product')

97 add('-dpb', '--disable_progress_bars', type=_str2bool, default=False, nargs='?', const=True,

98 help='whether to disable all progress bars during processing')

99 add('--path_earthSunDist', type=str, default=None,

100 help='input path of the earth sun distance model')

101 add('--path_solar_irr', type=str, default=None,

102 help='input path of the solar irradiance model')

103 add('--scale_factor_toa_ref', type=int, default=None,

104 help='scale factor to be applied to TOA reflectance result')

105 add('--enable_keystone_correction', type=_str2bool, default=False, nargs='?', const=True,

106 help='Enable keystone correction')

107 add('--enable_vnir_swir_coreg', type=_str2bool, default=False, nargs='?', const=True,

108 help='Enable VNIR/SWIR co-registration')

109 add('--path_reference_image', type=str, default=None,

110 help='Reference image for co-registration.')

111 add('--polymer_root', type=str, default=None,

112 help='Polymer root directory (that contains the subdirectory for ancillary data)')

113 add('--enable_ac', type=_str2bool, default=True, nargs='?', const=True,

114 help="Enable atmospheric correction using SICOR algorithm (default: True). If False, the L2A output contains "

115 "top-of-atmosphere reflectance")

116 add('--mode_ac', type=str, default=None, nargs='?',

117 help="3 modes to determine which atmospheric correction is applied at which surfaces (default: land): "

118 "('land', water', 'combined')")

119 add('--polymer_additional_results', type=_str2bool, default=True, nargs='?', const=True,

120 help="Enable the generation of additional results when running ACwater/POLYMER (default: True)")

121 add('--auto_download_ecmwf', type=_str2bool, default=True, nargs='?', const=True,

122 help='Automatically download ECMWF AUX data when running Polymer atmospheric correction for water surfaces')

123 add('--scale_factor_boa_ref', type=int, default=10000,

124 help='Scale factor to be applied to BOA reflectance result')

125 add('--threads', type=int, default=-1,

126 help='Number of threads in ACwater Polymer: 0 for single thread; < 0 for as many as there are CPUs; '

127 'and > 0 gives the number of threads')

128 add('--blocksize', type=int, default=100,

129 help='Block size in ACwater Polymer')

130 add('--run_smile_P', type=_str2bool, default=False, nargs='?', const=True,

131 help='Enable extra smile detection and correction (provider smile coefficients are ignored)')

132 add('--run_deadpix_P', type=_str2bool, default=False, nargs='?', const=True,

133 help='Enable dead pixel correction')

134 add('--deadpix_P_algorithm', type=str, default="spatial",

135 help="Algorithm for dead pixel correction ('spectral' or 'spatial')")

136 add('--deadpix_P_interp_spectral', type=str, default="linear",

137 help="Spectral interpolation algorithm to be used during dead pixel correction "

138 "('linear', 'quadratic', 'cubic')")

139 add('--deadpix_P_interp_spatial', type=str, default="linear",

140 help="Spatial interpolation algorithm to be used during dead pixel correction "

141 "('linear', 'nearest', 'zero', 'slinear', 'quadratic', 'cubic')")

142 add('--ortho_resampAlg', type=str, default='bilinear',

143 help="Ortho-rectification resampling algorithm ('nearest', 'bilinear', 'gauss', 'cubic', 'cubic_spline', "

144 "'lanczos', 'average', 'mode', 'max', 'min', 'med', 'q1', 'q3')")

145 add('--vswir_overlap_algorithm', type=str, default='swir_only',

146 help="Algorithm specifying how to deal with the spectral bands in the VNIR/SWIR spectral overlap region "

147 "('order_by_wvl', 'average', 'vnir_only', 'swir_only')")

148 add('-tgtprj', '--target_projection_type', type=str, default='UTM',

149 help="Projection type of the raster output files ('UTM', 'Geographic') (default: 'UTM')")

150 add('-tgtepsg', '--target_epsg', type=int, default=None,

151 help="Custom EPSG code of the target projection (overrides target_projection_type)")

152 add('-tgtgrid', '--target_coord_grid', nargs=4, type=float, default=None,

153 help="Custom target coordinate grid where is output is resampled to ([x0, x1, y0, y1], e.g., [0, 30, 0, 30])")

154

155 # link parser to run function

156 parser.set_defaults(func=run_job)

157

158 return parser

159

160

161def parsedArgs_to_user_opts(cli_args: argparse.Namespace) -> dict:

162 """Convert argparse Namespace object to dictionary of explicitly given parameters.

163

164 NOTE: All options that have not been given explicitly (None values) are removed. Reason: EnPTConfig prefers

165 directly passed arguments against those that are passed withi a JSON config file.

166 So, e.g., if CPUs=None (default), the 'CPUs' parameter given within a JSON config file would be overridden.

167

168 => only override JSON configuration if parameters are explicitly given (e.g., CPUs is set to 10)

169 => if json_opts are given: default options are overridden with the options in the JSON config.

170

171 :param cli_args: options as parsed by the argparse.ArgumentParser

172 """

173 # convert argparse Namespace object to dictionary

174 opts = {k: v for k, v in vars(cli_args).items() if not k.startswith('_') and k != 'func'}

175

176 # activate absolute coreg if a reference image is given (the argparser does not separate these two options)

177 if opts['path_reference_image']:

178 opts['enable_absolute_coreg'] = True

179

180 # remove those options that have not been given explicitly (None values)

181 user_opts = dict()

182 for k, v in opts.items():

183 # values are None if they are not given by the user -> don't pass to set_config

184 if v is None:

185 continue

186 else:

187 user_opts.update({k: v})

188

189 return user_opts

190

191

192def get_config(cli_args: argparse.Namespace):

193 return EnPTConfig(**parsedArgs_to_user_opts(cli_args))

194

195

196def run_job(config: EnPTConfig):

197 CTR = EnPT_Controller(config)

198 CTR.run_all_processors()

199

200

201def _str2bool(v):

202 """Convert string parameter to bool.

203

204 From: https://stackoverflow.com/a/43357954/2952871

205

206 :param v:

207 :return:

208 """

209 if isinstance(v, bool):

210 return v

211 if v.lower() in ('yes', 'true', 't', 'y', '1'):

212 return True

213 elif v.lower() in ('no', 'false', 'f', 'n', '0'):

214 return False

215 else:

216 raise argparse.ArgumentTypeError('Boolean value expected.')

217

218

219def main(parsed_args: argparse.Namespace = None) -> int:

220 """Run the argument parser and forward the arguments to the linked functions.

221

222 :param parsed_args: argparse.Namespace instance of already parsed arguments

223 (allows to call main() from test_cli_parser.py while passing specific arguments)

224

225 :return: exitcode (0: all fine, >=1: failed)

226 """

227 if not parsed_args:

228 parsed_args = get_enpt_argparser().parse_args() # type: argparse.Namespace

229

230 parsed_args.func(get_config(parsed_args))

231

232 print('\nready.')

233

234 return 0

235

236

237if __name__ == '__main__':

238 sys.exit(main()) # pragma: no cover