IO

Input/output functions for reading and writing matRad-compatible data formats.

matRad_readMHD(filename)

matRad NRRD reader

call

[cube, metadata] = matRad_readMHD(filename)

Input:

filename – full path to mhd or mha file

Output:

cube – the read cube
metadata – metadata from header information

References: [1] https://itk.org/Wiki/MetaIO/Documentation

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_exportDij(filename, dij, stf, metadata)

matRad physical dose writer

call

matRad_exportDij(filename,dij,stf,…: additionalFields,additionalKeyValuePairs)

Input:

filename – full output path, including the file extension
dij – matRad dij struct
stf – matRad stf struct
metadata – struct of metadata

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_readNifTI(filename)

matRad NifTI reader

call

[cube, metadata] = matRad_readNifTI(filename)

Input:

filename – full path to .nii(.gz) file

Output:

cube – the read cube
metadata – metadata from header information

References: [1] http://teem.sourceforge.net/nrrd/format.html5

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_importPatient(ctFile, maskFiles, hlutFilename)

matRad patient import from binary files (CT and masks)

call

[ct,cst] = matRad_importPatient(cubeFile,maskFiles) [ct,cst] = matRad_importPatient(cubeFile,maskFiles, hlutFilename)

Input:

ctFile – path to CT file. If HLUT is not set, values are interpreted as HU and interpolated to ED.
maskFiles – cell array with filenames to the masks if maskFiels contains a folder, all contained and recognized data files are treated as masks
hlutFilname – (optional) HLUT, (n,2) array. if set to ‘default’, we will use a default HLUT

Output:

ct ct struct for use with matlab
cst cst struct for use with matlab

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_supportedBinaryFormats()

matRad function to obtain supported binary formats

call

[read,write] = matRad_supportedBinaryFormats()

input:

Output:

read cell array with file filter in first column, name in second – column, and handle to read function in third column
write cell array with file filter in first column, name in second – column, and handle to write function in third column

References: [1] http://teem.sourceforge.net/nrrd/format.html5

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeNifTI(filepath, cube, metadata)

matRad NifTI reader

call

[cube, metadata] = matRad_writeNifTI(filename)

Input:: filename – full path to .nii(.gz) file
Output:: file will be written to disk

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_readCube(filename)

matRad Cube read wrapper determines the extension and assigns the appropriate reader to it

call

matRad_readCube(filename)

Input:: filename – full path of the file

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeNRRD(filename, cube, metadata)

matRad NRRD writer

call

matRad_writeNRRD(filename,cube,datatype,…: additionalFields,additionalKeyValuePairs)

Input:

filename – full output path, including the nrrd extension
cube – cube that is to be written
metadata – struct of metadata. Writer will wrap the existing metadata to nrrd standard-specific fields [1].

References: [1] http://teem.sourceforge.net/nrrd/format.html5

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeMHD(filepath, cube, metadata)

matRad function to write mha files

call

matRad_writeMHA(filepath,cube,metadata)

Input:

filepath – full filename (with extension)
cube – 3D array to be written into file
metadata – struct of metadata. Writer will wrap the existing metadata to MHA standard-specific fields Necessary fieldnames are: - resolution: [x y z] - datatype: numeric MATLAB-Datatype

Output:

file will be written to disk

References: https://itk.org/Wiki/MetaIO/Documentation

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeCube(filepath, cube, datatype, metadata)

matRad wrapper for Cube export

call

[saved_metadata] = matRad_writeCube(filepath,cube,meta)

Input:

filepath – full output path. needs the right extension to choose the appropriate writer
cube – cube that is to be written
datatype – MATLAB numeric datatype
metadata – meta-information in struct. Necessary fieldnames are: - resolution: [x y z] Optional: - axisPermutation (matRad default [2 1 3]) - coordinateSystem (matRad default ‘LPS’) - imageOrigin (as used in DICOM) - dataUnit (i.e. Gy..) - dataName (i.e. dose, ED, …) - compress (true/false) (default chosen by writer)

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_readHLUT(filename)

matRad function to read HLUT from filename

call

hlut = matRad_readHLUT(filename)

Input:: filename – hlut filename
Output:: hlut – lookup table

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeVTK(filepath, cube, metadata)

matRad function to write vtk cubes

call

matRad_writeVTK(filepath,cube,metadata)

Input:

filepath – full filename (with extension)
cube – 3D array to be written into file
metadata – struct of metadata. Writer will wrap the existing metadata to VTK standard-specific fields Necessary fieldnames are: - resolution: [x y z] - datatype: numeric MATLAB-Datatype

Output:

file will be written to disk

References

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_writeMHA(filepath, cube, metadata)

matRad function to write mha files

call

matRad_writeMHA(filepath,cube,metadata)

Input:

filepath – full filename (with extension)
cube – 3D array to be written into file
metadata – struct of metadata. Writer will wrap the existing metadata to MHA standard-specific fields Necessary fieldnames are: - resolution: [x y z] - datatype: numeric MATLAB-Datatype

Output:

file will be written to disk

References: https://itk.org/Wiki/MetaIO/Documentation

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.

matRad_readBinData(binFile, cubeDim): Instance of MatRad_Config class

matRad_readNRRD(filename)

matRad NRRD reader

call

[cube, metadata] = matRad_readNRRD(filename)

Input:

filename – full path to nrrd file

Output:

cube – the read cube
metadata – metadata from header information

References: [1] http://teem.sourceforge.net/nrrd/format.html5

This file is part of the matRad project. It is subject to the license terms in the LICENSE file found in the top-level directory of this distribution and at https://github.com/e0404/matRad/LICENSE.md. No part of the matRad project, including this file, may be copied, modified, propagated, or distributed except according to the terms contained in the LICENSE file.