add support for whaterver maryam is useing
This commit is contained in:
Carl Philipp Klemm
parent
c78fa5bd42
commit
551e30b098
@ -1,16 +1,15 @@
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cmake_minimum_required(VERSION 3.0)
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project(mdaptoeis)
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project(dataformaters)
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set(SRC_FILES
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src/main.cpp
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set(COMMON_SRC_FILES
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src/tokenize.cpp
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src/common.cpp
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)
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add_executable(${PROJECT_NAME} ${SRC_FILES})
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target_link_libraries( ${PROJECT_NAME} -leisgenerator)
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target_include_directories(${PROJECT_NAME} PRIVATE)
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target_compile_options(${PROJECT_NAME} PRIVATE
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set(COMMON_LINK_LIBRARIES -leisgenerator)
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add_compile_options(
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"-Wall"
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"-Wno-reorder"
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"-Wfatal-errors"
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@ -19,8 +18,22 @@ target_compile_options(${PROJECT_NAME} PRIVATE
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"-g"
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"-fno-strict-aliasing"
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)
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set_property(TARGET ${PROJECT_NAME} PROPERTY CXX_STANDARD 17)
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add_executable(madaptoeis ${COMMON_SRC_FILES} src/madap.cpp)
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target_link_libraries(madaptoeis ${COMMON_LINK_LIBRARIES})
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set_property(TARGET madaptoeis PROPERTY CXX_STANDARD 17)
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install(TARGETS madaptoeis RUNTIME DESTINATION bin)
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add_executable(relaxistoeis ${COMMON_SRC_FILES} src/relaxis.cpp)
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target_link_libraries(relaxistoeis ${COMMON_LINK_LIBRARIES} -lrelaxisloaderpp)
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set_property(TARGET relaxistoeis PROPERTY CXX_STANDARD 17)
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install(TARGETS relaxistoeis RUNTIME DESTINATION bin)
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add_executable(maryamtoeis ${COMMON_SRC_FILES} src/maryam.cpp)
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target_link_libraries(maryamtoeis ${COMMON_LINK_LIBRARIES})
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set_property(TARGET maryamtoeis PROPERTY CXX_STANDARD 17)
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install(TARGETS maryamtoeis RUNTIME DESTINATION bin)
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -s")
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install(TARGETS ${PROJECT_NAME} RUNTIME DESTINATION bin)
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135
src/main.cpp
135
src/main.cpp
@ -1,135 +0,0 @@
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#include <eisgenerator/translators.h>
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#include <eisgenerator/eistype.h>
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#include <iostream>
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#include <string>
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#include <vector>
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#include <filesystem>
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#include "csvBackend.h"
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#include "tokenize.h"
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struct ModelData
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{
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std::string modelStr;
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std::string id;
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size_t classNum;
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size_t classIndex;
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double temperature;
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std::vector<eis::DataPoint> data;
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};
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void trimBrackets(std::string& str)
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{
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if(str[0] == '[')
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str.erase(str.begin());
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if(str.back() == ']')
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str.pop_back();
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}
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std::vector<eis::DataPoint> parseEisDataFromMadapArrays(std::string& freqArray, std::string& realArray, std::string& imaginaryArray)
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{
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assert(realArray.size() > 2);
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assert(imaginaryArray.size() > 2);
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trimBrackets(realArray);
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trimBrackets(imaginaryArray);
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trimBrackets(freqArray);
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std::vector<std::string> freqTokens = tokenize(freqArray, ',');
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std::vector<std::string> realTokens = tokenize(realArray, ',');
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std::vector<std::string> imaginaryTokens = tokenize(imaginaryArray, ',');
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assert(realTokens.size() == freqTokens.size() && realTokens.size() == imaginaryTokens.size());
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std::vector<eis::DataPoint> data;
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data.reserve(freqTokens.size());
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for(size_t i = 0; i < freqTokens.size(); ++i)
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data.push_back(eis::DataPoint(std::complex<fvalue>(std::stod(realTokens[i]), std::stod(imaginaryTokens[i])), 2*M_PI*std::stod(freqTokens[i])));
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std::sort(data.begin(), data.end(), [](const eis::DataPoint& a, const eis::DataPoint& b){return a.omega < b.omega;});
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return data;
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}
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bool saveData(const ModelData& data, const std::filesystem::path& outDir)
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{
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std::filesystem::path filename("madapExport_");
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std::string modelStrWithoutParams = data.modelStr;
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eis::purgeEisParamBrackets(modelStrWithoutParams);
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filename.concat(modelStrWithoutParams);
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filename.concat("_");
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filename.concat(std::to_string(data.classIndex));
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filename.concat(".csv");
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if(!saveToDisk(data.data, outDir/filename, data.modelStr + ", " + data.id + "@" + std::to_string(data.temperature)))
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{
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std::cerr<<"Unable to save to "<<outDir/filename;
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return false;
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}
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return true;
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}
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bool checkDir(const std::filesystem::path& outDir)
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{
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if(!std::filesystem::is_directory(outDir))
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{
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if(!std::filesystem::create_directory(outDir))
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{
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std::cerr<<outDir<<" dose not exist and can not be created\n";
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return false;
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}
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}
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return true;
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}
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int main(int argc, char** argv)
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{
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if(argc < 2)
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{
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std::cerr<<"a file name is required\n";
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return 1;
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}
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io::CSVReader<7, io::trim_chars<' ', '\t'>, io::no_quote_escape<';'>> csvFile(argv[1]);
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csvFile.read_header(io::ignore_extra_column, "experimentID", "temperature", "frequency",
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"real_impedance", "imaginary_impedance", "EIS_fittedParameters", "EIS_circuit");
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if(!csvFile.next_line())
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return 1;
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if(!csvFile.next_line())
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return 1;
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std::string frequencyArray;
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std::string realArray;
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std::string imaginaryArray;
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std::string paramArray;
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std::string circutString;
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std::string idStr;
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double temperature;
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std::vector<std::pair<std::string, size_t>> modelStrings;
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if(!checkDir("./out"))
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return 1;
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while(csvFile.read_row(idStr, temperature, frequencyArray, realArray, imaginaryArray, paramArray, circutString))
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{
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ModelData data;
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data.modelStr = eis::madapToEis(circutString, paramArray);
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data.id = idStr;
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auto iterator = std::find_if(modelStrings.begin(), modelStrings.end(),
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[circutString](std::pair<std::string, size_t>& pair){return circutString == pair.first;});
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if(iterator != modelStrings.end())
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{
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++iterator->second;
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data.classIndex = iterator->second;
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data.classNum = std::distance(modelStrings.begin(), iterator);
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}
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else
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{
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modelStrings.push_back(std::pair<std::string, size_t>(circutString, 0));
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data.classIndex = 0;
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data.classNum = modelStrings.size()-1;
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std::cout<<"found "<<circutString<<" as new class "<<data.classNum<<'\n';
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}
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data.temperature = temperature;
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data.data = parseEisDataFromMadapArrays(frequencyArray, realArray, imaginaryArray);
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saveData(data, "./out");
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}
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}
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49
src/maryam.cpp
Normal file
49
src/maryam.cpp
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@ -0,0 +1,49 @@
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#include <iostream>
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#include <filesystem>
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#include <eisgenerator/translators.h>
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#include <eisgenerator/eistype.h>
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#include "csvBackend.h"
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#include "common.h"
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int main(int argc, char** argv)
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{
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if(argc < 4)
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{
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std::cerr<<"Usage: "<<(argc > 0 ? argv[0] : "NULL")<<" [OUTDIR] [MODEL] [FILENAME(S)]\n";
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return 1;
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}
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std::filesystem::path outDir(argv[1]);
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if(!checkDir(outDir))
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return 1;
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try
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{
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for(int i = 3; i < argc; ++i)
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{
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io::CSVReader<3, io::trim_chars<' '>, io::no_quote_escape<'\t'>> csvFile(argv[i]);
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if(!csvFile.next_line())
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return 1;
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csvFile.read_header(io::ignore_extra_column, "Impedance Real part", "Impedance Imaginary Part", "Frequency [Hz]");
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std::string frequency;
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std::string real;
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std::string imaginary;
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ModelData data;
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data.modelStr = eis::relaxisToEis(argv[2]);
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data.id = std::to_string(i-3);
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while(csvFile.read_row(real, imaginary, frequency))
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data.data.push_back(eis::DataPoint(std::complex<fvalue>(std::stod(real), std::stod(imaginary)), std::stod(frequency)*2*M_PI));
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saveData("maryam", data, outDir, argv[i]);
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}
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}
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catch (const std::invalid_argument& err)
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{
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std::cerr<<"Could not read file "<<err.what();
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return 1;
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}
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return 0;
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}
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