~~NOTOC~~ ===== sxrsort3d ===== 3D 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. \\