shift algorithms

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

  • None: in this case only the motors position / volume position will be used and 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

  • shift-grid: apply estimated stitch on an area for several shifts and pick the one with the highest score. Scores method can be ‘tv’ (total variation), ‘1/tv’, ‘std’ (standard deviation), ‘1/std’ and can be specify by the score_method key.

Settings of the shift search can be done with the axis_X_params keyword from the configuration file. Synthax is like key1=value1,key2=value2. For now valid keys are: And some parameter can also be specified like to set 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 keywork the axis_x_params can contain:

  • img_reg_method: detailled upper

  • window_size: size of the window for the ‘shift-grid’ algorithm’.

  • overlap_size: size to apply stitching. If not provided 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

  • score_method: method to use in order to compute score for the ‘shift-grid’ algorithm. Values can be ‘tv’ (total variation), ‘1/tv’, ‘std’ (standard deviation), ‘1/std’.