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gui.ui
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<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>MainWindow</class>
<widget class="QMainWindow" name="MainWindow">
<property name="windowModality">
<enum>Qt::WindowModal</enum>
</property>
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>795</width>
<height>666</height>
</rect>
</property>
<property name="windowTitle">
<string>EfsTA</string>
</property>
<widget class="QWidget" name="centralwidget">
<layout class="QGridLayout" name="gridLayout_7">
<item row="0" column="0">
<widget class="QStackedWidget" name="UI_stack">
<property name="currentIndex">
<number>1</number>
</property>
<widget class="QWidget" name="Experiment">
<layout class="QGridLayout" name="gridLayout_19">
<item row="1" column="0">
<widget class="QPushButton" name="Exp_TA">
<property name="text">
<string>Transient Absorption</string>
</property>
</widget>
</item>
<item row="0" column="0" colspan="3">
<widget class="QTextBrowser" name="Exp_Introduction">
<property name="html">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">This program is used to analyse data collected from transient spectroscopy measurements, using a matrix reconstruction algorithm. At the moment you can select between &quot;Transient Absorption&quot; and &quot;Transient EPR&quot;. If you pick &quot;Transient Absorption&quot;, you will first get the opportunity to chirp-correct your data.</span></p></body></html></string>
</property>
</widget>
</item>
<item row="1" column="2">
<widget class="QPushButton" name="Exp_trEPR">
<property name="text">
<string>Transient EPR</string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="GVD">
<layout class="QGridLayout" name="gridLayout_20">
<item row="1" column="1">
<widget class="QPushButton" name="GVD_skip">
<property name="text">
<string>Skip Correction</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QPushButton" name="GVD_correct">
<property name="text">
<string>Correct Data</string>
</property>
</widget>
</item>
<item row="0" column="0" colspan="2">
<widget class="QTextBrowser" name="GVD_explaination">
<property name="html">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">Click on &quot;Correct Data&quot; to correct your data, otherwise click on &quot;Skip Correction&quot;.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">For the correction background data and OKE / Chirp data are recommended but only the sample data is required.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">If OKE / Chirp data is available you can let the program remove unwanted data spikes automatically or you can select an option to choose the wanted data points manually.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">If no OKE / Chirp data is available you can still perform a correction, however the accuracy and quality of the corrected data may suffer.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">On the image on the right you can see the result of a correction using OKE data.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">In addition to correcting the chirp you can also correct the data around the excitation wavelength for scattering. To do this select the option &quot;Scattering&quot; and provide the excitation wavelength.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">If anything is unclear, you can read the manual </span><a href="https://github.com/4-DMAPandSadness/EfsTA/blob/main/User%20Guide.md"><span style=" font-size:11pt; text-decoration: underline; color:#0000ff;">here</span></a><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> or hover with your mouse over any interactable object in this user interface and a tooltip will show up and explain what you have to do or show you an example.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p></body></html></string>
</property>
<property name="openExternalLinks">
<bool>true</bool>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="QLabel" name="GVD_image">
<property name="text">
<string><html><head/><body><p><img src=":/Plots/images/example plots/Chirp_Example.png"/></p></body></html></string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="Chirp">
<layout class="QGridLayout" name="gridLayout_22">
<item row="0" column="0" colspan="5">
<widget class="QLineEdit" name="Chirp_Sample_Dir">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the filepath of the sample measurement or use the &quot;Browse&quot;-button on the right.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">/home/user/documents/fsta_measurements/[...]sample_1_raw.file_ending</p></body></html></string>
</property>
<property name="text">
<string/>
</property>
<property name="placeholderText">
<string>Sample Measurment Path</string>
</property>
</widget>
</item>
<item row="3" column="5" rowspan="13">
<widget class="QGroupBox" name="Chirp_options">
<property name="title">
<string>Options</string>
</property>
<layout class="QGridLayout" name="gridLayout_23">
<item row="0" column="0">
<widget class="QCheckBox" name="Chirp_Manually">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If selected points for the curve fit can be selected manually with a lasso, otherwise points will be selected automatically and data spikes will be removed automatically.<br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-style:italic;">Note:</span></p>
<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-style:italic;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If chirp is rather scattered, it is recommended to select the points manually.</p></body></html></string>
</property>
<property name="text">
<string>Select Chirp Points Manually</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QCheckBox" name="Chirp_Scatter">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If selected enables the correction of the data around the excitation wavelength to remove scattering.</p></body></html></string>
</property>
<property name="text">
<string>Scatter</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QSpinBox" name="Chirp_Header">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the number of lines skipped in the data files. (Default: 0)</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The first 10 lines of the file contain information about the measurment and not actual data points.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">10</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Note: This value will be applied to all three files.</p></body></html></string>
</property>
<property name="specialValueText">
<string>Lines Skipped In Files</string>
</property>
</widget>
</item>
<item row="2" column="0" colspan="5">
<widget class="QLineEdit" name="Chirp_Chirp_Dir">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the filepath of the chirp / OKE measurement or use the &quot;Browse&quot;-button on the right.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">/home/user/documents/fsta_measurements/[...]OKE.file_ending</p></body></html></string>
</property>
<property name="text">
<string/>
</property>
<property name="placeholderText">
<string>Chirp Measurment Path</string>
</property>
</widget>
</item>
<item row="14" column="0">
<widget class="QPushButton" name="Chirp_Done">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Starts the chirp correction.</p></body></html></string>
</property>
<property name="text">
<string>Correct the Data and move on to analysis</string>
</property>
</widget>
</item>
<item row="0" column="5">
<widget class="QPushButton" name="Chirp_Browse_Sample">
<property name="toolTip">
<string><html><head/><body><p>Click to open a directory dialog and select the file containing the sample measurment data.</p></body></html></string>
</property>
<property name="text">
<string>Browse</string>
</property>
</widget>
</item>
<item row="2" column="5">
<widget class="QPushButton" name="Chirp_Browse_Chirp">
<property name="toolTip">
<string><html><head/><body><p>Click to open a directory dialog and select the file containing the chirp/OKE measurment data.</p></body></html></string>
</property>
<property name="text">
<string>Browse</string>
</property>
</widget>
</item>
<item row="1" column="5">
<widget class="QPushButton" name="Chirp_Browse_Solvent">
<property name="toolTip">
<string><html><head/><body><p>Click to open a directory dialog and select the file containing the solvent/background measurment data.</p></body></html></string>
</property>
<property name="text">
<string>Browse</string>
</property>
</widget>
</item>
<item row="1" column="0" colspan="5">
<widget class="QLineEdit" name="Chirp_Solvent_Dir">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the filepath of the background / pure solvent measurement or use the &quot;Browse&quot;-button on the right.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">/home/user/documents/fsta_measurements/[...]solvent.file_ending</p></body></html></string>
</property>
<property name="text">
<string/>
</property>
<property name="placeholderText">
<string>Solvent Measurment Path</string>
</property>
</widget>
</item>
<item row="8" column="0">
<widget class="QLineEdit" name="Chirp_Scale">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the <span style=" font-style:italic;">OD</span>-value for the calculation of the scaling factor for the background/solvent measurement using formula (a) according to [1].</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">(a)<span style=" font-style:italic;"> f</span> = (1-10<span style=" font-style:italic; vertical-align:super;">-OD</span>) / (2.3 * <span style=" font-style:italic;">OD</span>)</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The OD-value is 0.171.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">0.171</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">[1] Lorenc, M., Ziolek, M., Naskrecki, R. <span style=" font-style:italic;">et al.Appl Phys B </span><span style=" font-weight:600;">2002, </span><span style=" font-style:italic;">74</span>, 19–27.</p></body></html></string>
</property>
<property name="text">
<string/>
</property>
<property name="placeholderText">
<string>Background Scaling Factor</string>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLineEdit" name="Chirp_Wave_Range">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the upper and lower bound for the wavelength range of interest.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Data measured from 200 to 900 nm but relevant range is only from 350 to 800 nm.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">350, 800</p></body></html></string>
</property>
<property name="placeholderText">
<string>Wavelength Range</string>
</property>
</widget>
</item>
<item row="10" column="0">
<widget class="QLineEdit" name="Chirp_Exclude_Wave">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the excitation wavelength or the wavelength where the scattering occurs.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">The sample was excited at 400 nm.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">400</p></body></html></string>
</property>
<property name="text">
<string/>
</property>
<property name="placeholderText">
<string>Scatter Wavelength</string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="Analysis">
<layout class="QGridLayout" name="gridLayout_18">
<item row="0" column="0">
<widget class="QTabWidget" name="Analysis_stack">
<property name="currentIndex">
<number>0</number>
</property>
<widget class="QWidget" name="Introduction">
<attribute name="title">
<string>Tutorial</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_4">
<item row="0" column="0">
<widget class="QTextBrowser" name="Quick_Tutorial">
<property name="html">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">To start your analysis, go through all the tabs and make your various inputs. You have to choose between GLA and GTA but after one is complete you can always go back und do the other one.</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">Multiple input parameters NEED to be separated by a comma except if it is stated otherwise. For decimal points use a dot. If anything is unclear, you can read the manual </span><a href="https://github.com/4-DMAPandSadness/EfsTA/blob/main/README.md"><span style=" font-size:11pt; text-decoration: underline; color:#0000ff;">here</span></a><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> or hover with your mouse over any interactable object in this user interface and a tooltip will show up and explain what you have to do or show you an example.</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">In the &quot;Data&quot; tab you can select the directory in which the measured data are saved and, if necessary, specify the data range which should be analysed. </span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">The data </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-weight:600;">need</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> to be separated into </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-weight:600;">three</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> files ending with </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;">time.* </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">or</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;"> delays.*</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">, </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;">field</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> or </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;">lambda.*</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> and ta</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;">spectra.* </span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">or</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;"> eprspectra.*</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">, depending on which kind of data you want to analyse</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt; font-style:italic;">.</span><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;"> </span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">The results will be saved in the data directory. You will find a new folder called &quot;analysis&quot;, which will contain all the plots and the reconstructed spectra.</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">In the &quot;GLA&quot; or &quot;GTA&quot; tab you can select the analysis method and input various parameters. For Global Target Analysis (GTA) there are three options:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">(i) you can choose one of the eight preset kinetic models</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">(ii) you can input and save your own kinetic model in form of a simple transition equation</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">(iii) you can skip all the models and input a kinetic matrix directly</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">In the &quot;Plotting&quot; tab you can select from a variety of different plots for your data. You can also use this tab to plot the raw data, to help you determine your lifetime guesses.</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">In the &quot;Input Confirmation&quot; tab you will find an overview of all your input parameters that will be used for the analysis. If everything appears to be correct, you can confirm your input and start the analysis.</span></p>
<p style="-qt-paragraph-type:empty; margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'MS Shell Dlg 2'; font-size:11pt;"><br /></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">If you encounter any problems or have suggestions, feel free to email me:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'MS Shell Dlg 2'; font-size:11pt;">lucas.traenkle@gmx.net</span></p></body></html></string>
</property>
<property name="openExternalLinks">
<bool>true</bool>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="Data">
<attribute name="title">
<string>Data</string>
</attribute>
<layout class="QGridLayout" name="gridLayout">
<item row="0" column="0" colspan="2">
<widget class="QLineEdit" name="Data_directory">
<property name="toolTip">
<string><html><head/><body><p>Input the directory of the folder containing the data or use the &quot;Browse&quot;-button on the right.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>/home/user/documents/fsta_measurements/sample_1</p><p>If the raw data was chirp corrected using this program, no action is needed.</p></body></html></string>
</property>
<property name="whatsThis">
<string/>
</property>
<property name="placeholderText">
<string>Data Directory</string>
</property>
</widget>
</item>
<item row="0" column="2">
<widget class="QPushButton" name="Data_browse">
<property name="toolTip">
<string><html><head/><body><p>Click to open a directory dialog and select the data directory. There should be only three <span style=" font-style:italic;">.txt-</span>files ending with <span style=" font-weight:600;">taspectra.txt, delays.txt </span>and<span style=" font-weight:600;"> lambda.txt </span>for TA or <span style=" font-weight:600;">eprspectra.txt, time.txt </span>and<span style=" font-weight:600;"> field.txt</span>.</p><p>If the raw data was chirp corrected using this program, no action is needed.</p></body></html></string>
</property>
<property name="text">
<string>Browse</string>
</property>
</widget>
</item>
<item row="1" column="0" colspan="3">
<widget class="QGroupBox" name="Data_Modification">
<property name="title">
<string>Data Modification</string>
</property>
<layout class="QGridLayout" name="gridLayout_2">
<item row="5" column="0">
<widget class="QLineEdit" name="Data_wavelength_input_ub">
<property name="toolTip">
<string><html><head/><body><p>Set a lower bound for the wavelength range to be analysed. This is optional and can be left empty. If left empty, all wavelengths from the lower bound upwards will be used.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>The data was measured for wavelengths ranging from 330 nm to 800 nm , but only the data up to 750 nm is relevant.</p><p><span style=" font-weight:600;">Input:</span></p><p>750</p></body></html></string>
</property>
<property name="placeholderText">
<string>Upper Wavelength / Field Bound (Optional)</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QLineEdit" name="Data_delay_input_lb">
<property name="toolTip">
<string><html><head/><body><p>Set a lower bound for the time frame to be analysed. This is optional and can be left empty. If left empty, all delays up to the upper bound will be used.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>The data was measured for delays ranging from -10 ps to 4000 ps, but to exclude artifacts at 0 ps the evaluation should start at 0.4 ps.</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>0.4</p></body></html></string>
</property>
<property name="placeholderText">
<string>Lower Delay / Time Bound (Optional)</string>
</property>
</widget>
</item>
<item row="3" column="0">
<widget class="QLineEdit" name="Data_delay_input_ub">
<property name="toolTip">
<string><html><head/><body><p>Set an upper bound for the time frame to be analysed. This is optional and can be left empty. If left empty, all delays from the lower bound upwards will be used.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>The data was measured for delays ranging from -10 ps to 4000 ps, but to the data is only relevant up to 3000 ps.</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>3000</p></body></html></string>
</property>
<property name="placeholderText">
<string>Upper Delay / Time Bound (Optional)</string>
</property>
</widget>
</item>
<item row="4" column="0">
<widget class="QLineEdit" name="Data_wavelength_input_lb">
<property name="toolTip">
<string><html><head/><body><p>Set a lower bound for the wavelength range to be analysed. This is optional and can be left empty. If left empty, all wavelengths up to the upper bound will be used.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>The data was measured for wavelengths ranging from 330 nm to 800 nm , but only the data starting at 350 nm is relevant.</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>350</p></body></html></string>
</property>
<property name="placeholderText">
<string>Lower Wavelength / Field Bound(Optional)</string>
</property>
</widget>
</item>
<item row="6" column="0">
<widget class="QLineEdit" name="Data_input_multiplier">
<property name="toolTip">
<string><html><head/><body><p>Set a multiplier for the absorption data. This is optional and can be left empty. If left empty, the data won't be changed.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>If the data was measured in ODU but the values are around 0,00X, the data can be multiplied by a factor of 1000 so the data will be displayed as mODU.</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>1000</p></body></html></string>
</property>
<property name="placeholderText">
<string>ΔA Data Multiplier (Optional)</string>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="2" column="1">
<spacer name="spacer_clear_cache">
<property name="orientation">
<enum>Qt::Horizontal</enum>
</property>
<property name="sizeHint" stdset="0">
<size>
<width>731</width>
<height>20</height>
</size>
</property>
</spacer>
</item>
<item row="2" column="2">
<widget class="QPushButton" name="Data_clear_cache">
<property name="toolTip">
<string><html><head/><body><p>Clears the saved inputs from previous evaluations.</p></body></html></string>
</property>
<property name="text">
<string>Clear Cache</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QPushButton" name="Data_backToChirp">
<property name="text">
<string>Back To Chirp</string>
</property>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="GLA">
<attribute name="title">
<string>GLA</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_8">
<item row="0" column="0">
<widget class="QGroupBox" name="GLA_Select">
<property name="title">
<string>Select GLA</string>
</property>
<layout class="QGridLayout" name="gridLayout_17">
<item row="0" column="0">
<widget class="QRadioButton" name="GLA_radio">
<property name="toolTip">
<string><html><head/><body><p>If selected the data will be analysed using Global Lifetime Analysis. This automatically unselects all other analysis options.</p></body></html></string>
</property>
<property name="text">
<string>GLA</string>
</property>
<property name="checked">
<bool>false</bool>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="0" column="1">
<widget class="QGroupBox" name="GLA_Algorithm">
<property name="title">
<string>Algorithm Choices</string>
</property>
<layout class="QGridLayout" name="gridLayout_13">
<item row="0" column="0">
<widget class="QComboBox" name="GLA_algorithm_optimize">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the algorithm used by the optimize function to minimize the Chi-Square function. The default algorithm is &quot;Nelder-Mead&quot;.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-style:italic;">Note:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For more information read the documentation for &quot;scipy.optimize.minimize&quot;.</p></body></html></string>
</property>
<item>
<property name="text">
<string>Nelder-Mead</string>
</property>
</item>
<item>
<property name="text">
<string>least_squares</string>
</property>
</item>
<item>
<property name="text">
<string>Powell</string>
</property>
</item>
<item>
<property name="text">
<string>CG</string>
</property>
</item>
<item>
<property name="text">
<string>BFGS</string>
</property>
</item>
<item>
<property name="text">
<string>L-BFGS-B</string>
</property>
</item>
<item>
<property name="text">
<string>TNC</string>
</property>
</item>
<item>
<property name="text">
<string>COBYLA</string>
</property>
</item>
<item>
<property name="text">
<string>SLSQP</string>
</property>
</item>
<item>
<property name="text">
<string>trust-constr</string>
</property>
</item>
<item>
<property name="text">
<string>basinhopping</string>
</property>
</item>
<item>
<property name="text">
<string>ampgo</string>
</property>
</item>
</widget>
</item>
</layout>
</widget>
</item>
<item row="1" column="0" colspan="2">
<widget class="QGroupBox" name="GLA_Tau_Input">
<property name="title">
<string>Initial Lifetime Guesses</string>
</property>
<layout class="QGridLayout" name="gridLayout_12">
<item row="0" column="0">
<widget class="QLineEdit" name="GLA_input_tau">
<property name="toolTip">
<string><html><head/><body><p>Input the guessed lifetimes for the global lifetime analysis.</p><p>After the input press ENTER to select fixed values.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p>Three species with different lifetimes.</p><p>τ<span style=" vertical-align:sub;">1</span> = 1.2 ps; τ<span style=" vertical-align:sub;">2</span> = 106 ps; τ<span style=" vertical-align:sub;">3</span> = 900 ns</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>1.2, 106, 900000</p></body></html></string>
</property>
<property name="placeholderText">
<string>τ-values</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QGroupBox" name="GLA_fix_box">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">After confirming your lifetime input with ENTER, here you can select which of the input lifetimes should be optimize and which ones should remain fixed, if there are any.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Three species with different lifetimes.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">τ<span style=" vertical-align:sub;">1</span> = 1.2 ps; τ<span style=" vertical-align:sub;">2</span> = 106 ps; τ<span style=" vertical-align:sub;">3</span> = 900 ns</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Only τ<span style=" vertical-align:sub;">1 </span>and τ<span style=" vertical-align:sub;">2 </span>are in the timescale of the measurment and therefore contribute to the fit in a meaningful way. τ<span style=" vertical-align:sub;">3 </span>will remain fixed.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> ◎ ◎ ◉</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">1.2 106 900000</p></body></html></string>
</property>
<property name="title">
<string>Fixed Values</string>
</property>
<layout class="QHBoxLayout" name="GLA_fix_layout"/>
</widget>
</item>
</layout>
</widget>
</item>
</layout>
</widget>
<widget class="QWidget" name="GTA">
<attribute name="title">
<string>GTA</string>
</attribute>
<layout class="QGridLayout" name="gridLayout_11">
<item row="0" column="0">
<widget class="QGroupBox" name="GTA_Custom_Matrix">
<property name="title">
<string>Model Selection</string>
</property>
<layout class="QGridLayout" name="gridLayout_10">
<item row="2" column="0">
<widget class="QRadioButton" name="GTA_radio_custom_matrix">
<property name="toolTip">
<string><html><head/><body><p>If selected the data will be analysed through Global Target Analysis using your kinetic matrix. This automatically unselects all other analysis options and is only recommended for advanced users.</p></body></html></string>
</property>
<property name="text">
<string>Custom Matrix</string>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QRadioButton" name="GTA_radio_custom_model">
<property name="toolTip">
<string><html><head/><body><p>If selected the data will be analysed through Global Target Analysis using one of your own kinetic models. This automatically unselects all other analysis options.</p></body></html></string>
</property>
<property name="text">
<string>Custom Model</string>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
<item row="0" column="0">
<widget class="QRadioButton" name="GTA_radio_preset_model">
<property name="toolTip">
<string><html><head/><body><p>If selected the data will be analysed through Global Target Analysis using one of the eight preset kinetic models. This automatically unselects all other analysis options.</p></body></html></string>
</property>
<property name="text">
<string>Preset Model</string>
</property>
<property name="autoExclusive">
<bool>false</bool>
</property>
</widget>
</item>
</layout>
</widget>
</item>
<item row="2" column="1">
<widget class="QGroupBox" name="GTA_Custom_Model">
<property name="title">
<string>Custom Model</string>
</property>
<layout class="QGridLayout" name="gridLayout_16">
<item row="2" column="0" colspan="2">
<widget class="QLineEdit" name="GTA_input_custom_model_equation">
<property name="toolTip">
<string><html><head/><body><p>Input the transition equation for the kinetic model.</p><p>Input has to be in the following form:</p><p>For species only use capital letters from <span style=" font-weight:600; font-style:italic;">A</span> to <span style=" font-weight:600; font-style:italic;">Z </span>in alphabetical order. If there are 3 species only the letters A,B and C should be used not something like A,Q and F. For decays into the &quot;void&quot; (e.q. a species decays back to the ground state) use a non-capital <span style=" font-weight:600; font-style:italic;">v</span>. These &quot;void decays&quot; only have to be declared once per species.</p><p>For arrows use &quot;-&gt;&quot; or nothing. But the input must be consistent either every decay is denoted by an arrow or none are.</p><p>If the decays split or go backwards, write it as a new sequence separated by &quot;;&quot;.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p><img src=":/Tooltips/images/tooltips/reaction example.png"/></p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>A-&gt;B-&gt;C-&gt;v;B-&gt;A;A-&gt;C</p><p>or to make the input a bit easier:</p><p>ABCv;BA;AC</p><p><span style=" font-style:italic;">Note:</span></p><p>Although species C appears twice, the void decay is only input once.</p></body></html></string>
</property>
<property name="placeholderText">
<string>Transition Equation</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QPushButton" name="GTA_custom_model_save">
<property name="toolTip">
<string><html><head/><body><p>Saves the currently input equation, if there is one.</p></body></html></string>
</property>
<property name="text">
<string>Save</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QPushButton" name="GTA_custom_model_del">
<property name="toolTip">
<string><html><head/><body><p>Deletes the currently selected equation, if there is one.</p></body></html></string>
</property>
<property name="text">
<string>Delete</string>
</property>
</widget>
</item>
<item row="3" column="0" colspan="2">
<widget class="QLineEdit" name="GTA_input_custom_model_tau">
<property name="toolTip">
<string><html><head/><body><p>Input the guessed lifetimes for the kinetic model.</p><p>Lifetimes need to be input in the same order as the transition arrows are in the equation.</p><p>After the input press ENTER to select fixed values.</p><p><span style=" font-weight:600; text-decoration: underline;">Example:</span></p><p><img src=":/Tooltips/images/tooltips/reaction example wt.png"/></p><p>Transition equation: ABCv;BA;AC</p><p><span style=" font-weight:600; text-decoration: underline;">Input:</span></p><p>1,80,4000,3,30<br/></p></body></html></string>
</property>
<property name="placeholderText">
<string>τ-values</string>
</property>
</widget>
</item>
<item row="0" column="0" colspan="2">
<widget class="QComboBox" name="GTA_input_custom_model_saved_equations">
<property name="toolTip">
<string><html><head/><body><p>Displays the saved models from previous evaluations.</p></body></html></string>
</property>
<property name="duplicatesEnabled">
<bool>false</bool>
</property>
</widget>
</item>
<item row="4" column="0" colspan="2">
<widget class="QGroupBox" name="GTA_custom_model_fix_box">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">After confirming your lifetime input with ENTER, here you can select which of the input lifetimes should be optimize and which ones should remain fixed, if there are any.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Three species with different lifetimes.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">τ<span style=" vertical-align:sub;">1</span> = 1 ps; τ<span style=" vertical-align:sub;">2</span> = 80 ps; τ<span style=" vertical-align:sub;">3</span> = 4000 ps; τ<span style=" vertical-align:sub;">4 </span>= 3 ps; τ<span style=" vertical-align:sub;">5</span> = 30 ps</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">τ<span style=" vertical-align:sub;">1 </span>is wellknown to be 1 ps and τ<span style=" vertical-align:sub;">3</span> is not really in the timescale of the measurement and therefore these two will remain fixed.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">◉ ◎ ◉ ◎ ◎ </p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> 1 80 4000 3 30</p></body></html></string>
</property>
<property name="title">
<string>Fixed Values</string>
</property>
<layout class="QHBoxLayout" name="GTA_custom_model_fix_layout"/>
</widget>
</item>
</layout>
</widget>
</item>
<item row="3" column="0">
<widget class="QGroupBox" name="GTA_algorith">
<property name="title">
<string>Algorithm Choices</string>
</property>
<layout class="QGridLayout" name="gridLayout_21">
<item row="0" column="0">
<widget class="QComboBox" name="GTA_algorithm_optimize">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Select the algorithm used by the optimize function to minimize the Chi-Square function. The default algorithm is &quot;Nelder-Mead&quot;.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-style:italic;">Note:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For more information read the documentation for &quot;scipy.optimize.minimize&quot;.</p></body></html></string>
</property>
<item>
<property name="text">
<string>Nelder-Mead</string>
</property>
</item>
<item>
<property name="text">
<string>least_squares</string>
</property>
</item>
<item>
<property name="text">
<string>Powell</string>
</property>
</item>
<item>
<property name="text">
<string>CG</string>
</property>
</item>
<item>
<property name="text">
<string>BFGS</string>
</property>
</item>
<item>
<property name="text">
<string>L-BFGS-B</string>
</property>
</item>
<item>
<property name="text">
<string>TNC</string>
</property>
</item>
<item>
<property name="text">
<string>COBYLA</string>
</property>
</item>
<item>
<property name="text">
<string>SLSQP</string>
</property>
</item>
<item>
<property name="text">
<string>trust-constr</string>
</property>
</item>
<item>
<property name="text">
<string>basinhopping</string>
</property>
</item>
<item>
<property name="text">
<string>ampgo</string>
</property>
</item>
</widget>
</item>
<item row="1" column="0">
<widget class="QComboBox" name="GTA_algorithm_initial_value_problem">
<property name="toolTip">
<string><html><head/><body><p>Select the algorithm used by the ivp solver to solve the differential equations for the concentrations of each species. The default algorithm is &quot;LSODA&quot;.</p><p><span style=" font-style:italic;">Note:</span></p><p>For more information read the documentation for &quot;scipy.integrate.solve_ivp&quot;.</p></body></html></string>
</property>
<item>
<property name="text">
<string>LSODA</string>
</property>
</item>
<item>
<property name="text">
<string>BDF</string>
</property>
</item>
<item>
<property name="text">
<string>RK45</string>
</property>
</item>
<item>
<property name="text">
<string>RK23</string>
</property>
</item>
<item>
<property name="text">
<string>DOP853</string>
</property>
</item>
<item>
<property name="text">
<string>Radau</string>
</property>
</item>
</widget>
</item>
</layout>
</widget>
</item>
<item row="0" column="1">
<widget class="QGroupBox" name="GTA_Model_Input">
<property name="title">
<string>Preset Model</string>
</property>
<layout class="QGridLayout" name="gridLayout_9">
<item row="1" column="0">
<widget class="QLineEdit" name="GTA_input_preset_model_tau">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Input the guessed lifetimes for the kinetic model.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Lifetimes need to be input in the same order as the transition arrows are in the equation.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">After the input press ENTER to select fixed values.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><img src=":/Tooltips/images/tooltips/preset tau example.png" /></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For this example Model 2 would be suited.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">1,80</p></body></html></string>
</property>
<property name="placeholderText">
<string>τ-values</string>
</property>
</widget>
</item>
<item row="2" column="0">
<widget class="QGroupBox" name="GTA_preset_model_fix_box">
<property name="toolTip">
<string><!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
<html><head><meta name="qrichtext" content="1" /><style type="text/css">
p, li { white-space: pre-wrap; }
</style></head><body style=" font-family:'Sans Serif'; font-size:9pt; font-weight:400; font-style:normal;">
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">After confirming your lifetime input with ENTER, here you can select which of the input lifetimes should be optimize and which ones should remain fixed, if there are any.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Example:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Two species with different lifetimes.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">τ<span style=" vertical-align:sub;">1</span> = 1 ps; τ<span style=" vertical-align:sub;">2</span> = 80 ps</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Both lifetimes are in the timescale of the measurement and therefore no lifetime will be fixed.</p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600; text-decoration: underline;">Input:</span></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"> ◎ ◎ </p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">1.2 106</p></body></html></string>
</property>
<property name="title">
<string>Fixed Values</string>
</property>
<layout class="QHBoxLayout" name="GTA_preset_model_fix_layout"/>
</widget>
</item>
<item row="0" column="0">
<widget class="QComboBox" name="GTA_preset_model_selection">
<property name="toolTip">
<string><html><head/><body><p>Select a kinetic model, through which the data will be analysed.</p><p><span style=" text-decoration: underline;">General linear consecutive models for any amount of species:</span></p><p>Model 1: A -&gt; B -&gt; C ... -&gt; Z -&gt; void</p><p>Model 2: A -&gt; B -&gt; C ... -&gt; Z</p><p><span style=" text-decoration: underline;">Specific consecutive models for a certain amount of species with branching:</span></p><p>Model 3: A -&gt; B -&gt; C -&gt; D; B -&gt; D</p><p>Model 4: A -&gt; B -&gt; C -&gt; D -&gt; E; B -&gt; E</p><p>Model 5: A -&gt; B -&gt; C -&gt; D -&gt; E; C -&gt; E</p><p>Model 6: A -&gt; B -&gt; C -&gt; D -&gt; E -&gt; F; C -&gt; F</p><p>Model 7: A -&gt; B; A -&gt; C</p><p>Model 8: A -&gt; B ; B -&gt; C ; B -&gt; D</p></body></html></string>
</property>
<item>
<property name="text">
<string>Model 1</string>
</property>
</item>
<item>
<property name="text">
<string>Model 2</string>
</property>
</item>
<item>
<property name="text">
<string>Model 3</string>
</property>
</item>
<item>
<property name="text">
<string>Model 4</string>
</property>
</item>
<item>
<property name="text">
<string>Model 5</string>
</property>
</item>
<item>
<property name="text">
<string>Model 6</string>
</property>
</item>
<item>
<property name="text">
<string>Model 7</string>
</property>
</item>
<item>
<property name="text">
<string>Model 8</string>
</property>
</item>
</widget>
</item>
</layout>
</widget>
</item>