Difference between revisions of "AnyWave:CommandLine"

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=Process files=
 
AnyWave can also process data files, running a specific process (plugin) to a bunch a files or directories.<br/>
 
The keyword to do that kind of opteration is :<br/>
 
'''--run <plugin name | json file | json string>'''<br/>
 
To run a plugin, the user must set all the required parameters as well as input and output options.<br/>
 
The other requirement is that the plugin CAN run in batch mode.<br/>
 
See the dedicated section to see how to make your plugin compatible or simply browse the list of compatible built-in plugins.<br/>
 
There is a list of common command line keywords that can be used anytime by every plug-ins:<br/>
 
'''--input_file <file>''' set the file to process.<br/>
 
'''--input_dir <dir>''' sets the input directory to use.<br/>
 
'''--output_dir <dir>''' sets the output directory. The location where the plugin should generate its results.<br/>
 
'''--output_file <file>''' sets the name of the processing output file.<br/>
 
'''--output_prefix <string>''' sets the prefix of the output file.<br/>
 
'''--hp <value>''' sets the high pass filter value to use.<br/>
 
'''--lp <value>''' sets the low pass filter value to use.<br/>
 
'''--notch <value>''' sets the notch filter value to use.<br/>
 
<br/>
 
==Setup parameters and run a processing plugin==
 
Processing a file relies on a specific plugin which need to be setup using specific parameters.<br/>
 
There are several ways to setup plugin parameters and run it:<br/>
 
1. use a json file to describe all the parameters.<br/>
 
2. use a json string to describe all the parameters.<br/>
 
3. use a plugin which declares its parameters.<br/>
 
<br/>
 
'''Examples''':<br/>
 
Suppose we want to run a processing using a plugin named ''ProcessPlugin''.<br/>
 
This ''ProcessPlugin'' requires two parameters, a time window (s) and a threshold value.<br/>
 
The expected parameters are :  time_window, threshold.<br/>
 
If the plugin published its required arguments to AnyWave, you can do :<br/>
 
<syntaxhighlight lang='bash'>
 
anywave --run ProcessPlugin --input_file d:\data\my_file.eeg --time_window 4 --threshold 0.3
 
</syntaxhighlight>
 
Note the input_file common keyword that set the data file to be processed by the plugin.<br/>
 
If the command fails, you'd probably need to use the json way:<br/>
 
Create a parameters.json file as follow:<br/>
 
<syntaxhighlight lang='java'>
 
{
 
"plugin" : "ProcessPlugin",
 
"time_window" : 4,
 
"threshold" : 0.3
 
}
 
</syntaxhighlight>
 
and use the command line:<br/>
 
<syntaxhighlight lang='bash'>
 
anywave --run parameters.json --input_file d:\data\my_file.eeg
 
</syntaxhighlight>
 
This way AnyWave will read the parameters from the json file and setup the plugin accordingly.<br/>
 
Note the you can also use the common keywords inside your json file:<br/>
 
<syntaxhighlight lang='java'>
 
{
 
"plugin" : "ProcessPlugin",
 
"input_file" : "d:\\data\\my_file.eeg",
 
"time_window" : 4,
 
"threshold" : 0.3
 
}
 
</syntaxhighlight>
 
Although it does not make sense there to specify input_file, you can do it.
 
You can also write down the json string on the command line after the --run keyword:<br/>
 
<syntaxhighlight lang='bash'>
 
anywave --run "{ """plugin""" : """ProcessPlugin""", """time_window""" : 4, """threshold""" : 0.3 }" --input_file d:\data\my_file.eeg
 
</syntaxhighlight>
 

Revision as of 12:49, 14 April 2020

This is a way to run AnyWave in non GUI mode to process files.
Passing arguments to anywave can be done using the double dash syntax:

anywave --arg1 <value> --arg2 <value> --arg3

An argument may have a value.
There is a list of common arguments that can be used anytime for every command line operation:
--input_file <file> set the file to process.
--input_dir <dir> sets the input directory to use.
--output_dir <dir> sets the output directory. The location where the plugin should generate its results.
--output_file <file> sets the name of the processing output file.
--output_prefix <string> sets the prefix of the output file.
--hp <value> sets the high pass filter value to use.
--lp <value> sets the low pass filter value to use.
--notch <value> sets the notch filter value to use.

Command Line Operations
convert a file to BIDS Run a plugin