From 121669078f948d3e2160e11ef30b0c8410eaddfa Mon Sep 17 00:00:00 2001
From: Carl Philipp Klemm <philipp@uvos.xyz>
Date: Fri, 10 Feb 2023 14:18:21 +0100
Subject: [PATCH] Move common stuff in seperate trabanslation unit Rename main
 to madap

---
 src/common.cpp | 44 ++++++++++++++++++++++++++
 src/common.h   | 13 ++++++++
 src/madap.cpp  | 83 ++++++++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 140 insertions(+)
 create mode 100644 src/common.cpp
 create mode 100644 src/common.h
 create mode 100644 src/madap.cpp

diff --git a/src/common.cpp b/src/common.cpp
new file mode 100644
index 0000000..40465cb
--- /dev/null
+++ b/src/common.cpp
@@ -0,0 +1,44 @@
+#include "common.h"
+
+#include <eisgenerator/eistype.h>
+#include <eisgenerator/translators.h>
+#include <iostream>
+
+bool saveData(const std::string& exportName, const ModelData& data, const std::filesystem::path& outDir, const std::filesystem::path& originFile)
+{
+	std::filesystem::path filename;
+	std::string modelStrWithoutParams = data.modelStr;
+	eis::purgeEisParamBrackets(modelStrWithoutParams);
+	size_t classIndex = 0;
+
+	do
+	{
+		filename.assign(exportName);
+		filename.concat("_");
+		filename.concat(modelStrWithoutParams);
+		filename.concat("_");
+		filename.concat(std::to_string(classIndex));
+		filename.concat(".csv");
+		++classIndex;
+	} while(std::filesystem::exists(outDir/filename));
+
+	if(!saveToDisk(data.data, outDir/filename, data.modelStr + ", " + data.id + ", \"" + std::string(originFile.filename()) + "\""))
+	{
+		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;
+}
diff --git a/src/common.h b/src/common.h
new file mode 100644
index 0000000..d655935
--- /dev/null
+++ b/src/common.h
@@ -0,0 +1,13 @@
+#include <filesystem>
+#include <vector>
+#include <eisgenerator/eistype.h>
+
+struct ModelData
+{
+	std::string modelStr;
+	std::string id;
+	std::vector<eis::DataPoint> data;
+};
+
+bool saveData(const std::string& exportName, const ModelData& data, const std::filesystem::path& outDir, const std::filesystem::path& originFile);
+bool checkDir(const std::filesystem::path& outDir);
diff --git a/src/madap.cpp b/src/madap.cpp
new file mode 100644
index 0000000..92fbdaf
--- /dev/null
+++ b/src/madap.cpp
@@ -0,0 +1,83 @@
+#include <eisgenerator/translators.h>
+#include <eisgenerator/eistype.h>
+#include <iostream>
+#include <string>
+#include <vector>
+#include <filesystem>
+
+#include "csvBackend.h"
+#include "tokenize.h"
+#include "common.h"
+
+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;
+}
+
+int main(int argc, char** argv)
+{
+	if(argc < 2)
+	{
+		std::cerr<<"Usage: "<<(argc > 0 ? argv[0] : "NULL")<<" [FILE] [OUTDIR]\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::filesystem::path outDir("./out");
+	if(argc == 3)
+		outDir = argv[2];
+
+	if(!checkDir(outDir))
+		return 1;
+
+	while(csvFile.read_row(idStr, temperature, frequencyArray, realArray, imaginaryArray, paramArray, circutString))
+	{
+		ModelData data;
+		data.modelStr = eis::madapToEis(circutString, paramArray);
+		data.id = idStr;
+
+		data.data = parseEisDataFromMadapArrays(frequencyArray, realArray, imaginaryArray);
+		saveData("madap", data, outDir, argv[1]);
+	}
+}