#File clitkAffineTransform.ggo
package "clitkAffineTransform"
version "1.0"
purpose "Resample with or without affine transform of 2D, 3D, 4D images or vector fields"

option "config"	  	- "Config file"			  string  	no
option "verbose"   	v "Verbose"			  flag		off

section "I/O"
option "input"		i "Input image filename"                                          string yes
option "output"    	o "Output image filename"                                         string yes
option "like"    	l "Resample output this image (size, spacing, origin, direction)" string no
option "transform_grid" - "Apply affine transform to input grid for output's"             flag   off

section "Options"
option "size"		- "New output size if different from input"  	int 	no 	multiple
option "spacing"	- "New output spacing if different from input" 	double 	no 	multiple
option "spacinglike"	- "New output spacing like this image" 	        string  no
option "origin"		- "New output origin if different from input" 	double 	no 	multiple
option "direction"	- "New output direction if different from input" double no 	multiple
option "matrix"		m "Affine matrix (homogene) filename"		string  no
option "elastix"	e "Read EulerTransform from elastix output file (combine if multiple)"	string  no
option "rotate"		r "Rotation to apply (radians)"	                double	no	multiple
option "translate"	t "Translation to apply (mm)"		        double  no	multiple
option "pad"		- "Edge padding value" 				double 	no 	default="0.0"
option "adaptive"		- "Adapt the size, spacing or the origin when one of the previous tag is on (use previous clitkResampleImage)" flag off

section "Interpolation"
option "interp"		- "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT"	int  	no  default="1"
option "interpOrder"	- "Order if BLUT or BSpline (0-5)"		        int  	no  default="3"
option "interpSF"	- "Sampling factor if BLUT"			        int  	no  default="20"
option "interpVF"	- "Interpolation: 0=NN, 1=Linear, 2=BSpline, 3=BLUT"	int  	no  default="1"
option "interpVFOrder"	- "Order if BLUT or BSpline (0-5)"		        int  	no  default="3"
option "interpVFSF"	- "Sampling factor if BLUT"			        int  	no  default="20"

section "Gaussian filtering"
option "gauss" g "Apply gaussian filter before (sigma in mm) (default=0.0)" double no multiple
option "autogauss" - "Apply gaussian filter before with auto sigma when downsampling (default=off)" flag off