import os
from rainbow.datafile import DataFile
from rainbow.datadirectory import DataDirectory
from rainbow import agilent, waters
[docs]
def read(path, prec=0, hrms=False, requested_files=None, telemetry=False):
"""
Reads a chromatogram data directory. Main method of the package.
Increasing the precision may drastically increase memory usage for \
larger files. Specifying a higher precision mainly affects the \
parsing of MS data, because intensities are summed within the given \
precision for each ylabel.
Max precision available for Agilent MS data is 1.
Max precision recommended for Waters MS data is 3.
Agilent HRMS parsing may be slow. Set the flag to enable it.
For Agilent .dx archives, instrument telemetry traces (e.g. pressure, \
temperature) are skipped unless the telemetry flag is set.
Args:
path (str): Path of the directory.
prec (int, optional): Number of decimals to round ylabels.
hrms (bool, optional): Flag for Agilent HRMS parsing.
requested_files (list, optional): List of filenames to parse.
telemetry (bool, optional): Flag for Agilent .dx telemetry traces.
Returns:
DataDirectory representing the directory.
"""
ext = os.path.splitext(path)[1] if isinstance(path, str) else ''
if ext.lower() == '.dx':
if not isinstance(path, str) or not os.path.isfile(path):
raise Exception(f"{path} is not a file.")
elif not isinstance(path, str) or not os.path.isdir(path):
raise Exception(f"{path} is not a directory.")
if not isinstance(prec, int) or prec < 0:
raise Exception(f"Invalid precision: {prec}.")
if not isinstance(hrms, bool):
raise Exception(f"The hrms flag must be a boolean.")
if requested_files is not None and not isinstance(requested_files, list):
raise Exception(f"The requested_files argument must be a list.")
if requested_files:
requested_files = list(map(str.lower, requested_files))
datadir = None
if ext.upper() == '.D' or ext.lower() == '.dx':
datadir = agilent.read(path, prec, hrms, requested_files, telemetry)
elif ext.lower() == '.raw':
datadir = waters.read(path, prec, requested_files)
if datadir is None:
raise Exception(f"Rainbow cannot read {path}.")
return datadir