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pipeline:utilities:sxrelion2sphire [2018/07/12 12:16]
moriya 		pipeline:utilities:sxrelion2sphire [2018/08/22 12:02]
fmerino
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 ===== sxrelion2sphire ===== ===== sxrelion2sphire =====
-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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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_star_file : Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset. Entries for Micrographs category are required. If it does not contain some entries associated with CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset, then the script does not produced the related output file(s). (default required string) +  ; input_star_file : Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset. Entries for Micrographs category are required. If some entries associated with CTF Estimation, Particle Extraction, 3D Alignment, or/and Random Subset are missing, then the script does not produced the related output file(s). (default required string) 
-  ; output_directory : Output directory: All the results will be written in here. This directory will be created automatically and it must not exist previously. (default required string)+  ; output_directory : Output directory: All the results will be written in here. It cannot be an existing one. (default required string)
  
   ; %%--%%relion_project_dir : RELION project directory: Path to RELION project directory associated with the RELION STAR file. By default, the program assume the current directory is the RELION project directory. (default none)   ; %%--%%relion_project_dir : RELION project directory: Path to RELION project directory associated with the RELION STAR file. By default, the program assume the current directory is the RELION project directory. (default none)
   ; %%--%%star_section : Section title in STAR file: The section title in the RELION star file where the data should be extracted. (default data_)   ; %%--%%star_section : Section title in STAR file: The section title in the RELION star file where the data should be extracted. (default data_)
   ; %%--%%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)+  ; %%--%%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 file: Save a stack file in HDF file format instead of 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)+  ; %%--%%cs_save_as_hdf : Save stack as HDF file: Save 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)
  
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 || 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:sxwindow|sxwindow]]. (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:sxrewindow|sxrewindow]]. (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 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) ||
 || *_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) || || *_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_relion || RELION's image name (_rlnImageName) which the script extracted this particle image. || || ptcl_source_relion || RELION's image name (_rlnImageName) which the script extracted this particle image. ||
 || ptcl_source_image || Micrograph path (relative path) where RELION extracted this particle image. || || ptcl_source_image || Micrograph path (relative path) where RELION extracted this particle image. ||
-|| 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_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. ||
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 ==== Developer Notes ==== ==== Developer Notes ====
 === 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 sxwindow.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.
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 || 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:sxheader|sxheader]] %%--%%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:sxheader|sxheader]] %%--%%params=xform.projection. (requires 3D Alignment Category) ||
-|| sphire_stack_chunk*.txt || Text file containing a list of particle IDs for the subset (typically #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:sxheader|sxheader]] %%--%%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:sxheader|sxheader]] to extract information from the output stack or rewindowed stack with the output SPHIRE rebox files using [[pipeline:window:sxrewindow|sxrewindow]].
pipeline/utilities/sxrelion2sphire.txt · Last modified: 2019/04/02 10:57 by lusnig

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