Difference between revisions of "AnyWave:CommandLine"
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| − | + | __NOTOC__ | |
| + | {| style="text-align: center; margin: auto;" | ||
| + | |+ Command Line Operations | ||
| + | |- | ||
| + | | [[File:Menu_cli_tobids.png|400px|link=AnyWave:CLi_toBIDS|'''convert a file to BIDS''']] || [[File:Menu_cli_process.png|400px|link=AnyWave:CLI_runPlugin|'''Run a plugin''']] | ||
| + | |- | ||
| + | |} | ||
| + | AnyWave allows the user to process data using the command line.<br/> | ||
| + | Passing arguments to anywave can be done using the double dash syntax:<br/> | ||
| + | <syntaxhighlight lang='bash'> | ||
| + | anywave --arg1 <value> --arg2 <value> --arg3 | ||
| + | </syntaxhighlight> | ||
| + | An argument may have a value.<br/> | ||
| + | There is a list of common arguments that can be used anytime for every command line operation:<br/> | ||
| + | '''--input_file <file>''' set the file to process.<br/> | ||
| + | '''--input_dir <dir>''' sets the input directory to use.<br/> | ||
| + | '''--marker_file <file>''' sets the marker file (.mrk) to use. (path must be absolute)<br/> | ||
| + | '''--montage_file <file>''' sets the montage file (.mtg) to use. (path must be absolute)<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/> | ||
| + | '''--skip_bad_chanels <true|false|yes|no>''' default is true. Set it false to force anywave to also add bad channels to processing input.<br/> | ||
| + | '''--create_montage <bipolar_ieeg|none>''' create a montage from data file and use it as input for processing. ''bipolar_ieeg'' means seeg alike bipolar. ''none'' will force AnyWave to ignore .mtg file that may be present along with the data file.<br/> | ||
| + | '''--use_markers "markers"''' specify the markers to use for processing. sets --use_markers all_data to force AnyWave to use a global marker for the whole data as input.<br/> | ||
| + | '''--skip_markers "markers"''' specify the markers to avoid while processing. Can be used with use_markers. if --use_markers all_data is set, this option is ignored.<br/> | ||
| + | <br/> | ||
| + | '''--log_dir <directory>''' set the output log directory. Every log files generated by the command line will be placed in that directory. The directory must exist.<br/> | ||
| + | '''--run <plugin name>''' start processing data using a plugin. This will required to specify plugin related options.<br/> | ||
| + | <br/> | ||
| + | Example:<br/> | ||
| + | Running h² computation on a seeg data file:<br/> | ||
| + | <syntaxhighlight lang="bash"> | ||
| + | anywave --run h2 --time_window 4 --step 1 --max_lag 0.1 --hp 1 --lp 45 --input_file d:\data\seeg\data.vhdr | ||
| + | </syntaxhighlight> | ||
Latest revision as of 15:27, 15 October 2020
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AnyWave allows the user to process data using the command line.
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.
--marker_file <file> sets the marker file (.mrk) to use. (path must be absolute)
--montage_file <file> sets the montage file (.mtg) to use. (path must be absolute)
--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.
--skip_bad_chanels <true|false|yes|no> default is true. Set it false to force anywave to also add bad channels to processing input.
--create_montage <bipolar_ieeg|none> create a montage from data file and use it as input for processing. bipolar_ieeg means seeg alike bipolar. none will force AnyWave to ignore .mtg file that may be present along with the data file.
--use_markers "markers" specify the markers to use for processing. sets --use_markers all_data to force AnyWave to use a global marker for the whole data as input.
--skip_markers "markers" specify the markers to avoid while processing. Can be used with use_markers. if --use_markers all_data is set, this option is ignored.
--log_dir <directory> set the output log directory. Every log files generated by the command line will be placed in that directory. The directory must exist.
--run <plugin name> start processing data using a plugin. This will required to specify plugin related options.
Example:
Running h² computation on a seeg data file:
anywave --run h2 --time_window 4 --step 1 --max_lag 0.1 --hp 1 --lp 45 --input_file d:\data\seeg\data.vhdr
