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pipeline:utilities:sxpipe_restacking [2018/08/07 22:04] moriya |
pipeline:utilities:sxpipe_restacking [2019/04/02 10:59] lusnig [Output] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxrewindow | + | ===== sp_pipe restacking |
- | Particle Reextraction: Rewindow particles from micrographs using the information | + | Restacking: Generate all necessary |
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Usage in command line | Usage in command line | ||
- | | + | |
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxrewindow exists in both MPI and non-MPI versions (Running MPI version | + | sp_pipe restacking |
- | There are several modes to run the program: | + | Do restacking |
- | \\ __1. All Micrographs Mode - Process all micrographs in a directory: | + | sp_pipe.py restacking |
- | \\ Specify path pattern of input micrographs and rebox files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between a associated pair of input micrograph and rebox file. BDB files can not be selected as input micrographs. Finally, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed. | + | |
- | mpirun | + | |
- | \\ You can also ignore per-particle | + | Generate the reboxing information of all particle |
- | mpirun | + | |
- | + | ||
- | \\ __2. Selected Micrographs Mode - Process all micrographs in a selection list file:__ | + | sp_pipe.py restacking |
- | \\ In addition to input micrographs path pattern, rebox files path pattern, and output directry arguments, specify a name of micrograph selection list text file using --selection_list option. In this mode, only micrographs in the selection list which matches the file name part of the pattern (ignoring the directory paths) will be processed. If a micrograph name in the selection list does not exists in the directory specified by the micrograph path pattern, processing of the micrograph will be skipped. | + | |
- | mpirun | + | |
- | \\ __3. Single Micrograph Mode - Process a single micrograph: | + | Generate |
- | \\ In addition to input micrographs path pattern, rebox files path pattern, CTF paramters source, and output directry arguments, specify a single micrograph name using --selection_list option. In this mode, only the specified single micrograph will be processed. If this micrograph name does not matches the file name part of the pattern (ignoring the directory paths), the process will exit without processing it. If this micrograph name matches the file name part of the pattern but does not exists | + | |
- | | + | |
- | \\ For negative staining data, use --skip_invert. | + | Do both restacking and reboxing to generate both the virtual stack and reboxing information of only particle images associated to the micrographs in the selection list. |
- | mpirun | + | |
- | \\ **NOTE:** Please remember to adjust box_size also when setting mic_resample_ratio < 0.1. | + | sp_pipe.py restacking ' |
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_pattern | + | ; input_bdb_stack_path |
- | ; input_rebox_pattern : Input rebox path pattern: Specify path pattern of input rebox files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). The substring at the variable part must be same between the associated input micrograph. (default required string) | + | ; output_directory : Output directory: The results will be written here. It cannot |
- | ; output_directory : Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string) | + | |
- | ; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph | + | ; %%--%%selection_list : Micrograph/ |
- | ; %%--%%box_size | + | ; %%--%%shift3d_x |
- | ; %%--%%skip_invert | + | ; %%--%%shift3d_y : 3D y-shift [Pixels]: 3D y-shift value. (default 0) |
+ | ; %%--%%shift3d_z : 3D z-shift [Pixels]: 3D z-shift value. (default | ||
+ | ; %%--%%save_vstack : Save virtual stack: Use this option to save the virtual stack. By default, the virtual stack will not be generated. (default | ||
+ | ; %%--%%sv_vstack_basename | ||
+ | ; %%--%%reboxing : Generate reboxing information: | ||
+ | ; %%--%%rb_box_size : Particle box size [Pixels]: For %%--%%reboxing option, specify | ||
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=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%mic_resample_ratio : Image size reduction factor (<1): Use a value between 0.0 and 1.0 (excluding 0.0). The new pixel size will be automatically recalculated and stored in CTF paramers when mic_resample_ratio < 1.0 is used. (default 1.0) | ||
- | ; %%--%%swap_ctf_params : Swap CTF parameters: Swaps CTF parameters by setting the CTF parameters in the specified CTER partres file while ignoring the CTF parameters in the input rebox parameters file. Typically, specify the file produced by sxcter and normally called partres.txt. Alternatively, | ||
- | ; %%--%%check_consistency : Check consistency of dataset: Create a text file containing the list of Micrograph ID entries might have inconsitency among the provided dataset. (i.e. mic_consistency_check_info_TIMESTAMP.txt). (default False) | ||
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===== Output ===== | ===== Output ===== | ||
- | Inside | + | === List of output Files === |
+ | || **File Name** || **Discription** || | ||
+ | || micrographs_in_input_stack.txt || Micrograph selection text file containing the list of micrograph basenames extracted from the input stack. This file can be used as micrograph selection text file of [[pipeline: | ||
+ | || micrographs_in_output_dataset.txt || Micrograph selection text file containing the list of micrograph in the output | ||
+ | || input_stack_particle_id_for_output_dataset.txt || Particle selection text file containing | ||
+ | || ctf_params_for_output_dataset.txt || CTF parameters text file containing CTF parameters of all particle images in the output dateset. This projection parameters can be used as inputs of [[pipeline: | ||
+ | || original_proj_params_for_output_dataset.txt || Projection parameters text file containing **original** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: | ||
+ | || centered_proj_params_for_output_dataset.txt || Projection parameters text file containing **centered** projection parameters of all particle images in the output dateset. This projection parameters can be imported to the reboxed stack using [[pipeline: | ||
+ | || original/ | ||
+ | || centered/${MICROGRAPH_ROOTNAME}_centered.box || The list of centered (or transformed) coordinates. These files can be used as inputs of [[pipeline: | ||
+ | || EMAN2DB/${VSTACK_BASENAME}.dbd || The output virtual stack. This stack can be directly used as input stack of [[pipeline:meridien: | ||
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===== Description ===== | ===== Description ===== | ||
This command executes the following processes: | This command executes the following processes: | ||
- | - Takes micrographs | + | - Extract the following information stored in the header of each particle image. |
- | - Normalization is done by subtracting | + | * source micrograph path (ptcl_source_image). |
- | - Micrographs are applied a Gaussian high-pass filter equivalent | + | * CTF parameters if exist (ctf). |
+ | * projection parameters if exist (xform.projection). | ||
+ | * box center coordinates within the micrograph (ptcl_source_coord). | ||
+ | - Save the list of extracted micrograph names to an output file. | ||
+ | - If provided, apply the selection list to extracted | ||
+ | - Save the list of selected micrograph names to an output file. | ||
+ | - Extract only particle | ||
+ | - Save the list of selected particle image IDs to an output file. | ||
+ | - Save the CTF parameters | ||
+ | - Save the original projection parameters of selected particle images to output file. | ||
+ | - Transform the projection parameters of selected particle images | ||
+ | - Convert | ||
+ | - Transform the coordinates based on the projection parameters and user-provided 3D shift, and then save the results to output files. | ||
+ | - Create the output virtual stack if necessary | ||
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==== Developer Notes ==== | ==== Developer Notes ==== | ||
+ | === 2018/03/05 Toshio Moriya === | ||
+ | Wish list: | ||
+ | * Setting %%--%%box_size to zero (default value) should save the coordinates file in SPHIRE format | ||
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==== Author / Maintainer ==== | ==== Author / Maintainer ==== | ||
- | Toshio Moriya | + | Christos Gatsogiannis and Toshio Moriya |
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==== Keywords ==== | ==== Keywords ==== | ||
- | Category 1:: FUNDAMENTALS, | + | Category 1:: APPLICATIONS |
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==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxrewindow.py | + | sparx/bin/sp_pipe.py |
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==== See also ==== | ==== See also ==== | ||
- | [[pipeline:utilities:sxpipe_restacking]], [[pipeline: | + | [[pipeline:window:sxwindow|sp_window]], [[pipeline: |
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