pipeline:viper:sp_proj_compare

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pipeline:viper:sp_proj_compare [2019/12/11 18:26]
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+  ​sp_proj_compare.py stack input_volume outdir --mode=viper --projparams=angles_file --projselect=img_selection_file --prjmethod=interpolation_method --delta=angular_increment --matchshift=shift_range --matchrad=outer_radius --matchstep=ring_step --symmetry=optional_symmetry --refineparams=refinement_params --partselect=substack_select --refineshift=shift_range --outliers=max_angle_diff --refinerad=outer_radius --refinestep=ring_step --alignmethod=2d_alignment_method --display --verbose
  
-[{{ :​pipeline:​viper:​projcompare_1_3.png?​600 |Projections of ribosome (EMDB 10028). For each image in the montage, the lef is the projection ​is a projection, and the right is the class average. }}]+[{{ :​pipeline:​viper:​projcompare_1_3.png?​600 |Projections of ribosome (EMDB 10028). For each image in the montage, the left is a projection, and the right is the class average. }}]
  
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 \\ __1. Use projections angles from VIPER/​RVIPER __: \\ __1. Use projections angles from VIPER/​RVIPER __:
  
-  sp_proj_compare.py Class2D/​best.hdf Initial3D/​main001/​run002/​rotated_volume.hdf Compare --mode viper --classangles ​Initial3D/​main001/​run002/​rotated_reduced_params.txt --classselect ​Initial3D/​main001/​index_keep_images.txt+  sp_proj_compare.py Class2D/​best.hdf Initial3D/​main001/​run002/​rotated_volume.hdf Compare --mode viper --projparams ​Initial3D/​main001/​run002/​rotated_reduced_params.txt --projselect ​Initial3D/​main001/​index_keep_images.txt
  
 Note 1: The projection angles are not required if present in the image header. ​ When in doubt, include this file explicitly. Note 1: The projection angles are not required if present in the image header. ​ When in doubt, include this file explicitly.
  
-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/​best.hdf Initial3D/​main001/​average_volume.hdf Compare/​Meridien --mode=meridien --partangles ​Refine3D/​final_params_037.txt --partselect Substack/​isac_substack_particle_id_list.txt --outliers=15+  sp_proj_compare.py Class2D/​best.hdf Initial3D/​main001/​average_volume.hdf Compare/​Meridien --mode=meridien --refineparams ​Refine3D/​final_params_037.txt --partselect Substack/​isac_substack_particle_id_list.txt --outliers=15
  
 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 ​: VIPER - Projection parameter file : Parameter file containing projection angles. Not required if the projection parameters are stored in the header of the input images, which for ISAC2 is generally not the case. In RVIPER, this file is of the form main003/​run002/​rotated_reduced_params.txt. This file is not required if the angles have already been written to the header. (default None) : %%--%%mode==viperĀ +  ; %%--%%projparams ​: VIPER - Projection parameter file : Parameter file containing projection angles. Not required if the projection parameters are stored in the header of the input images, which for ISAC2 is generally not the case. In RVIPER, this file is of the form main003/​run002/​rotated_reduced_params.txt. This file is not required if the angles have already been written to the header. (default None) : %%--%%mode==viperĀ 
-  ; %%--%%classselect ​: VIPER - Image selection file : Input selection containing list of images to be included from the input stack. ​ For instance, 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. (default None) : %%--%%mode==viper+  ; %%--%%projselect ​: VIPER - Image selection file : Input selection containing list of images to be included from the input stack. ​ For instance, 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. (default None) : %%--%%mode==viper
   ; %%--%%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 ​: MERIDIEN - Alignment parameter file : Input refinement parameter file. (default None) : %%--%%mode==meridien+  ; %%--%%refineparams ​: MERIDIEN - Alignment parameter file : Input refinement parameter file. (default None) : %%--%%mode==meridien
   ; %%--%%partselect : MERIDIEN - Particle selection file : Input substack selection file if particles removed before refinement (e.g., Substack/​isac_substack_particle_id_list.txt). (default None) : %%--%%mode==meridien   ; %%--%%partselect : MERIDIEN - Particle selection file : Input substack selection file if particles removed before refinement (e.g., Substack/​isac_substack_particle_id_list.txt). (default None) : %%--%%mode==meridien
   ; %%--%%outliers : MERIDIEN - Outlier angle : Particles differing from average Euler angle by more than this threshold (in degrees) will be excluded from average calculation,​ by default keeps all. (default None) : %%--%%mode==meridien   ; %%--%%outliers : MERIDIEN - Outlier angle : Particles differing from average Euler angle by more than this threshold (in degrees) will be excluded from average calculation,​ by default keeps all. (default None) : %%--%%mode==meridien
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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 ​: MERIDIEN - Alignment method : Valid choices are apsh and scf. (default apsh) : %%--%%mode==meridien
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  • pipeline/viper/sp_proj_compare.txt
  • Last modified: 2020/08/10 23:16
  • by shaikh