[Compiling|Functional][UNIT TESTS NEEDED]

- Correct human name for combing scans parameter
- put oweness on subclass to define the update origin (case by case problem)
- add nullptr checks and Error messaging

Author: nyoungbq

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/ReadH5EspritData.cpp

@@ -23,6 +23,19 @@ Result<> ReadH5EspritData::operator()()
   return execute();
 }
 
+// -----------------------------------------------------------------------------
+Result<> ReadH5EspritData::updateOrigin(const std::string& scanName)
+{
+  /*
+   * Unfortunately, the file does not have the correct data to find an origin.
+   * This means that the origin will remain {0,0,0}.
+   *
+   * Down the line, if a solution crops up, look to ReadH5Oina.cpp for an example
+   * implementation.
+   */
+  return {};
+}
+
 // -----------------------------------------------------------------------------
 Result<> ReadH5EspritData::copyRawEbsdData(int index)
 {

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/ReadH5EspritData.hpp

@@ -33,6 +33,8 @@ class ORIENTATIONANALYSIS_EXPORT ReadH5EspritData : public IEbsdOemReader<H5Espr
 
   Result<> operator()();
 
+  Result<> updateOrigin(const std::string& scanName) override;
+
   Result<> copyRawEbsdData(int index) override;
   Result<> copyRawEbsdData(const std::string& scanName) override;
 

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/ReadH5OinaData.cpp

@@ -60,6 +60,33 @@ Result<> ReadH5OinaData::operator()()
   return execute();
 }
 
+// -----------------------------------------------------------------------------
+Result<> ReadH5OinaData::updateOrigin(const std::string& scanName)
+{
+  const DataPath imagePath({scanName});
+
+  auto& imageGeom = m_DataStructure.getDataRefAs<ImageGeom>(imagePath);
+  const usize totalCells = imageGeom.getNumberOfCells();
+
+  const auto* xPos = reinterpret_cast<float32*>(m_Reader->getPointerByName(EbsdLib::Ctf::X));
+  if(xPos == nullptr)
+  {
+    return MakeErrorResult(-9970, fmt::format("{}({}): Function {}: Error. Cannot find {} in supplied scan file ({})", "IEbsdOemReader", __FILE__, __LINE__, EbsdLib::Ctf::X, m_Reader->getFileName()));
+  }
+  const auto* yPos = reinterpret_cast<float32*>(m_Reader->getPointerByName(EbsdLib::Ctf::Y));
+  if(yPos == nullptr)
+  {
+    return MakeErrorResult(-9971, fmt::format("{}({}): Function {}: Error. Cannot find {} in supplied scan file ({})", "IEbsdOemReader", __FILE__, __LINE__, EbsdLib::Ctf::Y, m_Reader->getFileName()));
+  }
+
+  float32 minX = *std::min_element(xPos, xPos + totalCells);
+  float32 minY = *std::min_element(yPos, yPos + totalCells);
+
+  imageGeom.setOrigin(minX, minY, 0.0f);
+
+  return {};
+}
+
 // -----------------------------------------------------------------------------
 Result<> ReadH5OinaData::copyRawEbsdData(int index)
 {

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/Algorithms/ReadH5OinaData.hpp

@@ -25,6 +25,7 @@ class ORIENTATIONANALYSIS_EXPORT ReadH5OinaData : public IEbsdOemReader<H5OINARe
 
   Result<> operator()();
 
+  Result<> updateOrigin(const std::string& scanName) override;
   Result<> copyRawEbsdData(int index) override;
   Result<> copyRawEbsdData(const std::string& scanName) override;
 };

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadH5EspritDataFilter.cpp

@@ -71,7 +71,7 @@ Parameters ReadH5EspritDataFilter::parameters() const
                                                                 /* OEMEbsdScanSelectionParameter::AllowedManufacturers{EbsdLib::OEM::Bruker, EbsdLib::OEM::DREAM3D},*/
                                                                 OEMEbsdScanSelectionParameter::EbsdReaderType::Esprit, OEMEbsdScanSelectionParameter::ExtensionsType{".h5", ".hdf5"}));
   params.insertLinkableParameter(std::make_unique<BoolParameter>(
-      k_CombineScans_Key, "Combine Scans", "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
+      k_CombineScans_Key, "Stack Scans Along Z Axis", "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
   params.insert(std::make_unique<Float32Parameter>(k_ZSpacing_Key, "Z Spacing (Microns)", "The spacing in microns between each layer.", 1.0f));
   params.insert(std::make_unique<VectorFloat32Parameter>(k_Origin_Key, "Origin", "The origin of the volume", std::vector<float32>{0.0F, 0.0F, 0.0F}, std::vector<std::string>{"x", "y", "z"}));
   params.insert(std::make_unique<Float32Parameter>(k_ZSpacing_Key, "Z Spacing (Microns)", "The spacing in microns between each layer.", 1.0f));

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadH5OimDataFilter.cpp

@@ -80,8 +80,9 @@ Parameters ReadH5OimDataFilter::parameters() const
   params.insert(std::make_unique<OEMEbsdScanSelectionParameter>(k_SelectedScanNames_Key, "Scan Names", "The name of the scan in the .h5 file. EDAX can store multiple scans in a single file",
                                                                 OEMEbsdScanSelectionParameter::ValueType{}, OEMEbsdScanSelectionParameter::EbsdReaderType::Oim,
                                                                 OEMEbsdScanSelectionParameter::ExtensionsType{".h5"}));
-  params.insertLinkableParameter(std::make_unique<BoolParameter>(
-      k_CombineScans_Key, "Combine Scans", "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
+  params.insertLinkableParameter(
+      std::make_unique<BoolParameter>(k_CombineScans_Key, "Stack Scans Along Z Axis",
+                                      "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
   params.insert(std::make_unique<Float32Parameter>(k_ZSpacing_Key, "Z Spacing (Microns)", "The spacing in microns between each layer.", 1.0f));
   params.insert(std::make_unique<VectorFloat32Parameter>(k_Origin_Key, "Origin", "The origin of the volume", std::vector<float32>{0.0F, 0.0F, 0.0F}, std::vector<std::string>{"x", "y", "z"}));
   params.insert(std::make_unique<Float32Parameter>(k_ZSpacing_Key, "Z Spacing (Microns)", "The spacing in microns between each layer.", 1.0f));

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ReadH5OinaDataFilter.cpp

@@ -66,8 +66,9 @@ Parameters ReadH5OinaDataFilter::parameters() const
   params.insert(std::make_unique<OEMEbsdScanSelectionParameter>(k_SelectedScanNames_Key, "Scan Names", "The name of the scan in the .h5oina file. Oxford can store multiple scans in a single file",
                                                                 OEMEbsdScanSelectionParameter::ValueType{}, OEMEbsdScanSelectionParameter::EbsdReaderType::H5Oina,
                                                                 OEMEbsdScanSelectionParameter::ExtensionsType{".h5oina"}));
-  params.insertLinkableParameter(std::make_unique<BoolParameter>(
-      k_CombineScans_Key, "Combine Scans", "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
+  params.insertLinkableParameter(
+      std::make_unique<BoolParameter>(k_CombineScans_Key, "Stack Scans Along Z Axis",
+                                      "If true combines each of the multiple scans into a single image geometry along the z axis, else each will result in an individual geometry", true));
   params.insert(std::make_unique<BoolParameter>(k_EdaxHexagonalAlignment_Key, "Convert Hexagonal X-Axis to EDAX Standard",
                                                 "Whether or not to convert a Hexagonal phase to the EDAX standard for x-axis alignment", true));
   params.insert(std::make_unique<BoolParameter>(k_ConvertPhaseToInt32_Key, "Convert Phase Data to Int32", "Native Phases data value is uint8. Convert to Int32 for better filter compatibility", true));

src/Plugins/OrientationAnalysis/src/OrientationAnalysis/utilities/IEbsdOemReader.hpp

@@ -81,13 +81,6 @@ class ORIENTATIONANALYSIS_EXPORT IEbsdOemReader
         auto& imageGeom = m_DataStructure.getDataRefAs<ImageGeom>(DataPath({currentScanName}));
         imageGeom.setUnits(IGeometry::LengthUnit::Micrometer);
         copyDataResults = copyRawEbsdData(currentScanName);
-
-        if(copyDataResults.invalid())
-        {
-          return copyDataResults;
-        }
-
-        copyDataResults = updateOrigin(currentScanName);
       }
 
       if(copyDataResults.invalid())
@@ -133,8 +126,7 @@ class ORIENTATIONANALYSIS_EXPORT IEbsdOemReader
     const DataPath cellEnsembleAM = imagePath.createChildPath(m_InputValues->CellEnsembleAttributeMatrixName);
     auto& crystalStructures = m_DataStructure.getDataRefAs<UInt32Array>(cellEnsembleAM.createChildPath(EbsdLib::AngFile::CrystalStructures));
     auto& materialNames = m_DataStructure.getDataRefAs<StringArray>(cellEnsembleAM.createChildPath(EbsdLib::AngFile::MaterialName));
-    auto& latticeConstantsArray =
-        m_DataStructure.getDataRefAs<Float32Array>(cellEnsembleAM.createChildPath(EbsdLib::AngFile::LatticeConstants));
+    auto& latticeConstantsArray = m_DataStructure.getDataRefAs<Float32Array>(cellEnsembleAM.createChildPath(EbsdLib::AngFile::LatticeConstants));
     Float32Array::store_type* latticeConstants = latticeConstantsArray.getDataStore();
 
     crystalStructures[0] = EbsdLib::CrystalStructure::UnknownCrystalStructure;
@@ -160,28 +152,19 @@ class ORIENTATIONANALYSIS_EXPORT IEbsdOemReader
       latticeConstants->setComponent(phaseId, 5, lc[5]);
     }
 
-    return {};
+    if(m_InputValues->CombineScans)
+    {
+      // No need to update origin
+      return {};
+    }
+
+    return updateOrigin(scanName);
   }
 
+  virtual Result<> updateOrigin(const std::string& scanName) = 0;
+
   virtual Result<> copyRawEbsdData(int index) = 0;
   virtual Result<> copyRawEbsdData(const std::string& scanName) = 0;
-  virtual Result<> updateOrigin(const std::string& scanName)
-  {
-    const DataPath imagePath({scanName});
-
-    auto& imageGeom = m_DataStructure.getDataRefAs<ImageGeom>(imagePath);
-    const usize totalCells = imageGeom.getNumberOfCells();
-
-    const auto* xPos = reinterpret_cast<float32*>(m_Reader->getPointerByName(EbsdLib::Ang::XPosition));
-    const auto* yPos = reinterpret_cast<float32*>(m_Reader->getPointerByName(EbsdLib::Ang::YPosition));
-
-    float32 minX = *std::min_element(xPos, xPos + totalCells);
-    float32 minY = *std::min_element(yPos, yPos + totalCells);
-
-    imageGeom.setOrigin(minX, minY, 0.0f);
-
-    return {};
-  }
 
 protected:
   std::shared_ptr<T> m_Reader;