From e76fbf0b4b00121f1f4d7e10f6d1026172f91013 Mon Sep 17 00:00:00 2001
From: Matt McCormick <matt.mccormick@kitware.com>
Date: Sun, 19 Jan 2020 19:50:57 -0500
Subject: [PATCH] DOC: Use compare widget in notebooks

---
 examples/0_HelloRegistrationWorld.ipynb | 125 ++++++------------------
 examples/1_NumPyArray.ipynb             |  69 +++++--------
 examples/2_RegistrationParameters.ipynb |  60 +++---------
 3 files changed, 68 insertions(+), 186 deletions(-)

diff --git a/examples/0_HelloRegistrationWorld.ipynb b/examples/0_HelloRegistrationWorld.ipynb
index 67f0ac47..f8ed5d3b 100644
--- a/examples/0_HelloRegistrationWorld.ipynb
+++ b/examples/0_HelloRegistrationWorld.ipynb
@@ -9,12 +9,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
     "import itk\n",
-    "from itkwidgets import view, checkerboard"
+    "from itkwidgets import view, compare, checkerboard"
    ]
   },
   {
@@ -30,72 +30,33 @@
    "source": [
     "In image registration, we typically identify the two images as the fixed and moving image. Our goal is to find the spatial transformation that makes the moving image align with the fixed image.\n",
     "\n",
-    "First, let's load our **fixed image**."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fixed = itk.imread('data/CT_2D_head_fixed.mha', itk.F)"
+    "First, let's load our **fixed image** and the image we will align to our fixed image, the **moving image**."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 3,
    "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "e4158972d1a04e098425a4f40d0e7c4b",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "view(fixed, ui_collapsed=True)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "And the image we will align to our fixed image, the **moving image**."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
    "outputs": [],
    "source": [
+    "fixed = itk.imread('data/CT_2D_head_fixed.mha', itk.F)\n",
     "moving = itk.imread('data/CT_2D_head_moving.mha', itk.F)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "7a65180dd10d4e2ba85b81ade160e3ab",
+       "model_id": "b3ebeb5e96b64508a72580cd02bf86c3",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
       ]
      },
      "metadata": {},
@@ -103,7 +64,7 @@
     }
    ],
    "source": [
-    "view(moving, ui_collapsed=True)"
+    "compare(fixed, moving, ui_collapsed=True)"
    ]
   },
   {
@@ -115,13 +76,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "8c8f18d0f55344e7b3eb44b56a1f0bb6",
+       "model_id": "9c0aa44dab00479eb61af83594bab01a",
        "version_major": 2,
        "version_minor": 0
       },
@@ -139,7 +100,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -156,18 +117,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "ec232d21042e4f159272bec55c8a24a0",
+       "model_id": "30f9e21a18aa4ba3bbd0b07122785301",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
       ]
      },
      "metadata": {},
@@ -175,18 +136,18 @@
     }
    ],
    "source": [
-    "view(registered_moving, ui_collapsed=True)"
+    "compare(fixed, registered_moving, ui_collapsed=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a6e2d7c491ba4d50b45b35e03e85a475",
+       "model_id": "4aea9949acf8440d88d0e2106f41f21e",
        "version_major": 2,
        "version_minor": 0
       },
@@ -211,60 +172,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 11,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "92cdb0e11f354bd49916557e2d6be968",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "view(fixed)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
+    "fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)\n",
     "moving = itk.imread('data/CT_3D_lung_moving.mha', itk.F)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 13,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b52c532b5c724faaa5d22cbe4460a504",
+       "model_id": "3435f5147c574e35b581944cb40a3177",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=True, description='cmap'), Checkbox(va…"
       ]
      },
      "metadata": {},
@@ -272,18 +201,19 @@
     }
    ],
    "source": [
-    "view(moving)"
+    "# A human lung at different time points\n",
+    "compare(fixed, moving, link_cmap=True, link_gradient_opacity=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "103b7484068044fb84ed5f7911aad9d1",
+       "model_id": "b0bba114c9a44411880775350294b876",
        "version_major": 2,
        "version_minor": 0
       },
@@ -305,7 +235,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# With the default, conservative parameters, this can take a few minutes\n# on a low-compute-power system.\n",
+    "# With the default, conservative parameters, this can take a few minutes\n",
+    "# on a low-compute-power system.\n",
     "registered = itk.elastix_registration_method(fixed, moving)"
    ]
   },
diff --git a/examples/1_NumPyArray.ipynb b/examples/1_NumPyArray.ipynb
index 80fec27c..508f813e 100644
--- a/examples/1_NumPyArray.ipynb
+++ b/examples/1_NumPyArray.ipynb
@@ -9,14 +9,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
     "import itk\n",
     "import numpy as np\n",
     "import imageio\n",
-    "from itkwidgets import view, checkerboard"
+    "from itkwidgets import view, compare, checkerboard"
    ]
   },
   {
@@ -30,7 +30,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -39,7 +39,7 @@
        "numpy.ndarray"
       ]
      },
-     "execution_count": 2,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -52,31 +52,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "78f2904bb67d47acba76aa64a819ec1c",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "view(fixed, ui_collapsed=True)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {
@@ -85,7 +61,7 @@
        "numpy.ndarray"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -98,18 +74,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "bf30bacf63324268835c2f7adde53cca",
+       "model_id": "73d7960ef9194b41823abc916f85fad9",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
       ]
      },
      "metadata": {},
@@ -117,7 +93,7 @@
     }
    ],
    "source": [
-    "view(moving, ui_collapsed=True)"
+    "compare(fixed, moving, ui_collapsed=True)"
    ]
   },
   {
@@ -129,13 +105,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "efc57a3976414bddbf411285b209e7af",
+       "model_id": "6885b56476d74c1db2a58cedfe4da230",
        "version_major": 2,
        "version_minor": 0
       },
@@ -153,7 +129,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [
     {
@@ -162,7 +138,7 @@
        "numpy.ndarray"
       ]
      },
-     "execution_count": 11,
+     "execution_count": 8,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -175,18 +151,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "cfae6e764f134fe2ac0ef124ca5175e8",
+       "model_id": "b743e0733f84453db820d32a3ad9e718",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF2; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=False, description='cmap'), Checkbox(v…"
       ]
      },
      "metadata": {},
@@ -194,7 +170,7 @@
     }
    ],
    "source": [
-    "view(registered, ui_collapsed=True)"
+    "compare(fixed, registered, ui_collapsed=True)"
    ]
   },
   {
@@ -212,7 +188,7 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "b277130b1b2b46aa8336ee94872c9a24",
+       "model_id": "33eb1427d33a4c9293ac5c60ad74c2d3",
        "version_major": 2,
        "version_minor": 0
       },
@@ -227,6 +203,13 @@
    "source": [
     "checkerboard(fixed, registered, pattern=10)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {
diff --git a/examples/2_RegistrationParameters.ipynb b/examples/2_RegistrationParameters.ipynb
index e1354c95..e1fe938c 100644
--- a/examples/2_RegistrationParameters.ipynb
+++ b/examples/2_RegistrationParameters.ipynb
@@ -9,12 +9,12 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 29,
    "metadata": {},
    "outputs": [],
    "source": [
     "import itk\n",
-    "from itkwidgets import view, checkerboard"
+    "from itkwidgets import view, compare, checkerboard"
    ]
   },
   {
@@ -28,7 +28,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -37,17 +37,17 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 31,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Self (0x55e28544c5e0)\n",
+      "Self (0x55e2865a1e60)\n",
       "  RTTI typeinfo:   elastix::ParameterObject\n",
       "  Reference Count: 1\n",
-      "  Modified Time: 56\n",
+      "  Modified Time: 24798\n",
       "  Debug: Off\n",
       "  Object Name: \n",
       "  Observers: \n",
@@ -106,60 +106,28 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 5,
-   "metadata": {},
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "85298f1bfb5d40bcb220771e8f155595",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    }
-   ],
-   "source": [
-    "view(fixed)"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 32,
    "metadata": {},
    "outputs": [],
    "source": [
+    "fixed = itk.imread('data/CT_3D_lung_fixed.mha', itk.F)\n",
     "moving = itk.imread('data/CT_3D_lung_moving.mha', itk.F)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 33,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "9511aa67abc14a0d97c3fe7e29607618",
+       "model_id": "8d7dd936320443d6826241e66ffdcb0a",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "Viewer(geometries=[], gradient_opacity=0.22, point_sets=[], rendered_image=<itkImagePython.itkImageF3; proxy o…"
+       "AppLayout(children=(HBox(children=(Label(value='Link:'), Checkbox(value=True, description='cmap'), Checkbox(va…"
       ]
      },
      "metadata": {},
@@ -167,18 +135,18 @@
     }
    ],
    "source": [
-    "view(moving)"
+    "compare(fixed, moving, link_cmap=True, link_gradient_opacity=True)"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 34,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "a67097d976ae47adb5365419b32d2b9e",
+       "model_id": "cd073f8997944143afd3e585ce3c3c09",
        "version_major": 2,
        "version_minor": 0
       },