inr%u

Option Description
inr%u -anisotropicDiffusion [%f %f %f %b %f %s %b] compute the anisotropic diffusion of the image. The first parameter is the time step dt (dt>0). The second parameter is the diffusion time tmax with tmax>=dt. Indeed, (tmax/dt) is the number of iterations. The third parameter is the quantile quant that set the gradient threshold (0
inr%u -arith <%f | inr%u> > Perform given arithmetic operation. Either a constant is use with each voxel or another same size inrimage is used. Zero division returns 0. Overflows are no handled.
inr%u -chamfer [2D|3D] [thres %f] [malandain3x3x3|chamfer5x5x5] Compute a chamfer map.
inr%u -components inr%u+ Set vectorial components of a vectorial inrimage with given scalar inrimages. There should be as many components as inrimage vectorial dimension.
inr%u -connexe [con <4|6|8|18|26>] [tcc %i] [ncc %u|max] [lt %v ht %v] [hyster [tcc_ht %i] ] [output ] Extract connexe components from an inrimage. Binarize input image using low threshold (lt) and high threshold (ht) if any (hysteresis thresholding). Extract connexe components with given (con) connectivity. tcc is the minimal size of cc kept, ncc is the number of cc kept (sorted with respect to their size), max selects only largest cc. The output type indicates whether to return a binary image or a labelled cc image.
inr%u -convolute [filterSize %u] Convolute inrimage with a filter of given size. Available filters are gaussian (X or Y or Z or 2D or 3D), first derivative X, Y or Z-wise and second derivative X, Y or Z-wise.
inr%u -copy duplicate image and return new image id
inr%u -crop crop inrimage with given box (from org to end or centered on center and with given size)
inr%u -cropHistogramm [min %v] [max %v] [bg %v] Threshold inrimage between min and max values. Voxel between min an max included are not modified. Other voxels are set to bg value.
inr%u -curvature compute 2D inrimage curvature: (Ixx*Iy^2 - 2*Ix*Iy*Ixy + Iyy*Ix^2) / (Ix^2 + Iy^2)^(3/2)
inr%u -destroy destroy inrimage
inr%u -dft [2D|3D] Compute DFT (Discrete Fourier Transform) of image using the FFT algorithm. If image is scalar, the direct transform is computed. If image is vectorial and vdim is 2, the inverse transform is computed.
inr%u -eval function string (do not use spaces) Evaluates expression in function string.Supports the following arithmetic operators in the following order: ^(power),/(division) or *(multiplication) and +(addition) or -(subtraction). Operators with the same priority are processed from left to right. All other operators have lowest priority and therefor processed from left to right as well. Special operators: |<(minimum), |>(maximum). Logical Operators(returns 1=true,0=false): <=(Smaller or equal), >=(Larger or equal), ==(equal), >(larger), <(smaller), &&(and), ||(or). Standard functions (angles are in radians): abs(), exp(), ceil()(rounds upwards), floor()(rounds downwards), log(), sqrt(), sin(), cos(), tan(), asin(), acos(), atan(), sinh(), cosh(), tanh(). Global functions (returns a scalar and calculates value based on the expression given as input to the function)): mean, min(minimum value), max(maximum value), med(median), std(estimated standard deviation), var(estimated variance). Variables: x,y,z (pixel positions), inrX(X can be any number of a valid image). Examples: inr3 -eval inr1|
inr%u -extrapolation [nearest|tozero] get or set extrapolation method
inr%u -fill bg %v fg %v [2D|3D] Fill-in 2D or 3D regions of inrimage. Contours with fg color on a bg background are filled with fg value.
inr%u -flip [X|Y|Z] flip along given direction
inr%u -floating return true if inrimage type is floating point, false otherwise
inr%u -glbounds [min %%v] [max %%v] get/set inrimage min and max grey level values
inr%u -gradient [sigma %f] [2D|3D] [rec [marta|gaussian|deriche] | sobel] [dir ] [max] [lt %f] Compute inrimage gradient either using recursive filters (rec with Marta, Deriche gaussian or Deriche step-edge approximation) or sobel masks (sobel). sigma represents filter standard deviation (rec) or filter size (sobel). A low thresholding is applied on resulting gradient image if lt option is specified. Only gradient extrema along gradient direction are kept with max. The dir option allow to get gradient vectors (dir vectors) or to generate a gradient directions map (as a 8-bits image whose voxel value index a direction vector among 180 vectors sampling all directions, dir sample).
inr%u -histogram returns the image histogram
inr%u -interpolation [nearest|trilin] get or set interpolation method
inr%u -isolateRegion zero voxel outside region (from org to end or centered on center and with given size)
inr%u -kind returns the name of the object kind associated with a given object
inr%u -laplacian [sigma %f] [marta|gaussian|deriche] Compute inrimage laplacian using recursive filters.
inr%u -logic < inr%u | not> apply given logical operator
inr%u -mel inr%u [ixo %u] [iyo %u] [izo %u] [ixi %i] [iyi %i] [izi %i] [idx %u] [idy %u] [idz %u] mel two inrimages (ixi, iyi, izi is input image block corner, and idx, idy, idz its size; ixo, iyo, izo is output image block corner).
inr%u -morpho [dil|ero|close|open|tophat|invtophat|grad|lowgrad|uppgrad|median] [ [con <4|6|8|10|18|26>] | [struct %s] ] [i %u] [binary | greylevel] Binarize inrimage and apply given morphological operator.
inr%u -name %s get/set image name
inr%u -noise [white mean=%f|gaussian|us] [dev %f] [org %u %u %u | center %u %u %u] [end %u %u %u | size %u %u %u] Creates a noisy box inside an inrimage. The output is either a white gaussian noise with given mean (white), a gaussian noise added to image (gaussian, default) or an ultrasound like multiplicative noise (us)
inr%u -oversample Oversample an image so that its new size is xdim*ydim*zdim. New size should be greater thant oler one.
inr%u -recfilter [sigma %f] [marta|gaussian|deriche] Apply recursive filter on inrimage (with Marta, Deriche gaussian or Deriche step-edge approximation). Available filters are gaussian (X or Y or Z or 2D or 3D), first derivative X, Y or Z-wise and second derivative X, Y or Z-wise.
inr%u -redraw force inrimage to be redisplayed in any viewer it appears
inr%u -region [%d %d %d %d %d %d] get or set region in which operations should be performed method. not used by all operations. negative values mean lower or higher bound, as appropriate.
inr%u -resample Resample an image so that its new size is xdim*ydim*zdim. Under sampled images are approximated by picking a trilinearly interpolated value in the originale image (i.e. there is no voxel averaging computation).
inr%u -save %s save image (using image name if no new name is given)
inr%u -size get image size
inr%u -slicecams return a list of slicecams associated with the image
inr%u -split split a vectorial inrimage in as many scalar inrimages as vector dimensions and return list of created inrimages
inr%u -switch switch two directions
inr%u -threshold [min %v] [max %v] [bg %v] [fg %v] Threshold inrimage between min and max values. Voxel between min an max included are set to fg value. Other voxels are set to bg value.
inr%u -transform [nearest|trilinear|cspline] [2D|3D] <-mat %s> [-def %s %s %s] [-inv] [-dim %u] Resample an image with a mat4 and a deformation field. Resampling may be nearest, trilinear, cspline and in 2D or 3D. The -inv option allows to resample with the inversed matrix. The matrix and the displacement field are allways supposed to go from the result image to the input image
inr%u -type [[cast|scale] <8bits|16bits|s16bits|32bits|s32bits|64bits|s64bits|float|double|rgb|rgba|floatVector|doubleVector>] get/set inrimage type
inr%u -undersample undersample image with given step in X, Y and Z direction, or with stepX step in X direction, stepY step in Y direction, stepZ step in Z direction.
inr%u -vectorial return true if inrimage type is vectorial, false otherwise
inr%u -voxel [%f %f %f] get/set inrimage voxels size
inr%u -windowing [min %v] [max %v] Creates an unsigned char image after Windowing the image between min and max values
inr%u -zeroRegion zero voxel inside region (from org to end or centered on center and with given size)