teem-puller (1)

teem-puller [@file ...] [-int <int>] [-enr <spec>] \fR

/usr/bin/teem-puller: Command-line interface to the "pull" library. 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).

• [-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 pop cntl (bool); default: "true"

• -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 pop cntl 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"

-nss <# 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 <# pnts/vox> = number of points per voxel to start in simulation

(need to have a seed thresh vol, overrides "-np") (unsigned 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 wrt scale (double);

default: "0.0"

• -wall <k> = spring constant on walls (double); default: "0.0"

• -eip <k> = amount by which its 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> = output volume (string); default: "-"

• -eob <base> = save extra info (besides position), and use this

• string as the base of the filenames. Not using this means the extra info is not saved. (string); default: ""

The full documentation for Teem is maintained as a Texinfo manual. If the info and Teem programs are properly installed at your site, the command

• info Teem

should give you access to the complete manual.