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):
"""
Converrt ANDI files(.cdf) -> intensity matrices for processing & peak detection
:param cdffile:
:return: list of intensity matrices
"""
data = ANDI_reader(cdffile)
#data.info() # prints info about the data
return build_intensity_matrix(data)
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
from pyms.GCMS.Function import build_intensity_matrix
from pyms.Baseline.TopHat import tophat_im
# read the raw data
andi_file = "/x/PyMS/data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
# build an intensity matrix object from the data
im = build_intensity_matrix(data)
# Use TopHat baseline correction on all IC's in the IM
print "Smoothing ..."
im_base_corr = tophat_im(im, struct="1.5m")
print "Done"
# find the IC for derivatisation product ion before smoothing
ic = im.get_ic_at_index(73)
# find the IC for derivatisation product ion after smoothing
ic_base_corr = im_base_corr.get_ic_at_index(73)
ic.write("output/ic.dat",minutes=True)
ic_base_corr.write("output/ic_smooth.dat",minutes=True)
from pyms.GCMS.IO.ANDI.Function import ANDI_reader 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 # # get the ion chromatogram for some m/z channel (73) ic = im.get_ic_at_mass(73) plot_ic(ic, line_label = '73', plot_title = 'TIC and ICs for m/z = 73 & 147')
def matrix_from_cdf(cdffile):
data = ANDI_reader(cdffile)
#data.info() # prints info about the data
return build_intensity_matrix(data)
"""proc.py
"""
import sys
sys.path.append("/x/PyMS")
from pyms.GCMS.IO.JCAMP.Function import JCAMP_reader
from pyms.GCMS.Function import build_intensity_matrix
# read the raw data as a GCMS_data object
jcamp_file = "/x/PyMS/data/gc01_0812_066.jdx"
data = JCAMP_reader(jcamp_file)
# IntensityMatrix
# must build intensity matrix before accessing any intensity matrix methods.
# bin interval of 0.5, eg. for double charge ions
print "intensity matrix, bin interval = 0.5, boundary +/- 0.25"
im = build_intensity_matrix(data, 0.5, 0.25, 0.25)
print " -> size of intensity matrix (#scans, #bins):", im.get_size()
print " -> start mass:", im.get_min_mass()
print " -> end mass:", im.get_max_mass()
index = im.get_index_of_mass(73.3)
print " -> the index of the nearest mass to 73.3m/z is:", index
print " -> the nearest mass to 73.3m/z is:", im.get_mass_at_index(index)
# e.g. /home/anahid/sample1.cdf andi_file_1 = "The file with data from sample 1" andi_file_2 = "The file with data from sample 2" data_1 = ANDI_reader(andi_file_1) data_2 = ANDI_reader(andi_file_2) # 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_1 = build_intensity_matrix(data_1) im_2 = build_intensity_matrix(data_2) # # quant_ion_mass is the ion you wish to compare between samples # quant_ion_mass = 104 #for example # get the ion chromatogram for some m/z channel ic_1 = im_1.get_ic_at_mass(quant_ion_mass) ic_2 = im_2.get_ic_at_mass(quant_ion_mass) ics = [ic_1, ic_2]
