This shows you the differences between two versions of the page.
Both sides previous revision Previous revision | Next revision Both sides next revision | ||
pipeline:sort3d:sxsort3d_depth [2018/06/20 13:12] 127.0.0.1 external edit |
pipeline:sort3d:sxsort3d_depth [2018/08/22 11:58] fmerino |
||
---|---|---|---|
Line 2: | Line 2: | ||
===== sxsort3d_depth ===== | ===== sxsort3d_depth ===== | ||
- | 3D Clustering - SORT3D_DEPTH: | + | 3D Clustering - SORT3D_DEPTH: |
\\ | \\ | ||
Line 18: | Line 18: | ||
There are two ways of running this command. | There are two ways of running this command. | ||
- | \\ __1. 3D sorting from meridien iteration__: | + | \\ __1. 3D sorting from meridien iteration__: |
mpirun -np 48 sxsort3d_depth.py --refinement_dir=' | mpirun -np 48 sxsort3d_depth.py --refinement_dir=' | ||
- | \\ __2. 3D sorting from stack__: | + | \\ __2. 3D sorting from stack__: |
mpirun -np 48 sxsort3d_depth.py --instack=' | mpirun -np 48 sxsort3d_depth.py --instack=' | ||
Line 27: | Line 27: | ||
===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; %%--%%refinement_dir : Meridien | + | ; %%--%%refinement_dir : Meridien |
- | ; %%--%%instack : Input images stack: | + | ; %%--%%instack : Input images stack: |
- | ; %%--%%output_dir : Output directory: | + | ; %%--%%output_dir : Output directory: |
- | ; %%--%%niter_for_sorting : 3D refinement iteration ID: Specify the iteration | + | ; %%--%%niter_for_sorting : Iteration |
- | ; %%--%%nxinit : Initial image size: Image size used for MGSKmeans in case of starting sorting from a data stack. By default, the program determines window size. Specific to stack mode. (default -1) | + | ; %%--%%nxinit : Initial image size: Image size used for MGSKmeans in case of starting sorting from a data stack. By default, the program determines window size. Option is valid only for stack mode. (default -1) |
- | ; %%--%%mask3D : 3D mask: File path of the global 3D mask for clustering. (default none) | + | ; %%--%%mask3D : 3D mask: A string denotes file path of the global 3D mask for clustering. Imported from 3D refinement unless user wishes a different one in meridien iteration mode. (default none) |
- | ; %%--%%focus : Focus 3D mask: File path of a binary 3D mask for focused clustering. (default none) | + | ; %%--%%focus : Focus 3D mask: A string denotes file path of a binary 3D mask for focused clustering. (default none) |
- | ; %%--%%radius : Estimated particle radius [Pixels]: | + | ; %%--%%radius : Estimated particle radius [Pixels]: |
- | ; %%--%%sym : Point-group symmetry: | + | ; %%--%%sym : Point-group symmetry: |
- | ; %%--%%img_per_grp : Number of images per group: User expected group size. This value is critical for a successful 3D clustering. (default 1000) | + | ; %%--%%img_per_grp : Number of images per group: User expected group size in integer. (default 1000) |
- | ; %%--%%img_per_grp_split_rate : Group splitting rate: Rate for splitting | + | ; %%--%%img_per_grp_split_rate : Group splitting rate: An integer value denotes split rate of the group size(%%--%%img_per_grp). (default 1) |
- | ; %%--%%minimum_grp_size : Minimum size of reproducible class: | + | ; %%--%%minimum_grp_size : Minimum size of reproducible class: |
- | ; %%--%%do_swap_au : Swap flag: Randomly swap a certain number of accounted elements per cluster with the unaccounted elements. If the processing with the default values are extremely slow or stalled, please use this --do_swap_au option and set --swap_ratio to a large value (15.0[%] is a good start point). (default False) | + | ; %%--%%do_swap_au : Swap flag: A boolean flag to control random swapping |
- | ; %%--%%swap_ratio : Swap percentage [%]: Specify a swap percentage between 0.0[%] and 50.0[%]. | + | ; %%--%%swap_ratio : Swap percentage [%]: the percentage |
; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). It will be used to evaluate the number of CPUs per node from user-provided MPI setting. By default, it uses 2GB * (number of CPUs per node). (default -1.0) | ; %%--%%memory_per_node : Memory per node [GB]: User provided information about memory per node in GB (NOT per CPU). It will be used to evaluate the number of CPUs per node from user-provided MPI setting. By default, it uses 2GB * (number of CPUs per node). (default -1.0) | ||
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%depth_order : Depth order: | + | ; %%--%%depth_order : Depth order: |
- | ; %%--%%stop_mgskmeans_percentage : Stop MGSKmeans | + | ; %%--%%stop_mgskmeans_percentage : Image assignment |
; %%--%%nsmear : Number of smears for sorting: Fill it with 1 if user does not want to use all smears. (default -1) | ; %%--%%nsmear : Number of smears for sorting: Fill it with 1 if user does not want to use all smears. (default -1) | ||
- | ; %%--%%orientation_groups : Number of orientation groups: Number of orientation groups in the asymmetric unit. (default 100) | + | ; %%--%%orientation_groups : Number of orientation groups: Number of orientation groups in an asymmetric unit. (default 100) |
; %%--%%not_include_unaccounted : Do unaccounted reconstruction: | ; %%--%%not_include_unaccounted : Do unaccounted reconstruction: | ||
; %%--%%notapplybckgnoise : Use background noise flag: Flag to turn off background noise. (default False question reversed in GUI) | ; %%--%%notapplybckgnoise : Use background noise flag: Flag to turn off background noise. (default False question reversed in GUI) | ||
- | ; %%--%%random_group_elimination_threshold : Random group elimination threshold: | + | ; %%--%%random_group_elimination_threshold : Random group elimination threshold: |
\\ | \\ | ||
Line 63: | Line 63: | ||
\\ | \\ | ||
===== Description ===== | ===== Description ===== | ||
- | sxsort3d_depth finds out stable members by carrying out two-way comparison of two independent Kmeans clustering | + | sxsort3d_depth |
\\ | \\ | ||
Line 70: | Line 70: | ||
|| %%--%%depth_order || The parameter resembles the previous option number of independent runs but it controls sorting in an different way. The default value of 2 is a good choice. || | || %%--%%depth_order || The parameter resembles the previous option number of independent runs but it controls sorting in an different way. The default value of 2 is a good choice. || | ||
|| %%--%%minimum_grp_size || This parameter selects qualified clusters and controls Kmeans clustering stability. The suggested value would be between img_per_grp/ | || %%--%%minimum_grp_size || This parameter selects qualified clusters and controls Kmeans clustering stability. The suggested value would be between img_per_grp/ | ||
- | || %%--%%stop_mgskmeans_percentage || Even though this option is not new, here the suggestion would be not to set it too small. 5.0 - 10.0 is a good choice. || | + | || %%--%%stop_mgskmeans_percentage || The suggestion would be not to set it too small. 5.0 - 10.0 is a good choice. || |
|| %%--%%orientation_groups || It divides the asymmetric unit into the specified number of orientation groups and cast the data orientation parameters into them. It is meant to prevent sorting by angle, i.e., assign certain angle to one group, for example top views to one group and side views to another. || | || %%--%%orientation_groups || It divides the asymmetric unit into the specified number of orientation groups and cast the data orientation parameters into them. It is meant to prevent sorting by angle, i.e., assign certain angle to one group, for example top views to one group and side views to another. || | ||
|| %%--%%swap_ratio || A ratio of randomly replaced particles in a group, it is meant to prevent premature convergence. When the program obtains both stable groups and unaccounted elements, it reassigns unaccounted elements back to stable groups, and continues sorting. Before re-assignment of unaccounted elements, the program swaps some elements of stable groups with unaccounted ones using this specified swap_ratio. || | || %%--%%swap_ratio || A ratio of randomly replaced particles in a group, it is meant to prevent premature convergence. When the program obtains both stable groups and unaccounted elements, it reassigns unaccounted elements back to stable groups, and continues sorting. Before re-assignment of unaccounted elements, the program swaps some elements of stable groups with unaccounted ones using this specified swap_ratio. || | ||
Line 142: | Line 142: | ||
\\ | \\ | ||
- |