Package mgui.io.standard.nifti

Class NiftiVolumeLoader

java.lang.Object

mgui.io.FileLoader

mgui.io.domestic.shapes.InterfaceShapeLoader

mgui.io.domestic.shapes.VolumeFileLoader

mgui.io.standard.nifti.NiftiVolumeLoader

All Implemented Interfaces:

InterfaceIO, IconObject

public class NiftiVolumeLoader
extends VolumeFileLoader

File loader to read Analyze 7.5 format volume files. Has methods to read from both header (.hdr) and volume (.img) files. See http://www.mayo.edu/PDF/ANALYZE75.pdf for details on this format.

Since:

1.0

Version:

1.0

Author:

Andrew Reid

Field Summary

Fields

Modifier and Type	Field	Description
java.io.File	header
boolean	is_nifti
java.io.File	transform
java.io.File	volume

Fields inherited from class mgui.io.domestic.shapes.VolumeFileLoader

dataMax, dataMin, flipX, flipY, flipZ, maxAlpha, minAlpha, setAlpha

Fields inherited from class mgui.io.FileLoader

dataFile, dataURL, options

Constructor Summary

Constructors

Constructor	Description
NiftiVolumeLoader()
NiftiVolumeLoader(java.io.File input)
NiftiVolumeLoader(java.io.File input, boolean trans)

Method Summary

Modifier and Type	Method	Description
Box3D	getBoundingBox()
java.io.File	getFile()	Returns the current data file for this loader.
int	getVolCount()
VolumeMetadata	getVolumeMetadata()	Returns a set of metadata describing the current volume file.
InterfaceIOType	getWriterComplement()	Returns the InterfaceIOType of a FileWriter which is the complement of this loader; i.e., writes what this loader reads with identical encoding.
boolean	hasVol(int v)
protected void	init(java.io.File input, boolean trans)
NiftiMetadata	readHeader()
void	setFile(java.io.File input)	Sets the current File for this loader.
protected boolean	setVolume3DBlocking(Volume3DInt volume3d, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
void	writeHeader(NiftiMetadata h)

Methods inherited from class mgui.io.domestic.shapes.VolumeFileLoader

getDefaultOptions, getObjectIcon, getSupportedObjects, getVolume3D, getVolume3D, getVolume3D, getVolume3D, getVolume3D, getVolume3DCustom, load, loadObject, loadShape, loadVolume, loadVolume, loadVolume, setAlpha, setAlpha, setVolume3D, setVolume3D, setVolume3D, setVolume3D, setVolume3DWorker

Methods inherited from class mgui.io.FileLoader

getComplementIOType, getFailureMessage, getIOType, getOptions, getProgressMessage, getSuccessMessage, getTitle, load, load, loadObject, loadObject, loadObject, setOptions, setURL, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Details

header

public java.io.File header

volume

public java.io.File volume

transform

public java.io.File transform

is_nifti

public boolean is_nifti

Constructor Details

NiftiVolumeLoader

public NiftiVolumeLoader()

NiftiVolumeLoader

public NiftiVolumeLoader(java.io.File input)

NiftiVolumeLoader

public NiftiVolumeLoader(java.io.File input,
boolean trans)

Method Details

setFile

public void setFile(java.io.File input)

Description copied from class: FileLoader

Sets the current File for this loader. Sets the URL to null.

Specified by:

setFile in interface InterfaceIO

Overrides:

setFile in class FileLoader

getFile

public java.io.File getFile()

Description copied from class: FileLoader

Returns the current data file for this loader.

Overrides:

getFile in class FileLoader

Returns:

init

protected void init(java.io.File input,
boolean trans)
             throws java.io.IOException

Throws:

java.io.IOException

getBoundingBox

public Box3D getBoundingBox()

readHeader

public NiftiMetadata readHeader()

getVolumeMetadata

public VolumeMetadata getVolumeMetadata()
                                 throws java.io.IOException,
java.io.FileNotFoundException

Description copied from class: VolumeFileLoader

Returns a set of metadata describing the current volume file.

Specified by:

getVolumeMetadata in class VolumeFileLoader

Returns:

Throws:

java.io.IOException

java.io.FileNotFoundException

writeHeader

public void writeHeader(NiftiMetadata h)

hasVol

public boolean hasVol(int v)

getVolCount

public int getVolCount()

Overrides:

getVolCount in class VolumeFileLoader

setVolume3DBlocking

protected boolean setVolume3DBlocking(Volume3DInt volume3d,
java.lang.String column,
int v,
VolumeInputOptions options,
ProgressUpdater progress)
                               throws ShapeIOException

Specified by:

setVolume3DBlocking in class VolumeFileLoader

Throws:

ShapeIOException

getWriterComplement

public InterfaceIOType getWriterComplement()

Description copied from class: FileLoader

Returns the InterfaceIOType of a FileWriter which is the complement of this loader; i.e., writes what this loader reads with identical encoding. Transfer between loader and writer should be lossless.

Returns null if no complement is defined.

Overrides:

getWriterComplement in class FileLoader

Returns: