merge master

code/plugins/reformat_plugin.py

@@ -3,26 +3,7 @@
 import shutil
 
 # open a text file ending with .md and append a paragraph to it
-def reformat_plugin(dirpath, plugin_name):
-    plugins_dir = '../../plugins'
-    index_file = os.path.join(plugins_dir, 'index.md')
-    shutil.copyfile(os.path.join(dirpath, 'README.md'), index_file)
-    with open(index_file) as f:
-        text = f.read()
-        append_text = '''---
-layout: default
-title: {plugin_name}
-long_title: {plugin_name}
-parent: Plugins
----
-'''.format(plugin_name=plugin_name)
-        text = append_text + text
-        with open(index_file, 'w') as out:
-            out.write(text)
-
-# open a text file ending with .md and append a paragraph to it
-# Usage: python test.py <filename>.md
-def append_to_file(filepath, filename, parent, output_file):
+def reformat_wiki_pages(filepath, filename, parent, output_file):
     with open(filepath) as f:
         text = f.read()
         append_text = '''---
@@ -42,53 +23,36 @@ def reformat_plugin_dir(plugin_input_dir, plugin_name, order, plugin_type='wiki'
     plugin_output_dir = os.path.join('../../plugins', plugin_name)
     if not os.path.exists(plugin_output_dir):
         os.makedirs(plugin_output_dir)
+
     # copy image directory from input to output dir
     if os.path.exists(os.path.join(plugin_input_dir, 'images')):
         shutil.copytree(os.path.join(plugin_input_dir, 'images'), os.path.join(plugin_output_dir, 'images'), dirs_exist_ok=True)
 
     index_file = os.path.join(plugin_output_dir, 'index.md')
-    if plugin_type == 'wiki':
-        shutil.copyfile(os.path.join(plugin_input_dir, 'Home.md'), index_file)
-        with open(index_file) as f:
-            text = f.read()
-            append_text = '''---
+    shutil.copyfile(os.path.join(plugin_input_dir, 'README.md'), index_file)
+    with open(index_file) as f:
+        text = f.read()
+        append_text = '''---
 layout: default
 title: {plugin_name}
 long_title: {plugin_name}
 parent: Plugins
-categories: plugins
 has_children: true
 nav_order: {order}
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/{plugin_name}).
 
 '''.format(plugin_name=plugin_name, order=order)
-            text = append_text + text
-            with open(index_file, 'w') as out:
-                out.write(text)
+        text = append_text + text
+        with open(index_file, 'w') as out:
+            out.write(text)
 
-        for root, dirs, files in os.walk(plugin_input_dir):
+    if plugin_type == 'wiki':
+        wiki_plugin_input_dir = plugin_input_dir + '.wiki'
+        for root, dirs, files in os.walk(wiki_plugin_input_dir):
             for file in files:
                 if file.endswith('.md') and not file.startswith('index') and not file.startswith('Home'):
-                    append_to_file(os.path.join(plugin_input_dir, file), file.strip('.md'), plugin_name, os.path.join(plugin_output_dir, file))
-    else:
-        shutil.copyfile(os.path.join(plugin_input_dir, 'README.md'), index_file)
-        with open(index_file) as f:
-            text = f.read()
-            append_text = '''---
-layout: default
-title: {plugin_name}
-long_title: {plugin_name}
-parent: Plugins
-nav_order: {order}
----
-To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/{plugin_name}).
-
-'''.format(plugin_name=plugin_name, order=order)
-            text = append_text + text
-            with open(index_file, 'w') as out:
-                out.write(text)
-
+                    reformat_wiki_pages(os.path.join(wiki_plugin_input_dir, file), file.strip('.md'), plugin_name, os.path.join(plugin_output_dir, file))
 # main
 def main():
     if len(sys.argv) != 5:

code/plugins/update_plugins.py

@@ -17,10 +17,15 @@ def update_repo(repo, order, plugin_type='readme'):
         os.chdir(repo_path)
         run_command('git pull')
     else:
-        if plugin_type == "wiki":
-            run_command(f'git clone https://github.com/sccn/{repo}.wiki.git {repo_path}')
+        run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}')
+
+    if plugin_type == "wiki":
+        wiki_repo_path = f"{repo_path}.wiki"
+        if os.path.exists(wiki_repo_path):
+            os.chdir(wiki_repo_path)
+            run_command('git pull')
         else:
-            run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}')
+            run_command(f'git clone https://github.com/sccn/{repo}.wiki.git {wiki_repo_path}')
 
     os.chdir(current_dir)
     script = 'reformat_plugin.py'
@@ -31,20 +36,26 @@ def update_repo(repo, order, plugin_type='readme'):
     # if 'github' not in current directory, create it
     if not os.path.exists('github'):
         os.makedirs('github')
-    if len(sys.argv) == 0:
+    wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
+    readme_plugins = ['ARfitStudio', 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
+    if len(sys.argv) == 1:
         order = 1
-        wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata']
         for plugin in wiki_plugins:
             update_repo(plugin, order, 'wiki')
             order += 1
-        readme_plugins = ['ARfitStudio', 'roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
         for plugin in readme_plugins:
             update_repo(plugin, order, "readme")
             order += 1
-    elif len(sys.argv) == 3:
+    elif len(sys.argv) == 2:
         plugin_name = sys.argv[1]
-        plugin_type = sys.argv[2]
-        update_repo(plugin_name, 1, plugin_type)
+        if plugin_name not in wiki_plugins and plugin_name not in readme_plugins:
+            print(f"Plugin {plugin_name} not found.")
+            sys.exit(1)
+
+        plugin_type = 'wiki' if plugin_name in wiki_plugins else 'readme'
+        plugin_order = wiki_plugins.index(plugin_name) + 1 if plugin_type == 'wiki' else len(wiki_plugins) + readme_plugins.index(plugin_name) + 1
+
+        update_repo(plugin_name, plugin_order, plugin_type)
     else:
-        print('Usage: python update_plugins.py <plugin_name> <plugin_type>')
+        print('Usage: python update_plugins.py <plugin_name>')
         sys.exit(1)

code/plugins/update_plugins.sh

@@ -0,0 +1,12 @@
+#!/bin/bash
+
+DIRECTORY="/path/to/directory"
+
+if [ -d "$DIRECTORY" ]; then
+    # Directory exists, pull changes
+    cd "$DIRECTORY"
+    git pull
+else
+    # Directory doesn't exist, clone from GitHub
+    git clone https://github.com/username/repository.git "$DIRECTORY"
+fi

plugins/ARfitStudio/index.md

@@ -3,6 +3,7 @@ layout: default
 title: ARfitStudio
 long_title: ARfitStudio
 parent: Plugins
+has_children: true
 nav_order: 7
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ARfitStudio).

plugins/EEG-BIDS/index.md

@@ -3,6 +3,7 @@ layout: default
 title: EEG-BIDS
 long_title: EEG-BIDS
 parent: Plugins
+has_children: true
 nav_order: 9
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/EEG-BIDS).

plugins/ICLabel/index.md

@@ -3,6 +3,7 @@ layout: default
 title: ICLabel
 long_title: ICLabel
 parent: Plugins
+has_children: true
 nav_order: 13
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/ICLabel).

plugins/NFT/index.md

@@ -3,119 +3,31 @@ layout: default
 title: NFT
 long_title: NFT
 parent: Plugins
-categories: plugins
 has_children: true
 nav_order: 3
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/NFT).
 
-### Open Source Matlab Toolbox for Neuroelectromagnetic Forward Head Modeling
+Pre-compiled binaries for the following 3rd party programs are distributed
+within the NFT toolbox for convinience of the users. The binaries are compiled
+for 32 and 64 bit Linux distributions.
 
-![right](NFTsmall.jpg "wikilink")
+All of these programs have opensource licenses and provide full source-code.
+Please visit home-pages of individual programs for more information on usage,
+source-code and license information.
 
-### What is NFT?
+ASC: Adaptive skeleton climbing
+homepage: http://www.cse.cuhk.edu.hk/~ttwong/papers/asc/asc.html
 
-Neuroelectromagnetic Forward Modeling Toolbox (NFT) is a MATLAB toolbox
-for generating realistic head models from available data (MRI and/or
-electrode locations) and for computing numerical solutions for solving
-the forward problem of electromagnetic source imaging (Zeynep Akalin
-Acar & S. Makeig, 2010). NFT includes tools for segmenting scalp, skull,
-cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic
-resonance (MR) images. The Boundary Element Method (BEM) is used for the
-numerical solution of the forward problem. After extracting the
-segmented tissue volumes, surface BEM meshes may be generated. When a
-subject MR image is not available, a template head model may be warped
-to 3-D measured electrode locations to obtain an individualized BEM head
-model. Toolbox functions can be called from either a graphic user
-interface (gui) compatible with EEGLAB (sccn.ucsd.edu/eeglab), or from
-the MATLAB command line. Function help messages and a user tutorial are
-included. The toolbox is freely available for noncommercial use and open
-source development under the GNU Public License.
+QSLIM: Quadric-based surface simplification
+homepage: http://mgarland.org/software/qslim.html
 
-### Why NFT?
+BEM_MATRIX: The METU-FP Toolkit
+homepage: http://www.eee.metu.edu.tr/metu-fp/
 
-The NFT is released under an open source license, allowing researchers
-to contribute and improve on the work for the benefit of the
-neuroscience community. By bringing together advanced head modeling and
-forward problem solution methods and implementations within an easy to
-use toolbox, the NFT complements EEGLAB, an open source toolkit under
-active development. Combined, NFT and EEGLAB form a freely available EEG
-(and in future, MEG) source imaging solution.
+PROCMESH: Mesh correction and processing. No web page yet. Please contact NFT developers for source code.
 
-The toolbox implements the major aspects of realistic head modeling and
-forward problem solution from available subject information:
+MATITK: Matlab and ITK
+homepage: http://www.sfu.ca/~vwchu/matitk.html
 
-1.  Segmentation of T1-weighted MR images: The preferred method of
-    generating a realistic head model is to use a 3-D whole-head
-    structural MR image of the subject's head. The toolbox can generate
-    a segmentation of scalp, skull, CSF and brain tissues from a
-    T1-weighted image.
-
-2.  High-quality BEM meshes: The accuracy of the BEM solution depends on
-    the quality of the underlying mesh that models tissue
-    conductance-change boundaries. To avoid numerical instabilities, the
-    mesh must be topologically correct with no self-intersections. It
-    should represent the surface using high-quality elements while
-    keeping the number of elements as small as possible. The NFT can
-    create high-quality linear surface BEM meshes from the head
-    segmentation.
-
-3.  Warping a template head model: When a whole-head structural MR image
-    of the subject is not available, a semi-realistic head model can be
-    generated by warping a standard template BEM mesh to the digitized
-    electrode coordinates (instead of vice versa).
-
-4.  Registration of electrode positions with the BEM mesh: The digitized
-    electrode locations and the BEM mesh must be aligned to compute
-    accurate forward problem solutions and lead field matrices.
-
-5.  Accurate high-performance forward problem solution: The NFT uses a
-    high-performance BEM implementation from the open source METU-FP
-    Toolkit for bioelectromagnetic field computations.
-
-### Required Resources
-
-Matlab 7.0 or later running under any operating system (Linux, Windows).
-A large amount of RAM is useful - at least 2 GB (4-8 GB recommended for
-forward problem solution of realistic head models). The Matlab Image
-Processing toolbox is also recommended.
-
-### NFT Reference Paper
-
-Zeynep Akalin Acar & Scott Makeig, [Neuroelectromagnetic Forward Head
-Modeling
-Toolbox](http://sccn.ucsd.edu/%7Escott/pdf/Zeynep_NFT_Toolbox10.pdf).
-<em>Journal of Neuroscience Methods</em>, 2010
-
-Download
---------
-
-To download the NFT, go to the [NFT download
-page](http://sccn.ucsd.edu/nft/).
-
-NFT User's Manual
------------------
-
--   [Chapter 01: Getting Started with NFT](Chapter_01_Getting_Started_with_NFT "wikilink")
--   [Chapter 02: Head Modeling from MR Images](Chapter_02_Head_Modeling_from_MR_Images "wikilink")
--   [Chapter 03: Forward Model Generation](Chapter_03_Forward_Model_Generation "wikilink")
--   [Chapter 04: NFT Examples](Chapter_04_NFT_Examples "wikilink")
--   [Chapter 05: NFT Commands and Functions](Chapter_05_NFT_Commands_and_Functions "wikilink")
--   [Appendix A: BEM Mesh Format](NFT_Appendix_A)
--   [Appendix B: Function Reference](NFT_Appendix_B)
--   [Appendix C: Effect of brain-to-skull conductivity ratio estimate](NFT_Appendix_C)
-
-
--   [Click here to download the NFT User Manual as a PDF book](NFT_Tutorial.pdf)
-
-<div align=right>
-
-Creation and documentation by:
-
-Zeynep Akalin Acar
-
-Project Scientist
-
-[email protected]
-
-</div>
+Note: The MATITK shared libraries are installed in the 'mfiles' directory.

plugins/NIMA/index.md

@@ -3,6 +3,7 @@ layout: default
 title: NIMA
 long_title: NIMA
 parent: Plugins
+has_children: true
 nav_order: 26
 ---
 To view the plugin source code, please visit the plugin's [GitHub repository](https://github.com/sccn/NIMA).