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_savitzky_golay_intensity_matrix(im, tic):
# Use Savitzky-Golay filtering to smooth all IC's in the IM
im_smooth = savitzky_golay_im(im)
assert isinstance(im_smooth, 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_smooth = im_smooth.get_ic_at_index(73)
assert isinstance(ic_smooth, IonChromatogram)
# TODO: value assertions
savitzky_golay_im(im, degree=5)
savitzky_golay_im(im, window=5)
# Test Errors
for obj in [test_string, *test_numbers, *test_lists, test_dict]:
with pytest.raises(TypeError):
savitzky_golay_im(obj) # type: ignore
for obj in [test_string, test_float, *test_lists, test_dict]:
with pytest.raises(TypeError):
savitzky_golay_im(im, degree=obj) # type: ignore
for obj in [test_float, *test_lists, test_dict]:
with pytest.raises(TypeError):
savitzky_golay_im(im, window=obj) # type: ignore
"""proc.py
"""
# This file has been replaced by jupyter/NoiseSmoothing.ipynb
from pyms.GCMS.IO.ANDI import ANDI_reader
from pyms.IntensityMatrix import build_intensity_matrix
from pyms.Noise.SavitzkyGolay import savitzky_golay_im
# 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 Savitzky-Golay filtering to smooth all IC's in the IM
print("Smoothing ...")
im_smooth = savitzky_golay_im(im)
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_smooth = im_smooth.get_ic_at_index(73)
ic.write("output/ic.dat", minutes=True)
ic_smooth.write("output/ic_smooth.dat", minutes=True)
"""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.Noise.SavitzkyGolay import savitzky_golay_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 Savitzky-Golay filtering to smooth all IC's in the IM
print "Smoothing ..."
im_smooth = savitzky_golay_im(im)
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_smooth = im_smooth.get_ic_at_index(73)
ic.write("output/ic.dat",minutes=True)
ic_smooth.write("output/ic_smooth.dat",minutes=True)