milxDeformableModelApp.cxx File Reference

A swiss-army knife of deformable model/surface processing. This application implements single/batch processing of models with various processing options found in the SMILI library.You are able to transform, orient etc. a number of surfaces easily via the commandline with this application (use –help). This application uses the milxDeformableModel class to do all processing. More...

#include <vector>
#include <tclap/CmdLine.h>
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkMultiThreader.h>
#include <vtkPolyDataCollection.h>
#include <vtkTransformCollection.h>
#include <milxFile.h>
#include <milxDeformableModel.h>

Go to the source code of this file.

Typedefs
typedef std::vector< std::string >::iterator	stringiterator
typedef unsigned char	charPixelType
typedef itk::Image< charPixelType, milx::imgDimension >	charImageType

Enumerations
enum	operations {   none = 0, convert, duplicate, cat,   split, scale, decimate, smooth,   laplacian, thresholdscalars, flip, diffscalars,   copyscalars, diffscalarspairs, statscalars, removescalars,   mse, procrustes, icp, clip,   voxelise, orient, flat, none = 0,   info, convert, print, csv,   none = 0, info, convert, labelinfo,   rescale, invert, relabel, smooth,   bilateral, median, gradmag, laplacian,   distancemap, threshold, Otsu, crop,   mask, resample, match, checker,   add, diff, mean, merge,   cast, flip, none = 0, convert,   duplicate, cat, split, scale,   decimate, smooth, laplacian, thresholdscalars,   clip, flip, diffscalars, copyscalars,   diffscalarspairs, statscalars, removescalars, mse,   procrustes, icp }

Functions
int	main (int argc, char *argv[])

Detailed Description

A swiss-army knife of deformable model/surface processing. This application implements single/batch processing of models with various processing options found in the SMILI library.

You are able to transform, orient etc. a number of surfaces easily via the commandline with this application (use –help). This application uses the milxDeformableModel class to do all processing.

Usage: Concatenate surfaces

$ milxModelApp *.vtk --cat -o initial.vtk

Split surfaces based on knowledge of known components of that surface

milxModelApp --split combined_new_weights.vtk --component Atlas_MRI_surface_R_ace.vtk --component Atlas_MRI_surface_R_fem.vtk -p split_ 

Copy scalars from atlas mesh to other meshes in directory and output to another directory with same names

milxModelApp --scalarcopy focus_atlases/focus_bladder_atlas.vtk results/bladder/asm_bladder_*.vtk -p results_scalars/bladder/

Clip meshes in directory keeping only parts with value of 1 and output to another directory with same names

milxModelApp --clip 1 results_scalars/bladder/asm_bladder_*.vtk -p results_clipped/bladder/

Compute scalars stats (mean, variance etc. per point) of meshes in directory and output single mesh (of first mesh) with stats as arrays in mesh

milxModelApp --scalarstats Hausdorff/bladder/bladder__*.vtk -o bladder_stats.vtk

Definition in file milxDeformableModelApp.cxx.

Function Documentation

main()

int main	(	int	argc,
		char *	argv[]
	)

Program Info

Process Arguments

Optional

Clamped Optional

Switches

XOR Switches

Mandatory

Deformable model options

Add argumnets

XOR args

Deformable model args

Parse the argv array.

Get the value parsed by each arg.

Setup ITK Threads

Deformable model value parsed by each arg.

Check operation

Check Deformable model operations

Partition list into two if option given

Open files

Deformable model open files

Geometric transforms potentially associated with the 'collection' item (e.g. with –icp).

Operate

Todo:

leak here?

Deformable Model ops

Write result

Definition at line 75 of file milxDeformableModelApp.cxx.