from glue.core import BaseData
from glue_jupyter.bqplot.image import BqplotImageView
from jdaviz.core.registries import viewer_registry
from jdaviz.configs.cubeviz.plugins.mixins import WithSliceIndicator, WithSliceSelection
from jdaviz.configs.default.plugins.viewers import JdavizViewerMixin
from jdaviz.configs.specviz.plugins.viewers import SpecvizProfileView
from jdaviz.core.freezable_state import FreezableBqplotImageViewerState
from jdaviz.configs.cubeviz.plugins.cube_listener import CubeListenerData, MINVOL
import numpy as np
from astropy import units as u
try:
import sounddevice as sd
except ImportError:
pass
__all__ = ['CubevizImageView', 'CubevizProfileView']
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@viewer_registry("cubeviz-image-viewer", label="Image 2D (Cubeviz)")
class CubevizImageView(JdavizViewerMixin, WithSliceSelection, 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:pixelboxzoommatch', 'jdaviz:boxzoom',
'jdaviz:pixelpanzoommatch', 'jdaviz:panzoom'],
['bqplot:truecircle', 'bqplot:rectangle', 'bqplot:ellipse',
'bqplot:circannulus'],
['jdaviz:spectrumperspaxel'],
['jdaviz:sidebar_plot', 'jdaviz:sidebar_export']
]
default_class = None
_state_cls = FreezableBqplotImageViewerState
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
# provide reference from state back to viewer to use for zoom syncing
self.state._set_viewer(self)
self._subscribe_to_layers_update()
self.state.add_callback('reference_data', self._initial_x_axis)
# Hide axes by default
self.state.show_axes = False
self.sonified_cube = None
self.stream = None
self.sonification_wl_ranges = None
self.sonification_wl_unit = None
self.volume_level = None
self.stream_active = True
self.data_menu._obj.dataset.add_filter('is_cube_or_image')
@property
def _default_spectrum_viewer_reference_name(self):
return self.jdaviz_helper._default_spectrum_viewer_reference_name
@property
def _default_flux_viewer_reference_name(self):
return self.jdaviz_helper._default_flux_viewer_reference_name
@property
def _default_uncert_viewer_reference_name(self):
return self.jdaviz_helper._default_uncert_viewer_reference_name
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]
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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"
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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)]
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def start_stream(self):
if self.stream and not self.stream.closed and self.stream_active:
self.stream.start()
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def stop_stream(self):
if self.stream and not self.stream.closed and self.stream_active:
self.stream.stop()
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def update_sonified_cube(self, x, y):
if (not self.sonified_cube or not hasattr(self.sonified_cube, 'newsig') or
not hasattr(self.sonified_cube, 'sigcube')):
return
self.sonified_cube.newsig = self.sonified_cube.sigcube[x, y, :]
self.sonified_cube.cbuff = True
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def update_listener_wls(self, wranges, wunit):
self.sonification_wl_ranges = wranges
self.sonification_wl_unit = wunit
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def update_sound_device(self, device_index):
if not self.sonified_cube:
return
self.stop_stream()
self.stream = sd.OutputStream(samplerate=self.sample_rate, blocksize=self.buffer_size,
device=device_index, channels=1, dtype='int16',
latency='low', callback=self.sonified_cube.player_callback)
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def update_volume_level(self, level):
if not self.sonified_cube:
return
self.volume_level = level
self.sonified_cube.atten_level = int(1/np.clip((level/100.)**2, MINVOL, 1))
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def get_sonified_cube(self, sample_rate, buffer_size, device, assidx, ssvidx,
pccut, audfrqmin, audfrqmax, eln, use_pccut):
spectrum = self.active_image_layer.layer.get_object(statistic=None)
wlens = spectrum.wavelength.to('m').value
flux = spectrum.flux.value
self.sample_rate = sample_rate
self.buffer_size = buffer_size
if self.sonification_wl_ranges:
wdx = np.zeros(wlens.size).astype(bool)
for r in self.sonification_wl_ranges:
# index just the spectral subregion
wdx = np.logical_or(wdx,
np.logical_and(wlens >= r[0].to_value(u.m),
wlens <= r[1].to_value(u.m)))
wlens = wlens[wdx]
flux = flux[:, :, wdx]
pc_cube = np.percentile(np.nan_to_num(flux), np.clip(pccut, 0, 99), axis=-1)
# clip zeros and remove NaNs
clipped_arr = np.nan_to_num(np.clip(flux, 0, np.inf), copy=False)
# make a rough white-light image from the clipped array
whitelight = np.expand_dims(clipped_arr.sum(-1), axis=2)
if use_pccut:
# subtract any percentile cut
clipped_arr -= np.expand_dims(pc_cube, axis=2)
# and re-clip
clipped_arr = np.clip(clipped_arr, 0, np.inf)
self.sonified_cube = CubeListenerData(clipped_arr ** assidx, wlens, duration=0.8,
samplerate=sample_rate, buffsize=buffer_size,
wl_unit=self.sonification_wl_unit,
audfrqmin=audfrqmin, audfrqmax=audfrqmax,
eln=eln, vol=self.volume_level)
self.sonified_cube.sonify_cube()
self.sonified_cube.sigcube = (
self.sonified_cube.sigcube * pow(whitelight / whitelight.max(),
ssvidx)).astype('int16')
self.stream = sd.OutputStream(samplerate=sample_rate, blocksize=buffer_size, device=device,
channels=1, dtype='int16', latency='low',
callback=self.sonified_cube.player_callback)
self.sonified_cube.cbuff = True
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@viewer_registry("cubeviz-profile-viewer", label="Profile 1D (Cubeviz)")
class CubevizProfileView(SpecvizProfileView, WithSliceIndicator):
# categories: zoom resets, zoom, pan, subset, select tools, shortcuts
tools_nested = [
['jdaviz:homezoom', 'jdaviz:prevzoom'],
['jdaviz:boxzoom', 'jdaviz:xrangezoom', 'jdaviz:yrangezoom'],
['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):
kwargs.setdefault('default_tool_priority', ['jdaviz:selectslice'])
super().__init__(*args, **kwargs)
@property
def _default_flux_viewer_reference_name(self):
return self.jdaviz_helper._default_flux_viewer_reference_name
