pyFAI.gui package

The package pyFAI.gui contains mainly the code of the graphical user interface widgets. This code is not intended to be used by users of pyFAI as a library hence it makes little sense to document it all here. Only documentation on the Jupyter tools are exposed.

pyFAI.gui.cli_calibration module

pyFAI.gui.jupyter module

pyFAI.gui.matplotlib module

pyFAI.gui.peak_picker module

Semi-graphical tool for peak-picking and extracting visually control points from an image with Debye-Scherer rings

class pyFAI.gui.peak_picker.PeakPicker(data, reconst=False, mask=None, pointfile=None, calibrant=None, wavelength=None, detector=None, method='massif')

Bases: object

This class is in charge of peak picking, i.e. find bragg spots in the image Two methods can be used : massif or blob

VALID_METHODS = ['massif', 'blob', 'watershed']
__init__(data, reconst=False, mask=None, pointfile=None, calibrant=None, wavelength=None, detector=None, method='massif')
Parameters

  • data – input image as numpy array

  • reconst – shall masked part or negative values be reconstructed (wipe out problems with pilatus gaps)

  • mask – area in which keypoints will not be considered as valid

  • pointfile –

property append_mode
closeGUI()
contour(data, cmap='autumn', linewidths=2, linestyles='dashed')

Overlay a contour-plot

Parameters

data – 2darray with the 2theta values in radians…

display_points(minIndex=0, reset=False)

display all points and their ring annotations :param minIndex: ring index to start with :param reset: remove all point before re-displaying them

finish(filename=None, callback=None)

Ask the ring number for the given points

Parameters

  • filename – file with the point coordinates saved

  • callback –

Returns

list of control points

gui(log=False, maximize=False, pick=True, widget_klass=None)

Display the GUI

Parameters

  • log – show z in log scale

  • maximize – set to true to maximize window

  • pick – activate pixel picking

  • widget_klass – provide the MplCalibWidget (either Qt or Jupyter) to instanciate the widget

Returns

None

help = ['Please select rings on the diffraction image. In parenthesis, some modified shortcuts for single button mouse (Apple):', ' * Right-click (click+n):         try an auto find for a ring', ' * Right-click + Ctrl (click+b):  create new group with one point', ' * Right-click + Shift (click+v): add one point to current group', ' * Right-click + m (click+m):     find more points for current group', ' * Center-click or (click+d):     erase current group', ' * Center-click + 1 or (click+1): erase closest point from current group']
init(method, sync=True)

Unified initializer

load(filename)

load a filename and plot data on the screen (if GUI)

massif_contour(data)

Overlays a mask over a diffraction image

Parameters

data – mask to be overlaid

on_minus_pts_clicked(*args)

callback function

on_plus_pts_clicked(*args)

callback function

onclick_append_1_point(yx, ring=None)

Right-click + Shift (click+v): add one point to current group

Parameters

xy – 2tuple of coordinates

onclick_append_more_points(yx, ring)

Right-click + m (click+m): find more points for current group

onclick_erase_1_point(yx, ring)

Center-click + 1 or (click+1): erase closest point from current group

onclick_erase_grp(yx, ring)

Center-click or (click+d): erase current group

onclick_new_grp(yx, ring)

new_grp Right-click (click+n): try an auto find for a ring

onclick_option(*args)

callback function

onclick_refine(*args)

callback function

onclick_single_point(yx, ring)

Right-click + Ctrl (click+b): create new group with one single point

peaks_from_area(**kwargs)

Return the list of peaks within an area

Parameters

  • mask – 2d array with mask.

  • Imin – minimum of intensity above the background to keep the point

  • keep – maximum number of points to keep

  • method – enforce the use of detection using “massif” or “blob” or “watershed”

  • ring – ring number to which assign the points

  • dmin – minimum distance between two peaks (in pixels)

  • seed – good starting points.

Returns

list of peaks [y,x], [y,x], …]

remove_grp(lbl)

remove a group of points

Parameters

lbl – label of the group of points

reset()

Reset control point and graph (if needed)

sync_init()
pyFAI.gui.peak_picker.preprocess_image(data, log=False, clip=0.001)

Preforms the pre-processing of the image

Parameters

  • data – the input image

  • log – set to apply logarithmic intensity scale

  • clip – discard pixel fraction which are too weak/intense

Returns

scaled image, bounds