def detect_one_run(run, args):
infile = os.path.join(args.indir, run)
print "processing GC-MS file:", infile
# sys.stdout("processing GCSM run:", run)
# load the input GC-MS file
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim(args.trimstart + "m", args.trimend + "m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
im = build_intensity_matrix_i(data)
# would be nice to do noise_mult*noise_level using the noise level AFTER smoothing,
# but i can't seem to get the TIC for the smoothed IM.
peak_list = call_peaks(im, tic, True, args)
return peak_list, run
def detect_one_run(run, args):
infile = os.path.join(args.indir, run)
print "processing GC-MS file:", infile
# sys.stdout("processing GCSM run:", run)
# load the input GC-MS file
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim(args.trimstart+"m",args.trimend+"m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
im = build_intensity_matrix_i(data)
# would be nice to do noise_mult*noise_level using the noise level AFTER smoothing,
# but i can't seem to get the TIC for the smoothed IM.
peak_list = call_peaks(im, tic, True, args)
return peak_list, run
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
def load_run(infile):
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim("4.0m", "20.0m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
return build_intensity_matrix_i(data), tic
def load_run(infile):
try:
if args.ftype == 'CDF':
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
data = ANDI_reader(infile)
elif args.ftype == 'JDX':
#data = JCAMP_reader(in_file)
data = pyms.GCMS.IO.JCAMP.Function.JCAMP_OpenChrom_reader(infile)
else:
raise ValueError('can only load ANDI (CDF) or JDX files!')
except:
print "Failure to load input file ", infile
else:
data.trim("4.0m", "20.0m")
# get TIC. Would prefer to get from smoothed IM but API is faulty!
tic = data.get_tic()
# integer mass
return build_intensity_matrix_i(data), tic
"""proc.py
"""
import sys
sys.path.append("/x/PyMS/")
from pyms.GCMS.IO.ANDI.Function import ANDI_reader
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Baseline.TopHat import tophat
# read the raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
# get the TIC
tic = data.get_tic()
# apply noise smoothing and baseline correction
tic1 = savitzky_golay(tic)
tic2 = tophat(tic1, struct="1.5m")
# save smoothed/baseline corrected TIC
tic.write("output/tic.dat", minutes=True)
tic1.write("output/tic_smooth.dat", minutes=True)
tic2.write("output/tic_smooth_bc.dat", minutes=True)
from pyms.GCMS.Function import build_intensity_matrix from pyms.Display.Function import plot_ic # read the raw data as a GCMS_data object andi_file = "/x/PyMS/data/gc01_0812_066.cdf" data = ANDI_reader(andi_file) # IntensityMatrix # must build intensity matrix before accessing any intensity matrix methods. # default, float masses with interval (bin interval) of one from min mass print "default intensity matrix, bin interval = 1, boundary +/- 0.5" im = build_intensity_matrix(data) # # IonChromatogram # # TIC from raw data tic = data.get_tic() # save TIC to a file #Call function to store a plot of the TIC plot_ic(tic, line_label = 'TIC', plot_title = 'TIC for gc01_0812_066')