inital commit

CMakeLists.txt

@@ -0,0 +1,26 @@
+cmake_minimum_required(VERSION 3.0)
+
+project(mdaptoeis)
+
+set(SRC_FILES
+	src/main.cpp
+	src/tokenize.cpp
+	)
+
+add_executable(${PROJECT_NAME} ${SRC_FILES})
+target_link_libraries( ${PROJECT_NAME} -leisgenerator)
+target_include_directories(${PROJECT_NAME} PRIVATE)
+target_compile_options(${PROJECT_NAME} PRIVATE
+	"-Wall"
+	"-Wno-reorder"
+	"-Wfatal-errors"
+	"-ffast-math"
+	"-ftree-vectorize"
+	"-g"
+	"-fno-strict-aliasing"
+	)
+set_property(TARGET ${PROJECT_NAME} PROPERTY CXX_STANDARD 17)
+
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -s")
+
+install(TARGETS ${PROJECT_NAME} RUNTIME DESTINATION bin)

src/main.cpp

@@ -0,0 +1,135 @@
+#include <eisgenerator/translators.h>
+#include <eisgenerator/eistype.h>
+#include <iostream>
+#include <string>
+#include <vector>
+#include <filesystem>
+
+#include "csvBackend.h"
+#include "tokenize.h"
+
+struct ModelData
+{
+	std::string modelStr;
+	std::string id;
+	size_t classNum;
+	size_t classIndex;
+	double temperature;
+	std::vector<eis::DataPoint> data;
+};
+
+void trimBrackets(std::string& str)
+{
+	if(str[0] == '[')
+		str.erase(str.begin());
+	if(str.back() == ']')
+		str.pop_back();
+}
+
+std::vector<eis::DataPoint> parseEisDataFromMadapArrays(std::string& freqArray, std::string& realArray, std::string& imaginaryArray)
+{
+	assert(realArray.size() > 2);
+	assert(imaginaryArray.size() > 2);
+	trimBrackets(realArray);
+	trimBrackets(imaginaryArray);
+	trimBrackets(freqArray);
+
+	std::vector<std::string> freqTokens = tokenize(freqArray, ',');
+	std::vector<std::string> realTokens = tokenize(realArray, ',');
+	std::vector<std::string> imaginaryTokens = tokenize(imaginaryArray, ',');
+	assert(realTokens.size() == freqTokens.size() && realTokens.size() == imaginaryTokens.size());
+
+	std::vector<eis::DataPoint> data;
+	data.reserve(freqTokens.size());
+	for(size_t i = 0; i < freqTokens.size(); ++i)
+		data.push_back(eis::DataPoint(std::complex<fvalue>(std::stod(realTokens[i]), std::stod(imaginaryTokens[i])), 2*M_PI*std::stod(freqTokens[i])));
+
+	std::sort(data.begin(), data.end(), [](const eis::DataPoint& a, const eis::DataPoint& b){return a.omega < b.omega;});
+	return data;
+}
+
+bool saveData(const ModelData& data, const std::filesystem::path& outDir)
+{
+	std::filesystem::path filename("madapExport_");
+	std::string modelStrWithoutParams = data.modelStr;
+	eis::purgeEisParamBrackets(modelStrWithoutParams);
+	filename.concat(modelStrWithoutParams);
+	filename.concat("_");
+	filename.concat(std::to_string(data.classIndex));
+	filename.concat(".csv");
+	if(!saveToDisk(data.data, outDir/filename, data.modelStr + ", " + data.id + "@" + std::to_string(data.temperature)))
+	{
+		std::cerr<<"Unable to save to "<<outDir/filename;
+		return false;
+	}
+	return true;
+}
+
+bool checkDir(const std::filesystem::path& outDir)
+{
+	if(!std::filesystem::is_directory(outDir))
+	{
+		if(!std::filesystem::create_directory(outDir))
+		{
+			std::cerr<<outDir<<" dose not exist and can not be created\n";
+			return false;
+		}
+	}
+	return true;
+}
+
+int main(int argc, char** argv)
+{
+	if(argc < 2)
+	{
+		std::cerr<<"a file name is required\n";
+		return 1;
+	}
+
+	io::CSVReader<7, io::trim_chars<' ', '\t'>, io::no_quote_escape<';'>> csvFile(argv[1]);
+	csvFile.read_header(io::ignore_extra_column, "experimentID", "temperature", "frequency",
+		"real_impedance", "imaginary_impedance", "EIS_fittedParameters", "EIS_circuit");
+
+	if(!csvFile.next_line())
+		return 1;
+	if(!csvFile.next_line())
+		return 1;
+
+	std::string frequencyArray;
+	std::string realArray;
+	std::string imaginaryArray;
+	std::string paramArray;
+	std::string circutString;
+	std::string idStr;
+	double temperature;
+	std::vector<std::pair<std::string, size_t>> modelStrings;
+
+	if(!checkDir("./out"))
+		return 1;
+
+	while(csvFile.read_row(idStr, temperature, frequencyArray, realArray, imaginaryArray, paramArray, circutString))
+	{
+		ModelData data;
+		data.modelStr = eis::madapToEis(circutString, paramArray);
+		data.id = idStr;
+		auto iterator = std::find_if(modelStrings.begin(), modelStrings.end(),
+									 [circutString](std::pair<std::string, size_t>& pair){return circutString == pair.first;});
+		if(iterator != modelStrings.end())
+		{
+			++iterator->second;
+			data.classIndex = iterator->second;
+			data.classNum = std::distance(modelStrings.begin(), iterator);
+		}
+		else
+		{
+			modelStrings.push_back(std::pair<std::string, size_t>(circutString, 0));
+			data.classIndex = 0;
+			data.classNum = modelStrings.size()-1;
+			std::cout<<"found "<<circutString<<" as new class "<<data.classNum<<'\n';
+		}
+		data.temperature = temperature;
+		data.data = parseEisDataFromMadapArrays(frequencyArray, realArray, imaginaryArray);
+		saveData(data, "./out");
+	}
+
+}

src/tokenize.cpp

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+#include "tokenize.h"
+
+std::vector<std::string> tokenize(const std::string& str, const char delim, const char ignBracketStart, const char ignBracketEnd)
+{
+	std::stringstream ss(str);
+	std::vector<std::string> tokens;
+
+	std::string token;
+	size_t bracketCounter = 0;
+	for(char ch : str)
+	{
+		if(ch == delim && bracketCounter == 0)
+		{
+			tokens.push_back(token);
+			token.clear();
+		}
+		else
+		{
+			token.push_back(ch);
+		}
+
+		if(ignBracketStart == ch)
+			++bracketCounter;
+		else if(ignBracketEnd == ch)
+			--bracketCounter;
+	}
+	if(bracketCounter == 0)
+		tokens.push_back(token);
+	return tokens;
+}

src/tokenize.h

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+#pragma once
+#include <string>
+#include <vector>
+#include <sstream>
+
+std::vector<std::string> tokenize(const std::string& str, const char delim = ' ', const char ignBracketStart = '\0', const char ignBracketEnd = '\0');