rename project and files to niCHART

Author: ashishsingh18

LICENSE

@@ -1,3 +1,3 @@
-By using NiBAx, the user agrees to the following license:
+By using niCHART, the user agrees to the following license:
 
 See https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html 

MANIFEST.in

@@ -1,2 +1,2 @@
-include NiBAx/plugins/loadsave/MUSE_ROI_Dictionary.csv
+include niCHART/plugins/loadsave/MUSE_ROI_Dictionary.csv
 include README.md

README.md

@@ -1,28 +1,28 @@
-# [NiBAx] The neuro-imaging brain aging chart
+# [niCHART] The neuro-imaging brain aging chart
 
 [![Codacy Badge](https://app.codacy.com/project/badge/Grade/7aadb18130574bd5b85b978cd709fe2c)](https://www.codacy.com/gh/CBICA/NiBAx/dashboard?utm_source=github.com&utm_medium=referral&utm_content=CBICA/NiBAx&utm_campaign=Badge_Grade)
 
 | :construction:
   <font size="+1">This software and documentation is under development!
                   Check out up-to-date documentation at
-                  [cbica.github.io/NiBAx/](https://cbica.github.io/NiBAx/) </font> :construction: |
+                  [cbica.github.io/niCHART/](https://cbica.github.io/niCHART/) </font> :construction: |
 |-----------------------------------------|
 
-The neuro-imaging brain aging chart **[NiBAχ]** is a comprehensive solution to
+The neuro-imaging brain aging chart **[niCHART]** is a comprehensive solution to
 analyze standard structural and functional brain MRI data across studies.
-**[NiBAχ]** and the associated pre-processing tools implement computational
+**[niCHART]** and the associated pre-processing tools implement computational
 morphometry, functional signal analysis, quality control, statistical
 harmonization, data standardization, interactive visualization, and extraction
 of expressive imaging signatures.
 
 This `README` is intended for contributors and developers.
 User documentation is available at
-[cbica.github.io/NiBAx/](https://cbica.github.io/NiBAx/).
+[cbica.github.io/niCHART/](https://cbica.github.io/niCHART/).
 
 
 <figure>
-  <img src="NiBAx/resources/workflow.gif" alt="[NiBAχ] Demo"/>
-  <figcaption>Demonstration of the [NiBAχ] graphical user interface.</figcaption>
+  <img src="niCHART/resources/workflow.gif" alt="[niCHART] Demo"/>
+  <figcaption>Demonstration of the [niCHART] graphical user interface.</figcaption>
 </figure>
 
 
@@ -37,23 +37,23 @@ python --version # should be 3.8.8 or newer
 
 
 ### Prepare conda environment
-Assuming current working directory is `NiBAx` and containing the source code
-cloned from https://github.com/CBICA/NiBAx.git.
+Assuming current working directory is `niCHART` and containing the source code
+cloned from https://github.com/CBICA/niCHART.git.
 
 Ensure Anaconda is installed. Follow instructions for user's operating system [here](https://docs.anaconda.com/anaconda/install/index.html). After Anaconda has been installed, be sure to exit and reopen any 
 command line windows to use `conda` command
 
 
 ```shell
-conda create -n NiBAx python=3.8.8  
-conda activate NiBAx
+conda create -n niCHART python=3.8.8  
+conda activate niCHART
 python -m pip install --upgrade pip
 ```
 
 
 ### Prepare environment in Linux (CUBIC)
-Assuming current working directory is `NiBAx` and containing the source code
-cloned from https://github.com/CBICA/NiBAx.git.
+Assuming current working directory is `niCHART` and containing the source code
+cloned from https://github.com/CBICA/niCHART.git.
 
 ```shell
 python -m venv .env
@@ -62,8 +62,8 @@ python -m pip install --upgrade pip
 ```
 
 ### Prepare environment for PowerShell (Windows 10 or 11)
-Assuming current working directory is `NiBAx` and containing the source code
-cloned from https://github.com/CBICA/NiBAx.git.
+Assuming current working directory is `niCHART` and containing the source code
+cloned from https://github.com/CBICA/niCHART.git.
 
 ```shell
 python -m venv .env
@@ -72,21 +72,21 @@ python -m pip install --upgrade pip
 ```
 
 
-### Install the [NiBAx] software
-To install the [NiBAx], install it in a virtual or conda environment.
+### Install the [niCHART] software
+To install the [niCHART], install it in a virtual or conda environment.
 Depending on the desired version, use one of the following
 commands to install it.
 
 ```shell
-# Editable version for development after cloning https://github.com/CBICA/NiBAx.git 
+# Editable version for development after cloning https://github.com/CBICA/niCHART.git 
 python -m pip install -U -e .
 poetry install
 
 # Version from pull request (#57 in this example) for testing proposed changes
-python -m pip install -U git+https://github.com/CBICA/NiBAx.git@refs/pull/57/head
+python -m pip install -U git+https://github.com/CBICA/niCHART.git@refs/pull/57/head
 
 # Main version of toolbox
-python -m pip install -U git+https://github.com/CBICA/NiBAx.git
+python -m pip install -U git+https://github.com/CBICA/niCHART.git
 ```
 
 
@@ -95,13 +95,13 @@ After proper installation, the standalone graphical user interface can be launch
 in the terminal with:
 
 ```shell
-NiBAx
+niCHART
 ```
 
 The data file can be passed as command line argument `--data_file` as shown below.
 
 ```shell
-NiBAx --data_file istaging.pkl.gz
+niCHART --data_file istaging.pkl.gz
 ```
 
 ## Build executable package for Windows 10/11
@@ -114,12 +114,12 @@ briefcase update
 briefcase package
 ```
 
-The result is an installer `NiBAx.msi` that will install the app in the
+The result is an installer `niCHART.msi` that will install the app in the
 user's profile. The installation does not require administrator rights.
 
 ## Disclaimer
 - The software has been designed for research purposes only and has neither been reviewed nor approved for clinical use by the Food and Drug Administration (FDA) or by any other federal/state agency.
 - By using NiBAx, the user agrees to the following license: https://www.med.upenn.edu/cbica/software-agreement-non-commercial.html
 
 ## Contact
-For more information and support, please post on the [Discussions](https://github.com/CBICA/NiBAx/discussions) section or contact <a href="mailto:[email protected]">CBICA Software</a>.
+For more information and support, please post on the [Discussions](https://github.com/CBICA/niCHART/discussions) section or contact <a href="mailto:[email protected]">CBICA Software</a>.

docs/conf.py

@@ -19,7 +19,7 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'NiBAχ'
+project = 'niCHART'
 copyright = '2022, CBICA, University of Pennsylvania'
 author = 'Ashish Singh'
 
@@ -51,7 +51,7 @@
     'sphinx.ext.autosectionlabel',
 ]
 
-autoapi_dirs = ['../NiBAx']
+autoapi_dirs = ['../niCHART']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -120,7 +120,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'NiBAxdoc'
+htmlhelp_basename = 'niCHARTdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -147,7 +147,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, 'NiBAx.tex', 'NiBAx Documentation',
+    (master_doc, 'niCHART.tex', 'niCHART Documentation',
      'Ashish Singh', 'manual'),
 ]
 
@@ -157,7 +157,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    (master_doc, 'NiBAx', 'NiBAx Documentation',
+    (master_doc, 'niCHART', 'niCHART Documentation',
      [author], 1)
 ]
 
@@ -168,7 +168,7 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    (master_doc, 'NiBAx', 'NiBAx Documentation',
+    (master_doc, 'niCHART', 'niCHART Documentation',
      author, 'Ahmed Abdulkadir', 'The neuro-imaging brain aging chart',
      'Miscellaneous'),
 ]
@@ -281,6 +281,6 @@
 
 html_context['display_github'] = True
 html_context['github_user'] = 'CBICA'
-html_context['github_repo'] = 'NiBAx'
+html_context['github_repo'] = 'niCHART'
 html_context['github_version'] = 'main/docs/'
 

NiBAx/__init__.py renamed to niCHART/__init__.py

@@ -2,17 +2,17 @@
 """
 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/NiBAx/blob/main/LICENSE
+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 NiBAx.mainwindow import MainWindow
-from NiBAx.NiBAxCmdApp import NiBAxCmdApp
+from niCHART.mainwindow import MainWindow
+from niCHART.niCHARTCmdApp import niCHARTCmdApp
 
 def main():
-    parser = argparse.ArgumentParser(description='NiBAx Data Visualization and Preparation')
+    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('--MUSE_harmonization_model_file', type=str, help='MUSE 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)
@@ -37,13 +37,13 @@ def main():
             if((data_file == None) or (MUSE_harmonization_model_file == None) or (output_file == None)):
                 print("Please provide '--data_file', '--harmonization_model_file' and optionally '--output_file_name' to compute harmonized volumes.")
                 exit()
-            App = NiBAxCmdApp()
+            App = niCHARTCmdApp()
             App.LoadData(data_file).Harmonize(MUSE_harmonization_model_file, output_file)
         if(compute_spares):
             if((data_file == None) or (SPARE_model_file == None) or (output_file == None)):
                 print("Please provide '--data_file', '--MUSE_harmonization_model_file', '--SPARE_model_file' and optionally '--output_file_name' to compute spares.")
                 exit()
-            NiBAxCmdApp().LoadData(data_file).Harmonize(MUSE_harmonization_model_file, output_file).ComputeSpares(SPARE_model_file, output_file)
+            niCHARTCmdApp().LoadData(data_file).Harmonize(MUSE_harmonization_model_file, output_file).ComputeSpares(SPARE_model_file, output_file)
 
     else:
         app = QtWidgets.QApplication(sys.argv)

NiBAx/__main__.py renamed to niCHART/__main__.py

@@ -2,17 +2,17 @@
 """
 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/NiBAx/blob/main/LICENSE
+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 NiBAx.mainwindow import MainWindow
-from NiBAx.NiBAxCmdApp import NiBAxCmdApp
+from niCHART.mainwindow import MainWindow
+from niCHART.niCHARTCmdApp import niCHARTCmdApp
 
 def main():
-    parser = argparse.ArgumentParser(description='NiBAx Data Visualization and Preparation')
+    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('--MUSE_harmonization_model_file', type=str, help='MUSE 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)
@@ -39,13 +39,13 @@ def main():
             if((data_file == None) or (MUSE_harmonization_model_file == None) or (output_file == None)):
                 print("Please provide '--data_file', '--harmonization_model_file' and optionally '--output_file_name' to compute harmonized volumes.")
                 exit()
-            NiBAxCmdApp.LoadData(data_file)
-            NiBAxCmdApp().Harmonize(MUSE_harmonization_model_file, output_file)
+            niCHARTCmdApp.LoadData(data_file)
+            niCHARTCmdApp().Harmonize(MUSE_harmonization_model_file, output_file)
         if(compute_spares):
             if((data_file == None) or (SPARE_model_file == None) or (output_file == None)):
                 print("Please provide '--data_file', '--MUSE_harmonization_model_file', '--SPARE_model_file' and optionally '--output_file_name' to compute spares.")
                 exit()
-            NiBAxCmdApp().ComputeSpares(SPARE_model_file,output_file)
+            niCHARTCmdApp().ComputeSpares(SPARE_model_file,output_file)
 
     else:
         app = QtWidgets.QApplication(sys.argv)

NiBAx/aboutdialog.py renamed to niCHART/aboutdialog.py

@@ -2,13 +2,13 @@
 """
 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/NiBAx/blob/main/LICENSE
+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 NiBAx.resources import resources
+from niCHART.resources import resources
 
 class AboutDialog(QtWidgets.QDialog):
     def __init__(self,parent=None):

NiBAx/aboutdialog.ui renamed to niCHART/aboutdialog.ui

@@ -17,7 +17,7 @@
    </size>
   </property>
   <property name="windowTitle">
-   <string>About NiBAx</string>
+   <string>About niCHART</string>
   </property>
   <layout class="QVBoxLayout" name="verticalLayout">
    <item>
@@ -52,12 +52,12 @@ p, li { white-space: pre-wrap; }
 &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;NiBAx facilitates preparation of neuro-imaging data for machine learning applications.&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;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/NiBAx&quot;&gt;&lt;span style=&quot; text-decoration: underline; color:#0000ff;&quot;&gt;https://github.com/CBICA/NiBAx&lt;/span&gt;&lt;/a&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 NiBAx, 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;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;

NiBAx/core/__init__.py renamed to niCHART/core/__init__.py

@@ -3,7 +3,7 @@
 Author: Ashish Singh
 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/NiBAx/blob/main/LICENSE
+Use of this source code is governed by license located in license file: https://github.com/CBICA/niCHART/blob/main/LICENSE
 """
 
 from yapsy.IPlugin import IPlugin