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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362
|
#!/usr/bin/env python
import sys
import optparse
from importlib import import_module
from glue import __version__
from glue.logger import logger
def parse(argv):
""" Parse argument list, check validity
:param argv: Arguments passed to program
*Returns*
A tuple of options, position arguments
"""
usage = """usage: %prog [options] [FILE FILE...]
# start a new session
%prog
# start a new session and load a file
%prog image.fits
#start a new session with multiple files
%prog image.fits catalog.csv
#restore a saved session
%prog saved_session.glu
or
%prog -g saved_session.glu
#run a script
%prog -x script.py
#run the test suite
%prog -t
"""
parser = optparse.OptionParser(usage=usage,
version=str(__version__))
parser.add_option('-x', '--execute', action='store_true', dest='script',
help="Execute FILE as a python script", default=False)
parser.add_option('-g', action='store_true', dest='restore',
help="Restore glue session from FILE", default=False)
parser.add_option('-t', '--test', action='store_true', dest='test',
help="Run test suite", default=False)
parser.add_option('-c', '--config', type='string', dest='config',
metavar='CONFIG',
help='use CONFIG as configuration file')
parser.add_option('-v', '--verbose', action='store_true',
help="Increase the vebosity level", default=False)
parser.add_option('--no-maximized', action='store_true', dest='nomax',
help="Do not start Glue maximized", default=False)
parser.add_option('--startup', dest='startup', type='string',
help="Startup actions to carry out", default='')
parser.add_option('--auto-merge', dest='auto_merge', action='store_true',
help="Automatically merge any data passed on the command-line", default='')
parser.add_option('--faulthandler', dest='faulthandler', action='store_true',
help="Run glue with the built-in faulthandler to debug segmentation faults", default=False)
err_msg = verify(parser, argv)
if err_msg:
sys.stderr.write('\n%s\n' % err_msg)
parser.print_help()
sys.exit(1)
return parser.parse_args(argv)
def verify(parser, argv):
""" Check for input errors
:param parser: OptionParser instance
:param argv: Argument list
:type argv: List of strings
*Returns*
An error message, or None
"""
opts, args = parser.parse_args(argv)
err_msg = None
if opts.script and opts.restore:
err_msg = "Cannot specify -g with -x"
elif opts.script and opts.config:
err_msg = "Cannot specify -c with -x"
elif opts.script and len(args) != 1:
err_msg = "Must provide a script\n"
elif opts.restore and len(args) != 1:
err_msg = "Must provide a .glu file\n"
return err_msg
def load_data_files(datafiles):
"""Load data files and return a list of datasets"""
from glue.core.data_factories import load_data
datasets = []
for df in datafiles:
datasets.append(load_data(df))
return datasets
def run_tests():
from glue import test
test()
def start_glue(gluefile=None, config=None, datafiles=None, maximized=True,
startup_actions=None, auto_merge=False):
"""Run a glue session and exit
Parameters
----------
gluefile : str
An optional ``.glu`` file to restore.
config : str
An optional configuration file to use.
datafiles : str
An optional list of data files to load.
maximized : bool
Maximize screen on startup. Otherwise, use default size.
auto_merge : bool, optional
Whether to automatically merge data passed in `datafiles` (default is `False`)
"""
import glue
# Some Qt modules are picky in terms of being imported before the
# application is set up, so we import them here. We do it here rather
# than in get_qapp since in the past, including this code in get_qapp
# caused severe issues (e.g. segmentation faults) in plugin packages
# during testing.
try:
from qtpy import QtWebEngineWidgets # noqa
except ImportError: # Not all PyQt installations have this module
pass
from glue.utils.qt.decorators import die_on_error
from glue.utils.qt import get_qapp
app = get_qapp()
splash = get_splash()
splash.show()
# Start off by loading plugins. We need to do this before restoring
# the session or loading the configuration since these may use existing
# plugins.
load_plugins(splash=splash, require_qt_plugins=True)
from glue.app.qt import GlueApplication
datafiles = datafiles or []
hub = None
from qtpy.QtCore import QTimer
timer = QTimer()
timer.setInterval(1000)
timer.setSingleShot(True)
timer.timeout.connect(splash.close)
timer.start()
if gluefile is not None:
with die_on_error("Error restoring Glue session"):
app = GlueApplication.restore_session(gluefile, show=False)
return app.start(maximized=maximized)
if config is not None:
glue.env = glue.config.load_configuration(search_path=[config])
data_collection = glue.core.DataCollection()
hub = data_collection.hub
splash.set_progress(100)
session = glue.core.Session(data_collection=data_collection, hub=hub)
ga = GlueApplication(session=session)
if datafiles:
with die_on_error("Error reading data file"):
datasets = load_data_files(datafiles)
ga.add_datasets(datasets, auto_merge=auto_merge)
if startup_actions is not None:
for name in startup_actions:
ga.run_startup_action(name)
return ga.start(maximized=maximized)
def execute_script(script):
""" Run a python script and exit.
Provides a way for people with pre-installed binaries to use
the glue library
"""
from glue.utils.qt.decorators import die_on_error
with die_on_error("Error running script"):
with open(script) as fin:
exec(fin.read())
sys.exit(0)
def get_splash():
"""Instantiate a splash screen"""
from glue.app.qt.splash_screen import QtSplashScreen
splash = QtSplashScreen()
return splash
def main(argv=sys.argv):
opt, args = parse(argv[1:])
if opt.verbose:
logger.setLevel("INFO")
if opt.faulthandler:
import faulthandler
faulthandler.enable()
logger.info("Input arguments: %s", sys.argv)
# Global keywords for Glue startup.
kwargs = {'config': opt.config,
'maximized': not opt.nomax,
'auto_merge': opt.auto_merge}
if opt.startup:
kwargs['startup_actions'] = opt.startup.split(',')
if opt.test:
return run_tests()
elif opt.restore:
start_glue(gluefile=args[0], **kwargs)
elif opt.script:
execute_script(args[0])
else:
has_file = len(args) == 1
has_files = len(args) > 1
has_py = has_file and args[0].endswith('.py')
has_glu = has_file and args[0].endswith('.glu')
if has_py:
execute_script(args[0])
elif has_glu:
start_glue(gluefile=args[0], **kwargs)
elif has_file or has_files:
start_glue(datafiles=args, **kwargs)
else:
start_glue(**kwargs)
_loaded_plugins = set()
_installed_plugins = set()
REQUIRED_PLUGINS = ['glue.plugins.coordinate_helpers',
'glue.core.data_exporters',
'glue.io.formats.fits']
REQUIRED_PLUGINS_QT = ['glue.plugins.tools.pv_slicer.qt',
'glue.viewers.image.qt',
'glue.viewers.scatter.qt',
'glue.viewers.histogram.qt',
'glue.viewers.table.qt']
def load_plugins(splash=None, require_qt_plugins=False):
# Search for plugins installed via entry_points. Basically, any package can
# define plugins for glue, and needs to define an entry point using the
# following format:
#
# entry_points = """
# [glue.plugins]
# webcam_importer=glue_exp.importers.webcam:setup
# vizier_importer=glue_exp.importers.vizier:setup
# dataverse_importer=glue_exp.importers.dataverse:setup
# """
#
# where ``setup`` is a function that does whatever is needed to set up the
# plugin, such as add items to various registries.
import setuptools
logger.info("Loading external plugins using "
"setuptools=={0}".format(setuptools.__version__))
from glue._plugin_helpers import iter_plugin_entry_points, PluginConfig
config = PluginConfig.load()
n_plugins = len(list(iter_plugin_entry_points()))
for iplugin, item in enumerate(iter_plugin_entry_points()):
if item.module_name not in _installed_plugins:
_installed_plugins.add(item.name)
if item.module_name in _loaded_plugins:
logger.info("Plugin {0} already loaded".format(item.name))
continue
if not config.plugins[item.name]:
continue
# We don't use item.load() because that then checks requirements of all
# the imported packages, which can lead to errors like this one that
# don't really matter:
#
# Exception: (pytest 2.6.0 (/Users/tom/miniconda3/envs/py27/lib/python2.7/site-packages),
# Requirement.parse('pytest>=2.8'), set(['astropy']))
#
# Just to be clear, this kind of error does indicate that there is an
# old version of a package in the environment, but this can confuse
# users as importing astropy directly would work (as setuptools then
# doesn't do a stringent test of dependency versions). Often this kind
# of error can occur if there is a conda version of a package and and
# older pip version.
try:
module = import_module(item.module_name)
function = getattr(module, item.attrs[0])
function()
except Exception as exc:
# Here we check that some of the 'core' plugins load well and
# raise an actual exception if not.
if item.module_name in REQUIRED_PLUGINS:
raise
elif item.module_name in REQUIRED_PLUGINS_QT and require_qt_plugins:
raise
else:
logger.info("Loading plugin {0} failed "
"(Exception: {1})".format(item.name, exc))
else:
logger.info("Loading plugin {0} succeeded".format(item.name))
_loaded_plugins.add(item.module_name)
if splash is not None:
splash.set_progress(100. * iplugin / float(n_plugins))
try:
config.save()
except Exception as e:
logger.warn("Failed to load plugin configuration")
# Reload the settings now that we have loaded plugins, since some plugins
# may have added some settings. Note that this will not re-read settings
# that were previously read.
from glue._settings_helpers import load_settings
load_settings()
if __name__ == "__main__":
sys.exit(main(sys.argv)) # pragma: no cover
|