puller - Man Page
command-line interface to the “pull” library
Synopsis
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>]
Options
- @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: “”
Notes
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).
See Also
gprobe(1), ilk(1), mrender(1), miter(1), nrrdSanity(1), overrgb(1), tend(1), unu(1), vprobe(1)
Referenced By
gprobe(1), ilk(1), miter(1), mrender(1), nrrdSanity(1), overrgb(1), tend(1), unu(1), vprobe(1).