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consolidate stretch histogram code (#2538)
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* consolidate stretch curve and colorbar code
* remove multilayer support
* hide stretch histogram in multiselect, advanced options to accordion
* show stretch curve by default
* ensure colorbar updated at start
* update tests
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@kecnry
kecnry authored Oct 27, 2023
1 parent 6e010c2 commit 7855702
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Showing 4 changed files with 166 additions and 175 deletions.
210 changes: 85 additions & 125 deletions jdaviz/configs/default/plugins/plot_options/plot_options.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -266,7 +266,7 @@ class PlotOptions(PluginTemplateMixin):
stretch_hist_nbins = IntHandleEmpty(25).tag(sync=True)
stretch_histogram_widget = Unicode().tag(sync=True)

stretch_curve_visible = Bool().tag(sync=True)
stretch_curve_visible = Bool(True).tag(sync=True)

subset_visible_value = Bool().tag(sync=True)
subset_visible_sync = Dict().tag(sync=True)
Expand Down Expand Up @@ -477,6 +477,19 @@ def state_attr_for_line_visible(state):

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='vmin', color='#c75d2c')
self.stretch_histogram.add_line(
label='stretch_curve',
x=[], y=[],
ynorm='vmin',
color="#007BA1", # "inactive" blue
opacities=[0.5],
)
self.stretch_histogram.add_scatter(
label='stretch_knots',
x=[], y=[],
ynorm='vmin',
color="#007BA1", # "inactive" blue
)
self.stretch_histogram.add_scatter('colorbar', x=[], y=[], ynorm='vmin', marker='square', stroke_width=33) # noqa: E501
with self.stretch_histogram.figure.hold_sync():
self.stretch_histogram.figure.axes[0].label = 'pixel value'
Expand Down Expand Up @@ -726,23 +739,24 @@ def _update_stretch_histogram(self, msg={}):

# update the n_bins since this may be a new layer
self._histogram_nbins_changed()
# update the curve/colorbar
self._update_stretch_curve(msg)

@observe('is_active', 'image_color_mode_value', 'image_color_value', 'image_colormap_value',
@observe('image_color_mode_value', 'image_color_value', 'image_colormap_value',
'image_contrast_value', 'image_bias_value',
'stretch_hist_nbins',
'stretch_curve_visible',
'stretch_function_value', 'stretch_vmin_value', 'stretch_vmax_value',
'stretch_hist_nbins', 'stretch_hist_zoom_limits')
)
@skip_if_no_updates_since_last_active()
def _update_stretch_histogram_colorbar(self, msg={}):
"""Renders a colorbar on top of the histogram."""
def _update_stretch_curve(self, msg=None):
if not self._viewer_is_image_viewer() or not hasattr(self, 'stretch_histogram'):
# don't update histogram if selected viewer is not an image viewer,
# or the stretch histogram hasn't been initialized:
return

if self.multiselect:
with self.stretch_histogram.hold_sync():
self.stretch_histogram._marks["colorbar"].x = []
self.stretch_histogram._marks["colorbar"].y = []
self.stretch_histogram.clear_marks('stretch_curve', 'stretch_knots', 'colorbar')
return

if len(self.layer.selected_obj):
Expand All @@ -753,135 +767,81 @@ def _update_stretch_histogram_colorbar(self, msg={}):

if isinstance(layer.layer, GroupedSubset):
# don't update histogram for subsets:
self.stretch_histogram.clear_marks('stretch_curve', 'stretch_knots', 'colorbar')
return

# Cannot use layer.state because it can be out-of-sync
with self.stretch_histogram.hold_sync():
color_mode = self.image_color_mode_value
interval = ManualInterval(self.stretch_vmin.value, self.stretch_vmax.value)
contrast_bias = ContrastBiasStretch(self.image_contrast_value, self.image_bias_value)
stretch = stretches.members[self.stretch_function_value]

# NOTE: Index 0 in marks is assumed to be the bin centers.
x = self.stretch_histogram.figure.marks[0].x
y = np.ones_like(x)

# Copied from the __call__ internals of glue/viewers/image/composite_array.py
data = interval(x)
data = contrast_bias(data, out=data)
data = stretch(data, out=data)

if color_mode == 'Colormaps':
cmap = colormaps[self.image_colormap.text]
if hasattr(cmap, "get_bad"):
bad_color = cmap.get_bad().tolist()[:3]
layer_cmap = cmap.with_extremes(bad=bad_color + [self.image_opacity_value])
else:
layer_cmap = cmap

# Compute colormapped image
plane = layer_cmap(data)

else: # Monochromatic
# Get color
color = COLOR_CONVERTER.to_rgba_array(self.image_color_value)[0]
plane = data[:, np.newaxis] * color
plane[:, 3] = 1

plane = np.clip(plane, 0, 1, out=plane)
ipycolors = [matplotlib.colors.rgb2hex(p, keep_alpha=False) for p in plane]

self.stretch_histogram._marks["colorbar"].x = x
self.stretch_histogram._marks["colorbar"].y = y
self.stretch_histogram._marks["colorbar"].colors = ipycolors

@observe('is_active', 'stretch_vmin_value', 'stretch_vmax_value', 'layer_selected',
'stretch_hist_nbins', 'image_contrast_value', 'image_bias_value',
'stretch_curve_visible')
@skip_if_no_updates_since_last_active()
def _update_stretch_curve(self, msg=None):
mark_label_prefix = "stretch_curve: "
knots_label_prefix = "stretch_knots: "

if not self._viewer_is_image_viewer() or not hasattr(self, 'stretch_histogram'):
# don't update histogram if selected viewer is not an image viewer,
# or the stretch histogram hasn't been initialized:
return

if not self.stretch_curve_visible:
# clear marks if curve is not visible:
for existing_mark_label, mark in self.stretch_histogram.marks.items():
if (existing_mark_label.startswith(mark_label_prefix) or
existing_mark_label.startswith(knots_label_prefix)):
# clear this mark
mark.x = []
mark.y = []
return

for layer in self.layer.selected_obj:
if isinstance(layer.layer, GroupedSubset):
# don't update histogram for subsets:
continue

# clear old mark, if it exists:
mark_label = f'{mark_label_prefix}{layer.label}'
mark_exists = mark_label in self.stretch_histogram.marks

knot_label = f"{knots_label_prefix}{layer.label}"
# create the new/updated mark following the colormapping
# procedure in glue's CompositeArray:
interval = ManualInterval(self.stretch_vmin.value, self.stretch_vmax.value)
contrast_bias = ContrastBiasStretch(layer.state.contrast, layer.state.bias)
stretch = stretches.members[layer.state.stretch]
layer_cmap = layer.state.cmap

if isinstance(stretch, SplineStretch):
knot_x = (self.stretch_vmin_value +
stretch.x * (self.stretch_vmax_value - self.stretch_vmin_value))
knot_y = stretch.y
# create the new/updated stretch curve following the colormapping
# procedure in glue's CompositeArray:
interval = ManualInterval(self.stretch_vmin_value, self.stretch_vmax_value)
contrast_bias = ContrastBiasStretch(self.image_contrast_value, self.image_bias_value)
stretch = stretches.members[self.stretch_function_value]
layer_cmap = layer.state.cmap

# show the colorbar
color_mode = self.image_color_mode_value

# NOTE: Index 0 in marks is assumed to be the bin centers.
x = self.stretch_histogram.figure.marks[0].x
y = np.ones_like(x)

# Copied from the __call__ internals of glue/viewers/image/composite_array.py
data = interval(x)
data = contrast_bias(data, out=data)
data = stretch(data, out=data)

if color_mode == 'Colormaps':
cmap = colormaps[self.image_colormap.text]
if hasattr(cmap, "get_bad"):
bad_color = cmap.get_bad().tolist()[:3]
layer_cmap = cmap.with_extremes(bad=bad_color + [self.image_opacity_value])
else:
knot_x, knot_y = [], []
layer_cmap = cmap

# Compute colormapped image
plane = layer_cmap(data)

else: # Monochromatic
# Get color
color = COLOR_CONVERTER.to_rgba_array(self.image_color_value)[0]
plane = data[:, np.newaxis] * color
plane[:, 3] = 1

plane = np.clip(plane, 0, 1, out=plane)
ipycolors = [matplotlib.colors.rgb2hex(p, keep_alpha=False) for p in plane]

colorbar_mark = self.stretch_histogram.marks['colorbar']
colorbar_mark.x = x
colorbar_mark.y = y
colorbar_mark.colors = ipycolors

# show "knot" locations if the stretch_function is a spline
if isinstance(stretch, SplineStretch) and self.stretch_curve_visible:
knot_mark = self.stretch_histogram.marks['stretch_knots']
knot_mark.x = (self.stretch_vmin_value +
stretch.x * (self.stretch_vmax_value - self.stretch_vmin_value))
# scale to 0.9 so always falls below colorbar (same as for stretch_curve)
# (may need to revisit this when supporting dragging)
knot_mark.y = 0.9 * stretch.y
else:
self.stretch_histogram.clear_marks('stretch_knots')

if self.stretch_curve_visible:
# create a photoshop style "curve" for the stretch function
curve_x = np.linspace(self.stretch_vmin.value, self.stretch_vmax.value, 50)
curve_y = interval(curve_x, clip=False)
curve_y = contrast_bias(curve_y, out=curve_y, clip=False)
curve_y = stretch(curve_y, out=curve_y, clip=False)
curve_y = layer_cmap(curve_y)[:, 0]

for existing_mark_label, mark in self.stretch_histogram.marks.items():
if mark_label == existing_mark_label:
# update this mark
mark.x = curve_x
mark.y = curve_y
elif existing_mark_label.startswith(mark_label_prefix):
# clear this mark
mark.x = []
mark.y = []

if not mark_exists:
self.stretch_histogram.add_line(
mark_label,
x=curve_x,
y=curve_y,
ynorm=True,
color="#007BA1", # "inactive" blue
opacities=[0.5],
)

if not mark_exists:
self.stretch_histogram.add_scatter(
label=knot_label,
x=knot_x,
y=knot_y,
ynorm=True,
color="#0a6774"
)
else:
self.stretch_histogram.marks[knot_label].x = knot_x
self.stretch_histogram.marks[knot_label].y = knot_y
curve_mark = self.stretch_histogram.marks['stretch_curve']
curve_mark.x = curve_x
# scale to 0.9 so always falls below colorbar (same as for stretch_knots)
# (may need to revisit this when supporting dragging)
curve_mark.y = 0.9 * curve_y
else:
self.stretch_histogram.clear_marks('stretch_curve')

self.stretch_histogram._refresh_marks()
self.stretch_histogram._refresh_marks()

@observe('stretch_vmin_value')
def _stretch_vmin_changed(self, msg=None):
Expand Down
94 changes: 60 additions & 34 deletions jdaviz/configs/default/plugins/plot_options/plot_options.vue
View file
Original file line number Diff line number Diff line change
Expand Up @@ -345,7 +345,8 @@
></v-select>
</glue-state-sync-wrapper>

<glue-state-sync-wrapper :sync="stretch_vmin_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmin')">
<!-- for multiselect, show vmin/max here, otherwise they'll be in the "more stretch options" expandable section -->
<glue-state-sync-wrapper v-if="multiselect" :sync="stretch_vmin_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmin')">
<v-text-field
ref="stretch_vmin"
label="Stretch VMin"
Expand All @@ -355,7 +356,7 @@
></v-text-field>
</glue-state-sync-wrapper>

<glue-state-sync-wrapper :sync="stretch_vmax_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmax')">
<glue-state-sync-wrapper v-if="multiselect" :sync="stretch_vmax_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmax')">
<v-text-field
ref="stretch_vmax"
label="Stretch VMax"
Expand All @@ -365,40 +366,65 @@
></v-text-field>
</glue-state-sync-wrapper>

<div v-if="stretch_function_sync.in_subscribed_states">
<v-row>
<v-text-field
ref="stretch_hist_nbins"
label="Number of Bins"
v-model.number="stretch_hist_nbins"
type="number"
hint="The amount of bins used in the histogram."
persistent-hint
:rules="[() => stretch_hist_nbins !== '' || 'This field is required',
() => stretch_hist_nbins > 0 || 'Number of Bins must be greater than zero']"
></v-text-field>
</v-row>
<v-row>
<!-- z-index to ensure on top of the jupyter widget with negative margin-top -->
<v-switch
v-model="stretch_hist_zoom_limits"
class="hide-input"
label="Limit histogram to current zoom limits"
style="z-index: 1"
></v-switch>
</v-row>
<div v-if="stretch_function_sync.in_subscribed_states && !multiselect">
<jupyter-widget :widget="stretch_histogram_widget"/>
<v-row>
<v-switch
v-model="stretch_curve_visible"
class="hide-input"
label="Show stretch function curve"
style="z-index: 1"
></v-switch>
<!-- NOTE: height defined here should match that in the custom CSS rules
below for the bqplot class -->
<v-expansion-panels accordion>
<v-expansion-panel>
<v-expansion-panel-header v-slot="{ open }">
<span style="padding: 6px">More Stretch Options</span>
</v-expansion-panel-header>
<v-expansion-panel-content>
<v-row>
<v-text-field
ref="stretch_hist_nbins"
label="Number of Bins"
v-model.number="stretch_hist_nbins"
type="number"
hint="The amount of bins used in the histogram."
persistent-hint
:rules="[() => stretch_hist_nbins !== '' || 'This field is required',
() => stretch_hist_nbins > 0 || 'Number of Bins must be greater than zero']"
></v-text-field>
</v-row>
<v-row>
<v-switch
v-model="stretch_hist_zoom_limits"
class="hide-input"
label="Limit histogram to current zoom limits"
></v-switch>
</v-row>
<v-row>
<v-switch
v-model="stretch_curve_visible"
class="hide-input"
label="Show stretch function curve"
></v-switch>
</v-row>
<glue-state-sync-wrapper :sync="stretch_vmin_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmin')">
<v-text-field
ref="stretch_vmin"
label="Stretch VMin"
v-model.number="stretch_vmin_value"
type="number"
:step="stretch_vstep"
></v-text-field>
</glue-state-sync-wrapper>
<glue-state-sync-wrapper :sync="stretch_vmax_sync" :multiselect="multiselect" @unmix-state="unmix_state('stretch_vmax')">
<v-text-field
ref="stretch_vmax"
label="Stretch VMax"
v-model.number="stretch_vmax_value"
type="number"
:step="stretch_vstep"
></v-text-field>
</glue-state-sync-wrapper>
</v-expansion-panel-content>
</v-expansion-panel>
</v-expansion-panels>
</v-row>
<jupyter-widget :widget="stretch_histogram_widget"/>
</div>

</div>

<!-- IMAGE:IMAGE -->
<j-plugin-section-header v-if="image_visible_sync.in_subscribed_states">Image</j-plugin-section-header>
Expand Down
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