Created
August 24, 2023 14:42
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| { | |
| "cells": [ | |
| { | |
| "cell_type": "code", | |
| "execution_count": 1, | |
| "id": "a578193d-4ad4-42d7-9931-24cd43fdc469", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "import itk\n", | |
| "from itk import RTK as rtk\n", | |
| "import numpy as np" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 2, | |
| "id": "f5b214ba-8e42-48ae-9640-8358c7911026", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "volumeFName = \"myVolume.nrrd\"\n", | |
| "\n", | |
| "# Load CT Image\n", | |
| "CT = itk.imread(volumeFName, pixel_type=itk.F)\n", | |
| "\n", | |
| "# Direction control\n", | |
| "direction=np.array([[0.,1.,0.],[0.,0.,1.],[-1.,0.,0.]])\n", | |
| "CT.SetDirection(itk.matrix_from_array(direction))\n", | |
| "\n", | |
| "# Set the origin to be around 0 - center of rotation\n", | |
| "CT.SetOrigin([-0.5*(CT.GetLargestPossibleRegion().GetSize()[1]-1)*CT.GetSpacing()[1],\n", | |
| " -0.5*(CT.GetLargestPossibleRegion().GetSize()[2]-1)*CT.GetSpacing()[2],\n", | |
| " 0.5*(CT.GetLargestPossibleRegion().GetSize()[0]-1)*CT.GetSpacing()[0]])\n", | |
| "\n", | |
| "# Define the Image Type\n", | |
| "ImageType = itk.Image[itk.F,3]" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 3, | |
| "id": "07b5b12e-05ad-4c1f-beef-12960ff7aee7", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Empty Projection Stack\n", | |
| "ConstantImageSourceType = rtk.ConstantImageSource[ImageType]\n", | |
| "constantImageSource = ConstantImageSourceType.New()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 4, | |
| "id": "3e4bc5c0-253a-4483-92f8-e3424cf1ccc1", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# Define the origin, size, and spacing of the projection stack \n", | |
| "# Need to automatically get/calculate this info from the CT data\n", | |
| "origin = [-200, -200, -500.]\n", | |
| "nProjections = 360\n", | |
| "size = [1000,1000,nProjections]\n", | |
| "spacing = [0.39625,0.39625,0.625]\n", | |
| "\n", | |
| "constantImageSource.SetOrigin(origin)\n", | |
| "constantImageSource.SetSpacing(spacing)\n", | |
| "constantImageSource.SetSize(size)\n", | |
| "constantImageSource.SetConstant(0.)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 5, | |
| "id": "9c76cd79-83d6-473e-a900-bdf3f060e478", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "# RTK geometry\n", | |
| "geo = rtk.ThreeDCircularProjectionGeometry.New()\n", | |
| "firstAngle = 0.\n", | |
| "angularArc = 360.\n", | |
| "# Pull SID and SDD from Dicom Headers\n", | |
| "sid = 541 # Source to Isocenter Distance\n", | |
| "sdd = 949.075 # Source to Detector Distance\n", | |
| "\n", | |
| "for x in range(0,nProjections):\n", | |
| " angle = firstAngle + x * angularArc / nProjections\n", | |
| " geo.AddProjection(sid,sdd,angle)" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 6, | |
| "id": "4d19f728-963d-48b1-85b6-1aa050ebfb81", | |
| "metadata": {}, | |
| "outputs": [ | |
| { | |
| "data": { | |
| "text/plain": [ | |
| "0" | |
| ] | |
| }, | |
| "execution_count": 6, | |
| "metadata": {}, | |
| "output_type": "execute_result" | |
| } | |
| ], | |
| "source": [ | |
| "# Writing the geometry to disk\n", | |
| "xmlWriter = rtk.ThreeDCircularProjectionGeometryXMLFileWriter.New()\n", | |
| "xmlWriter.SetFilename ( 'geo.xml' )\n", | |
| "xmlWriter.SetObject ( geo )\n", | |
| "xmlWriter.WriteFile()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 7, | |
| "id": "d0a6c2c6-24cf-4af7-813e-d9b0bf31e960", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "JFPType = rtk.JosephForwardProjectionImageFilter[ImageType, ImageType]\n", | |
| "jfp = JFPType.New()\n", | |
| "\n", | |
| "jfp.SetGeometry(geo)\n", | |
| "jfp.SetInput(0,constantImageSource.GetOutput())\n", | |
| "jfp.SetInput(1,CT)\n", | |
| "jfp.Update()" | |
| ] | |
| }, | |
| { | |
| "cell_type": "code", | |
| "execution_count": 8, | |
| "id": "efc1c05b-5d8a-42f9-9e63-1e4aefb475c3", | |
| "metadata": {}, | |
| "outputs": [], | |
| "source": [ | |
| "itk.imwrite(jfp.GetOutput(), 'stack.tif')" | |
| ] | |
| } | |
| ], | |
| "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": "3.11.4" | |
| } | |
| }, | |
| "nbformat": 4, | |
| "nbformat_minor": 5 | |
| } |
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