ENH: Add ipynb examples Transformix, image, mesh, TranslationTransform

Added examples on how to use recently added TransformixFilter member functions, `SetTransform`, `SetInputMesh`, and `GetOutputMesh`.
InsightSoftwareConsortium · Nov 7, 2022 · db606f8 · db606f8
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diff --git a/examples/ITK_Example15_Transformix_image_TranslationTransform.ipynb b/examples/ITK_Example15_Transformix_image_TranslationTransform.ipynb
@@ -0,0 +1,146 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "4ba94dda",
+   "metadata": {},
+   "source": [
+    "# Minimal example on how to transform an image, using TransformixFilter with TranslationTransform"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5fc4a7b9",
+   "metadata": {},
+   "source": [
+    "This example shows how to transform an image, using `itk.TransformixFilter` with `itk.TranslationTransform`.\n",
+    "\n",
+    "Start by importing packages and creating an TransformixFilter object:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "852e83ee",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "import itk\n",
+    "import numpy as np\n",
+    "\n",
+    "print('Creating a TransformixFilter (might take a while, please wait)...\\n')\n",
+    "transformix_filter = itk.TransformixFilter[ImageType].New()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "65d4e03c",
+   "metadata": {},
+   "source": [
+    "Create the example input: a small (5x6) image, a translation (1, -2), and a rather trivial parameter map.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9fbb7de3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ImageType = itk.Image[itk.F, 2]\n",
+    "\n",
+    "number_of_columns = 5\n",
+    "number_of_rows = 6\n",
+    "\n",
+    "moving_image = ImageType.New()\n",
+    "moving_image.SetRegions([number_of_columns, number_of_rows])\n",
+    "moving_image.Allocate(True)\n",
+    "\n",
+    "# Set the pixel values consecutively to 1, 2, 3, ..., n.\n",
+    "pixel_value = 0\n",
+    "for row in range(number_of_rows):\n",
+    "    for column in range(number_of_columns):\n",
+    "        pixel_value += 1\n",
+    "        moving_image.SetPixel([column, row], pixel_value)\n",
+    "\n",
+    "print('Moving image:')\n",
+    "print(np.asarray(output_image))\n",
+    "print()\n",
+    "\n",
+    "translation = [1, -2]\n",
+    "print('Translation:', translation)\n",
+    "\n",
+    "transform = itk.TranslationTransform.New()\n",
+    "transform.SetOffset(translation)\n",
+    "\n",
+    "parameter_map = itk.elxParameterObjectPython.mapstringvectorstring()\n",
+    "parameter_map[\"Direction\"] = [\"1\", \"0\", \"0\", \"1\"]\n",
+    "parameter_map[\"Index\"] = [\"0\", \"0\"]\n",
+    "parameter_map[\"Origin\"] = [\"0\", \"0\"]\n",
+    "parameter_map[\"Size\"] = [str(number_of_columns), str(number_of_rows)]\n",
+    "parameter_map[\"Spacing\"] = [\"1\", \"1\"]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2947cf4a",
+   "metadata": {},
+   "source": [
+    "Pass the example input to the TransformixFilter object, apply the transformation, and retrieve the output image. Ready!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "26f9394e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "parameter_object = itk.ParameterObject.New()\n",
+    "parameter_object.AddParameterMap(parameter_map)\n",
+    "\n",
+    "transformix_filter.SetMovingImage(moving_image)\n",
+    "transformix_filter.SetTransformParameterObject(parameter_object)\n",
+    "transformix_filter.SetTransform(transform)\n",
+    "transformix_filter.Update()\n",
+    "\n",
+    "output_image = transformix_filter.GetOutput()\n",
+    "\n",
+    "print('Output image:')\n",
+    "print(np.asarray(output_image))\n",
+    "print()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f4832730",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "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": "3.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/examples/ITK_Example16_Transformix_mesh_TranslationTransform.ipynb b/examples/ITK_Example16_Transformix_mesh_TranslationTransform.ipynb
@@ -0,0 +1,136 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "fe72d689",
+   "metadata": {},
+   "source": [
+    "# Minimal example on how to transform a mesh of points, using TransformixFilter with TranslationTransform"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2ef87562",
+   "metadata": {},
+   "source": [
+    "This example shows how to transform a mesh, using `itk.TransformixFilter` with `itk.TranslationTransform`.\n",
+    "\n",
+    "Start by importing packages, defining a little print helper function, and creating an TransformixFilter object:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "852e83ee",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "import itk\n",
+    "\n",
+    "def print_mesh(mesh):\n",
+    "    for i in range(mesh.GetNumberOfPoints()):\n",
+    "            print(mesh.GetPoint(i), ' ', end='')\n",
+    "    print()    \n",
+    "    print()    \n",
+    "    \n",
+    "print('Creating a TransformixFilter (might take a while, please wait)...\\n')\n",
+    "transformix_filter = itk.TransformixFilter[ImageType].New()\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b09bb751",
+   "metadata": {},
+   "source": [
+    "Create the example input: a mesh of three points, a small translation (0.03125, 0.0625), a \"dummy\" (1x1) image, and a rather trivial parameter map."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "539fc713",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "input_mesh = itk.Mesh[itk.F, 2].New()\n",
+    "input_mesh.SetPoint(0, [0.0, 0.0])\n",
+    "input_mesh.SetPoint(1, [0.0, 1.0])\n",
+    "input_mesh.SetPoint(2, [1.0, 0.0])\n",
+    "\n",
+    "print('Input Mesh:')\n",
+    "print_mesh(input_mesh)\n",
+    "\n",
+    "translation = [0.03125, 0.0625]\n",
+    "print('Translation:', translation)\n",
+    "\n",
+    "transform = itk.TranslationTransform.New()\n",
+    "transform.SetOffset(translation)\n",
+    "ImageType = itk.Image[itk.F, 2]\n",
+    "\n",
+    "# A moving image is required for TransformixFilter, just create a very small one.\n",
+    "moving_image = ImageType.New()\n",
+    "moving_image.SetRegions([1, 1])\n",
+    "moving_image.Allocate(True)\n",
+    "\n",
+    "parameter_map = itk.elxParameterObjectPython.mapstringvectorstring()\n",
+    "parameter_map[\"Direction\"] = [\"1\", \"0\", \"0\", \"1\"]\n",
+    "parameter_map[\"Index\"] = [\"0\", \"0\"]\n",
+    "parameter_map[\"Origin\"] = [\"0\", \"0\"]\n",
+    "parameter_map[\"Size\"] = [\"1\", \"1\"]\n",
+    "parameter_map[\"Spacing\"] = [\"1\", \"1\"]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3c1541e7",
+   "metadata": {},
+   "source": [
+    "Pass the example input to the TransformixFilter object, apply the transformation, and retrieve the output mesh. Ready!"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "606a65b9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "parameter_object = itk.ParameterObject.New()\n",
+    "parameter_object.AddParameterMap(parameter_map)\n",
+    "\n",
+    "transformix_filter.SetMovingImage(moving_image)\n",
+    "transformix_filter.SetTransformParameterObject(parameter_object)\n",
+    "transformix_filter.SetTransform(transform)\n",
+    "transformix_filter.SetInputMesh(input_mesh)\n",
+    "transformix_filter.Update()\n",
+    "\n",
+    "output_mesh = transformix_filter.GetOutputMesh()\n",
+    "print('Output Mesh:')\n",
+    "print_mesh(output_mesh)"
+   ]
+  }
+ ],
+ "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": "3.7.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}