def main(args=None):
"""
This is the main function called by the `velplot` script.
"""
from astropy.utils.compat import argparse
from astropy.extern.configobj import configobj, validate
from pkg_resources import resource_stream
parser = argparse.ArgumentParser(
description='Creates a stacked velocity plot.\nTo dump a default '
'configuration file: velplot -d\nTo dump an extended '
'default configuration file: velplot -dd',
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('config', help='path to the configuration file')
config = resource_stream(__name__, '/config/velplot.cfg')
config_extended = resource_stream(__name__, '/config/velplot_extended.cfg')
spec = resource_stream(__name__, '/config/velplot_specification.cfg')
if len(sys.argv) > 1:
if sys.argv[1] == '-d':
cfg = ConfigObj(config)
cfg.filename = '{0}/velplot.cfg'.format(os.getcwd())
cfg.write()
return
elif sys.argv[1] == '-dd':
cfg = ConfigObj(config_extended)
cfg.filename = '{0}/velplot.cfg'.format(os.getcwd())
cfg.write()
return
args = parser.parse_args(args)
try:
cfg = configobj.ConfigObj(args.config, configspec=spec)
validator = validate.Validator()
cfg.validate(validator)
except:
raise IOError('Configuration file could not be read')
figname = cfg['FIGURE'].pop('filename')
# Create list of transitions:
fname = cfg['FIGURE'].pop('transitions')
print('Reading transitions from ', fname)
fh = open(fname)
transitions = list(fh)
fh.close()
# Don't include transitions that are commented out:
transitions = [transition for transition in transitions
if not transition.startswith('#')]
# Initialise figure:
velplot = VelocityPlot(transitions, **cfg['FIGURE'])
fname = cfg['DATA'].pop('filename')
if not fname:
raise IOError('no data to plot!')
# Get spectrum information and plot:
spectrum = (Table.read(fname) if fname.endswith('fits')
else ascii.read(fname))
wavelength = spectrum[cfg['DATA'].pop('wavelength_column')]
flux = spectrum[cfg['DATA'].pop('flux_column')]
error = spectrum[cfg['DATA'].pop('error_column')]
continuum = spectrum[cfg['DATA'].pop('continuum_column')]
velplot.plot_data(wavelength, flux, error, continuum, **cfg['DATA'])
# Get model information and plot if specified:
fname = cfg['MODEL'].pop('filename')
if fname:
ion = cfg['MODEL'].pop('ion_column')
redshift = cfg['MODEL'].pop('redshift_column')
logn = cfg['MODEL'].pop('logn_column')
b = cfg['MODEL'].pop('b_column')
if fname.endswith('f26'):
model = read_f26(fname)
absorbers = model.absorbers
else:
table = (Table.read(fname) if fname.endswith('fits')
else ascii.read(fname))
absorbers = [Absorber(row[ion], row[redshift], row[logn], row[b])
for row in table]
velplot.plot_models(absorbers, **cfg['MODEL'])
# Save:
if figname:
print('Saving to {0}'.format(figname))
velplot.savefig(figname)
# Display:
velplot.display()
class ConfigItem(metaclass=InheritDocstrings):
"""
A setting and associated value stored in a configuration file.
These objects should be created as members of
`ConfigNamespace` subclasses, for example::
class _Conf(config.ConfigNamespace):
unicode_output = config.ConfigItem(
False,
'Use Unicode characters when outputting values, and writing widgets '
'to the console.')
conf = _Conf()
Parameters
----------
defaultvalue : object, optional
The default value for this item. If this is a list of strings, this
item will be interpreted as an 'options' value - this item must be one
of those values, and the first in the list will be taken as the default
value.
description : str or None, optional
A description of this item (will be shown as a comment in the
configuration file)
cfgtype : str or None, optional
A type specifier like those used as the *values* of a particular key
in a ``configspec`` file of ``configobj``. If None, the type will be
inferred from the default value.
module : str or None, optional
The full module name that this item is associated with. The first
element (e.g. 'astropy' if this is 'astropy.config.configuration')
will be used to determine the name of the configuration file, while
the remaining items determine the section. If None, the package will be
inferred from the package within which this object's initializer is
called.
aliases : str, or list of str, optional
The deprecated location(s) of this configuration item. If the
config item is not found at the new location, it will be
searched for at all of the old locations.
Raises
------
RuntimeError
If ``module`` is `None`, but the module this item is created from
cannot be determined.
"""
# this is used to make validation faster so a Validator object doesn't
# have to be created every time
_validator = validate.Validator()
cfgtype = None
"""
A type specifier like those used as the *values* of a particular key in a
``configspec`` file of ``configobj``.
"""
def __init__(self,
defaultvalue='',
description=None,
cfgtype=None,
module=None,
aliases=None):
from astropy.utils import isiterable
if module is None:
module = find_current_module(2)
if module is None:
msg1 = 'Cannot automatically determine get_config module, '
msg2 = 'because it is not called from inside a valid module'
raise RuntimeError(msg1 + msg2)
else:
module = module.__name__
self.module = module
self.description = description
self.__doc__ = description
# now determine cfgtype if it is not given
if cfgtype is None:
if (isiterable(defaultvalue)
and not isinstance(defaultvalue, str)):
# it is an options list
dvstr = [str(v) for v in defaultvalue]
cfgtype = 'option(' + ', '.join(dvstr) + ')'
defaultvalue = dvstr[0]
elif isinstance(defaultvalue, bool):
cfgtype = 'boolean'
elif isinstance(defaultvalue, int):
cfgtype = 'integer'
elif isinstance(defaultvalue, float):
cfgtype = 'float'
elif isinstance(defaultvalue, str):
cfgtype = 'string'
defaultvalue = str(defaultvalue)
self.cfgtype = cfgtype
self._validate_val(defaultvalue)
self.defaultvalue = defaultvalue
if aliases is None:
self.aliases = []
elif isinstance(aliases, str):
self.aliases = [aliases]
else:
self.aliases = aliases
def __set__(self, obj, value):
return self.set(value)
def __get__(self, obj, objtype=None):
if obj is None:
return self
return self()
def set(self, value):
"""
Sets the current value of this ``ConfigItem``.
This also updates the comments that give the description and type
information.
Parameters
----------
value
The value this item should be set to.
Raises
------
TypeError
If the provided ``value`` is not valid for this ``ConfigItem``.
"""
try:
value = self._validate_val(value)
except validate.ValidateError as e:
msg = 'Provided value for configuration item {0} not valid: {1}'
raise TypeError(msg.format(self.name, e.args[0]))
sec = get_config(self.module)
sec[self.name] = value
@contextmanager
def set_temp(self, value):
"""
Sets this item to a specified value only inside a with block.
Use as::
ITEM = ConfigItem('ITEM', 'default', 'description')
with ITEM.set_temp('newval'):
#... do something that wants ITEM's value to be 'newval' ...
print(ITEM)
# ITEM is now 'default' after the with block
Parameters
----------
value
The value to set this item to inside the with block.
"""
initval = self()
self.set(value)
try:
yield
finally:
self.set(initval)
def reload(self):
""" Reloads the value of this ``ConfigItem`` from the relevant
configuration file.
Returns
-------
val
The new value loaded from the configuration file.
"""
self.set(self.defaultvalue)
baseobj = get_config(self.module, True)
secname = baseobj.name
cobj = baseobj
# a ConfigObj's parent is itself, so we look for the parent with that
while cobj.parent is not cobj:
cobj = cobj.parent
newobj = configobj.ConfigObj(cobj.filename, interpolation=False)
if secname is not None:
if secname not in newobj:
return baseobj.get(self.name)
newobj = newobj[secname]
if self.name in newobj:
baseobj[self.name] = newobj[self.name]
return baseobj.get(self.name)
def __repr__(self):
out = '<{}: name={!r} value={!r} at 0x{:x}>'.format(
self.__class__.__name__, self.name, self(), id(self))
return out
def __str__(self):
out = '\n'.join(
('{0}: {1}', ' cfgtype={2!r}', ' defaultvalue={3!r}',
' description={4!r}', ' module={5}', ' value={6!r}'))
out = out.format(self.__class__.__name__, self.name, self.cfgtype,
self.defaultvalue, self.description, self.module,
self())
return out
def __call__(self):
""" Returns the value of this ``ConfigItem``
Returns
-------
val
This item's value, with a type determined by the ``cfgtype``
attribute.
Raises
------
TypeError
If the configuration value as stored is not this item's type.
"""
def section_name(section):
if section == '':
return 'at the top-level'
else:
return f'in section [{section}]'
options = []
sec = get_config(self.module)
if self.name in sec:
options.append((sec[self.name], self.module, self.name))
for alias in self.aliases:
module, name = alias.rsplit('.', 1)
sec = get_config(module)
if '.' in module:
filename, module = module.split('.', 1)
else:
filename = module
module = ''
if name in sec:
if '.' in self.module:
new_module = self.module.split('.', 1)[1]
else:
new_module = ''
warn(
"Config parameter '{}' {} of the file '{}' "
"is deprecated. Use '{}' {} instead.".format(
name, section_name(module),
get_config_filename(filename), self.name,
section_name(new_module)), AstropyDeprecationWarning)
options.append((sec[name], module, name))
if len(options) == 0:
self.set(self.defaultvalue)
options.append((self.defaultvalue, None, None))
if len(options) > 1:
filename, sec = self.module.split('.', 1)
warn(
"Config parameter '{}' {} of the file '{}' is "
"given by more than one alias ({}). Using the first.".format(
self.name, section_name(sec),
get_config_filename(filename), ', '.join([
'.'.join(x[1:3]) for x in options if x[1] is not None
])), AstropyDeprecationWarning)
val = options[0][0]
try:
return self._validate_val(val)
except validate.ValidateError as e:
raise TypeError('Configuration value not valid:' + e.args[0])
def _validate_val(self, val):
""" Validates the provided value based on cfgtype and returns the
type-cast value
throws the underlying configobj exception if it fails
"""
# note that this will normally use the *class* attribute `_validator`,
# but if some arcane reason is needed for making a special one for an
# instance or sub-class, it will be used
return self._validator.check(self.cfgtype, val)
def main(args=None):
"""
This is the main function called by the `ivelplot` script.
"""
from astropy.utils.compat import argparse
from astropy.extern.configobj import configobj, validate
from pkg_resources import resource_stream
parser = argparse.ArgumentParser(
description='An interactive environment for absorption line '
'identification and Voigt profile \nfitting with VPFIT.\n'
'\nTo dump a default configuration file: ivelplot -d'
'\nTo dump an extended default configuration file: '
'ivelplot -dd',
formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('config', help='path to the configuration file')
parser.add_argument('-z', '--redshift', help='redshift')
parser.add_argument('--search', action='store_true',
help='display a general search list of ions')
parser.add_argument('--lyman', action='store_true',
help='display the Lyman series transitions')
parser.add_argument('--galactic', action='store_true',
help='display the common Galactic transitions')
parser.add_argument('--agn', action='store_true',
help='display the common AGN associated transitions')
config = resource_stream(__name__, '/config/ivelplot.cfg')
config_extended = resource_stream(
__name__, '/config/ivelplot_extended.cfg')
spec = resource_stream(__name__, '/config/ivelplot_specification.cfg')
if len(sys.argv) > 1:
if sys.argv[1] == '-d':
cfg = configobj.ConfigObj(config)
cfg.filename = '{0}/ivelplot.cfg'.format(os.getcwd())
cfg.write()
return
elif sys.argv[1] == '-dd':
cfg = configobj.ConfigObj(config_extended)
cfg.filename = '{0}/ivelplot.cfg'.format(os.getcwd())
cfg.write()
return
args = parser.parse_args(args)
try:
cfg = configobj.ConfigObj(args.config, configspec=spec)
validator = validate.Validator()
cfg.validate(validator)
except:
raise IOError('Configuration file could not be read')
fname = cfg['WINDOW'].pop('transitions')
if args.search:
fh = resource_stream(__name__, '/data/search.dat')
transitions = list(fh)
fh.close()
elif args.lyman:
fh = resource_stream(__name__, '/data/lyman.dat')
transitions = list(fh)
fh.close()
elif args.galactic:
fh = resource_stream(__name__, '/data/galactic.dat')
transitions = list(fh)
fh.close()
elif args.agn:
fh = resource_stream(__name__, '/data/agn.dat')
transitions = list(fh)
fh.close()
else:
print('Reading transitions from ', fname)
fh = open(fname)
transitions = list(fh)
fh.close()
transitions = [transition for transition in transitions
if not transition.startswith('#')]
fname = cfg['DATA'].pop('filename')
if not fname:
raise IOError('no data to plot!')
spectrum = Table.read(fname) if fname[-4:] == 'fits' else ascii.read(fname)
wavelength = spectrum[cfg['DATA'].pop('wavelength_column')]
flux = spectrum[cfg['DATA'].pop('flux_column')]
error = spectrum[cfg['DATA'].pop('error_column')]
continuum = spectrum[cfg['DATA'].pop('continuum_column')]
redshift = float(args.redshift) if args.redshift is not None else 0
cfg['MODEL']['system_width'] = (cfg['WINDOW']['vmax'] -
cfg['WINDOW']['vmin'])
cfg['MODEL']['absorbers'] = None
print(info)
app = QApplication(sys.argv)
app.aboutToQuit.connect(app.deleteLater)
desktop = app.desktop()
screen = desktop.screenGeometry()
width = screen.width() / desktop.physicalDpiX() * 0.88
fontsize = 0.7 * width
label_fontsize = 0.6 * width
cfg['WINDOW']['width'] = width
cfg['WINDOW']['fontsize'] = fontsize
cfg['WINDOW']['label_fontsize'] = label_fontsize
velocity_plot = InteractiveVelocityPlot(
fname, transitions, wavelength, flux, error, continuum, redshift,
**cfg)
velocity_plot.window.show()
output_stream = OutputStream()
output_stream.text_written.connect(velocity_plot.on_output)
sys.stdout = output_stream
sys.exit(app.exec_())