~~NOTOC~~

===== sxproj_compare =====
Compares re-projections to class averages.

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===== Usage =====

Usage in command line

  	sxproj_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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===== Typical usage =====

sxproj_compare compares re-projections of a 3D reconstruction to 2D images, typically class averages. There are three methods for this comparison:

\\ __1. Use projections angles from VIPER/RVIPER __:

  sxproj_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

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.

\\ __2. Run a simple iteration of projection-matching__:

  sxproj_compare.py Class2D/best.hdf Initial3D/main001/average_volume.hdf Compare/ProjMatch --mode=projmatch --delta 7.5

\\ __3. Use the orientation parameters from refinement__:

  sxproj_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

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 set of classified particles may be different from the set of refined particles -- for example when a substack is generated from a selection of good class averages -- and thus the particle numbers will not match.  The particle-selection file -- e.g., Substack/isac_substack_particle_id_list.txt -- will allow mapping of the particle number during classification to that during refinement.

Some particles may have been erroneously assigned to a class, as indiciated by a large angular distance between their projection angles and the average.  Such particles can be excluded from the calculation of the average angles with the --outliers option. Furthermore, a list of the remaining included particles will be written to the files OUTPUT_DIRECTORY/Byclass/goodpartsclass###.txt.
  
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===== Input =====
=== Main Parameters ===
  ; 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. (default required string)
  ; outdir : Directory where outputs will be written. (default required string)
  ; %%--%%mode : Comparison method. Choices are: viper, projmatch, and meridien. (default viper)
  ; %%--%%classangles : VIPER mode -- Parameters 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.
  ; %%--%%classselect : VIPER mode -- 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.
  ; %%--%%delta : ProjMatch mode -- Angular-sampling for reference projections.
  ; %%--%%symmetry : ProjMatch mode -- Symmetry, to limit angular projections. (default c1)
  ; %%--%%partangles : MERIDIEN mode -- Input refinement parameter file.
  ; %%--%%partselect : MERIDIEN mode -- Input substack selection file if particles removed before refinement (e.g., Substack/isac_substack_particle_id_list.txt). (default None) : %%--%%mode==meridien
  ; %%--%%outliers : MERIDIEN mode -- 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.

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=== Advanced Parameters ===
  ; %%--%%prjmethod : Interpolation method. Valid choices are trilinear (default), gridding, and nn.
  ; %%--%%display : Automatically pops up a window with the output montage.
  ; %%--%%verbose : Writes additional messages to the terminal during execution.
  ; %%--%%matchshift : ProjMatch mode -- Maximum shift to allow during translation alignment, pixels.
  ; %%--%%matchrad : ProjMatch mode -- Outer alignment radius, defaults to automatically-determined.
  ; %%--%%matchstep : ProjMatch mode -- Alignment radius step size, pixels.
  ; %%--%%refinerad : MERIDIEN mode -- Outer alignment radius, defaults to automatically-determined.
  ; %%--%%refineshift : MERIDIEN mode -- Maximum shift to allow during translation alignment, pixels.
  ; %%--%%refinestep : MERIDIEN mode -- Alignment radius step size.
  ; %%--%%align : MERIDIEN mode -- Alignment method. Valid choices are apsh (default) and scf.
  
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===== Output =====
  ; angles.txt : Text file of projection parameters of input images.
  ; proj.hdf : Stack of re-projections of input 3D reconstruction.
  ; comp-proj-reproj.hdf : Comparison of re-projections and 2D images.
 
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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====
As an input_volume, RVIPER's main003/average_volume.hdf also worked for me.  

VIPER (as opposed to RVIPER) includes all class averages, so an image selection file shouldn't be needed.

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==== Author / Maintainer ====
Tapu Shaikh

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sparx/bin/sxproj_compare.py

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==== See also ====

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==== Maturity ====
Beta:: Under evaluation and testing. Please let us know if there are any bugs.

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==== Bugs ====
There are no known bugs so far.

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