def matrix_from_cdf(cdffile, name): data = ANDI_reader(cdffile) print(name) data.info() tic = data.get_tic() noise_lvl = window_analyzer(tic) return build_intensity_matrix(data), noise_lvl
def matrix_from_cdf(cdffile, name): ''' Intakes a .cdf file and produces an intensity matrix and a noise level . The noise level info is obtained by producing a tic and using the window_analyzer method to extract a noise approximation. @param cdffile: Absolutepath to a .cdf file to be processed @param name: file name associated with .cdf file @return: An intensity matrix and a corresponding noise level value ''' data = ANDI_reader(cdffile) print(name) data.info() tic = data.get_tic() noise_lvl = window_analyzer(tic) print('nz=', noise_lvl) return build_intensity_matrix(data), noise_lvl
"""proc.py """ import sys sys.path.append("/x/PyMS") from pyms.GCMS.IO.ANDI.Function import ANDI_reader # read the raw data andi_file = "/x/PyMS/data/gc01_0812_066.cdf" data = ANDI_reader(andi_file) # info about raw data data.info() # trim data between scans 1000 and 2000 data.trim(1000, 2000) # info about trimmed raw data data.info() # reload data = ANDI_reader(andi_file) # trim data between retention times, 6.5 minutes to 21 minutes data.trim("6.5m", "21m") # info about trimmed raw data data.info()