deid.utils package¶

Submodules¶

deid.utils.actions.get_func(function_name)[source]¶

Get_func will return a function that is defined from a string.

the function is assumed to be in this file

Parameters:	a function from globals based on a name string (return) –

deid.utils.actions.get_timestamp(item_date, item_time=None, jitter_days=None, format=None)[source]¶

Get_timestamp will return (default) a UTC timestamp.

This will have some date and (optional) time. A different format can be provided to change default behavior. eg: “%Y%m%d”

deid.utils.actions.parse_keyvalue_pairs(pairs)[source]¶: Given a listing of extra arguments, parse into lookup dict.

deid.utils.actions.parse_value(dicom, value, item=None, field=None, funcs=None)[source]¶

Parse_value will parse the value field of an action.

This function returns either: 1. the string (string or from function) 2. a variable looked up (var:FieldName)

deid.utils.fileio.get_installdir()[source]¶: Get installation directory of the application

deid.utils.fileio.get_temporary_name(prefix=None, ext=None)[source]¶

Get a temporary name.

Get a temporary name, can be used for a directory or file. This does so without creating the file, and adds an optional prefix

Parameters:	prefix (if defined, add the prefix after deid) – ext (if defined, return the file extension appended. Do not specify ".") –

deid.utils.fileio.is_number(value)[source]¶: Determine if the value for a field is numeric

deid.utils.fileio.read_file(filename, mode='r')[source]¶

Read a file.

Parameters:	filename (the name of the file to write to) – mode (the mode to open the file, defaults to read (r)) –

deid.utils.fileio.read_json(filename, mode='r', ordered_dict=False)[source]¶

Open a file, “filename” and read the string as json

Parameters:	filename (the name of the file to write to) – mode (the mode to open the file, defaults to read (r)) – ordered_dict (If true, return an OrderedDict (default is False)) –

deid.utils.fileio.recursive_find(base, pattern=None)[source]¶

Recursively find files that match a pattern.

recursive find will yield dicom files in all directory levels below a base path. It uses get_dcm_files to find the files in the bases.

Parameters:	base (the base directory to search) – pattern (a pattern to match. If None, defaults to ""*) –

deid.utils.fileio.to_int(value)[source]¶: Convert a value (value) to int, if found to be otherwise

deid.utils.fileio.write_file(filename, content, mode='w')[source]¶

Write to file.

write_file will open a file, “filename” and write content, “content” and properly close the file

Parameters:	filename (the name of the file to write to) – content (the content to write to file) – mode (the mode to open the file, defaults to write (w)) –

deid.utils.fileio.write_json(json_obj, filename, mode='w', print_pretty=True)[source]¶

Write a json object to file

Parameters:	json_obj (the dict to print to json) – filename (the output file to write to) – pretty_print (if True, will use nicer formatting) –