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--- pipeline:meridien:sxmeridien [2019/04/02 09:43]
lusnig
+++ pipeline:meridien:sxmeridien [2021/02/01 15:16] (current)
shaikh
@@ Line 9: / Line 9: @@
 Usage in command line
-  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
+  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 --voldir=reconstruction_directory
@@ Line 48: / Line 48: @@
   ; %%--%%do_final : Do only final reconstruction: Specify the iteration which to perform final reconstruction. By setting to 0, program searches for the iteration that had best resolution, then performs correponding final reconstruction. Value must be zero or positive. (default -1)
+  ; %%--%%voldir : Output reconstruction directory: Directory in which the output reconstructions will be written. (default None)
   ; %%--%%local_refinement : Perform local refinement: Perform local refinement starting from user-provided orientation parameters stored in the header of input image stack. (default False)

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