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ENH: Remove dependency on EbsdLib for the Parameter. (BlueQuartzSoftw…
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…are#702)

Checks should be done down in the specific filter using this parameter

Signed-off-by: Michael Jackson <[email protected]>
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@imikejackson
imikejackson committed Oct 3, 2023
1 parent 27a4753 commit 32d735f
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Showing 8 changed files with 30 additions and 138 deletions.
4 changes: 0 additions & 4 deletions src/Plugins/ComplexCore/src/ComplexCore/Filters/ImportHDF5Dataset.cpp
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Expand Up @@ -126,10 +126,6 @@ IFilter::PreflightResult ImportHDF5Dataset::preflightImpl(const DataStructure& d

fs::path inputFilePath(inputFile);
std::string ext = inputFilePath.extension().string();
if(ext != ".h5" && ext != ".hdf5" && ext != ".dream3d")
{
return {nonstd::make_unexpected(std::vector<Error>{Error{-20002, fmt::format("The selected file '{}' is not an HDF5 file.", inputFilePath.filename().string())}})};
}

if(!fs::exists(inputFilePath))
{
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Binary file added src/Plugins/OrientationAnalysis/docs/Images/Hexagonal_Axis_Alignment.png
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2 changes: 1 addition & 1 deletion src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ImportH5EspritDataFilter.cpp
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Expand Up @@ -67,7 +67,7 @@ Parameters ImportH5EspritDataFilter::parameters() const
params.insertSeparator(Parameters::Separator{"Input Parameters"});
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::AllowedManufacturers{EbsdLib::OEM::Bruker, EbsdLib::OEM::DREAM3D},
/* OEMEbsdScanSelectionParameter::AllowedManufacturers{EbsdLib::OEM::Bruker, EbsdLib::OEM::DREAM3D},*/
OEMEbsdScanSelectionParameter::EbsdReaderType::Esprit, OEMEbsdScanSelectionParameter::ExtensionsType{".h5"}));
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"}));
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3 changes: 2 additions & 1 deletion src/Plugins/OrientationAnalysis/src/OrientationAnalysis/Filters/ImportH5OimDataFilter.cpp
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Expand Up @@ -64,7 +64,8 @@ Parameters ImportH5OimDataFilter::parameters() const
// Create the parameter descriptors that are needed for this filter
params.insertSeparator(Parameters::Separator{"Input Parameters"});
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::AllowedManufacturers{EbsdLib::OEM::EDAX},
OEMEbsdScanSelectionParameter::ValueType{},
/* OEMEbsdScanSelectionParameter::AllowedManufacturers{EbsdLib::OEM::EDAX},*/
OEMEbsdScanSelectionParameter::EbsdReaderType::Oim, OEMEbsdScanSelectionParameter::ExtensionsType{".h5"}));
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"}));
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106 changes: 4 additions & 102 deletions .../OrientationAnalysis/src/OrientationAnalysis/Parameters/OEMEbsdScanSelectionParameter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,6 @@
#include "complex/Common/StringLiteral.hpp"
#include "complex/Utilities/StringUtilities.hpp"

#include "H5Support/H5ScopedSentinel.h"
#include "H5Support/H5Utilities.h"

#include "EbsdLib/IO/BrukerNano/EspritConstants.h"
#include "EbsdLib/IO/BrukerNano/H5EspritReader.h"
#include "EbsdLib/IO/HKL/CtfFields.h"
#include "EbsdLib/IO/TSL/H5OIMReader.h"

#include <fmt/core.h>
#include <fmt/ranges.h>

Expand All @@ -28,10 +20,9 @@ constexpr StringLiteral k_ScanNames = "scan_names";

//-----------------------------------------------------------------------------
OEMEbsdScanSelectionParameter::OEMEbsdScanSelectionParameter(const std::string& name, const std::string& humanName, const std::string& helpText, const ValueType& defaultValue,
const AllowedManufacturers& allowedManufacturers, const EbsdReaderType& readerType, const ExtensionsType& extensionsType)
const EbsdReaderType& readerType, const ExtensionsType& extensionsType)
: ValueParameter(name, humanName, helpText)
, m_DefaultValue(defaultValue)
, m_AllowedManufacturers(allowedManufacturers)
, m_AvailableExtensions(extensionsType)
, m_ReaderType(readerType)
{
Expand Down Expand Up @@ -112,10 +103,10 @@ Result<std::any> OEMEbsdScanSelectionParameter::fromJson(const nlohmann::json& j
}

const auto orderCheck = json[k_StackingOrder].get<int32>();
if(orderCheck != EbsdLib::RefFrameZDir::LowtoHigh && orderCheck != EbsdLib::RefFrameZDir::HightoLow)
if(orderCheck != RefFrameZDir::k_LowtoHigh && orderCheck != RefFrameZDir::k_HightoLow)
{
return MakeErrorResult<std::any>(FilterParameter::Constants::k_Json_Value_Not_Enumeration, fmt::format("{}JSON value for key '{}' was not a valid ordering Value. [{}|{}] allowed.", prefix.view(),
k_StackingOrder.view(), EbsdLib::RefFrameZDir::LowtoHigh, EbsdLib::RefFrameZDir::HightoLow));
k_StackingOrder.view(), RefFrameZDir::k_LowtoHigh, RefFrameZDir::k_HightoLow));
}

ValueType value;
Expand Down Expand Up @@ -161,7 +152,7 @@ Result<std::any> OEMEbsdScanSelectionParameter::fromJson(const nlohmann::json& j
//-----------------------------------------------------------------------------
IParameter::UniquePointer OEMEbsdScanSelectionParameter::clone() const
{
return std::make_unique<OEMEbsdScanSelectionParameter>(name(), humanName(), helpText(), m_DefaultValue, m_AllowedManufacturers, m_ReaderType, m_AvailableExtensions);
return std::make_unique<OEMEbsdScanSelectionParameter>(name(), humanName(), helpText(), m_DefaultValue, m_ReaderType, m_AvailableExtensions);
}

//-----------------------------------------------------------------------------
Expand Down Expand Up @@ -193,98 +184,9 @@ Result<> OEMEbsdScanSelectionParameter::validate(const std::any& valueRef) const
{
return {nonstd::make_unexpected(std::vector<Error>{{-20032, fmt::format("File extension '{}' is not a valid file extension.", value.inputFilePath.extension().string())}})};
}

if(value.stackingOrder != EbsdLib::RefFrameZDir::LowtoHigh && value.stackingOrder != EbsdLib::RefFrameZDir::HightoLow)
{
errors.push_back({-20033, fmt::format("{} is not a valid value for the stacking order. Please choose either {} or {}", value.stackingOrder, EbsdLib::RefFrameZDir::LowtoHigh,
EbsdLib::RefFrameZDir::HightoLow)});
return {nonstd::make_unexpected(std::move(errors))};
}

std::list<std::string> scanNames;
int32 err = 0;
if(m_ReaderType == EbsdReaderType::Oim)
{
const H5OIMReader::Pointer reader = H5OIMReader::New();
reader->setFileName(value.inputFilePath.string());
err = reader->readScanNames(scanNames);
}
else
{
const H5EspritReader::Pointer reader = H5EspritReader::New();
reader->setFileName(value.inputFilePath.string());
err = reader->readScanNames(scanNames);
}

if(err < 0)
{
errors.push_back({-20034, fmt::format("H5 file '{}' could not be opened. Reported error code from the H5OIMReader class is '{}'", value.inputFilePath.string(), err)});
return {nonstd::make_unexpected(std::move(errors))};
}

const ManufacturerType manufacturer = ReadManufacturer(value.inputFilePath.string());
if(m_AllowedManufacturers.find(manufacturer) == m_AllowedManufacturers.end())
{
errors.push_back({-20035, fmt::format("Original data source type {} is not a valid manufacturer", fmt::underlying(manufacturer))});
return {nonstd::make_unexpected(std::move(errors))};
}

if(value.scanNames.empty())
{
errors.push_back({-20036, fmt::format("At least one scan must be chosen. Please select a scan from the list.")});
return {nonstd::make_unexpected(std::move(errors))};
}

return {};
}

//-----------------------------------------------------------------------------
OEMEbsdScanSelectionParameter::ManufacturerType OEMEbsdScanSelectionParameter::ReadManufacturer(const std::string& inputFile)
{
EbsdLib::OEM manuf = EbsdLib::OEM::Unknown;

const hid_t fid = H5Utilities::openFile(inputFile, true);
if(fid < 0)
{
return manuf;
}
H5ScopedFileSentinel sentinel(fid, false);
std::string dsetName;
std::list<std::string> names;
herr_t err = H5Utilities::getGroupObjects(fid, H5Utilities::CustomHDFDataTypes::Any, names);
auto findIter = std::find(names.begin(), names.end(), EbsdLib::H5OIM::Manufacturer);
if(findIter != names.end())
{
dsetName = EbsdLib::H5OIM::Manufacturer;
}

findIter = std::find(names.begin(), names.end(), EbsdLib::H5Esprit::Manufacturer);
if(findIter != names.end())
{
dsetName = EbsdLib::H5Esprit::Manufacturer;
}

std::string manufacturer("Unknown");
err = H5Lite::readStringDataset(fid, dsetName, manufacturer);
if(err < 0)
{
return manuf;
}
if(manufacturer == EbsdLib::H5OIM::EDAX)
{
manuf = EbsdLib::OEM::EDAX;
}
if(manufacturer == EbsdLib::H5Esprit::BrukerNano)
{
manuf = EbsdLib::OEM::Bruker;
}
if(manufacturer == "DREAM.3D")
{
manuf = EbsdLib::OEM::DREAM3D;
}
return manuf;
}

//-----------------------------------------------------------------------------
OEMEbsdScanSelectionParameter::ExtensionsType OEMEbsdScanSelectionParameter::getAvailableExtensions() const
{
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31 changes: 16 additions & 15 deletions ...ns/OrientationAnalysis/src/OrientationAnalysis/Parameters/OEMEbsdScanSelectionParameter.h
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,6 @@
#include "complex/Utilities/FilePathGenerator.hpp"
#include "complex/complex_export.hpp"

#include "EbsdLib/Core/EbsdLibConstants.h"

#include <filesystem>
#include <list>
#include <string>
Expand All @@ -16,6 +14,16 @@ namespace fs = std::filesystem;

namespace complex
{
/** @brief RefFrameZDir defined for the Stacking order of images into a 3D Volume. This is taken from
* EbsdLib. If EbsdLib changes, this should follow suit.
*/
namespace RefFrameZDir
{
inline constexpr uint32_t k_LowtoHigh = 0;
inline constexpr uint32_t k_HightoLow = 1;
inline constexpr uint32_t UnknownRefFrameZDirection = 2;
} // namespace RefFrameZDir

class COMPLEX_EXPORT OEMEbsdScanSelectionParameter : public ValueParameter
{

Expand All @@ -26,16 +34,16 @@ class COMPLEX_EXPORT OEMEbsdScanSelectionParameter : public ValueParameter
struct ValueType
{
fs::path inputFilePath;
int32 stackingOrder = EbsdLib::RefFrameZDir::LowtoHigh;
uint32_t stackingOrder = RefFrameZDir::k_LowtoHigh;
std::list<std::string> scanNames = {};
};
using ManufacturerType = EbsdLib::OEM;
using AllowedManufacturers = std::unordered_set<ManufacturerType>;

using ExtensionsType = std::unordered_set<std::string>;
enum EbsdReaderType : uint8
{
Oim = 0,
Esprit = 1
Esprit = 1,
H5Oina = 2
};

OEMEbsdScanSelectionParameter() = delete;
Expand All @@ -47,7 +55,8 @@ class COMPLEX_EXPORT OEMEbsdScanSelectionParameter : public ValueParameter
* @param helpText The help text that should be displayed to a user
* @param defaultValue The default value for the parameter
*/
OEMEbsdScanSelectionParameter(const std::string& name, const std::string& humanName, const std::string& helpText, const ValueType& defaultValue, const AllowedManufacturers& allowedManufacturers,
OEMEbsdScanSelectionParameter(const std::string& name, const std::string& humanName, const std::string& helpText, const ValueType& defaultValue,
/* const AllowedManufacturers& allowedManufacturers, */
const EbsdReaderType& readerType, const ExtensionsType& extensionsType);

~OEMEbsdScanSelectionParameter() override = default;
Expand Down Expand Up @@ -112,16 +121,8 @@ class COMPLEX_EXPORT OEMEbsdScanSelectionParameter : public ValueParameter
*/
EbsdReaderType getReaderType() const;

/**
* @brief
* @param inputFile
* @return
*/
static ManufacturerType ReadManufacturer(const std::string& inputFile);

private:
ValueType m_DefaultValue = {};
AllowedManufacturers m_AllowedManufacturers = {};
ExtensionsType m_AvailableExtensions = {};
EbsdReaderType m_ReaderType = {};
};
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4 changes: 4 additions & 0 deletions src/Plugins/OrientationAnalysis/src/OrientationAnalysis/utilities/ImportH5Data.hpp
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Expand Up @@ -20,6 +20,8 @@ struct ORIENTATIONANALYSIS_EXPORT ImportH5DataInputValues
DataPath ImageGeometryPath;
DataPath CellAttributeMatrixPath;
DataPath CellEnsembleAttributeMatrixPath;
bool EdaxHexagonalAlignment;
bool ConvertPhaseToInt32;
};

/**
Expand Down Expand Up @@ -55,6 +57,8 @@ class ORIENTATIONANALYSIS_EXPORT ImportH5Data
int index = 0;
for(const auto& currentScanName : m_InputValues->SelectedScanNames.scanNames)
{
m_MessageHandler({IFilter::Message::Type::Info, fmt::format("Importing Index {}", currentScanName)});

Result<> readResults = readData(currentScanName);
if(readResults.invalid())
{
Expand Down
18 changes: 3 additions & 15 deletions src/Plugins/OrientationAnalysis/wrapping/python/orientationanalysis.cpp
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Expand Up @@ -43,23 +43,11 @@ PYBIND11_MODULE(orientationanalysis, mod)
oemEbsdScanSelectionEbsdReaderType.value("Oim", OEMEbsdScanSelectionParameter::EbsdReaderType::Oim);
oemEbsdScanSelectionEbsdReaderType.value("Esprit", OEMEbsdScanSelectionParameter::EbsdReaderType::Esprit);

py::enum_<OEMEbsdScanSelectionParameter::ManufacturerType> oemEbsdScanSelectionManufacturerType(oemEbsdScanSelectionParameter, "ManufacturerType");
oemEbsdScanSelectionManufacturerType.value("EDAX", OEMEbsdScanSelectionParameter::ManufacturerType::EDAX);
oemEbsdScanSelectionManufacturerType.value("Oxford", OEMEbsdScanSelectionParameter::ManufacturerType::Oxford);
oemEbsdScanSelectionManufacturerType.value("Bruker", OEMEbsdScanSelectionParameter::ManufacturerType::Bruker);
oemEbsdScanSelectionManufacturerType.value("HEDM", OEMEbsdScanSelectionParameter::ManufacturerType::HEDM);
oemEbsdScanSelectionManufacturerType.value("Zeiss", OEMEbsdScanSelectionParameter::ManufacturerType::Zeiss);
oemEbsdScanSelectionManufacturerType.value("Phillips", OEMEbsdScanSelectionParameter::ManufacturerType::Phillips);
oemEbsdScanSelectionManufacturerType.value("ThermoFisher", OEMEbsdScanSelectionParameter::ManufacturerType::ThermoFisher);
oemEbsdScanSelectionManufacturerType.value("DREAM3D", OEMEbsdScanSelectionParameter::ManufacturerType::DREAM3D);
oemEbsdScanSelectionManufacturerType.value("Unknown", OEMEbsdScanSelectionParameter::ManufacturerType::Unknown);

BindParameterConstructor(h5EbsdReaderParameter);

oemEbsdScanSelectionParameter.def(
py::init<const std::string&, const std::string&, const std::string&, const OEMEbsdScanSelectionParameter::ValueType&, const OEMEbsdScanSelectionParameter::AllowedManufacturers&,
OEMEbsdScanSelectionParameter::EbsdReaderType, OEMEbsdScanSelectionParameter::ExtensionsType>(),
"name"_a, "human_name"_a, "help_text"_a, "default_value"_a, "allowed_manufacturers"_a, "reader_type"_a, "extensions_type"_a);
oemEbsdScanSelectionParameter.def(py::init<const std::string&, const std::string&, const std::string&, const OEMEbsdScanSelectionParameter::ValueType&, OEMEbsdScanSelectionParameter::EbsdReaderType,
OEMEbsdScanSelectionParameter::ExtensionsType>(),
"name"_a, "human_name"_a, "help_text"_a, "default_value"_a, "reader_type"_a, "extensions_type"_a);

internals.addConversion<H5EbsdReaderParameter>();
internals.addConversion<OEMEbsdScanSelectionParameter>();
Expand Down

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