ENH: Added ImageMomentsCalculator test and Jupyter example.

Utilities/CookieCutter/{{cookiecutter.example_name}}/Code.py

@@ -17,18 +17,15 @@
 import sys
 import itk
 
-if len(sys.argv) != 3:
-    print("Usage: " + sys.argv[0] + "<InputFileName> "
-          "<OutputFileName>")
-    sys.exit(1)
-
-parser = argparse.ArgumentParser(description='{{ cookiecutter.example_title }}.')
-parser.add_argument('input_image')
-parser.add_argument('output_image')
+parser = argparse.ArgumentParser(description="{{ cookiecutter.example_title }}.")
+parser.add_argument("input_image")
+parser.add_argument("output_image")
 args = parser.parse_args()
 
 input_image = itk.imread(args.input_image)
 
-output_image = itk.itkHelpers.camel_to_snake_case({{ cookiecutter.class_name }})(input_image)
+output_image = itk.itkHelpers.camel_to_snake_case({{cookiecutter.class_name}})(
+    input_image
+)
 
 itk.imwrite(output_image, args.output_image)

Utilities/CookieCutter/{{cookiecutter.example_name}}/Documentation.rst

@@ -30,19 +30,20 @@ Results
 Code
 ----
 
+Python
+......
+
+.. literalinclude:: Code.py
+   :language: python
+   :lines: 1,16-
+
 C++
 ...
 
 .. literalinclude:: Code.cxx
    :language: c++
    :lines: 18-
 
-Python
-......
-
-.. literalinclude:: Code.py
-   :language: python
-   :lines: 1,16-
 
 
 Classes demonstrated

src/Core/Common/IterateRegionWithAccessToIndexWithoutWriteAccess/Code.cxx

@@ -53,7 +53,7 @@ main(int argc, char * argv[])
   region.SetSize(regionSize);
   region.SetIndex(regionIndex);
 
-  itk::ImageRegionConstIteratorWithIndex<ImageType> imageIterator(image, image->GetLargestPossibleRegion());
+  itk::ImageRegionConstIteratorWithIndex<ImageType> imageIterator(image, region);
 
   while (!imageIterator.IsAtEnd())
   {

src/Filtering/ImageStatistics/CMakeLists.txt

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

src/Filtering/ImageStatistics/CalculateImageMoments/CMakeLists.txt

@@ -0,0 +1,36 @@
+cmake_minimum_required(VERSION 3.10.2)
+
+project( CalculateImageMoments )
+
+find_package( ITK REQUIRED )
+include( ${ITK_USE_FILE} )
+
+add_executable( CalculateImageMoments Code.cxx )
+target_link_libraries( CalculateImageMoments ${ITK_LIBRARIES} )
+
+install( TARGETS CalculateImageMoments
+  DESTINATION bin/ITKExamples/Filtering/ImageStatistics
+  COMPONENT Runtime
+)
+
+install( FILES Code.cxx CMakeLists.txt Code.py
+  DESTINATION share/ITKExamples/Code/Filtering/ImageStatistics/CalculateImageMoments
+  COMPONENT Code
+)
+
+enable_testing()
+
+set(input_image ${CMAKE_CURRENT_BINARY_DIR}/ellipse.mha)
+
+add_test( NAME CalculateImageMomentsTest
+  COMMAND ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CalculateImageMoments
+  ${input_image}
+)
+
+if( ITK_WRAP_PYTHON )
+  find_package(PythonInterp REQUIRED)
+  add_test( NAME CalculateImageMomentsTestPython
+    COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
+      ${input_image}
+    )
+endif()

src/Filtering/ImageStatistics/CalculateImageMoments/CalculateEllipseMoments.ipynb

@@ -0,0 +1,126 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "revolutionary-headquarters",
+   "metadata": {},
+   "source": [
+    "# Calculate Image Moments of an Ellipse\n",
+    "\n",
+    "Image moments can be used to determine the center of gravity or average pixel location of a binary object as well as the orientation of an object according to its axes of variation.\n",
+    "\n",
+    "The interactive plot below demonstrates how to calculate the image moments of an ellipse-defined mask."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "amino-atlantic",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import itk\n",
+    "import matplotlib.pyplot as plt\n",
+    "import numpy as np\n",
+    "from ipywidgets import interact"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "domestic-jenny",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "9460aeb87fea499c90c4e301da10ddce",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "interactive(children=(IntSlider(value=30, description='tx'), IntSlider(value=50, description='ty'), IntSlider(…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "output_size = [100, 100] # size of binary image containing the ellipse\n",
+    "\n",
+    "@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",
+    "def foo(tx=30, ty=50, a=5, b=10, theta=np.pi/4.0):\n",
+    "    '''\n",
+    "    Creates a binary image of an ellipse and calculates the image moments.  Major (purple) and minor (green)\n",
+    "    principal axes are displayed.\n",
+    "    \n",
+    "    Parameters\n",
+    "    ==========\n",
+    "    tx, ty : translation x and y\n",
+    "    a, b : ellipse horizontal and vertical widths before rotation\n",
+    "    theta : angle of rotation (radians)\n",
+    "    '''\n",
+    "    \n",
+    "    # ellipse starts as unit circle, use world transform to define final ellipse\n",
+    "    ellipse = itk.EllipseSpatialObject[2].New()\n",
+    "    ellipse_transform = itk.AffineTransform[itk.D, 2].New()\n",
+    "    ellipse_transform.Scale([a, b])\n",
+    "    ellipse_transform.Rotate2D(theta)\n",
+    "    ellipse_transform.Translate([tx, ty])\n",
+    "    ellipse.SetObjectToWorldTransform(ellipse_transform)\n",
+    "\n",
+    "    ellipse_img = itk.spatial_object_to_image_filter(input=ellipse, inside_value=1, outside_value=0, size=output_size)\n",
+    "\n",
+    "    momentor = itk.ImageMomentsCalculator.New(Image=ellipse_img)\n",
+    "    momentor.Compute()\n",
+    "\n",
+    "    centroid = momentor.GetCenterOfGravity()\n",
+    "    prin_axes = itk.array_from_matrix(momentor.GetPrincipalAxes())\n",
+    "    minor_axes = prin_axes[0]\n",
+    "    major_axes = prin_axes[1]\n",
+    "\n",
+    "    fig, ax = plt.subplots(figsize=[8,8])\n",
+    "    plt.imshow(ellipse_img, cmap='gray')\n",
+    "    plt.scatter(centroid[0], centroid[1])\n",
+    "\n",
+    "    minor_pt = centroid + minor_axes*5\n",
+    "    plt.plot([centroid[0], minor_pt[0]], [centroid[1], minor_pt[1]], color='green')\n",
+    "\n",
+    "    major_pt = centroid + major_axes*5\n",
+    "    plt.plot([centroid[0], major_pt[0]], [centroid[1], major_pt[1]], color='purple')\n",
+    "\n",
+    "    print(momentor)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "seasonal-sandwich",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "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": "3.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

src/Filtering/ImageStatistics/CalculateImageMoments/Code.cxx

@@ -0,0 +1,56 @@
+/*=========================================================================
+ *
+ *  Copyright NumFOCUS
+ *
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *
+ *         http://www.apache.org/licenses/LICENSE-2.0.txt
+ *
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and
+ *  limitations under the License.
+ *
+ *=========================================================================*/
+
+#include "itkImageFileReader.h"
+#include "itkImageFileWriter.h"
+#include "itkImageMomentsCalculator.h"
+
+int
+main(int argc, char * argv[])
+{
+  if (argc != 2)
+  {
+    std::cerr << "Usage: " << std::endl;
+    std::cerr << argv[0];
+    std::cerr << " <InputFileName>" << std::endl;
+    std::cerr << "Prints image moments from unsigned short binary image.";
+    std::cerr << std::endl;
+    return EXIT_FAILURE;
+  }
+  const char * inputFileName = argv[1];
+
+  constexpr unsigned int Dimension = 2;
+
+  using PixelType = unsigned short;
+  using ImageType = itk::Image<PixelType, Dimension>;
+
+  using ReaderType = itk::ImageFileReader<ImageType>;
+  ReaderType::Pointer reader = ReaderType::New();
+  reader->SetFileName(inputFileName);
+  reader->Update();
+
+  // clang-format off
+  using FilterType = itk::ImageMomentsCalculator<ImageType>;
+  // clang-format on
+  FilterType::Pointer filter = FilterType::New();
+  filter->SetImage(reader->GetOutput());
+  filter->Compute();
+  filter->Print(std::cout, 0);
+
+  return EXIT_SUCCESS;
+}

src/Filtering/ImageStatistics/CalculateImageMoments/Code.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+# Copyright NumFOCUS
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#        http://www.apache.org/licenses/LICENSE-2.0.txt
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import sys
+import itk
+import argparse
+
+parser = argparse.ArgumentParser(description="Calculate Image Moments.")
+parser.add_argument("input_image")
+
+args = parser.parse_args()
+input_image = itk.imread(args.input_image)
+momentor = itk.ImageMomentsCalculator.New(Image=input_image)
+momentor.Compute()
+print(momentor)

src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst

@@ -0,0 +1,76 @@
+Calculate Image Moments
+================================
+
+.. index::
+   single: ImageMomentsCalculator
+
+Synopsis
+--------
+
+
+Calculate image moments from binary images and an interactive ellipse.
+
+
+Results
+-------
+
+.. figure:: ellipse.mha
+  :alt: Input image
+
+  Input Image
+::
+  Output
+   ImageMomentsCalculator (000002037138BE90)
+     RTTI typeinfo:   class itk::ImageMomentsCalculator<class itk::Image<unsigned short,2> >
+     Reference Count: 1
+     Modified Time: 249
+     Debug: Off
+     Object Name:
+     Observers:
+       none
+     Image: 000002037138FDD0
+     Valid: 1
+     Zeroth Moment about origin: 153
+     First Moment about origin: [30, 50]
+     Second Moment about origin: 15.0458 -8.8366
+   -8.8366 15.0458
+
+     Center of Gravity: [30, 50]
+     Second central moments: 15.0458 -8.8366
+   -8.8366 15.0458
+
+     Principal Moments: [950, 3654]
+     Principal axes: 0.707107 0.707107
+   -0.707107 0.707107
+
+
+Jupyter Notebook
+-----------------
+
+.. image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/InsightSoftwareConsortium/ITKExamples/master?filepath=src%2FFiltering%2FImageStatistics%2FImageMomentsCalculator%2FCalculateEllipseMoments.ipynb
+
+Code
+----
+
+Python
+......
+
+.. literalinclude:: Code.py
+   :language: python
+   :lines: 1,16-
+
+C++
+...
+
+.. literalinclude:: Code.cxx
+   :language: c++
+   :lines: 18-
+
+
+
+
+Classes demonstrated
+--------------------
+
+.. breathelink:: itk::ImageMomentsCalculator

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

@@ -0,0 +1 @@
+a9dc7abe4d5745de06491d21addb54f561619732d71c98f250447c4fcf2c1444a60badbebaa3d646913e82fff75bfc753e2495c2d672d5bd7f85860fb8f8da0c