From fbc4127002017d954a14d15e79773ccec55ddb61 Mon Sep 17 00:00:00 2001
From: muschellij2 <muschellij2@gmail.com>
Date: Mon, 23 Mar 2020 14:15:17 -0400
Subject: [PATCH] N4 verbosity

---
 Examples/N4BiasFieldCorrection.cxx | 46 +++++++++++++++++++++++++-----
 1 file changed, 39 insertions(+), 7 deletions(-)

diff --git a/Examples/N4BiasFieldCorrection.cxx b/Examples/N4BiasFieldCorrection.cxx
index 7e5b5eb56..91c553abf 100644
--- a/Examples/N4BiasFieldCorrection.cxx
+++ b/Examples/N4BiasFieldCorrection.cxx
@@ -71,12 +71,6 @@ int N4( itk::ants::CommandLineParser *parser )
 {
   using RealType = float;
 
-  using ImageType = itk::Image<RealType, ImageDimension>;
-  typename ImageType::Pointer inputImage = nullptr;
-
-  using MaskImageType = itk::Image<RealType, ImageDimension>;
-  typename MaskImageType::Pointer maskImage = nullptr;
-
   bool verbose = false;
   typename itk::ants::CommandLineParser::OptionType::Pointer verboseOption =
     parser->GetOption( "verbose" );
@@ -84,15 +78,37 @@ int N4( itk::ants::CommandLineParser *parser )
     {
     verbose = parser->Convert<bool>( verboseOption->GetFunction( 0 )->GetName() );
     }
+  if( verbose )
+    {
+    std::cout << std::endl << "Creating ImageType" << std::endl;
+    }
+  using ImageType = itk::Image<RealType, ImageDimension>;
+  typename ImageType::Pointer inputImage = nullptr;
+
+  if( verbose )
+    {
+    std::cout << std::endl << "Creating MaskImageType" << std::endl;
+    }
+  using MaskImageType = itk::Image<RealType, ImageDimension>;
+  typename MaskImageType::Pointer maskImage = nullptr;
+
   if( verbose )
     {
     std::cout << std::endl << "Running N4 for "
              << ImageDimension << "-dimensional images." << std::endl << std::endl;
     }
 
+  if( verbose )
+    {
+    std::cout << std::endl << "Getting CorrecterType" << std::endl;
+    }
   using CorrecterType = itk::N4BiasFieldCorrectionImageFilter<ImageType, MaskImageType, ImageType>;
   typename CorrecterType::Pointer correcter = CorrecterType::New();
 
+  if( verbose )
+    {
+    std::cout << std::endl << "Reading in Input Image" << std::endl;
+    }
   typename itk::ants::CommandLineParser::OptionType::Pointer inputImageOption =
     parser->GetOption( "input-image" );
   if( inputImageOption && inputImageOption->GetNumberOfFunctions() )
@@ -117,9 +133,17 @@ int N4( itk::ants::CommandLineParser *parser )
 
   typename itk::ants::CommandLineParser::OptionType::Pointer maskImageOption =
     parser->GetOption( "mask-image" );
-  if( maskImageOption && maskImageOption->GetNumberOfFunctions() )
+  if( verbose )
     {
+    std::cout << std::endl << "maskImageOption: " << maskImageOption << std::endl;
+    }    
+  if( maskImageOption && maskImageOption->GetNumberOfFunctions() )
+    { 
     std::string inputMaskFile = maskImageOption->GetFunction( 0 )->GetName();
+    if( verbose )
+    {
+        std::cout << std::endl << "Reading in Mask file: " << inputMaskFile << std::endl;
+    }    
     ReadImage<MaskImageType>( maskImage, inputMaskFile.c_str() );
 
     isMaskImageSpecified = true;
@@ -140,6 +164,10 @@ int N4( itk::ants::CommandLineParser *parser )
   /**
    * check for negative values in the masked region
    */
+    if( verbose )
+    {
+        std::cout << std::endl << "Checking for Negative Values" << std::endl;
+    }
   using ThresholderType = itk::BinaryThresholdImageFilter<MaskImageType, MaskImageType>;
   typename ThresholderType::Pointer thresholder = ThresholderType::New();
   thresholder->SetInsideValue( itk::NumericTraits<typename MaskImageType::PixelType>::ZeroValue() );
@@ -148,6 +176,10 @@ int N4( itk::ants::CommandLineParser *parser )
   thresholder->SetUpperThreshold( itk::NumericTraits<typename MaskImageType::PixelType>::ZeroValue() );
   thresholder->SetInput( maskImage );
 
+    if( verbose )
+    {
+        std::cout << std::endl << "Running LabelStatisticsImageFilter" << std::endl;
+    }
   using StatsType = itk::LabelStatisticsImageFilter<ImageType, MaskImageType>;
   typename StatsType::Pointer statsOriginal = StatsType::New();
   statsOriginal->SetInput( inputImage );