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
|
#!/usr/bin/env python
"""This module describe nxtomomill applications which are available through
the silx launcher.
Your environment should provide a command `nxtomomill`. You can reach help with
`tomwer --help`, and check the version with `nxtomomill --version`.
"""
import logging
import sys
from collections import namedtuple
from silx.utils.launcher import Launcher as _Launcher
import nxtomomill.version
from nxtomomill.utils.io import deprecated_warning
logging.basicConfig()
DeprecationWarning = namedtuple(
"DeprecationWarning", ["since", "reason", "replacement"]
)
class Launcher(_Launcher):
"""
Manage launch of module.
Provides an API to describe available commands and feature to display help
and execute the commands.
"""
def __init__(
self, prog=None, usage=None, description=None, epilog=None, version=None
):
super().__init__(
prog=prog,
usage=usage,
description=description,
epilog=epilog,
version=version,
)
self._deprecations = {}
"deprecations with prog names as key and deprecation info as values"
def add_command(
self,
name=None,
module_name=None,
description=None,
command=None,
deprecated=False,
deprecated_since_version=None,
deprecated_reason=None,
deprecated_replacement=None,
):
super().add_command(
name=name, module_name=module_name, description=description, command=command
)
if deprecated:
self._deprecations[name] = DeprecationWarning(
since=deprecated_since_version,
reason=deprecated_reason,
replacement=deprecated_replacement,
)
def execute(self, argv=None):
if argv is None:
argv = sys.argv
if len(argv) <= 1:
self.print_help()
return 0
command_name = argv[1]
if command_name in self._deprecations:
deprecation_info = self._deprecations[command_name]
deprecated_warning(
type_="application",
name=command_name,
reason=deprecation_info.reason,
replacement=deprecation_info.replacement,
since_version=deprecation_info.since,
)
super().execute(argv=argv)
def print_help(self):
"""Print the help to stdout."""
usage = self.usage
if usage is None:
usage = "usage: {0.prog} [--version|--help] <command> [<args>]"
description = self.description
epilog = self.epilog
if epilog is None:
epilog = "See '{0.prog} help <command>' to read about a specific subcommand"
print(usage.format(self))
print("")
if description is not None:
print(description)
print("")
print("The {0.prog} commands are:".format(self))
commands = sorted(self._commands.keys())
for command in commands:
command = self._commands[command]
print(" {:15} {:s}".format(command.name, command.description))
print("")
print(epilog.format(self))
def main():
"""Main function of the launcher
This function is referenced in the setup.py file, to create a
launcher script generated by setuptools.
:returns: The execution status
"""
_version = nxtomomill.version.version
launcher = Launcher(prog="nxtomomill", version=_version)
launcher.add_command(
"nx-copy",
module_name="nxtomomill.app.nxcopy",
description="Copy one or several NXtomo to another location",
)
launcher.add_command(
"dxfile2nx",
module_name="nxtomomill.app.dxfile2nx",
description="Convert dx file to NXTomo",
)
launcher.add_command(
"patch-nx",
module_name="nxtomomill.app.patch_nx",
description="allow to patch an NXTomo entry",
)
launcher.add_command(
"tomoedf2nx",
module_name="nxtomomill.app.edf2nx",
description="convert spec-edf acquisition to nexus - hdf5",
deprecated=True,
deprecated_reason="remove `tomo` repetition. The shorter the better",
deprecated_replacement="edf2nx",
deprecated_since_version=0.5,
)
launcher.add_command(
"edf2nx",
module_name="nxtomomill.app.edf2nx",
description="convert spec-edf acquisition to nexus - hdf5"
"format to nx compliant file format",
)
launcher.add_command(
"edf2nx-check",
module_name="nxtomomill.app.edf2nx_check",
description="check a conversion from EDF to Nxtomo and optionally remove EDF files",
)
launcher.add_command(
"edf-quick-start",
module_name="nxtomomill.app.edfconfig",
description="create a configuration file to convert from spec-edf to NXtomo",
deprecated_replacement="edf-config",
deprecated_since_version=0.13,
)
launcher.add_command(
"edf-config",
module_name="nxtomomill.app.edfconfig",
description="create a configuration file to convert from spec-edf to NXtomo",
)
launcher.add_command(
"fluo-config",
module_name="nxtomomill.app.fluoconfig",
description="create a configuration file to convert from fluo-tomo to NXtomo",
)
launcher.add_command(
"fluo2nx",
module_name="nxtomomill.app.fluo2nx",
description="Converts from fluo-tomo to NXtomo",
)
launcher.add_command(
"tomoh52nx",
module_name="nxtomomill.app.h52nx",
description="convert bliss hdf5 to nexus hdf5",
deprecated=True,
deprecated_reason="remove `tomo` repetition. The shorter the better",
deprecated_replacement="h52nx",
deprecated_since_version=0.5,
)
launcher.add_command(
"h52nx",
module_name="nxtomomill.app.h52nx",
description="convert bliss hdf5 to nexus hdf5",
)
launcher.add_command(
"z-concatenate-scans",
module_name="nxtomomill.app.z_concatenate_scans",
description="Build a concatenation nexus file from a z-series",
)
launcher.add_command(
"zstages2nxs",
module_name="nxtomomill.app.zstages2nxs",
description="""creates all the target NXTomos for all the stages. Possibly reducing also reference scans for obtaining flats/dark""",
)
launcher.add_command(
"h5-quick-start",
module_name="nxtomomill.app.h5config",
description="Create a default configuration file",
deprecated_replacement="h5-config",
deprecated_since_version=0.13,
)
launcher.add_command(
"h5-config",
module_name="nxtomomill.app.h5config",
description="Create a default configuration file",
)
launcher.add_command(
"split-nxfile",
module_name="nxtomomill.app.split_nxfile",
description="Split a file containing several NXtomo into a one file per NXtomo",
)
launcher.add_command(
"fscan2nx",
module_name="nxtomomill.app.fscan2nx",
description="convert fscan hdf5 to nexus hdf5",
)
status = launcher.execute(sys.argv)
return status
if __name__ == "__main__":
# executed when using python -m PROJECT_NAME
status = main()
sys.exit(status)
|
