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pipeline:utilities:sxpipe_resample_micrographs

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pipeline:utilities:sxpipe_resample_micrographs [2018/06/20 13:12]
127.0.0.1 external edit 		pipeline:utilities:sxpipe_resample_micrographs [2018/08/22 11:35]
fmerino
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 \\ __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 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 (')). bdb files can not be selected as input micrographs. Next, set %%--%%resample_ratio to the desired resampling ratio.  Then, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.+\\ Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: sxgui.py automatically adds single quotes (')). bdb files cannot be selected as input micrographs. Next, set %%--%%resample_ratio to the desired resampling ratio.  Then, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.
   mpirun  -np  48  sxpipe.py  resample_micrographs  './mic*.hdf'  outdir_pipe_resample_micrographs  --resample_ratio=0.5   mpirun  -np  48  sxpipe.py  resample_micrographs  './mic*.hdf'  outdir_pipe_resample_micrographs  --resample_ratio=0.5
  
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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: sxgui.py automatically adds single quotes (\')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. bdb files can not be selected as input micrographs. (default required string) +  ; 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: sxgui.py automatically adds single quotes (\')). The substring at the variable part must be same between the associated pair of input micrograph and coordinates file. bdb files cannot be selected as input micrographs. (default required string) 
-  ; 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 be an existing one. (default required string)
  
   ; %%--%%resample_ratio : Resampling ratio: Specify ratio between new and original pixel size. Use a value between 0.0 and 1.0 (exclusive both ends). (default required float)   ; %%--%%resample_ratio : Resampling ratio: Specify ratio between new and original pixel size. Use a value between 0.0 and 1.0 (exclusive both ends). (default required float)
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 \\ \\
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pipeline/utilities/sxpipe_resample_micrographs.txt · Last modified: 2019/04/02 10:29 by lusnig

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