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Plugin plots to viewers (spacetelescope#2498)
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* create separate app instance with glue-viewer
* nested toolbar in plugin viewers
* migrate implementation for scatter viewers (radial profile, line profiles) and histogram (stretch in plot options)
* downsampling no longer necessary
* lose logic to ensure vmin/max markers are within viewer range (might be confusing)
* home button on histogram viewer is buggy
* update tests
* temporary workaround to segfault on some machines
* bump glue-jupyter to ensure scatter lines support
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@kecnry
kecnry authored Oct 12, 2023
1 parent ffde818 commit 2f24a20
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Showing 13 changed files with 324 additions and 183 deletions.
3 changes: 3 additions & 0 deletions CHANGES.rst
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Expand Up @@ -4,6 +4,9 @@
New Features
------------

- Plots in plugins now include basic zoom/pan tools for Plot Options,
Imviz Line Profiles, and Imviz's aperture photometry. [#2498]

Cubeviz
^^^^^^^

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19 changes: 12 additions & 7 deletions jdaviz/app.vue
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Expand Up @@ -360,7 +360,12 @@ a:active {
text-decoration: none;
}
.jdaviz-nested-toolbar {
.invert, .invert-if-dark.theme--dark {
filter: invert(1) saturate(1) brightness(100);
color: white;
}
.jdaviz-nested-toolbar, .plugin-nested-toolbar {
/* height of nested toolbar to match viewer toolbar height */
height: 42px;
margin-right: 4px;
Expand All @@ -371,12 +376,7 @@ a:active {
filter: invert(1) saturate(1) brightness(100);
}
.invert, .invert-if-dark.theme--dark {
filter: invert(1) saturate(1) brightness(100);
color: white;
}
.jdaviz-nested-toolbar .v-btn {
.jdaviz-nested-toolbar .v-btn, .plugin-nested-toolbar .v-btn {
height: 42px !important;
border: none !important;
min-width: 42px !important;
Expand All @@ -394,6 +394,11 @@ a:active {
background-color: #c75109 !important;
}
.plugin-nested-toolbar .v-btn--active, .plugin-nested-toolbar .v-btn:focus {
/* semi-transparent active color (orange) */
background-color: #c7510996 !important;
}
.v-divider.theme--dark {
/* make the v-divider standout more */
border-color: hsla(0,0%,100%,.35) !important;
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11 changes: 5 additions & 6 deletions jdaviz/components/plugin_plot.vue
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@@ -1,22 +1,22 @@
<template>
<div class="plugin-plot-component">
<v-row style="margin: 0px 0px -8px 0px !important" justify="end">
<div style="line-height: 64px; width=32px" class="only-show-in-tray">
<div class="plugin-plot-component" style="margin-bottom: 40px">
<v-row dense style="margin: 0px 0px -8px 0px !important">
<jupyter-widget class='plugin-nested-toolbar' :widget="toolbar"></jupyter-widget>
<v-spacer></v-spacer>
<div style="line-height: 40px; width=32px" class="only-show-in-tray">
<j-plugin-popout :popout_button="popout_button"></j-plugin-popout>
</div>
</v-row>

<v-row style="margin: -16px 0px 8px 0px !important">
<jupyter-widget :widget="figure" style="height: 100%; width: 100%" />
</v-row>

</div>
</template>

<script>
</script>


<style scoped>
.only-show-in-tray {
display: none;
Expand All @@ -33,5 +33,4 @@
width: 100%;
height: 480px;
}
</style>
11 changes: 7 additions & 4 deletions jdaviz/components/toolbar_nested.py
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Expand Up @@ -65,10 +65,13 @@ def __init__(self, viewer, tools_nested, default_tool_priority=[]):
self.default_tool_priority = default_tool_priority
self._handle_default_tool()

for msg in (AddDataMessage, RemoveDataMessage, ViewerAddedMessage, ViewerRemovedMessage,
SpectralMarksChangedMessage):
self.viewer.hub.subscribe(self, msg,
handler=lambda _: self._update_tool_visibilities())
# toolbars in the main app viewers need to respond to the data-collection, etc,
# but those in plugins do not
if hasattr(self.viewer, 'hub'):
for msg in (AddDataMessage, RemoveDataMessage, ViewerAddedMessage, ViewerRemovedMessage,
SpectralMarksChangedMessage):
self.viewer.hub.subscribe(self, msg,
handler=lambda _: self._update_tool_visibilities())

def _is_visible(self, tool_id):
# tools can optionally implement self.is_visible(). If not NotImplementedError
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6 changes: 3 additions & 3 deletions jdaviz/components/toolbar_nested.vue
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Expand Up @@ -4,8 +4,8 @@
<v-tooltip v-for="[id, {tooltip, img, menu_ind, has_suboptions, primary, visible}] of Object.entries(tools_data)" v-if="primary && visible" bottom>
<template v-slot:activator="{ on }">
<v-btn v-on="on" icon :value="id" style="min-width: 40px !important" @contextmenu="(e) => show_submenu(e, has_suboptions, menu_ind)">
<img :src="img" width="20px" @click.ctrl.stop=""/>
<v-icon small v-if="has_suboptions" class="suboptions-carrot" @click.ctrl.stop="">mdi-menu-down</v-icon>
<img class="invert-if-dark" :src="img" width="20px" @click.ctrl.stop=""/>
<v-icon small v-if="has_suboptions" class="suboptions-carrot invert-if-dark" @click.ctrl.stop="">mdi-menu-down</v-icon>
</v-btn>
</template>
<span>{{ tooltip }}{{has_suboptions ? " [right-click for alt. tools]" : ""}}</span>
Expand Down Expand Up @@ -81,7 +81,7 @@
}
</script>

<style>
<style scoped>
.suboptions-carrot {
transform: rotate(-45deg);
bottom: 0px;
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99 changes: 37 additions & 62 deletions jdaviz/configs/default/plugins/plot_options/plot_options.py
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Expand Up @@ -7,7 +7,6 @@
from traitlets import Any, Dict, Float, Bool, Int, List, Unicode, observe

from glue.core.subset_group import GroupedSubset
import bqplot
from glue.config import stretches
from glue.viewers.scatter.state import ScatterViewerState
from glue.viewers.profile.state import ProfileViewerState, ProfileLayerState
Expand Down Expand Up @@ -403,8 +402,13 @@ def state_attr_for_line_visible(state):
'stretch_vmax_value', 'stretch_vmax_sync',
state_filter=is_image)

self.stretch_histogram = Plot(self)
self.stretch_histogram.add_bins('histogram', color='gray')
self.stretch_histogram = Plot(self, viewer_type='histogram')
# NOTE: this is a current workaround so the histogram viewer doesn't crash when replacing
# data. Note also that passing x=[0] fails on SOME machines, so we'll pass [0, 1] instead
self.stretch_histogram._add_data('ref', x=[0, 1])
self.stretch_histogram.layers['ref'].state.visible = False
self.stretch_histogram._add_data('histogram', x=[0, 1])

self.stretch_histogram.add_line('vmin', x=[0, 0], y=[0, 1], ynorm=True, color='#c75d2c')
self.stretch_histogram.add_line('vmax', x=[0, 0], y=[0, 1], ynorm=True, color='#c75d2c')
self.stretch_histogram.figure.axes[0].label = 'pixel value'
Expand Down Expand Up @@ -606,16 +610,6 @@ def _update_stretch_histogram(self, msg={}):
y_max = y_limits.max()

arr = comp.data[y_min:y_max, x_min:x_max]

size = arr.shape[0] * arr.shape[1]
if size > 400**2:
xstep = max(1, round(arr.shape[1] / 400))
ystep = max(1, round(arr.shape[0] / 400))
arr = arr[::ystep, ::xstep]
stretch_hist_downsampled = [size, arr.shape[0] * arr.shape[1]]
else:
stretch_hist_downsampled = size

sub_data = arr.ravel()

else:
Expand All @@ -635,49 +629,34 @@ def _update_stretch_histogram(self, msg={}):

sub_data = comp.data[inds].ravel()

# downsampling not currently implemented for 2d spectrum
stretch_hist_downsampled = len(sub_data)

else:
# include all data, regardless of zoom limits
arr = comp.data
size = arr.shape[0] * arr.shape[1]
if size > 400**2:
xstep = max(1, round(arr.shape[1] / 400))
ystep = max(1, round(arr.shape[0] / 400))
arr = arr[::ystep, ::xstep]
stretch_hist_downsampled = [size, arr.shape[0] * arr.shape[1]]
else:
stretch_hist_downsampled = size

sub_data = arr.ravel()

# filter out nans (or else bqplot will fail)
if np.any(np.isnan(sub_data)):
sub_data = sub_data[~np.isnan(sub_data)]

hist_mark = self.stretch_histogram.marks['histogram']
with hist_mark.hold_sync():
hist_mark.sample = sub_data
self.stretch_histogram._update_data('histogram', x=sub_data)

if len(sub_data) > 0:
interval = PercentileInterval(95)
if len(sub_data) > 0:
hist_lims = interval.get_limits(sub_data)
hist_mark.min, hist_mark.max = hist_lims
# set the stepsize for vmin/vmax to be approximately 1% of the range of the
# histogram (within the percentile interval), rounded to 1-2 significant digits
# to avoid random step sizes. This logic is somewhat arbitrary and can be safely
# modified or eventually exposed to the user if that would be useful.
stretch_vstep = (hist_lims[1] - hist_lims[0]) / 100.
self.stretch_vstep = np.round(stretch_vstep, decimals=-int(np.log10(stretch_vstep))+1) # noqa
hist_mark.bins = self.stretch_hist_nbins
# in case only the sample has changed but its length has not,
# we'll force the traitlet to trigger a change
hist_mark.send_state('sample')
if isinstance(stretch_hist_downsampled, list):
title = f"{stretch_hist_downsampled[1]} of {stretch_hist_downsampled[0]} pixels"
else:
title = f"{stretch_hist_downsampled} pixels"
self.stretch_histogram.figure.title = title
hist_lims = interval.get_limits(sub_data)
# set the stepsize for vmin/vmax to be approximately 1% of the range of the
# histogram (within the percentile interval), rounded to 1-2 significant digits
# to avoid random step sizes. This logic is somewhat arbitrary and can be safely
# modified or eventually exposed to the user if that would be useful.
stretch_vstep = (hist_lims[1] - hist_lims[0]) / 100.
self.stretch_vstep = np.round(stretch_vstep, decimals=-int(np.log10(stretch_vstep))+1) # noqa

self.stretch_histogram.viewer.state.hist_x_min = hist_lims[0]
self.stretch_histogram.viewer.state.hist_x_max = hist_lims[1]

self.stretch_histogram.figure.title = f"{len(sub_data)} pixels"

# update the n_bins since this may be a new layer
self._histogram_nbins_changed()

@observe('is_active', 'stretch_vmin_value', 'stretch_vmax_value', 'layer_selected',
'stretch_hist_nbins', 'image_contrast_value', 'image_bias_value',
Expand Down Expand Up @@ -739,13 +718,7 @@ def _update_stretch_curve(self, msg=None):
opacities=[0.5],
)

# reorder marks so histogram is on top:
figure_marks = self.stretch_histogram.figure.marks
for i, fig_mark in enumerate(figure_marks):
if isinstance(fig_mark, bqplot.Bins):
hist_mark = figure_marks.pop(i)
break
self.stretch_histogram.figure.marks = figure_marks + [hist_mark]
self.stretch_histogram._refresh_marks()

@observe('stretch_vmin_value')
def _stretch_vmin_changed(self, msg=None):
Expand All @@ -756,18 +729,20 @@ def _stretch_vmax_changed(self, msg=None):
self.stretch_histogram.marks['vmax'].x = [self.stretch_vmax_value, self.stretch_vmax_value]

@observe("stretch_hist_nbins")
def _histogram_nbins_changed(self, msg):
if self.stretch_histogram is None or msg['new'] == '' or msg['new'] < 1:
def _histogram_nbins_changed(self, msg={}):
if self.stretch_histogram is None:
return
self.stretch_histogram.marks['histogram'].bins = self.stretch_hist_nbins

def set_histogram_x_limits(self, x_min=None, x_max=None):
# NOTE: leaving this out of user API until API is finalized with interactive setting
self.stretch_histogram.set_xlims(x_min, x_max)
if self.stretch_hist_nbins == '' or self.stretch_hist_nbins < 1:
return
self.stretch_histogram.viewer.state.hist_n_bin = self.stretch_hist_nbins
# for some reason, this resets the internal marks, so we need to ensure the manual
# marks are still plotted
self.stretch_histogram._refresh_marks()

def set_histogram_y_limits(self, y_min, y_max):
def set_histogram_limits(self, x_min=None, x_max=None, y_min=None, y_max=None):
# NOTE: leaving this out of user API until API is finalized with interactive setting
self.stretch_histogram.set_ylims(y_min, y_max)
self.stretch_histogram.set_lims(x_min=x_min, x_max=x_max,
y_min=y_min, y_max=y_max)

def _viewer_is_image_viewer(self):
# Import here to prevent circular import (and not at the top of the method so the import
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35 changes: 18 additions & 17 deletions jdaviz/configs/default/plugins/plot_options/tests/test_plot_options.py
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Expand Up @@ -72,46 +72,47 @@ def test_stretch_histogram(cubeviz_helper, spectrum1d_cube_with_uncerts):

assert po.stretch_histogram is not None

hist_mark = po.stretch_histogram.marks['histogram']
flux_cube_sample = hist_mark.sample
hist_lyr = po.stretch_histogram.layers['histogram']
flux_cube_sample = hist_lyr.layer.data['x']

# changing viewer should change results
po.viewer.selected = 'uncert-viewer'
assert not allclose(hist_mark.sample, flux_cube_sample)
assert not allclose(hist_lyr.layer.data['x'], flux_cube_sample)

po.viewer.selected = 'flux-viewer'
assert_allclose(hist_mark.sample, flux_cube_sample)
assert_allclose(hist_lyr.layer.data['x'], flux_cube_sample)

# change viewer limits
fv = cubeviz_helper.app.get_viewer('flux-viewer')
fv.state.x_max = 0.5 * fv.state.x_max
# viewer limits should not be affected by default
assert_allclose(hist_mark.sample, flux_cube_sample)
# (re-retrieve layer - it should not have changed)
hist_lyr = po.stretch_histogram.layers['histogram']
assert_allclose(hist_lyr.layer.data['x'], flux_cube_sample)

# set to listen to viewer limits, the length of the samples will change
# (in this case the layer itself has been replaced)
po.stretch_hist_zoom_limits = True
assert len(hist_mark.sample) != len(flux_cube_sample)
hist_lyr = po.stretch_histogram.layers['histogram']
assert len(hist_lyr.layer.data['x']) != len(flux_cube_sample)

po.stretch_vmin.value = 0.5
po.stretch_vmax.value = 1

assert po.stretch_histogram.marks['vmin'].x[0] == po.stretch_vmin.value
assert po.stretch_histogram.marks['vmax'].x[0] == po.stretch_vmax.value

assert hist_mark.bins == 25
assert po.stretch_histogram.viewer.state.hist_n_bin == 25
po.stretch_hist_nbins = 20
assert hist_mark.bins == 20
assert po.stretch_histogram.viewer.state.hist_n_bin == 20

po.set_histogram_x_limits(x_min=0.25, x_max=2)
assert po.stretch_histogram.figure.axes[0].scale.min == 0.25
assert po.stretch_histogram.figure.axes[0].scale.max == 2
po.set_histogram_limits(x_min=0.25, x_max=2)
assert po.stretch_histogram.viewer.state.x_min == 0.25
assert po.stretch_histogram.viewer.state.x_max == 2

po.set_histogram_y_limits(y_min=1, y_max=2)
assert po.stretch_histogram.figure.axes[1].scale.min == 1
assert po.stretch_histogram.figure.axes[1].scale.max == 2

po.stretch_vmin.value = hist_mark.min - 1
po.stretch_vmax.value = hist_mark.max + 1
po.set_histogram_limits(y_min=1, y_max=2)
assert po.stretch_histogram.viewer.state.y_min == 1
assert po.stretch_histogram.viewer.state.y_max == 2

assert po.stretch_histogram.marks['vmin'].x[0] == po.stretch_vmin.value
assert po.stretch_histogram.marks['vmax'].x[0] == po.stretch_vmax.value
Expand Down
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