From 3a8afcb8c85419fa8f0f9c2127443a271742769e Mon Sep 17 00:00:00 2001
From: Philip Cook <cookpa@pennmedicine.upenn.edu>
Date: Sun, 5 May 2024 20:41:36 -0400
Subject: [PATCH] ENH: Fix vol / area, update label filter

---
 .../GetConnectedComponentsFeatureImages.cxx   | 51 +++++++++++--------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/Examples/GetConnectedComponentsFeatureImages.cxx b/Examples/GetConnectedComponentsFeatureImages.cxx
index 71badd16e..648ff76c2 100644
--- a/Examples/GetConnectedComponentsFeatureImages.cxx
+++ b/Examples/GetConnectedComponentsFeatureImages.cxx
@@ -7,8 +7,7 @@
 #include "itkBinaryThresholdImageFilter.h"
 #include "itkConnectedComponentImageFilter.h"
 #include "itkRelabelComponentImageFilter.h"
-#include "itkLabelGeometryImageFilter.h"
-#include "itkLabelPerimeterEstimationCalculator.h"
+#include "itkLabelImageToShapeLabelMapFilter.h"
 #include "itkLabelStatisticsImageFilter.h"
 #include "itkMultiplyImageFilter.h"
 #include "itkSignedMaurerDistanceMapImageFilter.h"
@@ -47,11 +46,6 @@ GetConnectedComponentsFeatureImages(int itkNotUsed(argc), char * argv[])
   }
 
   typename ImageType::SpacingType spacing = inputImage->GetSpacing();
-  float                           prefactor = 1.0;
-  for (unsigned int d = 0; d < ImageDimension; d++)
-  {
-    prefactor *= static_cast<float>(spacing[d]);
-  }
 
   using RelabelerType = itk::RelabelComponentImageFilter<ImageType, ImageType>;
   typename RelabelerType::Pointer relabeler = RelabelerType::New();
@@ -78,18 +72,13 @@ GetConnectedComponentsFeatureImages(int itkNotUsed(argc), char * argv[])
     relabeler2->SetInput(filter->GetOutput());
     relabeler2->Update();
 
-    using GeometryFilterType = itk::LabelGeometryImageFilter<ImageType, RealImageType>;
+    using GeometryFilterType = itk::LabelImageToShapeLabelMapFilter<ImageType>;
     typename GeometryFilterType::Pointer geometry = GeometryFilterType::New();
     geometry->SetInput(relabeler2->GetOutput());
-    geometry->CalculatePixelIndicesOff();
-    geometry->CalculateOrientedBoundingBoxOff();
-    geometry->CalculateOrientedLabelRegionsOff();
-    geometry->Update();
+    geometry->ComputeOrientedBoundingBoxOff();
+    geometry->ComputePerimeterOn();
 
-    using AreaFilterType = itk::LabelPerimeterEstimationCalculator<ImageType>;
-    typename AreaFilterType::Pointer area = AreaFilterType::New();
-    area->SetImage(relabeler2->GetOutput());
-    area->Compute();
+    geometry->Update();
 
     itk::ImageRegionIteratorWithIndex<ImageType> It(relabeler->GetOutput(),
                                                     relabeler->GetOutput()->GetRequestedRegion());
@@ -108,12 +97,32 @@ GetConnectedComponentsFeatureImages(int itkNotUsed(argc), char * argv[])
         // [2] = eccentricity
         // [3] = elongation
 
-        float volume = prefactor * static_cast<float>(geometry->GetVolume(label));
+        try
+        {
+          auto labelObject = geometry->GetOutput()->GetLabelObject(label);
+          float volume = labelObject->GetPhysicalSize();
+
+          outputImages[0]->SetPixel(index, volume);
+          outputImages[1]->SetPixel(index, volume / static_cast<float>(labelObject->GetPerimeter()));
+
+          auto principalMoments = labelObject->GetPrincipalMoments();
+
+          float lambda1 = principalMoments[0];
+          float lambdaN = principalMoments[ImageDimension - 1];
+          float eccentricity = 0.0;
+
+          if (!itk::Math::FloatAlmostEqual(lambda1, 0.0f))
+          {
+            eccentricity = std::sqrt(1.0 - (lambda1 * lambda1) / (lambdaN * lambdaN));
+          }
 
-        outputImages[0]->SetPixel(index, volume);
-        outputImages[1]->SetPixel(index, static_cast<float>(area->GetPerimeter(label)) / volume);
-        outputImages[2]->SetPixel(index, geometry->GetEccentricity(label));
-        outputImages[3]->SetPixel(index, geometry->GetElongation(label));
+          outputImages[2]->SetPixel(index, eccentricity);
+          outputImages[3]->SetPixel(index, labelObject->GetElongation());
+        }
+        catch (itk::ExceptionObject & e)
+        {
+          std::cerr << "Could not find label " << label << std::endl;
+        }
       }
     }
   }