pipeline:utilities:sxrelion2sphire
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pipeline:utilities:sxrelion2sphire [2018/07/12 12:16] moriya |
pipeline:utilities:sxrelion2sphire [2019/04/02 10:56] lusnig [Output] |
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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 | ||
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| ===== Typical usage ===== | ===== Typical usage ===== | ||
| - | sxrelion2sphire | + | sp_relion2sphire |
| - | | + | |
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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, | + | ; input_star_file : Input RELION STAR file: Specify a STAR file generated by RELION. The file should contain parameters related to Micrographs, |
| - | ; 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 |
| ; %%--%%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 | + | ; %%--%%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 |
| - | ; %%--%%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 | + | ;%%--%%do_not_create_stack |
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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: | + | || *_micrographs.txt || Text file containing a list of micrograph names/paths (Micrograph selection file). It can be used as input of [[pipeline: |
| - | || *_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_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: |
| - | || Coordinates/ | + | || Coordinates/ |
| - | || Rebox/*.rbx || SPHIRE rebox files. One for each micrograph. These files can be used as inputs of [[pipeline: | + | || Rebox/*.rbx || SPHIRE rebox files. One for each micrograph. These files can be used as inputs of [[pipeline: |
| - | || EMAN2DB/ | + | || EMAN2DB/ |
| - | || *_stack.hdf || Stack of all particle images | + | |
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| || ptcl_source_relion || RELION' | || ptcl_source_relion || RELION' | ||
| || 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 | + | || ptcl_source_coord || Coordinates of this particle in the Micrograph in SPHIRE |
| || 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: | + | NOTE: If you run [[pipeline: |
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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 | + | These changes require user not to break the relative path whenever they move or copy the micrographs because |
| 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: | + | || sphire_stack_ctf.txt || Text file containing a list of CTF parameters. It can be used as an input of [[pipeline: |
| - | || sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline: | + | || sphire_stack_proj3d.txt || Text file containing a list of 3D projection parameters. It can be used as an input of [[pipeline: |
| - | || sphire_stack_chunk*.txt || Text file containing a list of particle IDs for the subset (typically | + | || 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: |
| - | To create these files, please use [[pipeline: | + | To create these files, please use [[pipeline: |
| \\ | \\ | ||
| ==== 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 |
| \\ | \\ | ||
| ==== See also ==== | ==== See also ==== | ||
| - | [[pipeline: | + | [[pipeline: |
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pipeline/utilities/sxrelion2sphire.txt · Last modified: 2019/04/02 10:57 by lusnig
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