from glue.core import BaseData
from glue_jupyter.bqplot.image import BqplotImageView
from glue_jupyter.bqplot.profile import BqplotProfileView
from glue_jupyter.table import TableViewer
from specutils import Spectrum1D
from astropy import units as u
from jdaviz.core.events import (AddDataToViewerMessage,
RemoveDataFromViewerMessage,
TableClickMessage)
from jdaviz.core.registries import viewer_registry
from jdaviz.core.freezable_state import FreezableBqplotImageViewerState
from jdaviz.configs.default.plugins.viewers import JdavizViewerMixin
__all__ = ['MosvizProfileView', 'MosvizImageView', 'MosvizProfile2DView',
'MosvizTableViewer']
[docs]@viewer_registry("mosviz-profile-viewer", label="Profile 1D (Mosviz)")
class MosvizProfileView(BqplotProfileView, JdavizViewerMixin):
default_class = Spectrum1D
# categories: zoom resets, zoom, pan, subset, select tools, shortcuts
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoom', 'jdaviz:xrangezoom'],
['jdaviz:panzoom', 'jdaviz:panzoom_x', 'jdaviz:panzoom_y'],
['bqplot:xrange'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._subscribe_to_layers_update()
self._initialize_toolbar_nested()
[docs] def data(self, cls=None):
return [layer_state.layer.get_object(cls=cls or self.default_class)
for layer_state in self.state.layers
if hasattr(layer_state, 'layer') and
isinstance(layer_state.layer, BaseData)]
[docs] def set_plot_axes(self):
data = self.data()[0]
# Set axes labels for the spectrum viewer
spectral_axis_unit_type = str(data.spectral_axis.unit.physical_type).title()
# flux_unit_type = data.flux.unit.physical_type.title()
flux_unit_type = "Flux density"
if data.spectral_axis.unit.is_equivalent(u.m):
spectral_axis_unit_type = "Wavelength"
elif data.spectral_axis.unit.is_equivalent(u.pixel):
spectral_axis_unit_type = "pixel"
label_0 = f"{spectral_axis_unit_type} [{data.spectral_axis.unit.to_string()}]"
self.figure.axes[0].label = label_0
self.figure.axes[1].label = f"{flux_unit_type} [{data.flux.unit.to_string()}]"
# Make it so y axis label is not covering tick numbers.
self.figure.axes[1].label_offset = "-50"
# Set Y-axis to scientific notation
self.figure.axes[1].tick_format = '0.1e'
[docs]@viewer_registry("mosviz-image-viewer", label="Image 2D (Mosviz)")
class MosvizImageView(BqplotImageView, JdavizViewerMixin):
# Whether to inherit tools from glue-jupyter automatically. Set this to
# False to have full control here over which tools are shown in case new
# ones are added in glue-jupyter in future that we don't want here.
inherit_tools = False
tools = ['jdaviz:homezoom', 'jdaviz:boxzoom',
'jdaviz:panzoom', 'bqplot:rectangle',
'bqplot:circle']
# categories: zoom resets, zoom, pan, subset, select tools, shortcuts
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoom'],
['jdaviz:panzoom'],
['bqplot:circle', 'bqplot:rectangle'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
default_class = None
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._subscribe_to_layers_update()
self._initialize_toolbar_nested()
[docs] def data(self, cls=None):
return [layer_state.layer # .get_object(cls=cls or self.default_class)
for layer_state in self.state.layers
if hasattr(layer_state, 'layer') and
isinstance(layer_state.layer, BaseData)]
[docs] def set_plot_axes(self):
self.figure.axes[1].tick_format = None
self.figure.axes[0].tick_format = None
self.figure.axes[1].label = "y: pixels"
self.figure.axes[0].label = "x: pixels"
# Make it so y axis label is not covering tick numbers.
self.figure.axes[1].label_offset = "-50"
[docs]@viewer_registry("mosviz-profile-2d-viewer", label="Spectrum 2D (Mosviz)")
class MosvizProfile2DView(BqplotImageView, JdavizViewerMixin):
# Due to limitations in CCDData and 2D data that has spectral and spatial
# axes, the default conversion class must handle cubes
default_class = Spectrum1D
# replace the default tools (which include rect and circle region)
# with only the tools we want (likely the same as in SpecvizProfileView)
inherit_tools = False
tools = ['jdaviz:homezoom',
'jdaviz:boxzoom',
'jdaviz:xrangezoom',
'jdaviz:panzoom',
'jdaviz:panzoom_x',
'bqplot:xrange']
# categories: zoom resets, zoom, pan, subset, select tools, shortcuts
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoom', 'jdaviz:xrangezoom'],
['jdaviz:panzoom', 'jdaviz:panzoom_x'],
['bqplot:xrange'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
_state_cls = FreezableBqplotImageViewerState
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._subscribe_to_layers_update()
self._initialize_toolbar_nested()
# Setup viewer option defaults
self.state.aspect = 'auto'
[docs] def data(self, cls=None):
return [layer_state.layer.get_object(cls=cls or self.default_class)
for layer_state in self.state.layers
if hasattr(layer_state, 'layer') and
isinstance(layer_state.layer, BaseData)]
[docs] def set_plot_axes(self):
self.figure.axes[0].visible = False
self.figure.axes[1].label = "y: pixels"
self.figure.axes[1].tick_format = None
self.figure.axes[1].label_location = "start"
# Make it so y axis label is not covering tick numbers.
self.figure.axes[1].label_offset = "-50"
[docs]@viewer_registry("mosviz-table-viewer", label="Table (Mosviz)")
class MosvizTableViewer(TableViewer, JdavizViewerMixin):
def __init__(self, session, *args, **kwargs):
super().__init__(session, *args, **kwargs)
self.figure_widget.observe(self._on_row_selected, names=['highlighted'])
# enable scrolling: # https://github.com/glue-viz/glue-jupyter/pull/287
self.widget_table.scrollable = True
self._selected_data = {}
self._shared_image = False
self.row_selection_in_progress = False
self._on_row_selected_begin = None
self._on_row_selected_end = None
[docs] def redraw(self):
# Overload to hide components - we do this via overloading instead of
# checking for changes in self.figure_widget.data because some components
# might be added inplace to the dataset.
if self.figure_widget.data is None:
self.figure_widget.hidden_components = []
else:
components_str = [cid.label for cid in self.figure_widget.data.main_components]
hidden = []
for colname in ['Images', '1D Spectra', '2D Spectra']:
if colname in components_str:
hidden.append(self.figure_widget.data.id[colname])
self.figure_widget.hidden_components = hidden
super().redraw()
@property
def nrows(self):
return self.widget_table.get_state()['total_length']
@property
def current_row(self):
return self.widget_table.highlighted
[docs] def select_row(self, n):
if n < 0 or n >= self.nrows:
raise ValueError("n must be between 0 and {}".format(self.nrows-1))
# compute and set the appropriate page
# NOTE: traitlets won't detect internal changes to a dict
options = self.widget_table.get_state()['options']
page = int(n / options['itemsPerPage']) + 1
if options['page'] != page:
self.widget_table.set_state({'options': {**options, 'page': page}})
self.widget_table.send_state()
# select and highlight the row
self.widget_table.highlighted = n
[docs] def next_row(self):
current_row = self.current_row
new_row = 0 if current_row == self.nrows - 1 else current_row + 1
self.select_row(new_row)
[docs] def prev_row(self):
current_row = self.current_row
new_row = self.nrows - 1 if current_row == 0 else current_row - 1
self.select_row(new_row)
def _on_row_selected(self, event):
if self._on_row_selected_begin:
self._on_row_selected_begin(event)
self.row_selection_in_progress = True
# Grab the index of the latest selected row
selected_index = event['new']
mos_data = self.session.data_collection['MOS Table']
# plugin data entries: select all in new row, deselect all others
for data_item in self.jdaviz_app.data_collection:
if data_item.meta.get('Plugin') is not None:
if data_item.meta.get('mosviz_row') == selected_index:
self.session.hub.broadcast(AddDataToViewerMessage(
'spectrum-viewer', data_item.label, sender=self))
else:
self.session.hub.broadcast(RemoveDataFromViewerMessage(
'spectrum-viewer', data_item.label, sender=self))
for component in mos_data.components:
comp_data = mos_data.get_component(component).data
selected_data = comp_data[selected_index]
if component.label == '1D Spectra':
prev_data = self._selected_data.get('spectrum-viewer')
if prev_data != selected_data:
if prev_data:
# This covers the cases where data is unit converted
# and the name is modified
all_prev_data = [x
for x in self.session.data_collection.labels
if prev_data in x]
for modified_prev_data in all_prev_data:
if modified_prev_data:
remove_data_from_viewer_message = RemoveDataFromViewerMessage(
'spectrum-viewer', modified_prev_data, sender=self)
self.session.hub.broadcast(remove_data_from_viewer_message)
add_data_to_viewer_message = AddDataToViewerMessage(
'spectrum-viewer', selected_data, sender=self)
self.session.hub.broadcast(add_data_to_viewer_message)
self._selected_data['spectrum-viewer'] = selected_data
if component.label == '2D Spectra':
prev_data = self._selected_data.get('spectrum-2d-viewer')
if prev_data != selected_data:
if prev_data:
remove_data_from_viewer_message = RemoveDataFromViewerMessage(
'spectrum-2d-viewer', prev_data, sender=self)
self.session.hub.broadcast(remove_data_from_viewer_message)
add_data_to_viewer_message = AddDataToViewerMessage(
'spectrum-2d-viewer', selected_data, sender=self)
self.session.hub.broadcast(add_data_to_viewer_message)
self._selected_data['spectrum-2d-viewer'] = selected_data
if component.label == 'Images':
prev_data = self._selected_data.get('image-viewer')
if prev_data != selected_data:
if prev_data:
remove_data_from_viewer_message = RemoveDataFromViewerMessage(
'image-viewer', prev_data, sender=self)
self.session.hub.broadcast(remove_data_from_viewer_message)
add_data_to_viewer_message = AddDataToViewerMessage(
'image-viewer', selected_data, sender=self)
self.session.hub.broadcast(add_data_to_viewer_message)
self._selected_data['image-viewer'] = selected_data
message = TableClickMessage(selected_index=selected_index,
shared_image=self._shared_image,
sender=self)
self.session.hub.broadcast(message)
self.row_selection_in_progress = False
if self._on_row_selected_end:
self._on_row_selected_end(event)
[docs] def set_plot_axes(self, *args, **kwargs):
return