def test_IntensityMatrix_custom(data):
# IntensityMatrix
# must build intensity matrix before accessing any intensity matrix methods.
# bin interval of 0.5, eg. for double charge ions
# intensity matrix, bin interval = 0.5, boundary +/- 0.25
im = build_intensity_matrix(data, 0.5, 0.25, 0.25)
assert isinstance(im, IntensityMatrix)
# size of intensity matrix (#scans, #bins)
assert isinstance(im.size, tuple)
assert im.size == (2103, 900)
# start mass
assert isinstance(im.min_mass, float)
assert im.min_mass == 50.2516
# end mass
assert isinstance(im.max_mass, float)
assert im.max_mass == 499.7516
# the index of the nearest mass to 73.3m/z
index = im.get_index_of_mass(73.3)
assert isinstance(index, int)
assert index == 46
# the nearest mass to 73.3m/z
assert isinstance(im.get_mass_at_index(index), float)
assert im.get_mass_at_index(index) == 73.2516
# get the list of masses (bin centers), and print the first ten
masses = im.mass_list
assert isinstance(masses, list)
assert masses[0] == 50.2516
def test_build_intensity_matrix_errors(data, obj):
with pytest.raises(
TypeError,
match="'<=' not supported between instances of '.*' and 'int'"):
build_intensity_matrix(data, bin_interval=obj)
with pytest.raises(TypeError, match="'bin_left' must be a number."):
build_intensity_matrix(data, bin_left=obj)
with pytest.raises(TypeError, match="'bin_right' must be a number."):
build_intensity_matrix(data, bin_right=obj)
with pytest.raises(TypeError, match="'min_mass' must be a number."):
build_intensity_matrix(data, min_mass=obj)
with pytest.raises(ValueError,
match="The bin interval must be larger than zero."):
build_intensity_matrix(data, bin_interval=0)
"""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# This file has been replaced by jupyter/NoiseSmoothing.ipynb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)
def test_build_intensity_matrix(data):
# todo
for obj in [test_dict, *test_lists, test_string, *test_numbers]:
with pytest.raises(TypeError):
build_intensity_matrix(obj)
for obj in [test_dict, *test_lists, test_string]:
with pytest.raises(TypeError):
build_intensity_matrix(data, bin_interval=obj)
for obj in [test_dict, *test_lists, test_string]:
with pytest.raises(TypeError):
build_intensity_matrix(data, bin_left=obj)
for obj in [test_dict, *test_lists, test_string]:
with pytest.raises(TypeError):
build_intensity_matrix(data, bin_right=obj)
for obj in [test_dict, *test_lists, test_string]:
with pytest.raises(TypeError):
build_intensity_matrix(data, min_mass=obj)
with pytest.raises(ValueError):
build_intensity_matrix(data, bin_interval=0)
# This file has been replaced by jupyter/IntensityMatrix.ipynb
import pathlib
data_directory = pathlib.Path(".").resolve().parent.parent / "pyms-data"
# Change this if the data files are stored in a different location
from pyms.GCMS.IO.JCAMP import JCAMP_reader
from pyms.IntensityMatrix import build_intensity_matrix
# read the raw data
jcamp_file = data_directory / "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.size)
print(im.mass_list[:10])
print(" -> start mass:", im.min_mass)
print(" -> end mass:", im.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))
def im(data):
# build an intensity matrix object from the data
return build_intensity_matrix(data)
def test_build_intensity_matrix_errors_data(obj):
with pytest.raises(TypeError, match="'data' must be a GCMS_data object"):
build_intensity_matrix(obj)
