From 29d0c5f754c27cb54c5c1d7970a870c71d8b9d85 Mon Sep 17 00:00:00 2001
From: Carl Philipp Klemm <philipp@uvos.xyz>
Date: Thu, 27 Jun 2024 15:16:04 +0200
Subject: [PATCH] Add header description field to EisSpectra, split EisSpectra
into a seperate translation unit
---
CMakeLists.txt | 1 +
eisgenerator/eistype.h | 190 +---------------------------
eisgenerator/spectra.h | 206 +++++++++++++++++++++++++++++++
eistype.cpp | 247 -------------------------------------
spectra.cpp | 274 +++++++++++++++++++++++++++++++++++++++++
strops.cpp | 5 +
strops.h | 5 +
test.cpp | 2 +-
8 files changed, 493 insertions(+), 437 deletions(-)
create mode 100644 eisgenerator/spectra.h
create mode 100644 spectra.cpp
diff --git a/CMakeLists.txt b/CMakeLists.txt
index fa71b8f..3c043c7 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -32,6 +32,7 @@ set(SRC_FILES
normalize.cpp
basicmath.cpp
eistype.cpp
+ spectra.cpp
strops.cpp
translators.cpp
randomgen.cpp
diff --git a/eisgenerator/eistype.h b/eisgenerator/eistype.h
index c71f87d..8670153 100644
--- a/eisgenerator/eistype.h
+++ b/eisgenerator/eistype.h
@@ -256,192 +256,6 @@ public:
}
};
-class EisSpectra
-{
-public:
- static constexpr int F_VERSION_MAJOR = 1;
- static constexpr int F_VERSION_MINOR = 0;
- static constexpr int F_VERSION_PATCH = 0;
- static constexpr char F_MAGIC[] = "EISF";
-
-public:
- std::vector<DataPoint> data;
- std::string model;
- std::string header;
- std::vector<double> labels;
- std::vector<std::string> labelNames;
-
-public:
- /**
- * @brief Constructs an EisSpectra.
- *
- * @param data Vector of the data points of the spectra.
- * @param model Model description string for this spectra.
- * @param header A free-form text that will be included in any save of this spectra.
- * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
- * @param labelNames An optional vector of names describing every input of the model.
- */
- EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
- std::vector<double> labels = std::vector<double>(),
- std::vector<std::string> labelNames = std::vector<std::string>());
-
- /**
- * @brief Constructs an EisSpectra.
- *
- * This function differs from the above only in the datatype of the label.
- *
- * @param data Vector of the data points of the spectra.
- * @param model Model description string for this spectra.
- * @param header A free-form text that will be included in any save of this spectra.
- * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
- * @param labelNames An optional vector of names describing every input of the model.
- */
- EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
- std::vector<float> labels, std::vector<std::string> labelNames = std::vector<std::string>());
-
- /**
- * @brief Constructs an EisSpectra.
- *
- * This function differs from the above only in the datatype of the label.
- *
- * @param data Vector of the data points of the spectra.
- * @param model Model description string for this spectra.
- * @param header A free-from text that will be included in any save of this spectra.
- * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
- * @param labelNames An optional vector of names describing every input of the model.
- */
- EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
- std::vector<size_t> labels, std::vector<std::string> labelNames = std::vector<std::string>());
-
- /**
- * @brief Constructs an EisSpectra.
- *
- * This function differs from the above only in the datatype of the label.
- *
- * @param data Vector of the data points of the spectra.
- * @param model Model description string for this spectra.
- * @param header A free-form text that will be included in any save of this spectra.
- * @param label A value corresponding to all inputs of the model.
- * @param maxLabel The number of inputs of the model.
- */
- EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
- size_t label, size_t maxLabel, std::vector<std::string> labelNames = std::vector<std::string>());
-
- /**
- * @brief Constructs a EisSpectra by loading an EIS file from disk.
- *
- * @throw eis::file_error if there is an error loading the file
- * @param path The path to the file.
- */
- EisSpectra(const std::filesystem::path& path){*this = loadFromDisk(path);}
-
- EisSpectra(){}
-
- /**
- * @brief Constructs a EisSpectra by loading a EIS file from disk.
- *
- * This function has the attribute [[nodiscard]]
- *
- * @throw eis::file_error if there is an error loading the file
- * @param path The path to the file.
- * @return The EisSpectra parsed from the file.
- */
- [[nodiscard]] static EisSpectra loadFromDisk(const std::filesystem::path& path);
-
- /**
- * @brief Constructs a EisSpectra by loading a EIS file from a stream.
- *
- * This function has the attribute [[nodiscard]]
- *
- * @throw eis::file_error if there is an error loading the file
- * @param stream The stream that contains the EIS file.
- * @return The EisSpectra parsed from the stream.
- */
- [[nodiscard]] static EisSpectra loadFromStream(std::istream& stream);
-
- /**
- * @brief Sets all input values up to a maximum given by maxLabel to the value given by label.
- *
- * @param label The value to apply to all inputs.
- * @param maxLabel The maximum number of values to set.
- */
- void setLabel(size_t label, size_t maxLabel);
-
- /**
- * @brief Gets the input value of this model, where it is a single value.
- *
- * @return The input value,
- */
- size_t getLabel();
-
- /**
- * @brief Sets the input values of this model.
- *
- * @param label The input values.
- */
- void setSzLabels(std::vector<size_t> label);
-
- /**
- * @brief Sets the input values of this model.
- *
- * @param label The input values.
- */
- void setLabels(const std::vector<double>& labelsIn);
-
- /**
- * @brief Sets the input values of this model.
- *
- * @param label The input values.
- */
- void setLabels(const std::vector<float>& labelsIn);
-
- /**
- * @brief Sets the input values of this model.
- *
- * @param label The input values.
- */
- std::vector<size_t> getSzLabels() const;
-
- /**
- * @brief Returns true if there are multiple inputs, false otherwise.
- *
- * @return true if there are multiple inputs, false otherwise.
- */
- bool isMulticlass();
-
- /**
- * @brief Returns the inputs as a vector.
- *
- * @return The inputs as a vector.
- */
- std::vector<fvalue> getFvalueLabels();
-
- /**
- * @brief Saves the spectra to disk.
- *
- * @param path A path to the file on disk where the spectra shall be saved.
- * @return true on success, false on failure.
- */
- bool saveToDisk(const std::filesystem::path& path) const;
-
- /**
- * @brief Saves the spectra in the given stream.
- *
- * @param stream A std::ostream into which the spectra will be saved.
- */
- void saveToStream(std::ostream& stream) const;
-};
-
-/**
- * @brief Deprecated function use eis::EisSpectra::saveToDisk instead.
- */
-[[deprecated]] bool saveToDisk(const EisSpectra& data, const std::filesystem::path& path);
-
-/**
- * @brief Deprecated function use eis::EisSpectra::loadFromDisk instead.
- */
-[[deprecated]] [[nodiscard]] EisSpectra loadFromDisk(const std::filesystem::path& path);
-
/**
* @brief Returns the a vector of DataPoints as a pair of valarrays.
*
@@ -468,6 +282,4 @@ std::ostream &operator<<(std::ostream &s, eis::DataPoint const& dp);
std::ostream &operator<<(std::ostream &s, eis::Range const& range);
-std::ostream &operator<<(std::ostream &s, eis::EisSpectra const& spectra);
-
-
+#include "spectra.h"
diff --git a/eisgenerator/spectra.h b/eisgenerator/spectra.h
new file mode 100644
index 0000000..2d7a430
--- /dev/null
+++ b/eisgenerator/spectra.h
@@ -0,0 +1,206 @@
+#pragma once
+/**
+ * @addtogroup TYPES
+ * @{
+ */
+
+#include <string>
+#include <vector>
+
+#include "eistype.h"
+
+namespace eis
+{
+
+class EisSpectra
+{
+public:
+ static constexpr int F_VERSION_MAJOR = 1;
+ static constexpr int F_VERSION_MINOR = 1;
+ static constexpr int F_VERSION_PATCH = 0;
+ static constexpr char F_MAGIC[] = "EISF";
+
+public:
+ std::vector<DataPoint> data;
+ std::string model;
+ std::string headerDescription;
+ std::string header;
+ std::vector<double> labels;
+ std::vector<std::string> labelNames;
+
+public:
+ /**
+ * @brief Constructs an EisSpectra.
+ *
+ * @param data Vector of the data points of the spectra.
+ * @param model Model description string for this spectra.
+ * @param header A free-form text that will be included in any save of this spectra.
+ * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
+ * @param labelNames An optional vector of names describing every input of the model.
+ */
+ EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
+ std::vector<double> labels = std::vector<double>(),
+ std::vector<std::string> labelNames = std::vector<std::string>());
+
+ /**
+ * @brief Constructs an EisSpectra.
+ *
+ * This function differs from the above only in the datatype of the label.
+ *
+ * @param data Vector of the data points of the spectra.
+ * @param model Model description string for this spectra.
+ * @param header A free-form text that will be included in any save of this spectra.
+ * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
+ * @param labelNames An optional vector of names describing every input of the model.
+ */
+ EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
+ std::vector<float> labels, std::vector<std::string> labelNames = std::vector<std::string>());
+
+ /**
+ * @brief Constructs an EisSpectra.
+ *
+ * This function differs from the above only in the datatype of the label.
+ *
+ * @param data Vector of the data points of the spectra.
+ * @param model Model description string for this spectra.
+ * @param header A free-from text that will be included in any save of this spectra.
+ * @param labels An optional vector of giving the values of the inputs of the model to get this spectra.
+ * @param labelNames An optional vector of names describing every input of the model.
+ */
+ EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
+ std::vector<size_t> labels, std::vector<std::string> labelNames = std::vector<std::string>());
+
+ /**
+ * @brief Constructs an EisSpectra.
+ *
+ * This function differs from the above only in the datatype of the label.
+ *
+ * @param data Vector of the data points of the spectra.
+ * @param model Model description string for this spectra.
+ * @param header A free-form text that will be included in any save of this spectra.
+ * @param label A value corresponding to all inputs of the model.
+ * @param maxLabel The number of inputs of the model.
+ */
+ EisSpectra(const std::vector<DataPoint>& data, const std::string& model, const std::string& header,
+ size_t label, size_t maxLabel, std::vector<std::string> labelNames = std::vector<std::string>());
+
+ /**
+ * @brief Constructs a EisSpectra by loading an EIS file from disk.
+ *
+ * @throw eis::file_error if there is an error loading the file
+ * @param path The path to the file.
+ */
+ EisSpectra(const std::filesystem::path& path){*this = loadFromDisk(path);}
+
+ EisSpectra(){}
+
+ /**
+ * @brief Constructs a EisSpectra by loading a EIS file from disk.
+ *
+ * This function has the attribute [[nodiscard]]
+ *
+ * @throw eis::file_error if there is an error loading the file
+ * @param path The path to the file.
+ * @return The EisSpectra parsed from the file.
+ */
+ [[nodiscard]] static EisSpectra loadFromDisk(const std::filesystem::path& path);
+
+ /**
+ * @brief Constructs a EisSpectra by loading a EIS file from a stream.
+ *
+ * This function has the attribute [[nodiscard]]
+ *
+ * @throw eis::file_error if there is an error loading the file
+ * @param stream The stream that contains the EIS file.
+ * @return The EisSpectra parsed from the stream.
+ */
+ [[nodiscard]] static EisSpectra loadFromStream(std::istream& stream);
+
+ /**
+ * @brief Sets all input values up to a maximum given by maxLabel to the value given by label.
+ *
+ * @param label The value to apply to all inputs.
+ * @param maxLabel The maximum number of values to set.
+ */
+ void setLabel(size_t label, size_t maxLabel);
+
+ /**
+ * @brief Gets the input value of this model, where it is a single value.
+ *
+ * @return The input value,
+ */
+ size_t getLabel();
+
+ /**
+ * @brief Sets the input values of this model.
+ *
+ * @param label The input values.
+ */
+ void setSzLabels(std::vector<size_t> label);
+
+ /**
+ * @brief Sets the input values of this model.
+ *
+ * @param label The input values.
+ */
+ void setLabels(const std::vector<double>& labelsIn);
+
+ /**
+ * @brief Sets the input values of this model.
+ *
+ * @param label The input values.
+ */
+ void setLabels(const std::vector<float>& labelsIn);
+
+ /**
+ * @brief Sets the input values of this model.
+ *
+ * @param label The input values.
+ */
+ std::vector<size_t> getSzLabels() const;
+
+ /**
+ * @brief Returns true if there are multiple inputs, false otherwise.
+ *
+ * @return true if there are multiple inputs, false otherwise.
+ */
+ bool isMulticlass();
+
+ /**
+ * @brief Returns the inputs as a vector.
+ *
+ * @return The inputs as a vector.
+ */
+ std::vector<fvalue> getFvalueLabels();
+
+ /**
+ * @brief Saves the spectra to disk.
+ *
+ * @param path A path to the file on disk where the spectra shall be saved.
+ * @return true on success, false on failure.
+ */
+ bool saveToDisk(const std::filesystem::path& path) const;
+
+ /**
+ * @brief Saves the spectra in the given stream.
+ *
+ * @param stream A std::ostream into which the spectra will be saved.
+ */
+ void saveToStream(std::ostream& stream) const;
+};
+
+/**
+ * @brief Deprecated function use eis::EisSpectra::saveToDisk instead.
+ */
+[[deprecated]] bool saveToDisk(const EisSpectra& data, const std::filesystem::path& path);
+
+/**
+ * @brief Deprecated function use eis::EisSpectra::loadFromDisk instead.
+ */
+[[deprecated]] [[nodiscard]] EisSpectra loadFromDisk(const std::filesystem::path& path);
+
+}
+
+std::ostream &operator<<(std::ostream &s, eis::EisSpectra const& spectra);
+
+/** @} */
diff --git a/eistype.cpp b/eistype.cpp
index 6061d79..638821c 100644
--- a/eistype.cpp
+++ b/eistype.cpp
@@ -20,14 +20,12 @@
//
#include "eistype.h"
-#include <fstream>
#include <sstream>
#include <string>
#include <vector>
#include "strops.h"
#include "log.h"
-#include "basicmath.h"
using namespace eis;
@@ -155,245 +153,6 @@ std::ostream &operator<<(std::ostream &s, Range const& range)
return s;
}
-EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn,
- const std::string& headerIn, std::vector<double> labelsIn, std::vector<std::string> labelNamesIn):
-data(dataIn), model(modelIn), header(headerIn), labels(labelsIn), labelNames(labelNamesIn)
-{
-
-}
-
-EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn,
- const std::string& headerIn, std::vector<float> labelsIn, std::vector<std::string> labelNamesIn):
-data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
-{
- setLabels(labelsIn);
-}
-
-EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn, const std::string& headerIn,
- std::vector<size_t> labelsIn, std::vector<std::string> labelNamesIn):
-data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
-{
- setSzLabels(labelsIn);
-}
-
-EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn, const std::string& headerIn,
- size_t label, size_t maxLabel, std::vector<std::string> labelNamesIn):
-data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
-{
- setLabel(label, maxLabel);
-}
-
-void EisSpectra::setLabel(size_t label, size_t maxLabel)
-{
- labels.assign(maxLabel, 0);
- labels[label] = 1;
-}
-
-void EisSpectra::setSzLabels(std::vector<size_t> labelsIn)
-{
- labels.assign(labelsIn.size(), 0);
- for(size_t i = 0; i < labelsIn.size(); ++i)
- labels[i] = static_cast<double>(labelsIn[i]);
-}
-
-std::vector<size_t> EisSpectra::getSzLabels() const
-{
- std::vector<size_t> out(labels.size());
- for(size_t i = 0; i < labels.size(); ++i)
- out[i] = static_cast<size_t>(labels[i]);
- return out;
-}
-
-size_t EisSpectra::getLabel()
-{
- for(size_t i = 0; i < labels.size(); ++i)
- if(labels[i] != 0)
- return i;
- return 0;
-}
-
-bool EisSpectra::isMulticlass()
-{
- bool foundFirst = false;
- for(size_t i = 0; i < labels.size(); ++i)
- {
- if(labels[i] != 0)
- {
- if(foundFirst)
- return true;
- else
- foundFirst = true;
- }
- }
- return false;
-}
-
-void EisSpectra::setLabels(const std::vector<float>& labelsIn)
-{
- labels.assign(labelsIn.size(), 0);
- for(size_t i = 0; i < labels.size(); ++i)
- labels[i] = labelsIn[i];
-}
-
-void EisSpectra::setLabels(const std::vector<double>& labelsIn)
-{
- labels = labelsIn;
-}
-
-std::vector<fvalue> EisSpectra::getFvalueLabels()
-{
- if constexpr(std::is_same<fvalue, double>::value)
- {
- #pragma GCC diagnostic push
- #pragma GCC diagnostic ignored "-Wstrict-aliasing"
- return *reinterpret_cast<std::vector<fvalue>*>(&labels);
- #pragma GCC diagnostic pop
- }
- else
- {
- std::vector<fvalue> out(labels.size());
- for(size_t i = 0; i < labels.size(); ++i)
- out[i] = static_cast<fvalue>(labels[i]);
- return out;
- }
-}
-
-void EisSpectra::saveToStream(std::ostream& stream) const
-{
- stream<<std::scientific;
- stream<<F_MAGIC<<", "<<std::to_string(F_VERSION_MAJOR)<<'.'
- <<std::to_string(F_VERSION_MINOR)<<'.'<<std::to_string(F_VERSION_PATCH)<<'\n';
-
- stream<<'"'<<model<<'"'<<(!header.empty() ? ", " : "");
- stream<<header;
-
- if(!labels.empty())
- {
- if(!labelNames.empty())
- {
- stream<<"\nlabelsNames\n";
- std::string labelLine;
- for(const std::string& name : labelNames)
- labelLine += "\"" + name + "\", ";
- labelLine.pop_back();
- labelLine.pop_back();
- stream<<labelLine;
- }
- stream<<"\nlabels\n";
-
- std::stringstream labelSs;
- for(double label : labels)
- labelSs<<label<<", ";
- std::string labelLine = labelSs.str();
- labelLine.pop_back();
- labelLine.pop_back();
- stream<<labelLine;
- }
-
- stream<<"\nomega, real, im\n";
-
- for(const eis::DataPoint& point : data)
- stream<<point.omega<<", "<<point.im.real()<<", "<<point.im.imag()<<'\n';
-}
-
-bool EisSpectra::saveToDisk(const std::filesystem::path& path) const
-{
- std::fstream file;
- file.open(path, std::ios_base::out | std::ios_base::trunc);
- if(!file.is_open())
- {
- Log(Log::ERROR)<<"can not open "<<path<<" for writing\n";
- return false;
- }
-
- saveToStream(file);
-
- file.close();
- return true;
-}
-
-EisSpectra EisSpectra::loadFromStream(std::istream& stream)
-{
- EisSpectra out;
- std::string line;
- std::getline(stream, line);
- std::vector<std::string> tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
-
- if(tokens.size() < 2 || tokens[0] != F_MAGIC)
- {
- throw file_error("not a valid EISGenerator file or stream");
- }
- else
- {
- std::vector<std::string> versionTokens = tokenize(tokens[1], '.');
- if(versionTokens.size() != 3 || std::stoi(versionTokens[0]) > F_VERSION_MAJOR || std::stoi(versionTokens[1]) > F_VERSION_MINOR)
- throw file_error("saved by a newer version of EISGenerator, can not open");
- }
-
- std::getline(stream, line);
- tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
- stripQuotes(tokens[0]);
- out.model = tokens[0];
- line.erase(line.begin(), line.begin()+tokens.size());
- out.header = line;
-
- while(stream.good())
- {
- std::getline(stream, line);
- if(line.starts_with("labelsNames"))
- {
- std::getline(stream, line);
- out.labelNames = tokenizeBinaryIgnore(line, ',', '"', '\\');
- continue;
- }
- else if(line.starts_with("labels"))
- {
- std::getline(stream, line);
- std::vector<std::string> tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
- for(const std::string& token : tokens)
- out.labels.push_back(std::stod(token));
- continue;
- }
- else if(line.empty() || line[0] == '#' || line.starts_with("omega"))
- {
- continue;
- }
- tokens = tokenize(line, ',');
- if(tokens.size() != 3)
- throw file_error("invalid line: " + line);
-
- #pragma GCC diagnostic push
- #pragma GCC diagnostic ignored "-Wnarrowing"
- if constexpr (std::is_same<fvalue, double>::value)
- out.data.push_back(DataPoint({std::stod(tokens[1]), std::stod(tokens[2])}, std::stod(tokens[0])));
- else
- out.data.push_back(DataPoint({std::stof(tokens[1]), std::stof(tokens[2])}, std::stof(tokens[0])));
- #pragma GCC diagnostic pop
-
- eis::removeDuplicates(out.data);
- }
-
- return out;
-}
-
-EisSpectra EisSpectra::loadFromDisk(const std::filesystem::path& path)
-{
- std::fstream file;
- file.open(path, std::ios_base::in);
- if(!file.is_open())
- throw file_error("can not open " + path.string() + " for reading\n");
-
- try
- {
- EisSpectra out = loadFromStream(file);
- return out;
- }
- catch(const file_error& err)
- {
- throw file_error(path.string() + std::string(": ") + err.what());
- }
-}
-
static VersionFixed version = {VERSION_MAJOR, VERSION_MINOR, VERSION_PATCH};
const VersionFixed& getVersion()
@@ -401,12 +160,6 @@ const VersionFixed& getVersion()
return version;
}
-std::ostream &operator<<(std::ostream &s, EisSpectra const& spectra)
-{
- spectra.saveToStream(s);
- return s;
-}
-
std::ostream &operator<<(std::ostream &s, DataPoint const& dp)
{
s<<dp.im;
diff --git a/spectra.cpp b/spectra.cpp
new file mode 100644
index 0000000..3c139fc
--- /dev/null
+++ b/spectra.cpp
@@ -0,0 +1,274 @@
+#include <fstream>
+
+#include "spectra.h"
+#include "eistype.h"
+#include "strops.h"
+#include "log.h"
+#include "basicmath.h"
+
+namespace eis
+{
+
+EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn,
+ const std::string& headerIn, std::vector<double> labelsIn, std::vector<std::string> labelNamesIn):
+data(dataIn), model(modelIn), header(headerIn), labels(labelsIn), labelNames(labelNamesIn)
+{
+
+}
+
+EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn,
+ const std::string& headerIn, std::vector<float> labelsIn, std::vector<std::string> labelNamesIn):
+data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
+{
+ setLabels(labelsIn);
+}
+
+EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn, const std::string& headerIn,
+ std::vector<size_t> labelsIn, std::vector<std::string> labelNamesIn):
+data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
+{
+ setSzLabels(labelsIn);
+}
+
+EisSpectra::EisSpectra(const std::vector<DataPoint>& dataIn, const std::string& modelIn, const std::string& headerIn,
+ size_t label, size_t maxLabel, std::vector<std::string> labelNamesIn):
+data(dataIn), model(modelIn), header(headerIn), labelNames(labelNamesIn)
+{
+ setLabel(label, maxLabel);
+}
+
+void EisSpectra::setLabel(size_t label, size_t maxLabel)
+{
+ labels.assign(maxLabel, 0);
+ labels[label] = 1;
+}
+
+void EisSpectra::setSzLabels(std::vector<size_t> labelsIn)
+{
+ labels.assign(labelsIn.size(), 0);
+ for(size_t i = 0; i < labelsIn.size(); ++i)
+ labels[i] = static_cast<double>(labelsIn[i]);
+}
+
+std::vector<size_t> EisSpectra::getSzLabels() const
+{
+ std::vector<size_t> out(labels.size());
+ for(size_t i = 0; i < labels.size(); ++i)
+ out[i] = static_cast<size_t>(labels[i]);
+ return out;
+}
+
+size_t EisSpectra::getLabel()
+{
+ for(size_t i = 0; i < labels.size(); ++i)
+ if(labels[i] != 0)
+ return i;
+ return 0;
+}
+
+bool EisSpectra::isMulticlass()
+{
+ bool foundFirst = false;
+ for(size_t i = 0; i < labels.size(); ++i)
+ {
+ if(labels[i] != 0)
+ {
+ if(foundFirst)
+ return true;
+ else
+ foundFirst = true;
+ }
+ }
+ return false;
+}
+
+void EisSpectra::setLabels(const std::vector<float>& labelsIn)
+{
+ labels.assign(labelsIn.size(), 0);
+ for(size_t i = 0; i < labels.size(); ++i)
+ labels[i] = labelsIn[i];
+}
+
+void EisSpectra::setLabels(const std::vector<double>& labelsIn)
+{
+ labels = labelsIn;
+}
+
+std::vector<fvalue> EisSpectra::getFvalueLabels()
+{
+ if constexpr(std::is_same<fvalue, double>::value)
+ {
+ #pragma GCC diagnostic push
+ #pragma GCC diagnostic ignored "-Wstrict-aliasing"
+ return *reinterpret_cast<std::vector<fvalue>*>(&labels);
+ #pragma GCC diagnostic pop
+ }
+ else
+ {
+ std::vector<fvalue> out(labels.size());
+ for(size_t i = 0; i < labels.size(); ++i)
+ out[i] = static_cast<fvalue>(labels[i]);
+ return out;
+ }
+}
+
+void EisSpectra::saveToStream(std::ostream& stream) const
+{
+ stream<<std::scientific;
+ stream<<F_MAGIC<<", "<<std::to_string(F_VERSION_MAJOR)<<'.'
+ <<std::to_string(F_VERSION_MINOR)<<'.'<<std::to_string(F_VERSION_PATCH)<<'\n';
+
+ stream<<'"'<<model<<'"'<<'\n'<<(headerDescription.empty() ? "None" : headerDescription)<<'\n'<<(header.empty() ? "None" : header);
+
+ if(!labels.empty())
+ {
+ if(!labelNames.empty())
+ {
+ stream<<"\nlabelsNames\n";
+ std::string labelLine;
+ for(const std::string& name : labelNames)
+ labelLine += "\"" + name + "\", ";
+ labelLine.pop_back();
+ labelLine.pop_back();
+ stream<<labelLine;
+ }
+ stream<<"\nlabels\n";
+
+ std::stringstream labelSs;
+ for(double label : labels)
+ labelSs<<label<<", ";
+ std::string labelLine = labelSs.str();
+ labelLine.pop_back();
+ labelLine.pop_back();
+ stream<<labelLine;
+ }
+
+ stream<<"\nomega, real, im\n";
+
+ for(const eis::DataPoint& point : data)
+ stream<<point.omega<<", "<<point.im.real()<<", "<<point.im.imag()<<'\n';
+}
+
+bool EisSpectra::saveToDisk(const std::filesystem::path& path) const
+{
+ std::fstream file;
+ file.open(path, std::ios_base::out | std::ios_base::trunc);
+ if(!file.is_open())
+ {
+ Log(Log::ERROR)<<"can not open "<<path<<" for writing\n";
+ return false;
+ }
+
+ saveToStream(file);
+
+ file.close();
+ return true;
+}
+
+EisSpectra EisSpectra::loadFromStream(std::istream& stream)
+{
+ EisSpectra out;
+ std::string line;
+ std::getline(stream, line);
+ std::vector<std::string> tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
+ VersionFixed fileVersion;
+
+ if(tokens.size() < 2 || tokens[0] != F_MAGIC)
+ {
+ throw file_error("not a valid EISGenerator file or stream");
+ }
+ else
+ {
+ std::vector<std::string> versionTokens = tokenize(tokens[1], '.');
+ if(versionTokens.size() != 3)
+ throw file_error("could not load file version from file");
+ fileVersion.major = std::stoi(versionTokens[0]);
+ fileVersion.minor = std::stoi(versionTokens[1]);
+ fileVersion.patch = std::stoi(versionTokens[3]);
+ if(fileVersion.major > F_VERSION_MAJOR || fileVersion.minor > F_VERSION_MINOR)
+ throw file_error("saved by a newer version of EISGenerator, can not open");
+ }
+
+ if(fileVersion.minor == F_VERSION_MINOR)
+ {
+ std::getline(stream, line);
+ out.model = line;
+ std::getline(stream, line);
+ out.headerDescription = line == "None" ? "" : line;
+ std::getline(stream, line);
+ out.header = line == "None" ? "" : line;
+ }
+ else
+ {
+ std::getline(stream, line);
+ tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
+ stripQuotes(tokens[0]);
+ out.model = tokens[0];
+ line.erase(line.begin(), line.begin()+tokens.size());
+ out.header = line;
+ }
+
+ while(stream.good())
+ {
+ std::getline(stream, line);
+ if(line.starts_with("labelsNames"))
+ {
+ std::getline(stream, line);
+ out.labelNames = tokenizeBinaryIgnore(line, ',', '"', '\\');
+ continue;
+ }
+ else if(line.starts_with("labels"))
+ {
+ std::getline(stream, line);
+ std::vector<std::string> tokens = tokenizeBinaryIgnore(line, ',', '"', '\\');
+ for(const std::string& token : tokens)
+ out.labels.push_back(std::stod(token));
+ continue;
+ }
+ else if(line.empty() || line[0] == '#' || line.starts_with("omega"))
+ {
+ continue;
+ }
+ tokens = tokenize(line, ',');
+ if(tokens.size() != 3)
+ throw file_error("invalid line: " + line);
+
+ #pragma GCC diagnostic push
+ #pragma GCC diagnostic ignored "-Wnarrowing"
+ if constexpr (std::is_same<fvalue, double>::value)
+ out.data.push_back(DataPoint({std::stod(tokens[1]), std::stod(tokens[2])}, std::stod(tokens[0])));
+ else
+ out.data.push_back(DataPoint({std::stof(tokens[1]), std::stof(tokens[2])}, std::stof(tokens[0])));
+ #pragma GCC diagnostic pop
+
+ eis::removeDuplicates(out.data);
+ }
+
+ return out;
+}
+
+EisSpectra EisSpectra::loadFromDisk(const std::filesystem::path& path)
+{
+ std::fstream file;
+ file.open(path, std::ios_base::in);
+ if(!file.is_open())
+ throw file_error("can not open " + path.string() + " for reading\n");
+
+ try
+ {
+ EisSpectra out = loadFromStream(file);
+ return out;
+ }
+ catch(const file_error& err)
+ {
+ throw file_error(path.string() + std::string(": ") + err.what());
+ }
+}
+
+}
+
+std::ostream &operator<<(std::ostream &s, eis::EisSpectra const& spectra)
+{
+ spectra.saveToStream(s);
+ return s;
+}
diff --git a/strops.cpp b/strops.cpp
index 5fc6644..767f8e0 100644
--- a/strops.cpp
+++ b/strops.cpp
@@ -25,6 +25,9 @@
#include "log.h"
+namespace eis
+{
+
char getOpposingBracketChar(const char ch)
{
switch(ch)
@@ -214,3 +217,5 @@ std::string stripWhitespace(const std::string& in)
}
return out;
}
+
+}
diff --git a/strops.h b/strops.h
index e844c74..6db94a2 100644
--- a/strops.h
+++ b/strops.h
@@ -24,6 +24,9 @@
#include <sstream>
#include <algorithm>
+namespace eis
+{
+
std::vector<std::string> tokenize(const std::string& str, const char delim = ' ', const char ignBracketStart = '\0',
const char ignBracketEnd = '\0', const char escapeChar = '\0');
std::vector<std::string> tokenizeBinaryIgnore(const std::string& str, const char delim, const char ignoreBraket = '\0',
@@ -40,3 +43,5 @@ std::string stripWhitespace(const std::string& in);
void stripQuotes(std::string& in);
size_t eisRemoveUnneededBrackets(std::string& in, long int bracketStart = -1);
+
+}
diff --git a/test.cpp b/test.cpp
index 5ed71c0..3727152 100644
--- a/test.cpp
+++ b/test.cpp
@@ -342,7 +342,7 @@ static bool modelConsistancy()
static bool uneededBrackets()
{
std::string tst("(c-(rc)-(r-c(r)))");
- eisRemoveUnneededBrackets(tst);
+ eis::eisRemoveUnneededBrackets(tst);
std::string expected("c-rc-(r-cr)");
if(tst == expected)
{
--
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