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pipeline:sort3d:sx3dvariability [2018/05/14 16:19]
127.0.0.1 external edit 		pipeline:sort3d:sx3dvariability [2018/06/20 13:12]
127.0.0.1 external edit
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 Usage in command line Usage in command line
  
-  sx3dvariability.py  prj_stack  --output_dir=DIRECTORY  --var3D=FILE_NAME  --ave3D=FILE_NAME  --img_per_grp=NUM_OF_IMAGES --sym=SYMMETRY  --CTF  --fl=LPF_CUTOFF_FREQ  --aa=LPF_FALLOFF_WIDTH  --symmetrize  --ave2D=FILE_NAME  --var2D=FILE_NAME  --VAR  --no_norm  --npad=PADDING_FACTOR  --decimate=FACTOR  --window=WINDOW_SIZE  --nvec=NUM_OF_EIGENVECTORS  --VERBOSE+  sx3dvariability.py  prj_stack  --output_dir=DIRECTORY  --var3D=FILE_NAME  --ave3D=FILE_NAME  --img_per_grp=NUM_OF_IMAGES --sym=SYMMETRY  --CTF  --fl=LPF_CUTOFF_FREQ  --aa=LPF_FALLOFF_WIDTH  --symmetrize  --var2D=FILE_NAME  --ave2D=FILE_NAME  --VAR  --no_norm  --npad=PADDING_FACTOR  --decimate=FACTOR  --window=WINDOW_SIZE  --nvec=NUM_OF_EIGENVECTORS  --VERBOSE
  
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   ; %%--%%img_per_grp : Number of projections: Specify the number of images from the angular neighbourhood that will be used to estimate 2D variance for each projection data. The larger the number the less noisy the estimate, but the lower the resolution. Usage of large number also results in rotational artifacts in variances that will be visible in 3D variability volume. (default 10)   ; %%--%%img_per_grp : Number of projections: Specify the number of images from the angular neighbourhood that will be used to estimate 2D variance for each projection data. The larger the number the less noisy the estimate, but the lower the resolution. Usage of large number also results in rotational artifacts in variances that will be visible in 3D variability volume. (default 10)
   ; %%--%%sym : Point-group symmetry: If the structure has symmetry higher than c1, the command requires symmetrization of the dataset, using %%--%%symmetrize option, before computing 3D variability. (default c1)   ; %%--%%sym : Point-group symmetry: If the structure has symmetry higher than c1, the command requires symmetrization of the dataset, using %%--%%symmetrize option, before computing 3D variability. (default c1)
-  ; %%--%%CTF : Use CTF: If set to true, the a CTF correction will be applied using the parameters found in the image headers. (default False value reversed in GUI)  +  ; %%--%%CTF : Use CTF correction: If set to true, CTF correction will be applied using the parameters found in the image headers. (default False value reversed in GUI)  
-  ; %%--%%fl : Low-pass filter frequency [1/Pixel]: Stop-band frequency of the low-pass filter to be applied to the images prior to variability calculation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). By default, no filtering. (default 0.0) +  ; %%--%%fl : Low-pass filter frequency [1/Pixel]: Stop-band frequency of the low-pass filter to be applied to the images prior to variability calculation but after decimation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). By default, no filtering. (default 0.0) 
-  ; %%--%%aa : Low-pass filter fall-off [1/Pixel]: Fall-off width of the low-pass filter to be applied to the images prior to variability calculation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). 0.01 works in most of cases. Effective only with %%--%%fl %%>%% 0.0 and %%--%%aa %%>%% 0.0 has to be specified. (default 0.0) +  ; %%--%%aa : Low-pass filter fall-off [1/Pixel]: Fall-off width of the low-pass filter to be applied to the images prior to variability calculation but after decimation. Specify it in absolute frequency (%%>%% 0.0 and %%<=%% 0.5). 0.01 works in most of cases. Effective only with %%--%%fl %%>%% 0.0 and %%--%%aa %%>%% 0.0 has to be specified. (default 0.0) 
   ; %%--%%symmetrize : Symmetrise input stack: Prepare input stack for handling symmetry. Please skip this preparation step if the structure is asymmetrical (i.e. c1), since it is required only when the structure has internal symmetry. Notice this step can be run with only one CPU and there is no MPI version for it. (default False)   ; %%--%%symmetrize : Symmetrise input stack: Prepare input stack for handling symmetry. Please skip this preparation step if the structure is asymmetrical (i.e. c1), since it is required only when the structure has internal symmetry. Notice this step can be run with only one CPU and there is no MPI version for it. (default False)
  
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   ; %%--%%no_norm : Apply normalization: Indicate if normalization should be applied or not. By default, apply normalization. (default False question reversed in GUI)   ; %%--%%no_norm : Apply normalization: Indicate if normalization should be applied or not. By default, apply normalization. (default False question reversed in GUI)
   ; %%--%%npad : Image padding factor: The number of time to pad the original images. The images will be padded to achieve the original size times this option. (default 2)   ; %%--%%npad : Image padding factor: The number of time to pad the original images. The images will be padded to achieve the original size times this option. (default 2)
-  ; %%--%%decimate : Image decimate factor: Reduce images by this factor and change the pixel size. Specify a value large than 1.0 to expand images, and less than 1.0 to shrink them. By default, it does not change size of images. (default 1.0) +  ; %%--%%decimate : Image decimate factor: Reduce images by this factor and change the pixel size. Specify a non-zero positive float value smaller than 1.0. By default, it does not change size of images. (default 1.0) 
-  ; %%--%%window : User smaller window size [Pixels]: Window (or clip) images using the specified size without changing pixel size. By default, use the original particle image size. (default 0)+  ; %%--%%window : Target image size [Pixels]: Window (or clip) images using the specified size without changing pixel size. The target window size cannot be larger than the size of decimated images. By default, use the original particle image size. (default 0)
   ; %%--%%nvec : Number of eigenvectors: By default, no PCA will be calculated. (default 0)   ; %%--%%nvec : Number of eigenvectors: By default, no PCA will be calculated. (default 0)
   ; %%--%%VERBOSE : Verbose: Print long output which is useful for debugging. (default False)   ; %%--%%VERBOSE : Verbose: Print long output which is useful for debugging. (default False)
pipeline/sort3d/sx3dvariability.txt · Last modified: 2019/04/02 10:51 by lusnig

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