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pipeline:utilities:sp_center_2d3d

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pipeline:utilities:sp_center_2d3d [2020/05/22 16:18]
shaikh
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
      
-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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 \\ \\
 ===== 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 =====
pipeline/utilities/sp_center_2d3d.txt · Last modified: 2022/03/01 15:13 by shaikh