Merge pull request #6003 from hjmjohnson/fix-nifti-lossless-metadata

ENH: Use NumberToString for lossless float metadata in NIfTI reader

Author: hjmjohnson

Documentation/docs/migration_guides/itk_6_migration_guide.md

@@ -213,6 +213,22 @@ The handful of manually wrapped long double functions were
 removed from python wrapping.
 
 
+IO modules write floating-point metadata with lossless precision
+-----------------------------------------------------------------
+
+`float` and `double` metadata values are now serialized using
+`itk::ConvertNumberToString()`, which produces the shortest decimal string
+that round-trips exactly — replacing the previous 6-significant-digit default.
+
+Affected modules: **NIfTI** (`scl_slope`, `scl_inter`, `pixdim`, spacing,
+and offset fields), **MetaImage**, **NRRD**, **VoxBoCUB**, **SpatialObject**,
+and **Mesh IO**.
+
+Tests that compare raw header text against golden baselines may fail because
+values previously written as e.g. `"1"` are now written as `"1.0000001"`.
+Replace exact string matches with numeric comparisons or regenerate baselines.
+Files not written by ITK are unaffected.
+
 Legacy GoogleTest Target Names Removed
 --------------------------------------
 

Modules/IO/MeshFreeSurfer/include/itkFreeSurferAsciiMeshIO.h

@@ -24,6 +24,7 @@
 #include "itkMakeUniqueForOverwrite.h"
 
 #include <fstream>
+#include "itkNumberToString.h"
 
 namespace itk
 {
@@ -117,13 +118,12 @@ class ITKIOMeshFreeSurfer_EXPORT FreeSurferAsciiMeshIO : public MeshIOBase
   void
   WritePoints(T * buffer, std::ofstream & outputFile, T label = T{})
   {
-    outputFile.precision(6);
     SizeValueType index = 0;
     for (SizeValueType ii = 0; ii < this->m_NumberOfPoints; ++ii)
     {
       for (unsigned int jj = 0; jj < this->m_PointDimension; ++jj)
       {
-        outputFile << std::fixed << buffer[index++] << "  ";
+        outputFile << ConvertNumberToString(buffer[index++]) << "  ";
       }
       outputFile << label << '\n';
     }

Modules/IO/Meta/include/itkMetaImageIO.h

@@ -22,6 +22,7 @@
 
 #include <fstream>
 #include "itkImageIOBase.h"
+#include "itkNumberToString.h"
 #include "itkSingletonMacro.h"
 #include "itkMetaDataObject.h"
 #include "metaObject.h"
@@ -220,7 +221,7 @@ MetaImageIO::WriteMatrixInMetaData(std::ostringstream &       strs,
     {
       for (unsigned int j = 0; j < VNColumns; ++j)
       {
-        strs << mval[i][j];
+        strs << ConvertNumberToString(mval[i][j]);
         if (i != VNRows - 1 || j != VNColumns - 1)
         {
           strs << ' ';

Modules/IO/Meta/src/itkMetaImageIO.cxx

@@ -21,26 +21,13 @@
 #include "itkIOCommon.h"
 #include "itksys/SystemTools.hxx"
 #include "itkMath.h"
+#include "itkNumberToString.h"
 #include "itkSingleton.h"
 #include "itkMakeUniqueForOverwrite.h"
 #include "metaImageUtils.h"
 
 #include <set>
 
-// Function to join strings with a delimiter similar to python's ' '.join([1, 2, 3 ])
-template <typename ContainerType, typename DelimiterType, typename StreamType>
-static auto
-joinElements(const ContainerType & elements, const DelimiterType & delimiter, StreamType & strs) -> void
-{
-  for (size_t i = 0; i < elements.size(); ++i)
-  {
-    strs << elements[i];
-    if (i != elements.size() - 1)
-    {
-      strs << delimiter;
-    }
-  }
-}
 
 namespace itk
 {
@@ -458,11 +445,11 @@ MetaImageIO::WriteImageInformation()
     }
     else if (ExposeMetaData<double>(metaDict, key, dval))
     {
-      strs << dval;
+      strs << ConvertNumberToString(dval);
     }
     else if (ExposeMetaData<float>(metaDict, key, fval))
     {
-      strs << fval;
+      strs << ConvertNumberToString(fval);
     }
     else if (ExposeMetaData<long>(metaDict, key, lval))
     {
@@ -510,7 +497,14 @@ MetaImageIO::WriteImageInformation()
     }
     else if (ExposeMetaData<std::vector<double>>(metaDict, key, vval))
     {
-      joinElements(vval, ' ', strs);
+      for (size_t i = 0; i < vval.size(); ++i)
+      {
+        if (i > 0)
+        {
+          strs << ' ';
+        }
+        strs << ConvertNumberToString(vval[i]);
+      }
     }
     else if (WriteMatrixInMetaData<1>(strs, metaDict, key) || WriteMatrixInMetaData<2>(strs, metaDict, key) ||
              WriteMatrixInMetaData<3>(strs, metaDict, key) || WriteMatrixInMetaData<4>(strs, metaDict, key) ||

Modules/IO/Meta/test/itkMetaImageIOMetaDataTest.cxx

@@ -21,6 +21,7 @@
 #include "itkRandomImageSource.h"
 #include "itkMetaDataObject.h"
 #include "itkMetaImageIO.h"
+#include "itkNumberToString.h"
 #include "itkTestingMacros.h"
 
 
@@ -341,5 +342,60 @@ itkMetaImageIOMetaDataTest(int argc, char * argv[])
     return 1; // error
   }
 
+  // Precision test: verify that double and float metadata round-trips without
+  // the 6-digit truncation introduced by default stream precision.
+  //
+  // With default stream precision the MetaImageIO write path serialised a
+  // double like 1.2345678901234568 as "1.23457", which on read-back parses
+  // to a different double bit-pattern.  itk::ConvertNumberToString() produces
+  // the shortest decimal string that round-trips exactly.
+  //
+  // These checks FAIL against the unfixed MetaImageIO and PASS with the fix.
+  {
+    // Values chosen to require more than 6 significant decimal digits.
+    constexpr double hpDouble = 1.2345678901234568;
+    constexpr float  hpFloat = 1.2345679f;
+
+    ImageType::Pointer        precImage(source->GetOutput());
+    itk::MetaDataDictionary & precDict = precImage->GetMetaDataDictionary();
+    itk::EncapsulateMetaData<double>(precDict, std::string("high_precision_double"), hpDouble);
+    itk::EncapsulateMetaData<float>(precDict, std::string("high_precision_float"), hpFloat);
+
+    WriteImage<ImageType>(precImage, argv[1]);
+
+    const ImageType::Pointer  precImage2 = ReadImage<ImageType>(argv[1]);
+    itk::MetaDataDictionary & precDict2 = precImage2->GetMetaDataDictionary();
+
+    // Extract raw string and parse back with exact equality to detect
+    // any bit-level precision loss from the string serialization.
+    std::string doubleStr;
+    if (!itk::ExposeMetaData<std::string>(precDict2, std::string("high_precision_double"), doubleStr))
+    {
+      std::cerr << "Key high_precision_double not found after round-trip\n";
+      return 1;
+    }
+    const double parsedDouble = std::stod(doubleStr);
+    if (parsedDouble != hpDouble)
+    {
+      std::cerr << "Double precision loss: stored " << itk::ConvertNumberToString(hpDouble) << " but string '"
+                << doubleStr << "' parses to " << itk::ConvertNumberToString(parsedDouble) << '\n';
+      return 1;
+    }
+
+    std::string floatStr;
+    if (!itk::ExposeMetaData<std::string>(precDict2, std::string("high_precision_float"), floatStr))
+    {
+      std::cerr << "Key high_precision_float not found after round-trip\n";
+      return 1;
+    }
+    const float parsedFloat = std::stof(floatStr);
+    if (parsedFloat != hpFloat)
+    {
+      std::cerr << "Float precision loss: stored " << itk::ConvertNumberToString(hpFloat) << " but string '" << floatStr
+                << "' parses to " << itk::ConvertNumberToString(parsedFloat) << '\n';
+      return 1;
+    }
+  }
+
   return 0;
 }

Modules/IO/NIFTI/src/itkNiftiImageIO.cxx

@@ -19,6 +19,7 @@
 #include "itkNiftiImageIO.h"
 #include "itkIOCommon.h"
 #include "itkMetaDataObject.h"
+#include "itkNumberToString.h"
 #include "itkAnatomicalOrientation.h"
 #include <nifti1_io.h>
 #include "itkNiftiImageIOConfigurePrivate.h"
@@ -645,17 +646,9 @@ NiftiImageIO::SetImageIOMetadataFromNIfTI()
     EncapsulateMetaData<std::string>(thisDic, dimKey.str(), dim.str());
   }
 
-  std::ostringstream intent_p1;
-  intent_p1 << m_Holder->ptr->intent_p1;
-  EncapsulateMetaData<std::string>(thisDic, "intent_p1", intent_p1.str());
-
-  std::ostringstream intent_p2;
-  intent_p2 << m_Holder->ptr->intent_p2;
-  EncapsulateMetaData<std::string>(thisDic, "intent_p2", intent_p2.str());
-
-  std::ostringstream intent_p3;
-  intent_p3 << m_Holder->ptr->intent_p3;
-  EncapsulateMetaData<std::string>(thisDic, "intent_p3", intent_p3.str());
+  EncapsulateMetaData<std::string>(thisDic, "intent_p1", ConvertNumberToString(m_Holder->ptr->intent_p1));
+  EncapsulateMetaData<std::string>(thisDic, "intent_p2", ConvertNumberToString(m_Holder->ptr->intent_p2));
+  EncapsulateMetaData<std::string>(thisDic, "intent_p3", ConvertNumberToString(m_Holder->ptr->intent_p3));
 
   std::ostringstream intent_code;
   intent_code << m_Holder->ptr->intent_code;
@@ -675,24 +668,17 @@ NiftiImageIO::SetImageIOMetadataFromNIfTI()
 
   for (int idx = 0; idx < 8; ++idx)
   {
-    std::ostringstream pixdim;
-    pixdim << m_Holder->ptr->pixdim[idx];
     std::ostringstream pixdimKey;
     pixdimKey << "pixdim[" << idx << ']';
-    EncapsulateMetaData<std::string>(thisDic, pixdimKey.str(), pixdim.str());
+    EncapsulateMetaData<std::string>(thisDic, pixdimKey.str(), ConvertNumberToString(m_Holder->ptr->pixdim[idx]));
   }
 
   std::ostringstream vox_offset;
   vox_offset << m_Holder->ptr->iname_offset;
   EncapsulateMetaData<std::string>(thisDic, "vox_offset", vox_offset.str());
 
-  std::ostringstream scl_slope;
-  scl_slope << m_Holder->ptr->scl_slope;
-  EncapsulateMetaData<std::string>(thisDic, "scl_slope", scl_slope.str());
-
-  std::ostringstream scl_inter;
-  scl_inter << m_Holder->ptr->scl_inter;
-  EncapsulateMetaData<std::string>(thisDic, "scl_inter", scl_inter.str());
+  EncapsulateMetaData<std::string>(thisDic, "scl_slope", ConvertNumberToString(m_Holder->ptr->scl_slope));
+  EncapsulateMetaData<std::string>(thisDic, "scl_inter", ConvertNumberToString(m_Holder->ptr->scl_inter));
 
   std::ostringstream slice_end;
   slice_end << m_Holder->ptr->slice_end;
@@ -706,21 +692,10 @@ NiftiImageIO::SetImageIOMetadataFromNIfTI()
   xyzt_units << SPACE_TIME_TO_XYZT(m_Holder->ptr->xyz_units, m_Holder->ptr->time_units);
   EncapsulateMetaData<std::string>(thisDic, "xyzt_units", xyzt_units.str());
 
-  std::ostringstream cal_max;
-  cal_max << m_Holder->ptr->cal_max;
-  EncapsulateMetaData<std::string>(thisDic, "cal_max", cal_max.str());
-
-  std::ostringstream cal_min;
-  cal_min << m_Holder->ptr->cal_min;
-  EncapsulateMetaData<std::string>(thisDic, "cal_min", cal_min.str());
-
-  std::ostringstream slice_duration;
-  slice_duration << m_Holder->ptr->slice_duration;
-  EncapsulateMetaData<std::string>(thisDic, "slice_duration", slice_duration.str());
-
-  std::ostringstream toffset;
-  toffset << m_Holder->ptr->toffset;
-  EncapsulateMetaData<std::string>(thisDic, "toffset", toffset.str());
+  EncapsulateMetaData<std::string>(thisDic, "cal_max", ConvertNumberToString(m_Holder->ptr->cal_max));
+  EncapsulateMetaData<std::string>(thisDic, "cal_min", ConvertNumberToString(m_Holder->ptr->cal_min));
+  EncapsulateMetaData<std::string>(thisDic, "slice_duration", ConvertNumberToString(m_Holder->ptr->slice_duration));
+  EncapsulateMetaData<std::string>(thisDic, "toffset", ConvertNumberToString(m_Holder->ptr->toffset));
 
   std::ostringstream descrip;
   descrip << m_Holder->ptr->descrip;
@@ -740,44 +715,28 @@ NiftiImageIO::SetImageIOMetadataFromNIfTI()
   EncapsulateMetaData<std::string>(thisDic, "sform_code", sform_code.str());
   EncapsulateMetaData<std::string>(thisDic, "sform_code_name", std::string(str_xform(m_Holder->ptr->sform_code)));
 
-  std::ostringstream quatern_b;
-  quatern_b << m_Holder->ptr->quatern_b;
-  EncapsulateMetaData<std::string>(thisDic, "quatern_b", quatern_b.str());
-
-  std::ostringstream quatern_c;
-  quatern_c << m_Holder->ptr->quatern_c;
-  EncapsulateMetaData<std::string>(thisDic, "quatern_c", quatern_c.str());
-
-  std::ostringstream quatern_d;
-  quatern_d << m_Holder->ptr->quatern_d;
-  EncapsulateMetaData<std::string>(thisDic, "quatern_d", quatern_d.str());
-
-  std::ostringstream qoffset_x;
-  qoffset_x << m_Holder->ptr->qoffset_x;
-  EncapsulateMetaData<std::string>(thisDic, "qoffset_x", qoffset_x.str());
-
-  std::ostringstream qoffset_y;
-  qoffset_y << m_Holder->ptr->qoffset_y;
-  EncapsulateMetaData<std::string>(thisDic, "qoffset_y", qoffset_y.str());
+  EncapsulateMetaData<std::string>(thisDic, "quatern_b", ConvertNumberToString(m_Holder->ptr->quatern_b));
+  EncapsulateMetaData<std::string>(thisDic, "quatern_c", ConvertNumberToString(m_Holder->ptr->quatern_c));
+  EncapsulateMetaData<std::string>(thisDic, "quatern_d", ConvertNumberToString(m_Holder->ptr->quatern_d));
+  EncapsulateMetaData<std::string>(thisDic, "qoffset_x", ConvertNumberToString(m_Holder->ptr->qoffset_x));
+  EncapsulateMetaData<std::string>(thisDic, "qoffset_y", ConvertNumberToString(m_Holder->ptr->qoffset_y));
+  EncapsulateMetaData<std::string>(thisDic, "qoffset_z", ConvertNumberToString(m_Holder->ptr->qoffset_z));
 
-  std::ostringstream qoffset_z;
-  qoffset_z << m_Holder->ptr->qoffset_z;
-  EncapsulateMetaData<std::string>(thisDic, "qoffset_z", qoffset_z.str());
-
-  std::ostringstream srow_x;
-  srow_x << m_Holder->ptr->sto_xyz.m[0][0] << ' ' << m_Holder->ptr->sto_xyz.m[0][1] << ' '
-         << m_Holder->ptr->sto_xyz.m[0][2] << ' ' << m_Holder->ptr->sto_xyz.m[0][3];
-  EncapsulateMetaData<std::string>(thisDic, "srow_x", srow_x.str());
-
-  std::ostringstream srow_y;
-  srow_y << m_Holder->ptr->sto_xyz.m[1][0] << ' ' << m_Holder->ptr->sto_xyz.m[1][1] << ' '
-         << m_Holder->ptr->sto_xyz.m[1][2] << ' ' << m_Holder->ptr->sto_xyz.m[1][3];
-  EncapsulateMetaData<std::string>(thisDic, "srow_y", srow_y.str());
-
-  std::ostringstream srow_z;
-  srow_z << m_Holder->ptr->sto_xyz.m[2][0] << ' ' << m_Holder->ptr->sto_xyz.m[2][1] << ' '
-         << m_Holder->ptr->sto_xyz.m[2][2] << ' ' << m_Holder->ptr->sto_xyz.m[2][3];
-  EncapsulateMetaData<std::string>(thisDic, "srow_z", srow_z.str());
+  for (int row = 0; row < 3; ++row)
+  {
+    std::string srowStr;
+    for (int col = 0; col < 4; ++col)
+    {
+      if (col > 0)
+      {
+        srowStr += ' ';
+      }
+      srowStr += ConvertNumberToString(m_Holder->ptr->sto_xyz.m[row][col]);
+    }
+    std::ostringstream srowKey;
+    srowKey << "srow_" << "xyz"[row];
+    EncapsulateMetaData<std::string>(thisDic, srowKey.str(), srowStr);
+  }
 
   std::ostringstream intent_name;
   intent_name << m_Holder->ptr->intent_name;