SeqIm - Prestipino/TEMpcPlot GitHub Wiki

class TEMpcPlot.SeqIm(filenames, filesangle=None, *args, **kwords)

sequence of images

this class is supposed to use a sequence of image. each element of the class is an image

Parameters

  • filenames (list) – list string describing the exception.
  • filesangle (str) – Human readable file with angles

Attributes

  • EwP (TEMpcPlot.EwaldPeaks) – Ewald peaks 3D set of peaks
  • rot_vect (list) – list of Rotation vector for each image
  • scale (list) – scale(magnification) of the images
  • ima (TEMpcPlot.Mimage) – current image of the sequence

SeqIm.D3_peaks(tollerance=15)

sum and correct the peaks of all images :param tollerance () = pixel tollerance to determine if a peak: in two images is the same peak.

SeqIm.find_peaks(rad_c=1.5, tr_c=0.02, dist=None, symf=None)

findf the peak allows to search again the peaks in all the image witht the same parameter

Parameters

  • tr_c (float) – total range coefficent the minimal intensity of the peak should be at list tr_c*self.ima.max()
  • rad_c (float) – coefficent in respect of the center radious peaks should be separate from at list self.rad*rad_c
  • dist – (float): maximum distance in pixel

Examples

Exp1.find_peaks()

SeqIm.help()

print class help

SeqIm.load(filename)

load a saved project it is necessary that images remain in the same relative position :param filename: filename to open :type filename: str

Examples

>>> exp1 = SeqIm.load('exp1.sqm')

SeqIm.plot(log=False, fig=None, ax=None, tool_b=None, *args, **kwds)

plot the images of the sequences with peaks

Parameters

  • log (Bool) – plot logaritm of intyensity

  • anf keyworg directly of matplotlib plot (aargs) –

Examples

Exp1.plot(log=True) Exp1.plot(True) Exp1.plot(1) Exp1.plot(0) Exp1.plot(vmin = 10, )

SeqIm.plot_cal(axes, log=False, *args, **kwds)

plot the images of the sequences with peaks

Parameters

  • base for reciprocal space as (axes) – one defined in EwP

  • log (Bool) – plot logaritm of intyensity

  • anf keyworg directly of matplotlib plot (aargs) –

Examples

>>> Exp1.plot(Exp1.EwP.axes, log=True) >>> Exp1.plot(Exp1.EwP.axes)

SeqIm.save(filesave)

save the project to open later formats available: None: pickel format good for python

Parameters filename (str) – filename to save

Examples

Exp1.save('exp1')