User Tools

Site Tools

pipeline:cter:sxcter

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
pipeline:cter:sxcter [2018/08/22 10:35]
fmerino 		pipeline:cter:sxcter [2019/04/02 10:27]
lusnig [See also]
Line 1: Line 1:
 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxcter =====+===== sp_cter =====
 CTF Estimation: Automated estimation of CTF parameters with error assessment, including Volta phase shift. CTF Estimation: Automated estimation of CTF parameters with error assessment, including Volta phase shift.
  
Line 9: Line 9:
 Usage in command line Usage in command line
  
-  sxcter.py  input_image_path  output_directory  --selection_list=SELECTION_TEXT_FILE  --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE  --Cs=CS  --voltage=VOLTAGE  --ac=AMP_CONTRAST  --f_start=FREA_START  --f_stop=FREQ_STOP  --kboot=KBOOT  --overlap_x=OVERLAP_X  --overlap_y=OVERLAP_Y  --edge_x=EDGE_X  --edge_y=EDGE_Y  --check_consistency  --stack_mode  --debug_mode  --vpp  --defocus_min=DEFOCUS_MIN  --defocus_max=DEFOCUS_MAX  --defocus_step=DEFOCUS_STEP  --phase_min=PHASE_MIN    --phase_max=PHASE_MAX  --phase_step==PHASE_STEP  --pap+  sp_cter.py  input_image_path  output_directory  --selection_list=SELECTION_TEXT_FILE  --wn=CTF_WINDOW_SIZE --apix=PIXEL_SIZE  --Cs=CS  --voltage=VOLTAGE  --ac=AMP_CONTRAST  --f_start=FREA_START  --f_stop=FREQ_STOP  --kboot=KBOOT  --overlap_x=OVERLAP_X  --overlap_y=OVERLAP_Y  --edge_x=EDGE_X  --edge_y=EDGE_Y  --check_consistency  --stack_mode  --debug_mode  --vpp  --defocus_min=DEFOCUS_MIN  --defocus_max=DEFOCUS_MAX  --defocus_step=DEFOCUS_STEP  --phase_min=PHASE_MIN    --phase_max=PHASE_MAX  --phase_step==PHASE_STEP  --pap --pws
  
 \\ \\
 ===== Typical usage ===== ===== Typical usage =====
  
-sxcter exists in for both MPI and non-MPI versions (Running MPI version does not require --MPI flag). +sp_cter exists in for both MPI and non-MPI versions (Running MPI version does not require --MPI flag). 
 \\ The program supports the phase shift estimation which induced by phase plate (e.g. Volta Phase Plate) with --vpp option. Please note that cter stores the estimated phase shift as amplitude contrast. By default, amplitude is used for the CTF model fitting but user can select power spectrum with --pap option (traditional method). \\ The program supports the phase shift estimation which induced by phase plate (e.g. Volta Phase Plate) with --vpp option. Please note that cter stores the estimated phase shift as amplitude contrast. By default, amplitude is used for the CTF model fitting but user can select power spectrum with --pap option (traditional method).
  
 \\ __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 (*), 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.+\\ 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 (\"). sp_gui.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 sp_cter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
  
 \\ __Selected Micrographs Mode - Process all micrographs in a selection list file:__ \\ __Selected Micrographs Mode - Process all micrographs in a selection list file:__
-\\ In addition to input micrographs path pattern and output directry arguments, specify a name of micrograph selection list text file using --selection_list option (e.g. output of sxgui_unblur.py or sxgui_cter.py). The file extension must be ".txt". 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 to input micrographs path pattern and output directry arguments, specify a name of micrograph selection list text file using --selection_list option (e.g. output of sp_gui_unblur.py or sp_gui_cter.py). The file extension must be ".txt". 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 -np 16 sxcter.py './mic*.hdf' outdir_cter --selection_list=mic_list.txt --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0+  mpirun -np 16 sp_cter.py './mic*.hdf' outdir_cter --selection_list=mic_list.txt --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
  
 \\ __Single Micrograph Mode - Process a single micrograph:__ \\ __Single Micrograph Mode - Process a single micrograph:__
 \\ 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. \\ 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+  sp_cter.py './mic*.hdf' outdir_cter --selection_list=mic0.hdf --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0
  
 \\ __Stack Mode - ProcessProcess a particle stack (Not supported by SPHIRE GUI)):__ \\ __Stack Mode - ProcessProcess a particle stack (Not supported by SPHIRE GUI)):__
-\\ Use --stack_mode option, then specify the path of particle stack file (without wild card "*") and output directory as arguments. This mode ignores --selection_list, --wn --overlap_x, --overlap_y, --edge_x, and --edge_y options. Use single processor for this mode. Not supported by SPHIRE GUI (sxgui.py). +\\ Use --stack_mode option, then specify the path of particle stack file (without wild card "*") and output directory as arguments. This mode ignores --selection_list, --wn --overlap_x, --overlap_y, --edge_x, and --edge_y options. Use single processor for this mode. Not supported by SPHIRE GUI (sp_gui.py). 
  
-  sxcter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode+  sp_cter.py bdb:stack outdir_cter --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --stack_mode
  
 \\ __All Micrographs Mode with Phase-Shift Estimation:__ \\ __All Micrographs Mode with Phase-Shift Estimation:__
 \\ defocus_min, defocus_max, defocus_step, phase_min, phase_max, and phase_step options are only applicable with --vpp option. \\ defocus_min, defocus_max, defocus_step, phase_min, phase_max, and phase_step options are only applicable with --vpp option.
  
-  mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --vpp --defocus_min=0.3 --defocus_max=9.0 --defocus_step=0.1 --phase_min=5.0 --phase_max=175.0 --phase_step=5+  mpirun -np 16 sp_cter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --vpp --defocus_min=0.3 --defocus_max=9.0 --defocus_step=0.1 --phase_min=5.0 --phase_max=175.0 --phase_step=5
  
 \\ __All Micrographs Mode with the CTF model fitting to power spectrum:__ \\ __All Micrographs Mode with the CTF model fitting to power spectrum:__
  
-  mpirun -np 16 sxcter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --pap+  mpirun -np 16 sp_cter.py './mic*.hdf' outdir_cter --wn=512 --apix=2.29 --Cs=2.0 --voltage=300 --ac=10.0 --pap
  
 \\ \\
 ===== 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 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)+  ; 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 sp_gui. (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)   ; 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 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)
Line 60: Line 59:
   ; %%--%%f_start : Lowest resolution [A]: Lowest resolution used in the CTF estimation. Determined automatically if not given. (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 used in the CTF estimation. Determined automatically if not given. (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 ===
 +  ; %%--%%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)
   ; %%--%%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 micrograph 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)
Line 69: Line 68:
   ; %%--%%edge_y : Edge y [pixels]: Specifies micrograph exclusion margin in the y direction. 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 an 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 sp_gui. (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! Estimate phase shift. (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) : %%--%%vpp==True 
-  ; %%--%%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) : %%--%%vpp==True 
-  ; %%--%%defocus_step : Defocus search step [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.1) +  ; %%--%%defocus_step : Defocus search step [um]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 0.1) : %%--%%vpp==True 
-  ; %%--%%phase_min : Minimum phase search [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 5.0) +  ; %%--%%phase_min : Minimum phase search [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 5.0) : %%--%%vpp==True 
-  ; %%--%%phase_max : Maximum phase search [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 175.0) +  ; %%--%%phase_max : Maximum phase search [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 175.0) : %%--%%vpp==True 
-  ; %%--%%phase_step : Phase search step [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 5.0)+  ; %%--%%phase_step : Phase search step [degrees]: UNDER DEVELOPMENT! This is applicable only with --vpp option. (default 5.0) : %%--%%vpp==True
   ; %%--%%pap : Use PW spectrum: UNDER DEVELOPMENT! Use power spectrum for CTF parameter search instead of amplitude. (default False)   ; %%--%%pap : Use PW spectrum: UNDER DEVELOPMENT! Use power spectrum for CTF parameter search instead of amplitude. (default False)
 +  ; %%--%%pws : Skip calculation of 2D power spectra: Will write periodograms to disk. (default False question reversed in GUI)
  
 \\ \\
 ===== Output ===== ===== Output =====
-After successful execution, sxcter will create in the output_directory:+After successful execution, sp_cter will create in the output_directory:
  
   - A CTF parameters file, written to ''partres.txt''   - A CTF parameters file, written to ''partres.txt''
Line 186: Line 186:
 \\ \\
 ==== Files ==== ==== Files ====
-sparx/bin/sxcter.py+sparx/bin/sp_cter.py
  
 \\ \\
 ==== See also ==== ==== See also ====
-[[pipeline:cter:sxgui_cter|sxgui_cter]], [[pipeline:window:sxwindow|sxwindow]]+[[pipeline:cter:sxcter|sp_gui_cter]], [[pipeline:window:sxwindow|sp_window]]
  
 \\ \\
Line 201: Line 201:
  
 \\ \\
 +
pipeline/cter/sxcter.txt · Last modified: 2019/04/02 10:28 by lusnig

Page Tools

Except where otherwise noted, content on this wiki is licensed under the following license: GNU Free Documentation License 1.3
GNU Free Documentation License 1.3 Donate Powered by PHP Valid HTML5 Valid CSS Driven by DokuWiki