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pipeline:subtract:sp_mask

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pipeline:subtract:sp_mask [2021/02/01 16:08]
shaikh 		pipeline:subtract:sp_mask [2021/10/11 17:07]
shaikh
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 Generate and Apply Mask : Make a soft mask of the region to be excluded. Generate and Apply Mask : Make a soft mask of the region to be excluded.
  
-\\ 
 ===== Usage ===== ===== Usage =====
  
 Usage in command line Usage in command line
  
-  sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --verbosity=verbosity_level+<code> 
 +    sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --fullmap=full_map --outdir=output_subtraction_directory --mapthresh=threshold --verbosity=verbosity_level
  
 +</code>
  
-\\ 
 ===== Typical usage ===== ===== Typical usage =====
  
-sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map.  There are six steps for this process (five within SPHIRE):+sp_signalsubtract comprises the steps needed to subtract masked regions from a map in order to focus on the remaining features from that map. There are six steps for this process (five within SPHIRE):
  
-\\ __1. [[avgfilt|Average and low-pass filter a map for segmentation]] __+\\ 
 +__1. [[:pipeline:subtract:avgfilt|Average and low-pass filter a map for segmentation]] __
  
-\\ __2. Locate regions to be subtracted __+\\ 
 +__2. Locate regions to be subtracted __
  
-\\ __3. Mask a soft mask of the region to be excluded __:+\\ 
 +__3. Mask a soft mask of the region to be excluded __: 
 +<code>
  
-  sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --outdir=output_subtraction_directory --fullmap=full_map --mapthresh=threshold+sp_signalsubtract.py sp_mask --map2mask=map_to_make_mask_from --outdir=output_subtraction_directory --fullmap=full_map --mapthresh=threshold
  
-The map to make a mask from (--map2mask) corresponds to the region that you want to subtract. +</code>
  
-!!!IMPORTANT!!! The full map which is to be multiplied by the mask (--fullmap) must NOT have been postprocessed (e.g., sharpened).  Otherwise, re-projections will not be optimally comparable to the experimental images.   +The map to make a mask from (–map2mask) corresponds to the region that you want to subtract.
-   +
-\\ __4. [[projsubtract|Compute re-projections of map to be subtracted, and subtract them from the original images]] __+
  
-\\ __5. [[pipeline:meridien:sxmeridien|Compute reconstruction of density remaining after signal-subtraction]] __+!!!IMPORTANT!!! The full map which is to be multiplied by the mask (–fullmap) must NOT have been postprocessed (e.g., sharpened). Otherwise, re-projections will not be optimally comparable to the experimental images.
  
-\\ __6. [[centershift|Center map of the remaining density]] __+[{{:pipeline:subtract:grouped.png?410 |Grouped segments}}][{{ pipeline:subtract:sp_mask.png?410|Final mask}}]
  
 \\ \\
 +__4. [[:pipeline:subtract:projsubtract|Compute re-projections of map to be subtracted, and subtract them from the original images]] __
 +
 +\\
 +__5. [[:pipeline:meridien:sxmeridien|Compute reconstruction of density remaining after signal-subtraction]] __
 +
 +\\
 +__6. [[:pipeline:subtract:centershift|Center map of the remaining density]] __
 +
 ===== Input ===== ===== Input =====
 +
 === Main Parameters === === Main Parameters ===
-  ; %%--%%map2mask : Map from which a mask will be generated. (default None) + 
-  ; %%--%%fullmap : Map which will be multiplied by the mask. (default None) +; ; <nowiki>--</nowiki>map2mask : : Map from which a mask will be generated. (default required string) ; ; <nowiki>--</nowiki>fullmap : : Map which will be multiplied by the mask. (default None) ; ; <nowiki>--</nowiki>outdir : : Directory where outputs will be written. (default required string) ; ; <nowiki>--</nowiki>mapthresh : : Full map will be initially binarized at this threshold. (default None) 
-  ; %%--%%outdir : Directory where outputs will be written. (default required string) +
-  ; %%--%%mapthresh : Full map will be initially binarized at this threshold. (default None) +
-   +
-\\+
 === Advanced Parameters === === Advanced Parameters ===
-  ; %%--%%verbosity : Verbosity level : Controls how much information will be written to the screen. (default 2) + 
-   +; ; <nowiki>--</nowiki>verbosity : : Verbosity level : : Controls how much information will be written to the screen. (default 2) 
-\\+
 ===== Output ===== ===== Output =====
-  ; mask_final.hdf : Final mask + 
-  ; vol_masked.hdf : Diagnostic masked input map +; ; mask_final.hdf : : Final mask ; ; vol_masked.hdf : : Diagnostic masked input map ; ; ctf_params.txt : : CTF parameter file 
-  ; ctf_params.txt : CTF parameter file +
-  +
-\\+
 ===== Description ===== ===== Description =====
  
-\\ 
 ==== Method ==== ==== Method ====
  
-\\ 
 ==== Reference ==== ==== Reference ====
  
-\\ 
 ==== Developer Notes ==== ==== Developer Notes ====
  
-\\ 
 ==== Author / Maintainer ==== ==== Author / Maintainer ====
 +
 Tapu Shaikh Tapu Shaikh
  
-\\ 
 ==== Keywords ==== ==== Keywords ====
 +
 Category 1:: APPLICATIONS Category 1:: APPLICATIONS
  
-\\ 
 ==== Files ==== ==== Files ====
 +
 sphire/bin/sp_signalsubtract.py sphire/bin/sp_signalsubtract.py
  
-\\ 
 ==== See also ==== ==== See also ====
  
-\\ 
 ==== Maturity ==== ==== Maturity ====
 +
 Beta:: Under evaluation and testing. Please let us know if there are any bugs. Beta:: Under evaluation and testing. Please let us know if there are any bugs.
  
-\\ 
 ==== Bugs ==== ==== Bugs ====
  
-\\ 
  
pipeline/subtract/sp_mask.txt · Last modified: 2021/10/11 17:13 by shaikh

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