def cdf_processing(fpath, structure):
with suppress_stdout():
# Read CDF
dat = ANDI_reader(fpath)
# Construct int matrix ~ (n_scan, n_mz)
im = build_intensity_matrix_i(dat)
# Basic noise and baseline corrections
smooth = savitzky_golay_im(im)
norm = tophat_im(smooth, struct=structure)
return norm
def test_tophat_im(im):
# Use TopHat baseline correction on all IC's in the IM
im_base_corr = tophat_im(im, struct="1.5m")
assert isinstance(im_base_corr, IntensityMatrix)
# find the IC for derivatisation product ion before smoothing
ic = im.get_ic_at_index(73)
assert isinstance(ic, IonChromatogram)
# find the IC for derivatisation product ion after smoothing
ic_base_corr = im_base_corr.get_ic_at_index(73)
assert isinstance(ic_base_corr, IonChromatogram)
"""proc.py
"""
from pyms.GCMS.IO.ANDI import ANDI_reader
from pyms.IntensityMatrix import build_intensity_matrix
from pyms.TopHat import tophat_im
# This file has been replaced by jupyter/BaselineCorrection.ipynb
# read the raw data
andi_file = "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)
def test_im_errors(self, im, struct, expects):
with pytest.raises(expects):
tophat_im(im, struct)
def test_im_errors(self, obj):
with pytest.raises(TypeError):
tophat_im(obj, "1m")