pipeline:viper:sp_mask

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pipeline:viper:sp_mask [2019/05/21 18:57]
shaikh
pipeline:viper:sp_mask [2019/05/21 18:59] (current)
shaikh
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 Create a binary mask dilated by 2 pixel using the binary threshold from chimera Create a binary mask dilated by 2 pixel using the binary threshold from chimera
  
-  sp_mask.py input_volume ​output_direcory ​--threshold=0.3 --edge_width=0 --ndilation=1+  sp_mask.py input_volume ​output_directory ​--threshold=0.3 --edge_width=0 --ndilation=1
  
 Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera
  
-  sp_mask.py input_volume ​output_direcory ​--threshold=0.3 --edge_width=5 --ndilation=1+  sp_mask.py input_volume ​output_directory ​--threshold=0.3 --edge_width=5 --ndilation=1
  
 Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera and masked by a soft edged cylinder to 80% (e.g. for helical reconstruction with a box size of 300) Create an adapted mask dilated by 2 pixel and a soft edge of 5 pixel using the binary threshold from chimera and masked by a soft edged cylinder to 80% (e.g. for helical reconstruction with a box size of 300)
  
-  sp_mask.py input_volume ​output_direcory ​--threshold=0.3 --edge_width=5 --ndilation=1 --second_mask_shape=cylinder --s_radius=40 --s_nx=240 --s_ny=240 --s_nz=240 --s_ndilation=1 --s_edge_width=5+  sp_mask.py input_volume ​output_directory ​--threshold=0.3 --edge_width=5 --ndilation=1 --second_mask_shape=cylinder --s_radius=40 --s_nx=240 --s_ny=240 --s_nz=240 --s_ndilation=1 --s_edge_width=5
  
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 === Main Parameters === === Main Parameters ===
   ; input_volume : Input image : Path to the 2D image or 3D Volume (default required string)   ; input_volume : Input image : Path to the 2D image or 3D Volume (default required string)
-  ; output_directory : Output directory : Output ​direcory ​path (default required string)+  ; output_directory : Output directory : Output ​directory ​path (default required string)
  
   ; %%--%%prefix : Output prefix : Prefix of the produced files (default sp_mask)   ; %%--%%prefix : Output prefix : Prefix of the produced files (default sp_mask)
  • pipeline/viper/sp_mask.txt
  • Last modified: 2019/05/21 18:59
  • by shaikh