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pipeline:sort3d:sxsort3d [2018/02/16 10:11]
127.0.0.1 external edit 		pipeline:sort3d:sxsort3d [2018/06/20 13:12]
127.0.0.1 external edit
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 Usage in command line Usage in command line
-  sxsort3d.py  stack  outdir  mask  --focus=3Dmask  --ir=inner_radius  --radius=outer_radius  --maxit=max_iter  --rs=ring_step  --xr=xr  --yr=yr  --ts=ts  --delta=angular_step  --an=angular_neighborhood  --center=centring_method  --nassign=nassign  --nrefine=nrefine  --CTF  --stoprnct=stop_percent  --sym=c1  --function=user_function  --independent=indenpendent_runs  --number_of_images_per_group=number_of_images_per_group  --low_pass_filter=low_pass_filter  --nxinit=nxinit  --unaccounted  --seed=random_seed  --smallest_group=smallest_group  --sausage  --chunk0=CHUNK0_FILE_NAME  --chunk1=CHUNK1_FILE_NAME  --PWadjustment=PWadjustment  --protein_shape=protein_shape  --upscale=upscale  --wn=wn --interpolation=method+ 
 +  sxsort3d.py  stack  outdir  mask  --focus=3Dmask  --radius=outer_radius  --delta=angular_step  --CTF  --sym=c1  --number_of_images_per_group=number_of_images_per_group  --nxinit=nxinit  --smallest_group=smallest_group  --chunk0=CHUNK0_FILE_NAME  --chunk1=CHUNK1_FILE_NAME  --ir=inner_radius  --maxit=max_iter  --rs=ring_step  --xr=xr  --yr=yr  --ts=ts  --an=angular_neighborhood  --center=centring_method  --nassign=nassign  --nrefine=nrefine  --stoprnct=stop_percent  --function=user_function  --independent=indenpendent_runs  --low_pass_filter=low_pass_filter  --unaccounted  --seed=random_seed  --sausage  --PWadjustment=PWadjustment  --protein_shape=protein_shape  --upscale=upscale  --wn=wn  --interpolation=method
  
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 sxsort3d exists only in MPI version. sxsort3d exists only in MPI version.
-  mpirun -np 176 --host n1,n5,n6,n8,n9,n10,n0,n4,n3,n7 sxsort3d.py bdb:data sort3d_outdir1 mask.hdf --focus=ribosome_focus.hdf --chunkdir=/data/n10/pawel/ribosome_frank/ri3/main013 --radius=52 --CTF --number_of_images_per_group=2000 --low_pass_filter=.125 --stoprnct=5 + 
 +  mpirun -np 192 sxsort3d.py bdb:data sort3d_outdir1 mask.hdf --focus=ribosome_focus.hdf --chunkdir=/data/n10/pawel/ribosome_frank/ri3/main013 --radius=52 --CTF --number_of_images_per_group=2000 --low_pass_filter=.125 --stoprnct=5
  
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 === Main Parameters === === Main Parameters ===
   ; stack : Input images stack: (default required string)   ; stack : Input images stack: (default required string)
-  ; mask : 3D mask: (default none)  +  ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string) 
-  ; focus : Focus 3D mask: Mask used for focused clustering (default none) +  ; mask : 3D mask: File path of the global 3D mask for clustering. (default none) 
-  ; radius : Outer radius for rotational correlation [Pixels]: Must be smaller than half the box size. Please set to the radius of the particle. (default -1) + 
-  ; delta : Angular step for projections: (default '2') +  ; %%--%%focus : Binary Focus 3D mask: Binary 3D mask used for focused clustering. (default none) 
-  ; CTF : Use CTF: Do a full CTF correction during the alignment. (default False)  +  ; %%--%%radius : Particle radius [Pixels]: Used as outer radius for rotational correlation.  Must be smaller than half the box size. (default -1) 
-  ; sym : Point-group symmetry: (default c1)  +  ; %%--%%delta : Angular step for projections [Degrees]: Angular step of reference projections. (default '2') 
-  ; number_of_images_per_group : Images per group: Critical number of images per group, defined by user. (default 1000)  +  ; %%--%%CTF : Use CTF: Do a full CTF correction during the alignment. (default False) 
-  ; nxinit : Initial image size for sorting: (default 64) +  ; %%--%%sym : Point-group symmetry: Point-group symmetry of the target structure. (default c1) 
-  ; smallest_group : Smallest group size: Minimum members for identified group. (default 500)  +  ; %%--%%number_of_images_per_group : Images per group: Critical value defined by user. It suggests program the number of groups. (default 1000) 
-  ; chunk0 : Chunk file name for 1st subset: Name of chunk file containing particle IDs of 1st subset (chunk0) for computing margin of error. (default none)  +  ; %%--%%nxinit : Initial image size for sorting: Initial image size for sorting. (default 64) 
-  ; chunk1 : Chunk file name for 2nd subset: Name of chunk file containing particle IDs of 2nd subset (chunk0) for computing margin of error. (default none) +  ; %%--%%smallest_group : Smallest group size: Minimum members for identified group. (default 500)  
 +  ; %%--%%chunk0 : Chunk file name for 1st halfset: Name of chunk file containing particle IDs of 1st halfset (chunk0) for computing margin of error. (default none) 
 +  ; %%--%%chunk1 : Chunk file name for 2nd halfset: Name of chunk file containing particle IDs of 2nd halfset (chunk1) for computing margin of error. (default none)
  
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 === Advanced Parameters === === Advanced Parameters ===
-  ; ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) +  ; %%--%%ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1) 
-  ; maxit : Maximum iterations: (default 25) +  ; %%--%%maxit : Maximum iterations: Maximum number of iteration. (default 25) 
-  ; rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1) +  ; %%--%%rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1) 
-  ; xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default 1) +  ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction will take place in -xr to +xr range. (default '1') 
-  ; yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be set as xr. (default -1) +  ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction will take place in -yr to +yr range.. If omitted, it will be set as xr. (default '-1') 
-  ; ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default 0.25) +  ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '0.25') 
-  ; an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1') +  ; %%--%%an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1') 
-  ; center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) +  ; %%--%%center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0) 
-  ; nassign : Number of reassignment iterations: Performed for each angular step. (default 1) +  ; %%--%%nassign : Number of reassignment iterations: Performed for each angular step. (default 1) 
-  ; nrefine : Number of alignment iterations: Performed for each angular step. (default 0) +  ; %%--%%nrefine : Number of alignment iterations: Performed for each angular step. (default 0) 
-  ; stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run.  (default 3.0)  +  ; %%--%%stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run.  (default 3.0) 
-  ; function : Reference preparation function: Function used to prepare the reference volume. (default do_volume_mrk02)  +  ; %%--%%function : Reference preparation function: Specify name of function used to prepare the reference volume. (default do_volume_mrk05) 
-  ; independent : Number of independent runs: Number of independent equal-Kmeans(default 3)  +  ; %%--%%independent : Number of independent runs: Number of independent equal-Kmeans. (default 3) 
-  ; low_pass_filter : Low-pass filter frequency [1/Pixel]: Low-pass filter used for the 3D sorting on the original image size. (default -1.0) +  ; %%--%%low_pass_filter : Low-pass filter frequency [1/Pixels]: Low-pass filter used for the 3D sorting on the original image size. Specify with absolute frequency. (default -1.0) 
-  ; unaccounted : Reconstruct unaccounted images: (default False)  +  ; %%--%%unaccounted : Reconstruct unaccounted images: Reconstruct unaccounted images. (default False) 
-  ; seed : Seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1)  +  ; %%--%%seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1) 
-  ; sausage : Use sausage filter: (default False)  +  ; %%--%%sausage : Use sausage filter: A way of filtering volume. (default False) 
-  ; PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum. (default none)  +  ; %%--%%PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum used for EM density map power spectrum correction. Typically, compute 1D power spectrum from PDB file. (default none) 
-  ; protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default 'g') +  ; %%--%%protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default 'g') 
-  ; upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume's power spectrum completely to the reference, while a value of 0 means no modification. (default 0.5)  +  ; %%--%%upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume's power spectrum completely to the reference, while a value of 0 means no modification. (default 0.5) 
-  ; wn : Target image size [Pixels]: If different than 0, then the images will be rescaled to fit this size. (default 0)  +  ; %%--%%wn : Target image size [Pixels]: Specify optimal window size for data processing. If different than 0, then the images will be rescaled to fit this size. (default 0) 
-  ; interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default '4nn')+  ; %%--%%interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default '4nn')
  
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 ===== Output ===== ===== Output =====
-  ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string) 
  
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 ===== Description ===== ===== Description =====
- +The clustering algorithm in the program combines a couple of computational techniques, equal-Kmeans clustering, K-means clustering, and reproducibility of clustering such that it not only has a strong ability but also a high efficiency to sort out heterogeneity of cryo-EM images. The command sxsort3d.py is the protocol I (P1). In this protocol, the user defines the group size and thus defines the number of group K. Then the total data is randomly assigned into K group and an equal-size K-means (size restricted K-means) is carried out. N independent equal-Kmeans runs would give N partition of the K groups assignment. Then, two-way comparison of these partitions gives the reproducible number of particles.
-The clustering algorithm in the program combines a couple of computational techniques, equal-Kmeans clustering, K-means clustering, and reproducibility of clustering such that it not only has a strong ability but also a high efficiency to sort out heterogeneity of cryo-EM images. The command sxsort3d.py is the protocol I {P1). In this protocol, the user defines the group size and thus defines the number of group K. Then the total data is randomly assigned into K group and an equal-size K-means (size restricted K-means) is carried out. N independent equal-Kmeans runs would give N partition of the K groups assignment. Then two-way comparison of these partitions gives the reproducible number of particles.+
  
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 ==== Reference ==== ==== Reference ====
-Described by A.Einstein in his first paper on spectrum of radiation +Described by A.Einstein in his first paper on spectrum of radiation from a house heater kept at room temperature. Journal of Irreproducible Results, 12, 1905, 12-1127. 
-from a house heater kept at room temperature. Journal of Irreproducible + 
-Results, 12, 1905, 12-1127.+\\ 
 +==== Developer Notes ====
  
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 ==== Author / Maintainer ==== ==== Author / Maintainer ====
 Zhong Huang Zhong Huang
 +
  
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 ==== Files ==== ==== Files ====
-applications.py+sparx/bin/sxsort3d.py
  
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 ==== See also ==== ==== See also ====
-[[sxrsort3d|sxrsort3d.py]]+[[pipeline:meridien:sxmeridien|sxmeridien]], [[pipeline:utilities:sxheader|sxheader]], [[[pipeline:sort3d:sx3dvariability|sx3dvariability]], [[pipeline:sort3d:sxrsort3d|sxrsort3d]], and [[pipeline:sort3d:sxsort3d_depth|sxsort3d_depth]].
  
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 ==== Maturity ==== ==== Maturity ====
-stable while under development:: Two programs (P1,P2) have been tested on both simulated and experimental ribosome data. For experimental ribosome data, P2 has a reproducible ratio-70-90%. P2 can 100%separate two conformations from the simulated ribosome data that contains 5 conformations. +Alpha:: Under development. Two programs (P1,P2) have been tested on both simulated and experimental ribosome data. For experimental ribosome data, P2 has a reproducible ratio-70-90%. P2 can 100%separate two conformations from the simulated ribosome data that contains 5 conformations. 
  
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-==== Known Bugs ==== +==== Bugs ==== 
-None.+There are no known bugs so far.
  
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pipeline/sort3d/sxsort3d.txt · Last modified: 2019/04/02 10:49 by lusnig

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