VoCentering

Summary

VoCentering

Process category

Brief description

Computational demand

for typical tomography data

(low, medium, high)

Comment(s)

Reference(s)

Common alternative process(es)

filter

To find an optimal value of CoR automatically.

High

Since the computational cost of this auto-centring process is high, it is normally applied to a small, representative subset of data (this can most conveniently be done with the aid of the preview parameter of this process).

Reliable method for calculating the center of rotation in parallel-beam tomography

VoCenteringIterative

Parameters

Brief description

Savu Configurator command

>>> disp -avv

-------------------------------------------------------------------------------------
 1) VoCentering(savu.plugins.centering.vo_centering)                                 
  A plugin to find the center of rotation per frame                                  
    1)                preview : []
    A slice list of required frames (sinograms) to use in the calulation of the
    centre of rotation (this will not reduce the data size for subsequent plugins).
    2)            start_pixel : None
    The approximate centre. If value is None, take the value from .nxs file else set
    to image centre.
    3)            search_area : (-50, 50)
    Search area from horizontal approximate centre of the image.
    4)            in_datasets : []
    Create a list of the dataset(s) to process.
    5)          search_radius : 6
    Use for fine searching.
    6)                  ratio : 0.5
    The ratio between the size of object and FOV of the camera.
    7)           out_datasets : ['cor_raw', 'cor_fit']
    The default names.
    8)   datasets_to_populate : []
    A list of datasets which require this information.
    9)               row_drop : 20
    Drop lines around vertical center of the mask.
   10)                   step : 0.5
    Step of fine searching.
-------------------------------------------------------------------------------------

>>>

Additional notes

Item	Parameter name	Parameter format	Example(s)		Comment(s)
Item	Parameter name	Parameter format	Parameter value	Effect	Comment(s)
1	preview				Note that the *preview* parameter has a nested-cumulative behaviour, i. e. if one specifies VoCentering's *preview* parameter together with NxtomoLoader's *preview* parameter, then VoCentering will effectively be selecting a subset from NxtomoLoader's own subset (rather than the entire dataset). Note also that VoCentering's subset must always be specified by indexing NxtomoLoader's own subset (rather than the entire dataset). For instance, one must set VoCentering's *preview* parameter to [:, 0, :] in order to select the initial slice of any dataset previously loaded by NxtomoLoader, which may, for example, be the [:, 123:456, :] subset of the entire dataset. If you use any kind of parameter tuning before applying VoCentering, then the latter will automatically receive (from the immediately preceding process) a dataset of order higher than 3. In this case, if you leave VoCentering's *preview* parameter at its default value (i.e. [ ]), then VoCentering will process the entire rank-4 data, which is hardly ever desired. To avoid this situation, you must set VoCentering's *preview* parameter to be a desired rank-3 slice of that incoming rank-4 dataset. For instance, if you have generated a dataset of shape (D, img_W, img_L, T) by subjecting the original (D, img_W, img_L) data to a single parameter-tuning operation, then your new, rank-4 dataset needs to be sliced in the last dimension, e. g. the [:, mid, :, 0] slice of that parameter-tuned dataset will give you the rank-3 subset containing the middle sinogram created with the initial value of your tuning parameter.
2	start_pixel				An initial estimate for the pixel coordinate of an optimal CoR.
3	search_area				If the value of the *search_area* parameter is set to the default interval of (-50, 50), then VoCentering will attempt to search for an optimal value of CoR in the (*start_pixel* - 50, *start_pixel* + 50) interval. For some datasets, this default range of search (100 pixel) may be not sufficiently large to include an optimal value of CoR, leading to subsequent sub-optimal reconstruction. Therefore, if the value of CoR determined by VoCentering is found to coincide with one of the search-interval limits (i. e. either start_pixel - 50 or *start_pixel* + 50), then this value of CoR may not necessarily be optimal, and one should then re-run VoCentering with a larger value of the *search_area* parameter to confirm this result.
4	in_datasets
5	search_radius
6	ratio
7	out_datasets
8	datasets_to_populate
9	row_drop
10	step				Floating-point or integer value in pixel units.

Usage

TBC.

VoCentering

Summary

Parameters

Brief description

Additional notes

Usage