Merge pull request #437 from widgetti/feat_clip_volume

feat: allow clipping of volumetric renderings

Author: maartenbreddels

docs/source/conf.py

@@ -81,8 +81,8 @@
 # from https://github.com/ipython/ipywidgets/blob/master/docs/source/conf.py
 _release = {}
 exec(compile(open('../../ipyvolume/_version.py').read(), '../../ipyvolume/_version.py', 'exec'), _release)
-version = '.'.join(map(str, _release['__version_tuple__'][:2]))
 release = _release['__version__']
+version = ".".join(_release['__version__'].split(".")[:2])
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -386,5 +386,6 @@
     'examples/popup': 'examples/screenshot/ipyvolume-popup-legend-iris.gif',
     'examples/lighting': 'examples/screenshot/volume-rendering-specular.gif',
     'examples/slice': 'examples/screenshot/ipyvolume-slice-head.gif',
+    'examples/volume-clipping': 'examples/screenshot/volume-clip.gif',
 }
 exclude_patterns = ['**.ipynb_checkpoints']

docs/source/examples.rst

@@ -15,6 +15,8 @@ Examples
    examples/lighting
    examples/popup
    examples/slice
+   examples/slice
+   examples/volume-clipping
 
 Feel free to contribute new examples:
 

docs/source/examples/screenshot/volume-clip.gif

@@ -0,0 +1,90 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "580c6579",
+   "metadata": {},
+   "source": [
+    "# Clipping of volume\n",
+    "\n",
+    "In order to inspect volumetric renderings, it may be useful to remove parts of it. Using the `clip_x_min`, `clip_x_max`, `clip_y_min`, `clip_y_max`, `clip_z_min` and `clip_z_max` traits, we can control which part of the volume is rendered. In the example below you can use the sliders labels 'xmin' and 'xmax' to inspect regions inside the volume."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c7e47337",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ipyvolume as ipv\n",
+    "fig = ipv.figure()\n",
+    "volume = ipv.examples.head(show=False, description=\"Patient X\")\n",
+    "ipv.show()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "34ea1395",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import ipywidgets as w\n",
+    "clip_min = w.IntSlider(description=\"xmin\", min=0, max=128, value=50)\n",
+    "clip_max = w.IntSlider(description=\"xmax\", min=0, max=128, value=100)\n",
+    "w.jslink((clip_min, 'value'), (volume, 'clip_x_min'))\n",
+    "w.jslink((clip_max, 'value'), (volume, 'clip_x_max'))\n",
+    "container = ipv.gcc()\n",
+    "container.children = container.children + [clip_min, clip_max]\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "81702c3d",
+   "metadata": {},
+   "source": [
+    "Note that you can also link the instance the `slice_x` trait of the figure to the `clip_x_max` trait. Now we can hold the shift key and the clip plane will follow the mouse cursor."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "68b54115",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "w.jslink((fig, 'slice_x'), (volume, 'clip_x_max'));"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "22f48b7f",
+   "metadata": {},
+   "source": [
+    "[screencapture](screenshot/volume-clip.gif)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.16"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/source/examples/volume-clipping.ipynb

@@ -12,7 +12,9 @@
                 <v-expansion-panel>
                     <v-expansion-panel-header>Misc</v-expansion-panel-header>
                     <v-expansion-panel-content>
-                        <jupyter-widget v-for="child in children" :key="child" :widget="child"></jupyter-widget>
+                        <div>
+                            <jupyter-widget v-for="child in children" :key="child" :widget="child"></jupyter-widget>
+                        </div>
                     </v-expansion-panel-content>
                 </v-expansion-panel>
                 <v-expansion-panel>

ipyvolume/vue/container.vue

@@ -193,6 +193,13 @@ class Volume(widgets.Widget, LegendData):
     extent = traitlets.Any().tag(sync=True)
     extent_original = traitlets.Any()
 
+    clip_x_min = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+    clip_x_max = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+    clip_y_min = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+    clip_y_max = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+    clip_z_min = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+    clip_z_max = traitlets.CFloat(None, allow_none=True).tag(sync=True)
+
     def __init__(self, **kwargs):
         super(Volume, self).__init__(**kwargs)
         self._update_data()

ipyvolume/widgets.py

@@ -118,6 +118,9 @@ class VolumeView extends widgets.WidgetView {
             this.renderer.rebuild_multivolume_rendering_material();
             this.renderer.update();
         });
+        this.model.on("change:clip_x_min change:clip_x_max change:clip_y_min change:clip_y_max change:clip_z_min change:clip_z_max", () => {
+            this.renderer.update();
+        });
 
         (window as any).last_volume = this; // for debugging purposes
 
@@ -168,6 +171,7 @@ class VolumeModel extends widgets.WidgetModel {
     };
 
     volume: any;
+    scales?: any;
     texture_volume: THREE.DataTexture;
     uniform_volumes_values: {
         data_range?: any,
@@ -321,27 +325,42 @@ class VolumeModel extends widgets.WidgetModel {
         return this.get("rendering_method") === "NORMAL";
     }
     set_scales(scales) {
-        const sx = createD3Scale(scales.x).range([0, 1]);
-        const sy = createD3Scale(scales.y).range([0, 1]);
-        const sz = createD3Scale(scales.z).range([0, 1]);
+        this.scales = scales;
+        this.update_geometry();
+    }
+    update_geometry() {
+        const sx = createD3Scale(this.scales.x).range([0, 1]);
+        const sy = createD3Scale(this.scales.y).range([0, 1]);
+        const sz = createD3Scale(this.scales.z).range([0, 1]);
 
         const extent = this.get("extent");
 
-       // normalized coordinates of the corners of the box
+        // return v, of the clipped value
+        const or_clip = (v, name) => {
+            const clip_value = this.get("clip_" + name);
+            if ((clip_value === undefined) || (clip_value === null)) {
+                return v;
+            }
+            return clip_value;
+        }
+
+        // normalized coordinates of the corners of the box
         const x0n = sx(extent[0][0]);
         const x1n = sx(extent[0][1]);
         const y0n = sy(extent[1][0]);
         const y1n = sy(extent[1][1]);
         const z0n = sz(extent[2][0]);
         const z1n = sz(extent[2][1]);
 
-        // clipped coordinates
-        const cx0 = Math.max(x0n,  0);
-        const cx1 = Math.min(x1n,  1);
-        const cy0 = Math.max(y0n,  0);
-        const cy1 = Math.min(y1n,  1);
-        const cz0 = Math.max(z0n,  0);
-        const cz1 = Math.min(z1n,  1);
+        // normalized coordinates of the corners of the box
+        // including the custom clipping, and viewport clipping
+        const cx0 = Math.max(sx(or_clip(extent[0][0], "x_min")), 0);
+        const cx1 = Math.min(sx(or_clip(extent[0][1], "x_max")), 1);
+        const cy0 = Math.max(sy(or_clip(extent[1][0], "y_min")), 0);
+        const cy1 = Math.min(sy(or_clip(extent[1][1], "y_max")), 1);
+        const cz0 = Math.max(sz(or_clip(extent[2][0], "z_min")), 0);
+        const cz1 = Math.min(sz(or_clip(extent[2][1], "z_max")), 1);
+
 
         // the clipped coordinates back to world space, then normalized to extend
         // these are example calculations, the transform goes into scale and offset uniforms below