Wednesday, August 12 2026 10:57:10
CIP
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Display graphs: unu resample: error saving nrrd to "\windows\temp\tmpagd6dg\ct-deconv.nrrd":
[nrrd] nrrdSave: couldn't fopen("\windows\temp\tmpagd6dg\ct-deconv.nrrd","wb"): No such file or directory
puller: trouble with volumes or infos:
[meet] meetPullVolLoadMulti: trouble loading mpv[0]->nin ("V")
[meet] [nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.nrrd","rb") failed: No such file or directory
ERROR: error parsing "\windows\temp\tmpagd6dg\pass1.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\pass1.nrrd","rb") failed: No such file or directory
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 "\windows\temp\tmpagd6dg\pass2.nrrd" as nrrd for "-pi" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\pass2.nrrd","rb") failed: No such file or directory
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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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 "\windows\temp\tmpagd6dg\ct-deconv.nrrd" as nrrd for "-i" option:
[nrrd] nrrdLoad: fopen("\windows\temp\tmpagd6dg\ct-deconv.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: "-"
E
======================================================================
ERROR: test_vessel_particles.test_vessel_particles
----------------------------------------------------------------------
Traceback (most recent call last):
File "D:\Projects\CIP-build\CIPPython-install\lib\site-packages\nose\case.py", line 197, in runTest
self.test(*self.arg)
File "D:\Projects\CIP-build\CIP-build\cip_python\particles\tests\test_vessel_particles.py", line 61, in test_vessel_particles
vp.clean_tmp_dir()
File "D:\Projects\CIP-build\CIP-build\cip_python\particles\chest_particles.py", line 592, in clean_tmp_dir
list_dir=os.listdir(self._tmp_dir)
WindowsError: [Error 3] The system cannot find the path specified: '\\windows\\temp\\tmpagd6dg/*.*'
-------------------- >> begin captured stdout << ---------------------
c:\windows\temp\tmpagd6dg
Resetting param groups...
Building param groups...
Starting pass 1...
Finished pass 1.
Starting pass 2...
Finished pass 2.
Starting pass 3...
Finished pass 3.
Probing...
Finished probing.
Saving to vtk...
Cleaning temporary directory...
--------------------- >> end captured stdout << ----------------------
----------------------------------------------------------------------
Ran 1 test in 0.156s
FAILED (errors=1)
