import numpy as np
from glue.core import BaseData
from glue.core.subset import RoiSubsetState, RangeSubsetState
from glue_jupyter.bqplot.image import BqplotImageView
from jdaviz.core.registries import viewer_registry
from jdaviz.core.marks import SliceIndicatorMarks, ShadowSpatialSpectral
from jdaviz.configs.default.plugins.viewers import JdavizViewerMixin
from jdaviz.configs.cubeviz.helper import layer_is_cube_image_data
from jdaviz.configs.imviz.helper import data_has_valid_wcs
from jdaviz.configs.specviz.plugins.viewers import SpecvizProfileView
__all__ = ['CubevizImageView', 'CubevizProfileView']
[docs]@viewer_registry("cubeviz-image-viewer", label="Image 2D (Cubeviz)")
class CubevizImageView(JdavizViewerMixin, BqplotImageView):
# categories: zoom resets, (zoom, pan), subset, select tools, shortcuts
# NOTE: zoom and pan are merged here for space consideration and to avoid
# overflow to second row when opening the tray
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoommatch', 'jdaviz:boxzoom',
'jdaviz:simplepanzoommatch', 'jdaviz:panzoom'],
['bqplot:circle', 'bqplot:rectangle', 'bqplot:ellipse'],
['jdaviz:spectrumperspaxel'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
default_class = None
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self._default_flux_viewer_reference_name = kwargs.get(
"flux_viewer_reference_name", "flux-viewer"
)
self._default_uncert_viewer_reference_name = kwargs.get(
"uncert_viewer_reference_name", "uncert-viewer"
)
self._default_spectrum_viewer_reference_name = kwargs.get(
"spectrum_viewer_reference_name", "spectrum-viewer"
)
self._subscribe_to_layers_update()
self.state.add_callback('reference_data', self._initial_x_axis)
self.label_mouseover = None
self.add_event_callback(self.on_mouse_or_key_event, events=['mousemove', 'mouseenter',
'mouseleave'])
[docs] def on_mouse_or_key_event(self, data):
# Find visible layers
visible_layers = [layer for layer in self.state.layers
if (layer.visible and layer_is_cube_image_data(layer.layer))]
if len(visible_layers) == 0:
return
if self.label_mouseover is None:
if 'g-coords-info' in self.session.application._tools:
self.label_mouseover = self.session.application._tools['g-coords-info']
else:
return
if data['event'] == 'mousemove':
# Display the current cursor coordinates (both pixel and world) as
# well as data values. For now we use the first dataset in the
# viewer for the data values.
# Extract first dataset from visible layers and use this for coordinates - the choice
# of dataset shouldn't matter if the datasets are linked correctly
active_layer = visible_layers[-1]
image = active_layer.layer
self.label_mouseover.icon = self.jdaviz_app.state.layer_icons.get(active_layer.layer.label) # noqa
# Extract data coordinates - these are pixels in the reference image
x = data['domain']['x']
y = data['domain']['y']
if x is None or y is None: # Out of bounds
self.label_mouseover.pixel = ""
self.label_mouseover.reset_coords_display()
self.label_mouseover.value = ""
return
maxsize = int(np.ceil(np.log10(np.max(image.shape[:2])))) + 3
fmt = 'x={0:0' + str(maxsize) + '.1f} y={1:0' + str(maxsize) + '.1f}'
self.label_mouseover.pixel = (fmt.format(x, y))
# TODO: This assumes data_collection[0] is the main reference
# data for this application. This section will need to be updated
# when that is no longer true.
# Hack to insert WCS for generated 2D and 3D images using FLUX cube WCS.
if 'Plugin' in image.meta:
coo_data = self.jdaviz_app.data_collection[0]
else:
coo_data = image
# Hack around various WCS propagation issues in Cubeviz.
if '_orig_wcs' in coo_data.meta:
coo = coo_data.meta['_orig_wcs'].pixel_to_world(x, y, self.state.slices[-1])[0].icrs
self.label_mouseover.set_coords(coo)
elif data_has_valid_wcs(coo_data):
try:
coo = coo_data.coords.pixel_to_world(x, y, self.state.slices[-1])[-1].icrs
except Exception:
self.label_mouseover.reset_coords_display()
else:
self.label_mouseover.set_coords(coo)
else:
self.label_mouseover.reset_coords_display()
# Extract data values at this position.
# Check if shape is [x, y, z] or [y, x] and show value accordingly.
if image.ndim == 3:
ix_shape = 0
iy_shape = 1
elif image.ndim == 2:
ix_shape = 1
iy_shape = 0
else: # pragma: no cover
raise ValueError(f'Cubeviz does not support ndim={image.ndim}')
if (-0.5 < x < image.shape[ix_shape] - 0.5 and -0.5 < y < image.shape[iy_shape] - 0.5
and hasattr(active_layer, 'attribute')):
attribute = active_layer.attribute
arr = image.get_component(attribute).data
unit = image.get_component(attribute).units
if image.ndim == 3:
value = arr[int(round(x)), int(round(y)), self.state.slices[-1]]
else: # 2
value = arr[int(round(y)), int(round(x))]
self.label_mouseover.value = f'{value:+10.5e} {unit}'
else:
self.label_mouseover.value = ''
elif data['event'] == 'mouseleave' or data['event'] == 'mouseenter':
self.label_mouseover.pixel = ""
self.label_mouseover.reset_coords_display()
self.label_mouseover.value = ""
def _initial_x_axis(self, *args):
# Make sure that the x_att is correct on data load
ref_data = self.state.reference_data
if ref_data and ref_data.ndim == 3:
for att_name in ["Right Ascension", "RA", "Galactic Longitude"]:
if att_name in ref_data.component_ids():
x_att = att_name
self.state.x_att_world = ref_data.id[x_att]
break
else:
x_att = "Pixel Axis 0 [z]"
self.state.x_att = ref_data.id[x_att]
[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] 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]@viewer_registry("cubeviz-profile-viewer", label="Profile 1D (Cubeviz)")
class CubevizProfileView(SpecvizProfileView):
# 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:selectslice', 'jdaviz:selectline'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
def __init__(self, *args, **kwargs):
# NOTE: super will initialize nested toolbar with
# default_tool_priority=['jdaviz:selectslice']
super().__init__(*args, **kwargs)
self._default_flux_viewer_reference_name = kwargs.get(
"flux_viewer_reference_name", "flux-viewer"
)
def _is_spatial_subset(self, layer):
# spatial subset layers will have the same data-label as the collapsed flux cube
ref_data_label = self.state.reference_data.label
return (isinstance(getattr(layer.layer, 'subset_state', None), RoiSubsetState)
and layer.layer.data.label == ref_data_label)
def _get_spatial_subset_layers(self):
return [ls for ls in self.state.layers if self._is_spatial_subset(ls)]
def _is_spectral_subset(self, layer):
ref_data_label = self.layers[0].layer.data.label
return (isinstance(getattr(layer.layer, 'subset_state', None), RangeSubsetState)
and layer.layer.data.label == ref_data_label)
def _get_spectral_subset_layers(self):
return [ls for ls in self.state.layers if self._is_spectral_subset(ls)]
def _get_marks_for_layers(self, layers):
layers_list = list(self.state.layers)
# here we'll assume that all custom marks are subclasses of Lines/GL but don't directly
# use Lines/LinesGL (so an isinstance check won't be sufficient here)
layer_marks = self.native_marks
# and now we'll assume that the marks are in the same order as the layers, this should
# be the case as long as the order isn't manually resorted. If for any reason the layer
# is added but the mark has not yet been created, this will ignore that entry rather than
# raising an IndexError.
inds = [layers_list.index(layer) for layer in layers]
return [layer_marks[ind] for ind in inds if ind < len(layer_marks)]
def _on_subset_delete(self, msg):
# delete any ShadowSpatialSpectral mark for which either of the spectral or spatial marks
# no longer exists
spectral_marks = self._get_marks_for_layers(self._get_spectral_subset_layers())
spatial_marks = self._get_marks_for_layers(self._get_spatial_subset_layers())
self.figure.marks = [m for m in self.figure.marks
if not (isinstance(m, ShadowSpatialSpectral) and
(m.spatial_spectrum_mark in spatial_marks or
m.spectral_subset_mark in spectral_marks))]
def _expected_subset_layer_default(self, layer_state):
"""
This gets called whenever the layer of an expected new subset is added, we want to set the
default for the linewidth depending on whether it is spatial or spectral, and handle
creating any necessary marks for spatial-spectral subset intersections.
"""
super()._expected_subset_layer_default(layer_state)
if not (self._is_spatial_subset(layer_state) or self._is_spectral_subset(layer_state)):
return
this_mark = self._get_marks_for_layers([layer_state])[0]
new_marks = []
if isinstance(layer_state.layer.subset_state, RoiSubsetState):
layer_state.linewidth = 1
# need to add marks for every intersection between THIS spatial subset and ALL spectral
spectral_marks = self._get_marks_for_layers(self._get_spectral_subset_layers())
for spectral_mark in spectral_marks:
new_marks += [ShadowSpatialSpectral(this_mark, spectral_mark)]
else:
layer_state.linewidth = 3
# need to add marks for every intersection between THIS spectral subset and ALL spatial
spatial_marks = self._get_marks_for_layers(self._get_spatial_subset_layers())
for spatial_mark in spatial_marks:
new_marks += [ShadowSpatialSpectral(spatial_mark, this_mark)]
# NOTE: += or append won't pick up on change
self.figure.marks = self.figure.marks + new_marks
@property
def slice_indicator(self):
for mark in self.figure.marks:
if isinstance(mark, SliceIndicatorMarks):
return mark
# SliceIndicatorMarks does not yet exist
slice_indicator = SliceIndicatorMarks(self)
self.figure.marks = self.figure.marks + slice_indicator.marks
return slice_indicator
def _update_slice_indicator(self, slice):
self.slice_indicator.slice = slice