EwaldPeaks
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