From d08dc033849733d4b9a61c7aea07c11f454f8ee1 Mon Sep 17 00:00:00 2001
From: Dung Truong <dt.young112@gmail.com>
Date: Thu, 15 Aug 2024 14:59:04 -0400
Subject: [PATCH] index file

---
 code/plugins/update_plugins.py | 24 ++++++++++++++++++---
 plugins/index.md               | 39 ++++++++++++++++++++++++++++++++--
 2 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/code/plugins/update_plugins.py b/code/plugins/update_plugins.py
index 3a3ebe4..d26e840 100644
--- a/code/plugins/update_plugins.py
+++ b/code/plugins/update_plugins.py
@@ -41,11 +41,29 @@ def update_repo(repo, formatted_name, order, plugin_type='readme', plugin_link="
     if not os.path.exists('plugins.json'):
         print('Error: plugins.json not found.')
         sys.exit(1)
+    
     plugin_info = json.load(open('plugins.json'))
     plugins = [plugin['name'] for plugin in plugin_info]
-    # wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'EEG-BIDS', 'nsgportal', 'clean_rawdata', 'amica', 'LIMO']
-    # readme_plugins = ['ARfitStudio', 'roiconnect', 'trimOutlier', 'PACT', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline','NIMA', 'firfilt']
-    # ordering = ['ICLabel', 'dipfit', 'EEG-BIDS', 'roiconnect', 'amica', 'cleanline', 'clean_rawdata', 'SIFT', 'zapline-plus', 'eegstats', 'trimOutlier', 'fMRIb', 'imat', 'nwbio', 'NIMA', 'PACT', 'NFT', 'PACTools', 'ARfitStudio', 'PowPowCAT', 'relica', 'std_dipoleDensity', 'viewprops', 'firfilt', 'groupSIFT', 'get_chanlocs', 'nsgportal']
+
+    # write index file
+    with open('../../plugins/index.md', 'w') as index_file:
+        text = '''---
+layout: default
+title: Plugins
+has_children: true
+has_toc: true
+nav_order: 7
+---
+'''
+        for cat in ['import', 'processing']:
+            text += f'## {cat.capitalize()}\n'
+            for plugin in [plugin for plugin in plugin_info if plugin['cat'] == cat]:
+                text += f'* [{plugin["name"]}](/plugins/{plugin["name"]}): {plugin["desc"]}\n'
+            
+            text += '\n'
+        
+        index_file.write(text)
+
     
     if len(sys.argv) == 1:
         for plugin in plugin_info:
diff --git a/plugins/index.md b/plugins/index.md
index 4ec507c..58ab51f 100644
--- a/plugins/index.md
+++ b/plugins/index.md
@@ -5,5 +5,40 @@ has_children: true
 has_toc: true
 nav_order: 7
 ---
-{%- assign children_list = site.pages | where: "parent", "Plugins" -%}
-{% include toc_nav.html nav=children_list %}
\ No newline at end of file
+## Import
+* [EEG-BIDS](/plugins/EEG-BIDS): Imports and export EEG data to the BIDS format
+* [NWB-io](/plugins/NWB-io): Import and export to the NWB format
+* [BVA-io](/plugins/BVA-io): input/output for Brain Vision Analyzer format
+* [MFF-matlab-io](/plugins/MFF-matlab-io): input/output for MFF EGI file format
+* [Neuroscan-io](/plugins/Neuroscan-io): input/output for Neuroscan file format
+* [CTFimport](/plugins/CTFimport): input/output for Neuroscan file format
+* [get_chanlocs](/plugins/get_chanlocs): Import scanned channel locations
+
+## Processing
+* [ICLabel](/plugins/ICLabel): Classifies independent components of EEG data
+* [Viewprops](/plugins/Viewprops): Advanced ICA component property viewing for IClabel
+* [DIPFIT](/plugins/DIPFIT): Localizes independent components of EEG data
+* [ROIconnect](/plugins/ROIconnect): Computes connectivity analysis between regions of interest
+* [AMICA](/plugins/AMICA): Computes Adaptive Mixture Independent Component Analysis
+* [Clean_rawdata](/plugins/Clean_rawdata): Rejects bad channels and bad portions of data using ASR
+* [LIMO](/plugins/LIMO): Linear Modeling of EEG data
+* [SIFT](/plugins/SIFT): Computes connectivity analysis between ICA components
+* [groupSIFT](/plugins/groupSIFT): Group-level SIFT analysis
+* [BrainBeats](/plugins/BrainBeats): Joint EEG/heart analysis
+* [Zapline-Plus](/plugins/Zapline-Plus): Removes line noise
+* [CleanLine](/plugins/CleanLine): Computes mixture model independent component analysis
+* [EEGstats](/plugins/EEGstats): Compute EEG statistics (power, alpha peak and asymmetry)
+* [trimOutlier](/plugins/trimOutlier): Removes EEG outliers
+* [fMRIb](/plugins/fMRIb): Removes fMRI artifacts in EEG
+* [IMAT](/plugins/IMAT): Finds independent modulators of EEG data
+* [NIMA](/plugins/NIMA): Clustering of ICA components using Measure-projection
+* [PACT](/plugins/PACT): Computes phase-amplitude coupling for ECoG
+* [NFT](/plugins/NFT): Localizes ICs using Neuroelectromagnetic Forward Head Modeling
+* [PACTools](/plugins/PACTools): Computes phase-amplitude coupling using different methods
+* [ARfitStudio](/plugins/ARfitStudio): Computes multivariate autoregressive models of EEG
+* [PowPowCAT](/plugins/PowPowCAT): Computes cross-frequency power-power coupling of ICs
+* [RELICA](/plugins/RELICA): Computes reliable ICA using Bootstrap
+* [std_dipoleDensity](/plugins/std_dipoleDensity): Computes ICA component dipole density
+* [FirFilt](/plugins/FirFilt): Filtering of EEG data
+* [NSGportal](/plugins/NSGportal): Performs computation on the Neuroscience Gateway
+