This shows you the differences between two versions of the page.
Next revision | Previous revision Last revision Both sides next revision | ||
pipeline:utilities:sp_eval_isac [2020/05/27 15:45] shaikh created |
pipeline:utilities:sp_eval_isac [2020/07/24 23:21] shaikh |
||
---|---|---|---|
Line 7: | Line 7: | ||
===== Usage ===== | ===== Usage ===== | ||
- | Usage in command line: | + | Usage in command line (beta version): |
- | sp_eval_isac.py input_class_avgs | + | sp_eval_isac.py input_class_avgs output_directory |
| | ||
| | ||
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
+ | [{{ : | ||
The purpose of sp_separate_class.py is to: | The purpose of sp_separate_class.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 | + | 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 | + | sp_eval_isac.py input_class_avgs output_directory |
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. | ||
Line 34: | Line 32: | ||
\\ __3. Downsample output image stack__: | \\ __3. Downsample output image stack__: | ||
- | sp_eval_isac.py input_class_avgs | + | sp_eval_isac.py input_class_avgs output_directory |
| | ||
\\ __4. Apply ISAC alignments to particles__: | \\ __4. Apply ISAC alignments to particles__: | ||
- | sp_eval_isac.py input_class_avgs | + | sp_eval_isac.py input_class_avgs output_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. | ||
Line 44: | Line 42: | ||
\\ __5. Compute eigenimages (basis images) for each class__: | \\ __5. Compute eigenimages (basis images) for each class__: | ||
- | sp_eval_isac.py input_class_avgs | + | sp_eval_isac.py input_class_avgs output_directory |
| | ||
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. | ||
Line 50: | Line 48: | ||
\\ __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 | + | sp_eval_isac.py input_class_avgs output_directory |
| | ||
If you ran sp_center_2d3d.py, | If you ran sp_center_2d3d.py, | ||
+ | |||
+ | \\ __7. Apply a Gaussian band-pass filter to an image stack (e.g., class averages)__: | ||
+ | sp_eval_isac.py input_class_avgs output_directory --particles=input_image_stack --align_isac_dir=isac_directory --write_centered --applyparams=centering_mode | ||
+ | |||
+ | 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: | ||
\\ | \\ | ||
Line 58: | Line 63: | ||
=== Main Parameters === | === Main Parameters === | ||
; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ : | ; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ : | ||
- | ; 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) | ||
Line 67: | Line 72: | ||
; %%--%%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: ' | ; %%--%%ctf : Applies CTF correction: ' | ||
+ | ; %%--%%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) |