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pipeline:cter:sxcter [2018/06/09 00:23]
moriya 		pipeline:cter:sxcter [2018/08/22 10:35]
fmerino
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 \\ __All Micrographs Mode - Process all micrographs in a directory:__ \\ __All Micrographs Mode - Process all micrographs in a directory:__
-\\ Specify a list of input micrographs using a wild card (*), called here input micrographs path pattern. Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). Running from the command line requires enclosing the string by single quotes (') or double quotes ("). sxgui.py will automatically adds single quotes to the string. BDB files can not be selected as input micrographs. Then, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.+\\ Specify a list of input micrographs using a wild card (*), here called input micrographs path pattern. Running from the command line requires enclosing the string by single quotes (\') or double quotes (\"). sxgui.py will automatically adds single quotes to the string. bdb files cannot be selected as input micrographs. Then, specify output directory where all outputs should be saved. In this mode, all micrographs matching the path pattern will be processed.
  
   mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0   mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
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 \\ __Single Micrograph Mode - Process a single micrograph:__ \\ __Single Micrograph Mode - Process a single micrograph:__
-\\ In addition to input micrographs path pattern 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 in the directory which specified by the micrograph path pattern, again the process will exit without processing it. Use single processor for this mode.+\\ One can 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. Use single processor for this mode.
  
   sxcter.py './mic*.hdf' outdir_cter --selection_list=mic0.hdf --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0   sxcter.py './mic*.hdf' outdir_cter --selection_list=mic0.hdf --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
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 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_image_path : Input micrograph path pattern: Specify input micrographs path pattern with a wild card (*) for any of Micrograph Modes. Images of BDB format can not be used as input micrographs. As an advanced option, a particle stack file path can also be supplied here when using --stack_mode. However, Stack Mode is not supported by sxgui. (default required string) +  ; input_image_path : Input micrograph path pattern: Specify input micrographs path pattern with a wild card (*) for any of Micrograph Modes. Images in bdb format cannot be used as input micrographs. In an advanced option, a particle stack file path can also be given using --stack_mode. However, Stack Mode is not supported by sxgui. (default required string) 
-  ; output_directory : Output directory: The CTF parameters (partres file), rotationally averaged power spectra (rotinf), and micrograph thumbnails (thumb files) will be written here. This directory will be created automatically and it must not exist previously. (default required string)+  ; output_directory : Output directory: The CTF parameters (partres file), rotationally averaged power spectra (rotinf), and micrograph thumbnails (thumb files) will be written here. It cannot be an existing one. (default required string)
  
   ; %%--%%selection_list : Micrograph selection file: Specify path of a micrograph selection list text file for Selected Micrographs Mode. The file extension must be '.txt'. Alternatively, the file name of a single micrograph can be specified for Single Micrograph Mode. (default none)   ; %%--%%selection_list : Micrograph selection file: Specify path of a micrograph selection list text file for Selected Micrographs Mode. The file extension must be '.txt'. Alternatively, the file name of a single micrograph can be specified for Single Micrograph Mode. (default none)
-  ; %%--%%wn : CTF window size [Pixels]: The size should be slightly larger than particle box size. This will be ignored in Stack Mode. (default 512)+  ; %%--%%wn : CTF window size [Pixels]: The window size should be slightly larger than particle box size. This will be ignored in Stack Mode. (default 512)
   ; %%--%%apix : Pixel size [A]: The pixel size of input micrograph(s) or images in input particle stack. (default -1.0)   ; %%--%%apix : Pixel size [A]: The pixel size of input micrograph(s) or images in input particle stack. (default -1.0)
   ; %%--%%Cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default 2.0)   ; %%--%%Cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default 2.0)
   ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0)   ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default 300.0)
-  ; %%--%%ac : Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0) +  ; %%--%%ac : Amplitude contrast [%]: The amplitude contrast is in the range of 7% - 14%. The value  depends on the thickness of the ice embedding the particles, among other factors. (default 10.0) 
-  ; %%--%%f_start : Lowest resolution [A]: Lowest resolution to be considered in the CTF estimation. Determined automatically by default. (default -1.0) +  ; %%--%%f_start : Lowest resolution [A]: Lowest resolution used in the CTF estimation. Determined automatically if not given. (default -1.0) 
-  ; %%--%%f_stop : Highest resolution [A]: Highest resolution to be considered in the CTF estimation. Determined automatically by default. (default -1.0)+  ; %%--%%f_stop : Highest resolution [A]: Highest resolution used in the CTF estimation. Determined automatically if not given. (default -1.0)
  
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
   ; %%--%%kboot : Number of CTF estimates per micrograph: Used for error assessment. (default 16)   ; %%--%%kboot : Number of CTF estimates per micrograph: Used for error assessment. (default 16)
-  ; %%--%%overlap_x : X overlap [%]: Overlap between the windows in the x direction. This will be ignored in Stack Mode. (default 50) +  ; %%--%%overlap_x : X overlap [%]: Overlap between micrograph windows in the x direction. This will be ignored in Stack Mode. (default 50) 
-  ; %%--%%overlap_y : Y overlap [%]: Overlap between the windows in the y direction. This will be ignored in Stack Mode. (default 50) +  ; %%--%%overlap_y : Y overlap [%]: Overlap between micrograph windows in the y direction. This will be ignored in Stack Mode. (default 50) 
-  ; %%--%%edge_x : Edge x [pixels]: Defines the edge of the tiling area in the x direction. Normally it does not need to be modified. This will be ignored in Stack Mode. (default 0) +  ; %%--%%edge_x : Edge x [pixels]: Specifies micrograph exclusion margin in the x direction. This will be ignored in Stack Mode. (default 0) 
-  ; %%--%%edge_y : Edge y [pixels]: Defines the edge of the tiling area in the y direction. Normally it does not need to be modified. This will be ignored in Stack Mode. (default 0)+  ; %%--%%edge_y : Edge y [pixels]: Specifies micrograph exclusion margin in the y direction. This will be ignored in Stack Mode. (default 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)
-  ; %%--%%stack_mode : Use stack mode: Use a stack as the input. Please set the file path of a stack as the first argument and output directory for the second argument. This is advanced option. Not supported by sxgui. (default False)+  ; %%--%%stack_mode : Use stack mode: Use a stack as the input. Please set the file path of a stack as the first argument and output directory for the second argument. This is an advanced option. Not supported by sxgui. (default False)
   ; %%--%%debug_mode : Enable debug mode: Print out debug information. (default False)   ; %%--%%debug_mode : Enable debug mode: Print out debug information. (default False)
-  ; %%--%%vpp : Volta Phase Plate Dataset: UNDER DEVELOPMENT! Also estimate phase shift as amplitude contrast. Use this option to estimate phase shift induced by Volta Phase Plate imaging. (default False)+  ; %%--%%vpp : Volta Phase Plate Dataset: UNDER DEVELOPMENT! Estimate phase shift. (default False)
   ; %%--%%defocus_min : Minimum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.3)   ; %%--%%defocus_min : Minimum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.3)
   ; %%--%%defocus_max : Maximum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 9.0)   ; %%--%%defocus_max : Maximum defocus search [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 9.0)
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 || 4 || Pixel size [A] || || 4 || Pixel size [A] ||
 || 5 || B-factor [A%%^%%2] || || 5 || B-factor [A%%^%%2] ||
-|| 6 || Total amplitude contrast [%], which can include estimated Volta phase shift ||+|| 6 || Amplitude contrast [%] (it can include estimated Volta phase shift) ||
 || 7 || Astigmatism amplitude [um] || || 7 || Astigmatism amplitude [um] ||
 || 8 || Astigmatism angle [degrees] || || 8 || Astigmatism angle [degrees] ||
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 || 15 || Frequency at which the signal drops by 50% due to estimated error of defocus alone [1/A] || || 15 || Frequency at which the signal drops by 50% due to estimated error of defocus alone [1/A] ||
 || 16 || Frequency at which the signal drops by 50% due to estimated error of defocus and astigmatism [1/A] || || 16 || Frequency at which the signal drops by 50% due to estimated error of defocus and astigmatism [1/A] ||
-|| 17 || Frequency at which the CTF oscillation can no longer be modelled correctly due the pixel size of the image [1/A] ||+|| 17 || Frequency at which the CTF cannot be correctly represented in a discrete form (pixel size is too large) [1/A] ||
 || 18 || NOT IMPLEMENTED YET! Maximum frequency limit (visual-impression-based)[A] || || 18 || NOT IMPLEMENTED YET! Maximum frequency limit (visual-impression-based)[A] ||
 || 19 || NOT IMPLEMENTED YET! Reserved spot for other means of maximum frequency limit or error criterion. Possibly originated from external program || || 19 || NOT IMPLEMENTED YET! Reserved spot for other means of maximum frequency limit or error criterion. Possibly originated from external program ||
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 \\ \\
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pipeline/cter/sxcter.txt · Last modified: 2019/04/02 10:28 by lusnig

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