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teem-unu(1) [debian man page]

teem-unu(1)							   User Commands						       teem-unu(1)

teem-unu - Utah Nrrd Utilities command-line interface DESCRIPTION
"teem-unu" is a command-line interface to much of the functionality in "nrrd", a C library for raster data processing. Nrrd is one library in the "Teem" collection of libraries. More information about Teem is at <>. Users are strongly encouraged to join the teem-users mailing list: <>. This is the primary forum for feedback, questions, and feature requests. The utility of unu is mainly as a pre-processing tool for getting data into a type, encoding, format, or dimensions best suited for some visualization or rendering task. Also, slices and projections are effective ways to visually inspect the contents of a dataset. Especially useful commands include make, resample, crop, slice, project, histo, dhisto, quantize, and save. Full documentation for each command is shown by typing the command alone, e.g., "unu make". Unu can process CT and MRI volume datasets, grayscale and color images, time-varying volumes of vector fields (5-D arrays), and more. Currently supported formats are plain text files (2-D float arrays), NRRD, VTK structured points, and PNG and PNM images. "unu make -bs -1" can read from DICOM files. "unu save" can generate EPS files. Supported encodings are raw, ascii, hex, gzip, and bzip2. Much of the functionality of unu derives from chaining multiple invocations together with pipes ("|"), minimizing the need to save out intermediate files. For example, if "data.raw.gz" is a gzip'ed 256 x 256 x 80 volume of raw floats written from a PC, then the following will save to "zsum.png" a histogram equalized sum- mation projection along the slowest axis: unu make -i data.raw.gz -t float -s 256 256 80 -e gzip -en little | unu project -a 2 -m sum | unu heq -b 2000 -s 1 | unu quantize -b 8 -o zsum.png If unu or nrrd repeatedly proves itself useful for your research, an acknowledgment to that effect in your publication would be greatly appreciated, such as (for LaTeX): "Dataset processing performed with the { t unu} tool (or the { t nrrd} library), part of the { t Teem} toolkit available at { t $<$$>$}" Formats available: nrrd pnm png vtk text eps Nrrd data encodings available: raw ascii hex gz bz2 SEE ALSO
The full documentation for teem-unu is maintained as a Texinfo manual. If the info and teem-unu programs are properly installed at your site, the command info teem-unu should give you access to the complete manual. 1.10.0 December 10, 2008 teem-unu(1)

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TEEM(1) 							   User Commands							   TEEM(1)

/usr/bin/teem-puller - Command-line interface to the "pull" library. SYNOPSIS
teem-puller [@file ...] [-int <int>] [-enr <spec>] fR DESCRIPTION
/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 <ker- nel>] [-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: "" SEE ALSO
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. Teem version 1.11.0 April 2012 TEEM(1)
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