A collection of tools that make DAPT easy to use, especially with PhysiCell. The sample_db and create_settings_file() methods are helpful with anyone using DAPT. The rest of the methods are used specifically for PhysiCell pipelines., default_settings='PhysiCell_settings_default.xml', save_settings='PhysiCell_settings.xml', off_limits=[])

Create a PhysiCell XML settings file given a dictionary of paramaters. This function works by having a default_settings file which contains the generic XML structure. Each key in parameters` then contains the paths to each XML tag in the ``default_settings file. The value of that tag is then set to the value in the associated key. If a key in parameters does not exist in the default_settings XML file then it is ignored. If a key in parameters also exists in off_limits then it is ignored.

  • paramaters (dict) – A dictionary of paramaters where the key is the path to the xml variable and the value is the desired value in the XML file.
  • default_settings (str) – the path to the default xml file
  • save_settings (str) – the path to the output xml file
  • off_limits (list) – a list of keys that should not be inserted into the XML file., pid=None)

Creates a file where each line contains a key from the parameters and its associated key, separated by a semicolon.

  • parameters (dict) – the paramaters to be saved in the file
  • pid (str) – the parameter id of the current parameter run. If you don’t give an id then the id in parameters will be used.

Zip all of the important PhysiCell items.

Parameters:pid (str) – the id of the current parameter run
Returns:The name of the zipped file

Emulating make data-cleanup-light: remove .mat, .xml, .svg, .txt, .pov. You can optionally remove zipped files by setting remove-zip equal to True or remove *.mp4 by setting remove-movie to True in the config file.

Parameters:config (Config) – A config object, optionally given.'sample_db.csv', delimiter=', ')

Create a sample Delimited_file database. The sample table is shown below. This method will create a file specified in the file_name attribute using the delimiter specified by delimiter.

id start-time end-time status a b c
t1 2019-09-06 17:23 2019-09-06 17:36 finished 2 4 6
t2       10 10  
t3       10 -10  
  • file_name (str) – the file name of the file to create and use for the database. The default value is sample_db.csv.
  • delimiter (str) – the delimiter to use for the file. The default is a ,.

A Delimited_file object using the file_name specified.