import os
import pathlib
import re
import uuid
import warnings
from inspect import isclass
from ipywidgets import widget_serialization
import ipyvue
from astropy.nddata import CCDData, NDData
from astropy.io import fits
from echo import CallbackProperty, DictCallbackProperty, ListCallbackProperty
from ipygoldenlayout import GoldenLayout
from ipysplitpanes import SplitPanes
from traitlets import Dict, Bool, Unicode, Any
from specutils import Spectrum1D, SpectralRegion
import matplotlib.cm as cm
import numpy as np
from glue.core.exceptions import IncompatibleAttribute
from glue.config import colormaps, data_translator
from glue.config import settings as glue_settings
from glue.core import BaseData, HubListener, Data, DataCollection
from glue.core.link_helpers import LinkSame
from glue.plugins.wcs_autolinking.wcs_autolinking import WCSLink, IncompatibleWCS
from glue.core.message import (DataCollectionAddMessage,
DataCollectionDeleteMessage,
SubsetCreateMessage,
SubsetUpdateMessage,
SubsetDeleteMessage)
from glue.core.state_objects import State
from glue.core.subset import Subset, RangeSubsetState, RoiSubsetState
from glue_astronomy.spectral_coordinates import SpectralCoordinates
from glue_jupyter.app import JupyterApplication
from glue_jupyter.common.toolbar_vuetify import read_icon
from glue_jupyter.state_traitlets_helpers import GlueState
from glue_jupyter.bqplot.profile import BqplotProfileView
from ipyvuetify import VuetifyTemplate
from jdaviz import __version__
from jdaviz.core.config import read_configuration, get_configuration
from jdaviz.core.events import (LoadDataMessage, NewViewerMessage, AddDataMessage,
SnackbarMessage, RemoveDataMessage,
AddDataToViewerMessage, RemoveDataFromViewerMessage,
ViewerAddedMessage, ViewerRemovedMessage)
from jdaviz.core.registries import (tool_registry, tray_registry, viewer_registry,
data_parser_registry)
from jdaviz.core.tools import ICON_DIR
from jdaviz.utils import SnackbarQueue, alpha_index
from ipypopout import PopoutButton
__all__ = ['Application']
SplitPanes()
GoldenLayout()
CONTAINER_TYPES = dict(row='gl-row', col='gl-col', stack='gl-stack')
EXT_TYPES = dict(flux=['flux', 'sci'],
uncert=['ivar', 'err', 'var', 'uncert'],
mask=['mask', 'dq'])
# Set default opacity for data layers to 1 instead of 0.8 in
# some glue-core versions
glue_settings.DATA_ALPHA = 1
custom_components = {'j-tooltip': 'components/tooltip.vue',
'j-external-link': 'components/external_link.vue',
'j-docs-link': 'components/docs_link.vue',
'j-viewer-data-select': 'components/viewer_data_select.vue',
'j-viewer-data-select-item': 'components/viewer_data_select_item.vue',
'j-layer-viewer-icon': 'components/layer_viewer_icon.vue',
'j-tray-plugin': 'components/tray_plugin.vue',
'j-play-pause-widget': 'components/play_pause_widget.vue',
'j-plugin-section-header': 'components/plugin_section_header.vue',
'j-number-uncertainty': 'components/number_uncertainty.vue',
'j-plugin-popout': 'components/plugin_popout.vue',
'plugin-table': 'components/plugin_table.vue',
'plugin-dataset-select': 'components/plugin_dataset_select.vue',
'plugin-subset-select': 'components/plugin_subset_select.vue',
'plugin-viewer-select': 'components/plugin_viewer_select.vue',
'plugin-layer-select': 'components/plugin_layer_select.vue',
'plugin-add-results': 'components/plugin_add_results.vue',
'plugin-auto-label': 'components/plugin_auto_label.vue',
'glue-state-sync-wrapper': 'components/glue_state_sync_wrapper.vue'}
_verbosity_levels = ('debug', 'info', 'warning', 'error')
# Register pure vue component. This allows us to do recursive component instantiation only in the
# vue component file
for name, path in custom_components.items():
ipyvue.register_component_from_file(None, name,
os.path.join(os.path.dirname(__file__), path))
ipyvue.register_component_from_file('g-viewer-tab', "container.vue", __file__)
class ApplicationState(State):
"""
The application state object contains all the current front-end state,
including the loaded data name references, the active viewers, plugins,
and layout.
This state object allows for nested callbacks in mutable objects like
dictionaries and makes it so incremental changes to nested values
propagate to the traitlet in order to trigger a UI re-render.
"""
drawer = CallbackProperty(
False, docstring="State of the plugins drawer.")
logger_overlay = CallbackProperty(
False, docstring="State of the logger history overlay.")
snackbar = DictCallbackProperty({
'show': False,
'test': "",
'color': None,
'timeout': 3000,
'loading': False
}, docstring="State of the quick toast messages.")
snackbar_queue = SnackbarQueue()
snackbar_history = ListCallbackProperty(docstring="Previously dismissed snackbar items")
settings = DictCallbackProperty({
'data': {
'auto_populate': False,
'parser': None
},
'visible': {
'menu_bar': True,
'toolbar': True,
'tray': True,
'tab_headers': True,
},
'viewer_labels': True,
'dense_toolbar': True,
'context': {
'notebook': {
'max_height': '600px'
}
},
'layout': {
}
}, docstring="Top-level application settings.")
icons = DictCallbackProperty({
'radialtocheck': read_icon(os.path.join(ICON_DIR, 'radialtocheck.svg'), 'svg+xml'),
'checktoradial': read_icon(os.path.join(ICON_DIR, 'checktoradial.svg'), 'svg+xml')
}, docstring="Custom application icons")
viewer_icons = DictCallbackProperty({}, docstring="Indexed icons (numbers) for viewers across the app") # noqa
layer_icons = DictCallbackProperty({}, docstring="Indexed icons (letters) for layers across the app") # noqa
data_items = ListCallbackProperty(
docstring="List of data items parsed from the Glue data collection.")
tool_items = ListCallbackProperty(
docstring="Collection of toolbar items displayed in the application.")
tray_items = ListCallbackProperty(
docstring="List of plugins displayed in the sidebar tray area.")
tray_items_open = CallbackProperty(
[], docstring="The plugin(s) opened in sidebar tray area.")
tray_items_filter = CallbackProperty(
'', docstring='User-filter on tray items')
stack_items = ListCallbackProperty(
docstring="Nested collection of viewers constructed to support the "
"Golden Layout viewer area.")
[docs]class Application(VuetifyTemplate, HubListener):
"""
The main application object containing implementing the ipyvue/vuetify
template instructions for composing the interface.
"""
_metadata = Dict({"mount_id": "content"}).tag(sync=True)
state = GlueState().tag(sync=True)
template_file = __file__, "app.vue"
loading = Bool(False).tag(sync=True)
config = Unicode("").tag(sync=True)
vdocs = Unicode("").tag(sync=True)
popout_button = Any().tag(sync=True, **widget_serialization)
def __init__(self, configuration=None, *args, **kwargs):
super().__init__(*args, **kwargs)
self._jdaviz_helper = None
self._verbosity = 'warning'
self._history_verbosity = 'info'
self.popout_button = PopoutButton(self)
# Generate a state object for this application to maintain the state of
# the user interface.
self.state = ApplicationState()
# The application handler stores the state of the data and the
# underlying glue infrastructure
self._application_handler = JupyterApplication(
settings={'new_subset_on_selection_tool_change': True,
'single_global_active_tool': False})
# Add a reference to this application to the Glue session object. This
# allows the jdaviz Application object to then be accessed via e.g.
# viewer.session.jdaviz_app
self._application_handler.session.jdaviz_app = self
# Create a dictionary for holding non-ipywidget viewer objects so we
# can reference their state easily since glue does not store viewers
self._viewer_store = {}
# Parse the yaml configuration file used to compose the front-end UI
self.load_configuration(configuration)
# If true, link data on load. If false, do not link data to speed up
# data loading
self.auto_link = kwargs.pop('auto_link', True)
# Subscribe to messages indicating that a new viewer needs to be
# created. When received, information is passed to the application
# handler to generate the appropriate viewer instance.
self.hub.subscribe(self, NewViewerMessage,
handler=self._on_new_viewer)
# Subscribe to messages indicating new data should be loaded into the
# application
self.hub.subscribe(self, LoadDataMessage,
handler=lambda msg: self.load_data(msg.path))
# Subscribe to the event fired when data is added to the application-
# level data collection object
self.hub.subscribe(self, DataCollectionAddMessage,
handler=self._on_data_added)
# Subscribe to the event fired when data is deleted from the
# application-level data collection object
self.hub.subscribe(self, DataCollectionDeleteMessage,
handler=self._on_data_deleted)
self.hub.subscribe(self, AddDataToViewerMessage,
handler=lambda msg: self.add_data_to_viewer(
msg.viewer_reference, msg.data_label))
self.hub.subscribe(self, RemoveDataFromViewerMessage,
handler=lambda msg: self.remove_data_from_viewer(
msg.viewer_reference, msg.data_label))
# Subscribe to snackbar messages and tie them to the display of the
# message box
self.hub.subscribe(self, SnackbarMessage,
handler=self._on_snackbar_message)
# Add a fitted_models dictionary that the helpers (or user) can access
self.fitted_models = {}
# Internal cache so we don't have to keep calling get_object for the same Data.
# Key should be (data_label, statistic) and value the translated object.
self._get_object_cache = {}
self.hub.subscribe(self, SubsetUpdateMessage,
handler=lambda msg: self._clear_object_cache(msg.subset.label))
# Add new and inverse colormaps to Glue global state. Also see ColormapRegistry in
# https://github.com/glue-viz/glue/blob/main/glue/config.py
new_cms = (['Rainbow', cm.rainbow],
['Seismic', cm.seismic],
['Reversed: Gray', cm.gray_r],
['Reversed: Viridis', cm.viridis_r],
['Reversed: Plasma', cm.plasma_r],
['Reversed: Inferno', cm.inferno_r],
['Reversed: Magma', cm.magma_r],
['Reversed: Hot', cm.hot_r],
['Reversed: Rainbow', cm.rainbow_r])
for cur_cm in new_cms:
if cur_cm not in colormaps.members:
colormaps.add(*cur_cm)
# Subscribe to messages that result in changes to the layers
self.hub.subscribe(self, AddDataMessage,
handler=self._on_layers_changed)
self.hub.subscribe(self, RemoveDataMessage,
handler=self._on_layers_changed)
self.hub.subscribe(self, SubsetCreateMessage,
handler=self._on_layers_changed)
self.hub.subscribe(self, SubsetDeleteMessage,
handler=self._on_layers_changed)
@property
def hub(self):
"""
Reference to the stored application handler `~glue.core.hub.Hub` instance
for the application.
"""
return self._application_handler.data_collection.hub
@property
def session(self):
"""
Reference to the stored `~glue.core.session.Session` instance
maintained by Glue for this application.
"""
return self._application_handler.session
@property
def data_collection(self):
"""
Reference to the stored `~glue.core.data_collection.DataCollection` instance,
used to maintain the the data objects that been loaded into the application
this session.
"""
return self._application_handler.data_collection
@property
def verbosity(self):
"""
Verbosity of the application for popup snackbars, choose from ``'debug'``,
``'info'``, ``'warning'`` (default), or ``'error'``.
"""
return self._verbosity
@verbosity.setter
def verbosity(self, val):
if val not in _verbosity_levels:
raise ValueError(f'Invalid verbosity: {val}')
self._verbosity = val
@property
def history_verbosity(self):
"""
Verbosity of the logger history, choose from ``'debug'``, ``'info'`` (default),
``'warning'``, or ``'error'``.
"""
return self._history_verbosity
@history_verbosity.setter
def history_verbosity(self, val):
if val not in _verbosity_levels:
raise ValueError(f'Invalid verbosity: {val}')
self._history_verbosity = val
def _on_snackbar_message(self, msg):
"""
Displays a toast message with an editable message that be dismissed
manually or will dismiss automatically after a timeout.
Whether the message shows as a snackbar popup is controlled by ``self.verbosity``,
whether the message is added to the history log is controlled by ``self.history_verbosity``.
Parameters
----------
msg : `~glue.core.SnackbarMessage`
The Glue snackbar message containing information about displaying
the message box.
"""
# https://material-ui.com/customization/palette/ provides these options:
# success, info, warning, error, secondary, primary
# We have these options:
# debug, info, warning, error
# Therefore:
# * debug is not used, it is more for the future if we also have a logger.
# * info lets everything through
# * success, secondary, and primary are treated as info (not sure what they are used for)
# * None is also treated as info (when color is not set)
popup_level = _verbosity_levels.index(self.verbosity)
history_level = _verbosity_levels.index(self.history_verbosity)
def _color_to_level(color):
if color in _verbosity_levels:
return color
# could create dictionary mapping if we need anything more advanced
return 'info'
msg_level = _verbosity_levels.index(_color_to_level(msg.color))
self.state.snackbar_queue.put(self.state, msg,
history=msg_level >= history_level,
popup=msg_level >= popup_level)
def _on_layers_changed(self, msg):
if hasattr(msg, 'data'):
layer_name = msg.data.label
elif hasattr(msg, 'subset'):
layer_name = msg.subset.label
else:
raise NotImplementedError(f"cannot recognize new layer from {msg}")
if layer_name not in self.state.layer_icons:
self.state.layer_icons = {**self.state.layer_icons,
layer_name: alpha_index(len(self.state.layer_icons))}
def _link_new_data(self, reference_data=None, data_to_be_linked=None):
"""
When additional data is loaded, check to see if the spectral axis of
any components are compatible with already loaded data. If so, link
them so that they can be displayed on the same profile1D plot.
"""
if self.config == 'imviz': # Imviz does its own thing
return
elif not self.auto_link:
return
elif self.config == 'mosviz' and self.get_viewer('spectrum-viewer').state.reference_data:
# Mosviz turns auto_link to False in order to batch
# link the data after they have all been loaded.
# It then reverts auto_link to True, which means that when
# plugin data is added from mosviz, it can use the following line
# to set reference data.
reference_data = self.get_viewer('spectrum-viewer').state.reference_data.label
dc = self.data_collection
# This will need to be changed for cubeviz to support multiple cubes
default_refdata_index = 0
if self.config == 'mosviz':
# In Mosviz, first data is always MOS Table. Use the next data
default_refdata_index = 1
ref_data = dc[reference_data] if reference_data else dc[default_refdata_index]
linked_data = dc[data_to_be_linked] if data_to_be_linked else dc[-1]
if 'Trace' in linked_data.meta:
links = [LinkSame(linked_data.components[1], ref_data.components[0]),
LinkSame(linked_data.components[0], ref_data.components[1])]
dc.add_link(links)
return
elif linked_data.meta.get('Plugin', None) == 'SpectralExtraction':
links = [LinkSame(linked_data.components[0], ref_data.components[0]),
LinkSame(linked_data.components[1], ref_data.components[1])]
dc.add_link(links)
return
# The glue-astronomy SpectralCoordinates currently seems incompatible with glue
# WCSLink. This gets around it until there's an upstream fix.
if isinstance(linked_data.coords, SpectralCoordinates):
wc_old = ref_data.world_component_ids[-1]
wc_new = linked_data.world_component_ids[0]
self.data_collection.add_link(LinkSame(wc_old, wc_new))
return
try:
if linked_data.meta.get("Plugin", None) == 'GaussianSmooth':
raise AttributeError
dc.add_link(WCSLink(ref_data, linked_data))
except (AttributeError, IncompatibleWCS):
pc_ref = [str(id).split(" ")[-1][1] for id in ref_data.pixel_component_ids]
pc_linked = [str(id).split(" ")[-1][1] for id in linked_data.pixel_component_ids]
links = []
# This code loops through the returned locations of the x, y, and z
# axes in the pixel_coordinate_ids of the reference data. It matches
# the axes with the pixel_coordinate_ids of the linked data and links
# those axes. There are special rules for linking 2D and 3D data, which
# is as follows: 2D y to 3D z and 2D x to 3D y, and vice versa in the
# case of moment map and collapse data because they need to be transposed.
# See github comment:
# https://github.com/spacetelescope/jdaviz/pull/1412#discussion_r907630682
len_linked_pixel = len(linked_data.pixel_component_ids)
for ind, pixel_coord in enumerate(pc_ref):
ref_index = ind
if (len_linked_pixel == 2 and
(linked_data.meta.get("Plugin", None) in
['MomentMap', 'Collapse'])):
if pixel_coord == 'z':
linked_index = pc_linked.index('x')
elif pixel_coord == 'y':
linked_index = pc_linked.index('y')
else:
continue
elif len_linked_pixel == 2:
if pixel_coord == 'z':
linked_index = pc_linked.index('y')
elif pixel_coord == 'y':
linked_index = pc_linked.index('x')
else:
continue
elif pixel_coord in pc_linked:
linked_index = pc_linked.index(pixel_coord)
else:
continue
links.append(LinkSame(ref_data.pixel_component_ids[ref_index],
linked_data.pixel_component_ids[linked_index]))
dc.add_link(links)
[docs] def load_data(self, file_obj, parser_reference=None, **kwargs):
"""
Provided a path to a data file, open and parse the data into the
`~glue.core.data_collection.DataCollection` for this session.
For some parsers, this also attempts to find WCS links that exist
between data components.
Parameters
----------
file_obj : str or file-like
File object for the data to be loaded.
parser_reference : str or `None`
The actual data parser to use. It must already be registered
to glue's data parser registry. This is mainly for internal use.
**kwargs : dict
Additional keywords to be passed into the parser defined by
``parser_reference``.
"""
self.loading = True
try:
try:
# Properly form path and check if a valid file
file_obj = pathlib.Path(file_obj)
if not file_obj.exists():
msg_text = "Error: File {} does not exist".format(file_obj)
snackbar_message = SnackbarMessage(msg_text, sender=self,
color='error')
self.hub.broadcast(snackbar_message)
raise FileNotFoundError("Could not locate file: {}".format(file_obj))
else:
# Convert path to properly formatted string (Parsers do not accept path objs)
file_obj = str(file_obj)
except TypeError:
# If it's not a str/path type, it might be a compatible class.
# Pass to parsers to see if they can accept it
pass
# attempt to get a data parser from the config settings
parser = None
data = self.state.settings.get('data', None)
if parser_reference:
parser = data_parser_registry.members.get(parser_reference)
elif data and isinstance(data, dict):
data_parser = data.get('parser', None)
if data_parser:
parser = data_parser_registry.members.get(data_parser)
if parser is not None:
parser(self, file_obj, **kwargs)
else:
self._application_handler.load_data(file_obj)
except Exception: # Reset state on uncaught errors
cfg_name = self.state.settings.get('configuration', 'unknown')
if cfg_name in ('mosviz', ): # Add more as needed.
self.data_collection.clear()
raise
finally:
self.loading = False
[docs] def get_viewer(self, viewer_reference):
"""
Return a `~glue_jupyter.bqplot.common.BqplotBaseView` viewer instance.
This is *not* an ``IPyWidget``. This is stored here because
the state of the viewer and data methods that allow add/removing data
to the viewer exist in a wrapper around the core ``IPyWidget``, which
is needed to interact with the data rendered within a viewer.
Notes
-----
This is only used in cases where the viewers have been pre-defined
in the configuration file. Otherwise, viewers are not stored via
reference.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the yaml configuration file.
Returns
-------
`~glue_jupyter.bqplot.common.BqplotBaseView`
The viewer class instance.
"""
return self._viewer_by_reference(viewer_reference)
[docs] def get_viewer_by_id(self, vid):
"""Like :meth:`get_viewer` but use ID instead of reference name.
This is useful when reference name is `None`.
"""
return self._viewer_store.get(vid)
[docs] def get_data_from_viewer(self, viewer_reference, data_label=None,
cls='default', include_subsets=True):
"""
Returns each data component currently rendered within a viewer
instance. Viewers themselves store a default data type to which the
Glue data components are transformed upon retrieval. This can be
optionally overridden with the ``cls`` keyword.
Notes
-----
This is only used in cases where the viewers have been pre-defined
in the configuration file. Otherwise, viewers are not stored via
reference.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the yaml configuration file.
data_label : str, optional
Optionally provide a label to retrieve a specific data set from the
viewer instance.
cls : class
The class definition the Glue data components get transformed to
when retrieved. This requires that a working set of translation
functions exist in the ``glue_astronomy`` package. See
https://github.com/glue-viz/glue-astronomy for more info.
If this is the special string ``'default'``, the ``default_class``
attribute of the viewer referenced by ``viewer_reference`` is used.
include_subsets : bool
Whether to include subset layer data that exists in the viewer but
has not been included in the core data collection object.
Returns
-------
data : dict
A dict of the transformed Glue data objects, indexed to
corresponding viewer data labels.
"""
viewer = self.get_viewer(viewer_reference)
cls = viewer.default_class if cls == 'default' else cls
if cls is not None and not isclass(cls):
raise TypeError(
"cls in get_data_from_viewer must be a class, None, or "
"the 'default' string.")
data = {}
# If the viewer also supports collapsing, then grab the user's chosen
# statistic for collapsing data
if hasattr(viewer.state, 'function'):
statistic = viewer.state.function
else:
statistic = None
for layer_state in viewer.state.layers:
label = layer_state.layer.label
if (hasattr(layer_state, 'layer') and
(data_label is None or label == data_label)):
# For raw data, just include the data itself
if isinstance(layer_state.layer, BaseData):
layer_data = layer_state.layer
if cls is not None:
# If data is one-dimensional, assume that it can be
# collapsed via the defined statistic
if 'Trace' in layer_data.meta:
layer_data = layer_data.get_object()
elif cls == Spectrum1D:
layer_data = layer_data.get_object(cls=cls,
statistic=statistic)
else:
layer_data = layer_data.get_object(cls=cls)
# If the shape of the data is 2d, then use CCDData as the
# output data type
elif len(layer_data.shape) == 2:
layer_data = layer_data.get_object(cls=CCDData)
data[label] = layer_data
# For subsets, make sure to apply the subset mask to the
# layer data first
elif isinstance(layer_state.layer, Subset):
if include_subsets:
layer_data = layer_state.layer
if cls is not None:
handler, _ = data_translator.get_handler_for(cls)
try:
layer_data = handler.to_object(layer_data,
statistic=statistic)
except IncompatibleAttribute:
continue
data[label] = layer_data
# If a data label was provided, return only the corresponding data, otherwise return all:
return data.get(data_label, data)
[docs] def get_subsets_from_viewer(self, viewer_reference, data_label=None, subset_type=None):
"""
Returns the subsets of a specified viewer converted to astropy regions
objects.
It should be noted that the subset translation machinery lives in the
glue-astronomy repository. Currently, the machinery only works on 2D
data for cases like range selection. For e.g. a profile viewer that is
ostensibly just a view into a 3D data set, it is necessary to first
reduce the dimensions of the data, then retrieve the subset information
as a regions object. This means that the returned y extents in the
region are not strictly representative of the subset range in y.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the yaml configuration file.
data_label : str, optional
Optionally provide a label to retrieve a specific data set from the
viewer instance.
subset_type : str, optional
Optionally specify either "spectral" or "spatial" to return only
subsets created in a profile (spectrum) viewer or image viewer,
respectively.
Returns
-------
data : dict
A dict of the transformed Glue subset objects, with keys
representing the subset name and values as astropy regions
objects.
"""
viewer = self.get_viewer(viewer_reference)
data = self.get_data_from_viewer(viewer_reference,
data_label,
cls=None)
regions = {}
def _get_all_subregions(mask, spec_axis_data):
"""
Return all subregions within a subset.
Parameters
----------
mask : list
List of indices in spec_axis_data that are part of the subset.
spec_axis_data : list
List of spectral axis values.
Returns
-------
combined_spec_region : `~specutils.SpectralRegion`
SpectralRegion object containing all subregions of the subset.
"""
if len(mask) == 0:
# Mask should only be 0 if ApplyROI is used to incorrectly
# create subsets via the API
raise ValueError("Mask has length 0, ApplyROI may have been used incorrectly")
current_edge = 0
combined_spec_region = None
for index in range(1, len(mask)):
# Find spot where mask == True is for a different region of the subset
# i.e. mask = [0, 1, 4, 5]
# mask[2] != mask[1] + 1
if mask[index] != mask[index - 1] + 1:
subset_region = spec_axis_data[mask[current_edge]: mask[index - 1] + 1]
if not combined_spec_region:
combined_spec_region = SpectralRegion(min(subset_region),
max(subset_region))
else:
combined_spec_region += SpectralRegion(min(subset_region),
max(subset_region))
current_edge = index
# Get last region within the subset
if current_edge != index:
subset_region = spec_axis_data[mask[current_edge]: mask[index] + 1]
# No if check here because len(mask) must be greater than 1
# so combined_spec_region will have been instantiated in the for loop
if combined_spec_region is None:
combined_spec_region = SpectralRegion(min(subset_region), max(subset_region))
else:
combined_spec_region += SpectralRegion(min(subset_region), max(subset_region))
return combined_spec_region
if data_label is not None:
data = {data_label: data}
for key, value in data.items():
if isinstance(value, Subset):
# Get the component type in a compound subset
if hasattr(value.subset_state, "state1"):
this_type = type(value.subset_state.state1)
else:
this_type = type(value.subset_state)
# Skip spatial or spectral subsets if only the other is wanted
if subset_type == "spectral" or isinstance(viewer, BqplotProfileView):
if this_type == RoiSubsetState:
continue
elif subset_type == "spatial" or not isinstance(viewer, BqplotProfileView):
if this_type == RangeSubsetState:
continue
# Range selection on a profile is currently not supported in
# the glue translation machinery for astropy regions, so we
# have to do it manually. Only data that is 2d is supported,
# therefore, if the data is already 2d, simply use as is.
if value.data.ndim == 2:
region = value.data.get_selection_definition(
subset_id=key, format='astropy-regions')
regions[key] = region
continue
# There is a special case for 1d data (which is also not
# supported currently). We now eschew the use of the
# translation machinery entirely and construct the astropy
# region ourselves.
elif value.data.ndim == 1:
# Grab the data units from the glue-astronomy spectral axis
# TODO: this needs to be much simpler; i.e. data units in
# the glue component objects
# Cases where there is a single subset
if '_orig_wcs' in value.data.meta: # Hack for Cubeviz WCS propagation
data_wcs = value.data.meta['_orig_spec']
else:
data_wcs = value.data.coords
subregions_in_subset = _get_all_subregions(
np.where(value.to_mask() == True)[0], # noqa
data_wcs.spectral_axis)
regions[key] = subregions_in_subset
continue
temp_data = self.get_data_from_viewer(viewer_reference, value.label)
if isinstance(temp_data, Spectrum1D):
# Note that we look for mask == False here, rather than True above,
# because specutils masks are the reverse of Glue (of course)
subregions_in_subset = _get_all_subregions(
np.where(~temp_data.mask)[0], # noqa
temp_data.spectral_axis)
regions[key] = subregions_in_subset
continue
# Get the pixel coordinate [z] of the 3D data, repeating the
# wavelength axis. This doesn't seem strictly necessary as it
# returns the same data if the pixel axis is [y] or [x]
xid = value.data.pixel_component_ids[0]
# Construct a new data object collapsing over one of the
# spatial dimensions. This is necessary because the astropy
# region translation machinery in glue-astronomy does not
# support non-2D data, even for range objects.
stat_func = 'median'
if hasattr(viewer.state, 'function'):
stat_func = viewer.state.function
# Compute reduced data based on the current viewer's statistic
# function. This doesn't seem particularly useful, but better
# to be consistent.
reduced_data = Data(x=value.data.compute_statistic(
stat_func, value.data.id[xid],
subset_state=value.subset_state.copy(), axis=1))
# Instantiate a new data collection since we need to compose
# the collapsed data with the current subset state. We use a
# new data collection so as not to inference with the one used
# by the application.
temp_data_collection = DataCollection()
temp_data_collection.append(reduced_data)
# Get the data id of the pixel axis that will be used in the
# range composition. This is the wavelength axis for the new
# 2d data.
xid = reduced_data.pixel_component_ids[1]
# Create a new subset group to hold our current subset state
subset_group = temp_data_collection.new_subset_group(
label=value.label, subset_state=value.subset_state.copy())
# Set the subset state axis to the wavelength pixel coordinate
subset_group.subsets[0].subset_state.att = xid
# Use the associated collapsed subset data to get an astropy
# regions object dependent on the extends of the subset.
# **Note** that the y values in this region object are not
# useful, only the x values are.
region = subset_group.subsets[0].data.get_selection_definition(
format='astropy-regions')
regions[key] = region
return regions
[docs] def add_data(self, data, data_label=None, notify_done=True):
"""
Add data to the Glue ``DataCollection``.
Parameters
----------
data : any
Data to be stored in the ``DataCollection``. This must either be
a `~glue.core.data.Data` instance, or an arbitrary data instance
for which there exists data translation functions in the
glue astronomy repository.
data_label : str, optional
The name associated with this data. If none is given, label is pulled
from the input data (if `~glue.core.data.Data`) or a generic name is
generated.
notify_done: bool
Flag controlling whether a snackbar message is set when the data is
added to the app. Set to False to avoid overwhelming the user if
lots of data is getting loaded at once.
"""
if not data_label and hasattr(data, "label"):
data_label = data.label
data_label = self.return_unique_name(data_label)
if data_label in self.data_collection.labels:
warnings.warn(f"Overwriting existing data entry with label '{data_label}'")
self.data_collection[data_label] = data
# Send out a toast message
if notify_done:
snackbar_message = SnackbarMessage(
f"Data '{data_label}' successfully added.", sender=self, color="success")
self.hub.broadcast(snackbar_message)
[docs] def return_data_label(self, loaded_object, ext=None, alt_name=None, check_unique=True):
"""
Returns a unique data label that can be safely used to load data into data collection.
Parameters
----------
loaded_object : str or object
The path to a data file or FITS HDUList or image object or Spectrum1D or
NDData array or numpy.ndarray.
ext : str, optional
The extension (or other distinguishing feature) of data used to identify it.
For example, "filename[FLUX]" where "FLUX" is the ext value.
alt_name : str, optional
Alternate names that can be used if none of the options provided are valid.
check_unique : bool
Included so that this method can be used with data label retrieval in addition
to generation.
Returns
-------
data_label : str
A unique data label that at its root is either given by the user at load time
or created by Jdaviz using a description of the loaded filetype.
"""
data_label = None
if loaded_object is None:
pass
elif isinstance(loaded_object, str):
# This is either the full file path or the basename or the user input data label
if loaded_object.lower().endswith(('.jpg', '.jpeg', '.png')):
file_format = loaded_object.lower().split(".")[-1]
loaded_object = os.path.splitext(os.path.basename(loaded_object))[0]
data_label = f"{loaded_object}[{file_format}]"
elif os.path.isfile(loaded_object) or os.path.isdir(loaded_object):
# File that is not an image file
data_label = os.path.splitext(os.path.basename(loaded_object))[0]
else:
# Not a file path so assumed to be a data label
data_label = loaded_object
elif isinstance(loaded_object, fits.hdu.hdulist.HDUList):
if hasattr(loaded_object, 'file_name'):
data_label = f"{loaded_object.file_name}[HDU object]"
else:
data_label = "Unknown HDU object"
elif isinstance(loaded_object, Spectrum1D):
data_label = "Spectrum1D"
elif isinstance(loaded_object, NDData):
data_label = "NDData"
elif isinstance(loaded_object, np.ndarray):
data_label = "Array"
if data_label is None and alt_name is not None and isinstance(alt_name, str):
data_label = alt_name
elif data_label is None:
data_label = "Unknown"
if check_unique:
data_label = self.return_unique_name(data_label, ext=ext)
return data_label
[docs] def return_unique_name(self, data_label, ext=None):
if data_label is None:
data_label = "Unknown"
# This regex checks for any length of characters that end
# with a space followed by parenthesis with a number inside.
# If there is a match, the space and parenthesis section will be
# removed so that the remainder of the label can be checked
# against the data_label.
check_if_dup = re.compile(r"(.*)(\s\(\d*\))$")
labels = self.data_collection.labels
number_of_duplicates = 0
max_number = 0
for label in labels:
# If label is a duplicate of another label
if re.fullmatch(check_if_dup, label):
label_split = label.split(" ")
label_without_dup = " ".join(label_split[:-1])
label = label_without_dup
# Remove parentheses and cast to float
number_dup = int(label_split[-1][1:-1])
# Used to keep track the max number of duplicates,
# even if not all duplicates are loaded (or some
# are renamed)
if number_dup > max_number:
max_number = number_dup
if ext and f"{data_label}[{ext}]" == label:
number_of_duplicates += 1
elif ext is None and data_label == label:
number_of_duplicates += 1
if ext:
data_label = f"{data_label}[{ext}]"
if number_of_duplicates > 0:
data_label = f"{data_label} ({number_of_duplicates})"
# It is possible to add data named "test (1)" and then
# add another data named "test" and return_unique_name will see the
# first test and assume the second is the duplicate, appending
# "(1)" to the end. This overwrites the original data and
# causes issues. This block alters the duplicate number to be something unique
# (one more than the max number duplicate found)
# if a duplicate is still found in data_collection.
if data_label in self.data_collection.labels:
label_split = data_label.split(" ")
label_without_dup = " ".join(label_split[:-1])
data_label = f"{label_without_dup} ({max_number + 1})"
return data_label
[docs] def add_data_to_viewer(self, viewer_reference, data_label,
visible=True, clear_other_data=False):
"""
Plots a data set from the data collection in the specific viewer.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the yaml configuration file.
data_label : str
The Glue data label found in the ``DataCollection``.
visible : bool
Whether the layer should be initialized as visibile.
clear_other_data : bool
Removes all other currently plotted data and only shows the newly
defined data set.
"""
if ('mosviz_row' in self.state.settings and
not (self.get_viewer("table-viewer").row_selection_in_progress) and
self.data_collection[data_label].meta['mosviz_row'] !=
self.state.settings['mosviz_row']):
raise NotImplementedError("Intra-row plotting not supported. "
"Please use the table viewer to change rows")
viewer_item = self._get_viewer_item(viewer_reference)
if viewer_item is None:
raise ValueError(f"Could not identify viewer with reference {viewer_reference}")
self.set_data_visibility(viewer_item, data_label, visible=visible, replace=clear_other_data)
def _set_plot_axes_labels(self, viewer_id):
"""
Sets the plot axes labels to be the units of the data to be loaded.
Parameters
----------
viewer_id : str
The UUID associated with the desired viewer item.
"""
viewer = self._viewer_by_id(viewer_id)
viewer.set_plot_axes()
[docs] def remove_data_from_viewer(self, viewer_reference, data_label):
"""
Removes a data set from the specified viewer.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the yaml configuration file.
data_label : str
The Glue data label found in the ``DataCollection``.
"""
viewer_item = self._get_viewer_item(viewer_reference)
viewer_id = viewer_item['id']
viewer = self.get_viewer_by_id(viewer_id)
[data] = [x for x in self.data_collection if x.label == data_label]
viewer.remove_data(data)
viewer._layers_with_defaults_applied = [layer_info for layer_info in viewer._layers_with_defaults_applied # noqa
if layer_info['data_label'] != data.label] # noqa
remove_data_message = RemoveDataMessage(data, viewer,
viewer_id=viewer_id,
sender=self)
self.hub.broadcast(remove_data_message)
# update data menu entry
selected_items = viewer_item['selected_data_items']
data_id = self._data_id_from_label(data_label)
if data_id in selected_items:
_ = selected_items.pop(data_id)
def _data_id_from_label(self, label):
"""
Retrieve the data item given the Glue ``DataCollection`` data label.
Parameters
----------
label : str
Label associated with the ``DataCollection`` item. This is also the
name shown in the data list.
Returns
-------
dict
The data item dictionary containing the id and name of the given
data set.
"""
for data_item in self.state.data_items:
if data_item['name'] == label:
return data_item['id']
[docs] def get_viewer_ids(self, prefix=None):
"""Return a list of available viewer IDs.
Parameters
----------
prefix : str or `None`
If not `None`, only return viewer IDs with given prefix
(case-sensitive). Otherwise, all viewer IDs are returned.
Returns
-------
vids : list of str
Sorted list of viewer IDs.
"""
all_keys = sorted(self._viewer_store.keys())
if isinstance(prefix, str):
vids = [k for k in all_keys if k.startswith(prefix)]
else:
vids = all_keys
return vids
[docs] def get_viewer_reference_names(self):
"""Return a list of available viewer reference names."""
# Cannot sort because of None
return [self._viewer_item_by_id(vid).get('reference') for vid in self._viewer_store]
def _get_first_viewer_reference_name(
self, require_no_selected_data=False,
require_spectrum_viewer=False,
require_spectrum_2d_viewer=False,
require_table_viewer=False,
require_flux_viewer=False,
require_image_viewer=False
):
"""
Return the viewer reference name of the first available viewer.
Optionally use ``require_no_selected_data`` to require that the
viewer has not yet loaded data, or e.g. ``require_spectrum_viewer``
to require that the viewer supports spectrum visualization.
"""
from jdaviz.configs.imviz.plugins.viewers import ImvizImageView
from jdaviz.configs.specviz.plugins.viewers import SpecvizProfileView
from jdaviz.configs.cubeviz.plugins.viewers import CubevizProfileView, CubevizImageView
from jdaviz.configs.mosviz.plugins.viewers import (
MosvizTableViewer, MosvizProfile2DView
)
spectral_viewers = (SpecvizProfileView, CubevizProfileView)
spectral_2d_viewers = (MosvizProfile2DView, )
table_viewers = (MosvizTableViewer, )
image_viewers = (ImvizImageView, CubevizImageView)
flux_viewers = (CubevizImageView, )
for vid in self._viewer_store:
viewer_item = self._viewer_item_by_id(vid)
is_returnable = (
(require_no_selected_data and not len(viewer_item['selected_data_items'])) or
(not require_no_selected_data)
)
if require_spectrum_viewer:
if isinstance(self._viewer_store[vid], spectral_viewers) and is_returnable:
return viewer_item['reference']
elif require_spectrum_2d_viewer:
if isinstance(self._viewer_store[vid], spectral_2d_viewers) and is_returnable:
return viewer_item['reference']
elif require_table_viewer:
if isinstance(self._viewer_store[vid], table_viewers) and is_returnable:
return viewer_item['reference']
elif require_image_viewer:
if isinstance(self._viewer_store[vid], image_viewers) and is_returnable:
return viewer_item['reference']
elif require_flux_viewer:
if isinstance(self._viewer_store[vid], flux_viewers) and is_returnable:
return viewer_item['reference']
else:
if is_returnable:
return viewer_item['reference']
def _viewer_by_id(self, vid):
"""
Viewer instance by id.
Parameters
----------
vid : str
The UUID associated with the parent viewer item dictionary.
Returns
-------
`~glue_jupyter.bqplot.common.BqplotBaseView`
The viewer class instance.
"""
return self._viewer_store.get(vid)
def _viewer_item_by_id(self, vid):
"""
Retrieve a viewer item dictionary by id.
Parameters
----------
vid : str
The UUID associated with the desired viewer item.
Returns
-------
viewer_item : dict
The dictionary containing the viewer instances and associated
attributes.
"""
def find_viewer_item(stack_items):
for stack_item in stack_items:
for viewer_item in stack_item.get('viewers'):
if viewer_item.get('id') == vid:
return viewer_item
if len(stack_item.get('children')) > 0:
result = find_viewer_item(stack_item.get('children'))
if result is not None:
return result
viewer_item = find_viewer_item(self.state.stack_items)
return viewer_item
def _viewer_by_reference(self, reference):
"""
Viewer instance by reference defined in the yaml configuration file.
Parameters
----------
reference : str
Reference for viewer defined in the yaml configuration file.
Returns
-------
`~glue_jupyter.bqplot.common.BqplotBaseView`
The viewer class instance.
"""
viewer_item = self._viewer_item_by_reference(reference)
return self._viewer_store[viewer_item['id']]
def _viewer_item_by_reference(self, reference):
"""
Retrieve a viewer item dictionary by reference.
Parameters
----------
reference : str
Reference for viewer defined in the yaml configuration file.
Returns
-------
viewer_item : dict
The dictionary containing the viewer instances and associated
attributes.
"""
def find_viewer_item(stack_items):
out_viewer_item = None
for stack_item in stack_items:
for viewer_item in stack_item.get('viewers'):
if viewer_item['reference'] == reference:
out_viewer_item = viewer_item
break
if len(stack_item.get('children')) > 0:
out_viewer_item = find_viewer_item(stack_item.get('children'))
return out_viewer_item
viewer_item = find_viewer_item(self.state.stack_items)
return viewer_item
def _get_viewer_item(self, ref_or_id):
"""
Retrieve a viewer item dictionary by reference or id (trying reference first).
Parameters
----------
ref_or_id : str
Reference or ID for viewer defined in the yaml configuration file.
Returns
-------
viewer_item : dict
The dictionary containing the viewer instances and associated
attributes.
"""
if isinstance(ref_or_id, dict):
return ref_or_id
viewer_item = self._viewer_item_by_reference(ref_or_id)
if viewer_item is None: # Maybe they mean the ID
viewer_item = self._viewer_item_by_id(ref_or_id)
return viewer_item
[docs] def vue_destroy_viewer_item(self, cid):
"""
Callback for when viewer area tabs are destroyed. Finds the viewer item
associated with the provided id and removes it from the ``stack_items``
list.
Parameters
----------
cid : str
The viewer ID associated with the viewer item dictionary.
"""
def remove(stack_items):
for stack in stack_items:
for viewer in stack['viewers']:
if viewer['id'] == cid:
stack['viewers'].remove(viewer)
if len(stack.get('children', [])) > 0:
stack['children'] = remove(stack['children'])
for empty_stack in [s for s in stack_items
if not s['viewers'] and not s.get('children')]:
stack_items.remove(empty_stack)
return stack_items
remove(self.state.stack_items)
# Also remove the viewer from the stored viewer instance dictionary
if cid in self._viewer_store:
del self._viewer_store[cid]
self.hub.broadcast(ViewerRemovedMessage(cid, sender=self))
[docs] def vue_data_item_unload(self, event):
"""
Callback for selection events in the front-end data list when clicking to unload an entry
from the viewer.
"""
data_label = self._get_data_item_by_id(event['item_id'])['name']
self.remove_data_from_viewer(event['id'], data_label)
[docs] def vue_data_item_visibility(self, event):
self.set_data_visibility(event['id'],
self._get_data_item_by_id(event['item_id'])['name'],
visible=event['visible'], replace=event.get('replace', False))
[docs] def set_data_visibility(self, viewer_reference, data_label, visible=True, replace=False):
"""
Set the visibility of the layers corresponding to ``data_label`` in a given viewer.
Parameters
----------
viewer_reference : str
Reference (or ID) of the viewer
data_label : str
Label of the data to set the visiblity. If not already loaded in the viewer, the
data will automatically be loaded before setting the visibility
visible : bool
Whether to set the layer(s) to visible.
replace : bool
Whether to disable the visilility of all other layers in the viewer
"""
viewer_item = self._get_viewer_item(viewer_reference)
viewer_id = viewer_item['id']
viewer = self.get_viewer_by_id(viewer_id)
# if the data_label is in the app, but not loaded in the viewer, automatically load it first
viewer_data_labels = [layer.layer.label for layer in viewer.layers]
if data_label not in viewer_data_labels:
dc_labels = [data.label for data in self.data_collection]
if data_label not in dc_labels:
if os.path.exists(data_label):
raise ValueError(f'The data label "{data_label}" is not available '
f'to add to the viewer, but it does specify a file path. '
f'If you intended to load the data from that file, use the '
f'`load_data` method or similar.')
raise ValueError(
f"No data item found with label '{data_label}'. Label must be one "
"of:\n\t" + "\n\t".join(dc_labels))
[data] = [x for x in self.data_collection if x.label == data_label]
viewer.add_data(data, percentile=95, color=viewer.color_cycler())
add_data_message = AddDataMessage(data, viewer,
viewer_id=viewer_id,
sender=self)
self.hub.broadcast(add_data_message)
# set visibility state of all applicable layers
for layer in viewer.layers:
if layer.layer.data.label == data_label:
if visible and not layer.visible:
layer.visible = True
layer.update()
else:
layer.visible = visible
# if replace, do another loop (we do a second loop to ensure the visible layer is added
# first BEFORE other layers are removed)
if replace:
for layer in viewer.layers:
if layer.layer.data.label != data_label:
layer.visible = False
# update data menu - selected_data_items should be READ ONLY, not modified by the user/UI
selected_items = viewer_item['selected_data_items']
data_id = self._data_id_from_label(data_label)
selected_items[data_id] = 'visible' if visible else 'hidden'
if replace:
for id in selected_items:
if id != data_id:
selected_items[id] = 'hidden'
# Sets the plot axes labels to be the units of the most recently
# active data.
viewer_data_labels = [layer.layer.label for layer in viewer.layers]
if len(viewer_data_labels) > 0 and getattr(self._jdaviz_helper, '_in_batch_load', 0) == 0:
active_data = self.data_collection[viewer_data_labels[0]]
if (hasattr(active_data, "_preferred_translation")
and active_data._preferred_translation is not None):
self._set_plot_axes_labels(viewer_id)
if self.config == 'imviz':
viewer.on_limits_change() # Trigger compass redraw
[docs] def vue_data_item_remove(self, event):
self.data_collection.remove(self.data_collection[event['item_name']])
[docs] def vue_close_snackbar_message(self, event):
"""
Callback to close a message in the snackbar when the "close"
button is clicked.
"""
self.state.snackbar_queue.close_current_message(self.state)
[docs] def vue_call_viewer_method(self, event):
viewer_id, method = event['id'], event['method']
args = event.get('args', [])
kwargs = event.get('kwargs', {})
return getattr(self._viewer_store[viewer_id], method)(*args, **kwargs)
def _get_data_item_by_id(self, data_id):
return next((x for x in self.state.data_items
if x['id'] == data_id), None)
def _on_data_added(self, msg):
"""
Callback for when data is added to the internal ``DataCollection``.
Adds a new data item dictionary to the ``data_items`` state list and
links the new data to any compatible previously loaded data.
Parameters
----------
msg : `~glue.core.message.DataCollectionAddMessage`
The Glue data collection add message containing information about
the new data.
"""
# We don't need to link the first data to itself
if len(self.data_collection) > 1:
self._link_new_data()
data_item = self._create_data_item(msg.data)
self.state.data_items.append(data_item)
def _clear_object_cache(self, data_label=None):
if data_label is None:
self._get_object_cache.clear()
else:
# keys are (data_label, statistic) tuples
self._get_object_cache = {k: v for k, v in self._get_object_cache.items()
if k[0] != data_label}
def _on_data_deleted(self, msg):
"""
Callback for when data is removed from the internal ``DataCollection``.
Removes the data item dictionary in the ``data_items`` state list.
Parameters
----------
msg : `~glue.core.message.DataCollectionAddMessage`
The Glue data collection add message containing information about
the new data.
"""
for data_item in self.state.data_items:
if data_item['name'] == msg.data.label:
self.state.data_items.remove(data_item)
self._clear_object_cache(msg.data.label)
@staticmethod
def _create_data_item(data):
ndims = len(data.shape)
wcsaxes = data.meta.get('WCSAXES', None)
if wcsaxes is None:
# then we'll need to determine type another way, we want to avoid
# this when we can though since its not as cheap
component_ids = [str(c) for c in data.component_ids()]
if data.label == 'MOS Table':
typ = 'table'
elif 'Trace' in data.meta:
typ = 'trace'
elif ndims == 1:
typ = '1d spectrum'
elif ndims == 2 and wcsaxes is not None:
if wcsaxes == 3:
typ = '2d spectrum'
elif wcsaxes == 2:
typ = 'image'
else:
typ = 'unknown'
elif ndims == 2 and wcsaxes is None:
typ = '2d spectrum' if 'Wavelength' in component_ids else 'image'
elif ndims == 3:
typ = 'cube'
else:
typ = 'unknown'
# we'll expose any information we need here. For "meta", not all entries are guaranteed
# to be serializable, so we'll just send those that we need.
return {
'id': str(uuid.uuid4()),
'name': data.label,
'locked': False,
'ndims': data.ndim,
'type': typ,
'meta': {k: v for k, v in data.meta.items() if k in ['Plugin', 'mosviz_row']},
'children': []}
@staticmethod
def _create_stack_item(container='gl-stack', children=None, viewers=None):
"""
Convenience method for generating stack item dictionaries.
Parameters
----------
container : str
The GoldenLayout container type used to encapsulate the children
items within this stack item.
children : list
List of children stack item dictionaries used for recursively
including layout items within each GoldenLayout component cell.
viewers : list
List of viewer item dictionaries containing the information used
to render the viewer and associated tool widgets.
Returns
-------
dict
Dictionary containing information for this stack item.
"""
children = [] if children is None else children
viewers = [] if viewers is None else viewers
return {
'id': str(uuid.uuid4()),
'container': container,
'children': children,
'viewers': viewers}
def _next_viewer_num(self, prefix):
all_vids = self.get_viewer_ids(prefix=prefix)
if len(all_vids) == 0:
return 0
# Assume name-num format
last_vid = all_vids[-1]
last_num = int(last_vid.split('-')[-1])
return last_num + 1
def _create_viewer_item(self, viewer, vid=None, name=None, reference=None):
"""
Convenience method for generating viewer item dictionaries.
Parameters
----------
viewer : `~glue_jupyter.bqplot.common.BqplotBaseView`
The ``Bqplot`` viewer instance.
vid : str or `None`, optional
The ID of the viewer.
name : str or `None`, optional
The name shown in the GoldenLayout tab for this viewer.
If `None`, it is the same as viewer ID.
reference : str, optional
The reference associated with this viewer as defined in the yaml
configuration file.
Returns
-------
dict
Dictionary containing information for this viewer item.
"""
if vid is None:
pfx = self.state.settings.get('configuration', str(name))
n = self._next_viewer_num(pfx)
vid = f"{pfx}-{n}"
# There is a viewer.LABEL inherited from glue-jupyter but there was
# objection in using it here because it is not hidden, so we use our
# own attribute instead.
viewer._reference_id = vid # For reverse look-up
self.state.viewer_icons.setdefault(vid, len(self.state.viewer_icons)+1)
return {
'id': vid,
'name': name or vid,
'widget': "IPY_MODEL_" + viewer.figure_widget.model_id,
'toolbar': "IPY_MODEL_" + viewer.toolbar.model_id if viewer.toolbar else '', # noqa
'layer_options': "IPY_MODEL_" + viewer.layer_options.model_id,
'viewer_options': "IPY_MODEL_" + viewer.viewer_options.model_id,
'selected_data_items': {}, # noqa data_id: visibility state (visible, hidden, mixed), READ-ONLY
'visible_layers': {}, # label: {color, label_suffix}, READ-ONLY
'config': self.config, # give viewer access to app config/layout
'data_open': False,
'collapse': True,
'reference': reference}
def _on_new_viewer(self, msg, vid=None, name=None):
"""
Callback for when the `~jdaviz.core.events.NewViewerMessage` message is
raised. This method asks the application handler to generate a new
viewer and then created the associated stack and viewer items.
Parameters
----------
msg : `~jdaviz.core.events.NewViewerMessage`
The message received from the ``Hub`` broadcast.
vid : str or `None`
ID of the viewer. If `None`, it is auto-generated
from configuration settings.
name : str or `None`
Name of the viewer. If `None`, it is auto-generated
from class name.
Returns
-------
viewer : `~glue_jupyter.bqplot.common.BqplotBaseView`
The new viewer instance.
"""
viewer = self._application_handler.new_data_viewer(
msg.cls, data=msg.data, show=False)
viewer.figure_widget.layout.height = '100%'
links_control_plugin = self._jdaviz_helper.plugins.get('Links Control', None)
if links_control_plugin is not None:
viewer.state.linked_by_wcs = links_control_plugin.link_type.selected == 'WCS'
elif len(self._viewer_store):
# The plugin would only not exist for instances of Imviz where the user has
# intentionally removed the Links Control plugin, but in that case we will
# adopt "linked_by_wcs" from the first (assuming all are the same)
# NOTE: deleting the default viewer is forbidden both by API and UI, but if
# for some reason that was the case here, linked_by_wcs will default to False
viewer.state.linked_by_wcs = list(self._viewer_store.values())[0].state.linked_by_wcs
if msg.x_attr is not None:
x = msg.data.id[msg.x_attr]
viewer.state.x_att = x
# Create the viewer item dictionary
if name is None:
name = vid
new_viewer_item = self._create_viewer_item(
viewer=viewer, vid=vid, name=name, reference=name
)
new_stack_item = self._create_stack_item(
container='gl-stack',
viewers=[new_viewer_item])
# Store the glupyter viewer object so we can access the add and remove
# data methods in the future
vid = new_viewer_item['id']
self._viewer_store[vid] = viewer
# Add viewer locally
self.state.stack_items.append(new_stack_item)
self.session.application.viewers.append(viewer)
# Send out a toast message
self.hub.broadcast(ViewerAddedMessage(vid, sender=self))
return viewer
[docs] def load_configuration(self, path=None, config=None):
"""
Parses the provided input into a configuration
dictionary and populates the appropriate state values
with the results. Provided input can either be a
configuration YAML file or a pre-made configuration
dictionary.
Parameters
----------
path : str, optional
Path to the configuration file to be loaded. In the case where this
is ``None``, it loads the default configuration. Optionally, this
can be provided as name reference. **NOTE** This optional way to
define the configuration will be removed in future versions.
config : dict, optional
A dictionary of configuration settings to be loaded. The dictionary
contents should be the same as a YAML config file specification.
"""
# reset the application state
self._reset_state()
# load the configuration from the yaml file or configuration object
assert not (path and config), 'Cannot specify both a path and a config object!'
if config:
assert isinstance(config, dict), 'configuration object must be a dictionary'
else:
# check if the input path is actually a dict object
if isinstance(path, dict):
config = path
else:
config = read_configuration(path=path)
# store the loaded config object
self._loaded_configuration = config
# give the vue templates access to the current config/layout
self.config = config['settings'].get('configuration', 'unknown')
self.vdocs = 'latest' if 'dev' in __version__ else 'v'+__version__
self.state.settings.update(config.get('settings'))
def compose_viewer_area(viewer_area_items):
stack_items = []
for item in viewer_area_items:
stack_item = self._create_stack_item(
container=CONTAINER_TYPES[item.get('container')])
stack_items.append(stack_item)
for view in item.get('viewers', []):
viewer = self._application_handler.new_data_viewer(
viewer_registry.members.get(view['plot'])['cls'],
data=None, show=False)
viewer.figure_widget.layout.height = '100%'
viewer_item = self._create_viewer_item(
name=view.get('name'),
viewer=viewer,
reference=view.get('reference'))
self._viewer_store[viewer_item['id']] = viewer
stack_item.get('viewers').append(viewer_item)
if len(item.get('children', [])) > 0:
child_stack_items = compose_viewer_area(
item.get('children'))
stack_item['children'] = child_stack_items
return stack_items
if config.get('viewer_area') is not None:
stack_items = compose_viewer_area(config.get('viewer_area'))
self.state.stack_items.extend(stack_items)
# Add the toolbar item filter to the toolbar component
for name in config.get('toolbar', []):
tool = tool_registry.members.get(name)(app=self)
self.state.tool_items.append({
'name': name,
'widget': "IPY_MODEL_" + tool.model_id
})
self._application_handler._tools[name] = tool
for name in config.get('tray', []):
tray = tray_registry.members.get(name)
tray_registry_options = tray.get('viewer_reference_name_kwargs', {})
# Optional keyword arguments are required to initialize some
# tray items. These kwargs specify the viewer reference names that are
# assumed to be present in the configuration.
optional_tray_kwargs = dict()
# If viewer reference names need to be passed to the tray item
# constructor, pass the names into the constructor in the format
# that the tray items expect.
for opt_attr, [opt_kwarg, get_name_kwargs] in tray_registry_options.items():
opt_value = getattr(
self, opt_attr, self._get_first_viewer_reference_name(**get_name_kwargs)
)
if opt_value is None:
continue
optional_tray_kwargs[opt_kwarg] = opt_value
tray_item_instance = tray.get('cls')(
app=self, **optional_tray_kwargs
)
tray_item_label = tray.get('label')
# store a copy of the tray name in the instance so it can be accessed by the
# plugin itself
tray_item_instance._plugin_name = tray_item_label
self.state.tray_items.append({
'name': name,
'label': tray_item_label,
'widget': "IPY_MODEL_" + tray_item_instance.model_id
})
def _reset_state(self):
""" Resets the application state """
self.state = ApplicationState()
self._application_handler._tools = {}
[docs] def get_configuration(self, path=None, section=None):
"""Returns a copy of the application configuration.
Returns a copy of the configuration specification. If path
is not specified, returns the currently loaded configuration.
Parameters
----------
path : str, optional
path to the configuration file to be retrieved.
section : str, optional
A section of the configuration to retrieve.
Returns
-------
cfg : dict
A configuration specification dictionary.
"""
config = None
if not path:
config = self._loaded_configuration
cfg = get_configuration(path=path, section=section, config=config)
return cfg
[docs] def get_tray_item_from_name(self, name):
"""Return the instance of a tray item for a given name.
This is useful for direct programmatic access to Jdaviz plugins
registered under tray items.
Parameters
----------
name : str
The name used when the plugin was registered to
an internal `~jdaviz.core.registries.TrayRegistry`.
Returns
-------
tray_item : obj
The instance of the plugin registered to tray items.
Raises
------
KeyError
Name not found.
"""
from ipywidgets.widgets import widget_serialization
tray_item = None
for item in self.state.tray_items:
if item['name'] == name or item['label'] == name:
ipy_model_id = item['widget']
tray_item = widget_serialization['from_json'](ipy_model_id, None)
break
if tray_item is None:
raise KeyError(f'{name} not found in app.state.tray_items')
return tray_item