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pipeline:utilities:sp_center_2d3d [2020/05/22 15:17] shaikh created |
pipeline:utilities:sp_center_2d3d [2021/02/18 16:24] shaikh |
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | [{{ : | + | [{{ : |
The purpose of sp_center_2d3d.py is to: | The purpose of sp_center_2d3d.py is to: | ||
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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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sp_center_2d3d.py volume_to_be_centered output_directory --mode=blob --volradius=volume_radius | sp_center_2d3d.py volume_to_be_centered output_directory --mode=blob --volradius=volume_radius | ||
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- | If you volume to be centered isn't round, try the radius in the smallest dimension. | + | If your volume to be centered isn't round, try the radius in the smallest dimension. |
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; %%--%%pad : In acf mode (2D or 3D), factor by which images will be padded. (default 2) | ; %%--%%pad : In acf mode (2D or 3D), factor by which images will be padded. (default 2) | ||
; %%--%%stem : In 3D acf mode, stem for output filenames. (default acf) | ; %%--%%stem : In 3D acf mode, stem for output filenames. (default acf) | ||
- | ; %%--%%ndilation : In 2D acf mode, number of dilations (see sp_mask.py for more information). (default 3) | + | ; %%--%%ndilation : In 2D acf mode, number of dilations (see sp_mask.py for more information). (default 3)[{{ : |
; %%--%%nerosion : In 2D acf mode, number of erosions (see sp_mask.py for more information). (default 0) | ; %%--%%nerosion : In 2D acf mode, number of erosions (see sp_mask.py for more information). (default 0) | ||
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===== Output ===== | ===== Output ===== | ||
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; stkmask_centered.hdf : In 2D acf mode, binarized images after centering | ; stkmask_centered.hdf : In 2D acf mode, binarized images after centering | ||
; stkavgs_centered.hdf : In 2D acf mode, input images after centering | ; stkavgs_centered.hdf : In 2D acf mode, input images after centering |