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ENH: Add ipynb examples Transformix, image, mesh, TranslationTransform
Added examples on how to use recently added TransformixFilter member functions, `SetTransform`, `SetInputMesh`, and `GetOutputMesh`.
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examples/ITK_Example15_Transformix_image_TranslationTransform.ipynb
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,127 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "4ba94dda", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Minimal example on how to transform an image, using TransformixFilter with TranslationTransform" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 3, | ||
| "id": "852e83ee", | ||
| "metadata": { | ||
| "scrolled": true | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Moving image:\n", | ||
| " 1 2 3 4 5 \n", | ||
| " 6 7 8 9 10 \n", | ||
| "11 12 13 14 15 \n", | ||
| "16 17 18 19 20 \n", | ||
| "21 22 23 24 25 \n", | ||
| "26 27 28 29 30 \n", | ||
| "\n", | ||
| "Creating a TransformixFilter (might take a while, please wait)...\n", | ||
| "\n", | ||
| "Output image:\n", | ||
| " 0 0 0 0 0 \n", | ||
| " 0 0 0 0 0 \n", | ||
| " 2 3 4 5 0 \n", | ||
| " 7 8 9 10 0 \n", | ||
| "12 13 14 15 0 \n", | ||
| "17 18 19 20 0 \n", | ||
| "\n" | ||
| ] | ||
| } | ||
| ], | ||
| "source": [ | ||
| "import itk\n", | ||
| "\n", | ||
| "def print_image(image):\n", | ||
| " image_size = image.GetBufferedRegion().GetSize()\n", | ||
| " for row in range(image_size[1]):\n", | ||
| " for column in range(image_size[0]):\n", | ||
| " print('{:>2}'.format(int(image.GetPixel([column, row]))), ' ', end='')\n", | ||
| " print() \n", | ||
| " print()\n", | ||
| "\n", | ||
| "transform = itk.TranslationTransform.New()\n", | ||
| "transform.SetOffset([1, -2])\n", | ||
| "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_image(moving_image)\n", | ||
| "\n", | ||
| "input_mesh = itk.Mesh[itk.F, 2].New()\n", | ||
| "input_mesh.SetPoint(0, [0.0, 0.0])\n", | ||
| "input_mesh.SetPoint(1, [1.0, 2.0])\n", | ||
| "\n", | ||
| "print('Creating a TransformixFilter (might take a while, please wait)...\\n')\n", | ||
| "transformix_filter = itk.TransformixFilter[ImageType].New()\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\"]\n", | ||
| "\n", | ||
| "parameter_object = itk.ParameterObject.New()\n", | ||
| "parameter_object.AddParameterMap(parameter_map)\n", | ||
| "\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_image(output_image)" | ||
| ] | ||
| } | ||
| ], | ||
| "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 | ||
| } |
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examples/ITK_Example16_Transformix_mesh_TranslationTransform.ipynb
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|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "fe72d689", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Minimal example on how to transform a mesh of points, using TransformixFilter with TranslationTransform" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": 8, | ||
| "id": "852e83ee", | ||
| "metadata": { | ||
| "scrolled": true | ||
| }, | ||
| "outputs": [ | ||
| { | ||
| "name": "stdout", | ||
| "output_type": "stream", | ||
| "text": [ | ||
| "Input Mesh:\n", | ||
| "itkPointF2 ([0, 0]) itkPointF2 ([0, 1]) itkPointF2 ([1, 0]) \n", | ||
| "\n", | ||
| "Creating a TransformixFilter (might take a while, please wait)...\n", | ||
| "\n", | ||
| "Output Mesh:\n", | ||
| "itkPointF2 ([0.03125, 0.0625]) itkPointF2 ([0.03125, 1.0625]) itkPointF2 ([1.03125, 0.0625]) \n", | ||
| "\n" | ||
| ] | ||
| } | ||
| ], | ||
| "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", | ||
| "transform = itk.TranslationTransform.New()\n", | ||
| "transform.SetOffset([0.03125, 0.0625])\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", | ||
| "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", | ||
| "print('Creating a TransformixFilter (might take a while, please wait)...\\n')\n", | ||
| "transformix_filter = itk.TransformixFilter[ImageType].New()\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\"]\n", | ||
| "\n", | ||
| "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 | ||
| } |