pwem.utils module

pwem.utils.cleanFileName(fn, warn=True)[source]

Cleans any character that later on might cause shell parsing errors like “(“, “)”, ” ” and warns about it if warn is true.

Parameters
  • fn – file to be cleaned

  • warn – Optional (True). Logs

pwem.utils.convertPixToLength(samplingRate, length)[source]
pwem.utils.fnMatching(itemId, filesDict, objType='Micrograph')[source]

Check if in an object (micrograph, ctf, etc…) its files are matched

Parameters
  • itemId – Is micName, baseName, tsId,…(is not objId)

  • filesDict – The keys are the base name of the file to import without the extension, and the values can be a path (e.g. path of the ctf files when importing ctf) or an object (e.g. micrographs when importing coordinates).

  • objType – This parameter is informative to complete the log messages to know what is being imported.

Returns

A tuple with the key and the value of filesDict that matches itemId

pwem.utils.getCmdPath(*paths)[source]
pwem.utils.getMatchingFiles(path, sort=False)[source]
pwem.utils.getPWEMPath(*paths)[source]
pwem.utils.getTemplatePath(*paths)[source]
pwem.utils.loadSetFromDb(dbName, dbPrefix='')[source]
pwem.utils.round_to_nearest(number, base)[source]
Rounds number to the nearest integer: E.g: pass base=5 to round to the nearest

number multiple of 5

Parameters
  • number – number to be rounded

  • base – integer to limit the rounding to

pwem.utils.runProgram(program, params)[source]

Runs an em program setting its environment matching a prefix

pwem.utils.splitRange(minValue, maxValue, splitNum=10, roundTo=2)[source]

returns a list of “splitNum” items with values ranging from minValue to maxValue, equally divided :param minValue: value to start from :param maxValue: value to stop :param splitNum: number of splits, limits included :param roundTo: default to 2, rounding decimal value :return: list with the split