grapa.datatypes.graphSIMS.GraphSIMS

class grapa.datatypes.graphSIMS.GraphSIMS(filename: str | List[str] | List | ndarray = '', complement: dict | str | List[dict | str] = '', silent: bool = True, config: str | None = 'auto', log_active: bool = False)

Bases: Graph

msmtid is an id based on the initial datafile name, in order to be able to process simultaneously several SIMS measurements class must be written like instance of self is actually a Graph object, not a GraphSIMS. Cannot call a method of GraphSIMS as method of self.

__init__(filename: str | List[str] | List | ndarray = '', complement: dict | str | List[dict | str] = '', silent: bool = True, config: str | None = 'auto', log_active: bool = False)

default constructor. Calls method reset.

Methods

ROI_GUI2idx(msmtid, ROI)

appendReplaceCurveRatio(msmtid, ratioCurves, ...)

savgol: 2-element list width and degree for Savistky-Golay smoothening

appendReplaceCurveRatioGUI(ratioCurves, curveId)

appendReplaceCurveRatioGUISmt(ratioCurves, ...)

Creates a Curve computed as a ratio of Curves.

check_saturation(curve)

getCurve(msmtid, element[, silent, returnIdx])

getLayerBoundaries(msmtid)

getRatio(msmtid, ROI, ratioCurves[, ...])

getRatioGUI(ROI, ratioCurves[, msmtid, ...])

Computes a ratio of curves within a ROI.

getRatioProcessRatiocurves(ratioCurves)

isFileReadable(_filename, fileext[, line1, ...])

readDataFromFile(attributes, **_kwargs)

setLayerBoundaries(msmtid, ROI)

setLayerBoundariesDepthParameters(msmtid, ...)

setLayerBoundariesDepthParametersGUI(depth, ROI)

Calibrate depth by linear scaling of input x axis, given two positions and a corresponding distance.

setYieldCoefs(msmtid[, elementYield, ifAuto])

targetRatioSetYield(msmtid, ROI, ...[, silent])

targetRatioSetYieldGUI(ROI, ratioCurves, ...)

Adjust the relative SIMS yield of the Curve of a given element, such that the Curve ratio ratioCurves has the chosen value target within the selected range of interest ROI.

Attributes

AXISLABELS

FILEIO_GRAPHTYPE

SHORTCUTS

THRESHOLD_SATURATION

TOHIDE

YIELDS

appendReplaceCurveRatio(msmtid, ratioCurves, curveId, attributes={}, savgol=None)

savgol: 2-element list width and degree for Savistky-Golay smoothening

appendReplaceCurveRatioGUISmt(ratioCurves, curveId, SGw, SGd, msmtid=None)

Creates a Curve computed as a ratio of Curves.

Parameters:

  • ratioCurves – which Curve ratio is to be computed

  • curveId – give it a beautiful label (e.g. “GGI”)

  • SGw – width of a Savitsky-Golay smooth to apply to the elemental traces prior to combination, using window and degree. No effect if w 1 d 1. Possibly suitable smoothing w 21 d 3.

  • SGd – degree of the Savitsky-Golay smoothing.

  • msmtid – identifier for the Curves to consider.

getRatioGUI(ROI, ratioCurves, msmtid=None, ifROIisIdx=False)

Computes a ratio of curves within a ROI.

Parameters:

  • ROI – range of interest, in units of input x data. [x_min, x_max]

  • ratioCurves – which Curve ratio is to be adjusted

  • msmtid – identifier for the Curves to consider.

  • ifROIisIdx – if True, the ROI is given in units of index. If False, in terms of (calibrated) depth.

setLayerBoundariesDepthParametersGUI(depth, ROI, msmtid=None)

Calibrate depth by linear scaling of input x axis, given two positions and a corresponding distance.

Parameters:

  • depth – known depth difference of ROI

  • ROI – range of interest, in units of input x data. [xmin, xmax].

  • msmtid – identifier for the Curves to consider.

targetRatioSetYieldGUI(ROI, ratioCurves, element, target, msmtid=None)

Adjust the relative SIMS yield of the Curve of a given element, such that the Curve ratio ratioCurves has the chosen value target within the selected range of interest ROI.

Parameters:

  • ROI – range of interest, in units of input x data. [x_min, x_max].

  • ratioCurves – which Curve ratio is to be adjusted

  • element – which element the yield has to be adjusted

  • target – the known integrated ratio we want to reach by adjusting the element yield

  • msmtid – identifier for the Curves to consider.