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pipeline:viper:sp_proj_compare

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pipeline:viper:sp_proj_compare [2019/06/18 10:15]
shaikh 		pipeline:viper:sp_proj_compare [2019/12/11 18:33]
shaikh
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   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 --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
  
 +[{{ :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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 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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 === Main Parameters === === Main Parameters ===
   ; stack : Input images stack : Set of 2D images to be compared. (default required string)   ; stack : Input images stack : Set of 2D images to be compared. (default required string)
-  ; input_volume : Input volume : Reconstruction for which re-projections will be computed. In RVIPER, this file is of the form main003/run002/rotated_volume.hdf. This volume must have the same dimensions as the input images. (default required string)+  ; input_volume : Input volume : Reconstruction for which re-projections will be computed. In RVIPER, this file is of the form main003/run002/rotated_volume.hdf : This volume must have the same dimensions as the input images. (default required string)
   ; 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==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==viper
-  ; %%--%%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+  ; %%--%%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_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
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 \\ \\
 ==== Files ==== ==== Files ====
-sparx/bin/sp_proj_compare.py+sphire/bin/sp_proj_compare.py
  
 \\ \\
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 ==== Bugs ==== ==== Bugs ====
-There are no known bugs so far.+2019/06/18 Strange behavior when the volume/image dimension is odd. In the meantime, will pad by 1.
  
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pipeline/viper/sp_proj_compare.txt ยท Last modified: 2020/08/10 23:16 by shaikh

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