Renamed NiBAxV2 to NiChart.

LICENSE

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+By using NiChart, the user agrees to the following license:
+
+See https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html 

MANIFEST.in

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+include NiChart/plugins/loadsave/MUSE_ROI_Dictionary.csv
+include README.md

NiChart/NiChartCmdApp.py

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+# This Python file uses the following encoding: utf-8
+"""
+contact: [email protected]
+Copyright (c) 2018 University of Pennsylvania. All rights reserved.
+Use of this source code is governed by license located in license file: https://github.com/CBICA/NiChart/blob/main/LICENSE
+"""
+
+from PyQt5 import QtCore, QtGui, QtWidgets
+import os
+import pandas as pd
+from NiChart.core.dataio import DataIO
+from NiChart.core.model.datamodel import DataModel
+
+class NiChartCmdApp:
+    def __init__(self):
+        pass
+
+if __name__ == '__main__':
+    main()

NiChart/__init__.py

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+# This Python file uses the following encoding: utf-8
+"""
+contact: [email protected]
+Copyright (c) 2018 University of Pennsylvania. All rights reserved.
+Use of this source code is governed by license located in license file: https://github.com/CBICA/NiChart/blob/main/LICENSE
+"""
+
+from PyQt5 import QtCore, QtGui, QtWidgets
+import argparse
+import os, sys
+from NiChart.mainwindow import MainWindow
+from NiChart.NiChartCmdApp import NiChartCmdApp
+
+def main():
+    parser = argparse.ArgumentParser(description='NiChart Data Visualization and Preparation')
+    parser.add_argument('--data_file', type=str, help='Data file containing data frame.', default=None, required=False)
+    parser.add_argument('--dict_file', type=str, help='Dict file containing data dictionary.', default=None, required=False)
+    parser.add_argument("-nogui", action="store_true", help="Launch application in CLI mode to do data processing without any visualization or graphical user interface.")
+
+    args = parser.parse_args(sys.argv[1:])
+
+    data_file = args.data_file
+    dict_file = args.dict_file
+    noGUI = args.nogui
+
+    if(noGUI):
+        app = QtCore.QCoreApplication(sys.argv)
+        if(compute_spares):
+            if((data_file == None) or (SPARE_model_file == None) or (output_file == None)):
+                print("Please provide '--data_file', '--SPARE_model_file' and '--output_file_name' to compute spares.")
+                exit()
+            NiChartCmdApp().ComputeSpares(data_file, SPARE_model_file, output_file)
+    else:
+        app = QtWidgets.QApplication(sys.argv)
+
+        # Set the style sheet
+        with open('./style.qss', 'r') as f:         ## FIXME this is absolute path to curr dir
+            style = f.read()
+        app.setStyleSheet(style)
+
+        mw = MainWindow(dataFile = data_file, dictFile = dict_file)
+        mw.show()
+
+        sys.exit(app.exec_())
+
+if __name__ == '__main__':
+    main()

NiChart/__main__.py

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+# This Python file uses the following encoding: utf-8
+"""
+contact: [email protected]
+Copyright (c) 2018 University of Pennsylvania. All rights reserved.
+Use of this source code is governed by license located in license file: https://github.com/CBICA/NiChart/blob/main/LICENSE
+"""
+
+from PyQt5 import QtCore, QtGui, QtWidgets
+import argparse
+import os, sys
+from NiChart.mainwindow import MainWindow
+from NiChart.NiChartCmdApp import NiChartCmdApp
+
+def main():
+    parser = argparse.ArgumentParser(description='NiChart Data Visualization and Preparation')
+    parser.add_argument('--data_file', type=str, help='Data file containing data frame.', default=None, required=False)
+    parser.add_argument('--harmonization_model_file', type=str, help='Harmonization model file.', default=None, required=False)
+    parser.add_argument('--SPARE_model_file', type=str, help='Model file for SPARE-scores.', default=None, required=False)
+    parser.add_argument('--harmonize', type=str, help='Do harmonization or not.', default=None, required=False)
+    parser.add_argument('--compute_spares', type=str, help='Compute SPARE-scores or not.', default=None, required=False)
+    parser.add_argument('--output_file_name', type=str, help='Name of the output file with extension.', default=None, required=False)
+    parser.add_argument("-nogui", action="store_true", help="Launch application in CLI mode to do data processing without any visualization or graphical user interface.")
+
+    args = parser.parse_args(sys.argv[1:])
+
+    data_file = args.data_file
+    harmonization_model_file = args.harmonization_model_file
+    SPARE_model_file = args.SPARE_model_file
+    harmonize = args.harmonize
+    compute_spares = args.compute_spares
+    output_file = args.output_file_name
+    noGUI = args.nogui
+
+
+    if(noGUI):
+        app = QtCore.QCoreApplication(sys.argv)
+        if(compute_spares):
+            if((data_file == None) or (SPARE_model_file == None) or (output_file == None)):
+                print("Please provide '--data_file', '--SPARE_model_file' and '--output_file_name' to compute spares.")
+                exit()
+            NiChartCmdApp().ComputeSpares(data_file,SPARE_model_file,output_file)
+    else:
+        app = QtWidgets.QApplication(sys.argv)
+
+        with open('./style.qss', 'r') as f:
+            style = f.read()
+            # Set the current style sheet
+        app.setStyleSheet(style)
+
+
+        mw = MainWindow(dataFile=data_file,
+                        harmonizationModelFile=harmonization_model_file,
+                        SPAREModelFile=SPARE_model_file)
+        mw.show()
+
+        #sys.exit(app.exec_())
+
+if __name__ == '__main__':
+    main()

NiChart/aboutdialog.py

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+# This Python file uses the following encoding: utf-8
+"""
+contact: [email protected]
+Copyright (c) 2018 University of Pennsylvania. All rights reserved.
+Use of this source code is governed by license located in license file: https://github.com/CBICA/NiChart/blob/main/LICENSE
+Author: Ashish Singh
+"""
+
+from PyQt5 import QtCore, QtWidgets, uic
+import os
+from NiChart.resources import resources
+
+class AboutDialog(QtWidgets.QDialog):
+    def __init__(self,parent=None):
+        super(AboutDialog,self).__init__(parent)
+        self.SetupUi()
+        self.SetupConnections()
+
+    def SetupConnections(self):
+        self.buttonBox.accepted.connect(self.OnOkBtnClicked)
+
+    def OnOkBtnClicked(self):
+        self.hide()
+
+    def SetupUi(self):
+        root = os.path.dirname(__file__)
+        self.ui = uic.loadUi(os.path.join(root, 'aboutdialog.ui'), self)

NiChart/aboutdialog.ui

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+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Dialog</class>
+ <widget class="QDialog" name="Dialog">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>716</width>
+    <height>395</height>
+   </rect>
+  </property>
+  <property name="minimumSize">
+   <size>
+    <width>0</width>
+    <height>0</height>
+   </size>
+  </property>
+  <property name="windowTitle">
+   <string>About NiChart</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <layout class="QHBoxLayout" name="horizontalLayout">
+     <item>
+      <widget class="QLabel" name="imagearea">
+       <property name="maximumSize">
+        <size>
+         <width>256</width>
+         <height>256</height>
+        </size>
+       </property>
+       <property name="text">
+        <string/>
+       </property>
+       <property name="pixmap">
+        <pixmap>resources/NiChartLogo.png</pixmap>
+       </property>
+       <property name="scaledContents">
+        <bool>true</bool>
+       </property>
+      </widget>
+     </item>
+     <item>
+      <widget class="QLabel" name="label">
+       <property name="text">
+        <string>&lt;!DOCTYPE HTML PUBLIC &quot;-//W3C//DTD HTML 4.0//EN&quot; &quot;http://www.w3.org/TR/REC-html40/strict.dtd&quot;&gt;
+&lt;html&gt;&lt;head&gt;&lt;meta name=&quot;qrichtext&quot; content=&quot;1&quot; /&gt;&lt;style type=&quot;text/css&quot;&gt;
+p, li { white-space: pre-wrap; }
+&lt;/style&gt;&lt;/head&gt;&lt;body style=&quot; font-family:'MS Shell Dlg 2'; font-size:7.875pt; font-weight:400; font-style:normal;&quot;&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt; font-weight:600;&quot;&gt;Version 0.1 &lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt; font-weight:600;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:8pt;&quot;&gt;© &lt;/span&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt;University of Pennsylvania&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt;NiChart facilitates preparation of neuro-imaging data for machine learning applications.&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;https://github.com/CBICA/NiChart&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;https://github.com/CBICA/NiChart&lt;/span&gt;&lt;/a&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt; font-weight:600;&quot;&gt;License&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt;By using NiChart, the user agrees to the following license:&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;a href=&quot;https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html&quot;&gt;&lt;span style=&quot; font-size:8pt; text-decoration: underline; color:#0000ff;&quot;&gt;https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html&lt;/span&gt;&lt;/a&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt; &lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt; font-weight:600;&quot;&gt;Developers:&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt;Ahmed Abdulkadir, Ashish Singh, Randa Melhem&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:9pt;&quot;&gt;&lt;br /&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt; font-weight:600;&quot;&gt;Documentation Writers:&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;&quot;&gt;&lt;span style=&quot; font-size:9pt;&quot;&gt;Ahmed Abdulkadir, Ashish Singh, Randa Melhem&lt;/span&gt;&lt;/p&gt;
+&lt;p style=&quot;-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:8pt; text-decoration: underline; color:#0000ff;&quot;&gt;&lt;br /&gt;&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
+       </property>
+       <property name="wordWrap">
+        <bool>true</bool>
+       </property>
+       <property name="openExternalLinks">
+        <bool>true</bool>
+       </property>
+      </widget>
+     </item>
+    </layout>
+   </item>
+   <item>
+    <widget class="QDialogButtonBox" name="buttonBox">
+     <property name="orientation">
+      <enum>Qt::Horizontal</enum>
+     </property>
+     <property name="standardButtons">
+      <set>QDialogButtonBox::Ok</set>
+     </property>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <resources/>
+ <connections>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>accepted()</signal>
+   <receiver>Dialog</receiver>
+   <slot>accept()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>248</x>
+     <y>254</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>157</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>buttonBox</sender>
+   <signal>rejected()</signal>
+   <receiver>Dialog</receiver>
+   <slot>reject()</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>316</x>
+     <y>260</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>286</x>
+     <y>274</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>