import os
from importlib.machinery import SourceFileLoader
import sys
import types
import warnings
from collections import namedtuple
from glue.utils import format_choices
"""
Objects used to configure Glue at runtime.
"""
__all__ = ['Registry', 'SettingRegistry', 'ExporterRegistry',
'ColormapRegistry', 'DataFactoryRegistry',
'LinkFunctionRegistry', 'LinkHelperRegistry', 'ViewerToolRegistry',
'ProfileFitterRegistry', 'data_factory',
'link_function', 'link_helper', 'colormaps', 'exporters', 'settings',
'fit_plugin', 'auto_refresh', 'importer', 'DictRegistry',
'DataExporterRegistry', 'data_exporter',
'SubsetMaskExporterRegistry', 'SubsetMaskImporterRegistry',
'LayerArtistMakerRegistry', 'layer_artist_maker',
'SessionPatchRegistry', 'session_patch',
'AutoLinkerRegistry', 'autolinker',
'DataTranslatorRegistry', 'data_translator',
'SubsetDefinitionTranslatorRegistry', 'subset_state_translator',
'UnitConverterRegistry', 'unit_converter',
'StretchRegistry', 'stretches']
CFG_DIR = os.path.join(os.path.expanduser('~'), '.glue')
[docs]class Registry(object):
"""Container to hold groups of objects or settings.
Registry instances are used by Glue to track objects
used for various tasks like data linking, widget creation, etc.
They have the following properties:
- A `members` property, which lists each item in the registry
- A `default_members` function, which can be overridden to lazily
initialize the members list
- A call interface, allowing the instance to be used as a decorator
for users to add new items to the registry in their config files
"""
def __init__(self):
self._members = []
self._lazy_members = []
self._loaded = False
[docs] @property
def members(self):
""" A list of the members in the registry.
The return value is a list. The contents of the list
are specified in each subclass"""
self._load_lazy_members()
if not self._loaded:
self._members = self.default_members() + self._members
self._loaded = True
return self._members
[docs] def default_members(self):
"""The member items provided by default. These are put in this
method so that code is only imported when needed"""
return []
[docs] def add(self, value):
"""
Add a new item to the registry.
"""
self._members.append(value)
[docs] def lazy_add(self, value):
"""
Add a reference to a plugin which will be loaded when needed.
"""
self._lazy_members.append(value)
def _load_lazy_members(self):
from glue.plugins import load_plugin
while self._lazy_members:
plugin = self._lazy_members.pop()
load_plugin(plugin)
def __iter__(self):
return iter(self.members)
def __len__(self):
return len(self.members)
def __contains__(self, value):
return value in self.members
[docs] def __call__(self, arg):
"""This is provided so that registry instances can be used
as decorators. The decorators should add the decorated
code object to the registry, and return the original function"""
self.add(arg)
return arg
[docs]class DictRegistry(Registry):
"""
Base class for registries that are based on dictionaries instead of lists
of objects.
"""
def __init__(self):
self._members = {}
self._lazy_members = []
self._loaded = False
[docs] @property
def members(self):
self._load_lazy_members()
if not self._loaded:
defaults = self.default_members()
for key in defaults:
if key in self._members:
self._members[key].extend(defaults[key])
else:
self._members[key] = defaults[key]
self._loaded = True
return self._members
[docs] def default_members(self):
return {}
[docs]class SettingRegistry(DictRegistry):
"""Stores key/value settings that code can use to customize Glue
Each member is a tuple of 3 items:
- key: the setting name [str]
- value: the default setting [object]
- validator: A function which tests whether the input is a valid value,
and raises a ValueError if invalid. On valid input,
returns the (possibly sanitized) setting value.
"""
def __init__(self):
super(SettingRegistry, self).__init__()
self._validators = {}
self._defaults = {}
[docs] def add(self, key, default=None, validator=None):
if validator is None:
validator = lambda x: x
self._defaults[key] = validator(default)
self._validators[key] = validator
def __getattr__(self, attr):
if attr.startswith('_'):
raise AttributeError("No such setting: {0}".format(attr))
else:
if attr in self._members:
return self._members[attr]
elif attr in self._defaults:
return self._defaults[attr]
else:
raise AttributeError("No such setting: {0}".format(attr))
def __setattr__(self, attr, value):
if attr.startswith('_'):
object.__setattr__(self, attr, value)
elif attr in self:
self._members[attr] = self._validators[attr](value)
else:
raise AttributeError("No such setting: {0}".format(attr))
def __dir__(self):
return sorted(self._members.keys())
def __contains__(self, setting):
return setting in self._defaults
def __iter__(self):
for key in self._defaults:
value = self._members.get(key, self._defaults[key])
yield key, value, self._validators[key]
def __str__(self):
s = ""
for name, value, validator in self:
s += "{0}: {1}\n".format(name, value)
return s
[docs] def reset_defaults(self):
self._members.clear()
[docs] def is_default(self, setting):
return setting in self._defaults and setting not in self._members
class CLIParserRegistry(Registry):
"""
Registry for parsers that can be used to interpret arguments to the
:func:`~glue.qglue` function.
The members property is a list of parsers, each represented as a named tuple
with ``data_class``, ``parser`` and ``priority`` attributes, where ``class``
defines the class for which to use the parser, and ``parser`` is a function
that takes the input data and returns a list of glue
:class:`~glue.core.data.Data` objects. The ``parser`` functions should take two
arguments: the variable containing the data being parsed, and a label. In
addition, the priority (defaulting to 0) can be specified in case one wants
to make sure sub-classes get tested before more general classes. The
priority should be a numerical value, and the larger it is the higher the
priority.
"""
item = namedtuple('DataFactory', 'data_class parser priority')
def add(self, data_class, parser, priority=0):
"""
Add a new parser
Parameters
----------
data_class : class
The type of of data for which to use the specified parser
parser : func
The function to use to parse the input data
priority : int, optional
The priority, which is used to determine the order in which to check
the parsers.
"""
self.members.append(self.item(data_class, parser, priority))
def __call__(self, data_class, priority=0):
def adder(func):
if isinstance(data_class, tuple):
for dc in data_class:
self.add(dc, func, priority=priority)
else:
self.add(data_class, func, priority=priority)
return func
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: -x.priority):
yield member
class DataImportRegistry(Registry):
"""
Stores functions which can import data.
The members property is a list of importers, each represented as a
``(label, load_function)`` tuple. The ``load_function`` should take no
arguments and return a list of :class:`~glue.core.data.Data` objects.
"""
def add(self, label, importer):
"""
Add a new importer
:param label: Short label for the importer
:type label: str
:param importer: importer function
:type importer: function()
"""
self.members.append((label, importer))
def __call__(self, label):
def adder(func):
self.add(label, func)
return func
return adder
[docs]class AutoLinkerRegistry(Registry):
"""
Registry for auto-linking functions that given a data collection can suggest
links.
The members property is a list of auto-linking plugins, each represented as
a ``(label, function)`` tuple. The ``function`` should take a reference to
the data collection.
"""
[docs] def add(self, label, function):
"""
Add a new auto-linking function.
Parameters
----------
label : str
Short label for the plugin
function : func
The plugin function
"""
self.members.append((label, function))
[docs] def __call__(self, label):
def adder(func):
self.add(label, func)
return func
return adder
[docs]class ExporterRegistry(Registry):
"""Stores functions which can export an application to an output file
The members property is a list of exporters, each represented
as a (label, save_function, can_save_function, outmode) tuple.
save_function takes an (application, path) as input, and saves
the session
can_save_function takes an application as input, and raises an
exception if saving this session is not possible
outmode is a string, with one of 3 values:
'file': indicates that exporter creates a file
'directory': exporter creates a directory
'label': exporter doesn't write to disk, but needs a label
"""
[docs] def add(self, label, exporter, checker, outmode=None):
"""
Add a new exporter
Parameters
----------
label : str
Short label for the exporter
exporter : func
Exporter function which takes two arguments: the application and
optionally the path or label to create. This function should raise
an exception if export isn't possible.
checker : func
Function that checks if saving is possible, which takes one
argument: the application.
outmode : str or `None`
Indicates what kind of output is created. This can be either set to
``'file'``, ``'directory'``, ``'label'``, or `None`.
"""
self.members.append((label, exporter, checker, outmode))
[docs]class ColormapRegistry(Registry):
"""Stores colormaps for the Image Viewer. The members property is
a list of colormaps, each represented as a [name,cmap] pair.
"""
[docs] def default_members(self):
import matplotlib.cm as cm
members = []
members.append(['Gray', cm.gray])
members.append(['Viridis', cm.viridis])
members.append(['Plasma', cm.plasma])
members.append(['Inferno', cm.inferno])
members.append(['Magma', cm.magma])
members.append(['Purple-Blue', cm.PuBu])
members.append(['Yellow-Green-Blue', cm.YlGnBu])
members.append(['Yellow-Orange-Red', cm.YlOrRd])
members.append(['Red-Purple', cm.RdPu])
members.append(['Blue-Green', cm.BuGn])
members.append(['Hot', cm.hot])
members.append(['Red-Blue', cm.RdBu])
members.append(['Red-Yellow-Blue', cm.RdYlBu])
members.append(['Purple-Orange', cm.PuOr])
members.append(['Purple-Green', cm.PRGn])
return members
[docs] def add(self, label, cmap):
"""
Add colormap *cmap* with label *label*.
"""
self.members.append([label, cmap])
def __getitem__(self, cmap_name):
for name, cmap in self.members:
if name == cmap_name:
return cmap
raise KeyError(cmap_name)
[docs] def name_from_cmap(self, cmap_desired):
for name, cmap in self.members:
if cmap is cmap_desired or cmap.name == cmap_desired.name:
return name
raise ValueError("Could not find name for colormap")
[docs]class DataFactoryRegistry(Registry):
"""Stores data factories. Data factories take filenames as input,
and return :class:`~glue.core.data.Data` instances
The members property returns a list of (function, label, identifier,
priority) namedtuples:
- Function is the factory that creates the data object
- label is a short human-readable description of the factory
- identifier is a function that takes ``(filename, **kwargs)`` as input
and returns True if the factory can open the file
- priority is a numerical value that indicates how confident the data
factory is that it should read the data, relative to other data
factories. For example, a highly specialized FITS reader for specific
FITS file types can be given a higher priority than the generic FITS
reader in order to take precedence over it.
New data factories can be registered via::
@data_factory('label_name', identifier=identifier, priority=10)
def new_factory(file_name):
...
If not specified, the priority defaults to 0.
"""
item = namedtuple('DataFactory', 'function label identifier priority deprecated')
[docs] def __call__(self, label, identifier=None, priority=None, default='', deprecated=False):
if identifier is None:
identifier = lambda *a, **k: False
if priority is None:
if deprecated:
priority = -1000
else:
priority = 0
def adder(func):
self.add(self.item(func, label, identifier, priority, deprecated))
return func
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: (-x.priority, x.label)):
yield member
[docs]class DataExporterRegistry(Registry):
"""
Stores data exporters. Data exporters take a data/subset object as input
followed by a filename.
"""
item = namedtuple('DataFactory', 'function label extension')
[docs] def __call__(self, label, extension=[]):
def adder(func):
self.add(self.item(func, label, extension))
return func
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: x.label):
yield member
[docs]class SubsetMaskExporterRegistry(DataExporterRegistry):
"""
Stores mask exporters. Mask exporters should take a filename followed by
a dictionary of Numpy boolean arrays all with the same dimensions.
"""
item = namedtuple('SubsetMaskExporter', 'function label extension')
[docs]class SubsetMaskImporterRegistry(DataExporterRegistry):
"""
Stores mask importers. Mask importers should take a filename and return a
dictionary of Numpy boolean arrays.
"""
item = namedtuple('SubsetMaskImporter', 'function label extension')
[docs]class DataTranslatorRegistry(Registry):
"""
Stores data translators, which are classes that define methods to translate
between :class:`~glue.core.data.Data` objects and other kinds of data
containers.
"""
item = namedtuple('DataTranslator', 'target_cls handler priority')
[docs] def __call__(self, target_cls, priority=0):
def adder(handler_cls):
self.add(self.item(target_cls, handler_cls(), priority))
return handler_cls
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: -x.priority):
yield member
[docs] def remove(self, target_cls):
for member in self.members[:]:
if member.target_cls is target_cls:
self.members.remove(member)
[docs] @property
def supported_classes(self):
return [tr.target_cls for tr in self]
[docs] def get_handler_for(self, data_or_class):
for translator in self:
if isinstance(data_or_class, translator.target_cls) or data_or_class is translator.target_cls:
handler = translator.handler
preferred = translator.target_cls
break
else:
if isinstance(data_or_class, type):
raise TypeError("Could not find a class to translate objects of "
"type Data to {0}".format(data_or_class.__name__))
else:
raise TypeError("Could not find a class to translate objects of "
"type {0} to Data".format(data_or_class.__class__.__name__))
return handler, preferred
[docs]class SubsetDefinitionTranslatorRegistry(Registry):
"""
Stores subset state translators, which are classes that define methods to
translate between :class:`~glue.core.subset.SubsetState` objects and other
kinds of selection representations.
"""
item = namedtuple('SubsetDefinitionTranslator', 'format handler priority')
[docs] def __call__(self, format, priority=0):
def adder(handler_cls):
self.add(self.item(format, handler_cls(), priority))
return handler_cls
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: -x.priority):
yield member
[docs] def remove(self, format):
for member in self.members[:]:
if member.format is format:
self.members.remove(member)
[docs] @property
def supported_classes(self):
return [tr.target_cls for tr in self]
[docs] def get_handler_for(self, format):
for translator in self:
if translator.format == format:
return translator.handler
all_formats = [translator.format for translator in self]
if format is None:
raise ValueError("Subset state handler format not set - should be one of:" + format_choices(all_formats))
else:
raise ValueError("Invalid subset state handler format '{0}' - should be one of:".format(format) + format_choices(all_formats))
[docs]class UnitConverterRegistry(DictRegistry):
"""
Stores unit converters, which are classes that can be used to determine
conversion between units and find equivalent units to other units.
"""
[docs] def add(self, label, converter_cls):
if label in self.members:
raise ValueError("Unit converter class '{0}' already registered".format(label))
else:
self.members[label] = converter_cls
[docs] def __call__(self, label):
def adder(converter_cls):
self.add(label, converter_cls)
return converter_cls
return adder
[docs]class StretchRegistry(DictRegistry):
"""
Stores custom stretches
"""
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._display = {}
[docs] def add(self, label, stretch_cls, display=None):
if label in self.members:
raise ValueError("Stretch class '{0}' already registered".format(label))
else:
self.members[label] = stretch_cls
self._display[label] = display or label
[docs] def __call__(self, label):
def adder(stretch_cls):
self.add(label, stretch_cls)
return stretch_cls
return adder
[docs] def display_func(self, label):
return self._display[label]
[docs]class LinkFunctionRegistry(Registry):
"""Stores functions to convert between quantities
The members property is a list of (function, info_string,
output_labels) namedtuples. ``info_string`` describes what the
function does. ``output_labels`` is a list of names for each output.
``category`` is a category in which the link function will appear (defaults
to 'General').
New link functions can be registered via
@link_function(info="maps degrees to arcseconds",
output_labels=['arcsec'])
def degrees2arcsec(degrees):
return degrees * 3600
Link functions are expected to receive and return numpy arrays
"""
item = namedtuple('LinkFunction', 'function info output_labels category')
[docs] def __call__(self, info="", output_labels=None, category='General'):
out = output_labels or []
def adder(func):
self.add(self.item(func, info, out, category))
return func
return adder
[docs]class LinkHelperRegistry(Registry):
"""
Stores helper objects that compute many ComponentLinks at once
Link helpers can either be functions or subclasses of
`~glue.core.link_helpers.LinkCollection`. If a function, it should take a
list of `~glue.core.component_id.ComponentIDs` as inputs, and returns an
iterable of `~glue.core.component_link.ComponentLink` objects.
A link helper should only link components between two datasets, and the
order of the inputs to the function should be the
`~glue.core.component_id.ComponentIDs` of the first dataset, followed by
the ones for the second dataset. Human-readable names for the input and
output components should be given using ``input_labels`` and
``output_labels``
New link helpers can be registered with e.g.::
@link_helper('Links degrees and arcseconds in both directions',
input_labels=['degree'], output_labels=['arcsecond'])
def new_helper(degree, arcsecond):
return [ComponentLink([degree], arcsecond, using=lambda d: d*3600),
ComponentLink([arcsecond], degree, using=lambda a: a/3600)]
"""
item = namedtuple('LinkHelper', 'helper category')
[docs] def __call__(self, info=None, input_labels=None, output_labels=None, category='General'):
if input_labels is not None and output_labels is None:
warnings.warn('Specifying @link_helper without giving output_labels is '
'deprecated and will be removed in future. See the '
'documentation about how to specify output_labels', UserWarning)
def adder(func):
from glue.core.link_helpers import LinkCollection, functional_link_collection
if not issubclass(func, LinkCollection):
func = functional_link_collection(func, description=info,
labels1=input_labels or [],
labels2=output_labels or [])
self.add(self.item(func, category))
return func
return adder
[docs]class ProfileFitterRegistry(Registry):
item = namedtuple('ProfileFitter', 'cls')
[docs] def add(self, cls):
"""
Add colormap *cmap* with label *label*.
"""
self.members.append(cls)
[docs] def default_members(self):
from glue.core.fitters import __FITTERS__
return list(__FITTERS__)
class BooleanSetting(object):
def __init__(self, default=True):
self.state = default
def __call__(self, state=None):
if state not in [None, True, False]:
raise ValueError("Invalid True/False setting: %s" % state)
if state is not None:
self.state = state
return self.state
[docs]class LayerArtistMakerRegistry(Registry):
"""
A registry that allows customization of layer artists based on the data
and viewer type.
"""
item = namedtuple('LayerArtistMaker', 'label function priority')
[docs] def add(self, label, function, priority=0):
"""
Add a new plugin for providing custom layer artists.
Plugins take the form of functions that take two arguments - the data or
subset being added, and the viewer. The function should either return a
`~glue.viewers.common.layer_artist.LayerArtist` sub-class object or
`None`.
Parameters
----------
label : str
Name for the plugin
function : callable
The function that returns layer artists
priority : int, optional
Set this to a higher number if multiple plugins are present
and you want your plugin to take precedence over another.
"""
self.members.append(self.item(label, function, priority))
[docs] def __call__(self, label, priority=0):
def adder(func):
self.add(label, func, priority=priority)
return func
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: -x.priority):
yield member
[docs]class SessionPatchRegistry(Registry):
"""A registry that allows in-place patch of the session file"""
item = namedtuple('SessionPatch', 'function priority')
[docs] def add(self, function, priority=0):
"""
Add a new plugin for providing custom in-place session patch.
Plugins take the form of functions that take one argument: the session
object (a dictionary). It should returns `None`.
Parameters
----------
function : callable
The function apply the patch *in-place*
priority : int, optional
Set this to a higher number if multiple plugins are present
and you want your plugin to take precedence over another.
"""
self.members.append(self.item(function, priority))
[docs] def __call__(self, priority=0):
def adder(func):
self.add(func, priority=priority)
return func
return adder
def __iter__(self):
for member in sorted(self.members, key=lambda x: -x.priority):
yield member
layer_artist_maker = LayerArtistMakerRegistry()
viewer_tool = ViewerToolRegistry()
link_function = LinkFunctionRegistry()
link_helper = LinkHelperRegistry()
colormaps = ColormapRegistry()
importer = DataImportRegistry()
exporters = ExporterRegistry()
settings = SettingRegistry()
fit_plugin = ProfileFitterRegistry()
cli_parser = CLIParserRegistry()
autolinker = AutoLinkerRegistry()
session_patch = SessionPatchRegistry()
# watch loaded data files for changes?
auto_refresh = BooleanSetting(False)
enable_contracts = BooleanSetting(False)
# Data and subset I/O
data_factory = DataFactoryRegistry()
data_exporter = DataExporterRegistry()
subset_mask_exporter = SubsetMaskExporterRegistry()
subset_mask_importer = SubsetMaskImporterRegistry()
data_translator = DataTranslatorRegistry()
subset_state_translator = SubsetDefinitionTranslatorRegistry()
# Units
unit_converter = UnitConverterRegistry()
# Stretch classes
from astropy.visualization import (LinearStretch, SqrtStretch, AsinhStretch,
LogStretch)
stretches = StretchRegistry()
stretches.add('linear', LinearStretch, display='Linear')
stretches.add('sqrt', SqrtStretch, display='Square Root')
stretches.add('arcsinh', AsinhStretch, display='Arcsinh')
stretches.add('log', LogStretch, display='Logarithmic')
# Backward-compatibility
qglue_parser = cli_parser
def load_configuration(search_path=None):
"""
Find and import a config.py file
Returns:
The module object
Raises:
Exception, if no module was found
"""
search_order = search_path or _default_search_order()
result = types.ModuleType('config')
for config_file in search_order:
dir = os.path.dirname(config_file)
try:
sys.path.append(dir)
loader = SourceFileLoader('config', config_file)
config = types.ModuleType(loader.name)
loader.exec_module(config)
result = config
except IOError:
pass
except Exception as e:
if isinstance(e, Warning):
# avoid hard-raising warnings if they were turned into errors
# see https://github.com/glue-viz/glue/issues/2263
warnings.warn(e, category=type(e))
else:
raise type(e)(
"Error loading config file %s:\n%s" % (config_file, e),
sys.exc_info()[2]
)
finally:
sys.path.remove(dir)
return result
def _default_search_order():
"""
The default configuration file search order:
* current working directory
* environ var GLUERC
* HOME/.glue/config.py
* Glue's own default config
"""
search_order = [os.path.join(os.getcwd(), 'config.py')]
if 'GLUERC' in os.environ:
search_order.append(os.environ['GLUERC'])
search_order.append(os.path.join(CFG_DIR, 'config.py'))
return search_order[::-1]
# ##### Now define global settings ######
GRAY = '#7F7F7F'
BLUE = "#1F78B4"
GREEN = "#33A02C"
RED = "#E31A1C"
ORANGE = "#FF7F00"
PURPLE = "#6A3D9A"
YELLOW = "#FFFF99"
BROWN = "#8C510A"
PINK = "#FB9A99"
LIGHT_BLUE = "#A6CEE3"
LIGHT_GREEN = "#B2DF8A"
LIGHT_RED = "#FB9A99"
LIGHT_ORANGE = "#FDBF6F"
LIGHT_PURPLE = "#CAB2D6"
settings.add('SUBSET_COLORS', [RED, GREEN, BLUE, BROWN, ORANGE, PURPLE, PINK], validator=list)
settings.add('DATA_COLOR', '#595959')
settings.add('DATA_ALPHA', 0.8, validator=float)
settings.add('BACKGROUND_COLOR', '#FFFFFF')
settings.add('FOREGROUND_COLOR', '#000000')
settings.add('SHOW_LARGE_DATA_WARNING', True, validator=bool)
settings.add('SHOW_INFO_PROFILE_OPEN', True, validator=bool)
settings.add('SHOW_WARN_PROFILE_DUPLICATE', True, validator=bool)
settings.add('FONT_SIZE', -1.0, validator=float)
settings.add('AUTOLINK', {}, validator=dict)
def check_unit_converter(value):
if value != 'default' and value not in unit_converter.members:
raise KeyError(f'Unit converter {value} is not defined')
return value
settings.add('UNIT_CONVERTER', 'default', validator=check_unit_converter)
# It is difficult to emit deprecation warnigns for the following, so we just
# import these if glue-qt is installed. We can still remove these in future if
# needed but because we can't easily deprecate, we should leave them for a
# little while.
try:
from glue_qt.config import (QtClientRegistry, qt_client, # noqa
LayerActionRegistry, layer_action,
MenubarPluginRegistry, menubar_plugin,
PreferencePanesRegistry, preference_panes,
StartupActionRegistry, startup_action,
QtFixedLayoutTabRegistry, qt_fixed_layout_tab,
KeyboardShortcut, keyboard_shortcut)
except ImportError:
pass
