puller - Man Page

puller [@file ...] [-int <int>] [-enr <spec>] [-ens <spec>] [-enw <spec>] [-efs <bool>] [-nave <bool>] [-cbst <bool>] [-noadd] [-usa <bool>] [-pcet <bool>] [-nobin] [-lti <bool>] [-por <bool>] [-npcwza <bool>] [-ubfgl <bool>] [-ratb <bool>] [-svec <vec>] [-gssr <rad>] [-v <verbosity>] -vol <vol0 vol1 ...> -info <info0 info1 ...> [-k00 <kern00>] [-k11 <kern11>] [-k22 <kern22>] [-sscp <path>] [-kssb <kernel>] [-kssr <kernel>] [-nss <# scl smpls>] [-np <# points>] [-halton] [-ppv <# pnts/vox>] [-ppvzr <z range>] [-jit <jitter>] [-pi <npos>] [-step <step>] [-csm <step>] [-snap <# iters>] [-maxi <# iters>] [-stim <# iters>] [-maxci <# iters>] [-irad <scale>] [-srad <scale>] [-bws <bin width>] [-alpha <alpha>] [-beta <beta>] [-gamma <gamma>] [-theta <theta>] [-wall <k>] [-eip <k>] [-ess <scl>] [-oss <scl>] [-edmin <frac>] [-edpcmin <frac>] [-fnnm <frac>] [-pcp <period>] [-iad <# iters>] [-icb <# iters>] [-ac3c <ac3c>] [-sit <sit>] [-rng <seed>] [-pbm <mod>] [-eiphl <hl>] [-nt <# threads>] [-nprob <prob>] [-pprob <prob>] [-addlog <fname>] [-o <nout>] [-eob <base>]

@file ...

response file(s) containing command-line arguments

-int <int>

inter-particle energy type (interaction type); default: “justr”

-enr <spec>

inter-particle energy, radial component (energy specification); default: “cotan”

-ens <spec>

inter-particle energy, scale component (energy specification); default: “zero”

-enw <spec>

windowing to create locality with additive scale-space interaction (“-int add”) (energy specification); default: “butter:16,0.8”

-efs <bool>

whether or not strength contributes to particle-image energy (bool); default: “false”

-nave <bool>

whether or not to nix points at edge of volume, where gage had to invent values for kernel support (bool); default: “false”

-cbst <bool>

during initialization, try constraint satisfaction before testing seedThresh (bool); default: “false”

-noadd

turn off adding during population control

-usa <bool>

allow volumes to have different shapes (false is safe as different volume sizes are often accidental) (bool); default: “false”

-pcet <bool>

use neighbor-counting “enough” heuristic to bail out of population control (bool); default: “false”

-nobin

turn off spatial binning (which prevents multi-threading from being useful), for debugging or speed-up measurement

-lti <bool>

impose liveThresh on initialization (bool); default: “true”

-por <bool>

permute points during rebinning (bool); default: “true”

-npcwza <bool>

no population control with zero alpha (bool); default: “false”

-ubfgl <bool>

use beta for gamma learning (bool); default: “false”

-ratb <bool>

be choosy when adding points to bins to avoid overlap (bool); default: “true”

-svec <vec>

if non-zero (length), vector to use for displaying scale in 3-space (3 doubles); default: “0 0 0”

-gssr <rad>

if non-zero (length), scaling of scale to cylindrical tensors (double); default: “0.0”

-v <verbosity>

verbosity level (int); default: “1”

-vol <vol0 vol1 ...>

input volumes, in format <filename>:<kind>:<volname> (1 or more meetPullVols)

-info <info0 info1 ...>

info definitions, in format <info>[-c]:<volname>:<item>[:<zero>:<scale>] (1 or more meetPullInfos)

-k00 <kern00>

kernel for gageKernel00 (kernel specification); default: “cubic:1,0”

-k11 <kern11>

kernel for gageKernel11 (kernel specification); default: “cubicd:1,0”

-k22 <kern22>

kernel for gageKernel22 (kernel specification); default: “cubicdd:1,0”

-sscp <path>

path (without trailing /) for where to read/write pre-blurred volumes for scale-space (string); default: “./”

-kssb <kernel>

blurring kernel, to sample scale space (kernel specification); default: “ds:1,5”

-kssr <kernel>

kernel for reconstructing from scale space samples (kernel specification); default: “hermite”

-nssr <# scl smpls>

if using “-ppv”; number of samples along scale axis for each spatial position (unsigned int); default: “1”

-np <# points>

number of points to start in system (unsigned int); default: “1000”

-halton

use Halton sequence initialization instead of uniform random

-ppv <# p[nts/vox>

number of points per voxel to start in simulation (need to have a seed threshold volume, overrides “-np”) (int); default: “0”

-ppvzr <z range>

range of Z slices (1st num < 2nd num) to do ppv in, or, “1 0”) for whole volume (2 unsigned ints); default: “1 0”

-jit <jitter>

amount of jittering to do with ppv (double); default: “0”

-pi <npos>

4-by-N array of positions to start at (overrides “-np” (nrrd); default: “”

-step <step>

initial step size for gradient descent (double); default: “1”

-csm <step>

convergence criterion for constraint satisfaction (double); default: “0.0001”

-snap <# iters>

if non-zero, # iters between saved snapshots (unsigned int); default: “0”

-maxi <# iters>

if non-zero, max # iterations to run whole system (unsigned int); default: “0”

-stim <# iters>

if non-zero, max # iterations to allow a particle to be stuck before nixing (unsigned int); default: “5”

-maxci <# iters>

if non-zero, max # iterations for contraint enforcement (unsigned int); default: “15”

-irad <scale>

particle radius in spatial domain (double); default: “1”

-srad <scale>

particle radius in scale domain (double); default: “1”

-bws <bin width>

spatial bin width as multiple of spatial radius (double); default: “1.001”

-alpha <alpha>

blend between particle-image (alpha=0) and inter-particle (alpha=1) energies (double); default: “0.5”

-beta <beta>

when using Phi2 energy, blend between pure space repulsion (beta=0) and scale attraction (beta=1) (double); default: “1.0”

-gamma <gamma>

scaling factor on energy from strength (double); default: “1.0”

-theta <theta>

slope of increasing livethresh with respect to scale (double); default: “0.0”

-wall <k>

spring constant on walls (double); default: “0.0”

-eip <k>

amount by which it’s okay for per-particle energy to increase during gradient descent process (double); default: “0.0”

-ess <scl>

when energy goes up instead of down, scale step size by this (double); default: “0.5”

-oss <scl>

opportunistic scaling (hopefully up, >1) of step size on every iteration (double); default: “1.0”

-edmin <frac>

convergence threshold: stop when fractional improvement (decrease) in energy dips below this (double); default: “0.0001”

-edpcmin <frac>

population control is triggered when energy improvement goes below this threshold (double); default: “0.01”

-fnnm <frac>

don’t nix if this fraction (or more) of neighbors have been nixed (double); default: “0.25”

-pcp <period>

# iters to wait between attempts at population control (unsigned int); default: “20”

-iad <# iters>

# iters to run descent on tentative new points during PC (unsigned int); default: “10”

-icb <# iters>

periodicity of calling rendering callback (unsigned int); default: “1”

-ac3c <ac3c>

allow codimensions 3 constraints (bool); default: “false”

-sit <sit>

scale is tau (bool); default: “false”

-rng <seed>

base seed value for RNGs (unsigned int); default: “42”

-pbm <mod>

progress bin mod (unsigned int); default: “50”

-eiphl <hl>

half-life of energyIncreasePermute(“-eip”) (unsigned int); default: “0”

-nt <# threads>

number of threads hoover should use (int); default: “1”

-nprob <prob>

do full neighbor discovery with this probability (double); default: “1.0”

-pprob <prob>

probe local image values with this probability (double); default: “1.0”

-addlog <fname>

name of file in which to log all particle additions (string); default: “”

-o <nout>

filename for saving computed positions (string); default: “-”

-eob <base>

save extra info (besides position), and use this string as the base of the filenames. Not using this eans the extra info is not saved. (string); default: “”

Published research using this tool or the “pull” library should cite the paper: Gordon L. Kindlmann, Ra{\'u}l San Jos{\'e} Est{\'e}par, Stephen M. Smith, Carl-Fredrik Westin. Sampling and Visualizing Creases with Scale-Space Particles. IEEE Trans. on Visualization and Computer Graphics, 15(6):1415-1424 (2009).

gprobe(1), ilk(1), mrender(1), miter(1), nrrdSanity(1), overrgb(1), tend(1), unu(1), vprobe(1)

gprobe(1), ilk(1), miter(1), mrender(1), nrrdSanity(1), overrgb(1), tend(1), unu(1), vprobe(1).