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===== sxproj_compare =====
Compare Re-projections : Compare re-projections to class averages.

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===== Usage =====

Usage in command line

  	sxproj_compare.py stack input_volume --outdir=output_directory --angles=projection_parameters --select=img_selection_file --display --verbose


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===== Typical usage =====

sxproj_compare compares re-projections of a 3D reconstruction to 2D images, typically class averages.

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===== Input =====
=== Main Parameters ===
  ; 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. (default required string)
  ; %%--%%outdir : Output directory : Directory where outputs will be written. (default none).
  ; %%--%%angles : Projection parameters : Import 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. (default none)  
  ; %%--%%select : 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, will not include all images, and thus will be excluded from the parameters file.  This file will have a name like main003/index_keep_image.txt. (default none)  

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=== Advanced Parameters ===
  ; %%--%%display : e2display : Automatically pops up a window with the output normalized montage. (default False) 
  ; %%--%%verbose : verbose : Writes additional messages to the terminal during execution. (default False)
  
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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 : Unnormalized comparison of re-projections and 2D images.
  ; comp-proj-reproj-normalized.hdf : Normalized 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 ====
For the 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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