Differences

This shows you the differences between two versions of the page.

--- pipeline:meridien:sxmeridien [2018/02/16 10:11]
127.0.0.1 external edit
+++ pipeline:meridien:sxmeridien [2018/02/20 13:19]
moriya
@@ 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  --initialshifts  --skip_prealignment  --memory_per_node=MEMORY_PER_NODE  --xr=XR  --ts=TS  --center_method=CENTER_METHOD  --target_radius=TARGET_RADIUS  --an=ANGULAR_NEIGHBORHOOD  --shake=SHAKE  --small_memory  --ccfpercentage=CCFPERCENTAGE  --nonorm  --function=USER_FUNCTION
+  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
 \\
@@ Line 18: / Line 18: @@
 There are five ways to run the program:
-\\ __1. Standard fresh run__: The 3D refinement starts from exhaustive searches using initial reference volume.
+\\ __1. Standard fresh run:__
+\\ The 3D refinement starts from exhaustive searches using initial reference volume.
   mpirun -np 64 sxmeridien.py bdb:sparx_stack meridien_fresh_outdir ref3d.hdf --sym=c5  --initialshifts  --radius=120  --mask3D=mask3d.hdf
-\\ __2. Standard continuation run__: Simple restart where the 3D refinement restarts after the last fully finished iteration of meridien fresh run or local refinement run. One can change some parameters, but that MPI settings have to be the same.
+\\ __2. Standard continuation run:__
+\\ Simple restart where the 3D refinement restarts after the last fully finished iteration of meridien fresh run or local refinement run. One can change some parameters, but that MPI settings have to be the same.
   mpirun -np 64 sxmeridien.py meridien_fresh_outdir --radius=100
-\\ __3. Local refinement from stack__: The restricted search of 3D refinement starts from user-provided orientation parameters stored in stack header. Note that delta has to be %%<=%% 3.75.
+\\ __3. Local refinement from stack:__
+\\ The restricted search of 3D refinement starts from user-provided orientation parameters stored in stack header. Note that delta has to be %%<=%% 3.75.
   mpirun -np 64 sxmeridien.py --local_refinement bdb:sparx_stack meridien_local_outdir --delta=1.875 --xr=2.0  --inires=5.5  --sym=c5  --radius=120  --mask3D=mask3d.hdf
-\\ __4. Local refinement from meridien iteration__: The restricted search of 3D refinement restarts after the last fully finished iteration of meridien fresh run or local refinement run. One can change some parameters, but MPI settings have to be the same.
+\\ __4. Local refinement from meridien iteration:__
+\\ The restricted search of 3D refinement restarts after the last fully finished iteration of meridien fresh run or local refinement run. One can change some parameters, but MPI settings have to be the same.
   mpirun -np 64 sxmeridien.py --local_refinement meridien_fresh_outdir  --xr=0.6
-\\ __5. Final reconstruction only__: Do only final reconstruction using a fully finished iteration of meridien fresh run or local refinement run.
+\\ __5. Final reconstruction only:__
+\\ Do only final reconstruction using a fully finished iteration of meridien fresh run or local refinement run.
   mpirun -np 64 sxmeridien.py --do_final=21 meridien_fresh_outdir
@@ Line 48: / Line 53: @@
   ; %%--%%inires : Starting resolution [A]: Resolution of the initial volume used to start the refinement. Ignored in final reconstruction only. (default 25.0)
   ; %%--%%delta : Initial angular sampling step [Degrees]: Initial angular sampling step. Ignored in final reconstruction only. (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 only. (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. Ignored in final reconstruction only. (default 1.0)
   ; %%--%%initialshifts : Read shifts from header: Start refinement using orientation parameters in the input file header to jumpstart the procedure. Specific to standard run mode. Specific to standard run modes. (default False value reversed in GUI)
   ; %%--%%skip_prealignment : Do 2D pre-alignment step: Indicate if pre-alignment should be used or not. Do not use 2D pre-alignment if images are already centered. By default, do 2D pre-alignment. Specific to standard run modes. (default False question reversed in GUI)
@@ Line 54: / Line 61: @@
 \\
 === Advanced Parameters ===
-  ; %%--%%xr : Search range [Pixels]: Range for translation search in both directions. Search is +/-+xr. It can be fractional. Ignored in final reconstruction only. (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. Ignored in final reconstruction only. (default 1.0)
   ; %%--%%an : Angular neighborhood: Angular neighborhood for local search. Ignored in final reconstruction only. (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 76: / Line 81: @@
 \\
 ==== Reference ====
+\\
+==== Developer Notes ====
 \\
@@ Line 102: / Line 110: @@
 \\

User Tools

Site Tools

Differences

Page Tools