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pipeline:utilities:sp_center_2d3d

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pipeline:utilities:sp_center_2d3d [2020/05/22 15:18]
shaikh
pipeline:utilities:sp_center_2d3d [2021/02/18 16:24]
shaikh
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 \\ \\
 ===== Typical usage ===== ===== Typical usage =====
-[{{ :pipeline:utilities:center2d.png?225|Left: uncentered binarized images, right: centered}}]+[{{ :pipeline:utilities:center2d.png?220|Left: uncentered binarized images, right: centered}}]
 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
      
-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, [[pipeline:viper:sp_mask|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.
  
 \\ __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
      
-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)[{{ :pipeline:utilities:center3d.png?400|Gray: uncentered map, violet: bounding box, melon: acf}}]
   ; %%--%%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)
  
 \\ \\
 ===== Output ===== ===== Output =====
-[{{ :pipeline:utilities:center3d.png?225|Gray: uncentered map, violet: bounding box, melon: acf}}] 
   ; 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
pipeline/utilities/sp_center_2d3d.txt ยท Last modified: 2022/03/01 15:13 by shaikh