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pipeline:utilities:sp_center_2d3d

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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]
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
      
-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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   ; 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, or blob. (default acf)   ; %%--%%mode : Centering mode: acf, rt180, boundingbox, or blob. (default acf)
-  ; %%--%%threshsigma : Binarization threshold in 2D acf mode, in units of standard deviation. (default 0.0)+  ; %%--%%threshsigma : Binarization threshold in 2D acf mode, in units of standard deviation. (default 1.0)
   ; %%--%%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)
pipeline/utilities/sp_center_2d3d.txt ยท Last modified: 2022/03/01 15:13 by shaikh