diff --git a/code/plugins/README_plugin.py b/code/plugins/README_plugin.py deleted file mode 100644 index 49291ee4..00000000 --- a/code/plugins/README_plugin.py +++ /dev/null @@ -1,34 +0,0 @@ -import os -import sys -import shutil - -# open a text file ending with .md and append a paragraph to it -def reformat_plugin(dirpath, plugin_name): - plugins_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins' - index_file = os.path.join(plugins_dir, '{plugin_name}.md'.format(plugin_name=plugin_name)) - 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) - - -# main -def main(): - if len(sys.argv) != 3: - print('Usage: python README_plugin.py ') - sys.exit(1) - dirpath = sys.argv[1] - plugin_name = sys.argv[2] - reformat_plugin(dirpath, plugin_name) - -if __name__ == "__main__": - main() \ No newline at end of file diff --git a/code/plugins/Wiki_plugin.py b/code/plugins/Wiki_plugin.py deleted file mode 100644 index 072604f3..00000000 --- a/code/plugins/Wiki_plugin.py +++ /dev/null @@ -1,63 +0,0 @@ -import os -import sys -import shutil - -# open a text file ending with .md and append a paragraph to it -# Usage: python test.py .md -def append_to_file(filepath, filename, parent, output_file): - with open(filepath) as f: - text = f.read() - append_text = '''--- -layout: default -title: {filename} -long_title: {filename} -parent: {parent} -grand_parent: Plugins ---- -'''.format(filename=filename, parent=parent) - text = append_text + text - with open(output_file, 'w') as out: - out.write(text) - -def reformat_plugin_dir(plugin_input_dir, plugin_name): - # plugins_output_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins' - plugin_output_dir = os.path.join('/Users/dtyoung/Documents/EEGLAB/sccn.github.io/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') - shutil.copyfile(os.path.join(plugin_input_dir, 'Home.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 ---- -'''.format(plugin_name=plugin_name) - text = append_text + text - with open(index_file, 'w') as out: - out.write(text) - - for root, dirs, files in os.walk(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)) - -# main -def main(): - if len(sys.argv) != 3: - print('Usage: python test.py ') - sys.exit(1) - dirpath = sys.argv[1] - plugin_name = sys.argv[2] - reformat_plugin_dir(dirpath, plugin_name) - -if __name__ == "__main__": - main() \ No newline at end of file diff --git a/code/plugins/reformat_plugin.py b/code/plugins/reformat_plugin.py new file mode 100644 index 00000000..eb68b2a9 --- /dev/null +++ b/code/plugins/reformat_plugin.py @@ -0,0 +1,97 @@ +import os +import sys +import shutil + +# open a text file ending with .md and append a paragraph to it +def reformat_plugin(dirpath, plugin_name): + plugins_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/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 .md +def append_to_file(filepath, filename, parent, output_file): + with open(filepath) as f: + text = f.read() + append_text = '''--- +layout: default +title: {filename} +long_title: {filename} +parent: {parent} +grand_parent: Plugins +--- +'''.format(filename=filename, parent=parent) + text = append_text + text + with open(output_file, 'w') as out: + out.write(text) + +def reformat_plugin_dir(plugin_input_dir, plugin_name, plugin_type='wiki'): + # plugins_output_dir = '/Users/dtyoung/Documents/EEGLAB/sccn.github.io/plugins' + plugin_output_dir = os.path.join('/Users/dtyoung/Documents/EEGLAB/sccn.github.io/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 = '''--- +layout: default +title: {plugin_name} +long_title: {plugin_name} +parent: Plugins +categories: plugins +has_children: true +--- +'''.format(plugin_name=plugin_name) + text = append_text + text + with open(index_file, 'w') as out: + out.write(text) + + for root, dirs, files in os.walk(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 +--- +'''.format(plugin_name=plugin_name) + text = append_text + text + with open(index_file, 'w') as out: + out.write(text) + +# main +def main(): + if len(sys.argv) != 4: + print('Usage: python test.py ') + sys.exit(1) + dirpath = sys.argv[1] + plugin_name = sys.argv[2] + plugin_type = sys.argv[3] + reformat_plugin_dir(dirpath, plugin_name, plugin_type) + +if __name__ == "__main__": + main() \ No newline at end of file diff --git a/code/plugins/update_plugins.py b/code/plugins/update_plugins.py index 8513f766..c3c9c248 100644 --- a/code/plugins/update_plugins.py +++ b/code/plugins/update_plugins.py @@ -7,7 +7,7 @@ def run_command(command): print(f"Command failed: {command}\nError: {result.stderr}") return result -def update_repo(repo, script, type='readme'): +def update_repo(repo, script, plugin_type='readme'): print(f"Updating {repo}...") current_dir = os.getcwd() repo_path = os.path.join(current_dir, 'github', repo) @@ -16,22 +16,22 @@ def update_repo(repo, script, type='readme'): os.chdir(repo_path) run_command('git pull') else: - if type == "wiki": + if plugin_type == "wiki": run_command(f'git clone https://github.com/sccn/{repo}.wiki.git {repo_path}') else: run_command(f'git clone https://github.com/sccn/{repo}.git {repo_path}') os.chdir(current_dir) - run_command(f'python {script} {repo_path} {repo}') + run_command(f'python {script} {repo_path} {repo} {plugin_type}') if __name__ == "__main__": # if 'github' not in current directory, create it if not os.path.exists('github'): os.makedirs('github') - wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata'] - for plugin in wiki_plugins: - update_repo(plugin, "Wiki_plugin.py", 'wiki') - readme_plugins = ['roiconnect', 'EEG-BIDS', 'trimOutlier', 'groupSIFT', 'nwbio', 'ICLabel', 'dipfit', 'eegstats', 'PowPowCAT', 'PACTools', 'zapline-plus', 'amica', 'fMRIb', 'relica', 'std_dipoleDensity', 'imat', 'viewprops', 'cleanline', 'ARfitStudio ', 'NIMA', 'firfilt'] + # wiki_plugins = ['SIFT', 'get_chanlocs', 'NFT', 'PACT', 'nsgportal', 'clean_rawdata'] + # for plugin in wiki_plugins: + # update_repo(plugin, "reformat_plugin.py", 'wiki') + 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, "README_plugin.py") + update_repo(plugin, "reformat_plugin.py", "readme") diff --git a/plugins/ARfitStudio/images/Onchannels.png 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a/plugins/SIFT/Chapter-1.-Downloads.md b/plugins/SIFT/Chapter-1.-Downloads.md index fbc3b92d..87b5fc75 100644 --- a/plugins/SIFT/Chapter-1.-Downloads.md +++ b/plugins/SIFT/Chapter-1.-Downloads.md @@ -9,8 +9,7 @@ grand_parent: Plugins SIFT releases can be downloaded below -| You can install SIFT using the [EEGLAB Extension Manager](https://eeglab.org/others/EEGLAB_Extensions.html) (see also section 5.1). | -|------------------------------------------------------------------------------------------------------------------------| +You can install SIFT using the [EEGLAB Extension Manager](https://eeglab.org/others/EEGLAB_Extensions.html) (see also section 5.1). @@ -20,7 +19,7 @@ SIFT releases can be downloaded below - @@ -29,7 +28,7 @@ SIFT releases can be downloaded below +here. A longer video is available here.

70-page SIFT manual. It gives both SIFT methods theory and a practical guide to using SIFT using downloadable sample data (some of the content in the PDF document is outdated, and this wiki is more up-to-date). +

70-page SIFT manual. It gives both SIFT methods theory and a practical guide to using SIFT using downloadable sample data (some of the content in the PDF document is outdated, and this wiki is more up-to-date).

A short video lecture on the (very) basic theory and application of SIFT to modeling distributed brain dynamics in EEG is available -here. A longer video is available here.

diff --git a/plugins/SIFT/Chapter-5.1.-SIFT-install.md b/plugins/SIFT/Chapter-5.1.-SIFT-install.md index 00a1c3e7..d7d9efd9 100644 --- a/plugins/SIFT/Chapter-5.1.-SIFT-install.md +++ b/plugins/SIFT/Chapter-5.1.-SIFT-install.md @@ -25,8 +25,8 @@ Folder**) model-fitting algorithm. You must manually install as follows: Download the free ARfit package from . After downloading and -unzipping the ARfit package, place the **`/arfit/`** folder in -**`/external/`** where **** is the full path to +unzipping the ARfit package, place the **/arfit/** folder in +**SIFT-path/external/** where **SIFT-path** is the full path to the SIFT root directory. 6\) Once the EEGLAB main GUI is visible, you are good to go! You will diff --git a/plugins/SIFT/Chapter-5.2.-Loading-and-preparing-the-data.md b/plugins/SIFT/Chapter-5.2.-Loading-and-preparing-the-data.md index 0201d8f2..422ab1b3 100644 --- a/plugins/SIFT/Chapter-5.2.-Loading-and-preparing-the-data.md +++ b/plugins/SIFT/Chapter-5.2.-Loading-and-preparing-the-data.md @@ -25,7 +25,7 @@ options set. From the EEGLAB menu select **File > Memory and other options**. Ma Now let’s load our sample datasets in EEGLAB. We will first load the *RespWrong.set* file and then *RespCorr.set* located in the -**`/Data/`** folder (click on [Chapter 1. Downloads](Chapter-1.-Downloads) to download the data). +**SIFT-path/Data/** folder (click on [Chapter 1. Downloads](Chapter-1.-Downloads) to download the data). ![Image:images/SIFTfig5.jpg](images/SIFTfig5.jpg ) diff --git a/plugins/amica.md b/plugins/amica/index.md similarity index 100% rename from plugins/amica.md rename to plugins/amica/index.md diff --git a/plugins/dipfit.md b/plugins/dipfit/index.md similarity index 94% rename from plugins/dipfit.md rename to plugins/dipfit/index.md index 93d1103f..c6fe8d57 100644 --- a/plugins/dipfit.md +++ b/plugins/dipfit/index.md @@ -12,7 +12,7 @@ A major obstacle to using EEG data to visualize macroscopic brain dynamics is th Documentation ==== -For documentation see https://eeglab.org/tutorials/09_source/DIPFIT.html +For documentation see [https://eeglab.org/tutorials/09_source/DIPFIT.html](https://eeglab.org/tutorials/09_source/DIPFIT.html) Version history ===== diff --git a/plugins/eegstats.md b/plugins/eegstats/index.md similarity index 100% rename from plugins/eegstats.md rename to plugins/eegstats/index.md diff --git a/plugins/fMRIb.md b/plugins/fMRIb/index.md similarity index 100% rename from plugins/fMRIb.md rename to plugins/fMRIb/index.md diff --git a/plugins/firfilt.md b/plugins/firfilt/index.md similarity index 100% rename from plugins/firfilt.md rename to plugins/firfilt/index.md diff --git a/plugins/groupSIFT/images/Groupsift1.jpg b/plugins/groupSIFT/images/Groupsift1.jpg new file mode 100644 index 00000000..d2f6cba1 Binary files /dev/null and b/plugins/groupSIFT/images/Groupsift1.jpg differ diff --git a/plugins/groupSIFT/images/Groupsift2.jpg b/plugins/groupSIFT/images/Groupsift2.jpg new file mode 100644 index 00000000..e046262d Binary files /dev/null and b/plugins/groupSIFT/images/Groupsift2.jpg differ diff --git a/plugins/groupSIFT/images/Mccon_currentdefault2.png b/plugins/groupSIFT/images/Mccon_currentdefault2.png new file mode 100644 index 00000000..f6e803a3 Binary files /dev/null and b/plugins/groupSIFT/images/Mccon_currentdefault2.png differ diff --git a/plugins/groupSIFT/images/Mccon_gfwer2.png b/plugins/groupSIFT/images/Mccon_gfwer2.png new file mode 100644 index 00000000..df7cf3b7 Binary files /dev/null and b/plugins/groupSIFT/images/Mccon_gfwer2.png differ diff --git a/plugins/groupSIFT/images/Nomcc_previousdefault2.png b/plugins/groupSIFT/images/Nomcc_previousdefault2.png new file mode 100644 index 00000000..e920af4d Binary files /dev/null and b/plugins/groupSIFT/images/Nomcc_previousdefault2.png differ diff --git a/plugins/groupSIFT.md b/plugins/groupSIFT/index.md similarity index 100% rename from plugins/groupSIFT.md rename to plugins/groupSIFT/index.md diff --git a/plugins/imat.md b/plugins/imat/index.md similarity index 100% rename from plugins/imat.md rename to plugins/imat/index.md diff --git a/plugins/nsgportal.md b/plugins/nsgportal.md deleted file mode 100644 index 663ae6e3..00000000 --- a/plugins/nsgportal.md +++ /dev/null @@ -1,16 +0,0 @@ ---- -layout: default -title: nsgportal -long_title: nsgportal -parent: Plugins ---- -# EEGLAB on NSG -An Open EEGLAB Portal to High-Performance Computing: As of late 2018, EEGLAB scripts may now be run on high-performance computing resources via the freely available Neuroscience Gateway Portal to the NSF-sponsored [Comet supercomputer](https://ucsdnews.ucsd.edu/pressrelease/sdsc_to_double_comet_supercomputers_graphic_processor_count/) of the [San Diego Supercomputer Center](https://sdsc.edu/). The home page of the Neuroscience Gateway is shown below. NSG accounts are free and are not limited to US users, but the portal may only be used for non-commercial purposes (see the [NSG Terms of Use](http://www.nsgportal.org/policy.html)). We also recommend you to watch the [NSG tutorial videos](https://www.nsgportal.org/tutorial.html). -
-drawing -
- -Like all (except personal!) supercomputers, Comet typically runs jobs in batch mode rather than in the interactive style of Matlab. However, Comet has all Matlab functions as well as EEGLAB functions and many plug-in extensions installed ready to be called from scripts. When a job submitted through the NSG portal is run, you will receive an email from NSG alerting you to download the results. This means that best uses of the Open EEGLAB Portal are for computationally intensive processes and/or for parallel, automated processing of large EEG studies. In the first category, we are now installing the most computationally intensive EEGLAB functions on comet: AMICA, RELICA, time/frequency analysis, SCALE-optimized individual subject head modeling via NFT, etc. We will give more information here about using these installed capabilities as they become available. - -To read a detailed overview of the Open EEGLAB Portal, browse a [conference paper submitted the IEEE/EMBS Neural Engineering Conference](https://sccn.ucsd.edu/~scott/pdf/Delorme_Open_EEGLAB_Portal_NER18.pdf) in San Francisco (March, 2019) and our [Neuroimage](https://www.sciencedirect.com/science/article/pii/S1053811920302652) article. - diff --git a/plugins/nwbio.md b/plugins/nwbio/index.md similarity index 100% rename from plugins/nwbio.md rename to plugins/nwbio/index.md diff --git a/plugins/relica/images/relica_cluster1.jpg b/plugins/relica/images/relica_cluster1.jpg new file mode 100644 index 00000000..2a723d5a Binary files /dev/null and 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