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READER: Implement Aztec .cpr/.crc reader for EBSD data. (#27)
Signed-off-by: Michael Jackson <mike.jackson@bluequartz.net>
1 parent c8d33e2 commit 3fc5c63

28 files changed

+1409
-29
lines changed

‎CMakePresets.json

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@@ -128,6 +128,10 @@
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"VCPKG_HOST_TRIPLET": {
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"type": "STRING",
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"value": "arm64-osx-dynamic"
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},
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"CMAKE_BUILD_TYPE": {
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"type": "STRING",
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"value": "Debug"
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}
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},
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"environment": {

‎Source/Apps/ParseAztecProject.cpp

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#include "EbsdLib/IO/HKL/CprReader.h"
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#include "EbsdLib/LaueOps/LaueOps.h"
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#include <iostream>
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namespace detail
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{
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// const std::string k_CprPath = "/Volumes/OWC_Express_1M2/DREAM3D_Troubleshoot_Data/Benjamin_Layer1/Layer1.cpr";
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const std::string k_CprPath = "/Volumes/OWC_Express_1M2/CPR_CRC_Test_Data/dg7kv5mcv3-1/17NZ42_Dauphinetwinnedsample_nearlyuntwinnedgrains.cpr";
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} // namespace detail
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std::string ConvertLaueGroupToString(int idx)
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{
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switch(idx)
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{
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case 0:
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return "Hexagonal_High";
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case 1:
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return "Cubic_High";
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case 2:
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return "Hexagonal_Low";
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case 3:
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return "Cubic_Low";
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case 4:
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return "Triclinic";
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case 5:
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return "Monoclinic";
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case 6:
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return "OrthoRhombic";
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case 7:
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return "Tetragonal_Low";
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case 8:
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return "Tetragonal_High";
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case 9:
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return "Trigonal_Low";
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case 10:
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return "Trigonal_High";
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case 11:
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return "UnknownCrystalStructure";
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}
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return "Undefined";
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}
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// -----------------------------------------------------------------------------
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int main(int argc, char* argv[])
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{
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// if(argc != 3)
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// {
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// std::cout << "Program .cpr and .crc files as input." << std::endl;
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// return 1;
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// }
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CprReader reader;
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reader.setFileName(detail::k_CprPath);
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int error = reader.readHeaderOnly();
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if(error < 0)
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{
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std::cout << "Reading Header Failed: " << error << "\n";
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return 1;
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}
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// reader.printHeader(std::cout);
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// Write out a compatible DREAM3D "Ensemble" File
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auto phases = reader.getPhaseVector();
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std::cout << "[EnsembleInfo]\n"
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<< "Number_Phases=" << phases.size() << std::endl;
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size_t idx = 0;
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for(const auto& phase : phases)
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{
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std::cout << std::endl;
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std::cout << "[" << ++idx << "]\n"
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<< "CrystalStructure=" << ConvertLaueGroupToString(phase->determineOrientationOpsIndex()) << "\n"
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<< "PhaseType=PrimaryPhase\n";
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}
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error = reader.readFile();
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if(error < 0)
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{
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std::cout << reader.getErrorMessage() << error << "\n";
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return 2;
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}
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// Dump all the data to the command line
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// std::cout << "Phase,Bands,Error,Euler1,Euler2,Euler3,MAD,BC,BS\n";
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// uint8_t* phasePtr = reader.getPhasePointer();
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// uint8_t* bandsPtr = reader.getBandCountPointer();
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// uint8_t* errorPtr = reader.getErrorPointer();
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// float* phi1Ptr = reader.getEuler1Pointer();
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// float* phiPtr = reader.getEuler2Pointer();
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// float* phi2Ptr = reader.getEuler3Pointer();
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// float* madPtr = reader.getMeanAngularDeviationPointer();
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// uint8_t* bcPtr = reader.getBandContrastPointer();
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// uint8_t* bsPtr = reader.getBandSlopePointer();
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//
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// size_t numScanPoints = reader.getNumberOfElements();
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// for(size_t i = 0; i < numScanPoints; i++)
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// {
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// std::cout << static_cast<int>(phasePtr[i]) << "," << static_cast<int>(bandsPtr[i]) << "," << static_cast<int>(errorPtr[i]) << "," << phi1Ptr[i] << "," << phiPtr[i] << "," << phi2Ptr[i] << ","
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// << madPtr[i] << "," << static_cast<int>(bcPtr[i]) << "," << static_cast<int>(bsPtr[i]) << std::endl;
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// }
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return 0;
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}

‎Source/Apps/SourceList.cmake

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@@ -26,6 +26,10 @@ target_include_directories(generate_ipf_legends
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PRIVATE
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"${EbsdLibProj_SOURCE_DIR}/3rdParty/canvas_ity/src")
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add_executable(ParseAztecProject ${EbsdLibProj_SOURCE_DIR}/Source/Apps/ParseAztecProject.cpp)
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target_link_libraries(ParseAztecProject PUBLIC EbsdLib)
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target_include_directories(ParseAztecProject PUBLIC ${EbsdLibProj_SOURCE_DIR}/Source)
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if(EbsdLib_INSTALL_FILES)
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install(FILES

‎Source/Apps/make_ipf.cpp

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@@ -49,7 +49,7 @@ class GenerateIPFColorsImpl
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std::vector<size_t> laueOpsIndex(m_PhaseInfos.size());
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for(size_t i = 0; i < laueOpsIndex.size(); i++)
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{
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laueOpsIndex[i] = m_PhaseInfos[i]->determineLaueGroup();
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laueOpsIndex[i] = m_PhaseInfos[i]->determineOrientationOpsIndex();
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}
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size_t totalPoints = m_CellEulerAngles.size() / 3;

‎Source/EbsdLib/Core/EbsdLibConstants.h

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#include "EbsdLib/Core/StringLiteral.hpp"
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/**
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* @file EbsdConstants.h
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* @brief This file contains many constants that are generic to the EBSD library
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UnknownNumType
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};
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inline std::string SupportedTypeList(NumericTypes::Names::Int8.str() + ", " + NumericTypes::Names::UInt8.str() + ", " + NumericTypes::Names::Int16.str() + ", " + NumericTypes::Names::UInt16.str() + ", " +
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NumericTypes::Names::Int32.str() + ", " + NumericTypes::Names::UInt32.str() + ", " + NumericTypes::Names::Int64.str() + ", " + NumericTypes::Names::UInt64.str() + ", " +
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NumericTypes::Names::Float.str() + ", " + NumericTypes::Names::Double.str() + ", " + NumericTypes::Names::Bool.str() + ", " + NumericTypes::Names::SizeT.str() );
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inline std::string SupportedTypeList(NumericTypes::Names::Int8.str() + ", " + NumericTypes::Names::UInt8.str() + ", " + NumericTypes::Names::Int16.str() + ", " + NumericTypes::Names::UInt16.str() +
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", " + NumericTypes::Names::Int32.str() + ", " + NumericTypes::Names::UInt32.str() + ", " + NumericTypes::Names::Int64.str() + ", " +
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NumericTypes::Names::UInt64.str() + ", " + NumericTypes::Names::Float.str() + ", " + NumericTypes::Names::Double.str() + ", " + NumericTypes::Names::Bool.str() +
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", " + NumericTypes::Names::SizeT.str());
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} // namespace NumericTypes
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/** @brief RefFrameZDir defined for the Stacking order of images into a 3D Volume */
@@ -295,4 +295,3 @@ inline constexpr double BP[6] = {0.0, 1.0, 0.5773502691896260, 0.414213562373095
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namespace LPs = LambertParametersType;
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} // namespace EbsdLib
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‎Source/EbsdLib/Core/StringLiteral.hpp

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#pragma once
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3-
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#include <stdexcept>
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#include <string>
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#include <string_view>
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using WStringLiteral = BasicStringLiteral<wchar_t>;
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using String16Literal = BasicStringLiteral<char16_t>;
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using String32Literal = BasicStringLiteral<char32_t>;
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} // namespace nx::core
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} // namespace EbsdLib
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#if 0
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template <class CharT>

‎Source/EbsdLib/IO/AngleFileLoader.h

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#pragma once
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#include <memory>
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#include <vector>
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#include <string>
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#include <vector>
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#include "EbsdLib/Core/EbsdDataArray.hpp"
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#include "EbsdLib/EbsdLib.h"

‎Source/EbsdLib/IO/BrukerNano/EspritPhase.cpp

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// -----------------------------------------------------------------------------
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//
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// -----------------------------------------------------------------------------
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unsigned int EspritPhase::determineLaueGroup()
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unsigned int EspritPhase::determineOrientationOpsIndex()
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{
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int sg = getIT();
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‎Source/EbsdLib/IO/BrukerNano/EspritPhase.h

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/**
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* @brief Returns the type of crystal structure for this phase.
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*/
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unsigned int determineLaueGroup();
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unsigned int determineOrientationOpsIndex();
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protected:
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EspritPhase();

‎Source/EbsdLib/IO/BrukerNano/H5EspritReader.h

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@@ -65,7 +65,7 @@ class EbsdLib_EXPORT H5EspritReader : public EbsdReader
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/**
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* @brief Returns the name of the class for H5EspritReader
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*/
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std::string getNameOfClass() const;
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std::string getNameOfClass() const override;
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/**
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* @brief Returns the name of the class for H5EspritReader
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*/

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