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--- pipeline:meridien:sxmeridien [2018/08/22 11:02]
fmerino
+++ pipeline:meridien:sxmeridien [2019/04/02 09:43]
lusnig
@@ Line 1: / Line 1: @@
 ~~NOTOC~~
-===== sxmeridien =====
+===== sp_meridien =====
 D Refinement: Performs 3D structure refinement using a quasi-Maximum Likelihood approach.
@@ Line 9: / Line 9: @@
 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 =====
-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:
@@ Line 20: / Line 21: @@
 \\ __1. Standard default run:__
 \\ 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:__
 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:__
 \\  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.:__
 \\  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:__
 \\ 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
@@ Line 54: / Line 55: @@
   ; %%--%%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)
-  ; %%--%%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)
-  ; %%--%%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)
 \\
 === 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)
   ; %%--%%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)
@@ Line 70: / Line 72: @@
   ; %%--%%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_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)
 \\
@@ Line 88: / Line 102: @@
 \\
 ==== Author / Maintainer ====
+Markus Stabrin
 Pawel A. Penczek
@@ Line 96: / Line 111: @@
 \\
 ==== Files ====
-sparx/bin/sxmeridien.py
+sparx/bin/sp_meridien.py
 \\
@@ Line 111: / Line 126: @@
 \\

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