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Merged
merged 12 commits into from
Jun 30, 2025
+149 −103
Merged

Add support for stretches in volume viewer #396

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d6a0a2f
Add support for stretches to the volume viewer.
Carifio24 May 21, 2025
f9a41bf
Add stretch_parameters to color properties.
Carifio24 May 21, 2025
70db7cd
Use dictionary for stretch templates for extensibility.
Carifio24 May 22, 2025
fc0fdb1
Codestyle fixes.
Carifio24 May 22, 2025
fded642
Update tests to include a stretch.
Carifio24 May 23, 2025
87d4be6
Add widget for controlling stretch to Jupyter controls.
Carifio24 May 22, 2025
8913f79
Bump required version of glue-core so that stretch state mixin is def…
Carifio24 May 22, 2025
8cba3a9
Use a registry instead of a dictionary for storing stretch GLSL.
Carifio24 May 27, 2025
106f16b
Fix duplicate widget from rebasing in UI file.
Carifio24 Jun 5, 2025
231eb9b
Fix another UI rebasing issue.
Carifio24 Jun 6, 2025
1499d61
Fix more UI rebasing issues.
Carifio24 Jun 26, 2025
5b3a652
Remove flip limits button per team discussions.
Carifio24 Jun 30, 2025
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48 changes: 38 additions & 10 deletions glue_vispy_viewers/volume/colors.py
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Original file line number Diff line number Diff line change
@@ -1,43 +1,71 @@
from glue.config import AsinhStretch, LinearStretch, LogStretch, SqrtStretch, DictRegistry
from matplotlib.colors import ListedColormap
from vispy.color import BaseColormap


def create_cmap_template(n):
class GLSLStretchRegistry(DictRegistry):

def add(self, stretch_cls, glsl):
self.members[stretch_cls] = glsl


stretch_glsl = GLSLStretchRegistry()
stretch_glsl.add(LogStretch, "log({stretch.a} * {parameter} + 1.0) / log({stretch.a} + 1.0)")
stretch_glsl.add(SqrtStretch, "sqrt({parameter})")
stretch_glsl.add(AsinhStretch,
"log({parameter} / {stretch.a} + sqrt(pow({parameter} / {stretch.a}, 2) + 1)) / "
"log(1.0 / {stretch.a} + sqrt(pow(1.0 / {stretch.a}, 2) + 1))")
stretch_glsl.add(LinearStretch, "{parameter}")


def create_cmap_template(n, stretch_glsl):
ts = tuple((i + 1) / n for i in range(n-1))
lines = [
"vec4 translucent_colormap(float t) {",
f" float s = {stretch_glsl};"
]
for i in range(n-1):
lines.append(f" if (t <= {(i+1) / n})")
for i, t in enumerate(ts):
lines.append(f" if (s <= {t})")
lines.append(f" {{ return $color_{i}; }}")
lines.append(f" return $color_{n-1};")
lines.append("}")

return "\n".join(lines)


def get_translucent_cmap(r, g, b):
def glsl_for_stretch(stretch, parameter="t"):
template = stretch_glsl.members.get(type(stretch), "{param}")
return template.format(stretch=stretch, parameter=parameter)


def get_translucent_cmap(r, g, b, stretch):

func = glsl_for_stretch(stretch)

class TranslucentCmap(BaseColormap):
glsl_map = """
vec4 translucent_fire(float t) {{
return vec4({0}, {1}, {2}, t);
return vec4({0}, {1}, {2}, {3});
}}
""".format(r, g, b)
""".format(r, g, b, func)

return TranslucentCmap()


def get_mpl_cmap(cmap):
def get_mpl_cmap(cmap, stretch):

if isinstance(cmap, ListedColormap):
colors = cmap.colors
n_colors = len(colors)
colors = [color + [index / n_colors] for index, color in enumerate(colors)]
ts = stretch([index / n_colors for index in range(len(colors))])
colors = [color + [t] for t, color in zip(ts, colors)]
else:
n_colors = 256
colors = [cmap(index / n_colors)[:3] + (index / n_colors,) for index in range(n_colors)]
ts = stretch([index / n_colors for index in range(n_colors)])
colors = [cmap(t)[:3] + (t,) for t in ts]

template = create_cmap_template(n_colors)
stretch_glsl = glsl_for_stretch(stretch)
template = create_cmap_template(n_colors, stretch_glsl)

class MatplotlibCmap(BaseColormap):
glsl_map = template
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6 changes: 6 additions & 0 deletions glue_vispy_viewers/volume/jupyter/layer_state_widget.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,11 @@ class Volume3DLayerStateWidget(v.VuetifyTemplate):

cmap_items = traitlets.List().tag(sync=True)

# Stretch

stretch_items = traitlets.List().tag(sync=True)
stretch_selected = traitlets.Int(allow_none=True).tag(sync=True)

subset = traitlets.Bool().tag(sync=True)

def __init__(self, layer_state):
Expand All @@ -37,6 +42,7 @@ def __init__(self, layer_state):
self.subset = isinstance(layer_state.layer, Subset)

link_glue_choices(self, layer_state, "attribute")
link_glue_choices(self, layer_state, "stretch")
link_glue_choices(self, layer_state, "color_mode")

self.cmap_items = [
Expand Down
3 changes: 3 additions & 0 deletions glue_vispy_viewers/volume/jupyter/layer_state_widget.vue
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,9 @@
<v-select label="color" :items="color_mode_items" v-model="color_mode_selected" hide-details />
</div>
</template>
<div>
<v-select label="stretch" :items="stretch_items" v-model="stretch_selected" hide-details />
</div>
<div>
<v-subheader class="pl-0 slider-label">opacity</v-subheader>
<glue-throttled-slider wait="300" max="1" step="0.01" :value.sync="glue_state.alpha" hide-details />
Expand Down
7 changes: 4 additions & 3 deletions glue_vispy_viewers/volume/layer_artist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
from ..common.layer_artist import VispyLayerArtist


COLOR_PROPERTIES = set(['cmap', 'color', 'color_mode'])
COLOR_PROPERTIES = set(['cmap', 'color', 'color_mode', 'stretch', 'stretch_parameters'])


class DataProxy(object):
Expand Down Expand Up @@ -160,9 +160,10 @@

def _update_cmap(self):
if self.state.color_mode == "Fixed":
cmap = get_translucent_cmap(*ColorConverter().to_rgb(self.state.color))
cmap = get_translucent_cmap(*ColorConverter().to_rgb(self.state.color),
self.state.stretch_object)
else:
cmap = get_mpl_cmap(self.state.cmap)
cmap = get_mpl_cmap(self.state.cmap, self.state.stretch_object)

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self._multivol.set_cmap(self.id, cmap)
self.redraw()
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5 changes: 4 additions & 1 deletion glue_vispy_viewers/volume/layer_state.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,12 +4,13 @@
delay_callback)
from glue.core.state_objects import StateAttributeLimitsHelper
from glue.core.data_combo_helper import ComponentIDComboHelper
from glue.viewers.common.stretch_state_mixin import StretchStateMixin
from ..common.layer_state import VispyLayerState

__all__ = ['VolumeLayerState']


class VolumeLayerState(VispyLayerState):
class VolumeLayerState(VispyLayerState, StretchStateMixin):
"""
A state object for volume layers
"""
Expand Down Expand Up @@ -39,6 +40,8 @@ def __init__(self, layer=None, **kwargs):

VolumeLayerState.color_mode.set_choices(self, ['Fixed', 'Linear'])

self.setup_stretch_callback()

self.add_callback('layer', self._on_layer_change)
if layer is not None:
self._on_layer_change()
Expand Down
151 changes: 74 additions & 77 deletions glue_vispy_viewers/volume/qt/layer_style_widget.ui
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
<x>0</x>
<y>0</y>
<width>292</width>
<height>214</height>
<height>246</height>
</rect>
</property>
<property name="windowTitle">
Expand All @@ -17,30 +17,48 @@
<property name="verticalSpacing">
<number>5</number>
</property>
<item row="9" column="2">
<widget class="QRadioButton" name="radio_subset_outline">
<property name="text">
<string>Outline</string>
</property>
</widget>
</item>
<item row="3" column="1" colspan="2">
<widget class="QComboBox" name="combotext_color_mode">
<property name="currentText">
<string>Fixed</string>
</property>
<property name="currentIndex">
<number>0</number>
</property>
<item>
<property name="text">
<string>Fixed</string>
</property>
</item>
<item>
<property name="text">
<string>Linear</string>
</property>
</item>
</widget>
</item>
<item row="4" column="0">
<widget class="QLabel" name="label_color">
<property name="text">
<string>Color:</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_color_mode">
<item row="0" column="0">
<widget class="QLabel" name="label_att">
<property name="text">
<string>Color mode:</string>
<string>Attribute:</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QLineEdit" name="valuetext_vmin"/>
</item>
<item row="1" column="3" alignment="Qt::AlignLeft">
<widget class="QLineEdit" name="valuetext_vmax"/>
</item>
<item row="5" column="1" colspan="3">
<widget class="QColormapCombo" name="combodata_cmap"/>
</item>
<item row="8" column="0" colspan="4">
<item row="8" column="0" colspan="3">
<widget class="QSlider" name="value_alpha">
<property name="maximum">
<number>100</number>
Expand All @@ -50,54 +68,24 @@
</property>
</widget>
</item>
<item row="4" column="1" colspan="3">
<widget class="QColorBox" name="color_color">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string/>
</property>
</widget>
</item>
<item row="0" column="1" colspan="3">
<widget class="QComboBox" name="combosel_attribute">
<property name="sizeAdjustPolicy">
<enum>QComboBox::AdjustToMinimumContentsLengthWithIcon</enum>
</property>
</widget>
</item>
<item row="9" column="0">
<widget class="QLabel" name="label_subset_mode">
<property name="text">
<string>Subset:</string>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QLabel" name="label_att">
<item row="9" column="1">
<widget class="QRadioButton" name="radio_subset_data">
<property name="text">
<string>Attribute:</string>
<string>Data</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLabel" name="label_color_mode"/>
</item>
<item row="1" column="0">
<widget class="QLabel" name="label_limits">
<property name="text">
<string>Limits:</string>
</property>
</widget>
</item>
<item row="9" column="3">
<widget class="QRadioButton" name="radio_subset_outline">
<item row="9" column="0">
<widget class="QLabel" name="label_subset_mode">
<property name="text">
<string>Outline</string>
<string>Subset:</string>
</property>
</widget>
</item>
Expand All @@ -108,42 +96,34 @@
</property>
</widget>
</item>
<item row="9" column="1">
<widget class="QRadioButton" name="radio_subset_data">
<item row="3" column="0">
<widget class="QLabel" name="label_color_mode">
<property name="text">
<string>Data</string>
<string>Color mode:</string>
</property>
</widget>
</item>
<item row="1" column="2" alignment="Qt::AlignHCenter">
<widget class="QToolButton" name="button_flip_limits">
<property name="styleSheet">
<string notr="true">padding: 0px</string>
<item row="6" column="1" colspan="2">
<widget class="QComboBox" name="combosel_stretch"/>
</item>
<item row="4" column="1" colspan="2">
<widget class="QColorBox" name="color_color">
<property name="sizePolicy">
<sizepolicy hsizetype="Preferred" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>⇄</string>
<string/>
</property>
</widget>
</item>
<item row="3" column="1" colspan="3">
<widget class="QComboBox" name="combotext_color_mode">
<property name="currentText">
<string>Fixed</string>
</property>
<property name="currentIndex">
<number>0</number>
</property>
<item>
<property name="text">
<string>Fixed</string>
</property>
</item>
<item>
<property name="text">
<string>Linear</string>
</property>
</item>
</widget>
<item row="1" column="1">
<widget class="QLineEdit" name="valuetext_vmin"/>
</item>
<item row="5" column="1" colspan="2">
<widget class="QColormapCombo" name="combodata_cmap"/>
</item>
<item row="10" column="1">
<spacer name="verticalSpacer">
Expand All @@ -158,6 +138,23 @@
</property>
</spacer>
</item>
<item row="0" column="1" colspan="2">
<widget class="QComboBox" name="combosel_attribute">
<property name="sizeAdjustPolicy">
<enum>QComboBox::AdjustToMinimumContentsLengthWithIcon</enum>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLabel" name="label_stretch">
<property name="text">
<string>Stretch</string>
</property>
</widget>
</item>
<item row="1" column="2" alignment="Qt::AlignLeft">
<widget class="QLineEdit" name="valuetext_vmax"/>
</item>
</layout>
</widget>
<customwidgets>
Expand Down
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