EwaldPeaks - Prestipino/TEMpcPlot GitHub Wiki

class TEMpcPlot.EwaldPeaks(positions, intensity, rot_vect=None, angles=None, r0=None, z0=None, pos0=None, scale=None, axes=None, set_cell=True)[¶]

Set of peaks position and intensity this class manages peaks position and intensity and the methods related to lattice indexing and refinement could be created as an attribute EwP of a SeqIm class by using methods D3_peaks or by sum with an another EwaldPeaks class with the same first image

Parameters

  • positions (list) – list containing the coordonates of peaks
  • intensity (list) – list containing the intensity of peaks

Variables

  • pos (list) – Ewald peaks 3D set of peaks
  • int (list) – list of Rotation vector for each image
  • pos_cal (np.array) – array witht he position in the new basis
  • rMT (np.array) – reciprocal metric tensor
  • axis (np.array) – reciprocal basis set, 3 coloums
  • cell (dict) – a dictionary witht the value of real space cell
  • graph (D3plot.D3plot) – graph Ewald peaks 3D set of peaks used to index

Examples:

Exp1.D3_peaks(tollerance=5)
Exp1.EwP is defined
EWT= Exp1.EwP + Exp2.EwP\

EwaldPeaks.create_layer(hkl, n, size=0.25, toll=0.15, mir=0, spg=None)

create a specific layer create a reciprocal space layer

Parameters

  • hkl (str) – constant index for the hkl plane to plot, format(‘k’)
  • n (float_,_ int) – value of hkl
  • size (float) – intensity scaling * if positive, scale intensity of each peaks respect the max * if negative, scale a common value for all peaks
  • mir (bool) – mirror in respect of n meaning =/-n
  • tollerance (float) – exclude from the plot peaks at higher distance
  • spg (str) – allows to index the peaks, and check if they are extinted

EwaldPeaks.load(filename)

load EwP in python format Example: >>>cr1 = EwaldPeaks.load(‘cr1.ewp’)

EwaldPeaks.plot()

open a D3plot graph :ivar ~EwaldPeaks.plot.graph: graph Ewald peaks 3D set of peaks used to index

EwaldPeaks.plot_int()

Plot instogramm of intensity of the peaks

plot_proj_int(cell=True)

plot peak presence instogramm as a function of the cell

EwaldPeaks.plot_reduce(tollerance=0.1, condition=None)

plot collapsed reciprocal space plot the position of the peaks in cell coordinatete and all reduced to a single cell. it create a self.reduce attribute containingt he graph

EwaldPeaks.refine_angles(axes=None, tollerance=0.1, zero_tol=0.1)

refine reciprocal cell basis refine the reciprocal cell basis in respect to data that are indexed in the tollerance range.

EwaldPeaks.refine_axang(axes=None, tollerance=0.1, zero_tol=0.1)

refine reciprocal cell basis refine the reciprocal cell basis in respect to data that are indexed in the tollerance range.

EwaldPeaks.refine_axes(axes=None, tollerance=0.1)

refine reciprocal cell basis refine the reciprocal cell basis in respect to data that are indexed in the tollerance range.

EwaldPeaks.save(filename, dictionary=False)

save EwP

EwaldPeaks.set_cell(axes=None, axes_std=None, tollerance=0.1, cond=None)

calculation of the cell effect the calculation to obtain the cell

Parameters

axis (np.array 3_,_3) – the new reciprocal basis to be used in the format if axis is not inoput the programm seach if a new basis has been defined graphically axes format: np.array([
[a1, b1, c1],
[a2, b2, c2],
[a3, b3, c3]])

Variables

  • self.rMT (np.array) – reciprocal metric tensor
  • self.cell (dict) – a dictionary witht the value of real space cell
  • self.rMT – reciprocal metric tensor
  • self.cell – a dictionary witht the value of real space cell