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pipeline:utilities:sp_eval_isac [2020/05/27 15:45]
shaikh created
pipeline:utilities:sp_eval_isac [2020/10/21 10:17] (current)
shaikh
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 ===== Usage ===== ===== Usage =====
  
-Usage in command line:+Usage in command line (beta version):
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_or_beautifier_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --ctf=ctf_mode --nvec=number_of_eigenimages --pca_radius=radius --chains_radius=radius --chains_exe=spchains_executable --applyparams=centering_mode --write_centered --debug --imgformat=image_format --verbosity=verbosity_level+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_or_beautifier_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --ctf=ctf_mode --nvec=number_of_eigenimages --pca_radius=radius --chains_radius=radius --chains_exe=spchains_executable --applyparams=centering_mode --write_centered --debug --imgformat=image_format --verbosity=verbosity_level
      
      
 \\ \\
 ===== Typical usage ===== ===== Typical usage =====
- +[{{ :pipeline:utilities:regular-evil-isac.png?275|Regular ISAC (top) vs. Evil ISAC (bottom)}}] 
-The purpose of sp_separate_class.py is to:  +The purpose of sp_eval_isac.py is to: 
   : write particle-membership lists for each class   : write particle-membership lists for each class
   : write separate stacks for each class,    : write separate stacks for each class, 
   : optionally low-pass filter and/or downsample the images, and   : optionally low-pass filter and/or downsample the images, and
   : optionally compute eigenimages (basis images) for each class   : optionally compute eigenimages (basis images) for each class
- 
 \\ __1. Standard usage: create separate stacks for each class__: \\ __1. Standard usage: create separate stacks for each class__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory +  sp_eval_isac.py input_class_avgs output_directory 
  
 \\ __2. Apply a low-pass filter to the image stacks__: \\ __2. Apply a low-pass filter to the image stacks__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --filt=filter_radius --apix=pixel_size+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --filt=filter_radius --apix=pixel_size
  
 Filter radius is in units of Angstroms. If --apix is not specified, program will assume units of pixels^-1.  Filter radius is in units of Angstroms. If --apix is not specified, program will assume units of pixels^-1. 
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 \\ __3. Downsample output image stack__: \\ __3. Downsample output image stack__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --shrink=shrink_factor
      
 \\ __4. Apply ISAC alignments to particles__: \\ __4. Apply ISAC alignments to particles__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_or_beautifier_directory+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_or_beautifier_directory
      
 Alignments used by ISAC or beautification will be applied to the particles. In addition, the average and variance for each map will be written. Alignments used by ISAC or beautification will be applied to the particles. In addition, the average and variance for each map will be written.
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 \\ __5. Compute eigenimages (basis images) for each class__: \\ __5. Compute eigenimages (basis images) for each class__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory --nvec=number_of_eigenimages --pca_radius=radius+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_directory --nvec=number_of_eigenimages --pca_radius=radius
      
 In addition to the average and variance, the requested number of eigenimages will be computed also. If --pca_radius is not provided, the whole image will be used to compute the eigenimages. In addition to the average and variance, the requested number of eigenimages will be computed also. If --pca_radius is not provided, the whole image will be used to compute the eigenimages.
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 \\ __6. Apply centering to each class as determined by sp_center_2d3d.py__: \\ __6. Apply centering to each class as determined by sp_center_2d3d.py__:
  
-  sp_eval_isac.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory --write_centered --applyparams=centering_mode+  sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_directory --write_centered --applyparams=centering_mode
      
 If you ran sp_center_2d3d.py, you can also apply those centering parameters to the individual particles.  The --write_centered flag will write out the particles; omitting the flag will simply write out the alignment parameters without applying them. The options for --applyparams are 'intshifts' for integer shifts and no rotation (i.e., no interpolation) and 'combined' (rotation and shifts). If you ran sp_center_2d3d.py, you can also apply those centering parameters to the individual particles.  The --write_centered flag will write out the particles; omitting the flag will simply write out the alignment parameters without applying them. The options for --applyparams are 'intshifts' for integer shifts and no rotation (i.e., no interpolation) and 'combined' (rotation and shifts).
 +
 +\\ __7. Apply a Gaussian band-pass filter to an image stack (e.g., class averages)__:[{{ :pipeline:utilities:plotbandpass.png?400|Shape of the band-pass filter}}]
 +  sp_eval_isac.py input_class_avgs output_directory --apix=pixel_size --bandpass_radius=bandpass_radius_angstroms
 +
 +The default beautifier settings (CTF-correction using a Wiener filter and power-spectrum adjustment) will amplify the low-resolution data, and may make the averages more difficult to interpret. A band-pass filter will dampen the lowest-resolution data, and also the high-resolution noise. This filtration may be helpful for recognizing smaller complexes.
 +
 +[{{pipeline:utilities:bandpass-example.png?400|(top) Beautified images and (bottom) band-pass filtered images, centered at 14 Angstroms}}]
  
 \\ \\
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 === Main Parameters === === Main Parameters ===
   ; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ :pipeline:utilities:class084.png?400|Filtered, aligned particles of TcdA1 corresponding to class #9 below}}]   ; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ :pipeline:utilities:class084.png?400|Filtered, aligned particles of TcdA1 corresponding to class #9 below}}]
-  ; input_image_stack : Particle image stack. (default required string) 
   ; output_directory : Directory where outputs will be written. (default required string)   ; output_directory : Directory where outputs will be written. (default required string)
 +  ; %%--%%particles : Particle image stack. (default required string)
   ; %%--%%filtrad : Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None)   ; %%--%%filtrad : Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None)
   ; %%--%%apix : Angstroms per pixel, might be downsampled already by ISAC2. (default None)   ; %%--%%apix : Angstroms per pixel, might be downsampled already by ISAC2. (default None)
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   ; %%--%%pca_radius : Radius (pixels) to use for computation of eigenimages. (default None)   ; %%--%%pca_radius : Radius (pixels) to use for computation of eigenimages. (default None)
   ; %%--%%ctf : Applies CTF correction: 'flip' for phase-flipping, 'wiener' for Wiener filter. (default None)   ; %%--%%ctf : Applies CTF correction: 'flip' for phase-flipping, 'wiener' for Wiener filter. (default None)
 +  ; %%--%%bandpass_radius : Radius for the center of the band-pass filter, Angstroms.
 +  ; %%--%%bandpass_width : Width of the band-pass filter, units absolute frequency (i.e., px^-1).
 +  ; %%--%%verbosity : Controls how much information to write to screen. (default 1)
      
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
-  ; %%--%%verbosity : Controls how much information to write to screen. (default 1) 
   ; %%--%%chains_radius : Runs sp_chains.py internally to order input class averages. (default None)   ; %%--%%chains_radius : Runs sp_chains.py internally to order input class averages. (default None)
   ; %%--%%chains_exe : Path for sp_chains.py if not the default. (default None)   ; %%--%%chains_exe : Path for sp_chains.py if not the default. (default None)
pipeline/utilities/sp_eval_isac.1590587132.txt.gz · Last modified: 2020/05/27 15:45 by shaikh