User Tools

Site Tools

pipeline:sort3d:sx3dvariability

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
pipeline:sort3d:sx3dvariability [2018/05/15 13:28]
moriya 		pipeline:sort3d:sx3dvariability [2018/08/22 10:31]
fmerino
Line 32: Line 32:
   ; %%--%%output_dir : Output directory: Specify path to the output directory of 3D Variability. By default, the program uses the current directory. However, GUI requires the path other than the current directory. (default required string)   ; %%--%%output_dir : Output directory: Specify path to the output directory of 3D Variability. By default, the program uses the current directory. However, GUI requires the path other than the current directory. (default required string)
   ; %%--%%var3D : Output 3D variability: Specify a file name to indicate if the program should write the reconstructed 3D variability map to the disk. The 3D volume will contain, for each voxel, a measure of the variability in the dataset. Careful, time consuming! (default none)   ; %%--%%var3D : Output 3D variability: Specify a file name to indicate if the program should write the reconstructed 3D variability map to the disk. The 3D volume will contain, for each voxel, a measure of the variability in the dataset. Careful, time consuming! (default none)
-  ; %%--%%ave3D : Output 3D average: Specify a file name to indicate if the program should write the reconstructed 3D average map to the disk. The 3D volume will be reconstructed from projections averaged within respective angular neighbourhood. It should be used to assess the resolvability and possible artifacts of the variability map. (default none) +  ; %%--%%ave3D : Output 3D average: Specify a file name to indicate if the program should write the reconstructed 3D average map to the disk. The 3D map will be reconstructed from projections averaged within respective angular neighbourhood. It should be used to assess the resolvability and possible artifacts of the variability map. (default none) 
-  ; %%--%%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 map. (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 correction: If set to true, 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) 
Line 48: Line 48:
   ; %%--%%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 non-zero positive float value smaller than 1.0. 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 : 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)+  ; %%--%%window : Target image size [Pixels]: Window (or clip) images using the specified size without changing pixel size. It is relative to the orignal window size. The target window size cannot be larger than the orignal image size. 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)
Line 93: Line 93:
  
 \\ \\
- 
pipeline/sort3d/sx3dvariability.txt · Last modified: 2019/04/02 10:51 by lusnig

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: GNU Free Documentation License 1.3
GNU Free Documentation License 1.3 Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki