Package mgui.io.domestic.shapes

Class VolumeFileLoader

java.lang.Object

mgui.io.FileLoader

mgui.io.domestic.shapes.InterfaceShapeLoader

mgui.io.domestic.shapes.VolumeFileLoader

All Implemented Interfaces:

InterfaceIO, IconObject

Direct Known Subclasses:

FSLVolumeLoader, InterfileLoader, NiftiVolumeLoader, VolFileLoader, WunilVolumeLoader

public abstract class VolumeFileLoader
extends InterfaceShapeLoader

Loader for reading from a volume (3D grid) file into a Volume3DInt object.

Since:

1.0

Version:

1.0

Author:

Andrew Reid

Field Summary

Fields

Modifier and Type	Field	Description
double	dataMax
double	dataMin
boolean	flipX
boolean	flipY
boolean	flipZ
protected float	maxAlpha
protected float	minAlpha
protected boolean	setAlpha

Fields inherited from class mgui.io.FileLoader

dataFile, dataURL, options

Constructor Summary

Constructors

Constructor	Description
VolumeFileLoader()

Method Summary

Modifier and Type	Method	Description
VolumeInputOptions	getDefaultOptions()	Returns a default set of options for loading a volume with this loader.
javax.swing.Icon	getObjectIcon()	Returns the Icon associated with this object.
java.util.ArrayList<java.lang.Class<?>>	getSupportedObjects()	Returns a list of classes for objects which are supported by this I/O interface
int	getVolCount()
Volume3DInt	getVolume3D()
Volume3DInt	getVolume3D(int t)	Load the volume at time point t.
Volume3DInt	getVolume3D(int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the metadata.
Volume3DInt	getVolume3D(VolumeInputOptions options)	Creates and returns a grid based on the parameters in options.
Volume3DInt	getVolume3D(VolumeInputOptions options, int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the metadata.
protected Volume3DInt	getVolume3DCustom(VolumeInputOptions options, int v, ProgressUpdater progress_bar)	Creates and returns a grid based on the parameters in options.
abstract VolumeMetadata	getVolumeMetadata()	Returns a set of metadata describing the current volume file.
boolean	load(InterfaceIOOptions options, ProgressUpdater progress_bar)	Loads data from the set of files or URLs specified by options.
java.lang.Object	loadObject(ProgressUpdater progress_bar, InterfaceIOOptions options)	Loads data into an instance of the object corresponding to this loader.
InterfaceShape	loadShape(ShapeInputOptions options, ProgressUpdater progress_bar)	Loads a shape with the given options.
Volume3DInt	loadVolume()	Load the volume at the current file, with default options.
Volume3DInt	loadVolume(ProgressUpdater progress_bar)	Load the volume at the current file.
Volume3DInt	loadVolume(VolumeInputOptions options, ProgressUpdater progress_bar)	Load the volume at the current file, with the given options.
void	setAlpha(boolean set)
void	setAlpha(boolean set, float min, float max)
boolean	setVolume3D(Volume3DInt volume, int v, VolumeInputOptions options)
boolean	setVolume3D(Volume3DInt volume, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	setVolume3D(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
boolean	setVolume3D(Volume3DInt volume, VolumeInputOptions options)
protected abstract boolean	setVolume3DBlocking(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)
protected boolean	setVolume3DWorker(Volume3DInt volume, java.lang.String column, int v, VolumeInputOptions options, ProgressUpdater progress)

Methods inherited from class mgui.io.FileLoader

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

Methods inherited from class java.lang.Object

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

Field Details

setAlpha

protected boolean setAlpha

minAlpha

protected float minAlpha

maxAlpha

protected float maxAlpha

flipX

public boolean flipX

flipY

public boolean flipY

flipZ

public boolean flipZ

dataMax

public double dataMax

dataMin

public double dataMin

Constructor Details

VolumeFileLoader

public VolumeFileLoader()

Method Details

loadShape

public InterfaceShape loadShape(ShapeInputOptions options,
ProgressUpdater progress_bar)
                         throws java.io.IOException

Description copied from class: InterfaceShapeLoader

Loads a shape with the given options.

Specified by:

loadShape in class InterfaceShapeLoader

Returns:

Throws:

java.io.IOException

getVolCount

public int getVolCount()

getVolume3D

public Volume3DInt getVolume3D()

getVolumeMetadata

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

Returns a set of metadata describing the current volume file.

Returns:

Throws:

java.io.IOException

java.io.FileNotFoundException

loadObject

public java.lang.Object loadObject(ProgressUpdater progress_bar,
InterfaceIOOptions options)
                            throws java.io.IOException

Description copied from class: FileLoader

Loads data into an instance of the object corresponding to this loader. If loaded object is of type PersistentObject, this method should also set the file loader and reference URL for the object. TODO: make generic?

Overrides:

loadObject in class InterfaceShapeLoader

Parameters:

progress_bar - An optional progress updater. Can be null.

options - Options defining the loading process

Returns:

Throws:

java.io.IOException

loadVolume

public Volume3DInt loadVolume(VolumeInputOptions options,
ProgressUpdater progress_bar)

Load the volume at the current file, with the given options.

Parameters:

options -

progress_bar -

Returns:

loadVolume

public Volume3DInt loadVolume()

Load the volume at the current file, with default options.

Returns:

loadVolume

public Volume3DInt loadVolume(ProgressUpdater progress_bar)

Load the volume at the current file.

Parameters:

progress_bar -

Returns:

getVolume3D

public Volume3DInt getVolume3D(int t)
                        throws ShapeIOException

Load the volume at time point t.

Parameters:

t -

Returns:

Throws:

ShapeIOException

getVolume3D

public Volume3DInt getVolume3D(VolumeInputOptions options)

Creates and returns a grid based on the parameters in options.

Parameters:

options -

Returns:

getVolume3D

public Volume3DInt getVolume3D(int v,
ProgressUpdater progress_bar)

Creates and returns a grid based on the metadata.

Parameters:

options -

Returns:

getVolume3D

public Volume3DInt getVolume3D(VolumeInputOptions options,
int v,
ProgressUpdater progress_bar)

Creates and returns a grid based on the metadata.

Parameters:

options -

Returns:

getDefaultOptions

public VolumeInputOptions getDefaultOptions()

Returns a default set of options for loading a volume with this loader.

Returns:

getVolume3DCustom

protected Volume3DInt getVolume3DCustom(VolumeInputOptions options,
int v,
ProgressUpdater progress_bar)

Creates and returns a grid based on the parameters in options. Use this method to override the metadata if necessary.

Parameters:

options -

Returns:

setVolume3D

public boolean setVolume3D(Volume3DInt volume,
VolumeInputOptions options)
                    throws ShapeIOException

Throws:

ShapeIOException

setVolume3D

public boolean setVolume3D(Volume3DInt volume,
int v,
VolumeInputOptions options)
                    throws ShapeIOException

Throws:

ShapeIOException

setVolume3D

public boolean setVolume3D(Volume3DInt volume,
int v,
VolumeInputOptions options,
ProgressUpdater progress)
                    throws ShapeIOException

Throws:

ShapeIOException

setVolume3D

public boolean setVolume3D(Volume3DInt volume,
java.lang.String column,
int v,
VolumeInputOptions options,
ProgressUpdater progress)
                    throws ShapeIOException

Throws:

ShapeIOException

setVolume3DWorker

protected boolean setVolume3DWorker(Volume3DInt volume,
java.lang.String column,
int v,
VolumeInputOptions options,
ProgressUpdater progress)

setVolume3DBlocking

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

Throws:

ShapeIOException

setAlpha

public void setAlpha(boolean set,
float min,
float max)

setAlpha

public void setAlpha(boolean set)

load

public boolean load(InterfaceIOOptions options,
ProgressUpdater progress_bar)

Description copied from class: FileLoader

Loads data from the set of files or URLs specified by options. Loading is controlled by the specifications of options. If loaded object is of type PersistentObject, this method should also set the file loader and reference URL for the object.

This method should also set the URL reference and writer and loader attributes to match this one and its complement.

Overrides:

load in class InterfaceShapeLoader

progress_bar - An optional progress updater. Can be null.

Returns:

getObjectIcon

public javax.swing.Icon getObjectIcon()

Description copied from interface: IconObject

Returns the Icon associated with this object.

Specified by:

getObjectIcon in interface IconObject

Overrides:

getObjectIcon in class FileLoader

Returns:

getSupportedObjects

public java.util.ArrayList<java.lang.Class<?>> getSupportedObjects()

Description copied from interface: InterfaceIO

Returns a list of classes for objects which are supported by this I/O interface

Specified by:

getSupportedObjects in interface InterfaceIO

Overrides:

getSupportedObjects in class FileLoader

Returns: