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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 15:12] shaikh [Output] |
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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 ===== | ===== Output ===== | ||
- | ; stkmask_centered.hdf : In 2D acf mode, binarized images after centering | ||
- | ; stkavgs_centered.hdf : In 2D acf mode, input images after centering | ||
- | ; stkcompare.hdf : In 2D acf mode, montage of mask, centered image, and masked image | ||
- | ; stkcentered_rt180.hdf : In rt180 mode, input images after centering | ||
- | ; vol_acf_centered.hdf : In 3D acf mode, volume of interest after centering | ||
- | ; vol_blob_centered.hdf : In blob mode, volume of interest after centering | ||
- | ; vol_box_centered.hdf : In boundingbox mode, volume of interest after centering | ||
- | ; docshifts.txt : Shift parameters. Inputs will not be rotated. | ||
- | \\ | + | ; ; stkmask_centered.hdf : : In 2D acf mode, binarized images after centering ; ; stkavgs_centered.hdf : : In 2D acf mode, input images after centering ; ; stkcompare.hdf : : In 2D acf mode, montage of mask, centered image, and masked image ; ; stkcentered_rt180.hdf : : In rt180 mode, input images after centering ; ; vol_acf_centered.hdf : : In 3D acf mode, volume of interest after centering ; ; vol_blob_centered.hdf : : In blob mode, volume of interest after centering ; ; vol_box_centered.hdf : : In boundingbox mode, volume of interest after centering ; ; docshifts.txt : : Shift parameters. Inputs will not be rotated. |
===== Description ===== | ===== Description ===== |