ENH: Add CalculateImageMoments and fix cookiecutter and other issues.

DOC: Changed cookiecutter to put Python link first
DOC: Changed CalculateImageMoments to put Python link first
BUG: Removed extraneous lines in CMakeLists refering to output_image
ENH: Changed cookiecutter to use argparse for print_usage
ENH: Changed CalculateImageMoments to use argparse for print_usage
BUG: Fixed IterateRegionWithAccessToIndexWithoutWriteAccess/Code.cxx to use defined region instead of LargestPossibleRegion (Closes #270)

Added ellipse.png.sha512 so that the image would render.  Fixed whitespace and syntax issues with .rst.

Author: brad-t-moore

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

@@ -32,19 +32,20 @@ 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/CalculateImageMoments/CMakeLists.txt

@@ -29,7 +29,6 @@ add_test( NAME CalculateImageMomentsTest
 
 if( ITK_WRAP_PYTHON )
   find_package(PythonInterp REQUIRED)
-  string( REPLACE . "Python." output_image "${output_image}" )
   add_test( NAME CalculateImageMomentsTestPython
     COMMAND ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/Code.py
       ${input_image}

src/Filtering/ImageStatistics/CalculateImageMoments/CalculateEllipseMoments.ipynb

@@ -1,9 +1,21 @@
 {
  "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": 9,
-   "id": "protecting-hobby",
+   "execution_count": 1,
+   "id": "amino-atlantic",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -15,14 +27,14 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
-   "id": "dried-demographic",
+   "execution_count": 2,
+   "id": "domestic-jenny",
    "metadata": {},
    "outputs": [
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "12ddf6ab0ad54db19849293d0d20c252",
+       "model_id": "9460aeb87fea499c90c4e301da10ddce",
        "version_major": 2,
        "version_minor": 0
       },
@@ -84,7 +96,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "several-label",
+   "id": "seasonal-sandwich",
    "metadata": {},
    "outputs": [],
    "source": []

src/Filtering/ImageStatistics/CalculateImageMoments/Code.py

@@ -18,11 +18,6 @@
 import itk
 import argparse
 
-if len(sys.argv) != 2:
-    print("Usage: " + sys.argv[0] + "<InputFileName>")
-    print("Prints image moment information from binary image.")
-    sys.exit(1)
-
 parser = argparse.ArgumentParser(description="Calculate Image Moments.")
 parser.add_argument("input_image")
 

src/Filtering/ImageStatistics/CalculateImageMoments/Documentation.rst

@@ -1,50 +1,57 @@
+:name: CalculateImageMoments
+
 Calculate Image Moments
 ================================
 
 .. index::
    single: ImageMomentsCalculator
 
+.. toctree::
+  :maxdepth: 1
+
+  CalculateEllipseMoments.ipynb
+
 Synopsis
 --------
 
 
 Calculate image moments from binary images and an interactive ellipse.
 
-
 Results
 -------
 
-.. figure:: ellipse.mha
-  :scale: 50%
+Input Image
+
+.. figure:: ellipse.png
   :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
+
 ::
 
+  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
 -----------------
@@ -55,19 +62,21 @@ Jupyter Notebook
 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/Filtering/ImageStatistics/CalculateImageMoments/ellipse.png.sha512

@@ -0,0 +1 @@
+faafd547a568d258dc916d18058f6dae75ef3fe31e83ee500e71a9a253eb502961e362f18cfd5c5a4e2edab78341184a891016abee4718b286d564c24afedf35