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app.py
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app.py
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import operator
import os
import pathlib
import re
import uuid
import warnings
import ipyvue
from astropy import units as u
from astropy.nddata import NDData
from astropy.io import fits
from astropy.time import Time
from echo import CallbackProperty, DictCallbackProperty, ListCallbackProperty
from ipygoldenlayout import GoldenLayout
from ipysplitpanes import SplitPanes
import matplotlib.cm as cm
import numpy as np
from glue.config import colormaps, settings as glue_settings
from glue.core import HubListener
from glue.core.link_helpers import LinkSame, LinkSameWithUnits
from glue.core.message import (DataCollectionAddMessage,
DataCollectionDeleteMessage,
SubsetCreateMessage,
SubsetUpdateMessage,
SubsetDeleteMessage)
from glue.core.roi import CircularROI, CircularAnnulusROI, EllipticalROI, RectangularROI
from glue.core.state_objects import State
from glue.core.subset import (RangeSubsetState, RoiSubsetState,
CompositeSubsetState, InvertState)
from glue.core.units import unit_converter
from glue_astronomy.spectral_coordinates import SpectralCoordinates
from glue_astronomy.translators.regions import roi_subset_state_to_region
from glue_jupyter.app import JupyterApplication
from glue_jupyter.common.toolbar_vuetify import read_icon
from glue_jupyter.state_traitlets_helpers import GlueState
from ipypopout import PopoutButton
from ipyvuetify import VuetifyTemplate
from ipywidgets import widget_serialization
from traitlets import Dict, Bool, Unicode, Any
from specutils import Spectrum1D, SpectralRegion
from jdaviz import __version__
from jdaviz import style_registry
from jdaviz.core.config import read_configuration, get_configuration
from jdaviz.core.events import (LoadDataMessage, NewViewerMessage, AddDataMessage,
SnackbarMessage, RemoveDataMessage,
AddDataToViewerMessage, RemoveDataFromViewerMessage,
ViewerAddedMessage, ViewerRemovedMessage,
ViewerRenamedMessage, ChangeRefDataMessage)
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, data_has_valid_wcs, layer_is_table_data,
MultiMaskSubsetState, _wcs_only_label)
__all__ = ['Application', 'ALL_JDAVIZ_CONFIGS']
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'])
ALL_JDAVIZ_CONFIGS = ['cubeviz', 'specviz', 'specviz2d', 'mosviz', 'imviz']
@unit_converter('custom-jdaviz')
class UnitConverterWithSpectral:
def equivalent_units(self, data, cid, units):
if cid.label == "flux":
eqv = u.spectral_density(1 * u.m) # Value does not matter here.
list_of_units = set(list(map(str, u.Unit(units).find_equivalent_units(
include_prefix_units=True, equivalencies=eqv))) + [
'Jy', 'mJy', 'uJy',
'W / (m2 Hz)', 'W / (Hz m2)', # Order is different in astropy v5.3
'eV / (s m2 Hz)', 'eV / (Hz s m2)',
'erg / (s cm2)',
'erg / (s cm2 Angstrom)', 'erg / (Angstrom s cm2)',
'erg / (s cm2 Hz)', 'erg / (Hz s cm2)',
'ph / (s cm2 Angstrom)', 'ph / (Angstrom s cm2)',
'ph / (s cm2 Hz)', 'ph / (Hz s cm2)'
])
else: # spectral axis
# prefer Hz over Bq and um over micron
exclude = {'Bq', 'micron'}
list_of_units = set(list(map(str, u.Unit(units).find_equivalent_units(
include_prefix_units=True, equivalencies=u.spectral())))) - exclude
return list_of_units
def to_unit(self, data, cid, values, original_units, target_units):
# Given a glue data object (data), a component ID (cid), the values
# to convert, and the original and target units of the values, this method
# should return the converted values. Note that original_units
# gives the units of the values array, which might not be the same
# as the original native units of the component in the data.
if cid.label == "flux":
spec = data.get_object(cls=Spectrum1D)
if len(values) == 2:
# Need this for setting the y-limits
spec_limits = [spec.spectral_axis[0].value, spec.spectral_axis[-1].value]
eqv = u.spectral_density(spec_limits*spec.spectral_axis.unit)
else:
eqv = u.spectral_density(spec.spectral_axis)
else: # spectral axis
eqv = u.spectral()
return (values * u.Unit(original_units)).to_value(u.Unit(target_units), equivalencies=eqv)
# Set default opacity for data layers to 1 instead of 0.8 in
# some glue-core versions
glue_settings.DATA_ALPHA = 1
# Enable spectrum unit conversion.
glue_settings.UNIT_CONVERTER = 'custom-jdaviz'
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-previews-temp-disabled': 'components/plugin_previews_temp_disabled.vue', # noqa
'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-layer-select-tabs': 'components/plugin_layer_select_tabs.vue',
'plugin-editable-select': 'components/plugin_editable_select.vue',
'plugin-action-button': 'components/plugin_action_button.vue',
'plugin-add-results': 'components/plugin_add_results.vue',
'plugin-auto-label': 'components/plugin_auto_label.vue',
'plugin-file-import-select': 'components/plugin_file_import_select.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__)
style_registry.add((__file__, 'main_styles.vue'))
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,
'server_is_remote': False, # sets some defaults, should be set before loading the config
'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'),
'nuer': read_icon(os.path.join(ICON_DIR, 'right-east.svg'), 'svg+xml'),
'nuel': read_icon(os.path.join(ICON_DIR, 'left-east.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.")
style_widget = CallbackProperty(
'', docstring="Jupyter widget that won't be displayed but can apply css to the app"
)
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)
docs_link = Unicode("").tag(sync=True)
popout_button = Any().tag(sync=True, **widget_serialization)
style_registry_instance = 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)
self.style_registry_instance = style_registry.get_style_registry()
# 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 = {}
# 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)
# 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)
# Imviz linking
self._link_type = 'pixels'
if self.config == "imviz":
self._wcs_use_affine = None
# 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))
# 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 _add_style(self, path):
"""
Appends an addition vue file containing a <style> tag that will be applied on top of the
style defined in ``main_styles.vue``. This is useful for config-specific or downstream
styling at the app-level.
Parameters
----------
path : str or tuple
Path to a ``.vue`` file containing style rules to inject into the app.
"""
style_registry.add(path)
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
is_wcs_only = msg.data.meta.get(_wcs_only_label, False)
elif hasattr(msg, 'subset'):
layer_name = msg.subset.label
is_wcs_only = False
else:
raise NotImplementedError(f"cannot recognize new layer from {msg}")
wcs_only_refdata_icon = '' # blank - might be replaced with custom icon in the future
# any changes here should also be manually reflected in orientation.vue
orientation_icons = {'Default orientation': 'mdi-image-outline',
'North-up, East-left': 'nuel',
'North-up, East-right': 'nuer'}
if layer_name not in self.state.layer_icons:
if is_wcs_only:
self.state.layer_icons = {**self.state.layer_icons,
layer_name: orientation_icons.get(layer_name,
wcs_only_refdata_icon)}
else:
self.state.layer_icons = {
**self.state.layer_icons,
layer_name: alpha_index(len([ln for ln, ic in self.state.layer_icons.items()
if not ic.startswith('mdi-')]))
}
def _change_reference_data(self, new_refdata_label, viewer_id=None):
"""
Change reference data to Data with ``data_label``.
This does not work on data without WCS.
"""
if self.config != 'imviz':
# this method is only meant for Imviz for now
return
if viewer_id is None:
viewer = self._jdaviz_helper.default_viewer._obj
else:
viewer = self.get_viewer(viewer_id)
old_refdata = viewer.state.reference_data
if old_refdata is not None and ((new_refdata_label == old_refdata.label)
or (old_refdata.coords is None)):
# if there's no refdata change nor WCS, don't do anything:
return
if old_refdata is None:
return
# locate the central coordinate of old refdata in this viewer:
sky_cen = viewer._get_center_skycoord()
# estimate FOV in the viewer with old reference data:
fov_sky_init = viewer._get_fov()
new_refdata = self.data_collection[new_refdata_label]
# make sure new refdata can be selected:
refdata_choices = [choice.label for choice in viewer.state.ref_data_helper.choices]
if new_refdata_label not in refdata_choices:
viewer.state.ref_data_helper.append_data(new_refdata)
viewer.state.ref_data_helper.refresh()
# set the new reference data in the viewer:
viewer.state.reference_data = new_refdata
# also update the viewer item's reference data label:
viewer_ref = viewer.reference
viewer_item = self._get_viewer_item(viewer_ref)
viewer_item['reference_data_label'] = new_refdata.label
self.hub.broadcast(ChangeRefDataMessage(
new_refdata,
viewer,
viewer_id=viewer.reference,
old=old_refdata,
sender=self))
if (
all('_WCS_ONLY' in refdata.meta for refdata in [old_refdata, new_refdata]) and
viewer.shape is not None
):
# adjust zoom to account for new refdata if both the
# old and new refdata are WCS-only layers
# (which also ensures zoom_level is already determined):
fov_sky_final = viewer._get_fov()
viewer.zoom(
float(fov_sky_final / fov_sky_init)
)
# only re-center the viewer if all data layers have WCS:
has_wcs_per_data = [data_has_valid_wcs(d) for d in viewer.data()]
if all(has_wcs_per_data):
# re-center the viewer on previous location.
viewer.center_on(sky_cen)
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 self.config == 'cubeviz' and linked_data.ndim == 1:
ref_wavelength_component = dc[0].components[-2]
ref_flux_component = dc[0].components[-1]
linked_wavelength_component = dc[-1].components[1]
linked_flux_component = dc[-1].components[-1]
links = [
LinkSame(ref_wavelength_component, linked_wavelength_component),
LinkSame(ref_flux_component, linked_flux_component)
]
dc.add_link(links)
return
elif (linked_data.meta.get('Plugin', None) == 'SpectralExtraction' or
(linked_data.meta.get('Plugin', None) == ('GaussianSmooth') and
linked_data.ndim < 3 and # Cube linking requires special logic. See below
ref_data.ndim < 3)
):
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(LinkSameWithUnits(wc_old, wc_new))
return
# NOTE: if Cubeviz ever supports multiple cubes, we might want to reintroduce WCS-linking
# but will likely need affine approximation for performance
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(LinkSameWithUnits(ref_data.pixel_component_ids[ref_index],
linked_data.pixel_component_ids[linked_index]))
dc.add_link(links)
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
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
-----
If viewer does not have a reference, it is going to try to look
up the viewer using the given reference as ID.
Parameters
----------
viewer_reference : str
The reference to the viewer defined with the ``reference`` key
in the YAML configuration file.
Returns
-------
viewer : `~glue_jupyter.bqplot.common.BqplotBaseView`
The viewer class instance.
"""
return self._viewer_by_reference(viewer_reference, fallback_to_id=True)
def get_viewer_by_id(self, vid):
"""Like :meth:`get_viewer` but use ID directly instead of reference name.
This is useful when reference name is `None`.
"""
return self._viewer_store.get(vid)
def _get_wcs_from_subset(self, subset_state):
""" Usually WCS is subset.parent.coords, except special cubeviz case."""
if self.config == 'cubeviz':
parent_data = subset_state.attributes[0].parent
wcs = parent_data.meta.get("_orig_spatial_wcs", None)
else:
wcs = subset_state.xatt.parent.coords
return wcs
def get_subsets(self, subset_name=None, spectral_only=False,
spatial_only=False, object_only=False,
simplify_spectral=True, use_display_units=False,
include_sky_region=False):
"""
Returns all branches of glue subset tree in the form that subset plugin
can recognize.
Parameters
----------
subset_name : str
The subset name.
spectral_only : bool
Return only spectral subsets.
spatial_only : bool
Return only spatial subsets, except masked subsets (uncommon).
object_only : bool
Return only object relevant information and
leave out the region class name and glue_state.
simplify_spectral : bool
Return a composite spectral subset collapsed to a simplified
SpectralRegion.
use_display_units : bool, optional
Whether to convert to the display units defined in the
:ref:`Unit Conversion <unit-conversion>` plugin.
include_sky_region : bool
If True, for spatial subsets that have a WCS associated with their
parent data, return a sky region in addition to pixel region. If
subset is composite, a sky region for each constituent subset will
be returned.
Returns
-------
data : dict
Returns a nested dictionary with, for each subset, 'name', 'glue_state',
'region', 'sky_region' (set to None if not applicable), and 'subset_state'.
If subset is composite, each constituant subset will be included individually.
"""
dc = self.data_collection
subsets = dc.subset_groups
all_subsets = {}
for subset in subsets:
label = subset.label
if isinstance(subset.subset_state, CompositeSubsetState):
# Region composed of multiple ROI or Range subset
# objects that must be traversed
subset_region = self.get_sub_regions(subset.subset_state,
simplify_spectral, use_display_units,
get_sky_regions=include_sky_region)
elif isinstance(subset.subset_state, RoiSubsetState):
subset_region = self._get_roi_subset_definition(subset.subset_state,
to_sky=include_sky_region)
elif isinstance(subset.subset_state, RangeSubsetState):
# 2D regions represented as SpectralRegion objects
subset_region = self._get_range_subset_bounds(subset.subset_state,
simplify_spectral,
use_display_units)
elif isinstance(subset.subset_state, MultiMaskSubsetState):
subset_region = self._get_multi_mask_subset_definition(subset.subset_state)
else:
# subset.subset_state can be an instance of something else
# we do not know how to handle yet
all_subsets[label] = [{"name": subset.subset_state.__class__.__name__,
"glue_state": subset.subset_state.__class__.__name__,
"region": None,
"sky_region": None,
"subset_state": subset.subset_state}]
continue
# Is the subset spectral, spatial, temporal?
is_spectral = self._is_subset_spectral(subset_region)
is_temporal = self._is_subset_temporal(subset_region)
# Remove duplicate spectral regions
if is_spectral and isinstance(subset_region, SpectralRegion):
subset_region = self._remove_duplicate_bounds(subset_region)
if spectral_only and is_spectral:
if object_only and not simplify_spectral:
all_subsets[label] = [reg['region'] for reg in subset_region]
else:
all_subsets[label] = subset_region
elif spatial_only and not is_spectral:
if object_only:
all_subsets[label] = [reg['region'] for reg in subset_region]
else:
all_subsets[label] = subset_region
elif not spectral_only and not spatial_only:
# General else statement if no type was specified
if object_only and not isinstance(subset_region, SpectralRegion):
all_subsets[label] = [reg['region'] for reg in subset_region]
else:
all_subsets[label] = subset_region
if not (spectral_only or spatial_only) and is_temporal:
if object_only:
all_subsets[label] = [reg['region'] for reg in subset_region]
else:
all_subsets[label] = subset_region
# can this be done at the top to avoid traversing all subsets if only
# one is requested?
all_subset_names = [subset.label for subset in dc.subset_groups]
if subset_name and subset_name in all_subset_names:
return all_subsets[subset_name]
elif subset_name:
raise ValueError(f"{subset_name} not in {all_subset_names}")
else:
return all_subsets
def _is_subset_spectral(self, subset_region):
if isinstance(subset_region, SpectralRegion):
return True
elif isinstance(subset_region, list) and len(subset_region) > 0:
if isinstance(subset_region[0]['region'], SpectralRegion):
return True
return False
def _is_subset_temporal(self, subset_region):
if isinstance(subset_region, Time):
return True
elif isinstance(subset_region, list) and len(subset_region) > 0:
if isinstance(subset_region[0]['region'], Time):
return True
return False
def _remove_duplicate_bounds(self, spec_regions):
regions_no_dups = None
for region in spec_regions:
if not regions_no_dups:
regions_no_dups = region
elif region.bounds not in regions_no_dups.subregions:
regions_no_dups += region
return regions_no_dups
def _get_range_subset_bounds(self, subset_state,
simplify_spectral=True, use_display_units=False):
# TODO: Use global display units
# units = dc[0].data.coords.spectral_axis.unit
viewer = self.get_viewer(self._jdaviz_helper. _default_spectrum_viewer_reference_name)
data = viewer.data()
if data and len(data) > 0 and isinstance(data[0], Spectrum1D):
units = data[0].spectral_axis.unit
else:
raise ValueError("Unable to find spectral axis units")
if use_display_units:
# converting may result in flipping order (wavelength <-> frequency)
ret_units = self._get_display_unit('spectral')
subset_bounds = [(subset_state.lo * units).to(ret_units, u.spectral()),
(subset_state.hi * units).to(ret_units, u.spectral())]
spec_region = SpectralRegion(min(subset_bounds), max(subset_bounds))
else:
spec_region = SpectralRegion(subset_state.lo * units, subset_state.hi * units)
if not simplify_spectral:
return [{"name": subset_state.__class__.__name__,
"glue_state": subset_state.__class__.__name__,
"region": spec_region,
"sky_region": None, # not implemented for spectral, include for consistancy
"subset_state": subset_state}]
return spec_region
def _get_multi_mask_subset_definition(self, subset_state):
return [{"name": subset_state.__class__.__name__,
"glue_state": subset_state.__class__.__name__,
"region": subset_state.total_masked_first_data(),
"sky_region": None,
"subset_state": subset_state}]
def _get_roi_subset_definition(self, subset_state, to_sky=False):
# pixel region
roi_as_region = roi_subset_state_to_region(subset_state)
wcs = None
if to_sky:
wcs = self._get_wcs_from_subset(subset_state)
# if no spatial wcs on subset, we have to skip computing sky region for this subset
# but want to do so without raising an error (since many subsets could be requested)
roi_as_sky_region = None
if wcs is not None:
roi_as_sky_region = roi_as_region.to_sky(wcs)
return [{"name": subset_state.roi.__class__.__name__,
"glue_state": subset_state.__class__.__name__,
"region": roi_as_region,
"sky_region": roi_as_sky_region,
"subset_state": subset_state}]
def get_sub_regions(self, subset_state, simplify_spectral=True,
use_display_units=False, get_sky_regions=False):
if isinstance(subset_state, CompositeSubsetState):
if subset_state and hasattr(subset_state, "state2") and subset_state.state2:
one = self.get_sub_regions(subset_state.state1,
simplify_spectral, use_display_units,
get_sky_regions=get_sky_regions)
two = self.get_sub_regions(subset_state.state2,
simplify_spectral, use_display_units,
get_sky_regions=get_sky_regions)
if isinstance(one, list) and "glue_state" in one[0]:
one[0]["glue_state"] = subset_state.__class__.__name__