1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239 | # This Python module is part of the PyRate software package.
#
# Copyright 2020 Geoscience Australia
#
# 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.
"""
This Python module contains utilities to validate user input parameters
parsed in a PyRate configuration file.
"""
from configparser import ConfigParser
from pathlib import Path, PurePath
from typing import Union
from pyrate.constants import NO_OF_PARALLEL_PROCESSES
from pyrate.default_parameters import PYRATE_DEFAULT_CONFIGURATION
from pyrate.core.algorithm import factorise_integer
from pyrate.core.shared import extract_epochs_from_filename, InputTypes
from pyrate.core.config import parse_namelist, ConfigException, ORB_ERROR_DIR, TEMP_MLOOKED_DIR
def set_parameter_value(data_type, input_value, default_value, required, input_name):
if len(input_value) < 1:
input_value = None
if required: # pragma: no cover
raise ValueError("A required parameter is missing value in input configuration file: " + str(input_name))
if input_value is not None:
if str(data_type) in "path":
return Path(input_value)
return data_type(input_value)
return default_value
def validate_parameter_value(input_name, input_value, min_value=None, max_value=None, possible_values=None):
if isinstance(input_value, PurePath):
if not Path.exists(input_value): # pragma: no cover
raise ValueError("Given path: " + str(input_value) + " does not exist.")
if input_value is not None:
if min_value is not None:
if input_value < min_value: # pragma: no cover
raise ValueError(
"Invalid value for " + str(input_name) + " supplied: " + str(input_value) + ". Provide a value greater than or equal to " + str(min_value) + ".")
if input_value is not None:
if max_value is not None:
if input_value > max_value: # pragma: no cover
raise ValueError(
"Invalid value for " + str(input_name) + " supplied: " + str(input_value) + ". Provide a value less than or equal to " + str(max_value) + ".")
if possible_values is not None:
if input_value not in possible_values: # pragma: no cover
raise ValueError(
"Invalid value for " + str(input_name) + " supplied: " + str(input_value) + ". Provide a value from: " + str(possible_values) + ".")
return True
def validate_file_list_values(file_list, no_of_epochs):
if file_list is None: # pragma: no cover
raise ValueError("No value supplied for input file list: " + str(file_list))
files = parse_namelist(file_list)
for f in files:
if not Path(f).exists(): # pragma: no cover
raise ConfigException(f"{f} does not exist")
else:
matches = extract_epochs_from_filename(filename_with_epochs=f)
if len(matches) < no_of_epochs: # pragma: no cover
raise ConfigException(f"the number of epochs in {f} names are less the required number: {no_of_epochs}")
class MultiplePaths:
def __init__(self, out_dir: str, file_name: str, ifglksx: int = 1, ifgcropopt: int = 1,
input_type: InputTypes = InputTypes.IFG, tempdir: Union[Path, str] = TEMP_MLOOKED_DIR):
self.input_type = input_type
b = Path(file_name)
if b.suffix == ".tif":
self.unwrapped_path = None
converted_path = b # original file
self.sampled_path = Path(out_dir).joinpath(
b.stem + '_' + str(ifglksx) + "rlks_" + str(ifgcropopt) + "cr.tif")
else:
self.unwrapped_path = b.as_posix()
converted_path = Path(out_dir).joinpath(
b.stem.split('.')[0] + '_' + b.suffix[1:] + input_type.value).with_suffix('.tif')
self.sampled_path = converted_path.with_name(
converted_path.stem + '_' + str(ifglksx) + "rlks_" + str(ifgcropopt) + "cr.tif")
if not isinstance(tempdir, Path):
tempdir = Path(out_dir).joinpath(tempdir)
self.tmp_sampled_path = tempdir.joinpath(self.sampled_path.name).as_posix()
self.sampled_path = self.sampled_path.as_posix()
self.converted_path = converted_path.as_posix()
def __str__(self): # pragma: no cover
st = ""
if self.unwrapped_path is not None:
st += """\nunwrapped_path = """ + self.unwrapped_path
else:
st += """\nunwrapped_path = None"""
st += """
converted_path = """ + self.converted_path+"""
sampled_path = """ + self.sampled_path+"""
tmp_sampled_path = """ + self.tmp_sampled_path+"""
"""
return st
class Configuration:
def __init__(self, config_file_path):
parser = ConfigParser()
parser.optionxform = str
# mimic header to fulfil the requirement for configparser
with open(config_file_path) as stream:
parser.read_string("[root]\n" + stream.read())
for key, value in parser["root"].items():
self.__dict__[key] = value
# make output path, if not provided will error
Path(self.outdir).mkdir(exist_ok=True, parents=True)
# custom process sequence if 'process' section is provided in config
if 'process' in parser and 'steps' in parser['process']:
self.__dict__['process'] = list(filter(None, parser['process'].get('steps').splitlines()))
else:
self.__dict__['process'] = [
'orbfit',
'refphase',
'mst',
'apscorrect',
'maxvar',
'timeseries',
'stack'
]
# Validate required parameters exist.
required = {k for k, v in PYRATE_DEFAULT_CONFIGURATION.items() if v['Required']}
if not required.issubset(self.__dict__): # pragma: no cover
raise ValueError("Required configuration parameters: " + str(
required.difference(self.__dict__)) + " are missing from input config file.")
# handle control parameters
for parameter_name in PYRATE_DEFAULT_CONFIGURATION:
param_value = self.__dict__[parameter_name] if parameter_name in required or \
parameter_name in self.__dict__ else ''
self.__dict__[parameter_name] = set_parameter_value(PYRATE_DEFAULT_CONFIGURATION[parameter_name]["DataType"],
param_value,
PYRATE_DEFAULT_CONFIGURATION[parameter_name]["DefaultValue"],
PYRATE_DEFAULT_CONFIGURATION[parameter_name]["Required"],
parameter_name)
validate_parameter_value(parameter_name, self.__dict__[parameter_name],
PYRATE_DEFAULT_CONFIGURATION[parameter_name]["MinValue"],
PYRATE_DEFAULT_CONFIGURATION[parameter_name]["MaxValue"],
PYRATE_DEFAULT_CONFIGURATION[parameter_name]["PossibleValues"])
# bespoke parameter validation
if self.refchipsize % 2 != 1: # pragma: no cover
if self.refchipsize - 1 > 1:
# Configuration parameters refchipsize must be odd
# values too large (>101) will slow down the process without significant gains in results.
self.refchipsize = self.refchipsize - 1
# calculate rows and cols if not supplied
if hasattr(self, 'rows') and hasattr(self, 'cols'):
self.rows, self.cols = int(self.rows), int(self.cols)
else:
self.rows, self.cols = [int(num) for num in factorise_integer(NO_OF_PARALLEL_PROCESSES)]
# create a temporary directory if not supplied
if not hasattr(self, 'tmpdir'):
self.tmpdir = Path(self.outdir).joinpath("tmpdir")
else:
self.tmpdir = Path(self.tmpdir)
self.tmpdir.mkdir(parents=True, exist_ok=True)
# create orbfit error dir
self.orb_error_dir = Path(self.outdir).joinpath(ORB_ERROR_DIR)
self.orb_error_dir.mkdir(parents=True, exist_ok=True)
# create temp multilooked files dir
self.temp_mlooked_dir = Path(self.outdir).joinpath(TEMP_MLOOKED_DIR)
self.temp_mlooked_dir.mkdir(parents=True, exist_ok=True)
# var no longer used
self.APS_ELEVATION_EXT = None
self.APS_INCIDENCE_EXT = None
self.apscorrect = 0
self.apsmethod = 0
self.elevationmap = None
self.incidencemap = None
# define parallel processes that will run
self.NUMEXPR_MAX_THREADS = str(NO_OF_PARALLEL_PROCESSES)
# Validate file names supplied in list exist and contain correct epochs in file names
if self.cohfilelist is not None:
# if self.processor != 0: # not roipac
validate_file_list_values(self.cohfilelist, 1)
self.coherence_file_paths = self.__get_files_from_attr('cohfilelist', input_type=InputTypes.COH)
self.header_file_paths = self.__get_files_from_attr('hdrfilelist', input_type=InputTypes.HEADER)
self.interferogram_files = self.__get_files_from_attr('ifgfilelist')
self.dem_file = MultiplePaths(self.outdir, self.demfile, self.ifglksx, self.ifgcropopt,
input_type=InputTypes.DEM)
# backward compatibility for string paths
for key in self.__dict__:
if isinstance(self.__dict__[key], PurePath):
self.__dict__[key] = str(self.__dict__[key])
def __get_files_from_attr(self, attr, input_type=InputTypes.IFG):
val = self.__getattribute__(attr)
files = parse_namelist(val)
return [
MultiplePaths(self.outdir, p, self.ifglksx, self.ifgcropopt, input_type=input_type,
tempdir=self.temp_mlooked_dir) for p in files
]
def write_config_parser_file(conf: ConfigParser, output_conf_file: Union[str, Path]):
"""replacement function for write_config_file which uses dict instead of a ConfigParser instance"""
with open(output_conf_file, 'w') as configfile:
conf.write(configfile)
|