Wednesday, August 12 2026 09:54:44
CIP
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Display graphs: ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V" (in "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-on:VSN C:\Projects\CIP-Release12\CIP-build\cip_python\particles\tests/../../../Testing/Data/Input/vessel_vesselSeedsMask.nrrd:scalar:M") as meetPullVol for "-vol" option:
[meet] meetPullVolParse: couldn't parse "\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd" as kind
Usage: puller [@file ...] [-int <int>] [-enr <spec>] [-ens <spec>] \
[-enw <spec>] [-zz <bool>] [-efs <bool>] [-nave <bool>] [-cbst <bool>] \
[-noadd] [-usa <bool>] [-pcet <bool>] [-cipc <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>] [-bsp <boundary>] \
[-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"
-zz <bool> = always constrain Z=0, to process 2D images (bool);
default: "false"
-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"
-cipc <bool> = convergence test doesn't care if there has been
recent changes due to 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 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> = default blurring kernel, to sample scale space
(kernel specification); default: "dgauss:1,5"
-bsp <boundary> = default boundary behavior of scale-space blurring
(boundary specification); default: "wrap"
-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")
(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> = 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
means the extra info is not saved. (string);
default: ""
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V" (in "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-on:VSN") as meetPullVol for "-vol" option:
[meet] meetPullVolParse: couldn't parse "\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd" as kind
Usage: puller [@file ...] [-int <int>] [-enr <spec>] [-ens <spec>] \
[-enw <spec>] [-zz <bool>] [-efs <bool>] [-nave <bool>] [-cbst <bool>] \
[-noadd] [-usa <bool>] [-pcet <bool>] [-cipc <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>] [-bsp <boundary>] \
[-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"
-zz <bool> = always constrain Z=0, to process 2D images (bool);
default: "false"
-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"
-cipc <bool> = convergence test doesn't care if there has been
recent changes due to 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 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> = default blurring kernel, to sample scale space
(kernel specification); default: "dgauss:1,5"
-bsp <boundary> = default boundary behavior of scale-space blurring
(boundary specification); default: "wrap"
-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")
(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> = 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
means the extra info is not saved. (string);
default: ""
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V" (in "c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-o:V c:\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd:scalar:0-10-6.0-on:VSN") as meetPullVol for "-vol" option:
[meet] meetPullVolParse: couldn't parse "\users\jorge\appdata\local\temp\tmpsrcnjx\ct-deconv.nrrd" as kind
Usage: puller [@file ...] [-int <int>] [-enr <spec>] [-ens <spec>] \
[-enw <spec>] [-zz <bool>] [-efs <bool>] [-nave <bool>] [-cbst <bool>] \
[-noadd] [-usa <bool>] [-pcet <bool>] [-cipc <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>] [-bsp <boundary>] \
[-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"
-zz <bool> = always constrain Z=0, to process 2D images (bool);
default: "false"
-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"
-cipc <bool> = convergence test doesn't care if there has been
recent changes due to 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 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> = default blurring kernel, to sample scale space
(kernel specification); default: "dgauss:1,5"
-bsp <boundary> = default boundary behavior of scale-space blurring
(boundary specification); default: "wrap"
-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")
(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> = 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
means the extra info is not saved. (string);
default: ""
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
ERROR: error parsing "c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("c:\users\jorge\appdata\local\temp\tmpsrcnjx\pass3.nrrd","rb") failed: No such file or directory
Usage: gprobe -i <nin> -k <kind> [-v <verbosity>] -q <query> [-gmc <min \
gradmag>] [-ofs] [-seed <N>] [-c <bool>] [-zz <bool>] [-k00 <kern00>] \
[-k11 <kern11>] [-k22 <kern22>] [-rn] [-ssn <SS #>] [-ssr <scale \
range>] [-ssu] [-sso] [-kssb <kernel>] [-sbp <blur spec>] [-ssnd] \
[-ssnb <bias>] [-ssf <SS read/save format>] [-kssr <kernel>] [-s <sclX \
sclY sxlZ>] [-ssp <pos>] [-pg <nrrd>] [-pi <nrrd>] [-pp <pos ...>] \
[-eps <epsilon>] [-psi <p>] [-t <type>] [-o <nout>]
-i <nin> = input volume
-k <kind> = "kind" of volume ("scalar", "vector", "tensor",
or "dwi")
-v <verbosity> = verbosity level (int); default: "1"
-q <query> = the quantity (scalar, vector, or matrix) to learn
by probing (string)
-gmc <min gradmag> = For curvature-based queries, use zero when
gradient magnitude is below this (double);
default: "0.0"
-ofs = If only per-axis spacing is available, use that
to contrive full orientation info
-seed <N> = RNG seed; mostly for debugging (unsigned int);
default: "42"
-c <bool> = clamp positions as part of probing (bool);
default: "false"
-zz <bool> = enable "zeroZ" behavior in gage that partially
implements working with 3D images as if they are
2D (bool); default: "false"
-k00 <kern00> = kernel for gageKernel00; default: "tent"
-k11 <kern11> = kernel for gageKernel11; default: "cubicd:1,0"
-k22 <kern22> = kernel for gageKernel22; default: "cubicdd:1,0"
-rn = renormalize kernel weights at each new sample
location. "Accurate" kernels don't need this;
doing it always makes things go slower
-ssn <SS #> = how many scale-space samples to evaluate, or, 0
to turn-off all scale-space behavior (unsigned
int); default: "0"
-ssr <scale range> = range of scales in scale-space (2 doubles);
default: "nan nan"
-ssu = do uniform samples along sigma, and not (by
default) samples according to the effective
diffusion scale
-sso = if not using "-ssu", use pre-computed optimal
sigmas when possible
-kssb <kernel> = blurring kernel, to sample scale space;
default: "dgauss:1,5"
-sbp <blur spec> = complete specification of stack blur parms;
over-rides all previous "ss" options; default: ""
-ssnd = normalize derivatives by scale
-ssnb <bias> = bias on scale-based derivative normalization
(double); default: "0.0"
-ssf <SS read/save format> = printf-style format (including a "%u") for the
filenames from which to read pre-blurred volumes
computed for the stack, if they exist and match
the stack parameters, and where to save them if
they had to be re-computed. Leave this as empty
string to disable this. (string); default: ""
-kssr <kernel> = kernel for reconstructing from scale space
samples; default: "hermite"
-s <sclX sclY sxlZ> = scaling factor for resampling on each axis (>1.0
: supersampling); use "-ssp" (and "-psi")to
specify scale position of sampling (3 doubles);
default: "1 1 1"
-ssp <pos> = when using scale-space, scale-position at which
to probe (double); default: "0"
-pg <nrrd> = overrides "-s": 2-D nrrd which specifies origin
and direction vectors for sampling grid;
default: ""
-pi <nrrd> = overrides "-pv": probes at this list of 3-vec or
4-vec positions; default: ""
-pp <pos ...> = overrides "-pi": only sample at this specified
point (3..4 doubles); default: "nan nan nan"
-eps <epsilon> = if non-zero, and if query is a scalar, and if
using "pp" to query at a single point, then do
epsilon offset probes to calculate discrete
differences, to find the numerical gradient and
hessian (for debugging) (double); default: "0"
-psi <p> = whether the probe location specification (by any
of the four previous flags) are in index space
(bool); default: "false"
-t <type> = type of output volume (type); default: "float"
-o <nout> = output volume (string); default: "-"
'ReadNRRDsWriteVTK' is not recognized as an internal or external command,
operable program or batch file.
ERROR: In C:\Minonda\conda-bld\work\VTK-6.3.0\IO\Legacy\vtkDataReader.cxx, line 430
vtkPolyDataReader (00000000022E0590): Unable to open file: c:\users\jorge\appdata\local\temp\tmpsrcnjx\vessel_particles.vtk
ERROR: In C:\Minonda\conda-bld\work\VTK-6.3.0\Common\DataModel\vtkPointLocator.cxx, line 859
vtkPointLocator (00000000065066E0): No points to subdivide
ERROR: In C:\Minonda\conda-bld\work\VTK-6.3.0\Common\DataModel\vtkPointLocator.cxx, line 859
vtkPointLocator (00000000065066E0): No points to subdivide
