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pipeline:window:sxwindow [2018/06/20 13:12] 127.0.0.1 external edit |
pipeline:window:sxwindow [2019/04/02 10:26] lusnig [See also] |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxwindow | + | ===== sp_window |
Particle Extraction: Window particles from micrographs using the particle coordinates. | Particle Extraction: Window particles from micrographs using the particle coordinates. | ||
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Usage in command line | Usage in command line | ||
- | | + | |
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxwindow | + | sp_window |
There are several modes to run the program: | There are several modes to run the program: | ||
\\ __1. All Micrographs Mode - Process all micrographs in a directory: | \\ __1. All Micrographs Mode - Process all micrographs in a directory: | ||
- | \\ Specify path pattern of input micrographs and coordinates 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: | + | \\ Specify path pattern of input micrographs and coordinates files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: |
- | mpirun | + | mpirun |
\\ __2. Selected Micrographs Mode - Process all micrographs in a selection list file:__ | \\ __2. Selected Micrographs Mode - Process all micrographs in a selection list file:__ | ||
\\ In addition input micrographs path pattern, coordinates files path pattern, CTF paramters source, and output directry, 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. | \\ In addition input micrographs path pattern, coordinates files path pattern, CTF paramters source, and output directry, 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 | + | mpirun |
\\ __3. Single Micrograph Mode - Process a single micrograph: | \\ __3. Single Micrograph Mode - Process a single micrograph: | ||
\\ In addition input micrographs path pattern, coordinates files path pattern, CTF paramters source, and output directry, 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 in the directory which specified by the micrograph path pattern, again the process will exit without processing it. | \\ In addition input micrographs path pattern, coordinates files path pattern, CTF paramters source, and output directry, 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 in the directory which specified by the micrograph path pattern, again the process will exit without processing it. | ||
- | | + | |
\\ __4. For Negative Staining Dataset:__ | \\ __4. For Negative Staining Dataset:__ | ||
\\ Set the pixel size [A/Pixels] as the source of CTF paramters and use --skip_invert. | \\ Set the pixel size [A/Pixels] as the source of CTF paramters and use --skip_invert. | ||
- | mpirun | + | mpirun |
\\ **NOTE:** Please remember to adjust box_size also when setting resample_ratio < 0.1. | \\ **NOTE:** Please remember to adjust box_size also when setting resample_ratio < 0.1. | ||
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs 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: | + | ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: |
- | ; input_coordinates_pattern : Input coordinates path pattern: Specify path pattern of input coordinates 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: | + | ; input_coordinates_pattern : Input coordinates path pattern: Specify path pattern of input coordinates files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: |
- | ; input_ctf_params_source : CTF parameters source: Specify the file produced by sxcter | + | ; input_ctf_params_source : CTF parameters source: Specify the file produced by sp_cter |
- | ; 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) | + | ; output_directory : Output directory: The results will be written here. It cannot |
; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ||
- | ; %%--%%coordinates_format : Coordinate file format: Allowed values are ' | + | ; %%--%%coordinates_format : Coordinate file format: Allowed values are ' |
; %%--%%box_size : Particle box size [Pixels]: The x and y dimensions of square area to be windowed. The box size after resampling is assumed when resample_ratio < 1.0. (default 256) | ; %%--%%box_size : Particle box size [Pixels]: The x and y dimensions of square area to be windowed. The box size after resampling is assumed when resample_ratio < 1.0. (default 256) | ||
; %%--%%skip_invert : Invert image contrast: Indicate if image contrast should be inverted or not. Do not invert for negative staining data. By default, the image contrast will be inverted for cryo data. (default False question reversed in GUI) | ; %%--%%skip_invert : Invert image contrast: Indicate if image contrast should be inverted or not. Do not invert for negative staining data. By default, the image contrast will be inverted for cryo data. (default False question reversed in GUI) | ||
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\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%limit_ctf : Use CTF limit filter: Frequencies where CTF oscillations | + | ; %%--%%limit_ctf : Use CTF limit filter: Frequencies where CTF oscillations |
- | ; %%--%%astigmatism_error : Astigmatism error limit [Degrees]: Set astigmatism to zero for all micrographs where the angular error computed by sxcter | + | ; %%--%%astigmatism_error : Astigmatism error limit [Degrees]: Set astigmatism to zero for all micrographs where the angular error computed by sp_cter |
; %%--%%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 resample_ratio < 1.0 is used. (default 1.0) | ; %%--%%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 resample_ratio < 1.0 is used. (default 1.0) | ||
; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ; %%--%%check_consistency : Check consistency of inputs: Create a text file containing the list of inconsistent Micrograph ID entries (i.e. inconsist_mic_list_file.txt). (default False) | ||
+ | ; %%--%%filament_width : Filament width : Filament width for the creation of the rectangular mask. When -1 is selected it uses one third of the box size. (default -1) | ||
\\ | \\ | ||
===== Output ===== | ===== Output ===== | ||
- | Inside the output directory, the program will write a local BDB stack image for each micrograph. The files are named micrograph name with " | + | Inside the output directory, the program will write a local bdb stack image for each micrograph. The files are named micrograph name with " |
\\ | \\ | ||
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==== Developer Notes ==== | ==== Developer Notes ==== | ||
=== 2017/12/07 Toshio Moriya === | === 2017/12/07 Toshio Moriya === | ||
- | The format of '' | + | The format of '' |
\\ | \\ | ||
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\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxwindow.py | + | sparx/bin/sp_window.py |
\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
\\ | \\ |