Source code for glue.config

from __future__ import absolute_import, division, print_function

import os
import imp
import sys
import warnings
from collections import namedtuple

Objects used to configure Glue at runtime.

__all__ = ['Registry', 'SettingRegistry', 'ExporterRegistry',
           'ColormapRegistry', 'DataFactoryRegistry', 'QtClientRegistry',
           'LinkFunctionRegistry', 'LinkHelperRegistry', 'ViewerToolRegistry',
           'LayerActionRegistry', 'ProfileFitterRegistry', 'qt_client', 'data_factory',
           'link_function', 'link_helper', 'colormaps', 'exporters', 'settings',
           'fit_plugin', 'auto_refresh', 'importer', 'DictRegistry',
           'preference_panes', 'PreferencePanesRegistry',
           'DataExporterRegistry', 'data_exporter', 'layer_action',
           'SubsetMaskExporterRegistry', 'SubsetMaskImporterRegistry',
           'StartupActionRegistry', 'startup_action', 'QtFixedLayoutTabRegistry',
           'qt_fixed_layout_tab', 'KeyboardShortcut', 'keyboard_shortcut',
           'LayerArtistMakerRegistry', 'layer_artist_maker', 'AutoLinkerRegistry',

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 QGlueParserRegistry(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:`` 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:`` 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 class MenubarPluginRegistry(Registry): """ Stores menubar plugins. The members property is a list of menubar plugins, each represented as a ``(label, function)`` tuple. The ``function`` should take two items which are a reference to the session and to the data collection respectively. """ def add(self, label, function): """ Add a new menubar plugin :param label: Short label for the plugin :type label: str :param function: function :type function: function() """ self.members.append((label, function)) def __call__(self, label): def adder(func): self.add(label, func) return func return adder
[docs]class PreferencePanesRegistry(DictRegistry): """ Stores preference panes The members property is a list of tuples of Qt widget classes that can have their own tab in the preferences window. """
[docs] def add(self, label, widget_cls): self._members[label] = widget_cls
def __iter__(self): for label in self._members: yield label, self._members[label]
[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 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',]) 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: 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:`` 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 QtClientRegistry(Registry): """ Stores QT widgets to visualize data. The members property is a list of Qt widget classes New widgets can be registered via:: @qt_client class CustomWidget(QMainWindow): ... """
[docs]class QtFixedLayoutTabRegistry(Registry): """ Stores Qt pre-defined tabs (non-MDI) New widgets can be registered via:: @qt_fixed_layout_tab class CustomTab(QWidget): ... """
[docs]class ViewerToolRegistry(DictRegistry):
[docs] def add(self, tool_cls): """ Add a tool class to the registry. The the ``tool_id`` attribute on the tool_cls should be set, and is used by the viewers to indicate which tools they want to """ if tool_cls.tool_id in self.members: raise ValueError("Tool ID '{0}' already registered".format(tool_cls.tool_id)) else: self.members[tool_cls.tool_id] = tool_cls
[docs] def __call__(self, tool_cls): self.add(tool_cls) return tool_cls
[docs]class StartupActionRegistry(DictRegistry):
[docs] def add(self, startup_name, startup_function): """ Add a startup function to the registry. This is a function that will get called once glue has been started and any data loaded, and can be used to set up specific layouts and create links. Startup actions are triggered by either specifying comma-separated names of actions on the command-line:: glue --startup=mystartupaction or by passing an iterable of startup action names to the ``startup`` keyword of ``GlueApplication``. The startup function will be given the session object and the data collection object. """ if startup_name in self.members: raise ValueError("A startup action with the name '{0}' already exists".format(startup_name)) else: self.members[startup_name] = startup_function
[docs] def __call__(self, name): def adder(func): self.add(name, func) return func return adder
[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 LayerActionRegistry(Registry): """ Stores custom menu actions available when the user select one or more datasets, subset group, or subset in the data collection view. This members property is a list of named tuples with the following attributes: * ``label``: the user-facing name of the action * ``tooltip``: the text that appears when hovering with the mouse over the action * ``callback``: the function to call when the action is triggered * ``icon``: an icon image to use for the layer action * ``single``: whether to show this action only when selecting single layers (default: `False`) * ``data``: if ``single`` is `True` whether to only show the action when selecting a dataset * ``subset_group``: if ``single`` is `True` whether to only show the action when selecting a subset group * ``subset``: if ``single`` is `True` whether to only show the action when selecting a subset The callback function is called with two arguments. If ``single`` is `True`, the first argument is the selected layer, otherwise it is the list of selected layers. The second argument is the `~glue.core.data_collection.DataCollection` object. """ item = namedtuple('LayerAction', 'label tooltip callback icon single data subset_group, subset')
[docs] def __call__(self, label, callback=None, tooltip=None, icon=None, single=False, data=False, subset_group=False, subset=False): # Backward-compatibility if callback is not None: self.add(self.item(label, tooltip, callback, icon, True, False, False, True)) return True def adder(func): self.add(self.item(label, tooltip, func, icon, single, data, subset_group, subset)) 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 KeyboardShortcut(DictRegistry): """ Stores keyboard shortcuts. The members property is a dictionary within a dictionary of keyboard shortcuts, which is represented as (viewer,(keybind,function)). The ``function`` should take one item, which is a reference to the session. """
[docs] def add(self, valid_viewers, keybind, function): """ Add a new keyboard shortcut Parameters ---------- arg1: list list of viewers where event can be fired arg2: Qt.Key type of key event arg3: function() function to be run that corresponds with key """ if valid_viewers: for viewer in valid_viewers: if viewer in self.members: if keybind in self.members[viewer]: raise ValueError("Keyboard shortcut '{0}' already registered in {1}".format(keybind, viewer)) else: self.members[viewer][keybind] = function else: self.members[viewer] = {keybind: function} else: if None in self.members: if keybind in self.members[None]: raise ValueError("Keyboard shortcut '{0}' already registered in {1}".format(keybind, None)) else: self.members[None][keybind] = function else: self.members[None] = {keybind: function}
[docs] def __call__(self, keybind, valid_viewers): def adder(func): self.add(valid_viewers, keybind, func) return func return adder
[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
layer_artist_maker = LayerArtistMakerRegistry() qt_client = QtClientRegistry() qt_fixed_layout_tab = QtFixedLayoutTabRegistry() viewer_tool = ViewerToolRegistry() link_function = LinkFunctionRegistry() link_helper = LinkHelperRegistry() colormaps = ColormapRegistry() importer = DataImportRegistry() exporters = ExporterRegistry() settings = SettingRegistry() fit_plugin = ProfileFitterRegistry() layer_action = LayerActionRegistry() menubar_plugin = MenubarPluginRegistry() preference_panes = PreferencePanesRegistry() qglue_parser = QGlueParserRegistry() startup_action = StartupActionRegistry() keyboard_shortcut = KeyboardShortcut() autolinker = AutoLinkerRegistry() # 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() # Backward-compatibility single_subset_action = layer_action def load_configuration(search_path=None): """ Find and import a file Returns: The module object Raises: Exception, if no module was found """ search_order = search_path or _default_search_order() result = imp.new_module('config') for config_file in search_order: dir = os.path.dirname(config_file) try: sys.path.append(dir) config = imp.load_source('config', config_file) result = config except IOError: pass except Exception as e: 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/ * Glue's own default config """ search_order = [os.path.join(os.getcwd(), '')] if 'GLUERC' in os.environ: search_order.append(os.environ['GLUERC']) search_order.append(os.path.join(CFG_DIR, '')) 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)