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Both sides previous revision Previous revision Next revision | Previous revision | ||
pipeline:viper:sp_proj_compare [2019/12/11 18:31] shaikh |
pipeline:viper:sp_proj_compare [2020/08/10 23:16] shaikh |
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Usage in command line | Usage in command line | ||
- | sp_proj_compare.py stack input_volume outdir --mode=viper --classangles=angles_file --classselect=img_selection_file --prjmethod=interpolation_method --delta=angular_increment --matchshift=shift_range --matchrad=outer_radius --matchstep=ring_step --symmetry=optional_symmetry --partangles=refinement_params --partselect=substack_select --refineshift=shift_range --outliers=max_angle_diff --refinerad=outer_radius --refinestep=ring_step --align=2d_alignment_method --display --verbose | + | |
- | [{{ : | + | [{{ : |
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\\ __1. Use projections angles from VIPER/ | \\ __1. Use projections angles from VIPER/ | ||
- | sp_proj_compare.py Class2D/ | + | sp_proj_compare.py Class2D/ |
Note 1: The projection angles are not required if present in the image header. | Note 1: The projection angles are not required if present in the image header. | ||
- | Note 2: RVIPER, if it finds a stable solution, may exclude some images, and thus their projection angles will be excluded from the parameters file. The file containing the list of included images will have a name like main003/index_keep_image.txt. | + | Note 2: RVIPER, if it finds a stable solution, may exclude some images, and thus their projection angles will be excluded from the parameters file. The file containing the list of included images will have a name like main003/index_keep_images.txt. |
\\ __2. Run a simple iteration of projection-matching__: | \\ __2. Run a simple iteration of projection-matching__: | ||
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\\ __3. Use the orientation parameters from refinement__: | \\ __3. Use the orientation parameters from refinement__: | ||
- | sp_proj_compare.py Class2D/ | + | sp_proj_compare.py Class2D/ |
The projection angle for a class will be calculated by taking the vector sum of the projection angles of the particles belonging to that class. | The projection angle for a class will be calculated by taking the vector sum of the projection angles of the particles belonging to that class. | ||
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; outdir : Output directory : Directory where outputs will be written. (default required string) | ; outdir : Output directory : Directory where outputs will be written. (default required string) | ||
; %%--%%mode : Comparison method : Choices are: viper, projmatch, and meridien. (default viper) | ; %%--%%mode : Comparison method : Choices are: viper, projmatch, and meridien. (default viper) | ||
- | ; %%--%%classangles | + | ; %%--%%projparams |
- | ; %%--%%classselect | + | ; %%--%%projselect |
; %%--%%delta : ProjMatch - Sampling angle : Angular-sampling for reference projections. (default 7.5) : %%--%%mode==projmatch | ; %%--%%delta : ProjMatch - Sampling angle : Angular-sampling for reference projections. (default 7.5) : %%--%%mode==projmatch | ||
; %%--%%symmetry : ProjMatch - Symmetry : To limit angular projections. (default c1) : %%--%%mode==projmatch | ; %%--%%symmetry : ProjMatch - Symmetry : To limit angular projections. (default c1) : %%--%%mode==projmatch | ||
- | ; %%--%%partangles | + | ; %%--%%refineparams |
; %%--%%partselect : MERIDIEN - Particle selection file : Input substack selection file if particles removed before refinement (e.g., Substack/ | ; %%--%%partselect : MERIDIEN - Particle selection file : Input substack selection file if particles removed before refinement (e.g., Substack/ | ||
; %%--%%outliers : MERIDIEN - Outlier angle : Particles differing from average Euler angle by more than this threshold (in degrees) will be excluded from average calculation, | ; %%--%%outliers : MERIDIEN - Outlier angle : Particles differing from average Euler angle by more than this threshold (in degrees) will be excluded from average calculation, | ||
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; %%--%%display : e2display : Automatically pops up a window with the output montage. (default False) | ; %%--%%display : e2display : Automatically pops up a window with the output montage. (default False) | ||
; %%--%%verbose : verbose : Writes additional messages to the terminal during execution. (default False) | ; %%--%%verbose : verbose : Writes additional messages to the terminal during execution. (default False) | ||
+ | ; %%--%%fullstack : VIPER - Input particle stack to which VIPER angles will be | ||
+ | added. (default None) : %%--%%mode==viper | ||
; %%--%%matchshift : ProjMatch - Maximum shift : Maximum shift to allow during translation alignment, pixels. (default 2) : %%--%%mode==projmatch | ; %%--%%matchshift : ProjMatch - Maximum shift : Maximum shift to allow during translation alignment, pixels. (default 2) : %%--%%mode==projmatch | ||
; %%--%%matchrad : ProjMatch - Outer radius : Outer alignment radius, defaults to automatically-determined. (default None) : %%--%%mode==projmatch | ; %%--%%matchrad : ProjMatch - Outer radius : Outer alignment radius, defaults to automatically-determined. (default None) : %%--%%mode==projmatch | ||
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; %%--%%refineshift : MERIDIEN - Maximum shift : Maximum shift to allow during translation alignment, pixels. (default 2) : %%--%%mode==meridien | ; %%--%%refineshift : MERIDIEN - Maximum shift : Maximum shift to allow during translation alignment, pixels. (default 2) : %%--%%mode==meridien | ||
; %%--%%refinestep : MERIDIEN - Radius step size : Alignment radius step size. (default 1) : %%--%%mode==meridien | ; %%--%%refinestep : MERIDIEN - Radius step size : Alignment radius step size. (default 1) : %%--%%mode==meridien | ||
- | ; %%--%%align : MERIDIEN - Alignment method : Valid choices are apsh and scf. (default apsh) : %%--%%mode==meridien | + | ; %%--%%alignmethod |
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\\ | \\ |