rainbow.datadirectory.DataDirectory

class DataDirectory(path, datafiles, metadata)[source]

Bases: object

Class representing a chromatogram data directory.

Parameters:

  • path (str) – Path of the directory.

  • datafiles (list) – All DataFile objects for the directory.

  • metadata (dict) – Metadata for the directory.

Attributes:

  • name (str) – Name of the DataDirectory.

  • datafiles (list) – DataFile objects with a detector. This does not include miscellaneous analog data.

  • detectors (set) – String detector names in the DataDirectory. Options: UV, MS, FID, CAD, ELSD.

  • by_name (dict) – Maps filenames to DataFile objects.

  • by_detector (dict) – Maps detector names to lists of DataFile objects.

  • analog (list) – DataFile objects with miscellaneous analog data.

  • metadata (dict) – Depends on the vendor.

get_info()[source]

Returns a string summary of the DataDirectory.

get_file(filename)[source]

Returns a DataFile object by filename.

Raises an exception if the filename is not in the DataDirectory.

Parameters:

filename (str) – DataFile name.

get_detector(detector)[source]

Returns a list of DataFile objects by detector.

Raises an exception if the detector is invalid.

Parameters:

detector (str) – Detector name.

list_analog()[source]

Prints a summary of the miscellaneous analog data.

extract_traces(filename, labels=None)[source]

Extracts data corresponding to the specified DataFile and labels.

Parameters:

  • filename (str) – DataFile name.

  • labels (int/float/list, optional) – Ylabel(s) to extract.

Returns:

2D numpy array containing data for the specified ylabel(s). The rows correspond to the ylabels and the columns corrrespond to the retention times.

export_csv(in_filename, out_filename, labels=None, delim=',')[source]

Outputs a CSV with data for the specified DataFile and labels.

Parameters:

  • in_filename (str) – DataFile name.

  • out_filename (str) – Filename for the output CSV.

  • labels (int/float/list, optional) – Ylabel(s) to export.

  • delim (str, optional) – Delimiter used in the output CSV.

plot(filename, label, **kwargs)[source]

Shows a basic matplotlib plot for the specified DataFile and label.

Parameters:

  • filename (str) – DataFile name.

  • label (int/float) – Ylabel to be plotted.

  • **kwargs (optional) – Keyword arguments for matplotlib.