Add notebook to try some 3D visualizations

RobotLocomotion · May 14, 2020 · 9b81dbe · 9b81dbe
1 parent 28565ce
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diff --git a/.binder/Dockerfile b/.binder/Dockerfile
@@ -5,21 +5,36 @@
 # named "latest" is not allowed, however they do not (yet) enforce that
 # restriction.
 FROM robotlocomotion/drake:latest
+
 ARG NB_USER=jovyan
 ARG NB_UID=1000
 ARG NB_GID=100
 EXPOSE 7000/tcp
 EXPOSE 8888/tcp
 RUN export DEBIAN_FRONTEND=noninteractive \
   && apt-get update -qq \
-  && apt-get install --no-install-recommends -qq \
+  && apt-get install --no-install-recommends -qq python3-pip \
     -o Dpkg::Options::=--force-confdef -o Dpkg::Options::=--force-confnew \
     -o Dpkg::Use-Pty=0 \
       locales \
       xvfb \
   && rm -rf /var/lib/apt/lists/* \
   && locale-gen en_US.UTF-8 \
   && useradd -d "/home/$NB_USER" -G $NB_GID -mU -s /bin/bash "$NB_USER"
+
+RUN pip3 install wheel
+RUN pip3 install itkwidgets
+RUN pip3 install itk
+RUN pip3 install open3d==0.9.0
+RUN pip3 install pandas
+RUN pip3 install pyntcloud
+
+RUN jupyter nbextension install --py --symlink --sys-prefix itkwidgets
+RUN jupyter nbextension enable --py --sys-prefix itkwidgets
+RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
+RUN jupyter nbextension install --py --symlink --sys-prefix open3d
+RUN jupyter nbextension enable --py --sys-prefix open3d
+
 ENV HOME="/home/$NB_USER" \
   LANG=en_US.UTF-8 \
   LANGUAGE=en_US.UTF-8 \
@@ -34,6 +49,8 @@ COPY ["tutorials/*.ipynb", "$HOME/tutorials/"]
 RUN chown -R $NB_UID:$NB_GID \
   /opt/drake/bin/binder-entrypoint \
   "$HOME/tutorials"
+
+ENV PYTHONPATH="/home/jovyan/.local/lib/python3.6/site-packages:$PYTHONPATH"
 USER "$NB_USER"
 ENTRYPOINT ["/opt/drake/bin/binder-entrypoint"]
 CMD ["jupyter", "notebook", "--ip", "0.0.0.0"]
diff --git a/tutorials/3dvisualization_tests.ipynb b/tutorials/3dvisualization_tests.ipynb
@@ -0,0 +1,341 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# 3D Visualization Examples"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "See https://github.com/RobotLocomotion/drake/issues/12645"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add and show `itkwidgets`  examples\n",
+    "\n",
+    "Demonstrate a few `itkwidgets` widget examples inside of this notebook.\n",
+    "\n",
+    "See https://github.com/InsightSoftwareConsortium/itkwidgets"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Necessary Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Import for the itkwidgets examples\n",
+    "# Assumes itk and itkwidgets have been installed\n",
+    "\n",
+    "import os\n",
+    "from urllib.request import urlretrieve\n",
+    "\n",
+    "import itk\n",
+    "from itkwidgets import view\n",
+    "\n",
+    "import vtk"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Vtk poly data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download data\n",
+    "file_name = 'Bunny.vtp'\n",
+    "if not os.path.exists(file_name):\n",
+    "    url = 'https://data.kitware.com/api/v1/file/5d23b917877dfcc902def289/download'\n",
+    "    urlretrieve(url, file_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reader = vtk.vtkXMLPolyDataReader()\n",
+    "reader.SetFileName(file_name)\n",
+    "reader.Update()\n",
+    "bunny = reader.GetOutput()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view(geometries=bunny)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cone_source = vtk.vtkConeSource()\n",
+    "cone_source.SetResolution(20)\n",
+    "cone_source.Update()\n",
+    "cone = cone_source.GetOutput()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view(geometries=cone)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### 3D Image"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download data\n",
+    "file_name = '005_32months_T2_RegT1_Reg2Atlas_ManualBrainMask_Stripped.nrrd'\n",
+    "if not os.path.exists(file_name):\n",
+    "    url = 'https://data.kitware.com/api/v1/file/564a5b078d777f7522dbfaa6/download'\n",
+    "    urlretrieve(url, file_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "image = itk.imread(file_name)\n",
+    "view(image, rotate=True, vmin=4000, vmax=17000, gradient_opacity=0.4)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Mesh\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Download data\n",
+    "file_name = 'cow.vtk'\n",
+    "if not os.path.exists(file_name):\n",
+    "    url = 'https://data.kitware.com/api/v1/file/5aa18c268d777f06857863fe/download'\n",
+    "    urlretrieve(url, file_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mesh = itk.meshread(file_name)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "view(geometries=mesh)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add and show `open3d` example\n",
+    "\n",
+    "Demonstrate an open3d example inside of this notebook.\n",
+    "See http://www.open3d.org/docs/release/tutorial/Basic/working_with_numpy.html"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Necessary Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import open3d as o3d\n",
+    "from open3d import JVisualizer"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# generate some neat n times 3 matrix using a variant of sync function\n",
+    "x = np.linspace(-3, 3, 401)\n",
+    "mesh_x, mesh_y = np.meshgrid(x, x)\n",
+    "z = np.sinc((np.power(mesh_x, 2) + np.power(mesh_y, 2)))\n",
+    "z_norm = (z - z.min()) / (z.max() - z.min())\n",
+    "xyz = np.zeros((np.size(mesh_x), 3))\n",
+    "xyz[:, 0] = np.reshape(mesh_x, -1)\n",
+    "xyz[:, 1] = np.reshape(mesh_y, -1)\n",
+    "xyz[:, 2] = np.reshape(z_norm, -1)\n",
+    "\n",
+    "# Pass xyz to Open3D.o3d.geometry.PointCloud and visualize\n",
+    "pcd = o3d.geometry.PointCloud()\n",
+    "pcd.points = o3d.utility.Vector3dVector(xyz)\n",
+    "\n",
+    "# http://www.open3d.org/docs/release/tutorial/Basic/jupyter.html\n",
+    "visualizer = JVisualizer()\n",
+    "visualizer.add_geometry(pcd)\n",
+    "visualizer.show()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Add and show `pyntcloud` example\n",
+    "\n",
+    "https://github.com/daavoo/pyntcloud/blob/master/README.rst\n",
+    "\n",
+    "Example Binder link:\n",
+    "https://mybinder.org/v2/gh/daavoo/pyntcloud/master?filepath=examples/[visualization]%20Polylines.ipynb\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "### Necessary Imports"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from pyntcloud import PyntCloud"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "positions = np.random.rand(1000, 3) * 10\n",
+    "positions -= positions.mean(0)\n",
+    "\n",
+    "points = pd.DataFrame(\n",
+    "    positions.astype(np.float32), \n",
+    "    columns=['x', 'y', 'z'])\n",
+    "\n",
+    "points[\"red\"] = (np.random.rand(1000) * 255).astype(np.uint8)\n",
+    "points[\"green\"] = (np.random.rand(1000) * 255).astype(np.uint8)\n",
+    "points[\"blue\"] = (np.random.rand(1000) * 255).astype(np.uint8)\n",
+    "\n",
+    "cloud = PyntCloud(points)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "lines = [\n",
+    "    {\n",
+    "        \"color\": \"red\",\n",
+    "        \"vertices\": [[0, 0, 0], [10, 0, 0]]\n",
+    "    },\n",
+    "    {\n",
+    "        \"color\": \"green\",\n",
+    "        \"vertices\": [[0, 0, 0], [0, 10, 0]]\n",
+    "    },\n",
+    "    {\n",
+    "        \"color\": \"blue\",\n",
+    "        \"vertices\": [[0, 0, 0], [0, 0, 10]]\n",
+    "    }\n",
+    "]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "cloud.plot(polylines=lines)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.6.9"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}