/usr/bin/teem-puller(1) Command-line interface to the pull library.


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: ""