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pipeline:meridien:sxmeridien [2018/08/22 11:02]
fmerino
pipeline:meridien:sxmeridien [2019/04/02 09:43] (current)
lusnig
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 ~~NOTOC~~ ~~NOTOC~~
  
-===== sxmeridien ​=====+===== sp_meridien ​=====
 3D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach. 3D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach.
  
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 Usage in command line Usage in command line
  
-  ​sxmeridien.py  stack  output_directory ​ initial_volume ​ --do_final=MERIDIEN_ITERATION_ID ​ --local_refinement ​ --radius=particle_radius ​ --mask3D=MASK3D ​ --symmetry=SYMMETRY ​ --inires=INITIAL_RESOLUTION ​ --delta=DELTA ​ --xr=XR ​ --ts=TS ​ --initialshifts ​ --skip_prealignment ​ --memory_per_node=MEMORY_PER_NODE ​ --center_method=CENTER_METHOD ​ --target_radius=TARGET_RADIUS ​ --an=ANGULAR_NEIGHBORHOOD ​ --shake=SHAKE ​ --small_memory ​ --ccfpercentage=CCFPERCENTAGE ​ --nonorm ​ --function=USER_FUNCTION+  ​sp_meridien.py  stack  output_directory ​ initial_volume ​ --do_final=MERIDIEN_ITERATION_ID ​ --local_refinement ​ --radius=particle_radius ​ --mask3D=MASK3D ​ --symmetry=SYMMETRY ​ --inires=INITIAL_RESOLUTION ​ --delta=DELTA ​ --xr=XR ​ --ts=TS ​ --initialshifts ​ --skip_prealignment ​ --memory_per_node=MEMORY_PER_NODE ​ --center_method=CENTER_METHOD ​ --target_radius=TARGET_RADIUS ​ --an=ANGULAR_NEIGHBORHOOD ​ --shake=SHAKE ​ --small_memory ​ --ccfpercentage=CCFPERCENTAGE ​ --nonorm ​ --function=USER_FUNCTION ​--function_ai=USER_FUNCTION_AI --group_by=GROUP_BY --theta_min=THETA_MIN --theta_max=THETA_MAX --even_angle_method=EVEN_ANGLE_METHOD --group_id=GROUP_ID --filament_width=FILAMENT_WIDTH --helical_rise=HELICAL_RISE --a_criterion=A_CRITERION --limit_improvement=LIMIT_IMPROVEMENT --plot_ang_dist=PLOT_ANG_DIST --main000=MAIN000 
  
 \\ \\
 ===== Typical usage ===== ===== Typical usage =====
  
-sxmeridien ​exists only in MPI version (Running MPI version does not require --MPI flag).+sp_meridien ​exists only in MPI version (Running MPI version does not require --MPI flag).
  
 There are five ways to run the program: There are five ways to run the program:
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 \\ __1. Standard default run:__ \\ __1. Standard default run:__
 \\ The standard refinement starts from exhaustive searches, uses initial reference structure \\ The standard refinement starts from exhaustive searches, uses initial reference structure
-  mpirun -np 64 --hostfile four_nodes.txt  ​sxmeridien.py  bdb:​sparx_stack vton1 mask15.hdf --sym=c5 ​ --initialshifts ​ --radius=120 ​ --mask3D=mask15.hdf ​   >1ovotn &+  mpirun -np 64 --hostfile four_nodes.txt  ​sp_meridien.py  bdb:​sparx_stack vton1 mask15.hdf --sym=c5 ​ --initialshifts ​ --radius=120 ​ --mask3D=mask15.hdf ​   >1ovotn &
  
 \\ __2. Restart after the last fully finished iteration:​__ \\ __2. Restart after the last fully finished iteration:​__
 One can change some parameters (MPI settings have to be the same) One can change some parameters (MPI settings have to be the same)
-  mpirun -np 64 --hostfile four_nodes.txt  ​sxmeridien.py  vton1 --radius=100 >2ovotn &+  mpirun -np 64 --hostfile four_nodes.txt  ​sp_meridien.py  vton1 --radius=100 >2ovotn &
  
 \\ __3. Local refinement:​__ \\ __3. Local refinement:​__
 \\  Local refinement starts from user-provided orientation parameters, delta has to be <= 3.75 \\  Local refinement starts from user-provided orientation parameters, delta has to be <= 3.75
-  mpirun -np 64 --hostfile four_nodes.txt ​sxmeridien.py --local_refinement bdb:​sparx_stack ​  vton3 --delta=1.875 --xr=2.0 ​ --inires=5.5 ​ --sym=c5 ​ --radius=120 ​ --mask3D=mask15.hdf >5ovotn &+  mpirun -np 64 --hostfile four_nodes.txt ​sp_meridien.py --local_refinement bdb:​sparx_stack ​  vton3 --delta=1.875 --xr=2.0 ​ --inires=5.5 ​ --sym=c5 ​ --radius=120 ​ --mask3D=mask15.hdf >5ovotn &
  
 \\ __4. Restart of local refinement after the last fully finished iteration.:​__ \\ __4. Restart of local refinement after the last fully finished iteration.:​__
 \\  One can change some parameters (MPI settings have to be the same) \\  One can change some parameters (MPI settings have to be the same)
-  mpirun -np 64 --hostfile four_nodes.txt  ​sxmeridien.py --local_refinement ​ vton3  --xr=0.6 >6ovotn &+  mpirun -np 64 --hostfile four_nodes.txt  ​sp_meridien.py --local_refinement ​ vton3  --xr=0.6 >6ovotn &
  
 \\ __5. Final reconstruction only:__ \\ __5. Final reconstruction only:__
 \\ Do only final reconstruction using a fully finished iteration of meridien (here number 21). \\ Do only final reconstruction using a fully finished iteration of meridien (here number 21).
-  mpirun -np 64 sxmeridien.py --do_final=21 ​ meridien_outdir+  mpirun -np 64 sp_meridien.py --do_final=21 ​ meridien_outdir
  
  
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   ; %%--%%inires : Starting resolution [A]: Resolution of the initial map used to start the refinement. Ignored in final reconstruction. (default 25.0)   ; %%--%%inires : Starting resolution [A]: Resolution of the initial map used to start the refinement. Ignored in final reconstruction. (default 25.0)
   ; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction. (default 7.5)   ; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction. (default 7.5)
-  ; %%--%%xr : Search range [Pixels]: Range for translation search in both directions. Search is +/-xr. It can be fractional. Ignored in final reconstruction. (default 5.0)  
-  ; %%--%%ts : Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. (default 1.0) 
   ; %%--%%initialshifts : Read shifts from header: Start refinement using translation parameters located in the input file header to jumpstart the procedure. Specific to standard run mode. (default False value reversed in GUI)   ; %%--%%initialshifts : Read shifts from header: Start refinement using translation parameters located in the input file header to jumpstart the procedure. Specific to standard run mode. (default False value reversed in GUI)
-  ; %%--%%skip_prealignment : Skip the 2D pre-alignment step: Indicate if pre-alignment should be omitted. ​ By default it is performed in order to find initial translation parameters. This accelerates convergence of the program. Do not use 2D pre-alignment if images are already centered. Specific to standard run modes. (default False question reversed in GUI)+  ; %%--%%skip_prealignment : Skip the 2D pre-alignment step: Indicate if pre-alignment should be omitted. ​ By default it is performed in order to find initial translation parameters. This accelerates convergence of the program. Do not use 2D pre-alignment if images are already centered. Specific to standard run modes. (default False) ​: %%--%%initialshifts==False
   ; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). By default, it uses 2GB * (number of CPUs per node). Used in all modes. (default -1.0)   ; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). By default, it uses 2GB * (number of CPUs per node). Used in all modes. (default -1.0)
  
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
 +  ; %%--%%xr : Search range [Pixels]: Range for translation search in both directions. Search is +/-xr. It can be fractional. Ignored in final reconstruction. (default 5.0) 
 +  ; %%--%%ts : Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. (default 1.0)
 +  ; %%--%%ts : Search step size [Pixels]: Step size of translation search in both directions. Search is within a circle of radius xr on a grid with steps ts. It can be fractional. (default 1.0)
   ; %%--%%an : Angular neighborhood:​ Angular neighborhood for local search. Used only in Local Refinement mode. Ignored in final reconstruction. (default -1.0)   ; %%--%%an : Angular neighborhood:​ Angular neighborhood for local search. Used only in Local Refinement mode. Ignored in final reconstruction. (default -1.0)
   ; %%--%%center_method : Centering method: Method for centering averages during initial 2D prealignment of data (0: no centering; -1: average shift method; For 1-7, see center_2D in utilities.py). Specific to standard run modes. (default -1)   ; %%--%%center_method : Centering method: Method for centering averages during initial 2D prealignment of data (0: no centering; -1: average shift method; For 1-7, see center_2D in utilities.py). Specific to standard run modes. (default -1)
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   ; %%--%%nonorm : Apply image norm correction: Indicate if image norm correction should be applied or not. By default, apply image norm correction. Ignored in final reconstruction. (default False question reversed in GUI)   ; %%--%%nonorm : Apply image norm correction: Indicate if image norm correction should be applied or not. By default, apply image norm correction. Ignored in final reconstruction. (default False question reversed in GUI)
   ; %%--%%function : Reference preparation function: Specify name of function that program should use to prepare the reference structure after each iteration. Ignored in final reconstruction. (default do_volume_mask)   ; %%--%%function : Reference preparation function: Specify name of function that program should use to prepare the reference structure after each iteration. Ignored in final reconstruction. (default do_volume_mask)
 +  ; %%--%%function_ai : Logic function: Specify name of function that the program should use to follow the specified logic. (default ai_spa)
 +  ; %%--%%group_by : Group name for chunks:​Group the particles by the specified header name before splitting them into chunks. (default ptcl_source_image)
 +  ; %%--%%theta_min : Theta min [degree]: ​ Minimum out-of-plane rotation value to use for the reference projection angles. Default is the full range from 0 to 180.(default -1)
 +  ; %%--%%theta_max : Theta max [degree]: ​ Maximum out-of-plane rotation value to use for the reference projection angles. Default is the full range from 0 to 180.(default -1)
 +  ; %%--%%even_angle_method : Even anle method: Method to use for even angle creation (S, M, P). (default S)
 +  ; %%--%%group_id : Outlier group ID: Group the particles by the header name for the outlier detection. By default do not do outlier detection. (default None)
 +  ; %%--%%filament_width : Filament width [px]: This is used to normalize the particles in case of filaments. A rectangular mask will be used instead of a circular one. (default None)
 +  ; %%--%%helical_rise : Helical rise [A]: Helical rise used to limit the shift along the helical axis to +-rise/2 (default None)
 +  ; %%--%%a_criterion : Convergence criterion A value: Convergence criterion multiplication for the criterion A. (default 0.75)
 +  ; %%--%%limit_improvement : Limit of improvements:​ Specify the number of iterations in a row without changes that will be considered convergence. (default 1)
 +  ; %%--%%plot_ang_dist : Plot angular distribution:​ Plot the angular distribution in every iteration. This will take some time for high symmetries.(default False)
 +  ; %%--%%main000 : Main000 folder: Main000 folder of a previous refinement to presever chunk and group information. By default it will assign new chunks and groups. (default none)
  
 \\ \\
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 \\ \\
 ==== Author / Maintainer ==== ==== Author / Maintainer ====
 +Markus Stabrin
 Pawel A. Penczek Pawel A. Penczek
  
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 \\ \\
 ==== Files ==== ==== Files ====
-sparx/bin/sxmeridien.py+sparx/bin/sp_meridien.py
  
 \\ \\
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 \\ \\
 +