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pipeline:utilities:sp_center_2d3d [2020/06/02 11:58] shaikh [Typical usage] |
pipeline:utilities:sp_center_2d3d [2022/03/01 15:13] (current) shaikh old revision restored (2021/02/18 16:24) |
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sp_center_2d3d.py input_binary_volume output_directory --applyshift=volume_to_be_centered | sp_center_2d3d.py input_binary_volume output_directory --applyshift=volume_to_be_centered | ||
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- | Generate the input binary volume using, for example, sp_mask.py. An adaptive mask is fine also; it will be thresholded. The mask will be centered, and those shifts will be applied to the volume to be shifted. | + | Generate the input binary volume using, for example, |
\\ __5. Center a binarized volume by finding a box that encloses it and centering that box__: | \\ __5. Center a binarized volume by finding a box that encloses it and centering that box__: | ||
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; output_directory : Directory where outputs will be written. (default required string) | ; output_directory : Directory where outputs will be written. (default required string) | ||
; %%--%%mode : Centering mode: acf, rt180, boundingbox, | ; %%--%%mode : Centering mode: acf, rt180, boundingbox, | ||
- | ; %%--%%threshsigma : Binarization threshold in 2D acf mode, in units of standard deviation. (default | + | ; %%--%%threshsigma : Binarization threshold in 2D acf mode, in units of standard deviation. (default |
; %%--%%applyshift : In 3D acf or boundingbox mode, volume to which shifts will be applied. (default None) | ; %%--%%applyshift : In 3D acf or boundingbox mode, volume to which shifts will be applied. (default None) | ||
; %%--%%volradius : In blob mode, radius of the Gaussian blob, in voxels, to which the input map will be aligned. (default None) | ; %%--%%volradius : In blob mode, radius of the Gaussian blob, in voxels, to which the input map will be aligned. (default None) |