Difference between revisions of "AnyWave:CLI ICA"
From WikiMEG
(→Arguments description for plugin ICA) |
(→using json file) |
||
| (17 intermediate revisions by one user not shown) | |||
| Line 8: | Line 8: | ||
|- | |- | ||
|input_file <file> | |input_file <file> | ||
| − | |MANDATORY | + | |'''MANDATORY''' |
|common argument | |common argument | ||
|- | |- | ||
| − | | modality | + | |modality <eeg,eeg,ieeg> |
| − | |MANDATORY | + | |'''MANDATORY''' |
| − | |channel modality | + | |channel modality |
|- | |- | ||
| − | | | + | |comp <value> |
| − | | | + | |'''MANDATORY''' |
| − | | | + | |number of components |
|- | |- | ||
| − | + | |hp <value> | |
| − | | | + | | OPTIONAL |
| − | | | + | |common hp argument. |
| − | | | + | |- |
| − | + | |lp <value> | |
| − | + | | OPTIONAL | |
| − | + | |common lp argument. | |
| − | | | + | |- |
| + | |downsampling <flag> | ||
| + | | OPTIONAL | ||
| + | |Downsampling data before computing. Default is false | ||
|- | |- | ||
| − | | | + | |infomax_extended <flag> |
| + | |OPTIONAL | ||
| + | |Use the extended option for Infomax. Default is false. | ||
|- | |- | ||
| − | | | + | |skip_bad <flag> |
| + | |OPTIONAL | ||
| + | |Skip bad channels. Default is true. | ||
|- | |- | ||
| − | | | + | |skip_markers <marker name> |
| + | |OPTIONAL | ||
| + | |common argument. ICA will skip all the data sections marked by the specified marker. | ||
|- | |- | ||
| − | | | + | |use_markers <marker name> |
| + | |OPTIONAL | ||
| + | |common argument. ICA will only compute on data sections marked by the specified marker. | ||
|- | |- | ||
| − | | | + | |output_dir <dir> |
| + | |OPTIONAL | ||
| + | |common argument. The result file will be placed in the specified directory path. | ||
|- | |- | ||
| − | | | + | |output_prefix <string> |
| + | |OPTIONAL | ||
| + | |common argument. The result file will be prefixed using the specified string. | ||
|} | |} | ||
| − | + | =Examples= | |
| − | + | run ica on meg data, just 70 components and filtering data in the 1-100Hz band.<br> | |
| − | + | <syntaxhighlight lang='bash'> | |
| − | + | anywave --run ica --input_file d:\data\meg\megdata.meg --modality meg --comp 70 --hp 1 --lp 100 | |
| − | + | </syntaxhighlight> | |
| − | + | run with extended flag and output result to a directory:<br/> | |
| + | <syntaxhighlight lang='bash'> | ||
| + | anywave --run ica --input_file d:\data\meg\megdata.meg --modality meg --comp 70 --hp 1 --lp 100 --infomax_extended true --output_dir d:\results | ||
| + | </syntaxhighlight> | ||
| + | =using json file= | ||
| + | Sometimes it makes sense to group the plugin's parameters in a json file for further re-use in a batch loop.<br/> | ||
| + | A JSON file also offers the capability to specify more than one value for some arguments like skip_markers, use markers.<br/> | ||
| + | Example of processing while skipping several artifacts parts of the data file:<br/> | ||
| + | json param.json:<br/> | ||
| + | <syntaxhighlight lang='java'> | ||
| + | { | ||
| + | "plugin" : "ica", | ||
| + | "modality" : "meg", | ||
| + | "comp" : 70, | ||
| + | "skip_markers" : ["artefacts", "bad", "rejected"] | ||
| + | } | ||
| + | </syntaxhighlight> | ||
| + | Then the command:<br/> | ||
| + | <syntaxhighlight lang='bash'> | ||
| + | anywave --run param.json --input_file d:\data\meeg\data.meg --hp 1 --lp 100 | ||
| + | </syntaxhighlight> | ||
Latest revision as of 16:48, 14 April 2020
Arguments description for plugin ICA
plugin name: ica
| argument | requirement | description |
|---|---|---|
| input_file <file> | MANDATORY | common argument |
| modality <eeg,eeg,ieeg> | MANDATORY | channel modality |
| comp <value> | MANDATORY | number of components |
| hp <value> | OPTIONAL | common hp argument. |
| lp <value> | OPTIONAL | common lp argument. |
| downsampling <flag> | OPTIONAL | Downsampling data before computing. Default is false |
| infomax_extended <flag> | OPTIONAL | Use the extended option for Infomax. Default is false. |
| skip_bad <flag> | OPTIONAL | Skip bad channels. Default is true. |
| skip_markers <marker name> | OPTIONAL | common argument. ICA will skip all the data sections marked by the specified marker. |
| use_markers <marker name> | OPTIONAL | common argument. ICA will only compute on data sections marked by the specified marker. |
| output_dir <dir> | OPTIONAL | common argument. The result file will be placed in the specified directory path. |
| output_prefix <string> | OPTIONAL | common argument. The result file will be prefixed using the specified string. |
Examples
run ica on meg data, just 70 components and filtering data in the 1-100Hz band.
anywave --run ica --input_file d:\data\meg\megdata.meg --modality meg --comp 70 --hp 1 --lp 100
run with extended flag and output result to a directory:
anywave --run ica --input_file d:\data\meg\megdata.meg --modality meg --comp 70 --hp 1 --lp 100 --infomax_extended true --output_dir d:\results
using json file
Sometimes it makes sense to group the plugin's parameters in a json file for further re-use in a batch loop.
A JSON file also offers the capability to specify more than one value for some arguments like skip_markers, use markers.
Example of processing while skipping several artifacts parts of the data file:
json param.json:
{ "plugin" : "ica", "modality" : "meg", "comp" : 70, "skip_markers" : ["artefacts", "bad", "rejected"] }
Then the command:
anywave --run param.json --input_file d:\data\meeg\data.meg --hp 1 --lp 100
