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--- pipeline:sort3d:sxrsort3d [2018/02/23 18:11]
moriya
+++ pipeline:sort3d:sxrsort3d [2018/06/20 13:12]
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-~~NOTOC~~
-===== sxrsort3d =====
-D Clustering - RSORT3D: Sort out 3D heterogeneity of 2D data whose 3D reconstruction parameters (xform.projection) have been determined already using 3D sorting.
-\\
-===== Usage =====
-Usage in command line
-  sxrsort3d.py  stack  outdir  mask  --previous_run1=sort3d_run1_directory  --previous_run2=sort3d_run2_directory  --focus=3D_focus_mask  --radius=outer_radius  --delta=angular_step  --CTF  --sym=symmetry  --number_of_images_per_group=images_per_group  --nxinit=nxinit  --smallest_group=smallest_group  --chunkdir=chunkdir  --ir=inner_radius  --maxit=max_iter  --rs=ring_step  --xr=xr  --yr=yr  --ts=ts  --an=angular_neighborhood  --center=centring_method  --nassign=nassign  --nrefine=nrefine  --stoprnct=stop_percent  --function=user_function  --independent=independent_runs  --low_pass_filter=low_pass_filter  --unaccounted  --seed=random_seed  --group_size_for_unaccounted=group_size_for_unaccounted  --sausage  --PWadjustment=PWadjustment  --protein_shape=protein_shape  --upscale=upscale  --wn=wn  --interpolation=method
-\\
-===== Typical usage =====
-sxrsort3d.py exists only in MPI version.
-  mpirun -np 192 sxrsort3d.py bdb:data rsort3d mask.hdf --previous_run1=sort3d1 --previous_run2=sort3d2 --radius=88 --maxit=25 --independent=3 --CTF --number_of_images_per_group=11000 --low_pass_filter=.20 --chunkdir=./ --sym=c4 --PWadjustment=pwrec.txt
-\\
-===== Input =====
-=== Main Parameters ===
-  ; stack : Input images stack: (default required string)
-  ; outdir : Output directory: There is a log.txt that describes the sequences of computations in the program. (default required string)
-  ; mask : 3D mask: (default none)
-  ; %%--%%previous_run1 : Directory of 1st sort3d run: (default required string)
-  ; %%--%%previous_run2 : Directory of 2nd sort3d run: (default required string)
-  ; %%--%%focus : Focus 3D mask: Mask used for focused clustering (default none)
-  ; %%--%%radius : Outer radius for rotational correlation [Pixels]: Must be smaller than half the box size. Please set to the radius of the particle. (default -1)
-  ; %%--%%delta : Angular step for projections: (default '2')
-  ; %%--%%CTF : Use CTF: Do a full CTF correction during the alignment. (default False)
-  ; %%--%%sym : Point-group symmetry: (default c1)
-  ; %%--%%number_of_images_per_group : Images per group: Critical number of images per group, defined by user. (default 1000)
-  ; %%--%%nxinit : Initial image size for sorting: (default 64)
-  ; %%--%%smallest_group : Smallest group size: Minimum members for identified group. (default 500)
-  ; %%--%%chunkdir : Directory containing chunk files: Typically, specify meridien output directory. A chunk file contains a list of particle IDs belonging to associated halfset. This information is used for computing margin of error. (default none)
-\\
-=== Advanced Parameters ===
-  ; %%--%%ir : Inner radius for rotational correlation [Pixels]: Must be bigger than 1. (default 1)
-  ; %%--%%maxit : Maximum iterations: (default 50)
-  ; %%--%%rs : Step between rings in rotational correlation: Must be bigger than 0. (default 1)
-  ; %%--%%xr : X search range [Pixels]: The translational search range in the x direction will take place in a +/xr range. (default '1')
-  ; %%--%%yr : Y search range [Pixels]: The translational search range in the y direction. If omitted it will be set as xr. (default '-1')
-  ; %%--%%ts : Translational search step [Pixels]: The search will be performed in -xr, -xr+ts, 0, xr-ts, xr, can be fractional. (default '0.25')
-  ; %%--%%an : Local angular search width [Degrees]: This defines the neighbourhood where the local angular search will be performed. (default '-1')
-  ; %%--%%center : Centering method: 0 - if you do not want the volume to be centered, 1 - center the volume using the center of gravity. (default 0)
-  ; %%--%%nassign : Number of reassignment iterations: Performed for each angular step. (default 1)
-  ; %%--%%nrefine : Number of alignment iterations: Performed for each angular step. (default 0)
-  ; %%--%%stoprnct : Assignment convergence threshold [%]: Used to asses convergence of the run. It is the minimum percentage of assignment change required to stop the run.  (default 3.0)
-  ; %%--%%function : Reference preparation function: Function used to prepare the reference volume. (default do_volume_mrk05)
-  ; %%--%%independent : Number of independent runs: Number of independent equal-Kmeans(default 3)
-  ; %%--%%low_pass_filter : Low-pass filter frequency [1/Pixel]: Low-pass filter used for the 3D sorting on the original image size. (default -1.0)
-  ; %%--%%unaccounted : Reconstruct unaccounted images: (default False)
-  ; %%--%%seed : Random seed: Seed used for the initial random assignment for EQ Kmeans. The program generates a random integer by default. (default -1)
-  ; %%--%%group_size_for_unaccounted : Unaccounted particles group size: (default 500)
-  ; %%--%%sausage : Use sausage filter: (default False)
-  ; %%--%%PWadjustment : Power spectrum reference: Text file containing a 1D reference power spectrum. (default none)
-  ; %%--%%protein_shape : Protein Shape: It defines protein preferred orientation angles. "g" is for globular proteins and "f" is for filament proteins. (default g)
-  ; %%--%%upscale : Power spectrum adjustment strength: This parameters adjusts how strongly the power spectrum of the volume should be modified to match the reference. A value of 1 brings the volume's power spectrum completely to the reference, while a value of 0 means no modification.  (default 0.5)
-  ; %%--%%wn : Target image size [Pixels]: If different than 0, then the images will be rescaled to fit this size. (default 0)
-  ; %%--%%interpolation : 3D interpolation method: Method interpolation in 3D. Options are tr1 or 4nn. (default 4nn)
-\\
-===== Output =====
-\\
-===== Description =====
-sxrsort3d.py finds out stable members by carrying out two-way comparison of two independent sxsort3d.py runs.
-For small tested datasets (real and simulated ribosome data around 10K particles), it gives 70%-90% reproducibility. However, this rate also depends on the choice of number of images per group and number of particles in the smallest group.
-\\
-=== Time and Memory ===
-On lonestar cluster of TACC, using 264 cpus, it takes about 2 hours and 23 minutes to accomplish 95953 128x128 images for one sxsort3d.py independent run, 2 hours 24 minutes to accomplish one independent sxrsort3d.py run with number_of_images_per_group set as 30000.
-\\
-==== Method ====
-K-means, equal K-means, reproducibility, two-way comparison.
-\\
-==== Reference ====
-Not published yet.
-\\
-==== Developer Notes ====
-\\
-==== Author / Maintainer ====
-Zhong Huang
-\\
-==== Keywords ====
-Category 1:: APPLICATIONS
-\\
-==== Files ====
-sparx/bin/sxrsort3d.py
-\\
-==== See also ====
-[[pipeline:meridien:sxmeridien|sxmeridien]], [[pipeline:utilities:sxheader|sxheader]], [[[pipeline:sort3d:sx3dvariability|sx3dvariability]], [[pipeline:sort3d:sxsort3d|sxsort3d]] and [[pipeline:sort3d:sxsort3d_depth|sxsort3d_depth]]
-\\
-==== Maturity ====
-Alpha:: Under development.
-\\
-==== Bugs ====
-There are no known bugs so far.
-\\

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