A B C D E F G H I L M N P R S T U V X

A

AbstractSequenceDescription<V extends BasicViewSetup,D extends BasicViewDescription<V>,L extends BasicImgLoader> - Class in mpicbg.spim.data.generic.sequence

A SPIM sequence consisting of a list of timepoints and a list of view setups.

AbstractSequenceDescription(TimePoints, Map<Integer, ? extends V>, L, MissingViews) - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

AbstractSequenceDescription() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

AbstractSequenceDescriptionUtils - Class in mpicbg.spim.data.generic.sequence

AbstractSequenceDescriptionUtils() - Constructor for class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils

AbstractSpimData<S extends AbstractSequenceDescription<?,?,?>> - Class in mpicbg.spim.data.generic

AbstractSpimData(File, S, ViewRegistrations) - Constructor for class mpicbg.spim.data.generic.AbstractSpimData

AbstractSpimData(URI, S, ViewRegistrations) - Constructor for class mpicbg.spim.data.generic.AbstractSpimData

AbstractSpimData() - Constructor for class mpicbg.spim.data.generic.AbstractSpimData

affine - Variable in class mpicbg.spim.data.registration.ViewTransformAffine

affineTransform3DElement(String, AffineGet) - Static method in class mpicbg.spim.data.XmlHelpers

Angle - Class in mpicbg.spim.data.sequence

Defines an angle which is part of the ViewSetup.

Angle(int, String, double, double[]) - Constructor for class mpicbg.spim.data.sequence.Angle

Angle(int, String) - Constructor for class mpicbg.spim.data.sequence.Angle

Angle(int) - Constructor for class mpicbg.spim.data.sequence.Angle

Angle() - Constructor for class mpicbg.spim.data.sequence.Angle

ANGLE_ROTATIONAXIS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ANGLE_ROTATIONDEGREES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ANGLE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

angleAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup

ANGLES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

asAffine3D() - Method in interface mpicbg.spim.data.registration.ViewTransform

A representation of this ViewTransform as a 3D AffineGet.

asAffine3D() - Method in class mpicbg.spim.data.registration.ViewTransformAffine

attributeMap - Variable in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

Maps attribute tag name to map from id to entity.

ATTRIBUTES_NAME_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

ATTRIBUTES_SPECIALIZED_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

ATTRIBUTES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

B

BASEPATH_TAG - Static variable in class mpicbg.spim.data.XmlKeys

BasicImgLoader - Interface in mpicbg.spim.data.generic.sequence

Provides images for a sequence.

BasicMultiResolutionImgLoader - Interface in mpicbg.spim.data.generic.sequence

A BasicImgLoader providing multiple resolutions of each image.

BasicMultiResolutionSetupImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence

A BasicSetupImgLoader providing multiple resolutions of each image.

BasicSetupImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence

Provides images for one setup of a sequence.

BasicViewDescription<V extends BasicViewSetup> - Class in mpicbg.spim.data.generic.sequence

TODO

BasicViewDescription(int, int, boolean, AbstractSequenceDescription<? extends V, ?, ?>) - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewDescription

TODO

BasicViewSetup - Class in mpicbg.spim.data.generic.sequence

An view setup is an Entity that may have a name, image size, and voxel size.

BasicViewSetup(int, String, Dimensions, VoxelDimensions) - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewSetup

BasicViewSetup() - Constructor for class mpicbg.spim.data.generic.sequence.BasicViewSetup

booleanElement(String, boolean) - Static method in class mpicbg.spim.data.XmlHelpers

BoundedTypeBasicImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence

C

changeIds(Collection<? extends Entity>, Map<Integer, Integer>) - Static method in class mpicbg.spim.data.generic.base.EntityUtils

changeIds(Collection<? extends Entity>, int...) - Static method in class mpicbg.spim.data.generic.base.EntityUtils

changeIds(AbstractSequenceDescription<V, ?, ?>, Map<Integer, Integer>) - Static method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils

changeIds(AbstractSequenceDescription<V, ?, ?>, int...) - Static method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescriptionUtils

changeViewsetupIds(ViewRegistrations, Map<Integer, Integer>) - Static method in class mpicbg.spim.data.registration.ViewRegistrationsUtils

changeViewsetupIds(ViewRegistrations, int...) - Static method in class mpicbg.spim.data.registration.ViewRegistrationsUtils

changeViewsetupIds(Collection<? extends ViewId>, Map<Integer, Integer>) - Static method in class mpicbg.spim.data.sequence.ViewIdUtils

Channel - Class in mpicbg.spim.data.sequence

Defines a channel which is part of the ViewSetup.

Channel(int, String) - Constructor for class mpicbg.spim.data.sequence.Channel

Construct a channel with the specified id and name.

Channel(int) - Constructor for class mpicbg.spim.data.sequence.Channel

Construct a Channel with the specified id.

Channel() - Constructor for class mpicbg.spim.data.sequence.Channel

CHANNEL_TAG - Static variable in class mpicbg.spim.data.XmlKeys

channelAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup

CHANNELS_TAG1 - Static variable in class mpicbg.spim.data.XmlKeys

compareTo(Angle) - Method in class mpicbg.spim.data.sequence.Angle

Compares the ids.

compareTo(Channel) - Method in class mpicbg.spim.data.sequence.Channel

Compares the ids.

compareTo(Illumination) - Method in class mpicbg.spim.data.sequence.Illumination

Compares the ids.

compareTo(Tile) - Method in class mpicbg.spim.data.sequence.Tile

Compares the ids.

compareTo(ViewId) - Method in class mpicbg.spim.data.sequence.ViewId

Order by timepoint id, then setup id.

compareTo(ViewSetup) - Method in class mpicbg.spim.data.sequence.ViewSetup

Compares the ids.

concatenateTransform(ViewTransform) - Method in class mpicbg.spim.data.registration.ViewRegistration

Concatenate a transform to the transform list and update the concatenated model.

createSequenceDescription() - Static method in class mpicbg.spim.data.SpimDataExample2

createSetups() - Static method in class mpicbg.spim.data.SpimDataExample2

createTimePoints() - Static method in class mpicbg.spim.data.SpimDataExample2

createViewDescription(int, int) - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

createViewDescription(int, int) - Method in class mpicbg.spim.data.sequence.SequenceDescription

createViewDescriptions() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

createViewRegistrations() - Static method in class mpicbg.spim.data.SpimDataExample2

createXmlIoForFormat(String) - Static method in class mpicbg.spim.data.generic.sequence.ImgLoaders

createXmlIoForImgLoaderClass(Class<T>) - Static method in class mpicbg.spim.data.generic.sequence.ImgLoaders

createXmlIoForName(String) - Static method in class mpicbg.spim.data.generic.base.ViewSetupAttributes

D

DefaultVoxelDimensions - Class in mpicbg.spim.data.sequence

A default implementation of VoxelDimensions with spacing of one for all dimensions and units of "pixel"s.

DefaultVoxelDimensions(int) - Constructor for class mpicbg.spim.data.sequence.DefaultVoxelDimensions

dimension(int) - Method in class mpicbg.spim.data.sequence.DefaultVoxelDimensions

Always returns one.

dimension(int) - Method in class mpicbg.spim.data.sequence.FinalVoxelDimensions

dimension(int) - Method in interface mpicbg.spim.data.sequence.VoxelDimensions

Get the size of a voxel in a given dimension d.

dimensions(double[]) - Method in class mpicbg.spim.data.sequence.DefaultVoxelDimensions

Sets all entries to one.

dimensions(double[]) - Method in class mpicbg.spim.data.sequence.FinalVoxelDimensions

dimensions(double[]) - Method in interface mpicbg.spim.data.sequence.VoxelDimensions

Write the size of a voxel in each dimension into double[].

dimensionsAsDoubleArray() - Method in interface mpicbg.spim.data.sequence.VoxelDimensions

Get the size of a voxel in each dimension as a new double[] array.

dimensionsElement(String, Dimensions) - Static method in class mpicbg.spim.data.XmlHelpers

doubleArrayElement(String, double[]) - Static method in class mpicbg.spim.data.XmlHelpers

Append a double array as space-separated list of values

doubleElement(String, double) - Static method in class mpicbg.spim.data.XmlHelpers

E

Entity - Class in mpicbg.spim.data.generic.base

Something that has a unique id.

Entity(int) - Constructor for class mpicbg.spim.data.generic.base.Entity

Entity() - Constructor for class mpicbg.spim.data.generic.base.Entity

EntityUtils - Class in mpicbg.spim.data.generic.base

EntityUtils() - Constructor for class mpicbg.spim.data.generic.base.EntityUtils

equals(Object) - Method in class mpicbg.spim.data.generic.base.Entity

Two Entitys are equal if they have the same Entity.getId().

equals(Object) - Method in class mpicbg.spim.data.sequence.ViewId

Two ViewId are equal if they have the same timepoint and setup ids.

exampleSequenceDescription() - Static method in class mpicbg.spim.data.SpimDataExample2

exampleTimePoints() - Static method in class mpicbg.spim.data.SpimDataExample2

exampleViewRegistrations() - Static method in class mpicbg.spim.data.SpimDataExample2

exampleViewSetups() - Static method in class mpicbg.spim.data.SpimDataExample2

F

FinalVoxelDimensions - Class in mpicbg.spim.data.sequence

An implementation of VoxelDimensions.

FinalVoxelDimensions(String, double...) - Constructor for class mpicbg.spim.data.sequence.FinalVoxelDimensions

FinalVoxelDimensions(VoxelDimensions) - Constructor for class mpicbg.spim.data.sequence.FinalVoxelDimensions

fromXml(Element) - Method in class mpicbg.spim.data.generic.base.XmlIoEntity

Create an object from the given element.

fromXml(Element) - Method in class mpicbg.spim.data.generic.base.XmlIoEntityMap

fromXml(Element) - Method in class mpicbg.spim.data.generic.base.XmlIoNamedEntity

fromXml(Element) - Method in class mpicbg.spim.data.generic.base.XmlIoSingleton

Create an object from the given element.

fromXml(Element, File) - Method in class mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription

fromXml(Element, URI) - Method in class mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription

fromXml(Element, File, AbstractSequenceDescription<?, ?, ?>) - Method in interface mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader

fromXml(Element, URI, AbstractSequenceDescription<?, ?, ?>) - Method in interface mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader

Subclasses that construct ImgLoaders that are able to read from sources other than local files should override this method.

fromXml(Element) - Method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

fromXml(Element) - Method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetups

fromXml(Element, File) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

fromXml(Element, URI) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

fromXml(Element) - Method in class mpicbg.spim.data.registration.XmlIoViewRegistration

fromXml(Element) - Method in class mpicbg.spim.data.registration.XmlIoViewRegistrations

Load ViewRegistrations from the given DOM element.

fromXml(Element) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

Load a ViewTransform from the given DOM element.

fromXml(Element) - Method in class mpicbg.spim.data.sequence.XmlIoAngle

fromXml(Element) - Method in class mpicbg.spim.data.sequence.XmlIoMissingViews

fromXml(Element) - Method in class mpicbg.spim.data.sequence.XmlIoTile

fromXml(Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

fromXmlAffine(Element) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

fromXmlGeneric(Element) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

fromXmlList(TimePoints, Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Create TimePointsPattern from < > element of type

fromXmlPattern(Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Create TimePointsPattern from < > element of type

fromXmlRange(TimePoints, Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Create TimePointsPattern from < > element of type

G

getAffineTransform3D(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getAffineTransform3D(Element, String, AffineTransform3D) - Static method in class mpicbg.spim.data.XmlHelpers

getAllAngles() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Angles occurring in any setups.

getAllAngles(Collection<? extends ViewSetup>) - Static method in class mpicbg.spim.data.sequence.ViewSetups

getAllAnglesOrdered() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Angles occurring in any setup, ordered by angle id.

getAllChannels() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Channels occurring in any setup.

getAllChannels(Collection<? extends ViewSetup>) - Static method in class mpicbg.spim.data.sequence.ViewSetups

getAllChannelsOrdered() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Channels occurring in any setup, ordered by channel id.

getAllIlluminations() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Illuminations occurring in any setups.

getAllIlluminations(Collection<? extends ViewSetup>) - Static method in class mpicbg.spim.data.sequence.ViewSetups

getAllIlluminationsOrdered() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Illuminations occurring in any setup, ordered by illumination id.

getAllTiles() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Tiles occurring in any setup.

getAllTiles(Collection<? extends ViewSetup>) - Static method in class mpicbg.spim.data.sequence.ViewSetups

getAllTilesOrdered() - Method in class mpicbg.spim.data.sequence.SequenceDescription

Get all Tiles occurring in any setup, ordered by tile id.

getAngle() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get stage rotation Angle.

getAttribute(Class<T>) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

getAttributes() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

getBasePath() - Method in class mpicbg.spim.data.generic.AbstractSpimData

Get the base path of the sequence.

getBasePathURI() - Method in class mpicbg.spim.data.generic.AbstractSpimData

getBoolean(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getBoolean(Element, String, boolean) - Static method in class mpicbg.spim.data.XmlHelpers

getChannel() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the Channel.

getDimensions(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getDimensions(Element, String, Dimensions) - Static method in class mpicbg.spim.data.XmlHelpers

getDouble(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getDouble(Element, String, double) - Static method in class mpicbg.spim.data.XmlHelpers

getDoubleArray(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getDoubleArray(Element, String, double[]) - Static method in class mpicbg.spim.data.XmlHelpers

getDoubleArrayAttribute(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getDoubleAttribute(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getEntityClass() - Method in class mpicbg.spim.data.generic.base.XmlIoEntity

getFloatImage(ViewId, boolean) - Method in interface mpicbg.spim.data.legacy.LegacyImgLoader

Get FloatType image.

getFloatImage(int, boolean, ImgLoaderHint...) - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

getFloatImage(int, boolean, ImgLoaderHint...) - Method in interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader

getFloatImage(int, int, boolean, ImgLoaderHint...) - Method in interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader

Get image at the specified timepoint and resolution level, converted to FloatType.

getFloatImage(int, boolean, ImgLoaderHint...) - Method in interface mpicbg.spim.data.sequence.SetupImgLoader

Get image at the specified timepoint, converted to FloatType.

getId() - Method in class mpicbg.spim.data.generic.base.Entity

Get the unique id of this entity.

getId() - Method in class mpicbg.spim.data.sequence.Angle

Get the unique id of this angle.

getId() - Method in class mpicbg.spim.data.sequence.Channel

Get the unique id of this channel.

getId() - Method in class mpicbg.spim.data.sequence.Illumination

Get the unique id of this illumination direction.

getId() - Method in class mpicbg.spim.data.sequence.Tile

Get the unique id of this location.

getId() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the unique id of this ViewSetup.

getIllumination() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the Illumination direction.

getImage(int, int, ImgLoaderHint...) - Method in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader

Get the image at the specified timepoint and resolution level.

getImage(int, ImgLoaderHint...) - Method in interface mpicbg.spim.data.generic.sequence.BasicSetupImgLoader

Get the image at the specified timepoint.

getImage(ViewId) - Method in interface mpicbg.spim.data.legacy.LegacyBasicImgLoader

Get the un-normalized image of the default pixel type of this BasicImgLoader.

getImage(int, ImgLoaderHint...) - Method in class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper.SetupImgLoaderWrapper

getImage(int, ImgLoaderHint...) - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

getImageSize(ViewId) - Method in interface mpicbg.spim.data.legacy.LegacyImgLoader

Get the size of an image.

getImageSize(int) - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

getImageSize(int) - Method in interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader

getImageSize(int, int) - Method in interface mpicbg.spim.data.sequence.MultiResolutionSetupImgLoader

Get the size of an image.

getImageSize(int) - Method in interface mpicbg.spim.data.sequence.SetupImgLoader

Get the size of an image.

getImageType() - Method in interface mpicbg.spim.data.generic.sequence.BasicSetupImgLoader

getImageType() - Method in interface mpicbg.spim.data.legacy.LegacyBasicImgLoader

getImageType() - Method in class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper.SetupImgLoaderWrapper

getImageType() - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

getImgLoader() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getInt(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getInt(Element, String, int) - Static method in class mpicbg.spim.data.XmlHelpers

getIntArray(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getIntArray(Element, String, int[]) - Static method in class mpicbg.spim.data.XmlHelpers

getIntAttribute(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getLocation() - Method in class mpicbg.spim.data.sequence.Tile

Get the the approximate location (as defined by the microscope meta-data).

getLongArray(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getLongArray(Element, String, long[]) - Static method in class mpicbg.spim.data.XmlHelpers

getMipmapResolutions() - Method in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader

Get the sub-sampling factors, indexed by resolution level and dimension.

getMipmapTransforms() - Method in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader

Get the transformation from coordinates of the sub-sampled image of a a resolution level to coordinates of the full resolution image.

getMissingViews() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getMissingViews() - Method in class mpicbg.spim.data.sequence.MissingViews

getModel() - Method in class mpicbg.spim.data.registration.ViewRegistration

Get the affine registration model of this view mapping local into world coordinates.

getName() - Method in class mpicbg.spim.data.generic.base.NamedEntity

getName() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Get the name of this setup.

getName() - Method in interface mpicbg.spim.data.registration.ViewTransform

Get the name of this transform.

getName() - Method in class mpicbg.spim.data.registration.ViewTransformAffine

getName() - Method in class mpicbg.spim.data.sequence.Angle

Get the name of this angle.

getName() - Method in class mpicbg.spim.data.sequence.Channel

Get the name of this channel.

getName() - Method in class mpicbg.spim.data.sequence.Illumination

Get the name of this illumination direction.

getName() - Method in class mpicbg.spim.data.sequence.Tile

Get the name of this tile.

getName() - Method in class mpicbg.spim.data.sequence.TimePoint

getName() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the name of this setup.

getNameForClass(Class<? extends Entity>) - Static method in class mpicbg.spim.data.generic.base.ViewSetupAttributes

getPattern() - Method in class mpicbg.spim.data.sequence.TimePointsPattern

getRelativePath(File, File) - Static method in class mpicbg.spim.data.XmlHelpers

getReplaceString(String, char) - Static method in class mpicbg.spim.data.sequence.IntegerPattern

Analyzes a file pattern and returns the number of digits as well as the replace pattern for a certain type, e.g.

getRotationAngleDegrees() - Method in class mpicbg.spim.data.sequence.Angle

Get the approximate rotation angle (as defined by the microscope meta-data).

getRotationAxis() - Method in class mpicbg.spim.data.sequence.Angle

Get the the approximate rotation axis (as defined by the microscope meta-data).

getSequenceDescription() - Method in class mpicbg.spim.data.generic.AbstractSpimData

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.generic.sequence.BasicImgLoader

Get the BasicSetupImgLoader for the specified view setup.

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader

Get the BasicMultiResolutionSetupImgLoader for the specified view setup.

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.generic.sequence.BoundedTypeBasicImgLoader

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.generic.sequence.TypedBasicImgLoader

getSetupImgLoader(int) - Method in class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper

getSetupImgLoader(int) - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.sequence.ImgLoader

Get the SetupImgLoader for the specified view setup.

getSetupImgLoader(int) - Method in interface mpicbg.spim.data.sequence.MultiResolutionImgLoader

Get the MultiResolutionSetupImgLoader for the specified view setup.

getSize() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Get the Dimensions of images from this setup.

getSize() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the Dimensions of images from this setup.

getTag() - Method in class mpicbg.spim.data.generic.base.XmlIoEntity

Get the tag name of the XML element that is written by this XmlIoEntity.

getTag() - Method in class mpicbg.spim.data.generic.base.XmlIoSingleton

Get the tag name of the XML element that is written by this XmlIoSingleton.

getTag() - Method in class mpicbg.spim.data.registration.XmlIoViewRegistration

Get the tag name of the XML element that is written by this class.

getTag() - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

Get the tag name of the XML element that is written by this class.

getText(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

getText(Element, String, String) - Static method in class mpicbg.spim.data.XmlHelpers

getTile() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the Tile.

getTimePoint() - Method in class mpicbg.spim.data.generic.sequence.BasicViewDescription

getTimePointId() - Method in class mpicbg.spim.data.sequence.ViewId

Get the timepoint id.

getTimePoints() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getTimePoints() - Method in class mpicbg.spim.data.sequence.TimePoints

getTimePointsOrdered() - Method in class mpicbg.spim.data.sequence.TimePoints

getTransformList() - Method in class mpicbg.spim.data.registration.ViewRegistration

Get the list of transforms.

getVersion(Element) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

getVersion() - Static method in class mpicbg.spim.data.Version

getViewDescription(int, int) - Method in class mpicbg.spim.data.sequence.SequenceDescription

convenience method.

getViewDescription(ViewId) - Method in class mpicbg.spim.data.sequence.SequenceDescription

convenience method.

getViewDescriptions() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getViewRegistration(int, int) - Method in class mpicbg.spim.data.registration.ViewRegistrations

getViewRegistration(ViewId) - Method in class mpicbg.spim.data.registration.ViewRegistrations

getViewRegistrations() - Method in class mpicbg.spim.data.generic.AbstractSpimData

getViewRegistrations() - Method in class mpicbg.spim.data.registration.ViewRegistrations

getViewRegistrationsOrdered() - Method in class mpicbg.spim.data.registration.ViewRegistrations

getViewSetup() - Method in class mpicbg.spim.data.generic.sequence.BasicViewDescription

getViewSetupId() - Method in class mpicbg.spim.data.sequence.ViewId

Get the setup id.

getViewSetups() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getViewSetupsOrdered() - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

getVoxelDimensions(Element, String) - Static method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

getVoxelDimensions(Element, String, VoxelDimensions) - Static method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

getVoxelSize() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Get the VoxelDimensions of images from this setup.

getVoxelSize(ViewId) - Method in interface mpicbg.spim.data.legacy.LegacyImgLoader

Get the voxel size of an image.

getVoxelSize(int) - Method in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

getVoxelSize(int) - Method in interface mpicbg.spim.data.sequence.SetupImgLoader

Get the voxel size of an image.

getVoxelSize() - Method in class mpicbg.spim.data.sequence.ViewSetup

Get the VoxelDimensions of images from this setup.

H

handledTags - Variable in class mpicbg.spim.data.generic.base.XmlIoEntity

handledTags - Variable in class mpicbg.spim.data.generic.base.XmlIoSingleton

hashCode() - Method in class mpicbg.spim.data.generic.base.Entity

hashCode() - Method in class mpicbg.spim.data.sequence.ViewId

hasLocation() - Method in class mpicbg.spim.data.sequence.Tile

Is the locations defined?

hasName() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Whether this setup has has a BasicViewSetup.getName().

hasName() - Method in interface mpicbg.spim.data.registration.ViewTransform

Whether this transform has has a ViewTransform.getName().

hasName() - Method in class mpicbg.spim.data.registration.ViewTransformAffine

hasName() - Method in class mpicbg.spim.data.sequence.ViewSetup

Whether this setup has has a ViewSetup.getName().

hasRotation() - Method in class mpicbg.spim.data.sequence.Angle

Is the approximate rotation defined?

hasSize() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Whether this setup has has a BasicViewSetup.getSize().

hasSize() - Method in class mpicbg.spim.data.sequence.ViewSetup

Whether this setup has has a ViewSetup.getSize().

hasVoxelSize() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

Whether this setup has has a BasicViewSetup.getVoxelSize().

hasVoxelSize() - Method in class mpicbg.spim.data.sequence.ViewSetup

Whether this setup has has a ViewSetup.getVoxelSize().

I

ID_TAG - Static variable in class mpicbg.spim.data.XmlKeys

Generic

identity() - Method in class mpicbg.spim.data.registration.ViewRegistration

Reset the ViewRegistration to the identity transform

idMap(Collection<T>) - Static method in class mpicbg.spim.data.generic.base.Entity

Helper method to create a id-to-entity map from a collection of entities.

Illumination - Class in mpicbg.spim.data.sequence

Defines an illumination direction which is part of the ViewSetup.

Illumination(int, String) - Constructor for class mpicbg.spim.data.sequence.Illumination

Construct an illumination direction with the specified id and name.

Illumination(int) - Constructor for class mpicbg.spim.data.sequence.Illumination

Construct an illumination direction with the specified id.

Illumination() - Constructor for class mpicbg.spim.data.sequence.Illumination

ILLUMINATION_TAG - Static variable in class mpicbg.spim.data.XmlKeys

illuminationAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup

ILLUMINATIONS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ImgLoader - Interface in mpicbg.spim.data.sequence

A BasicImgLoader that is able to also provide each image converted to FloatType.

IMGLOADER_FORMAT_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

IMGLOADER_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ImgLoaderHint - Interface in mpicbg.spim.data.generic.sequence

A hint to help BasicImgLoader to determine the best way to load an image.

ImgLoaderHints - Enum in mpicbg.spim.data.generic.sequence

Default set of ImgLoaderHint.

ImgLoaderIo - Annotation Type in mpicbg.spim.data.generic.sequence

Annotation for a class that creates a BasicImgLoader for a specific format (the format is specified in the XML "ImageLoader" element).

ImgLoaders - Class in mpicbg.spim.data.generic.sequence

ImgLoaders() - Constructor for class mpicbg.spim.data.generic.sequence.ImgLoaders

init(Element) - Method in interface mpicbg.spim.data.registration.ViewTransformGeneric

initialize the transform from a <> DOM element.

intArrayElement(String, int[]) - Static method in class mpicbg.spim.data.XmlHelpers

IntegerPattern - Class in mpicbg.spim.data.sequence

Class with static methods to deal with integer patterns defining ranges of numbers and create String instances based on simple expressions like {aaa} or {t}.

IntegerPattern() - Constructor for class mpicbg.spim.data.sequence.IntegerPattern

intElement(String, int) - Static method in class mpicbg.spim.data.XmlHelpers

isPathRelative(Element, String) - Static method in class mpicbg.spim.data.XmlHelpers

isPresent() - Method in class mpicbg.spim.data.generic.sequence.BasicViewDescription

TODO

L

LegacyBasicImgLoader<T> - Interface in mpicbg.spim.data.legacy

LegacyBasicImgLoaderWrapper<T,I extends LegacyBasicImgLoader<T>> - Class in mpicbg.spim.data.legacy

LegacyBasicImgLoaderWrapper(I) - Constructor for class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper

LegacyBasicImgLoaderWrapper.SetupImgLoaderWrapper - Class in mpicbg.spim.data.legacy

legacyImgLoader - Variable in class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper

LegacyImgLoader<T> - Interface in mpicbg.spim.data.legacy

legacyImgLoader - Variable in class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper

LegacyImgLoaderWrapper<T,I extends LegacyImgLoader<T>> - Class in mpicbg.spim.data.legacy

LegacyImgLoaderWrapper(I) - Constructor for class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper

LegacyImgLoaderWrapper.SetupImgLoaderWrapper - Class in mpicbg.spim.data.legacy

load(String) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

load(Reader, URI) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

Load SpimData from the given Reader (that can read from a local file, or S3 for example).

loadBasePathURI(Element, URI) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

loadPath(Element, String, String, File) - Static method in class mpicbg.spim.data.XmlHelpers

loadPath(Element, String, File) - Static method in class mpicbg.spim.data.XmlHelpers

loadPathURI(Element, String, String, URI) - Static method in class mpicbg.spim.data.XmlHelpers

loadPathURI(Element, String, URI) - Static method in class mpicbg.spim.data.XmlHelpers

longArrayElement(String, long[]) - Static method in class mpicbg.spim.data.XmlHelpers

M

main(String[]) - Static method in class mpicbg.spim.data.SpimDataExample

main(String[]) - Static method in class mpicbg.spim.data.SpimDataExample2

main(String[]) - Static method in class mpicbg.spim.data.SpimDataExample3

markMissingViews(Map<ViewId, D>, MissingViews) - Static method in class mpicbg.spim.data.generic.sequence.BasicViewDescription

MISSINGVIEW_SETUP_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

MISSINGVIEW_TAG - Static variable in class mpicbg.spim.data.XmlKeys

MISSINGVIEW_TIMEPOINT_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

MissingViews - Class in mpicbg.spim.data.sequence

MissingViews(Collection<? extends ViewId>) - Constructor for class mpicbg.spim.data.sequence.MissingViews

MissingViews() - Constructor for class mpicbg.spim.data.sequence.MissingViews

MISSINGVIEWS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

model - Variable in class mpicbg.spim.data.registration.ViewRegistration

The affine registration model of this view mapping local into world coordinates.

mpicbg.spim.data - package mpicbg.spim.data

mpicbg.spim.data.generic - package mpicbg.spim.data.generic

mpicbg.spim.data.generic.base - package mpicbg.spim.data.generic.base

mpicbg.spim.data.generic.sequence - package mpicbg.spim.data.generic.sequence

mpicbg.spim.data.legacy - package mpicbg.spim.data.legacy

mpicbg.spim.data.registration - package mpicbg.spim.data.registration

mpicbg.spim.data.sequence - package mpicbg.spim.data.sequence

MultiResolutionImgLoader - Interface in mpicbg.spim.data.sequence

An ImgLoader providing multiple resolutions of each image.

MultiResolutionSetupImgLoader<T> - Interface in mpicbg.spim.data.sequence

A SetupImgLoader providing multiple resolutions of each image.

N

name - Variable in class mpicbg.spim.data.registration.ViewTransformAffine

NAME_TAG - Static variable in class mpicbg.spim.data.XmlKeys

NamedEntity - Class in mpicbg.spim.data.generic.base

An Entity that has a name.

NamedEntity(int, String) - Constructor for class mpicbg.spim.data.generic.base.NamedEntity

NamedEntity() - Constructor for class mpicbg.spim.data.generic.base.NamedEntity

numDimensions() - Method in class mpicbg.spim.data.sequence.DefaultVoxelDimensions

numDimensions() - Method in class mpicbg.spim.data.sequence.FinalVoxelDimensions

numMipmapLevels() - Method in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader

Get number of resolution levels.

P

parseIntegerString(String) - Static method in class mpicbg.spim.data.sequence.IntegerPattern

Parse a pattern provided by the user defining a range of integers.

pathElement(String, File, File) - Static method in class mpicbg.spim.data.XmlHelpers

pathElementURI(String, URI, URI) - Static method in class mpicbg.spim.data.XmlHelpers

Returns an Element with the given tag name containing a String representation of the given path.

preconcatenateTransform(ViewTransform) - Method in class mpicbg.spim.data.registration.ViewRegistration

Pre-concatenate a transform to the transform list and update the concatenated model.

present - Variable in class mpicbg.spim.data.generic.sequence.BasicViewDescription

TODO

R

registerManually(Class<? extends XmlIoEntity<?>>) - Static method in class mpicbg.spim.data.generic.base.ViewSetupAttributes

Register an XmlIoEntity attribute IO class manually.

registerManually(Class<? extends XmlIoBasicImgLoader<?>>) - Static method in class mpicbg.spim.data.generic.sequence.ImgLoaders

Register an XmlIoBasicImgLoader class manually.

S

save(T, String) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

save(T, Writer, URI) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

Write spimData to the given Writer (that can write to a local file, or S3 for example).

sequenceDescription - Variable in class mpicbg.spim.data.generic.sequence.BasicViewDescription

SequenceDescription - Class in mpicbg.spim.data.sequence

SequenceDescription(TimePoints, Map<Integer, ViewSetup>) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription(TimePoints, Map<Integer, ViewSetup>, ImgLoader) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription(TimePoints, Map<Integer, ViewSetup>, ImgLoader, MissingViews) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription(TimePoints, Collection<ViewSetup>) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription(TimePoints, Collection<ViewSetup>, ImgLoader) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription(TimePoints, Collection<ViewSetup>, ImgLoader, MissingViews) - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SequenceDescription() - Constructor for class mpicbg.spim.data.sequence.SequenceDescription

SEQUENCEDESCRIPTION_TAG - Static variable in class mpicbg.spim.data.XmlKeys

SequenceDescription

setAngle(Angle) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the rotation Angle

setAttribute(T) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

setAttributeMap(HashMap<String, HashMap<Integer, ? extends Entity>>) - Method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

Set the attribute map.

setAttributes(Map<String, Entity>) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

setAttributes(Map<String, Entity>) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the attributes map.

setBasePath(File) - Method in class mpicbg.spim.data.generic.AbstractSpimData

setBasePathURI(URI) - Method in class mpicbg.spim.data.generic.AbstractSpimData

setChannel(Channel) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the Channel.

setIllumination(Illumination) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the Illumination direction.

setImgLoader(L) - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

setLocation(double[]) - Method in class mpicbg.spim.data.sequence.Tile

Set the approximate location (as defined by the microscope meta-data).

setMissingViews(MissingViews) - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

setMissingViews(Set<ViewId>) - Method in class mpicbg.spim.data.sequence.MissingViews

setName(String) - Method in class mpicbg.spim.data.generic.base.NamedEntity

setName(String) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

setName(String) - Method in class mpicbg.spim.data.sequence.Angle

Set the name of this angle.

setName(String) - Method in class mpicbg.spim.data.sequence.Channel

Set the name of this channel.

setName(String) - Method in class mpicbg.spim.data.sequence.Illumination

Set the name of this illumination direction.

setName(String) - Method in class mpicbg.spim.data.sequence.Tile

Set the name of this tile.

setPattern(String) - Method in class mpicbg.spim.data.sequence.TimePointsPattern

setPresent(boolean) - Method in class mpicbg.spim.data.generic.sequence.BasicViewDescription

setRotation(double[], double) - Method in class mpicbg.spim.data.sequence.Angle

Set the approximate rotation angle and axis (as defined by the microscope meta-data).

setSequenceDescription(S) - Method in class mpicbg.spim.data.generic.AbstractSpimData

setSize(Dimensions) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

setSize(Dimensions) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the Dimensions of images from this setup.

setTile(Tile) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the Tile.

setTimePoints(TimePoints) - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

setTimePoints(Collection<TimePoint>) - Method in class mpicbg.spim.data.sequence.TimePoints

setTimePoints(Map<Integer, TimePoint>) - Method in class mpicbg.spim.data.sequence.TimePoints

setup - Variable in class mpicbg.spim.data.sequence.ViewId

The setup id.

SetupImgLoader<T> - Interface in mpicbg.spim.data.sequence

A BasicSetupImgLoader that is able to also provide each image converted to FloatType.

SetupImgLoaderWrapper(int) - Constructor for class mpicbg.spim.data.legacy.LegacyBasicImgLoaderWrapper.SetupImgLoaderWrapper

SetupImgLoaderWrapper(int) - Constructor for class mpicbg.spim.data.legacy.LegacyImgLoaderWrapper.SetupImgLoaderWrapper

setViewRegistrations(ViewRegistrations) - Method in class mpicbg.spim.data.generic.AbstractSpimData

setViewRegistrations(Map<ViewId, ViewRegistration>) - Method in class mpicbg.spim.data.registration.ViewRegistrations

setViewSetups(Map<Integer, ? extends V>) - Method in class mpicbg.spim.data.generic.sequence.AbstractSequenceDescription

setVoxelSize(VoxelDimensions) - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

setVoxelSize(VoxelDimensions) - Method in class mpicbg.spim.data.sequence.ViewSetup

Set the VoxelDimensions of images from this setup.

size() - Method in class mpicbg.spim.data.sequence.TimePoints

sortById(L) - Static method in class mpicbg.spim.data.generic.base.Entity

Helper method to sort a list of entities by ascending id.

SpimData - Class in mpicbg.spim.data

SpimData(File, SequenceDescription, ViewRegistrations) - Constructor for class mpicbg.spim.data.SpimData

SpimData(URI, SequenceDescription, ViewRegistrations) - Constructor for class mpicbg.spim.data.SpimData

SpimData() - Constructor for class mpicbg.spim.data.SpimData

SPIMDATA_TAG - Static variable in class mpicbg.spim.data.XmlKeys

SpimData

SPIMDATA_VERSION_ATTRIBUTE_CURRENT - Static variable in class mpicbg.spim.data.XmlKeys

SPIMDATA_VERSION_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

SpimDataExample - Class in mpicbg.spim.data

SpimDataExample() - Constructor for class mpicbg.spim.data.SpimDataExample

SpimDataExample2 - Class in mpicbg.spim.data

The methods SpimDataExample2.exampleViewSetups(), SpimDataExample2.exampleTimePoints(), SpimDataExample2.exampleViewRegistrations(), and SpimDataExample2.exampleSequenceDescription() construct ViewSetups, TimePoints, ViewRegistrations, and SequenceDescription respectively.

SpimDataExample2() - Constructor for class mpicbg.spim.data.SpimDataExample2

SpimDataExample3 - Class in mpicbg.spim.data

SpimDataExample3() - Constructor for class mpicbg.spim.data.SpimDataExample3

SpimDataException - Exception in mpicbg.spim.data

SpimDataException() - Constructor for exception mpicbg.spim.data.SpimDataException

SpimDataException(String) - Constructor for exception mpicbg.spim.data.SpimDataException

SpimDataException(String, Throwable) - Constructor for exception mpicbg.spim.data.SpimDataException

SpimDataException(Throwable) - Constructor for exception mpicbg.spim.data.SpimDataException

SpimDataInstantiationException - Exception in mpicbg.spim.data

This exception is thrown when SpimData entities cannot be constructed (while loading).

SpimDataInstantiationException() - Constructor for exception mpicbg.spim.data.SpimDataInstantiationException

SpimDataInstantiationException(String) - Constructor for exception mpicbg.spim.data.SpimDataInstantiationException

SpimDataInstantiationException(String, Throwable) - Constructor for exception mpicbg.spim.data.SpimDataInstantiationException

SpimDataInstantiationException(Throwable) - Constructor for exception mpicbg.spim.data.SpimDataInstantiationException

SpimDataIOException - Exception in mpicbg.spim.data

This exception is thrown when an IO error occurs while reading or writing an XML file.

SpimDataIOException() - Constructor for exception mpicbg.spim.data.SpimDataIOException

SpimDataIOException(String) - Constructor for exception mpicbg.spim.data.SpimDataIOException

SpimDataIOException(String, Throwable) - Constructor for exception mpicbg.spim.data.SpimDataIOException

SpimDataIOException(Throwable) - Constructor for exception mpicbg.spim.data.SpimDataIOException

T

textElement(String, String) - Static method in class mpicbg.spim.data.XmlHelpers

Tile - Class in mpicbg.spim.data.sequence

Defines a tile that is part of the ViewSetup.

Tile(int, String, double[]) - Constructor for class mpicbg.spim.data.sequence.Tile

Tile(int, String) - Constructor for class mpicbg.spim.data.sequence.Tile

Tile(int) - Constructor for class mpicbg.spim.data.sequence.Tile

Tile() - Constructor for class mpicbg.spim.data.sequence.Tile

TILE_LOCATION_TAG - Static variable in class mpicbg.spim.data.XmlKeys

TILE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

tileAttributeKey - Static variable in class mpicbg.spim.data.sequence.ViewSetup

TILES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

TimePoint - Class in mpicbg.spim.data.sequence

TimePoint(int) - Constructor for class mpicbg.spim.data.sequence.TimePoint

TimePoint() - Constructor for class mpicbg.spim.data.sequence.TimePoint

timepoint - Variable in class mpicbg.spim.data.sequence.ViewId

The timepoint id.

TimePoints - Class in mpicbg.spim.data.sequence

TimePoints(Map<Integer, TimePoint>) - Constructor for class mpicbg.spim.data.sequence.TimePoints

TimePoints(Collection<TimePoint>) - Constructor for class mpicbg.spim.data.sequence.TimePoints

TimePoints() - Constructor for class mpicbg.spim.data.sequence.TimePoints

TIMEPOINTS_LIST_TYPE - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_PATTERN_TAG - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_PATTERN_TYPE - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_RANGE_FIRST - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_RANGE_LAST - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_RANGE_TYPE - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_TIMEPOINT_TAG - Static variable in class mpicbg.spim.data.XmlKeys

TIMEPOINTS_TYPE_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

TimePointsPattern - Class in mpicbg.spim.data.sequence

TimePointsPattern(String) - Constructor for class mpicbg.spim.data.sequence.TimePointsPattern

TimePointsPattern() - Constructor for class mpicbg.spim.data.sequence.TimePointsPattern

toString() - Method in class mpicbg.spim.data.generic.sequence.BasicViewSetup

toString() - Method in class mpicbg.spim.data.sequence.DefaultVoxelDimensions

toString() - Method in class mpicbg.spim.data.sequence.FinalVoxelDimensions

toString() - Method in class mpicbg.spim.data.sequence.ViewId

toXml(T) - Method in class mpicbg.spim.data.generic.base.XmlIoEntity

Create an XML element from the given object.

toXml(Map<Integer, ? extends T>) - Method in class mpicbg.spim.data.generic.base.XmlIoEntityMap

Sort the values in the entity map by id and add them to a new XmlIoSingleton.getTag() element.

toXml(Collection<T>) - Method in class mpicbg.spim.data.generic.base.XmlIoEntityMap

Add the values to a new XmlIoSingleton.getTag() element (in the iteration order of the collection).

toXml(T) - Method in class mpicbg.spim.data.generic.base.XmlIoNamedEntity

toXml() - Method in class mpicbg.spim.data.generic.base.XmlIoSingleton

Create an XML element from the given object.

toXml(T, File) - Method in class mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription

toXml(T, URI) - Method in class mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription

toXml(T, File) - Method in interface mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader

toXml(T, URI) - Method in interface mpicbg.spim.data.generic.sequence.XmlIoBasicImgLoader

Subclasses that construct ImgLoaders that are able to read from sources other than local files should override this method.

toXml(T) - Method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

toXml(Collection<T>) - Method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetups

toXml(T, File) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

toXml(T, URI) - Method in class mpicbg.spim.data.generic.XmlIoAbstractSpimData

toXml() - Method in interface mpicbg.spim.data.registration.ViewTransformGeneric

create a <> DOM element for this ViewTransform.

toXml(ViewRegistration) - Method in class mpicbg.spim.data.registration.XmlIoViewRegistration

toXml(ViewRegistrations) - Method in class mpicbg.spim.data.registration.XmlIoViewRegistrations

toXml(ViewTransform) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

toXml(Angle) - Method in class mpicbg.spim.data.sequence.XmlIoAngle

toXml(MissingViews) - Method in class mpicbg.spim.data.sequence.XmlIoMissingViews

toXml(Tile) - Method in class mpicbg.spim.data.sequence.XmlIoTile

toXml(TimePoints) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

toXmlAffine(ViewTransformAffine) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

toXmlGeneric(ViewTransformGeneric) - Method in class mpicbg.spim.data.registration.XmlIoViewTransform

toXmlList(TimePoints, Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Save TimePoints as a list of TimePoint.

toXmlPattern(TimePointsPattern, Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Save TimePointsPattern.

toXmlTryRange(TimePoints, Element) - Method in class mpicbg.spim.data.sequence.XmlIoTimePoints

Try to save a TimePoints list as a range.

transformList - Variable in class mpicbg.spim.data.registration.ViewRegistration

TypedBasicImgLoader<T> - Interface in mpicbg.spim.data.generic.sequence

U

unit() - Method in class mpicbg.spim.data.sequence.DefaultVoxelDimensions

unit() - Method in class mpicbg.spim.data.sequence.FinalVoxelDimensions

unit() - Method in interface mpicbg.spim.data.sequence.VoxelDimensions

Get the unit in which dimensions are specified.

updateModel() - Method in class mpicbg.spim.data.registration.ViewRegistration

Update the model by concatenating all transforms from the transform list.

V

valueOf(String) - Static method in enum mpicbg.spim.data.generic.sequence.ImgLoaderHints

Returns the enum constant of this type with the specified name.

values() - Static method in enum mpicbg.spim.data.generic.sequence.ImgLoaderHints

Returns an array containing the constants of this enum type, in the order they are declared.

Version - Class in mpicbg.spim.data

ViewDescription - Class in mpicbg.spim.data.sequence

ViewDescription(int, int, boolean, AbstractSequenceDescription<? extends ViewSetup, ?, ?>) - Constructor for class mpicbg.spim.data.sequence.ViewDescription

ViewId - Class in mpicbg.spim.data.sequence

Identifies a particular view as a combination of a TimePoint id and a ViewSetup id.

ViewId(int, int) - Constructor for class mpicbg.spim.data.sequence.ViewId

ViewIdUtils - Class in mpicbg.spim.data.sequence

ViewIdUtils() - Constructor for class mpicbg.spim.data.sequence.ViewIdUtils

ViewRegistration - Class in mpicbg.spim.data.registration

ViewRegistration(int, int) - Constructor for class mpicbg.spim.data.registration.ViewRegistration

Creates a new ViewRegistration object using the identity transformation

ViewRegistration(int, int, AffineTransform3D) - Constructor for class mpicbg.spim.data.registration.ViewRegistration

Creates a new ViewRegistration object using one AffineTransform3D transform.

ViewRegistration(int, int, ArrayList<ViewTransform>) - Constructor for class mpicbg.spim.data.registration.ViewRegistration

Creates a new ViewRegistration object using a list of ViewTransform transforms.

VIEWREGISTRATION_SETUP_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

VIEWREGISTRATION_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWREGISTRATION_TIMEPOINT_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

ViewRegistrations - Class in mpicbg.spim.data.registration

Only contains a Map from ViewId to ViewRegistration currently.

ViewRegistrations(Map<ViewId, ViewRegistration>) - Constructor for class mpicbg.spim.data.registration.ViewRegistrations

ViewRegistrations(Collection<ViewRegistration>) - Constructor for class mpicbg.spim.data.registration.ViewRegistrations

ViewRegistrations() - Constructor for class mpicbg.spim.data.registration.ViewRegistrations

VIEWREGISTRATIONS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ViewRegistrations

ViewRegistrationsUtils - Class in mpicbg.spim.data.registration

ViewRegistrationsUtils() - Constructor for class mpicbg.spim.data.registration.ViewRegistrationsUtils

ViewSetup - Class in mpicbg.spim.data.sequence

A collection of parameters describing the setup for a particular stack coming from a SPIM microscope (angle, illumination direction, etc).

ViewSetup(int, String, Dimensions, VoxelDimensions, Tile, Channel, Angle, Illumination) - Constructor for class mpicbg.spim.data.sequence.ViewSetup

TODO

ViewSetup(int, String, Dimensions, VoxelDimensions, Channel, Angle, Illumination) - Constructor for class mpicbg.spim.data.sequence.ViewSetup

TODO

VIEWSETUP_ANGLE_ID_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_ATTRIBUTES_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_CHANNEL_ID_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_ILLUMINATION_ID_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_SIZE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWSETUP_VOXELSIZE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ViewSetupAttributeIo - Annotation Type in mpicbg.spim.data.generic.base

ViewSetupAttributes - Class in mpicbg.spim.data.generic.base

ViewSetupAttributes() - Constructor for class mpicbg.spim.data.generic.base.ViewSetupAttributes

ViewSetups - Class in mpicbg.spim.data.sequence

Helper methods for dealing with ViewSetup collections.

ViewSetups() - Constructor for class mpicbg.spim.data.sequence.ViewSetups

VIEWSETUPS_TAG - Static variable in class mpicbg.spim.data.XmlKeys

ViewTransform - Interface in mpicbg.spim.data.registration

VIEWTRANSFORM_AFFINE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_CLASS_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_NAME_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_TYPE_ATTRIBUTE_NAME - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_TYPE_VALUE_AFFINE - Static variable in class mpicbg.spim.data.XmlKeys

VIEWTRANSFORM_TYPE_VALUE_GENERIC - Static variable in class mpicbg.spim.data.XmlKeys

ViewTransformAffine - Class in mpicbg.spim.data.registration

ViewTransformAffine(String, AffineTransform3D) - Constructor for class mpicbg.spim.data.registration.ViewTransformAffine

ViewTransformGeneric - Interface in mpicbg.spim.data.registration

VoxelDimensions - Interface in mpicbg.spim.data.sequence

VOXELDIMENSIONS_SIZE_TAG - Static variable in class mpicbg.spim.data.XmlKeys

VOXELDIMENSIONS_UNIT_TAG - Static variable in class mpicbg.spim.data.XmlKeys

voxelDimensionsElement(String, VoxelDimensions) - Static method in class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

X

XmlHelpers - Class in mpicbg.spim.data

XmlHelpers() - Constructor for class mpicbg.spim.data.XmlHelpers

XmlIoAbstractSequenceDescription<V extends BasicViewSetup,T extends AbstractSequenceDescription<V,?,?>> - Class in mpicbg.spim.data.generic.sequence

XmlIoAbstractSequenceDescription(Class<T>, XmlIoTimePoints, XmlIoEntityMap<V>, XmlIoMissingViews) - Constructor for class mpicbg.spim.data.generic.sequence.XmlIoAbstractSequenceDescription

XmlIoAbstractSpimData<S extends AbstractSequenceDescription<?,?,?>,T extends AbstractSpimData<S>> - Class in mpicbg.spim.data.generic

XmlIoAbstractSpimData(Class<T>, XmlIoAbstractSequenceDescription<?, S>, XmlIoViewRegistrations) - Constructor for class mpicbg.spim.data.generic.XmlIoAbstractSpimData

XmlIoAngle - Class in mpicbg.spim.data.sequence

XmlIoAngle() - Constructor for class mpicbg.spim.data.sequence.XmlIoAngle

XmlIoBasicImgLoader<T extends BasicImgLoader> - Interface in mpicbg.spim.data.generic.sequence

XmlIoBasicViewSetup<T extends BasicViewSetup> - Class in mpicbg.spim.data.generic.sequence

XmlIoBasicViewSetup(Class<T>) - Constructor for class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetup

XmlIoBasicViewSetups<T extends BasicViewSetup> - Class in mpicbg.spim.data.generic.sequence

Writes and reads collections of a specific BasicViewSetup subclass as an XML section.

XmlIoBasicViewSetups(Class<T>) - Constructor for class mpicbg.spim.data.generic.sequence.XmlIoBasicViewSetups

XmlIoChannel - Class in mpicbg.spim.data.sequence

XmlIoChannel() - Constructor for class mpicbg.spim.data.sequence.XmlIoChannel

XmlIoEntity<T extends Entity> - Class in mpicbg.spim.data.generic.base

Writes and reads objects of a specific subclass of Entity as XML elements.

XmlIoEntity(String, Class<T>) - Constructor for class mpicbg.spim.data.generic.base.XmlIoEntity

Construct a XmlIoEntity that writes and reads objects of the specified Class as XML elements with the specified tag name.

XmlIoEntityMap<T extends Entity> - Class in mpicbg.spim.data.generic.base

Writes and reads collections of a specific Entity subclass as an XML section.

XmlIoEntityMap(String, Class<T>, XmlIoEntity<T>) - Constructor for class mpicbg.spim.data.generic.base.XmlIoEntityMap

XmlIoIllumination - Class in mpicbg.spim.data.sequence

XmlIoIllumination() - Constructor for class mpicbg.spim.data.sequence.XmlIoIllumination

XmlIoMissingViews - Class in mpicbg.spim.data.sequence

XmlIoMissingViews() - Constructor for class mpicbg.spim.data.sequence.XmlIoMissingViews

XmlIoNamedEntity<T extends NamedEntity> - Class in mpicbg.spim.data.generic.base

XmlIoEntity for NamedEntity that also handles <>

XmlIoNamedEntity(String, Class<T>) - Constructor for class mpicbg.spim.data.generic.base.XmlIoNamedEntity

XmlIoSequenceDescription - Class in mpicbg.spim.data.sequence

XmlIoSequenceDescription() - Constructor for class mpicbg.spim.data.sequence.XmlIoSequenceDescription

XmlIoSingleton<T> - Class in mpicbg.spim.data.generic.base

Writes and reads objects of a specific class as XML elements.

XmlIoSingleton(String, Class<T>) - Constructor for class mpicbg.spim.data.generic.base.XmlIoSingleton

Construct a XmlIoSingleton that writes and reads objects of the specified Class as XML elements with the specified tag name.

XmlIoSpimData - Class in mpicbg.spim.data

XmlIoSpimData() - Constructor for class mpicbg.spim.data.XmlIoSpimData

XmlIoTile - Class in mpicbg.spim.data.sequence

XmlIoTile() - Constructor for class mpicbg.spim.data.sequence.XmlIoTile

XmlIoTimePoints - Class in mpicbg.spim.data.sequence

XmlIoTimePoints() - Constructor for class mpicbg.spim.data.sequence.XmlIoTimePoints

XmlIoViewRegistration - Class in mpicbg.spim.data.registration

XmlIoViewRegistration() - Constructor for class mpicbg.spim.data.registration.XmlIoViewRegistration

XmlIoViewRegistrations - Class in mpicbg.spim.data.registration

XmlIoViewRegistrations() - Constructor for class mpicbg.spim.data.registration.XmlIoViewRegistrations

XmlIoViewSetups - Class in mpicbg.spim.data.sequence

XmlIoViewSetups() - Constructor for class mpicbg.spim.data.sequence.XmlIoViewSetups

XmlIoViewTransform - Class in mpicbg.spim.data.registration

XmlIoViewTransform() - Constructor for class mpicbg.spim.data.registration.XmlIoViewTransform

XmlKeys - Class in mpicbg.spim.data

Definition of tag and attribute names.

XmlKeys() - Constructor for class mpicbg.spim.data.XmlKeys

xmlViewTransform - Variable in class mpicbg.spim.data.registration.XmlIoViewRegistrations

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