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Merged
merged 5 commits into from
Jun 30, 2025
Merged

ENH: Add StringArray Support To ReadCSVFile Filter #1339

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5b31cd8
Add support for importing string arrays in ReadCSVFile filter.
joeykleingers Jun 18, 2025
8bca45b
Remove quotes from strings before importing them.
joeykleingers Jun 23, 2025
8b7477b
Fix bug where headers were being cached when they shouldn't have been.
joeykleingers Jun 23, 2025
503ca6a
Add unit test that verifies that quotes are removed from strings.
joeykleingers Jun 23, 2025
f2370fc
Fix Python examples and pipelines.
joeykleingers Jun 24, 2025
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12 changes: 6 additions & 6 deletions src/Plugins/OrientationAnalysis/test/WriteGBCDGMTFileTest.cpp
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Expand Up @@ -101,7 +101,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = fmt::format("{}/6_6_Small_IN100_GBCD/small_in100_sigma_3_1.dat", unit_test::k_TestFilesDir);
data.customHeaders = {k_ExemplarGMT1, k_ExemplarGMT2, k_ExemplarGMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand All @@ -121,7 +121,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = outputFile.string();
data.customHeaders = {k_GMT1, k_GMT2, k_GMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand Down Expand Up @@ -187,7 +187,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = fmt::format("{}/6_6_Small_IN100_GBCD/small_in100_sigma_9_1.dat", unit_test::k_TestFilesDir);
data.customHeaders = {k_ExemplarGMT1, k_ExemplarGMT2, k_ExemplarGMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand All @@ -207,7 +207,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = outputFile.string();
data.customHeaders = {k_GMT1, k_GMT2, k_GMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand Down Expand Up @@ -273,7 +273,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = fmt::format("{}/6_6_Small_IN100_GBCD/small_in100_sigma_11_1.dat", unit_test::k_TestFilesDir);
data.customHeaders = {k_ExemplarGMT1, k_ExemplarGMT2, k_ExemplarGMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand All @@ -293,7 +293,7 @@ TEST_CASE("OrientationAnalysis::WriteGBCDGMTFileFilter", "[OrientationAnalysis][
ReadCSVData data;
data.inputFilePath = outputFile.string();
data.customHeaders = {k_GMT1, k_GMT2, k_GMT3};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32};
data.skippedArrayMask = {false, false, false};
data.startImportRow = 2;
data.delimiters = {' '};
Expand Down
8 changes: 4 additions & 4 deletions src/Plugins/OrientationAnalysis/test/WriteGBCDTriangleDataTest.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -92,8 +92,8 @@ TEST_CASE("OrientationAnalysis::WriteGBCDTriangleDataFilter: Valid filter execut
ReadCSVData data;
data.inputFilePath = fmt::format("{}/6_6_Small_IN100_GBCD/6_6_Small_IN100_GBCD_Triangles.ph", unit_test::k_TestFilesDir);
data.customHeaders = {k_Phi1Right, k_PhiRight, k_Phi2Right, k_Phi1Left, k_PhiLeft, k_Phi2Left, k_TriangleNormal0, k_TriangleNormal1, k_TriangleNormal2, k_SurfaceArea};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32, DataType::float32, DataType::float32,
DataType::float32, DataType::float64, DataType::float64, DataType::float64, DataType::float64};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32, CSVType::float32, CSVType::float32,
CSVType::float32, CSVType::float64, CSVType::float64, CSVType::float64, CSVType::float64};
data.skippedArrayMask = {false, false, false, false, false, false, false, false, false, false};
data.startImportRow = 6;
data.delimiters = {' '};
Expand All @@ -114,8 +114,8 @@ TEST_CASE("OrientationAnalysis::WriteGBCDTriangleDataFilter: Valid filter execut
ReadCSVData data;
data.inputFilePath = outputFile.string();
data.customHeaders = {k_Phi1Right, k_PhiRight, k_Phi2Right, k_Phi1Left, k_PhiLeft, k_Phi2Left, k_TriangleNormal0, k_TriangleNormal1, k_TriangleNormal2, k_SurfaceArea};
data.dataTypes = {DataType::float32, DataType::float32, DataType::float32, DataType::float32, DataType::float32,
DataType::float32, DataType::float64, DataType::float64, DataType::float64, DataType::float64};
data.dataTypes = {CSVType::float32, CSVType::float32, CSVType::float32, CSVType::float32, CSVType::float32,
CSVType::float32, CSVType::float64, CSVType::float64, CSVType::float64, CSVType::float64};
data.skippedArrayMask = {false, false, false, false, false, false, false, false, false, false};
data.startImportRow = 5;
data.delimiters = {' '};
Expand Down
4 changes: 2 additions & 2 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/ReadCSVFile.cpp
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Expand Up @@ -26,7 +26,7 @@ ReadCSVFile::ReadCSVFile() = default;

ReadCSVFile::~ReadCSVFile() noexcept = default;

Result<> ReadCSVFile::readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, usize headersLineNumber, const std::vector<DataType>& columnDataTypes,
Result<> ReadCSVFile::readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, usize headersLineNumber, const std::vector<CSVType>& columnDataTypes,
const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims, const std::vector<char>& delimiters, bool consecutiveDelimiters,
const std::atomic_bool& shouldCancel, const IFilter::MessageHandler& msgHandler)
{
Expand All @@ -39,7 +39,7 @@ Result<> ReadCSVFile::readFile(DataStructure& dataStructure, const std::string&
}

Result<> ReadCSVFile::readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, const std::vector<std::string>& columnHeaders,
const std::vector<DataType>& columnDataTypes, const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims,
const std::vector<CSVType>& columnDataTypes, const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims,
const std::vector<char>& delimiters, bool consecutiveDelimiters, const std::atomic_bool& shouldCancel, const IFilter::MessageHandler& msgHandler)
{
auto headers = columnHeaders;
Expand Down
9 changes: 5 additions & 4 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/Algorithms/ReadCSVFile.hpp
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Expand Up @@ -6,6 +6,7 @@
#include "simplnx/DataStructure/DataStructure.hpp"
#include "simplnx/Filter/Arguments.hpp"
#include "simplnx/Filter/IFilter.hpp"
#include "simplnx/Parameters/util/ReadCSVData.hpp"

namespace fs = std::filesystem;

Expand Down Expand Up @@ -46,11 +47,11 @@ class SIMPLNXCORE_EXPORT ReadCSVFile
ReadCSVFile& operator=(const ReadCSVFile&) = delete;
ReadCSVFile& operator=(ReadCSVFile&&) noexcept = delete;

Result<> readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, const std::vector<std::string>& columnHeaders,
const std::vector<DataType>& columnDataTypes, const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims,
const std::vector<char>& delimiters, bool consecutiveDelimiters, const std::atomic_bool& shouldCancel, const IFilter::MessageHandler& msgHandler);
Result<> readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, const std::vector<std::string>& columnHeaders, const std::vector<CSVType>& columnDataTypes,
const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims, const std::vector<char>& delimiters, bool consecutiveDelimiters,
const std::atomic_bool& shouldCancel, const IFilter::MessageHandler& msgHandler);

Result<> readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, usize headersLineNumber, const std::vector<DataType>& columnDataTypes,
Result<> readFile(DataStructure& dataStructure, const std::string& inputFilePath, usize importStartingRow, usize headersLineNumber, const std::vector<CSVType>& columnDataTypes,
const std::vector<bool>& columnsSkipped, const DataPath& groupPath, const std::vector<usize>& tupleDims, const std::vector<char>& delimiters, bool consecutiveDelimiters,
const std::atomic_bool& shouldCancel, const IFilter::MessageHandler& msgHandler);
};
Expand Down
21 changes: 16 additions & 5 deletions src/Plugins/SimplnxCore/src/SimplnxCore/Filters/ReadCSVFileFilter.cpp
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Expand Up @@ -8,6 +8,7 @@
#include "simplnx/DataStructure/IDataArray.hpp"
#include "simplnx/Filter/Actions/CreateArrayAction.hpp"
#include "simplnx/Filter/Actions/CreateAttributeMatrixAction.hpp"
#include "simplnx/Filter/Actions/CreateStringArrayAction.hpp"
#include "simplnx/Parameters/AttributeMatrixSelectionParameter.hpp"
#include "simplnx/Parameters/BoolParameter.hpp"
#include "simplnx/Parameters/DataGroupCreationParameter.hpp"
Expand Down Expand Up @@ -129,10 +130,13 @@ Result<> cacheHeaders(const ReadCSVData& readCsvData)
Result<> cacheFullFile(const ReadCSVData& readCsvData)
{
s_HeaderCache[s_InstanceId].FilePath = readCsvData.inputFilePath;
auto result = cacheHeaders(readCsvData);
if(result.invalid())
if(readCsvData.headerMode == ReadCSVData::HeaderMode::LINE && readCsvData.headersLine != s_HeaderCache[s_InstanceId].HeadersLine)
{
return result;
auto result = cacheHeaders(readCsvData);
if(result.invalid())
{
return result;
}
}

s_HeaderCache[s_InstanceId].TotalLines = nx::core::FileUtilities::LinesInFile(readCsvData.inputFilePath);
Expand Down Expand Up @@ -431,12 +435,19 @@ IFilter::PreflightResult ReadCSVFileFilter::preflightImpl(const DataStructure& d
continue;
}

DataType dataType = readCSVData.dataTypes[i];
CSVType csvType = readCSVData.dataTypes[i];
std::string name = headers[i];

DataPath arrayPath = groupPath;
arrayPath = arrayPath.createChildPath(name);
resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(dataType, tupleDims, std::vector<usize>{1}, arrayPath));
if(csvType == CSVType::string)
{
resultOutputActions.value().appendAction(std::make_unique<CreateStringArrayAction>(tupleDims, arrayPath));
}
else
{
resultOutputActions.value().appendAction(std::make_unique<CreateArrayAction>(ConvertCSVTypeToDataType(csvType), tupleDims, std::vector<usize>{1}, arrayPath));
}
}

return {std::move(resultOutputActions), {}};
Expand Down
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