pyms.Simulator

Provides functions for simulation of GCMS data.

Functions:

add_gaussc_noise(im, scale)	Adds noise to an IntensityMatrix object.
add_gaussc_noise_ic(ic, scale)	Adds noise drawn from a normal distribution with constant scale to an ion chromatogram.
add_gaussv_noise(im, scale, cutoff, prop)	Adds noise to an IntensityMatrix object.
add_gaussv_noise_ic(ic, scale, cutoff, prop)	Adds noise to an ic.
chromatogram(n_scan, x_zero, sigma, peak_scale)	Returns a simulated ion chromatogram of a pure component.
gaussian(point, mean, sigma, scale)	Calculates a point on a gaussian density function.
gcms_sim(time_list, mass_list, peak_list)	Simulator of GCMS data.

add_gaussc_noise(im, scale)

Adds noise to an IntensityMatrix object.

Parameters:

• im (BaseIntensityMatrix) – the intensity matrix object

• scale (float) – the scale of the normal distribution from which the noise is drawn

Author:

Sean O’Callaghan

add_gaussc_noise_ic(ic, scale)

Adds noise drawn from a normal distribution with constant scale to an ion chromatogram.

Parameters:

• ic (IonChromatogram) – The ion Chromatogram.

• scale (float) – The scale of the normal distribution.

Author:

Sean O’Callaghan

add_gaussv_noise(im, scale, cutoff, prop)

Adds noise to an IntensityMatrix object.

Parameters:

• im (BaseIntensityMatrix) – the intensity matrix object

• scale (int) – the scale of the normal distribution from which the noise is drawn

• cutoff (int) – The level below which the intensity of the ic at that point has no effect on the scale of the noise distribution

• scale – The scale of the normal distribution for ic values

• prop (float) – For intensity values above the cutoff, the scale is multiplied by the ic value multiplied by prop.

Author:

Sean O’Callaghan

add_gaussv_noise_ic(ic, scale, cutoff, prop)

Adds noise to an ic. The noise value is drawn from a normal distribution, the scale of this distribution depends on the value of the ic at the point where the noise is being added

Parameters:

• ic (IonChromatogram) – The IonChromatogram

• cutoff (int) – The level below which the intensity of the ic at that point has no effect on the scale of the noise distribution

• scale (int) – The scale of the normal distribution for ic values below the cutoff is modified for values above the cutoff

• prop (float) – For ic values above the cutoff, the scale is multiplied by the ic value multiplied by prop.

Author:

Sean O’Callaghan

chromatogram(n_scan, x_zero, sigma, peak_scale)

Returns a simulated ion chromatogram of a pure component.

The ion chromatogram contains a single gaussian peak.

Parameters:

• n_scan (int) – the number of scans

• x_zero (int) – The apex of the peak

• sigma (float) – The standard deviation of the distribution

• peak_scale (float) – the intensity of the peak at the apex

Author:

Sean O’Callaghan

Return type:

ndarray

gaussian(point, mean, sigma, scale)

Calculates a point on a gaussian density function.

f = s*exp(-((x-x0)^2)/(2*w^2))

Parameters:

• point (float) – The point currently being computed

• mean (int) – The apex of the peak

• sigma (float) – The standard deviation of the gaussian

• scale (float) – The height of the apex

Return type:

float

Returns:

a single value from a normal distribution

Author:

Sean O’Callaghan

gcms_sim(time_list, mass_list, peak_list)

Simulator of GCMS data.

Parameters:

• time_list (List[float]) – the list of scan times

• mass_list (List[float]) – the list of m/z channels

• peak_list (List[Peak]) – A list of peaks

Return type:

IntensityMatrix

Returns:

A simulated Intensity Matrix object

Author:

Sean O’Callaghan