import numpy as np
from functools import cached_property
from ipyvuetify import VuetifyTemplate
from glue.config import colormaps
from glue.core import HubListener
from glue.core.message import (DataCollectionAddMessage,
DataCollectionDeleteMessage,
SubsetCreateMessage,
SubsetDeleteMessage,
SubsetUpdateMessage)
from glue.core.subset import RoiSubsetState
from glue_jupyter.bqplot.image import BqplotImageView
from glue_jupyter.widgets.linked_dropdown import get_choices as _get_glue_choices
from specutils import Spectrum1D
from traitlets import Any, Bool, HasTraits, List, Unicode, observe
from jdaviz import __version__
from jdaviz.core.events import (AddDataMessage, RemoveDataMessage,
ViewerAddedMessage, ViewerRemovedMessage)
__all__ = ['TemplateMixin', 'PluginTemplateMixin',
'BasePluginComponent', 'BaseSelectPluginComponent',
'SubsetSelect', 'SpatialSubsetSelectMixin', 'SpectralSubsetSelectMixin',
'ViewerSelect', 'ViewerSelectMixin',
'DatasetSelect', 'DatasetSelectMixin',
'AutoLabel', 'AutoLabelMixin',
'AddResults', 'AddResultsMixin']
[docs]class TemplateMixin(VuetifyTemplate, HubListener):
config = Unicode("").tag(sync=True)
vdocs = Unicode("").tag(sync=True)
def __new__(cls, *args, **kwargs):
"""
Overload object creation so that we can inject a reference to the
`~glue.core.hub.Hub` class before components can be initialized. This makes it so
hub references on plugins can be passed along to components in the
call to the initialization method.
"""
app = kwargs.pop('app', None)
obj = super().__new__(cls, *args, **kwargs)
obj._app = app
# give the vue templates access to the current config/layout
obj.config = app.state.settings.get("configuration", "default")
# give the vue templates access to jdaviz version
obj.vdocs = 'latest' if 'dev' in __version__ else 'v'+__version__
# store references to all bqplot widgets that need to handle resizing
obj.bqplot_figs_resize = []
return obj
@property
def app(self):
"""
Allows access to the underlying Jdaviz application instance. This is
**not** access to the helper class, but instead the
`jdaviz.app.Application` object.
"""
return self._app
@property
def hub(self):
return self._app.session.hub
@property
def session(self):
return self._app.session
@property
def data_collection(self):
return self._app.session.data_collection
[docs]class PluginTemplateMixin(TemplateMixin):
"""
This base class can be inherited by all sidebar plugins to expose common functionality.
"""
disabled_msg = Unicode("").tag(sync=True)
plugin_opened = Bool(False).tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.app.state.add_callback('tray_items_open', self._mxn_update_plugin_opened)
self.app.state.add_callback('drawer', self._mxn_update_plugin_opened)
def _mxn_update_plugin_opened(self, new_value):
app_state = self.app.state
tray_names_open = [app_state.tray_items[i]['name'] for i in app_state.tray_items_open]
self.plugin_opened = app_state.drawer and self._registry_name in tray_names_open
[docs]class BasePluginComponent(HubListener):
"""
This base class handles attaching traitlets from the plugin itself to logic
handled within the component, support for caching and clearing caches on properties,
and common properties for accessing the app, etc.
"""
def __init__(self, plugin, **kwargs):
self._plugin_traitlets = {k: v for k, v in kwargs.items() if v is not None}
self._plugin = plugin
self._cached_properties = []
super().__init__()
def __getattr__(self, attr):
if attr[0] == '_' or attr not in self._plugin_traitlets.keys():
return super().__getattribute__(attr)
return getattr(self._plugin, self._plugin_traitlets.get(attr))
def __setattr__(self, attr, value, force_super=False):
if attr[0] == '_' or force_super or attr not in self._plugin_traitlets.keys():
return super().__setattr__(attr, value)
return setattr(self._plugin, self._plugin_traitlets.get(attr), value)
def _clear_cache(self, *attrs):
"""
provide convenience function to clearing the cache for cached_properties
"""
if not len(attrs):
attrs = self._cached_properties
for attr in attrs:
if attr in self.__dict__:
del self.__dict__[attr]
[docs] def add_observe(self, traitlet_name, handler, first=False):
self._plugin.observe(handler, traitlet_name)
if first:
# re-order the callbacks so this one is first
existing_callbacks = self._plugin._trait_notifiers[traitlet_name]['change']
new_order = [handler] + [other for other in existing_callbacks if other != handler]
self._plugin._trait_notifiers[traitlet_name]['change'] = new_order
@property
def plugin(self):
"""
Access the parent plugin object
"""
return self._plugin
@property
def app(self):
"""
Access the parent app object
"""
return self._plugin.app
@property
def hub(self):
"""
Access the hub attached to the parent plugin object
"""
return self._plugin.hub
@property
def viewer_dicts(self):
def _dict_from_viewer(viewer, viewer_item, index=None):
d = {'viewer': viewer, 'id': viewer_item['id']}
if viewer_item.get('reference') is not None:
d['reference'] = viewer_item['reference']
d['label'] = viewer_item['reference']
else:
d['reference'] = None
d['label'] = viewer_item['id']
if index is not None:
d['icon'] = f"mdi-numeric-{index+1}-circle-outline"
return d
return [_dict_from_viewer(viewer, self.app._viewer_item_by_id(vid), index)
for index, (vid, viewer) in enumerate(self.app._viewer_store.items())
if viewer.__class__.__name__ != 'MosvizTableViewer']
@cached_property
def spectrum_viewer(self):
return self._plugin.app.get_viewer("spectrum-viewer")
[docs]class BaseSelectPluginComponent(BasePluginComponent, HasTraits):
"""
This base class extends BasePluginComponent for common functionality for a select/dropdown
component. The subclasses MUST have an ``items`` traitlet as a list of dictionaries, with
'label' as the selection entry (and any other optional entries for styling, etc) and a
``selected`` string traitlet. The subclasses should also override ``selected_obj`` and may
choose to override ``_selected_changed`` (likely with a super call to keep the base logic).
"""
filters = List([]).tag(sync=True)
def __init__(self, *args, **kwargs):
# default_mode can be one of empty, first, default_text (requires default_text to be set)
default_mode = kwargs.pop('default_mode', 'empty')
default_text = kwargs.pop('default_text', None)
manual_options = kwargs.pop('manual_options', [])
self._viewers = kwargs.pop('viewers', None)
# we'll pop from kwargs now to avoid passing to the super.__init__, but need to
# wait for everything else to be set before setting to the traitlet
filters = kwargs.pop('filters', [])[:] # [:] needed to force copy from kwarg default
super().__init__(*args, **kwargs)
self._cached_properties = ["selected_obj", "selected_item"]
self._default_mode = default_mode
self._default_text = default_text
if default_text is not None and default_text not in manual_options:
manual_options = [default_text] + manual_options
self._manual_options = manual_options
self.items = [{"label": opt} for opt in manual_options]
# set default values for traitlets
if default_text is not None:
self.selected = default_text
if kwargs.get('multiselect'):
self.add_observe(kwargs.get('multiselect'), self._multiselect_changed)
# this callback MUST come first so that any plugins that use @observe have those
# callbacks triggered AFTER the cache is cleared and the value is checked against
# valid options
self.add_observe(kwargs.get('selected'), self._selected_changed, first=True)
self.filters = filters
@property
def is_multiselect(self):
if not hasattr(self, 'multiselect'):
return False
else:
return self.multiselect
@property
def default_text(self):
return self._default_text
@property
def manual_options(self):
return self._manual_options
# read-only access to manual options (cannot change after init)
@property
def cached_properties(self):
return self._cached_properties
[docs] def add_filter(self, *filters):
self.filters += [filter for filter in filters]
@property
def viewer_dicts(self):
all_viewer_dicts = super().viewer_dicts
if self._viewers is None:
return all_viewer_dicts
# filter to those provided (either by id or reference)
return [v for v in all_viewer_dicts
if v['reference'] in self._viewers or v['id'] in self._viewers]
@property
def viewer_refs(self):
return [v['reference'] for v in self.viewer_dicts]
@property
def viewer_ids(self):
return [v['id'] for v in self.viewer_dicts]
@property
def viewers(self):
return [v['viewer'] for v in self.viewer_dicts]
@property
def labels(self):
return [s['label'] for s in self.items if 'label' in s.keys()]
def _get_selected_item(self, selected):
for item in self.items:
if item['label'] == selected:
return item
return {}
@cached_property
def selected_item(self):
if self.is_multiselect:
items = [self._get_selected_item(selected) for selected in self.selected]
if not len(items):
return {}
return {k: [item[k] for item in items] for k in items[0].keys()}
return self._get_selected_item(self.selected)
@cached_property
def selected_obj(self):
raise NotImplementedError(f"selected_obj not implemented by {self.__class__.__name__}")
@property
def default_mode(self):
return self._default_mode
def _apply_default_selection(self):
# TODO: make this multi-ready
is_valid = self.selected in self.labels
if callable(self.default_mode):
# callable was defined and passed by the plugin or inheriting component.
# the callable takes the viewer component as input as well as the `is_valid` boolean
# which states if the current selection is already valid and returns the default label
# (to keep the current selection
self.selected = self.default_mode(self, is_valid=is_valid)
return
if is_valid:
# current selection is valid
return
if self.default_mode == 'first':
self.selected = self.labels[0] if len(self.labels) else ''
elif self.default_mode == 'default_text':
self.selected = self._default_text if self._default_text else ''
else:
self.selected = ''
def _is_valid_item(self, item, filter_callables={}):
for valid_filter in self.filters:
if isinstance(valid_filter, str):
# pull from the functions above (should be subclassed),
# will raise an error if not in locals
try:
valid_filter = filter_callables[valid_filter]
except KeyError:
raise ValueError(f"{valid_filter} not an implemented filter.")
if not valid_filter(item):
return False
return True
def _multiselect_changed(self, event):
self._clear_cache()
if self.is_multiselect:
self.selected = [self.selected]
elif isinstance(self.selected, list):
self.selected = self.selected[0]
else:
self._apply_default_selection()
def _selected_changed(self, event):
self._clear_cache()
if self.is_multiselect:
if not isinstance(event['new'], list):
self.selected = [event['new']]
return
if not np.all([item in self.labels + [''] for item in event['new']]):
self._apply_default_selection()
raise ValueError(f"not all items in {event['new']} are one of {self.labels}")
else:
if event['new'] not in self.labels + ['']:
self._apply_default_selection()
raise ValueError(f"{event['new']} not one of {self.labels}")
class LayerSelect(BaseSelectPluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``items`` (list of dicts with keys: label, color)
* ``selected`` (string)
Properties (in the object only):
* ``labels`` (list of labels corresponding to items)
* ``selected_item`` (dictionary in ``items`` coresponding to ``selected``, cached)
* ``selected_obj`` (layer object corresponding to ``selected``, cached)
To use in a plugin:
* create (empty) traitlets in the plugin
* register with all the automatic logic in the plugin's init by passing the string names
of the respective traitlets.
* use component in plugin template (see below)
* refer to properties above based on the interally stored reference to the
instantiated object of this component
* observe the traitlets created and defined in the plugin, as necessary
Example template (label and hint are optional)::
<plugin-layer-select
:items="layer_items"
:selected.sync="layer_selected"
:show_if_single_entry="true"
label="Layer"
hint="Select layer."
/>
"""
def __init__(self, plugin, items, selected, viewer,
multiselect=None,
default_text=None, manual_options=[], allowed_type=None,
default_mode='first'):
"""
Parameters
----------
plugin
the parent plugin object
items : str
the name of the items traitlet defined in ``plugin``
selected : str
the name of the selected traitlet defined in ``plugin``
viewer: str
the name of the traitlet defined in ``plugin`` storing the viewer(s) to expose the
layers
default_text : str or None
the text to show for no selection. If not provided or None, no entry will be provided
in the dropdown for no selection.
manual_options: list
list of options to provide that are not automatically populated by subsets. If
``default`` text is provided but not in ``manual_options`` it will still be included as
the first item in the list.
"""
super().__init__(plugin,
items=items,
selected=selected,
viewer=viewer,
multiselect=multiselect,
default_text=default_text,
manual_options=manual_options,
default_mode=default_mode)
self.hub.subscribe(self, AddDataMessage,
handler=lambda _: self._on_layers_changed())
self.hub.subscribe(self, RemoveDataMessage,
handler=lambda _: self._on_layers_changed())
self.hub.subscribe(self, SubsetCreateMessage,
handler=lambda _: self._on_layers_changed())
# will need SubsetUpdateMessage for name only (style shouldn't force a full refresh)
# self.hub.subscribe(self, SubsetUpdateMessage,
# handler=lambda _: self._on_layers_changed())
self.hub.subscribe(self, SubsetDeleteMessage,
handler=lambda _: self._on_layers_changed())
self.add_observe(viewer, self._on_viewer_changed)
self._on_layers_changed()
def _get_viewer(self, viewer):
# newer will likely be the viewer name in most cases, but viewer id in the case
# of additional viewers in imviz.
try:
return self.app.get_viewer(viewer)
except TypeError:
return self.app.get_viewer_by_id(viewer)
def _layer_to_dict(self, layer, index=None):
d = {"label": layer.layer.label, "color": layer.state.color}
if index is not None:
d['icon'] = f"mdi-alpha-{chr(97 + index)}-box-outline"
return d
def _on_viewer_changed(self, msg=None):
# we don't want to update the layers if we're just toggling between single and multi-select
old, new = msg['old'], msg['new']
if not isinstance(old, list):
old = [old]
if not isinstance(new, list):
new = [new]
if new != old:
self._clear_cache()
self._on_layers_changed()
def _valid_layer(self, viewer, layer):
if isinstance(viewer, BqplotImageView) and self.plugin.config == 'cubeviz':
# exclude spectral subsets in image viewers (but not in 2d spectrum viewers)
if hasattr(layer.state.layer, 'subset_state') and not isinstance(layer.state.layer.subset_state, RoiSubsetState): # noqa
return False
return True
@observe('filters')
def _on_layers_changed(self, msg=None):
# NOTE: _on_layers_changed is passed without a msg object during init
viewer_names = self.viewer
if not isinstance(viewer_names, list):
viewer_names = [viewer_names]
viewers = [self._get_viewer(viewer) for viewer in viewer_names]
manual_items = [{'label': label} for label in self.manual_options]
layers = [layer for viewer in viewers for layer in viewer.layers if self._valid_layer(viewer, layer)] # noqa
# remove duplicates - NOTE: by doing this, any color-mismatch between layers with the
# same name in different viewers will be randomly assigned within plot_options
# based on which was found _first.
layer_labels = [layer.layer.label for layer in layers]
_, inds = np.unique(layer_labels, return_index=True)
layers = [layers[i] for i in inds]
self.items = manual_items + [self._layer_to_dict(layer, index) for index, layer in enumerate(layers)] # noqa
self._apply_default_selection()
@cached_property
def selected_obj(self):
viewer_names = self.viewer
if not isinstance(viewer_names, list):
# case for single-select on the viewer select
viewer_names = [viewer_names]
selected = self.selected
if not isinstance(selected, list):
selected = [selected]
viewers = [self._get_viewer(viewer_name) for viewer_name in viewer_names]
layers = [[layer for layer in viewer.layers
if layer.layer.label in selected and self._valid_layer(viewer, layer)]
for viewer in viewers]
if not self.multiselect and len(layers) == 1:
return layers[0]
else:
return layers
class LayerSelectMixin(VuetifyTemplate, HubListener):
"""
Applies the LayerSelect component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``LayerSelectMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.layer``.
Example template (label and hint are optional)::
<plugin-layer-select
:items="layer_items"
:selected.sync="layer_selected"
:show_if_single_entry="true"
label="Layer"
hint="Select layer."
/>
"""
layer_items = List().tag(sync=True)
layer_selected = Any().tag(sync=True)
layer_viewer = Unicode().tag(sync=True)
layer_multiselect = Bool(False).tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.layer = LayerSelect(self,
'layer_items',
'layer_selected',
'layer_viewer',
'layer_multiselect')
[docs]class SubsetSelect(BaseSelectPluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``items`` (list of dicts with keys: label, color, type)
* ``selected`` (string)
* ``selected_has_subregions`` (bool, OPTIONAL)
Properties (in the object only):
* ``labels`` (list of labels corresponding to items)
* ``selected_item`` (dictionary in ``items`` coresponding to ``selected``, cached)
* ``selected_obj`` (subset object corresponding to ``selected``, cached)
Methods (in the object only):
* ``selected_min_max(cube)`` (quantity, only applicable for spectral subsets)
To use in a plugin:
* create (empty) traitlets in the plugin
* register with all the automatic logic in the plugin's init by passing the string names
of the respective traitlets. Pass ``allowed_type='spectral'`` or ``allowed_type='spatial'``
to only support spectral or spatial subsets, respectively.
* use component in plugin template (see below)
* refer to properties above based on the interally stored reference to the
instantiated object of this component
* observe the traitlets created and defined in the plugin, as necessary
Example template (label and hint are optional)::
<plugin-subset-select
:items="spectral_subset_items"
:selected.sync="spectral_subset_selected"
:show_if_single_entry="true"
label="Subset"
hint="Select subset."
/>
"""
def __init__(self, plugin, items, selected, selected_has_subregions=None,
viewers=None, default_text=None, manual_options=[], allowed_type=None,
default_mode='default_text'):
"""
Parameters
----------
plugin
the parent plugin object
items : str
the name of the items traitlet defined in ``plugin``
selected : str
the name of the selected traitlet defined in ``plugin``
selected_has_subregions: str
the name of the selected_has_subregions traitlet defined in ``plugin``, optional
viewers : list
the reference names or ids of the viewer to extract the subregion. If not provided o
None, will loop through all references.
default_text : str or None
the text to show for no selection. If not provided or None, no entry will be provided
in the dropdown for no selection.
manual_options: list
list of options to provide that are not automatically populated by subsets. If
``default`` text is provided but not in ``manual_options`` it will still be included as
the first item in the list.
allowed_type : str or None
whether to filter to 'spatial' or 'spectral' types of subsets. If not provided or None,
will include both entries.
"""
super().__init__(plugin,
items=items,
selected=selected,
selected_has_subregions=selected_has_subregions,
viewers=viewers,
default_text=default_text,
manual_options=manual_options,
default_mode=default_mode)
if allowed_type not in [None, 'spatial', 'spectral']:
raise ValueError("allowed_type must be None, 'spatial', or 'spectral'")
self._allowed_type = allowed_type
if selected_has_subregions is not None:
self.selected_has_subregions = False
self.hub.subscribe(self, SubsetUpdateMessage,
handler=lambda msg: self._update_subset(msg.subset, msg.attribute))
self.hub.subscribe(self, SubsetDeleteMessage,
handler=lambda msg: self._delete_subset(msg.subset))
# intialize any subsets that have already been created
for lyr in self.app.data_collection.subset_groups:
self._update_subset(lyr)
@staticmethod
def _subset_type(subset):
if isinstance(subset.subset_state, RoiSubsetState):
return 'spatial'
else:
return 'spectral'
def _selected_changed(self, event):
super()._selected_changed(event)
self._update_has_subregions()
def _subset_to_dict(self, subset):
# find layer artist in default spectrum-viewer
for viewer in self.viewers:
for layer in viewer.layers:
if layer.layer.label == subset.label:
color = layer.state.color
subset_type = self._subset_type(subset)
return {"label": subset.label, "color": color, "type": subset_type}
return {"label": subset.label, "color": False, "type": False}
def _delete_subset(self, subset):
# NOTE: calling .remove will not trigger traitlet update
self.items = [s for s in self.items
if s['label'] != subset.label]
if self.selected not in self.labels:
self._apply_default_selection()
def _update_subset(self, subset, attribute=None):
if self._allowed_type is not None and self._subset_type(subset) != self._allowed_type:
return
if subset.label not in self.labels:
# NOTE: this logic will need to be revisited if generic renaming of subsets is added
# see https://github.com/spacetelescope/jdaviz/pull/1175#discussion_r829372470
if subset.label.startswith('Subset'):
# NOTE: += will not trigger traitlet update
self.items = self.items + [self._subset_to_dict(subset)] # noqa
else:
# 'type' can be passed manually rather than coming from SubsetUpdateMessage.attribute
if attribute in ('style', 'type'):
# TODO: may need to add label and then rebuild the entire list if/when
# we add support for renaming subsets
# NOTE: in-line replacement (self.spectral_subset_items[i] = ...)
# will not trigger traitlet update
self.items = [s if s['label'] != subset.label
else self._subset_to_dict(subset)
for s in self.items]
if attribute == 'subset_state' and subset.label == self.selected:
# updated the currently selected subset
self._clear_cache("selected_obj", "selected_item")
self._update_has_subregions()
def _update_has_subregions(self):
if "selected_has_subregions" in self._plugin_traitlets.keys():
if self.selected in self._manual_options:
self.selected_has_subregions = False
else:
self.selected_has_subregions = len(self.selected_obj.subregions) > 1
@cached_property
def selected_obj(self):
if self.selected in self.manual_options or self.selected not in self.labels:
return None
subset_type = self.selected_item['type']
# NOTE: we use reference names here instead of IDs since get_subsets_from_viewer requires
# that. For imviz, this will mean we won't be able to loop through each of the viewers,
# but the original viewer should have access to all the subsets.
for viewer_ref in self.viewer_refs:
match = self.app.get_subsets_from_viewer(viewer_ref,
subset_type=subset_type).get(self.selected)
if match is not None:
return match
[docs] def selected_min_max(self, spectrum1d):
if self.selected_obj is None:
return np.nanmin(spectrum1d.spectral_axis), np.nanmax(spectrum1d.spectral_axis)
if self.selected_item.get('type') != 'spectral':
raise TypeError("This action is only supported on spectral-type subsets")
else:
return self.selected_obj.lower, self.selected_obj.upper
[docs]class SpectralSubsetSelectMixin(VuetifyTemplate, HubListener):
"""
Applies the SubsetSelect component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``SpectralSubsetSelectMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.spectral_subset``.
Example template (label and hint are optional)::
<plugin-subset-select
:items="spectral_subset_items"
:selected.sync="spectral_subset_selected"
:show_if_single_entry="true"
label="Spectral region"
hint="Select spectral region."
/>
"""
spectral_subset_items = List().tag(sync=True)
spectral_subset_selected = Unicode().tag(sync=True)
spectral_subset_selected_has_subregions = Bool(False).tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.spectral_subset = SubsetSelect(self,
'spectral_subset_items',
'spectral_subset_selected',
'spectral_subset_selected_has_subregions',
viewers=['spectrum-viewer'],
default_text='Entire Spectrum',
allowed_type='spectral')
[docs]class SpatialSubsetSelectMixin(VuetifyTemplate, HubListener):
"""
Applies the SubsetSelect component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``SpatialSubsetSelectMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.spatial_subset``.
Example template (label and hint are optional)::
<plugin-subset-select
:items="spatial_subset_items"
:selected.sync="spatial_subset_selected"
label="Spatial region"
hint="Select spatial region."
/>
"""
spatial_subset_items = List().tag(sync=True)
spatial_subset_selected = Unicode().tag(sync=True)
spatial_subset_selected_has_subregions = Bool(False).tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.spatial_subset = SubsetSelect(self,
'spatial_subset_items',
'spatial_subset_selected',
'spatial_subset_selected_has_subregions',
default_text='No Subset',
allowed_type='spatial')
[docs]class ViewerSelect(BaseSelectPluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``items`` (list of dicts with keys: id, reference, label)
* ``selected`` (string)
Properties (in the object only):
* ``ids`` (list of ids corresponding to ``items``)
* ``references`` (list of references corresponding to ``items``)
* ``labels`` (list of references falling back on ids corresponding to ``items``. These
are the values seen in the dropdown, although setting either id or reference to the traitlet
will still process correctly)
* ``selected_item`` (dict of the currently selected entry in ``items``)
* ``selected_id`` (string corresponding to the id of ``selected_item``)
* ``selected_obj`` (viewer item corresponding to ``selected``)
To use in a plugin:
* create traitlets with default values
* register with all the automatic logic in the plugin's init by passing the string names
of the respective traitlets
* use component in plugin template (see below)
* refer to properties above based on the interally stored reference to the
instantiated object of this component
Example template (label and hint are optional)::
<plugin-viewer-select
:items="viewer_items"
:selected.sync="viewer_selected"
label="Viewer"
hint="Select viewer."
/>
"""
def __init__(self, plugin, items, selected,
multiselect=None,
default_text=None, manual_options=[], default_mode='first'):
super().__init__(plugin, items=items, selected=selected,
multiselect=multiselect,
default_text=default_text, manual_options=manual_options,
default_mode=default_mode)
self.hub.subscribe(self, ViewerAddedMessage, handler=self._on_viewers_changed)
self.hub.subscribe(self, ViewerRemovedMessage, handler=self._on_viewers_changed)
# initialize viewer_items from original viewers
self._on_viewers_changed()
@property
def ids(self):
return [item['id'] for item in self.items]
@property
def references(self):
return [item['reference'] for item in self.items]
def _get_selected_item(self, selected):
if selected in self.manual_options:
return {}
item = super()._get_selected_item(selected)
if item:
return item
# try again but this time allow match to id alone. Note that _selected_changed
# will handle resetting the trait to the reference since it exists, but this
# will allow access to the underlying item/object for any observes in the meantime.
for item in self.items:
if item['id'] == selected:
return item
@property
def selected_id(self):
return self.selected_item.get('id', None)
@property
def selected_reference(self):
return self.selected_item.get('reference', None)
def _get_selected_obj(self, selected, selected_id):
if selected in self.manual_options or selected_id is None:
return None
return self.app.get_viewer_by_id(selected_id)
@cached_property
def selected_obj(self):
if self.is_multiselect and len(self.selected):
return [self._get_selected_obj(selected, selected_id)
for selected, selected_id in zip(self.selected, self.selected_id)]
return self._get_selected_obj(self.selected, self.selected_id)
def _selected_changed(self, event):
self._clear_cache()
if self.is_multiselect and isinstance(event['new'], list):
new_selected = []
for entry in event['new']:
if entry in self.labels + self.manual_options:
new_selected.append(entry)
elif entry in self.ids:
new_selected.append(self.labels[self.ids.index(entry)])
else:
raise ValueError(f"could not map {entry} to valid choice")
self.selected = new_selected
return
else:
if event['new'] not in self.labels + self.manual_options:
if self.selected in self.ids:
# provided id in place of ref
self.selected = self.labels[self.ids.index(self.selected)]
return
return super()._selected_changed(event)
def _is_valid_item(self, viewer):
def is_spectrum_viewer(viewer):
return 'ProfileView' in viewer.__class__.__name__
def is_image_viewer(viewer):
return 'ImageView' in viewer.__class__.__name__
return super()._is_valid_item(viewer, locals())
@observe('filters')
def _on_viewers_changed(self, msg=None):
# NOTE: _on_viewers_changed is passed without a msg object during init
# list of dictionaries with id, ref, ref_or_id
manual_items = [{'label': label} for label in self.manual_options]
self.items = manual_items + [{k: v for k, v in vd.items() if k != 'viewer'}
for vd in self.viewer_dicts if self._is_valid_item(vd['viewer'])] # noqa
self._apply_default_selection()
[docs]class ViewerSelectMixin(VuetifyTemplate, HubListener):
"""
Applies the ViewerSelect component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``ViewerSelectMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.viewer``.
Example template (label and hint are optional)::
<plugin-viewer-select
:items="viewer_items"
:selected.sync="viewer_selected"
label="Viewer"
hint="Select viewer."
/>
"""
viewer_items = List().tag(sync=True)
viewer_selected = Any().tag(sync=True)
viewer_multiselect = Bool(False).tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.viewer = ViewerSelect(self, 'viewer_items', 'viewer_selected', 'viewer_multiselect')
[docs]class DatasetSelect(BaseSelectPluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``items`` (list of dicts with keys: label)
* ``selected`` (string)
Properties (in the object only):
* ``selected_obj``
* ``selected_dc_item``
Methods (in the object only):
* ``get_object``
* ``add_filter`` (more useful for the mixin, when creating a custom component, pass ``filters``)
To use in a plugin:
* create traitlets with default values
* register with all the automatic logic in the plugin's init by passing the string names
of the respective traitlets
* use component in plugin template (see below)
* refer to properties above based on the interally stored reference to the
instantiated object of this component
Example template (label and hint are optional)::
<plugin-dataset-select
:items="dataset_items"
:selected.sync="dataset_selected"
label="Data"
hint="Select data."
/>
"""
def __init__(self, plugin, items, selected,
filters=['not_from_plugin_model_fitting', 'layer_in_viewers'],
default_mode='first'):
super().__init__(plugin, items=items, selected=selected, filters=filters,
default_mode=default_mode)
self._cached_properties += ["selected_dc_item"]
# Add/Remove Data are triggered when checked/unchecked from viewers
self.hub.subscribe(self, AddDataMessage, handler=self._on_data_changed)
self.hub.subscribe(self, RemoveDataMessage, handler=self._on_data_changed)
self.hub.subscribe(self, DataCollectionDeleteMessage, handler=self._on_data_changed)
# initialize items from original viewers
self._on_data_changed()
@property
def default_data_cls(self):
if self.app.config == 'imviz':
return None
return Spectrum1D
@cached_property
def selected_dc_item(self):
if self.selected not in self.labels:
# _apply_default_selection will override shortly anyways
return None
return next((x for x in self.app.data_collection if x.label == self.selected))
[docs] def get_object(self, *args, **kwargs):
if self.selected not in self.labels:
# _apply_default_selection will override shortly anyways
return None
return self.selected_dc_item.get_object(*args, **kwargs)
@cached_property
def selected_obj(self):
if self.selected not in self.labels:
# _apply_default_selection will override shortly anyways
return None
for viewer_ref in self.viewer_refs:
if viewer_ref is None:
# image viewers might not have a reference, but get_data_from_viewer
# does not take id
continue
match = self.app.get_data_from_viewer(viewer_ref, data_label=self.selected)
if match is not None:
if hasattr(match, 'get_object'):
# cube viewers return the data collection instance from get_data_from_viewer
return match.get_object(cls=self.default_data_cls)
return match
# handle the case of empty Application with no viewer, we'll just pull directly
# from the data collection
return self.get_object(cls=self.default_data_cls)
def _is_valid_item(self, data):
def not_from_plugin(data):
return data.meta.get('Plugin', None) is None
def not_from_plugin_model_fitting(data):
return data.meta.get('Plugin', None) != 'ModelFitting'
def has_metadata(data):
return hasattr(data, 'meta') and isinstance(data.meta, dict) and len(data.meta)
def layer_in_viewers(data):
if not len(self.app.get_viewer_reference_names()):
# then this is a bar Application object, so ignore this filter
return True
for viewer in self.viewers:
if data.label in [l.layer.label for l in viewer.layers]: # noqa E741
return True
return False
def layer_in_spectrum_viewer(data):
if not len(self.app.get_viewer_reference_names()):
# then this is a bar Application object, so ignore this filter
return True
return data.label in [l.layer.label for l in self.spectrum_viewer.layers] # noqa E741
def is_image(data):
return len(data.shape) == 3
return super()._is_valid_item(data, locals())
@observe('filters')
def _on_data_changed(self, msg=None):
# NOTE: _on_data_changed is passed without a msg object during init
# future improvement: don't recreate the entire list when msg is passed
self.items = [{"label": data.label} for data in self.app.data_collection
if self._is_valid_item(data)]
self._apply_default_selection()
# future improvement: only clear cache if the selected data entry was changed?
self._clear_cache(*self._cached_properties)
[docs]class DatasetSelectMixin(VuetifyTemplate, HubListener):
"""
Applies the DatasetSelect component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``DatasetSelectMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.dataset``.
Example template (label and hint are optional)::
<plugin-dataset-select
:items="dataset_items"
:selected.sync="dataset_selected"
label="Data"
hint="Select data."
/>
"""
dataset_items = List().tag(sync=True)
dataset_selected = Unicode().tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# NOTE: cannot be named self.data or will conflict with existing self.data traitlet!
self.dataset = DatasetSelect(self, 'dataset_items', 'dataset_selected')
[docs]class AutoLabel(BasePluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``value`` (string: user-provided label for the results data-entry. If ``auto``, changes
to ``default`` will update ``value``. Otherwise, changes to ``value`` will set
``auto`` to False.)
* ``default`` (string: plugin-determined default label that will be synced to ``value``
if/when ``auto`` is set to True)
* ``auto`` (bool: whether to sync ``default`` to ``value``)
* ``invalid_msg`` (string: validation string for the current value of ``value``.)
Example template::
<plugin-auto-label
:value.sync="value"
:default="comp_label_default"
:auto.sync="comp_label_auto"
:invalid_msg="invalid_msg"
hint="Label hint."
></plugin-auto-label>
"""
def __init__(self, plugin, value, default, auto,
invalid_msg):
super().__init__(plugin, value=value,
default=default, auto=auto,
invalid_msg=invalid_msg)
self.add_observe(default, self._on_set_to_default)
self.add_observe(auto, self._on_set_to_default)
def _on_set_to_default(self, msg={}):
if self.auto:
self.value = self.default
[docs]class AutoLabelMixin(VuetifyTemplate, HubListener):
"""
Applies the AutoLabel component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``AutoLabelMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.auto_label``.
Example template::
<plugin-auto-label
:value.sync="label"
:default="label_default"
:auto.sync="label_auto"
:invalid_msg="invalid_msg"
hint="Label hint."
></plugin-auto-label>
"""
label = Unicode().tag(sync=True)
label_default = Unicode().tag(sync=True)
label_auto = Bool(True).tag(sync=True)
label_invalid_msg = Unicode('').tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.auto_label = AddResults(self, 'label',
'label_default', 'label_auto',
'label_invalid_msg')
[docs]class AddResults(BasePluginComponent):
"""
Traitlets (in the object, custom traitlets in the plugin):
* ``label`` (string: user-provided label for the results data-entry. If ``label_auto``, changes
to ``label_default`` will update ``label``. Otherwise, changes to ``label`` will set
``label_auto`` to False.)
* ``label_default`` (string: plugin-determined default label that will be synced to ``label``
if/when ``label_auto`` is set to True)
* ``label_auto`` (bool: whether to sync ``label_default`` to ``label``)
* ``label_invalid_msg`` (string: validation string for the current value of ``label``. If
not an empty string, calls to ``add_results_from_plugin`` will raise an error.)
* ``label_overwrite`` (bool: whether the value of ``label`` already exists for a data-entry
from the same plugin)
* ``add_to_viewer_items`` (list of dicts: see ``ViewerSelect``)
* ``add_to_viewer_selected`` (string: name of the viewer to add the results,
see ``ViewerSelect``)
Methods:
* ``add_results_from_plugin``
Example template::
<plugin-add-results
:label.sync="results_label"
:label_default="results_label_default"
:label_auto.sync="results_label_auto"
:label_invalid_msg="results_label_invalid_msg"
:label_overwrite="results_label_overwrite"
label_hint="Label for the smoothed data"
:add_to_viewer_items="add_to_viewer_items"
:add_to_viewer_selected.sync="add_to_viewer_selected"
action_label="Apply"
action_tooltip="Apply the action to the data"
@click:action="apply"
></plugin-add-results>
"""
def __init__(self, plugin, label, label_default, label_auto,
label_invalid_msg, label_overwrite,
add_to_viewer_items, add_to_viewer_selected):
super().__init__(plugin, label=label,
label_default=label_default, label_auto=label_auto,
label_invalid_msg=label_invalid_msg, label_overwrite=label_overwrite,
add_to_viewer_items=add_to_viewer_items,
add_to_viewer_selected=add_to_viewer_selected)
# DataCollectionAdd/Delete are fired even if remain unchecked in all viewers
self.hub.subscribe(self, DataCollectionAddMessage,
handler=lambda _: self._on_label_changed())
self.hub.subscribe(self, DataCollectionDeleteMessage,
handler=lambda _: self._on_label_changed())
self.viewer = ViewerSelect(plugin, add_to_viewer_items, add_to_viewer_selected,
manual_options=['None'],
default_mode=self._handle_default_viewer_selected)
self.auto_label = AutoLabel(plugin, label, label_default, label_auto, label_invalid_msg)
self.add_observe(label, self._on_label_changed)
def _handle_default_viewer_selected(self, viewer_comp, is_valid):
if len(viewer_comp.items) == 2:
# then we're a switch, so we want to default to ON
return viewer_comp.labels[1]
else:
# then we're a dropdown, so want to default to None and force the user to choose
return 'None'
def _on_label_changed(self, msg={}):
if not len(self.label.strip()):
# strip will raise the same error for a label of all spaces
self.label_invalid_msg = 'label must be provided'
return
for data in self.app.data_collection:
if self.label == data.label:
if data.meta.get('Plugin', None) == self._plugin.__class__.__name__:
self.label_invalid_msg = ''
self.label_overwrite = True
return
else:
self.label_invalid_msg = 'label already in use'
self.label_overwrite = False
return
self.label_invalid_msg = ''
self.label_overwrite = False
[docs] def add_results_from_plugin(self, data_item):
"""
Add ``data_item`` to the app's data_collection according to the default or user-provided
label and adds to any requested viewers.
"""
if self.label_invalid_msg:
raise ValueError(self.label_invalid_msg)
data_item.meta['Plugin'] = self._plugin.__class__.__name__
if self.app.config == 'mosviz':
data_item.meta['mosviz_row'] = self.app.state.settings['mosviz_row']
replace = self.viewer.selected_reference != 'spectrum-viewer'
if self.label in self.app.data_collection:
if not replace:
self.app.remove_data_from_viewer(self.viewer.selected_reference, self.label)
self.app.data_collection.remove(self.app.data_collection[self.label])
self.app.add_data(data_item, self.label)
if self.add_to_viewer_selected != 'None':
# replace the contents in the selected viewer with the results from this plugin
# TODO: switch to an instance/classname check?
self.app.add_data_to_viewer(self.viewer.selected_id,
self.label, clear_other_data=replace)
[docs]class AddResultsMixin(VuetifyTemplate, HubListener):
"""
Applies the AddResults component as a mixin in the base plugin. This
automatically adds traitlets as well as new properties to the plugin with minimal
extra code. For multiple instances or custom traitlet names/defaults, use the
component instead.
To use in a plugin:
* add ``AddResultsMixin`` as a mixin to the class
* use the traitlets available from the plugin or properties/methods available from
``plugin.add_results``.
Example template::
<plugin-add-results
:label.sync="results_label"
:label_default="results_label_default"
:label_auto.sync="results_label_auto"
:label_invalid_msg="results_label_invalid_msg"
:label_overwrite="results_label_overwrite"
label_hint="Label for the smoothed data"
:add_to_viewer_items="add_to_viewer_items"
:add_to_viewer_selected.sync="add_to_viewer_selected"
action_label="Apply"
action_tooltip="Apply the action to the data"
@click:action="apply"
></plugin-add-results>
"""
results_label = Unicode().tag(sync=True)
results_label_default = Unicode().tag(sync=True)
results_label_auto = Bool(True).tag(sync=True)
results_label_invalid_msg = Unicode('').tag(sync=True)
results_label_overwrite = Bool().tag(sync=True)
add_to_viewer_items = List().tag(sync=True)
add_to_viewer_selected = Unicode().tag(sync=True)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.add_results = AddResults(self, 'results_label',
'results_label_default', 'results_label_auto',
'results_label_invalid_msg', 'results_label_overwrite',
'add_to_viewer_items', 'add_to_viewer_selected')
class PlotOptionsSyncState(BasePluginComponent):
"""
"""
def __init__(self, plugin, viewer_select, layer_select, glue_name,
value, sync, state_filter=None):
super().__init__(plugin, value=value, sync=sync)
self._state_filter = state_filter
self._linked_states = []
self._processing_change_from_glue = False
self._processing_change_to_glue = False
self._cached_properties = ["subscribed_states", "subscribed_icons"]
self._viewer_select = viewer_select
self._layer_select = layer_select
self._glue_name = glue_name
self.add_observe(viewer_select._plugin_traitlets['selected'], self._on_viewer_layer_changed)
self.add_observe(layer_select._plugin_traitlets['selected'], self._on_viewer_layer_changed)
self.add_observe(value, self._on_value_changed)
self._on_viewer_layer_changed()
def state_filter(self, state):
if self._state_filter is None:
return True
return self._state_filter(state)
@cached_property
def subscribed_states(self):
# states object that according to the viewer selection, we *should*
# link if this entry is found there
viewers = self._viewer_select.selected_obj
if not isinstance(viewers, list):
# which is the case for single-select
viewers = [viewers]
def _state_item(item):
if isinstance(item, list):
return [_state_item(item_i) for item_i in item]
elif item is None:
return None
else:
return item.state
viewer_states = [_state_item(viewer) for viewer in viewers]
layer_labels = self._layer_select.selected
if not isinstance(layer_labels, list):
layer_labels = [layer_labels]
# NOTE: accessing from self._layer_select.selected_obj would give us a per-viewer
# list, but we need a per-selected-layer list.
layer_states = []
for selected_layer_label in layer_labels:
layer_states.append([])
for viewer in viewers:
for layer in viewer.layers:
if layer.layer.label == selected_layer_label:
layer_states[-1].append(layer.state)
# subscribed states can still be nested list
return viewer_states + layer_states
@cached_property
def subscribed_icons(self):
# dictionary items giving information about the entries in subscribed_states
viewer_icons = self._viewer_select.selected_item.get('icon', [])
if not isinstance(viewer_icons, list):
viewer_icons = [viewer_icons]
layer_icons = self._layer_select.selected_item.get('icon', [])
if not isinstance(layer_icons, list):
layer_icons = [layer_icons]
return viewer_icons + layer_icons
@property
def linked_states(self):
# access glue state objects for which the callbacks are currently connected
return self._linked_states
def _get_glue_value(self, state):
if self._glue_name == 'cmap':
return getattr(state, self._glue_name).name
return getattr(state, self._glue_name)
def _get_glue_choices(self, state):
if self._glue_name == 'cmap':
return [{'text': cmap[0], 'value': cmap[1].name} for cmap in colormaps.members]
else:
values, labels = _get_glue_choices(state, self._glue_name)
return [{'text': l, 'value': v} for v, l in zip(values, labels)]
def _on_viewer_layer_changed(self, msg=None):
self._clear_cache(*self._cached_properties)
# clear existing callbacks - we'll re-create those we need later
for state in self.linked_states:
state.remove_callback(self._glue_name, self._on_glue_value_changed)
in_subscribed_states = False
icons = []
current_glue_values = []
self._linked_states = []
for states, icon in zip(self.subscribed_states, self.subscribed_icons):
if not isinstance(states, list):
states = [states]
for state in states:
if state is None or not self.state_filter(state):
continue
if self._glue_name is None or not hasattr(state, self._glue_name):
continue
in_subscribed_states = True
if icon not in icons:
icons.append(icon)
current_glue_values.append(self._get_glue_value(state))
self._linked_states.append(state) # these will be iterated when value is set
state.add_callback(self._glue_name, self._on_glue_value_changed)
if self.sync.get('choices') is None and \
(hasattr(getattr(type(state), self._glue_name), 'get_display_func')
or self._glue_name == 'cmap'):
# then we can access and populate the choices. We are assuming here
# that each state-instance with this same name will have the same
# choices and that those will not change. If we ever hookup options
# with changing choices, we'll need additional logic to sync to those
# and handle mixed state in the choices...
self.sync = {**self.sync, 'choices': self._get_glue_choices(state)}
self.sync = {**self.sync,
'in_subscribed_states': in_subscribed_states,
'icons': icons,
'mixed': len(np.unique(current_glue_values, axis=0)) > 1}
if len(current_glue_values):
# sync the initial value of the widget, avoiding recursion
self._on_glue_value_changed(current_glue_values[0])
def _update_mixed_state(self):
if len(self.linked_states) <= 1:
mixed = False
else:
current_glue_values = []
for state in self.linked_states:
current_glue_values.append(self._get_glue_value(state))
mixed = len(np.unique(current_glue_values, axis=0)) > 1
self.sync = {**self.sync,
'mixed': mixed}
def _on_value_changed(self, msg):
if self._processing_change_from_glue:
return
self._processing_change_to_glue = True
for glue_state in self.linked_states:
if self._glue_name == 'cmap':
cmap = None
for member in colormaps.members:
if member[1].name == msg['new']:
cmap = member[1]
break
setattr(glue_state, self._glue_name, cmap)
else:
setattr(glue_state, self._glue_name, msg['new'])
# need to recompute mixed state
self._update_mixed_state()
self._processing_change_to_glue = False
def _on_glue_value_changed(self, value):
if self._processing_change_to_glue:
return
self._processing_change_from_glue = True
if "Colormap" in value.__class__.__name__: # TODO: better logic
value = str(value)
elif isinstance(self.value, (int, float)) and self._glue_name != 'percentile':
# glue might pass us ints for float or vice versa, but our traitlets care
# so let's cast to the type expected by the traitlet to avoid having to
# use Any traitlets for all of these. We skip percentile as that needs
# to be an Any traitlet in order to handle "Custom"
value = type(self.value)(value)
self.value = value
# need to recompute mixed state
self._update_mixed_state()
self._processing_change_from_glue = False
def unmix_state(self):
self._on_value_changed({'new': self.value})
self.sync = {**self.sync,
'mixed': False}