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shift algorithms

In order to find shifts several methods are available (img_reg_method key):

  • None: in this case only the motor positions / volume position will be used together with the pixel size
  • skimage: use sci-kit image 'phase_cross_correlation' function with a specific space (real or fourier)
  • nabu-fft: use nabu find_shift_correlate function

Settings of the shift search can be done with the axis_X_params keyword from the configuration file. Syntax is key1=value1,key2=value2. For now valid keys are: And some parameters can also be specified, like setting the window search size with window_size.

  • first example: ask shift search over the axis 0 (aka z) with nabu-fft on a window of 400 px around the expected overlap.

    axis_0_params = overlap_size=;img_reg_method=nabu-fft;window_size=400
    
  • second example: ask the shifting algorithm to take the raw value of volume or scan for axis 2 (aka x)

    axis_2_params = img_reg_method=None;
    

Finally here is the list of the different keywords the axis_x_params can contain:

  • img_reg_method: detailed above
  • overlap_size: size to apply stitching. If not provided it will take the largest size possible.
  • low_pass: low pass filter value for filtering frames before shift research
  • high_pass: high pass filter value for filtering frames before shift research