def read_model_components(cfg_file):
"""Read model components from ``model_components/*.fits`` and return
a list of 2D component images with containment masks.
"""
cfg = configobj.ConfigObj(cfg_file)
column_names = ('Name', 'Type', 'GLON', 'GLAT', 'Sigma', 'Norm')
column_types = ('S25', 'S25', np.float32, np.float32, np.float32,
np.float32)
component_table = Table(names=column_names, dtype=column_types)
# Build data table
for component in cfg.keys():
type_ = cfg[component]['Type']
glon = cfg[component]['GLON']
glat = cfg[component]['GLAT']
sigma = cfg[component]['Sigma']
norm = cfg[component]['Norm']
component_table.add_row([component, type_, glon, glat, sigma, norm])
if os.path.exists('model_components/'):
read_fits_files(component_table)
else:
logging.error('No model components found. Please reuse morph_fit.')
if os.path.exists('fit.reg'):
read_region_file(component_table)
else:
compute_containment_radius(component_table)
logging.info('Computing containment radii')
return component_table
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 is_unedited_config_file(content, template_content=None):
"""
Determines if a config file can be safely replaced because it doesn't
actually contain any meaningful content, i.e. if it contains only comments
or is completely empty.
"""
buffer = io.StringIO(content)
raw_cfg = configobj.ConfigObj(buffer, interpolation=True)
# If any of the items is set, return False
return not any(len(v) > 0 for v in raw_cfg.values())
def obsdata(conf='observations.conf'):
"""Load the observation data."""
# C = configobj.ConfigObj(get_pkg_data_filename(conf))
C = configobj.ConfigObj(conf)
# map things from ConfigObj to dictionary of useful objects
obs = {}
for key, val in C.iteritems():
if key == 'psrs' or key == 'pulsars':
obs[key] = parse_pulsars(val)
else:
obs[key] = parse_telescope(key, val)
return obs
def is_unedited_config_file(content, template_content=None):
"""
Determines if a config file can be safely replaced because it doesn't
actually contain any meaningful content.
To meet this criteria, the config file must be either:
- All comments or completely empty
- An exact match to a "legacy" version of the config file prior to
Astropy 0.4, when APE3 was implemented and the config file
contained commented-out values by default.
"""
# We want to calculate the md5sum using universal line endings, so
# that even if the files had their line endings converted to \r\n
# on Windows, this will still work.
content = content.encode('latin-1')
# The jquery_url setting, present in 0.3.2 and later only, is
# effectively auto-generated by the build system, so we need to
# ignore it in the md5sum calculation for 0.3.2.
content = re.sub(br'\njquery_url\s*=\s*[^\n]+', b'', content)
# First determine if the config file has any effective content
buffer = io.BytesIO(content)
buffer.seek(0)
raw_cfg = configobj.ConfigObj(buffer, interpolation=True)
for v in raw_cfg.values():
if len(v):
break
else:
return True
# Now determine if it matches the md5sum of a known, unedited
# config file.
known_configs = set([
'7d4b4f1120304b286d71f205975b1286', # v0.3.2
'5df7e409425e5bfe7ed041513fda3288', # v0.3
'8355f99a01b3bdfd8761ef45d5d8b7e5', # v0.2
'4ea5a84de146dc3fcea2a5b93735e634' # v0.2.1, v0.2.2, v0.2.3, v0.2.4, v0.2.5
])
md5 = hashlib.md5()
md5.update(content)
digest = md5.hexdigest()
return digest in known_configs
def __init__(self, fname=None, obsfile=None, size=2**25):
obs = {}
conf = configobj.ConfigObj(r"{0}".format(obsfile))
for key, val in conf.iteritems():
obs[key] = val
self.dtype = obs["dtype"]
self.sample_rate = float(obs["srate"]) * u.MHz
dm = float(obs["dm"]) * u.pc / u.cm**3
self.dm = DispersionMeasure(dm)
self.thread_ids = list(obs["threads"])
self.fedge = np.array(obs["fedge"]).astype('float') * u.MHz
if 'forder' in obs:
self.forder = np.array(obs["forder"]).astype('int')
else:
self.forder = np.ones(len(self.fedge))
if 'ntrack' in obs:
self.ntrack = int(obs["ntrack"])
else:
self.ntrack = 64
if 'nIF' in obs:
self.nIF = int(obs["nIF"])
self.dt1 = 1 / self.sample_rate
self.size = size
self.f = self.fedge + self.forder * np.fft.rfftfreq(
size, self.dt1)[:, np.newaxis]
self.fref = np.amax(self.f)
self.dmloss = self.dm.time_delay(np.amin(self.f), self.fref)
self.samploss = int(
np.ceil((self.dmloss * self.sample_rate).decompose()).value)
self.step = int(size - 2**(np.ceil(np.log2(self.samploss))))
self.npol = len(self.thread_ids)
print("{0} and {1} samples lost to de-dispersion".format(
self.dmloss, self.samploss))
print("Taking blocks of {0}, steps of {1} samples".format(
self.size, self.step))
if fname:
self.open(fname)
def write_test_cfg_file(spacing=2.):
"""Write test fit.cfg file with 7 sources on a hexagonal grid.
Please specify sigma, excess in fit.cfg and spacing of the sources.
"""
cfg = configobj.ConfigObj('fit.cfg')
# Hexgonal test grid
positions = np.array([[0, 0], [0, 1], [1, 0.5], [1, -0.5], [0, -1],
[-1, -0.5], [-1, 0.5]]) * spacing
# Set source parameters
for i, pos in enumerate(positions):
cfg['Source{0}'.format(i)] = {}
cfg['Source{0}'.format(i)]['Type'] = 'Gaussian'
cfg['Source{0}'.format(i)]['GLON'] = pos[0] + 180
cfg['Source{0}'.format(i)]['GLAT'] = pos[1]
cfg['Source{0}'.format(i)]['Sigma'] = 1.
cfg['Source{0}'.format(i)]['Norm'] = 1.
cfg.write()
def get_config(packageormod=None, reload=False):
""" Gets the configuration object or section associated with a particular
package or module.
Parameters
-----------
packageormod : str or None
The package for which to retrieve the configuration object. If a
string, it must be a valid package name, or if `None`, the package from
which this function is called will be used.
reload : bool, optional
Reload the file, even if we have it cached.
Returns
-------
cfgobj : ``configobj.ConfigObj`` or ``configobj.Section``
If the requested package is a base package, this will be the
``configobj.ConfigObj`` for that package, or if it is a subpackage or
module, it will return the relevant ``configobj.Section`` object.
Raises
------
RuntimeError
If ``packageormod`` is `None`, but the package this item is created
from cannot be determined.
"""
if packageormod is None:
packageormod = find_current_module(2)
if packageormod 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:
packageormod = packageormod.__name__
packageormodspl = packageormod.split('.')
rootname = packageormodspl[0]
secname = '.'.join(packageormodspl[1:])
cobj = _cfgobjs.get(rootname, None)
if cobj is None or reload:
cfgfn = None
try:
# This feature is intended only for use by the unit tests
if _override_config_file is not None:
cfgfn = _override_config_file
else:
cfgfn = path.join(get_config_dir(), rootname + '.cfg')
cobj = configobj.ConfigObj(cfgfn, interpolation=False)
except OSError as e:
msg = ('Configuration defaults will be used due to ')
errstr = '' if len(e.args) < 1 else (':' + str(e.args[0]))
msg += e.__class__.__name__ + errstr
msg += f' on {cfgfn}'
warn(ConfigurationMissingWarning(msg))
# This caches the object, so if the file becomes accessible, this
# function won't see it unless the module is reloaded
cobj = configobj.ConfigObj(interpolation=False)
_cfgobjs[rootname] = cobj
if secname: # not the root package
if secname not in cobj:
cobj[secname] = {}
return cobj[secname]
else:
return cobj
def get_config(packageormod=None, reload=False, rootname=None):
""" Gets the configuration object or section associated with a particular
package or module.
Parameters
----------
packageormod : str or None
The package for which to retrieve the configuration object. If a
string, it must be a valid package name, or if ``None``, the package from
which this function is called will be used.
reload : bool, optional
Reload the file, even if we have it cached.
rootname : str or None
Name of the root configuration directory. If ``None`` and
``packageormod`` is ``None``, this defaults to be the name of
the package from which this function is called. If ``None`` and
``packageormod`` is not ``None``, this defaults to ``astropy``.
Returns
-------
cfgobj : ``configobj.ConfigObj`` or ``configobj.Section``
If the requested package is a base package, this will be the
``configobj.ConfigObj`` for that package, or if it is a subpackage or
module, it will return the relevant ``configobj.Section`` object.
Raises
------
RuntimeError
If ``packageormod`` is `None`, but the package this item is created
from cannot be determined.
"""
if packageormod is None:
packageormod = find_current_module(2)
if packageormod 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:
packageormod = packageormod.__name__
_autopkg = True
else:
_autopkg = False
packageormodspl = packageormod.split('.')
pkgname = packageormodspl[0]
secname = '.'.join(packageormodspl[1:])
if rootname is None:
if _autopkg:
rootname = pkgname
else:
rootname = 'astropy' # so we don't break affiliated packages
cobj = _cfgobjs.get(pkgname, None)
if cobj is None or reload:
cfgfn = None
try:
# This feature is intended only for use by the unit tests
if _override_config_file is not None:
cfgfn = _override_config_file
else:
cfgfn = path.join(get_config_dir(rootname=rootname),
pkgname + '.cfg')
cobj = configobj.ConfigObj(cfgfn, interpolation=False)
except OSError:
# This can happen when HOME is not set
cobj = configobj.ConfigObj(interpolation=False)
# This caches the object, so if the file becomes accessible, this
# function won't see it unless the module is reloaded
_cfgobjs[pkgname] = cobj
if secname: # not the root package
if secname not in cobj:
cobj[secname] = {}
return cobj[secname]
else:
return cobj
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()
foldspec, icount = fold(a.foldtype, a.filename, a.obsfile, a.tstart, a.polyco, a.dtype, a.Tint*u.s, a.tbin*u.s, a.nchan, a.ngate, a.size, a.dedisperse, a.pulsedetect)
# Write very basic fits file
# Arrange to [time, pol, freq, phase]
n = foldspec / icount[...,np.newaxis]
if a.foldtype == 'fold':
n = np.swapaxes(n, 1, 3)
n = np.swapaxes(n, 2, 3)
header = fits.Header(['filename', a.filename])
if a.tstart:
header.set('T0', a.tstart)
else:
header.set('T0', 'beginning of file')
header.set('polyco', a.polyco)
header.set('Tint', a.Tint)
header.set('dedisperse', a.dedisperse)
obs = {}
conf = configobj.ConfigObj(r"{0}".format(a.obsfile))
for key, val in conf.iteritems():
header.set('{0}'.format(key), '{0}'.format(val))
hdu = fits.PrimaryHDU(n, header)
hdu.writeto('{0}_{1}_{2}s_{3}chan_{4}gate.fits'
.format(a.foldtype, a.tstart, a.Tint, a.nchan, a.ngate))
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_())
