pipeline:utilities:sxprocess

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pipeline:utilities:sxprocess [2018/11/20 10:48]
shaikh [Typical usage]
pipeline:utilities:sxprocess [2019/04/08 16:15]
shaikh
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxprocess ​=====+===== sp_process ​=====
 Miscellaneous Commands: Carry out various SPARX commands on image series, and generate data and initialize database for demo script. Miscellaneous Commands: Carry out various SPARX commands on image series, and generate data and initialize database for demo script.
  
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 Usage in command line Usage in command line
  
-  ​sxprocess.py  inputfile ​ outputfile ​ micrograph_prefix ​ --order ​ --order_lookup ​ --order_metropolis ​ --order_pca ​ --initial=INITIAL ​ --circular ​ --radius=RADIUS ​ --changesize ​ --ratio=RATIO ​ --pw  --wn=WN ​ --phase_flip ​ --makedb=param1=value1:​param2=value2 ​ --generate_projections=param1=value1:​param2=value2 ​ --isacgroup=ISACGROUP ​ --isacselect ​ --params=PARAMS ​ --adjpw ​ --rotpw=ROTPW ​ --transformparams=TRANSFORMPARAMS ​ --importctf=IMPORTCTF ​ --input=INPUT ​ --defocuserror=DEFOCUSERROR ​ --astigmatismerror=ASTIGMATISMERROR ​ --scale=SCALE ​ --adaptive_mask ​ --nsigma=NSIGMA ​ --threshold=THRESHOLD ​ --ndilation=NDILATION ​ --kernel_size=KERNEL_SIZE  ​--gauss_standard_dev=GAUSS_STANDARD_DEV  ​--binary_mask ​ ​--bin_threshold=BIN_THRESHOLD ​ --ne=NE ​ --nd=ND ​ ​--combinemaps ​ --output_dir=DIRECTORY ​ --output=OUTPUT ​ --pixel_size=PIXEL_SIZE ​ --mask=MASK ​ --do_adaptive_mask ​ ​--mask_threshold=MASK_THRESHOLD ​ --cosine_edge=COSINE_EDGE ​ --dilation=DILATION  ​--mtf=MTF_FILE_NAME ​ --fsc_adj ​ --B_enhance=B_ENHANCE ​ --B_start=B_START ​ --B_stop=B_STOP ​ --fl=lpf_cutoff_freq ​ --aa=lpf_falloff ​ --window_stack ​ --box=BOX ​ --balance_angular_distribution ​ --max_occupy=MAX_ORIENTATIONS ​ --angstep=ANGULAR_STEP+  ​sp_process.py  inputfile ​ outputfile ​ micrograph_prefix ​ --order ​ --order_lookup ​ --order_metropolis ​ --order_pca ​ --initial=INITIAL ​ --circular ​ --radius=RADIUS ​ --changesize ​ --ratio=RATIO ​ --pw  --wn=WN ​ --phase_flip ​ --makedb=param1=value1:​param2=value2 ​ --generate_projections=param1=value1:​param2=value2 ​ --isacgroup=ISACGROUP ​ --isacselect ​ --params=PARAMS ​ --adjpw ​ --rotpw=ROTPW ​ --transformparams=TRANSFORMPARAMS ​ --importctf=IMPORTCTF ​ --input=INPUT ​ --defocuserror=DEFOCUSERROR ​ --astigmatismerror=ASTIGMATISMERROR ​ --scale=SCALE ​ --adaptive_mask ​ --nsigma=NSIGMA ​ --threshold=THRESHOLD  ​--mol_mass=MOL_MASS ​--ndilation=NDILATION --edge_type=EDGE_TYP ​--edge_width=EDGE_WIDTH ​--binary_mask ​ --combinemaps ​ --output_dir=DIRECTORY ​ --output=OUTPUT ​ --pixel_size=PIXEL_SIZE ​ --mask=MASK ​ --do_adaptive_mask ​  ​--mtf=MTF_FILE_NAME ​ --fsc_adj ​ --B_enhance=B_ENHANCE ​ --B_start=B_START ​ --B_stop=B_STOP ​ --fl=lpf_cutoff_freq ​ --aa=lpf_falloff ​ --window_stack ​ --box=BOX ​ --balance_angular_distribution ​ --max_occupy=MAX_ORIENTATIONS ​ --angstep=ANGULAR_STEP ​ ​--symmetry=SYMMETRY --nerosion=NEROSION --do_approx
  
 \\ \\
 ===== Typical usage ===== ===== Typical usage =====
  
-sxprocess ​does not support MPI.+sp_process ​does not support MPI.
  
  1. Phase flip a stack of images and write output to new file:  1. Phase flip a stack of images and write output to new file:
  
-  ​sxprocess.py  input_stack.hdf ​ output_stack.hdf ​ --phase_flip+  ​sp_process.py  input_stack.hdf ​ output_stack.hdf ​ --phase_flip
  
  2. Change size of image or map (resample, decimation or interpolation up). The process also changes the pixel size and window size accordingly.  2. Change size of image or map (resample, decimation or interpolation up). The process also changes the pixel size and window size accordingly.
  
-  ​sxprocess ​ ​input.hdf ​ output.hdf ​ --changesize ​ --ratio=0.5+  ​sp_process ​ ​input.hdf ​ output.hdf ​ --changesize ​ --ratio=0.5
  
  3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes.  3. Compute average power spectrum of a stack of 2D images with optional padding (option wn) with zeroes.
  
-  ​sxprocess.py  input_stack.hdf ​ powerspectrum.hdf ​ --pw  [--wn=1024]+  ​sp_process.py  input_stack.hdf ​ powerspectrum.hdf ​ --pw  [--wn=1024]
  
  4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf,​ with CTF applied to both projections and micrographs.  4. Generate a stack of projections bdb:data and micrographs with prefix mic (i.e., mic0.hdf, mic1.hdf etc) from structure input_structure.hdf,​ with CTF applied to both projections and micrographs.
  
-  ​sxprocess.py  input_structure.hdf ​ data mic  --generate_projections ​ format="​bdb":​apix=5.2:​CTF=True:​boxsize=64+  ​sp_process.py  input_structure.hdf ​ data mic  --generate_projections ​ format="​bdb":​apix=5.2:​CTF=True:​boxsize=64
  
  5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3).  5. Retrieve original image numbers in the selected ISAC group (here group 12 from generation 3).
  
-  ​sxprocess.py  bdb:​test3 ​ class_averages_generation_3.hdf ​ list3_12.txt ​ --isacgroup=12 ​ --params=originalid+  ​sp_process.py  bdb:​test3 ​ class_averages_generation_3.hdf ​ list3_12.txt ​ --isacgroup=12 ​ --params=originalid
  
  ​6. ​ Retrieve original image numbers of images listed in ISAC output stack of averages/  ​6. ​ Retrieve original image numbers of images listed in ISAC output stack of averages/
  
-  ​sxprocess.py  select1.hdf ​ ohk.txt+  ​sp_process.py  select1.hdf ​ ohk.txt
  
  7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file. Optionally use a tangent low-pass filter. ​ Also works for a stack of images, in which case the output is also a stack.  7. Adjust rotationally averaged power spectrum of an image to that of a reference image or a reference 1D power spectrum stored in an ASCII file. Optionally use a tangent low-pass filter. ​ Also works for a stack of images, in which case the output is also a stack.
  
-  ​sxprocess.py  vol.hdf ref.hdf ​ avol.hdf ​ < 0.25 0.2> ​ --adjpw +  ​sp_process.py  vol.hdf ref.hdf ​ avol.hdf ​ < 0.25 0.2> ​ --adjpw 
-  ​sxprocess.py  vol.hdf pw.txt ​  ​avol.hdf ​ < 0.25 0.2> ​ --adjpw+  ​sp_process.py  vol.hdf pw.txt ​  ​avol.hdf ​ < 0.25 0.2> ​ --adjpw
  
  8. Generate a 1D rotationally averaged power spectrum of an image.  8. Generate a 1D rotationally averaged power spectrum of an image.
  
-  ​sxprocess.py  vol.hdf ​ --rotwp=rotpw.txt+  ​sp_process.py  vol.hdf ​ --rotpw=rotpw.txt
  
 \\ Output will contain three columns: \\ Output will contain three columns:
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  9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.  9. Apply 3D transformation (rotation and/or shift) to a set of orientation parameters associated with projection data.
  
-  ​sxprocess.py  --transfromparams=phi,​theta,​psi,​tx,​ty,​tz ​ input.txt ​ output.txt+  ​sp_process.py  --transfromparams=phi,​theta,​psi,​tx,​ty,​tz ​ input.txt ​ output.txt
  
 The output file is then imported and 3D transformed map computed. The output file is then imported and 3D transformed map computed.
  
-  ​sxheader.py  bdb:p  --params=xform.projection ​ --import=output.txt +  ​sp_header.py  bdb:p  --params=xform.projection ​ --import=output.txt 
-  mpirun ​ -np  2  ​sxrecons3d_n.py  bdb:p tvol.hdf ​ --MPI+  mpirun ​ -np  2  ​sp_recons3d_n.py  bdb:p tvol.hdf ​ --MPI
  
 The reconstructed map is in the position of the map computed using the input.txt parameters and then transformed with rot_shift3D(vol,​ phi,​theta,​psi,​tx,​ty,​tz). The reconstructed map is in the position of the map computed using the input.txt parameters and then transformed with rot_shift3D(vol,​ phi,​theta,​psi,​tx,​ty,​tz).
  
-10. Import ctf parameters from the output of sxcter ​into windowed particle headers. ​+10. Import ctf parameters from the output of sp_cter ​into windowed particle headers. ​
 \\ There are three possible input files formats: (1) all particles are in one stack, (2) and/or (3) particles are in stacks, each stack corresponds to a single micrograph. In each case the particles should contain a name of the micrograph of origin stores using attribute name '​ptcl_source_image'​. Normally this is done by e2boxer.py during windowing. Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created. \\ There are three possible input files formats: (1) all particles are in one stack, (2) and/or (3) particles are in stacks, each stack corresponds to a single micrograph. In each case the particles should contain a name of the micrograph of origin stores using attribute name '​ptcl_source_image'​. Normally this is done by e2boxer.py during windowing. Particles whose defocus or astigmatism error exceed set thresholds will be skipped, otherwise, virtual stacks with the original way preceded by G will be created.
  
-  ​sxprocess.py  --input=bdb:​data ​ --importctf=outdir/​partres ​ --defocuserror=10.0 ​ --astigmatismerror=5.0+  ​sp_process.py  --input=bdb:​data ​ --importctf=outdir/​partres ​ --defocuserror=10.0 ​ --astigmatismerror=5.0
  
 \\ Output will be a vritual stack bdb:Gdata. \\ Output will be a vritual stack bdb:Gdata.
  
-  ​sxprocess.py  --input="​bdb:​directory/​stacks*" ​ --importctf=outdir/​partres ​ --defocuserror=10.0 ​ --astigmatismerror=5.0+  ​sp_process.py  --input="​bdb:​directory/​stacks*" ​ --importctf=outdir/​partres ​ --defocuserror=10.0 ​ --astigmatismerror=5.0
  
-To concatenate output files:+To concatenate output files,
  
   cd directory   cd directory
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 11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor. 11. Scale 3D shifts. The shifts in the input five columns text file with 3D orientation parameters will be DIVIDED by the scale factor.
  
-  ​sxprocess.py  orientationparams.txt ​ scaledparams.txt ​ scale=0.5+  ​sp_process.py  orientationparams.txt ​ scaledparams.txt ​ scale=0.5
  
 12. Generate soft-edged 3D mask from input 3D map automatically or using the user-provided threshold. 12. Generate soft-edged 3D mask from input 3D map automatically or using the user-provided threshold.
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 \\ Automatically compute the threshold to intially obtain the largest density cluster. \\ Automatically compute the threshold to intially obtain the largest density cluster.
  
-  ​sxprocess.py  vol3d.hdf ​ mask3d.hdf ​ --adaptive_mask ​ --nsigma=3.0 ​ --ndilation=1 ​ --kernel_size=9  ​--gauss_standard_dev=5+  ​sp_process.py  vol3d.hdf ​ mask3d.hdf ​ --adaptive_mask  ​--fl=12.0 --aa=0.02 --pixel_size=3.1 ​--nsigma=3.0 ​ --ndilation=1 ​ --edge_width=--edge_type="​G"​ --mol_mass=1500.0
  
 \\ Use the user-provided threshold to intially obtain the largest density cluster. \\ Use the user-provided threshold to intially obtain the largest density cluster.
  
-  ​sxprocess.py  vol3d.hdf ​ mask3d.hdf ​ --adaptive_mask --threshold=0.05 ​ -ndilation=0 ​ --kernel_size=9 ​ --gauss_standard_dev=5+  ​sp_process.py  vol3d.hdf ​ mask3d.hdf ​ --adaptive_mask --threshold=0.05  ​--ndilation=0 ​ --edge_width=5
  
 13. Generate binary 3D mask from input 3D map using the user-provided threshold. 13. Generate binary 3D mask from input 3D map using the user-provided threshold.
  
-  ​sxprocess.py  vol3d.hdf ​ mask3d.hdf ​ --binary_mask ​ --threshold=0.05 ​ --ne=3  ​--nd==3+  ​sp_process.py  vol3d.hdf ​ mask3d.hdf ​ --binary_mask ​ --threshold=0.05 ​ --ndilation=--nerosion=0
  
 14. PostRefiner - Post-refine maps or images by enhancing the power spectrum after 2D averaging, 3D refinement, or 3D sorting run. 14. PostRefiner - Post-refine maps or images by enhancing the power spectrum after 2D averaging, 3D refinement, or 3D sorting run.
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 \\ Options are independent of each others. \\ Options are independent of each others.
   * %%--%%do_adaptive_mask : =True when it is restored, the program adaptively creates adaptive mask file using summed two maps. This takes a couple of minutes. For map with dimension of 384*384*384,​ it takes 6 minutes.   * %%--%%do_adaptive_mask : =True when it is restored, the program adaptively creates adaptive mask file using summed two maps. This takes a couple of minutes. For map with dimension of 384*384*384,​ it takes 6 minutes.
-  * %%--%%mask_threshold ​  : The number of sigmas of summed two halves above image average used as the density ​threshold for creating adaptive surface mask. User can adjust it if the default value is too high or too low.+  * %%--%%threshold ​  : Adaptive mask threshold: Density ​threshold for creating adaptive surface mask. This threshold ​is the same as the threshold in e.g. UCSF Chimera.
   * %%--%%mtf ​             : For those high resolution maps, mtf correction would significantly enhance structural features.   * %%--%%mtf ​             : For those high resolution maps, mtf correction would significantly enhance structural features.
   * %%--%%fsc_adj ​         : FSC adjustment of power spectrum is inclined to increase the slope of power spectrum of the summed map.   * %%--%%fsc_adj ​         : FSC adjustment of power spectrum is inclined to increase the slope of power spectrum of the summed map.
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   * %%--%%fl ​              : =0.0, low-pass filter to resolution; >=0.5, low-pass filter to the given Angstrom; >0.0 AND <=0.5, low-pass filter to the given absolute frequency; =-1.0, no low-pass filter.   * %%--%%fl ​              : =0.0, low-pass filter to resolution; >=0.5, low-pass filter to the given Angstrom; >0.0 AND <=0.5, low-pass filter to the given absolute frequency; =-1.0, no low-pass filter.
  
-  ​sxprocess.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --output=postrefine_fullset_vol3d.hdf ​ --pixel_size=1.12 ​ --mask=mask3d.hdf ​  ​--mtf=mtf.txt ​ --fl=-1 ​  ​--fsc_adj +  ​sp_process.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --output=postrefine_fullset_vol3d.hdf ​ --pixel_size=1.12 ​ --mask=mask3d.hdf ​  ​--mtf=mtf.txt ​ --fl=-1 ​  ​--fsc_adj 
-  ​sxprocess.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --pixel_size=1.12 ​ --mask=mask3d.hdf ​  ​--mtf=aa.txt ​ --fl=4.7 ​ --aa=0.02 --fsc_adj +  ​sp_process.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --pixel_size=1.12 ​ --mask=mask3d.hdf ​  ​--mtf=aa.txt ​ --fl=4.7 ​ --aa=0.02 --fsc_adj 
-  ​sxprocess.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --output=postrefine_fullset_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280+  ​sp_process.py  --combinemaps ​ vol_0_unfil.hdf vol_1_unfil.hdf ​ --output_dir=outdir_postrefine ​ --output=postrefine_fullset_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280
  
 \\ (2) Cluster Maps Mode or Single Map Mode: \\ (2) Cluster Maps Mode or Single Map Mode:
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 \\ Note that this mode is mainly designed for SORT3D_DEPTH outputs but also applicable to ANY maps. \\ Note that this mode is mainly designed for SORT3D_DEPTH outputs but also applicable to ANY maps.
  
-  ​sxprocess.py  --combinemaps ​ vol_cluster*.hdf ​   --output_dir=outdir_postrefine_cluster_vols ​ --output=postrefine_cluster_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280+  ​sp_process.py  --combinemaps ​ vol_cluster*.hdf ​   --output_dir=outdir_postrefine_cluster_vols ​ --output=postrefine_cluster_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280
  
 \\ To process one single map, simply specify the input volume path (without wild card '​*'​). This executes the same processes as above but on one single map: \\ To process one single map, simply specify the input volume path (without wild card '​*'​). This executes the same processes as above but on one single map:
  
-  ​sxprocess.py  --combinemaps ​ vol.hdf ​ --output_dir=outdir_postrefine_single_vol ​ --output=spostrefine_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280+  ​sp_process.py  --combinemaps ​ vol.hdf ​ --output_dir=outdir_postrefine_single_vol ​ --output=spostrefine_vol3d.hdf ​ --pixel_size=1.12 ​ --do_adaptive_mask ​ --mtf=mtf.txt ​ --fl=3.9 ​ --aa=0.01 ​ --B_enhance=280
  
 \\ (3) Images Mode - for 2D images \\ (3) Images Mode - for 2D images
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 15. Window stack file -reduce size of images without changing the pixel size. 15. Window stack file -reduce size of images without changing the pixel size.
- sxprocess.py input.hdf output.hdf --box=new_box_size+ sp_process.py input.hdf output.hdf --box=new_box_size
  
 16. Pad stack file --pad images to a larger size and set surround background to request value (default 0.0). 16. Pad stack file --pad images to a larger size and set surround background to request value (default 0.0).
- sxprocess.py input.hdf output.hdf --box=new_box_size --background=3.0+ sp_process.py input.hdf output.hdf --box=new_box_size --background=3.0
  
 17. Create angular distribution .build file 17. Create angular distribution .build file
- sxprocess.py --angular_distribution ​ inputfile=example/​path/​params.txt --pixel_size=1.0 ​ --round_digit=5 ​ --box_size=500 ​ --particle_radius=175 ​ --cylinder_width=1 ​ --cylinder_length=10000+ sp_process.py --angular_distribution ​ inputfile=example/​path/​params.txt --pixel_size=1.0 ​ --round_digit=5 ​ --box_size=500 ​ --particle_radius=175 ​ --cylinder_width=1 ​ --cylinder_length=10000
   
 18. Subtract from images in the first stack images in the second stack and write results to the third stack. 18. Subtract from images in the first stack images in the second stack and write results to the third stack.
-\\ If the name of the output stack is the same as the second stack, the results will be written to the second stack (it will be overwritten).+   If the name of the output stack is the same as the second stack, the results will be written to the second 
 +   stack (it will be overwritten).
  
- sxprocess.py bdb:​orgstack bdb:​proj/​data ​ bdb:​proj/​sdata bdb:​proj/​odata --subtract_stack+ sp_process.py bdb:​orgstack bdb:​proj/​data ​ bdb:​proj/​sdata bdb:​proj/​odata --subtract_stack
   
 19. Balance angular distribution. ​ 19. Balance angular distribution. ​
-\\ Input ASCII file with 3D orientation parameters, compute a histogram of distribution of angles using user-provided angular step, retain a subset of randomly selected projection direction per angular bin using user-provided threshold, and write the list of the all retained projection directions.  ​+   Input ASCII file with 3D orientation parameters, compute a histogram 
 +   of distribution of angles using user-provided angular step, retain a subset of randomly selected 
 +   projection direction per angular bin using user-provided threshold, and write the list of the all 
 +   retained projection directions.  ​(In order to create a substack with retained images, use e2bdb.py 
 +   with options makevstack and list). 
 + 
 + sp_process.py --balance_angular_distribution ​ params.txt select.txt --max_occupy=100 --angstep=15 --symmetry=d3
  
- sxprocess.py --balance_angular_distribution ​ params.txt select.txt --max_occupy=100 --angstep=15 --symmetry=d3 
-\\ In order to create a substack with retained images, use e2bdb.py: 
- e2bdb.py bdb:​particle_directory#​input_stack --makevstack bdb:​particle_directory#​output_stack --list select.txt 
  
 \\ \\
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   ; %%--%%rotpw : Compute rotationally averaged power spectrum of the input image: Store in output text file with name as specified. (default none)   ; %%--%%rotpw : Compute rotationally averaged power spectrum of the input image: Store in output text file with name as specified. (default none)
  
-  ; %%--%%importctf : Import ​sxcter ​CTF parameters into stack file: Specify name of a file that contains CTF parameters produced by sxcter. (default none)+  ; %%--%%importctf : Import ​sp_cter ​CTF parameters into stack file: Specify name of a file that contains CTF parameters produced by sp_cter. (default none)
   ; %%--%%input : Input particle image stack file: CTF parameters will be imported into headers of images in the stack. (default none)   ; %%--%%input : Input particle image stack file: CTF parameters will be imported into headers of images in the stack. (default none)
-  ; %%--%%defocuserror : Defocus error threshold: Exclude micrographs whose relative defocus error as estimated by sxcter ​is larger than defocuserror percent. the error is computed as (std dev defocus)/​defocus*100%. (default 1000000.0) +  ; %%--%%defocuserror : Defocus error threshold: Exclude micrographs whose relative defocus error as estimated by sp_cter ​is larger than defocuserror percent. the error is computed as (std dev defocus)/​defocus*100%. (default 1000000.0) 
-  ; %%--%%astigmatismerror : Astigmatism error threshold: Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sxcter ​is larger than astigmatismerror degrees. (default 360.0)+  ; %%--%%astigmatismerror : Astigmatism error threshold: Set to zero astigmatism for micrographs whose astigmatism angular error as estimated by sp_cter ​is larger than astigmatismerror degrees. (default 360.0)
  
   ; %%--%%scale : Divide shifts in input 3D orientation parameters text file by the specified scale factor: (default -1.0)   ; %%--%%scale : Divide shifts in input 3D orientation parameters text file by the specified scale factor: (default -1.0)
  
   ; %%--%%adaptive_mask : Create soft-edged 3D mask: Create soft-edged 3D mask from the input structure. (default False)   ; %%--%%adaptive_mask : Create soft-edged 3D mask: Create soft-edged 3D mask from the input structure. (default False)
-  ; %%--%%nsigma ​Density standard deviation thresholdDefines the threshold used in the first step of the processing ​to generate a binary version of the structure. The threshold ​is set to <= mean + (nsigma x standard deviations). This option will not be used if the option ​threshold ​is larger than -9999.0. (default ​1.0) +  ; %%--%%use_mol_mass ​Use molecular mass GUI OPTION ONLY - Define if one want to use the molecular mass option as a masking ​threshold(default False: %%--%%threshold==-9999.0 ​%%--%%nsigma==1.0 %%--%%do_adaptive_mask==True 
-  ; %%--%%threshold : Binarization threshold: Defines the threshold used in the first step of the processing to generate a binary version of the input structure. If the value is lower-equal than the default, the option will be ignored and the threshold will be set according to nsigma method above. (default -9999.0) +  ; %%--%%threshold : Binarization threshold: Defines the threshold used in the first step of the processing to generate a binary version of the input structure. If the value is lower-equal than the default, the option will be ignored and the threshold will be set according to nsigma method above. (default -9999.0) ​: %%--%%nsigma==1.0 ​ %%--%%use_mol_mass==False %%--%%do_adaptive_mask==True 
-  ; %%--%%ndilation ​Mask extension cycles: The initial mask will be dilated ​(extended) the number ​of cycles. (default ​3+  ; %%--%%mol_mass ​Molecular mass [kDa]: The estimated molecular mass of the target particle in kilodalton. ​(default none: %%--%%use_mol_mass==True 
-  ; %%--%%kernel_size ​Gaussian kernel size [Pixels]: ​Size of the Gaussian kernel used for intermediate processing. ​(default ​11+  ; %%--%%nsigma : Density standard deviation threshold: Defines ​the threshold used in the first step of the processing to generate a binary version of the structure. The threshold is set to <= mean + (nsigma x standard deviations). This option will not be used if the option threshold is larger than -9999.0. (default ​1.0: %%--%%threshold==-9999.0 %%--%%use_mol_mass==False %%--%%do_adaptive_mask==True 
-  ; %%--%%gauss_standard_dev ​Kernel standard deviation ​[Pixels]: ​Standard deviation ​of the Gaussian smoothing ​used to produce smooth ​edge. (default ​9)+  ; %%--%%ndilation ​Dilation width [Pixels]: ​The pixel width to dilate ​the 3D binary volume corresponding to the specified molecular mass or density threshold prior to softening the edge (default ​3: %%--%%do_adaptive_mask==True 
 +  ; %%--%%edge_width ​Soft-edge width [Pixels]: ​The pixel width of transition area for soft-edged masking.(default 5) : %%--%%do_adaptive_mask==True 
 +  ; %%--%%edge_type : Soft-edge type: The type of soft-edge for moon-eliminator 3D mask and a moon-eliminated soft-edged 3D mask. Available methods are (1) \'​cosine\'​ for cosine soft-edged (used in PostRefiner) and (2) \'​gauss\'​ for gaussian soft-edge. (default ​cosine: %%--%%do_adaptive_mask==True
  
   ; %%--%%binary_mask : Create binary 3D mask: Create binary 3D mask from the input structure. (default False)   ; %%--%%binary_mask : Create binary 3D mask: Create binary 3D mask from the input structure. (default False)
-  ; %%--%%bin_threshold : Binarization threshold: Defines the threshold used in the first step of the processing to generate a binary version of the input structure. (default 0.0) +  ; %%--%%nerosion ​: Erosion ​value Number ​of times to erode binarized volume ​(default 0)
-  ; %%--%%ne ​: Erosion ​cyclesAfter initial binarization the structure is eroded to remove fragmented pieces ​of the map. (default 0) +
-  ; %%--%%nd : Dilation cycles: After erosing the binary structure is dilated back to smooth the surface and match the original size. (default 0)+
  
   ; %%--%%combinemaps : Post-refine structures or images: Post-refine structures or averages by enhancing their high-frequencies after 2D alignment, 3D refinement, or 3D sorting. Available modes are (1) Halfset Volumes Mode, (2) Cluster Volumes Mode or Single Volumes Mode, and (3) Images Mode. (1) The Halfset Volumes Mode combines a pair of unfiltered odd & even 3D density maps, then enhance the power spectrum at high frequencies. B-factor can be automatically estimated from these unfiltered halfset maps. This mode requires two arguments; use unfiltered hal-maps produced by MERIDIEN. (2) The Cluster Volumes Mode or Single Volumes Mode enhances the power spectrum of cluster maps, produced by SORT3D_DEPTH,​ at high frequencies. Only ad-hoc low-pass filter cutoff and B-factor can be used. This mode requires one argument (path pattern with wild card '​*'​ can be used to specify a list of single maps). It is mainly designed for SORT3D_DEPTH outputs but it is also applicable to ANY single map. (default False)   ; %%--%%combinemaps : Post-refine structures or images: Post-refine structures or averages by enhancing their high-frequencies after 2D alignment, 3D refinement, or 3D sorting. Available modes are (1) Halfset Volumes Mode, (2) Cluster Volumes Mode or Single Volumes Mode, and (3) Images Mode. (1) The Halfset Volumes Mode combines a pair of unfiltered odd & even 3D density maps, then enhance the power spectrum at high frequencies. B-factor can be automatically estimated from these unfiltered halfset maps. This mode requires two arguments; use unfiltered hal-maps produced by MERIDIEN. (2) The Cluster Volumes Mode or Single Volumes Mode enhances the power spectrum of cluster maps, produced by SORT3D_DEPTH,​ at high frequencies. Only ad-hoc low-pass filter cutoff and B-factor can be used. This mode requires one argument (path pattern with wild card '​*'​ can be used to specify a list of single maps). It is mainly designed for SORT3D_DEPTH outputs but it is also applicable to ANY single map. (default False)
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   ; %%--%%output : Output file name: File name of output final post-refined structure. (default vol_combined.hdf)   ; %%--%%output : Output file name: File name of output final post-refined structure. (default vol_combined.hdf)
   ; %%--%%pixel_size : Pixel size [A]: Pixel size of input data. (default 0.0)   ; %%--%%pixel_size : Pixel size [A]: Pixel size of input data. (default 0.0)
-  ; %%--%%mask : 3D mask file: Path to user-provided mask. (default none) +  ; %%--%%mask : 3D mask file: Path to user-provided mask. (default none) : %%--%%do_adaptive_mask==False 
-  ; %%--%%do_adaptive_mask : Apply adaptive mask: Program creates mask adaptively with given density threshold. (default False) +  ; %%--%%do_adaptive_mask : Apply adaptive mask: Program creates mask adaptively with given density threshold. (default False) ​: %%--%%mask==none 
-  ; %%--%%mask_threshold ​Adaptive ​mask thresholdThe number of sigmas of summed two halves above image average corresponding used as the density threshold ​for creating adaptive surface mask. Effective only with --do_adaptive_mask option. (default ​5.0+  ; %%--%%do_adaptive_mask ​Apply adaptive ​mask: Program creates mask adaptively with given density threshold. (default ​False: %%--%%mask==none 
-  ; %%--%%cosine_edge ​Cosine edge width [Pixels]Width of cosine transition area for soft-edge maskingEffective only with --do_adaptive_mask option. (default ​6.0) +  ; %%--%%do_approx ​Approximate valuesApproximate the values ​of the soft edge area instead of using the exact valuesThis will lead to a less smoothened mask, but will mirror the previous behaviour. (default ​False%%--%%edge_width!=0
-  ; %%--%%dilation : Surface dilation size [Pixels]: Size of surface dilation or erosion. Effective only with --do_adaptive_mask option. (default 6.0+
   ; %%--%%mtf : MTF file: Path to file contains the MTF (modulation transfer function) of the detector used. (default none)   ; %%--%%mtf : MTF file: Path to file contains the MTF (modulation transfer function) of the detector used. (default none)
   ; %%--%%fsc_adj : Apply FSC-based low-pass filter: Applies an FSC-based low-pass filter to the merged map before the B-factor estimation. Effective only in Halfset Volumes Mode. (default False)   ; %%--%%fsc_adj : Apply FSC-based low-pass filter: Applies an FSC-based low-pass filter to the merged map before the B-factor estimation. Effective only in Halfset Volumes Mode. (default False)
   ; %%--%%B_enhance : B-factor enhancement:​ 0.0: program automatically estimates B-factor using power spectrum at frequencies from B_start (usually 10 Angstrom) to the resolution determined by FSC143 (valid only in Halfset Volumes Mode; Non-zero positive value: program use the given value [A^2] to enhance map); -1.0: B-factor is not applied. (default 0.0)   ; %%--%%B_enhance : B-factor enhancement:​ 0.0: program automatically estimates B-factor using power spectrum at frequencies from B_start (usually 10 Angstrom) to the resolution determined by FSC143 (valid only in Halfset Volumes Mode; Non-zero positive value: program use the given value [A^2] to enhance map); -1.0: B-factor is not applied. (default 0.0)
-  ; %%--%%B_start : B-factor estimation lower limit [A]: Frequency in Angstrom defining lower boundary of B-factor estimation. Effective only in Halfset Volumes Mode with --B_enhance=0.0. (default 10.0) +  ; %%--%%B_start : B-factor estimation lower limit [A]: Frequency in Angstrom defining lower boundary of B-factor estimation. Effective only in Halfset Volumes Mode with --B_enhance=0.0. (default 10.0) : %%--%%B_enhance==0.0 
-  ; %%--%%B_stop : B-factor estimation upper limit [A]: Frequency in Angstrom defining upper boundary of B-factor estimation. Recommended to set the upper boundary to the frequency where fsc is smaller than 0.0. Effective only in Halfset Volumes Mode with --B_enhance=0.0. (default ​ 0.0)+  ; %%--%%B_stop : B-factor estimation upper limit [A]: Frequency in Angstrom defining upper boundary of B-factor estimation. Recommended to set the upper boundary to the frequency where fsc is smaller than 0.0. Effective only in Halfset Volumes Mode with --B_enhance=0.0. (default ​ 0.0) : %%--%%B_enhance==0.0
   ; %%--%%fl : Low-pass filter frequency [A]: 0.0: low-pass filter to resolution (valid only in Halfset Volumes Mode); A value larger than 0.5: low-pass filter to the value in Angstrom; -1.0: no low-pass filter. (default 0.0)   ; %%--%%fl : Low-pass filter frequency [A]: 0.0: low-pass filter to resolution (valid only in Halfset Volumes Mode); A value larger than 0.5: low-pass filter to the value in Angstrom; -1.0: no low-pass filter. (default 0.0)
-  ; %%--%%aa : Low-pass filter fall-off [1/Pixels]: Low-pass filter fall-off. Effective only when --fl option is not -1.0. (default 0.01)+  ; %%--%%aa : Low-pass filter fall-off [1/Pixels]: Low-pass filter fall-off. Effective only when --fl option is not -1.0. (default 0.01) : %%--fl%%!=-1.0
  
   ; %%--%%window_stack : Window stack images using a smaller window size: (default False)   ; %%--%%window_stack : Window stack images using a smaller window size: (default False)
   ; %%--%%box : New window size: (default 0)   ; %%--%%box : New window size: (default 0)
  
-  ; %%--%%balance_angular_distribution : Balance Angular Distribution:​ Balance ​an angular distribution of projection directions by removing ​their excess ​numbers, as determined by their angular histogram on a coarser grid, as specified by the angular_step option. (default False) +  ; %%--%%balance_angular_distribution : Balance Angular Distribution:​ Balance angular distribution of projection directions by removing excess ​particles, as determined by their angular histogram on a coarser grid, as specified by the angular_step option. (default False) 
-  ; %%--%%max_occupy : Maximum orientations per reference angle: Maximum number of angular orientations ​per reference angle. (default 1) +  ; %%--%%max_occupy : Maximum orientations per reference angle: Maximum number of particles ​per reference angle. (default ​-1) 
-  ; %%--%%angstep : Angular step of reference angles: angular step of reference angles, i.e., number of bins of angular histogram. (default ​15.0)+  ; %%--%%angstep ​: Angular increment: Angular step of reference angles. (default 15.0) 
 +  ; %%--%%symmetry : Point-group symmetry ​: angular step of reference angles, i.e., number of bins of angular histogram. (default ​c1)
  
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   ; %%--%%makedb : Generate a database file containing a set of parameters: One argument is required, name of key with which the database will be created. Fill in database with parameters specified as %%--%%makedb param1=value1:​param2=value2 (e.g. '​gauss_width'​=1.0:'​pixel_input'​=5.2:'​pixel_output'​=5.2:'​thr_low'​=1.0). (default none)   ; %%--%%makedb : Generate a database file containing a set of parameters: One argument is required, name of key with which the database will be created. Fill in database with parameters specified as %%--%%makedb param1=value1:​param2=value2 (e.g. '​gauss_width'​=1.0:'​pixel_input'​=5.2:'​pixel_output'​=5.2:'​thr_low'​=1.0). (default none)
  
-  ; %%--%%transformparams : Transform 3D projection orientation parameters: Using six 3D parameters (phi,​theta,​psi,​sx,sy,sz). input is %%--%%transformparams=45.,​66.,​12.,​-2,​3,​-5.5 desired six transformation of the reconstructed structure. output is file with modified orientation parameters. (default none)+  ; %%--%%transformparams : Transform 3D projection orientation parameters: Using six 3D parameters (phi,​theta,​psi,​sp_,sy,sz). input is %%--%%transformparams=45.,​66.,​12.,​-2,​3,​-5.5 desired six transformation of the reconstructed structure. output is file with modified orientation parameters. (default none)
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxprocess.py+sparx/bin/sp_process.py
  
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 +
  • pipeline/utilities/sxprocess.txt
  • Last modified: 2019/04/08 16:15
  • by shaikh