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pipeline:viper:sxviper [2018/06/20 13:12]
127.0.0.1 external edit 		pipeline:viper:sxviper [2019/04/02 10:52]
lusnig [See also]
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxviper ===== +===== sp_viper ===== 
-Initial 3D Model - VIPER: //ab initio// 3D structure determination using Validation of Individual Parameter Reproducibility (VIPER). Designed to determine a validated initial model using a small set of class averages produced by [[pipeline:isac:sxisac2|ISAC2]].+Initial 3D Model - VIPER: //ab initio// 3D structure determination using Validation of Individual Parameter Reproducibility (VIPER). Determines a validated initial model using a small set of class averages produced by [[pipeline:isac:sxisac2|ISAC2]].
  
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 Usage in command line Usage in command line
  
-  sxviper.py stack  directory  --radius=outer_radius  --sym=sym  --ir=inner_radius  --rs=ring_step  --xr=x_range  --yr=y_range  --ts=translational_search_step  --delta=angular_step  --center=center_type  --maxit1=max_iter1  --maxit2=max_iter2  --mask3D=mask3D  --moon_elimination=moon_elimination  --L2threshold=L2threshold  --ref_a=ref_a  --nruns=nruns  --doga=doga  --fl=fl  --aa=aa  --pwreference=pwreference  --debug+  sp_viper.py stack  directory  --radius=outer_radius  --sym=sym  --moon_elimination=moon_elimination  --ir=inner_radius  --rs=ring_step  --xr=x_range  --yr=y_range  --ts=translational_search_step  --delta=angular_step  --center=center_type  --maxit1=max_iter1  --maxit2=max_iter2  --mask3D=mask3D  --L2threshold=L2threshold  --ref_a=ref_a  --nruns=nruns  --doga=doga  --fl=fl  --aa=aa  --pwreference=pwreference  --debug
  
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 ===== Typical usage ===== ===== Typical usage =====
  
-sxrviper exists only in MPI version.+sp_rviper exists only in MPI version.
  
-  mpirun --npernode 16 -np 24 --host node1,node2 sxviper.py  stack output_directory --fl=0.25 --radius=30 --xr=2 --moon_elimination=750,4.84+  mpirun --npernode 16 -np 24 --host node1,node2 sp_viper.py  stack output_directory --fl=0.25 --radius=30 --xr=2 --moon_elimination=750,4.84
  
-A fast track option, that can be used to choose parameters in the appropriate ranges (for example, obtaining adequate spatial frequency filtering %%--%%fl) is provided below. Since it employs extreme values for some parameters this command can be used only for parameter tuning for the VIPER algorithm. +A faster version using restricted ranges of parameters.
  
-  mpirun --npernode 16 -np 16 --host node1 sxviper.py  stack output_directory --fl=0.25 --radius=30 --xr=1 --nruns=2   --L2threshold=1.0e300  --doga=-1+  mpirun --npernode 16 -np 16 --host node1 sp_viper.py  stack output_directory --fl=0.25 --radius=30 --xr=1 --nruns=2   --L2threshold=1.0e300  --doga=-1
  
-The VIPER program needs MPI environment to work properly. Number of used MPI processes **must be** a multiple of %%--%%nruns (default = 6). +The VIPER program exists only in MPI version.  Number of MPI processes **must be** a multiple of %%--%%nruns (default = 6). 
  
-Since VIPER makes use of group of processors working together, it is important from a time efficiency point of view to have processors within a group being allocated on the same node. This way any data exchange within the group does not use network traffic. The %%--%%npernode option of mpirun is useful in accomplishing this goal. As shown in the example below when %%--%%npernode is used  mpi allocates the ranks of the processors sequentially, not moving to the next node until the current one is filled.  If %%--%%npernode is not used then processors are allocated in a round robin fashion (i.e. jumping to the next node with each allocation). Since in VIPER, groups contain consecutively ranked processors, it is important to provide "%%--%%npernode XX", where XX is the number of processors per node.+Since VIPER uses group of processors working together, it is important for efficient execution to have processors within a group allocated to the same node. This way any data exchange within the group does not involve network traffic. The %%--%%npernode option of mpirun accomplishes this goal. As shown in the example below when %%--%%npernode is used  MPI allocates the ranks of the processors sequentially, not moving to the next node until the current one is filled.  If %%--%%npernode is not used then processors are allocated in a round robin fashion (i.e. jumping to the next node with each allocation). Since in VIPER, groups contain consecutively ranked processors, it is important to provide "%%--%%npernode XX", where XX is the number of processors per node.
  
 {{viper:npernode_rank.png?600}} {{viper:npernode_rank.png?600}}
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 ===== Input ===== ===== Input =====
 +
 === Main Parameters === === Main Parameters ===
-  ; stack : Input images stack: A small set of class averages produced by ISAC2. (default required string) +  ; stack : Input images stack: A small subset of class averages produced by ISAC2. (default required string) 
-  ; directory : Output directory: The directory will be automatically created and the results will be written here. If the directory already exists, results will be written there, possibly overwriting previous runs. (default required string)+  ; directory : Output directory: The automatically-created output directory will contain results. If the directory already exists, results will be written there, possibly overwriting previous runs. (default required string)
  
-  ; %%--%%radius : Target particle radius [Pixels]: Use the same value as in ISAC2. It has to be less than half the box size. (default 29) +  ; %%--%%radius : Particle radius [Pixels]: Use the same value as in ISAC2. It has to be less than half the box size. (default 29) 
-  ; %%--%%sym : Point-group symmetry: Point-group symmetry of the target particle. (default c1) +  ; %%--%%sym : Point-group symmetry: Point-group symmetry of the particle. (default c1) 
-  ; %%--%%moon_elimination : Eliminate disconnected regions: Used to removed disconnected pieces from the model. It requires as argument a comma separated string with the mass in KDa and the pixel size. (default none)+  ; %%--%%moon_elimination : Eliminate disconnected regions: Used to removed disconnected pieces from the model. As an argument it requires a comma-separated string with the mass in KDa and the pixel size in [A]. (default none)
  
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   ; %%--%%ir : Inner rotational search radius [Pixels]: Inner rotational search radius [Pixels]. (default 1)   ; %%--%%ir : Inner rotational search radius [Pixels]: Inner rotational search radius [Pixels]. (default 1)
   ; %%--%%rs : Ring step size [Pixels]: Step between rings used for the rotational search. (default 1)   ; %%--%%rs : Ring step size [Pixels]: Step between rings used for the rotational search. (default 1)
-  ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default '0')+  ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction. Search will +/-xr range in steps of ts. (default '0')
   ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be xr. (default '0')   ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be xr. (default '0')
   ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '1.0')   ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '1.0')
   ; %%--%%delta :  Projection angular step [Degrees]: Projection angular step. (default '2.0')   ; %%--%%delta :  Projection angular step [Degrees]: Projection angular step. (default '2.0')
-  ; %%--%%center : Center 3D template: 0: no centering; 1: center of gravity (default -1.0) +  ; %%--%%center : Center 3D template: -1: center of coordinates, 0: no centering; 1: center of gravity (default -1.0) 
-  ; %%--%%maxit1 : Maximum iterations - GA step: Maximum iterations for GA step. (default 400) +  ; %%--%%maxit1 : Maximum iterations - GA step: Maximum number of iterations for GA step. (default 400) 
-  ; %%--%%maxit2 : Maximum iterations - Finish step: Maximum iterations for Finish step. (default 50)+  ; %%--%%maxit2 : Maximum iterations - Finish step: Maximum iterations number of for Finish step. (default 50)
   ; %%--%%mask3D : 3D mask: Path to 3D mask file. (default sphere)   ; %%--%%mask3D : 3D mask: Path to 3D mask file. (default sphere)
-  ; %%--%%L2threshold : GA stop threshold: Defines the maximum relative dispersion of volumes' L2 norms. (default 0.03)+  ; %%--%%L2threshold : GA stop threshold: Defines the maximum relative dispersion of structures' L2 norms. (default 0.03)
   ; %%--%%ref_a : Projection generation method: Method for generating the quasi-uniformly distributed projection directions. S - Saff algorithm, or P - Penczek 1994 algorithm. (default S)   ; %%--%%ref_a : Projection generation method: Method for generating the quasi-uniformly distributed projection directions. S - Saff algorithm, or P - Penczek 1994 algorithm. (default S)
-  ; %%--%%nruns : GA population size: This defines the number of quasi-independent volumes generated. (default 6)+  ; %%--%%nruns : GA population size: This defines the number of quasi-independent structures generated. (default 6)
   ; %%--%%doga : Threshold to start GA: Do GA when the fraction of orientation that changes less than 1.0 degrees is at least this fraction. (default 0.1)   ; %%--%%doga : Threshold to start GA: Do GA when the fraction of orientation that changes less than 1.0 degrees is at least this fraction. (default 0.1)
   ; %%--%%fl : Low-pass filter frequency [1/Pixels]: Using a hyperbolic tangent low-pass filter. Specify with absolute frequency. (default 0.25)   ; %%--%%fl : Low-pass filter frequency [1/Pixels]: Using a hyperbolic tangent low-pass filter. Specify with absolute frequency. (default 0.25)
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 ===== Description ===== ===== Description =====
-  * This program uses a user-defined projection angle and translation shift to perform 3D reconstruction. The translation shifts, and step are not limited to integer number. For a given delta, the program will perform maxit round refinement. So the final refinement iteration is maxit*(number of delta values). +  * This program uses a Genetic Algorithm (GA) strategy to deliver a validated 3D ab initio structure.  It will first compute simultaneously ab initio structures 
-  * For the program to work, attributes xform.projection (Transform object containing three Euler angles and two in-plane shifts) have to be set in the header of each file.  If their values are not known, all should be set to zero. +  * whose number will be equal to the population size.  Next, it will compare solutions and apply evolutionary operators (merge some of the solutions) 
-  * The program will start alignment from the current alignment parameters xform.projection stored in file headers.  +  * to produce their offsprings, which subsequently are used as initial structures for the next generation of GA processing. 
-  * The program only change the alignment parameters in their header. The images in stack keep untouched. (Neither rotated nor shifted.)+  * By default, structures in the first generation are initialized randomly. 
 +  * However, the program will start alignment from the alignment parameters xform.projection stored in file headers, if provided.  
 +  * The program only change the alignment parameters in header. The images in stack are untouched. (Neither rotated nor shifted.)
  
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 ==== Files ==== ==== Files ====
-sparx/bin/sxviper.py+sparx/bin/sp_viper.py
  
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 ==== See also ==== ==== See also ====
-[[pipeline:isac:sxisac2|sxisac2]] and [[pipeline:viper:sxrviper|sxrviper]]+[[pipeline:isac:sxisac2|sp_isac2]] and [[pipeline:viper:sxrviper|sp_rviper]]
  
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pipeline/viper/sxviper.txt · Last modified: 2019/04/02 10:52 by lusnig

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