ENH: Simplification of the ImageSeriesReader nonuniform sampling dete…

…ction
InsightSoftwareConsortium · Dec 11, 2019 · 8c5d9e9 · 8c5d9e9
1 parent 98c5620
commit 8c5d9e9
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Showing 2 changed files with 18 additions and 30 deletions.
diff --git a/Modules/IO/ImageBase/include/itkImageSeriesReader.hxx b/Modules/IO/ImageBase/include/itkImageSeriesReader.hxx
@@ -26,6 +26,7 @@
 #include "itkMath.h"
 #include "itkProgressReporter.h"
 #include "itkMetaDataObject.h"
+#include <iomanip>
 
 namespace itk
 {
@@ -311,6 +312,7 @@ ImageSeriesReader<TOutputImage>::GenerateData()
     const bool insideRequestedRegion = requestedRegion.IsInside(sliceStartIndex);
     const int  iFileName = (m_ReverseOrder ? numberOfFiles - i - 1 : i);
     bool       nonUniformSampling = false;
+    double     spacingDeviation = 0.0;
 
     // check if we need this slice
     if (!insideRequestedRegion && !needToUpdateMetaDataDictionaryArray)
@@ -436,17 +438,15 @@ ImageSeriesReader<TOutputImage>::GenerateData()
               outputSpacing[this->m_NumberOfDimensionsInImage])) // either non-uniform sampling or missing slice
         {
           nonUniformSampling = true;
-          itkWarningMacro(<< "Non unform sampling or missing slices detected , expected "
-                          << outputSpacing[this->m_NumberOfDimensionsInImage] << " got: " << dirNnorm);
-
-          EncapsulateMetaData<bool>(output->GetMetaDataDictionary(),
-                                    "ITK_non_uniform_sampling",
-                                    true); // set metadata for the series reader output
+          spacingDeviation = Math::abs(outputSpacing[this->m_NumberOfDimensionsInImage] - dirNnorm);
+          itkWarningMacro(<< "Non uniform sampling or missing slices detected , expected " << std::setprecision(14)
+                          << outputSpacing[this->m_NumberOfDimensionsInImage] << " got: " << dirNnorm
+                          << " Deviation of:" << spacingDeviation << std::defaultfloat);
 
           needToUpdateMetaDataDictionaryArray = true;
-          if (Math::abs(outputSpacing[this->m_NumberOfDimensionsInImage] - dirNnorm) > maxSpacingDeviation)
+          if (spacingDeviation > maxSpacingDeviation)
           {
-            maxSpacingDeviation = Math::abs(outputSpacing[this->m_NumberOfDimensionsInImage] - dirNnorm);
+            maxSpacingDeviation = spacingDeviation;
             EncapsulateMetaData<double>(output->GetMetaDataDictionary(),
                                         "ITK_non_uniform_sampling_deviation",
                                         maxSpacingDeviation); // maximum deviation
@@ -471,7 +471,8 @@ ImageSeriesReader<TOutputImage>::GenerateData()
       *newDictionary = reader->GetImageIO()->GetMetaDataDictionary();
       if (nonUniformSampling)
       {
-        EncapsulateMetaData<bool>(*newDictionary, "ITK_non_uniform_sampling", true); // slice-specific information
+        // slice-specific information
+        EncapsulateMetaData<double>(*newDictionary, "ITK_non_uniform_sampling_deviation", spacingDeviation);
       }
       m_MetaDataDictionaryArray.push_back(newDictionary);
     }

diff --git a/Modules/IO/ImageBase/test/itkImageSeriesReaderSamplingTest.cxx b/Modules/IO/ImageBase/test/itkImageSeriesReaderSamplingTest.cxx
@@ -45,43 +45,30 @@ itkImageSeriesReaderSamplingTest(int ac, char * av[])
     Reader3DType::Pointer reader = Reader3DType::New();
     reader->SetFileNames(fnames);
     reader->Update();
-    bool globalNonUniformSampling = false;
-    if (itk::ExposeMetaData<bool>(
-          reader->GetOutput()->GetMetaDataDictionary(), "ITK_non_uniform_sampling", globalNonUniformSampling) &&
-        globalNonUniformSampling)
-    {
-      std::cout << "output ITK_non_uniform_sampling detected " << std::endl;
-    }
-    else
-    {
-      std::cout << "output ITK_non_uniform_sampling not found" << std::endl;
-      return EXIT_FAILURE;
-    }
-
-    double globalSamplingDeviation = 0.0;
+    double maxSamplingDeviation = 0.0;
     if (itk::ExposeMetaData<double>(
-          reader->GetOutput()->GetMetaDataDictionary(), "ITK_non_uniform_sampling_deviation", globalSamplingDeviation))
+          reader->GetOutput()->GetMetaDataDictionary(), "ITK_non_uniform_sampling_deviation", maxSamplingDeviation))
     {
-      std::cout << "output ITK_non_uniform_sampling_deviation = " << globalSamplingDeviation << std::endl;
+      std::cout << "global ITK_non_uniform_sampling_deviation detected : " << maxSamplingDeviation << std::endl;
     }
     else
     {
-      std::cout << "output ITK_non_uniform_sampling_deviation not found" << std::endl;
+      std::cout << "global ITK_non_uniform_sampling_deviation not found" << std::endl;
       return EXIT_FAILURE;
     }
 
     // iterate over all slices to detect offending slice
     for (auto d : *reader->GetMetaDataDictionaryArray())
     {
       itk::MetaDataDictionary theMetadata = *d;
-      bool                    nonUniformSampling = false;
-      if (itk::ExposeMetaData<bool>(theMetadata, "ITK_non_uniform_sampling", nonUniformSampling) && nonUniformSampling)
+      double                  samplingDeviation = 0.0;
+      if (itk::ExposeMetaData<double>(theMetadata, "ITK_non_uniform_sampling_deviation", samplingDeviation))
       {
-        std::cout << "slice ITK_non_uniform_sampling detected" << std::endl;
+        std::cout << "slice ITK_non_uniform_sampling_deviation detected: " << samplingDeviation << std::endl;
       }
       else
       {
-        std::cout << "slice ITK_non_uniform_sampling not detected" << std::endl;
+        std::cout << "slice ITK_non_uniform_sampling_deviation not detected" << std::endl;
       }
     }
   }