Command-line interface¶
CxSystem2 has five commands associated with the main functionalities of CxSystem2. Each of this commands have descriptive help commands.
cxsystem2¶
This command can be used to run a simulation using anatomy and configuration files:
$ cxsystem2 -h
cxsystem2 -- a cortex simulation software
Usage:
cxsystem2 (-h | --help)
cxsystem2 -a ANATOMY_FILE -p PHYSIOLOGY_FILE
cxsystem2 (-v | --version)
A cortex simulation framework called `CxSystem`.
Arguments:
PORT port number on which the BUI server runs
Options:
-h --help Show this screen
-v --version Show current cxsystem version
-a ANATOMY_FILE --anatomy=ANATOMY_FILE Sets the anatomy file path
-p PHYSIOLOGY_FILE --physiology=PHYSIOLOGY_FILE Sets the physiology file path
Description:
cxsystem2 -a ./anatomy.csv -p ./physiology.csv
runs the cxsystem using the anatomy file called anatomy.csv and physiology file called physiology.csv
cxsystem2 --anatomy ./anatomy.csv --physiology ./physiology.csv
runs the cxsystem using the anatomy file called anatomy.csv and physiology file called physiology.csv
cxvisualize¶
This command can be used to visualize the result of a simualtion using ViSimpl (available here
for download):
$ cxvisualize -h
cxvisualize -- cxsystem visualizer
Usage:
cxvisualize (-h | --help)
cxvisualize [ -d | -c ] FILEPATH
cxvisualize --rasterplot-pdf FOLDERPATH TIMESTAMP [--sampling-rate SAMPLINGRATE]
A tool for visualizing `CxSystem` spike data in ViSimpl.
Arguments:
FILENAME Path to results file
FOLDERPATH Path to folder containing array run files
TIMESTAMP Timestamp suffix of the arrayrun files
SAMPLINGRATE Sampling rate for the rasterplots
Options:
-h --help Show this screen
--rasterplot-pdf Generate a rasterplot pdf for arrayrun
-c --convert Convert results for use in ViSimpl
-d --delete Delete ViSimpl-related files after visualization
-s SAMPLINGRATE --sampling-rate=SAMPLINGRATE Sampling rate for raster plot (default is 1%)
Description:
cxvisualize ./results.gz
converts the results file into two CSVs and one JSON for ViSimpl, visualizes the result and does not remove the temp files
(actual visualization: ./visimpl -csv results_structure.csv results_spikes.csv -se results_subsets.json)
cxvisualize -d ./results.gz
converts the results file into two CSVs and one JSON for ViSimpl, visualizes the result and remove the temp files
cxvisualize -c ./results.gz
converts the results file into two CSVs and one JSON for ViSimpl (no visualization)
cxvisualize --rasterplot-pdf ./cobaeif 20191123_1353509
Generates a pdf of rasterplots of all groups in the folder with 20191123_1353509 timestamp
cxvisualize --rasterplot-pdf ./cobaeif 20191123_1353509 --sampling-rate=4%
Generates a pdf of rasterplots of all groups in the folder with timestamp 20191123_1353509 and sampling rate or 4%
cxconfig¶
CxSystem2 supports both csv and json file formats for the anatomy and physiology configurations. cxconfig can be used
to convert the json configuration files to csv and vice versa:
$ cxconfig -h
cxconfig -- cxsystem config file converter
Usage:
cxconfig (-h | --help)
cxconfig FILEPATH
A configuration file converter for `CxSystem`.
Arguments:
FILENAME Path to configuration file to convert
Options:
-h --help Show this screen
Description:
cxconfig ./sample_conf.json
converts the file `sample_conf.json` in current directory to csv and saves it as `sample_conf.csv`
cxconfig ./sample_conf.csv
converts the file `sample_conf.csv` in current directory to csv and saves it as `sample_conf.json`
cxcluster¶
After submitting jobs to cluster, CxSystem stores the data corresponding to the job to a metadata file. To retrieve the results
when they are ready, you can use the cxcluster command as follows:
$ cxcluster -h
cxcluster -- cxsystem cluster result downloader
Usage:
cxcluster (-h | --help)
cxcluster META_FILE_PATH
Downloads result data of `CxSystem` from cluster.
Arguments:
META_FILE_PATH Path to cluster run metadata file
Options:
-h --help Show this screen
Description:
cxcluster ./sample_meta.pkl
Uses the information in the metadata file to download the results if ready, and otherwise wait for the results.
User will be prompted for the remote password.
cxserver¶
You can use the cxserver command to run the browser user interface of the CxSystem2 in either http or https mode.
Note that running it in https mode requires oauth configurations for authentication:
$ cxserver -h
cxserver -- web server for cxsystem2
Usage:
cxserver (-h | --help)
cxserver [--port=PORT] [--no-browser]
cxserver --https [-p PROVIDERID -c CLIENTID -r REDIRECTURI -a AUTHORIZATION] [--port=PORT] [--no-browser]
cxserver --config -p PROVIDERID -c CLIENTID -r REDIRECTURI -a AUTHORIZATION
cxserver --config -w WORKSPACEPATH
cxserver --config -l LOGPATH
Web server for running the BUI for `cxsystem2`
Arguments:
PORT port number on which the BUI server runs
PROVIDERID provider id for OAuth2 client for authentication
CLIENTID client id for OAuth2 client for authentication
REDIRECTURI redirect url for OAuth2 client for authentication
AUTHORIZATION authorization url for OAuth2 client for authentication
WORKSPACEPATH path to the main workspace folder
LOGPATH path to the log folder
Options:
-h --help Show this screen
-v --version Show current cxsystem version
--https Run server with ssl certificate
--port=PORT Runs the server on port PORT
--config Rewrite the oauth config file with the new parameters
--no-browser Do not open browser after running the server
-p PROVIDERID --provider-id=PROVIDERID Sets the provider id
-c CLIENTID --client-id=CLIENTID Sets the client id
-r REDIRECTURI --redirect-uri=REDIRECTURI Sets the redirect url
-a AUTHORIZATION --authorization=AUTHORIZATION Sets the authorization url
-w WORKSPACE --workspace-path=WORKSPACE Sets the workspace path
-l LOGPATH --log-path=LOGPATH Sets the log path
Description:
cxserver
runs the cxsystem2 server without SSL certificate on a random port
cxserver --port=PORT
runs the server on a specific port number PORT
cxserver --https
runs the cxsystem using the ssl certificate and other parameters previously saved in the configuraiton file using --config
cxserver --config -p HBP -c f34780ff-7842-499c-8440-5777c28e360d -r https://127.0.0.1:4443 -a https://services.humanbrainproject.eu/oidc/authorize
config the configuration yaml file with the new oauth parameters
cxserver --config -w /cxworkspace
config the configuration yaml file with the new workspace path
cxserver --config -l /var/log/
config the configuration yaml file with the new log path