pipeline:utilities:sxrelion2sphire

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pipeline:utilities:sxrelion2sphire [2018/08/22 12:02]
fmerino
pipeline:utilities:sxrelion2sphire [2019/04/02 10:16]
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxrelion2sphire ​=====+===== sp_relion2sphire ​=====
 RELION to SPHIRE Conversion: Create several types of parameter text files and per-micrograph virtual stacks of particle images in bdb format from parameters stored in a RELION STAR file RELION to SPHIRE Conversion: Create several types of parameter text files and per-micrograph virtual stacks of particle images in bdb format from parameters stored in a RELION STAR file
  
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 Usage in command line Usage in command line
  
-  ​sxrelion2sphire.py  input_star_file ​ output_directory ​ --relion_project_dir=DIR_PATH ​ --star_section=STAR_SECTION  ​--outputs_root=ROOT_NAME_STRING ​  ​--box_size=BOX_SIZE ​ ​--create_stack  ​--cs_save_as_hdf+  ​sp_relion2sphire.py   ​input_star_file output_directory --relion_project_dir=DIR_PATH --star_section=SECTION_STRING ​--outputs_root=ROOT_NAME_STRING --box_size=BOX_SIZE --do_not_create_stack
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxrelion2sphire ​does not support MPI. +sp_relion2sphire ​does not support MPI. 
  
-  ​sxrelion2sphire.py  '​Particles.star' ​ '​Sphire_Project' ​ --box_size=256 ​ --create_stack+  ​sp_relion2sphire.py  '​Particles.star' ​ '​Sphire_Project' ​ --box_size=256 ​ --do_not_create_stack
   ​   ​
-  ​sxrelion2sphire.py  '​Refine3D/​run1_data.star'​ '​Sphire_Project' ​ --star_section='​data_images' ​ --box_size=100 ​ --create_stack+  ​sp_relion2sphire.py  '​Refine3D/​run1_data.star'​ '​Sphire_Project' ​ --star_section='​data_images' ​ --box_size=100 ​ --do_not_create_stack
   ​   ​
-  ​sxrelion2sphire.py  '​Relion_Project/​Refine3D/​run1_data.star' ​ '​Sphire_Project' ​ --relion_project_dir='​Relion_Project'​ --outputs_root='​my_protein' ​ --create_stack+  ​sp_relion2sphire.py  '​Relion_Project/​Refine3D/​run1_data.star' ​ '​Sphire_Project' ​ --relion_project_dir='​Relion_Project'​ --outputs_root='​my_protein' ​ --do_not_create_stack
  
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   ; %%--%%outputs_root : Root name of outputs: Specify the root name of all outputs. It cannot be empty string or only white spaces. (default sphire)   ; %%--%%outputs_root : Root name of outputs: Specify the root name of all outputs. It cannot be empty string or only white spaces. (default sphire)
   ; %%--%%box_size : Box size: Box size for particle extraction. It also controls the saved coordinates file format. If the given value is > 0, store the eman1 format. coordinate file. The coordinates of eman1 format is particle box corner associated with this box size. The coordinates of SPHIRE format is particle center. By default, use SPHIRE format. (default 0)   ; %%--%%box_size : Box size: Box size for particle extraction. It also controls the saved coordinates file format. If the given value is > 0, store the eman1 format. coordinate file. The coordinates of eman1 format is particle box corner associated with this box size. The coordinates of SPHIRE format is particle center. By default, use SPHIRE format. (default 0)
-  ; %%--%%create_stack : Create virtual stacks: Create per-micrograph virtual stacks of particle images in bdb format. By default, the program does not generate the stack of particle images because it takes a long time and the file size is large. (default False) 
  
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 === Advanced Parameters === === Advanced Parameters ===
-  ; %%--%%cs_save_as_hdf ​Save stack as HDF fileSave a stack file in HDF file format instead in bdb format. ​In this case, the stack file will contain all particle ​images in the input RELION STAR file. Effective only with %%--%%create_stack. (default False)+  ;%%--%%do_not_create_stack ​Skip virtual ​stack creationCreate per-micrograph virtual stacks without the actual particle meta information ​in BDB format. ​By defaultthe program does generate ​the stack of particle ​meta information. (default False))
  
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 || **File Name** || **Discription** || || **File Name** || **Discription** ||
-|| *_micrographs.txt || Text file containing a list of micrograph names/paths (Micrograph selection file). It can be used as input of [[pipeline:​cter:​sxcter|sxcter]], [[pipeline:​window:​sxwindow|sxwindow]], [[pipeline:​movie:​sxunblur|sxunblur]], [[pipeline:​movie:​sxsummovie|sxsummovie]], and [[pipeline:​utilities:​sxpipe_organize_micrographs|sxpipe ​organize_micrographs]]. (requires Micrographs Category) || +|| *_micrographs.txt || Text file containing a list of micrograph names/paths (Micrograph selection file). It can be used as input of [[pipeline:​cter:​sp_cter|sp_cter]], [[pipeline:​window:​sp_window|sp_window]], [[pipeline:​movie:​sp_unblur|sp_unblur]], [[pipeline:​movie:​sp_summovie|sp_summovie]], and [[pipeline:​utilities:​sp_pipe_organize_micrographs|sp_pipe ​organize_micrographs]]. (requires Micrographs Category) || 
-|| *_cter_partres.txt || Text file containing a list of CTF parameters in CTER format (CTER partres file). It can be used as an input of [[pipeline:​cter:​sxgui_cter|sxgui_cter]] and [[pipeline:​window:​sxwindow|sxwindow]]. (requires CTF Estimation Category) || +|| *_cter_partres.txt || Text file containing a list of CTF parameters in CTER format (CTER partres file). It can be used as an input of [[pipeline:​cter:​sp_gui_cter|sp_gui_cter]] and [[pipeline:​window:​sp_window|sp_window]]. (requires CTF Estimation Category) || 
-|| Coordinates/​*.box || Coordinates files. One for each micrograph. These files can be used as inputs of [[pipeline:​window:​sxwindow|sxwindow]]. (requires Particle Extraction Category) || +|| Coordinates/​*.box || Coordinates files. One for each micrograph. These files can be used as inputs of [[pipeline:​window:​sp_window|sp_window]]. (requires Particle Extraction Category) || 
-|| Rebox/*.rbx || SPHIRE rebox files. One for each micrograph. These files can be used as inputs of [[pipeline:​window:​sxrewindow|sxrewindow]]. (requires Particle Extraction Category) || +|| Rebox/*.rbx || SPHIRE rebox files. One for each micrograph. These files can be used as inputs of [[pipeline:​window:​sp_rewindow|sp_rewindow]]. (requires Particle Extraction Category) || 
-|| EMAN2DB/​*_stack.bdb || Per-micrograph virtual stacks of particle ​images ​in bdb format (only when %%--%%create_stack option without %%--%%cs_save_as_hdf is used) containing the header entries associated with the extracted information. (requires Particle Extraction Category) || +|| EMAN2DB/​*_stack.bdb || Per-micrograph virtual stacks of particle ​meta information ​in bdb format (only when %%--%%do_not_create_stack ​is not used) containing the header entries associated with the extracted information. (requires Particle Extraction Category) ||
-|| *_stack.hdf || Stack of all particle images in HDF format (only when %%--%%create_stack option with %%--%%cs_save_as_hdf ​is used) containing the header entries associated with the extracted information. (requires Particle Extraction Category) ||+
  
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 || ptcl_source_coord || Coordinates of this particle in the Micrograph in SPHIRE format. || || ptcl_source_coord || Coordinates of this particle in the Micrograph in SPHIRE format. ||
 || ptcl_source_coord_id || Coordinates ID in the original coordinate file RELION used. || || ptcl_source_coord_id || Coordinates ID in the original coordinate file RELION used. ||
 +|| data_path || Relative path to the original particle image location. ||
 || data_n || Serial particle image ID.  Here, it is same as ptcl_source_coord_id. || || data_n || Serial particle image ID.  Here, it is same as ptcl_source_coord_id. ||
 || resample_ratio || Resampling ratio of dimensions or pixel size of extracted particle images relative to micrograph. Here, it is always set to 1.0. || || resample_ratio || Resampling ratio of dimensions or pixel size of extracted particle images relative to micrograph. Here, it is always set to 1.0. ||
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 || chunk_id || Chunk ID (or Subset ID) where this particle belongs. || || chunk_id || Chunk ID (or Subset ID) where this particle belongs. ||
  
-NOTE: If you run [[pipeline:​window:​sxwindow|sxwindow]] using the coordinates files generated by this script, ptcl_source_coord_id will be reassigned. It can be different from the RELION'​s local particle ID (the number before '​@'​ in ptcl_source_relion).+NOTE: If you run [[pipeline:​window:​sp_window|sp_window]] using the coordinates files generated by this script, ptcl_source_coord_id will be reassigned. It can be different from the RELION'​s local particle ID (the number before '​@'​ in ptcl_source_relion).
  
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 ==== Developer Notes ==== ==== Developer Notes ====
 +=== 2018/09/17 Markus Stabrin ===
 +  - Remove image stack creation.
 +  - Created stacks only contain meta data.
 +  - Write bdb meta data stacks by default (Change %%--%%create_stack to %%--%%do_not_create_stack).
 +  - Remove %%--%%cs_save_as_hdf option.
 +
 === 2018/07/11 Toshio Moriya === === 2018/07/11 Toshio Moriya ===
   - Change default stack format from HDF to bdb (%%--%%cs_save_as_hdf). ​   - Change default stack format from HDF to bdb (%%--%%cs_save_as_hdf). ​
-    * By default, the script creates a local particle image stack for each micrograph like sxwindow.py.+    * By default, the script creates a local particle image stack for each micrograph like sp_window.py.
     * Likewise, because of synchronisation problem of subprocess execution, user must run particle stack command to create a virtual stack of all particles.     * Likewise, because of synchronisation problem of subprocess execution, user must run particle stack command to create a virtual stack of all particles.
   - Accept arbitrary output file name (%%--%%outputs_root).   - Accept arbitrary output file name (%%--%%outputs_root).
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     * The program appends the path of relion project directory to micrograph path extracted from the star file.     * The program appends the path of relion project directory to micrograph path extracted from the star file.
  
-These changes require user not to break the relative path whenever they move or copy the micrographs because ​sxrelion2sparx.py use full name including the path stored in the input RELION STAR file.+These changes require user not to break the relative path whenever they move or copy the micrographs because ​sp_relion2sparx.py use full name including the path stored in the input RELION STAR file.
  
 The program does not generate the following output files anymore. ​ The program does not generate the following output files anymore. ​
  
 || **File Name** || **Discription** || || **File Name** || **Discription** ||
-|| sphire_stack_ctf.txt || Text file containing a list of CTF parameters. It can be used as an input of [[pipeline:​utilities:​sxheader|sxheader]] %%--%%params=ctf. (requires CTF Estimation Category) || +|| sphire_stack_ctf.txt || Text file containing a list of CTF parameters. It can be used as an input of [[pipeline:​utilities:​sp_header|sp_header]] %%--%%params=ctf. (requires CTF Estimation Category) || 
-|| sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline:​utilities:​sxheader|sxheader]] %%--%%params=xform.projection. (requires 3D Alignment Category) || +|| sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline:​utilities:​sp_header|sp_header]] %%--%%params=xform.projection. (requires 3D Alignment Category) || 
-|| sphire_stack_chunk*.txt || Text file containing a list of particle IDs for the subset (#0 and #1). It can be used as an input of [[pipeline:​utilities:​sxheader|sxheader]] %%--%%params=chunk_id. (requires Random Subset Category) ||+|| sphire_stack_chunk*.txt || Text file containing a list of particle IDs for the subset (#0 and #1). It can be used as an input of [[pipeline:​utilities:​sp_header|sp_header]] %%--%%params=chunk_id. (requires Random Subset Category) ||
  
-To create these files, please use [[pipeline:​utilities:​sxheader|sxheader]] to extract information from the output stack or rewindowed stack with the output SPHIRE rebox files using [[pipeline:​window:​sxrewindow|sxrewindow]].+To create these files, please use [[pipeline:​utilities:​sp_header|sp_header]] to extract information from the output stack or rewindowed stack with the output SPHIRE rebox files using [[pipeline:​window:​sp_rewindow|sp_rewindow]].
  
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 ==== Author / Maintainer ==== ==== Author / Maintainer ====
 Toshio Moriya Toshio Moriya
 +Markus Stabrin
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxrelion2sphire.py+sparx/bin/sp_relion2sphire.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:​cter:​sxcter|sxcter]], [[pipeline:​cter:​sxgui_cter|sxgui_cter]], [[pipeline:​window:​sxwindow|sxwindow]], [[pipeline:​window:​sxrewindow|sxrewindow]], [[pipeline:​utilities:​sxheader|sxheader]], [[pipeline:​utilities:​sxpipe_organize_micrographs|sxpipe ​organize_micrographs]],​ [[pipeline:​movie:​sxunblur|sxunblur]], and [[pipeline:​movie:​sxsummovie|sxsummovie]].+[[pipeline:​cter:​sp_cter|sp_cter]], [[pipeline:​cter:​sp_gui_cter|sp_gui_cter]], [[pipeline:​window:​sp_window|sp_window]], [[pipeline:​window:​sp_rewindow|sp_rewindow]], [[pipeline:​utilities:​sp_header|sp_header]], [[pipeline:​utilities:​sp_pipe_organize_micrographs|sp_pipe ​organize_micrographs]],​ [[pipeline:​movie:​sp_unblur|sp_unblur]], and [[pipeline:​movie:​sp_summovie|sp_summovie]].
  
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 +
  • pipeline/utilities/sxrelion2sphire.txt
  • Last modified: 2019/04/02 10:57
  • by lusnig