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ENH: Added ImageMomentsCalculator test and Jupyter example.
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‎src/Filtering/ImageStatistics/CMakeLists.txt

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@@ -45,3 +45,5 @@ add_example(ComputeMinMaxVarianceMeanOfImage)
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#compare_to_baseline(EXAMPLE_NAME StatisticalPropertiesOfRegions
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# BASELINE_PREFIX OutputBaseline
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# )
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add_example(CalculateImageMoments)

‎src/Filtering/ImageStatistics/CalculateImageMoments/CMakeLists.txt

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cmake_minimum_required(VERSION 3.10.2)
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project( CalculateImageMoments )
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find_package( ITK REQUIRED )
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include( ${ITK_USE_FILE} )
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add_executable( CalculateImageMoments Code.cxx )
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target_link_libraries( CalculateImageMoments ${ITK_LIBRARIES} )
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install( TARGETS CalculateImageMoments
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DESTINATION bin/ITKExamples/Filtering/ImageStatistics
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COMPONENT Runtime
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)
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install( FILES Code.cxx CMakeLists.txt Code.py
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DESTINATION share/ITKExamples/Code/Filtering/ImageStatistics/CalculateImageMoments
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COMPONENT Code
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)
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enable_testing()
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set(input_image ${CMAKE_CURRENT_BINARY_DIR}/ellipse.mha)
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add_test( NAME CalculateImageMomentsTest
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COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CalculateImageMoments
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${input_image}
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)
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if( ITK_WRAP_PYTHON )
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find_package(PythonInterp REQUIRED)
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string( REPLACE . "Python." output_image "${output_image}" )
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add_test( NAME CalculateImageMomentsTestPython
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COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
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${input_image}
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)
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endif()

‎src/Filtering/ImageStatistics/CalculateImageMoments/CalculateEllipseMoments.ipynb

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 9,
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"id": "protecting-hobby",
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"metadata": {},
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"outputs": [],
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"source": [
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"import itk\n",
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"import matplotlib.pyplot as plt\n",
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"import numpy as np\n",
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"from ipywidgets import interact"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 32,
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"id": "dried-demographic",
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"metadata": {},
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"outputs": [
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{
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"data": {
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"application/vnd.jupyter.widget-view+json": {
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"model_id": "12ddf6ab0ad54db19849293d0d20c252",
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"version_major": 2,
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"version_minor": 0
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},
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"text/plain": [
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"interactive(children=(IntSlider(value=30, description='tx'), IntSlider(value=50, description='ty'), IntSlider(…"
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]
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},
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"metadata": {},
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"output_type": "display_data"
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}
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],
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"source": [
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"output_size = [100, 100] # size of binary image containing the ellipse\n",
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"\n",
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"@interact(tx=(0,output_size[0],1), ty=(0,output_size[1],1), a=(5,50,1), b=(5,50,1), theta=(0,2*np.pi,0.1))\n",
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"def foo(tx=30, ty=50, a=5, b=10, theta=np.pi/4.0):\n",
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" '''\n",
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" Creates a binary image of an ellipse and calculates the image moments. Major (purple) and minor (green)\n",
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" principal axes are displayed.\n",
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" \n",
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" Parameters\n",
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" ==========\n",
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" tx, ty : translation x and y\n",
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" a, b : ellipse horizontal and vertical widths before rotation\n",
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" theta : angle of rotation (radians)\n",
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" '''\n",
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" \n",
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" # ellipse starts as unit circle, use world transform to define final ellipse\n",
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" ellipse = itk.EllipseSpatialObject[2].New()\n",
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" ellipse_transform = itk.AffineTransform[itk.D, 2].New()\n",
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" ellipse_transform.Scale([a, b])\n",
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" ellipse_transform.Rotate2D(theta)\n",
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" ellipse_transform.Translate([tx, ty])\n",
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" ellipse.SetObjectToWorldTransform(ellipse_transform)\n",
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"\n",
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" ellipse_img = itk.spatial_object_to_image_filter(input=ellipse, inside_value=1, outside_value=0, size=output_size)\n",
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"\n",
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" momentor = itk.ImageMomentsCalculator.New(Image=ellipse_img)\n",
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" momentor.Compute()\n",
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"\n",
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" centroid = momentor.GetCenterOfGravity()\n",
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" prin_axes = itk.array_from_matrix(momentor.GetPrincipalAxes())\n",
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" minor_axes = prin_axes[0]\n",
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" major_axes = prin_axes[1]\n",
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"\n",
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" fig, ax = plt.subplots(figsize=[8,8])\n",
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" plt.imshow(ellipse_img, cmap='gray')\n",
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" plt.scatter(centroid[0], centroid[1])\n",
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"\n",
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" minor_pt = centroid + minor_axes*5\n",
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" plt.plot([centroid[0], minor_pt[0]], [centroid[1], minor_pt[1]], color='green')\n",
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"\n",
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" major_pt = centroid + major_axes*5\n",
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" plt.plot([centroid[0], major_pt[0]], [centroid[1], major_pt[1]], color='purple')\n",
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"\n",
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" print(momentor)\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "several-label",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.7.6"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}

‎src/Filtering/ImageStatistics/CalculateImageMoments/Code.cxx

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/*=========================================================================
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*
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* Copyright NumFOCUS
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0.txt
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*
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*=========================================================================*/
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#include "itkImageFileReader.h"
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#include "itkImageFileWriter.h"
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#include "itkImageMomentsCalculator.h"
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int
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main(int argc, char * argv[])
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{
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if (argc != 2)
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{
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std::cerr << "Usage: " << std::endl;
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std::cerr << argv[0];
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std::cerr << " <InputFileName>" << std::endl;
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std::cerr << "Prints image moments from unsigned short binary image.";
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std::cerr << std::endl;
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return EXIT_FAILURE;
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}
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const char * inputFileName = argv[1];
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constexpr unsigned int Dimension = 2;
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using PixelType = unsigned short;
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using ImageType = itk::Image<PixelType, Dimension>;
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using ReaderType = itk::ImageFileReader<ImageType>;
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ReaderType::Pointer reader = ReaderType::New();
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reader->SetFileName(inputFileName);
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reader->Update();
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// clang-format off
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using FilterType = itk::ImageMomentsCalculator<ImageType>;
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// clang-format on
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FilterType::Pointer filter = FilterType::New();
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filter->SetImage(reader->GetOutput());
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filter->Compute();
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filter->Print(std::cout, 0);
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return EXIT_SUCCESS;
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}

‎src/Filtering/ImageStatistics/CalculateImageMoments/Code.py

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#!/usr/bin/env python
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# Copyright NumFOCUS
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0.txt
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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import sys
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import itk
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import argparse
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if len(sys.argv) != 2:
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print("Usage: " + sys.argv[0] + "<InputFileName>")
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print("Prints image moment information from binary image.")
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sys.exit(1)
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parser = argparse.ArgumentParser(description="Calculate Image Moments.")
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parser.add_argument("input_image")
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args = parser.parse_args()
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input_image = itk.imread(args.input_image)
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momentor = itk.ImageMomentsCalculator.New(Image=input_image)
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momentor.Compute()
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print(momentor)

‎src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst

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Calculate Image Moments
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================================
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.. index::
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single: ImageMomentsCalculator
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Synopsis
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--------
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Calculate image moments from binary images and an interactive ellipse.
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Results
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-------
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.. figure:: ellipse.mha
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:scale: 50%
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:alt: Input image
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Input Image
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::
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Output
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ImageMomentsCalculator (000002037138BE90)
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RTTI typeinfo: class itk::ImageMomentsCalculator<class itk::Image<unsigned short,2> >
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Reference Count: 1
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Modified Time: 249
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Debug: Off
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Object Name:
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Observers:
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none
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Image: 000002037138FDD0
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Valid: 1
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Zeroth Moment about origin: 153
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First Moment about origin: [30, 50]
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Second Moment about origin: 15.0458 -8.8366
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-8.8366 15.0458
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Center of Gravity: [30, 50]
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Second central moments: 15.0458 -8.8366
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-8.8366 15.0458
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Principal Moments: [950, 3654]
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Principal axes: 0.707107 0.707107
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-0.707107 0.707107
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::
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Jupyter Notebook
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-----------------
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.. image:: https://mybinder.org/badge_logo.svg
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:target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKExamples/master?filepath=src%2FFiltering%2FImageStatistics%2FImageMomentsCalculator%2FCalculateEllipseMoments.ipynb
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Code
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----
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C++
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...
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.. literalinclude:: Code.cxx
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:language: c++
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:lines: 18-
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Python
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......
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.. literalinclude:: Code.py
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:language: python
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:lines: 1,16-
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Classes demonstrated
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--------------------
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.. breathelink:: itk::ImageMomentsCalculator

‎src/Filtering/ImageStatistics/CalculateImageMoments/ellipse.mha.sha512

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a9dc7abe4d5745de06491d21addb54f561619732d71c98f250447c4fcf2c1444a60badbebaa3d646913e82fff75bfc753e2495c2d672d5bd7f85860fb8f8da0c

‎src/Filtering/ImageStatistics/index.rst

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ComputeMinMaxVarianceMeanOfImage/Documentation.rst
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ComputePCAShapeFromSample/Documentation.rst
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StatisticalPropertiesOfRegions/Documentation.rst
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CalculateImageMoments/Documentation.rst

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