Serialized Form (Anchor - merged Javadoc across key repositories. This documentation is a work-in-progress. 0.0.1-SNAPSHOT API)

Package org.anchoranalysis.bean.define
- Class DefineAddException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.bean.exception
- Class BeanDuplicateException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1842384434578361294L
- Class BeanMisconfiguredException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  -6966810405755062033L
- Class BeanStrangeException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.bean.permute.assign
- Class AssignPermutationException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.bean.xml.exception
- Class BeanMisconfiguredXMLException extends AnchorCombinableException implements Serializable
  
  serialVersionUID:
  
  1L
- Class BeanXMLException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class LocalisedBeanException extends AnchorCombinableException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ProvisionFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.bean.xml.factory
- Class HelperDescribeXMLNode extends Object implements Serializable
Package org.anchoranalysis.core.exception
- Class AnchorCheckedException extends Exception implements Serializable
  
  serialVersionUID:
  
  1L
- Class AnchorNeverOccursException extends AnchorRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class AnchorRuntimeException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class CheckedUnsupportedOperationException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  7975790749088346594L
- Class CreateException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1842384434578361294L
- Class InitializeException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class OperationFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  -5014516097016484634L
- Class OperationFailedRuntimeException extends AnchorRuntimeException implements Serializable
  
  serialVersionUID:
  
  -5014516097016484634L
Package org.anchoranalysis.core.exception.combinable
- Class AnchorCombinableException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -6966810405755062033L
  - Serialized Fields
    - description
```
String description
```
      The (uncombined) description associated with the exception.
- Class SummaryException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.core.exception.friendly
- Class AnchorFriendlyCheckedException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class AnchorFriendlyRuntimeException extends AnchorRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class AnchorImpossibleSituationException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.core.functional
- Class CheckedStream.ConvertedToRuntimeException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - exception
```
Throwable exception
```
Package org.anchoranalysis.core.identifier.provider
- Class NamedProviderGetException extends AnchorCombinableException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.core.index
- Class GetOperationFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  4847382915351464834L
  - Serialized Fields
    - key
```
String key
```
      The key that was used in the operation that created this exception.
    - message
```
String message
```
      A message describing the failure.
- Class SetOperationFailedException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -3323720426335397452L
Package org.anchoranalysis.core.serialize
- Class DeserializationFailedException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  7824941062757840315L
Package org.anchoranalysis.core.system.path
- Class PathDifferenceException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.experiment
- Class ExperimentExecutionException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class JobExecutionException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  -7030930961354624998L
Package org.anchoranalysis.feature.calculate
- Class FeatureCalculationException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -907417952940489366L
- Class NamedFeatureCalculateException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - messageWithoutKey
```
String messageWithoutKey
```
      The message without any key identifier.
Package org.anchoranalysis.image.bean.nonbean
- Class UnitValueException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.bean.nonbean.segment
- Class SegmentationFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.bean.nonbean.spatial.arrange
- Class ArrangeStackException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.bean.unitvalue.distance
- Class DistancePhysical extends UnitValueDistance implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
double value
```
      The value in units of type unitType.
    - unitType
```
String unitType
```
      A string indicating type of units to use, as per SpatialUnits.
- Class DistanceVoxels extends UnitValueDistance implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - value
```
double value
```
      The distance in units of voxels.
- Class UnitValueDistance extends AnchorBean<UnitValueDistance> implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.core.dimensions
- Class IncorrectImageSizeException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class Resolution extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - res
```
Point3d res
```
      The resolution in each dimension, stored in meter units.
      If we change this, this may break some serialized annotations.
Package org.anchoranalysis.image.core.dimensions.size.suggestion
- Class SuggestionFormatException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.io
- Class ImageIOException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.image.voxel.binary.values
- Class BinaryValuesByte extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - off
```
byte off
```
      The byte representation of the value for off.
    - on
```
byte on
```
      The byte representation of the value for on.
Package org.anchoranalysis.image.voxel.datatype
- Class IncorrectVoxelTypeException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.inference.concurrency
- Class ConcurrentModelException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class CreateModelFailedException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.imagej.convert
- Class ImageJConversionException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.input
- Class InputReadFailedException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.input.csv
- Class CSVReaderException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.input.file
- Class FilesProviderException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.input.path
- Class DerivePathException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.input.path.matcher
- Class FindFilesException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.output.error
- Class OutputDirectoryAlreadyExistsException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class OutputWriteFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1036971819028250342L
Package org.anchoranalysis.io.output.namestyle
- Class IndexableOutputNameStyle extends OutputNameStyle implements Serializable
  
  serialVersionUID:
  
  -2393013576294162543L
- Class IntegerSuffixOutputNameStyle extends IndexableOutputNameStyle implements Serializable
  
  serialVersionUID:
  
  0L
  - Serialized Fields
    - prefix
```
String prefix
```
    - numberDigits
```
int numberDigits
```
- Class OutputNameStyle extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - outputName
```
String outputName
```
      An identifier used in rules to determine if an output is enabled or not.
- Class SimpleOutputNameStyle extends OutputNameStyle implements Serializable
  
  serialVersionUID:
  
  1L
- Class StringSuffixOutputNameStyle extends IndexableOutputNameStyle implements Serializable
  
  serialVersionUID:
  
  4582344790084798682L
  - Serialized Fields
    - outputFormatString
```
String outputFormatString
```
- Class WithoutOutputNameStyle extends OutputNameStyle implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.output.outputter
- Class BindFailedException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.io.output.path.prefixer
- Class PathPrefixerException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.launcher
- Class CommandLineException extends AnchorFriendlyRuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.launcher.executor.selectparam.path.convert
- Class InvalidPathArgumentException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.math.arithmetic
- Class RunningSum extends Object implements Serializable
  
  serialVersionUID:
  
  -2147459521030056604L
  - Serialized Fields
    - sum
```
double sum
```
      The running sum.
    - count
```
long count
```
      The running count.
Package org.anchoranalysis.mpp.bean.bound
- Class Bound extends MarkBounds implements Serializable
  
  serialVersionUID:
  
  -5447041367811327604L
- Class BoundDegrees extends BoundMinMax implements Serializable
  
  serialVersionUID:
  
  1281361242890359356L
- Class BoundMinMax extends Bound implements Serializable
  
  serialVersionUID:
  
  -493791653577617743L
  - Serialized Fields
    - delegate
```
ResolvedBound delegate
```
- Class BoundPhysicalExtent extends BoundMinMax implements Serializable
  
  serialVersionUID:
  
  -5440824428055546445L
- Class BoundUnitless extends BoundMinMax implements Serializable
  
  serialVersionUID:
  
  8738881592311859713L
- Class MarkBounds extends AnchorBean<MarkBounds> implements Serializable
  
  serialVersionUID:
  
  0L
- Class ResolvedBound extends AnchorBean<ResolvedBound> implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - min
```
double min
```
    - max
```
double max
```
Package org.anchoranalysis.mpp.bean.points.fitter
- Class InsufficientPointsException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class PointsFitterException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  6066348459108781534L
Package org.anchoranalysis.mpp.feature.addcriteria
- Class IncludeMarksFailureException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -4475636830799035389L
Package org.anchoranalysis.mpp.feature.energy
- Class EnergyTotal extends Object implements Serializable
  
  serialVersionUID:
  
  -595099053761257083L
  - Serialized Fields
    - total
```
double total
```
Package org.anchoranalysis.mpp.feature.energy.marks
- Class MarksWithEnergyBreakdown extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - marks
```
MarksWithTotalEnergy marks
```
    - individual
```
EnergySavedInd individual
```
- Class MarksWithTotalEnergy extends Object implements Serializable
  
  serialVersionUID:
  
  -7008599104878130986L
  - Serialized Fields
    - marks
```
MarkCollection marks
```
      The marks
    - energyTotal
```
double energyTotal
```
      The pre-annealed total energy
Package org.anchoranalysis.mpp.feature.energy.saved
- Class EnergySavedAll extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - energyTotal
```
double energyTotal
```
- Class EnergySavedInd extends Object implements Serializable
  
  serialVersionUID:
  
  -5205697546115728135L
  - Serialized Fields
    - energyTotal
```
double energyTotal
```
    - ind
```
ArrayList<E> ind
```
Package org.anchoranalysis.mpp.feature.error
- Class CheckException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.mpp.feature.mark
- Class EnergyMemoList extends Object implements Serializable
  
  serialVersionUID:
  
  9067220044867268357L
Package org.anchoranalysis.mpp.mark
- Class Mark extends Object implements Serializable
  
  serialVersionUID:
  
  3272456193681334471L
  - Serialized Fields
    - id
```
int id
```
- Class MarkCollection extends Object implements Serializable
  
  serialVersionUID:
  
  2398855316191681489L
  - Serialized Fields
    - marks
```
List<E> marks
```
      The underlying List that stores the Marks in the collection.
- Class MarkWithPosition extends Mark implements Serializable
  
  serialVersionUID:
  
  -6976277985708631268L
  - Serialized Fields
    - position
```
Point3d position
```
- Class UnsupportedMarkTypeException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -5855318973518035098L
- Class UpdateMarkSetException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -3084951824689469370L
Package org.anchoranalysis.mpp.mark.conic
- Class Circle extends MarkWithPositionAndSingleRadius implements Serializable
  
  serialVersionUID:
  
  8551900716243748046L
- Class ConicBase extends MarkWithPosition implements Serializable
  
  serialVersionUID:
  
  1680124471263339009L
- Class Ellipse extends ConicBase implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - shell
```
double shell
```
      The size of the shell, expressed as a ratio of the radius.
    - radii
```
Point2d radii
```
    - orientation
```
Orientation orientation
```
    - ellipsoidCalculator
```
EllipsoidMatrixCalculator ellipsoidCalculator
```
    - shellInternal
```
double shellInternal
```
    - shellExternal
```
double shellExternal
```
    - shellExternalOut
```
double shellExternalOut
```
    - shellInternalSquared
```
double shellInternalSquared
```
    - shellExternalSquared
```
double shellExternalSquared
```
    - shellExternalOutSquared
```
double shellExternalOutSquared
```
    - radiiShellMaxSquared
```
double radiiShellMaxSquared
```
- Class Ellipsoid extends ConicBase implements Serializable
  
  serialVersionUID:
  
  -2678275834893266874L
  - Serialized Fields
    - shell
```
double shell
```
    - innerCoreDistance
```
double innerCoreDistance
```
    - radii
```
Point3d radii
```
    - orientation
```
Orientation orientation
```
    - ellipsoidCalculator
```
EllipsoidMatrixCalculator ellipsoidCalculator
```
    - shellInnerCore
```
double shellInnerCore
```
    - shellInternal
```
double shellInternal
```
    - shellExternal
```
double shellExternal
```
    - shellExternalOut
```
double shellExternalOut
```
    - shellInnerCoreSquared
```
double shellInnerCoreSquared
```
    - shellInternalSquared
```
double shellInternalSquared
```
    - shellExternalSquared
```
double shellExternalSquared
```
    - shellExternalOutSquared
```
double shellExternalOutSquared
```
    - radiiShellMaxSq
```
double radiiShellMaxSq
```
- Class MarkWithPositionAndSingleRadius extends MarkWithPosition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - radius
```
double radius
```
    - radiusSq
```
double radiusSq
```
    - radiusExtraSq
```
double radiusExtraSq
```
    - boundRadius
```
Bound boundRadius
```
- Class Sphere extends MarkWithPositionAndSingleRadius implements Serializable
  
  serialVersionUID:
  
  -3526056946146656810L
Package org.anchoranalysis.mpp.mark.points
- Class LineSegment extends Mark implements Serializable
  
  serialVersionUID:
  
  6436383113190855927L
  - Serialized Fields
    - distanceToLineForInside
```
double distanceToLineForInside
```
- Class PointList extends PointListBase implements Serializable
  
  serialVersionUID:
  
  1718294470056379145L
  - Serialized Fields
    - set
```
Set<E> set
```
- Class PointListBase extends Mark implements Serializable
  
  serialVersionUID:
  
  6520431317406007141L
  - Serialized Fields
    - points
```
List<E> points
```
    - min
```
Point3d min
```
    - max
```
Point3d max
```
- Class Polygon extends PointListBase implements Serializable
  
  serialVersionUID:
  
  1718294470056379145L
  - Serialized Fields
    - region
```
ij.gui.PolygonRoi region
```
      A region of interest in ImageJ representing a polygon
    - area
```
double area
```
    - centroid
```
Point3d centroid
```
- Class PolygonCurve extends PointListBase implements Serializable
  
  serialVersionUID:
  
  -2043844259526872933L
  - Serialized Fields
    - distanceThreshold
```
double distanceThreshold
```
- Class RotatableBoundingBox extends MarkWithPosition implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - distanceToLeftBottom
```
Point3d distanceToLeftBottom
```
      Add to orientation to get the left-point and bottom-point (without rotation)
    - distanceToRightTop
```
Point3d distanceToRightTop
```
      Add to orientation to get the right-point and top-point (without rotation)
    - orientation
```
Orientation orientation
```
      An orientation in the 2D plane to rotate the bounding box by.
    - rotMatrix
```
RotationMatrix rotMatrix
```
    - rotMatrixInv
```
RotationMatrix rotMatrixInv
```
    - pointRelative
```
Point3d pointRelative
```
      Repeatedly reused when evaluating points. We instantiate it here, to avoid unnecessary heap allocation.
Package org.anchoranalysis.mpp.proposer
- Class ProposalAbnormalFailureException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
- Class ProposerException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.mpp.proposer.error
- Class ErrorNode extends Object implements Serializable
  
  serialVersionUID:
  
  -5769879460789165274L
- Class ErrorNodeException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  -4000166470139114311L
  - Serialized Fields
    - str
```
String str
```
- Class ErrorNodeImpl extends ErrorNode implements Serializable
  
  serialVersionUID:
  
  -3967665095180902654L
  - Serialized Fields
    - parent
```
ErrorNode parent
```
    - children
```
ArrayList<E> children
```
    - errorMessage
```
String errorMessage
```
- Class ErrorNodeNull extends ErrorNode implements Serializable
  
  serialVersionUID:
  
  5512508477564211253L
- Class ProposerFailureDescription extends Object implements Serializable
  
  serialVersionUID:
  
  4418671354471633349L
  - Serialized Fields
    - errorTree
```
DefaultTreeModel errorTree
```
    - root
```
ErrorNode root
```
Package org.anchoranalysis.mpp.segment.optimization
- Class OptimizationTerminatedEarlyException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1311039251626279919L
Package org.anchoranalysis.mpp.segment.optimization.feedback
- Class ReporterException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  -943590820981212617L
Package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- Class AggregatorException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  896694665077742955L
Package org.anchoranalysis.mpp.segment.optimization.feedback.period
- Class PeriodReceiverException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  8462423019988537940L
Package org.anchoranalysis.mpp.segment.optimization.kernel
- Class KernelCalculateEnergyException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  8395015058238556485L
- Class KernelDecision extends Object implements Serializable
  
  serialVersionUID:
  
  -5135255409310941727L
  - Serialized Fields
    - id
```
int id
```
    - description
```
String description
```
    - accepted
```
boolean accepted
```
    - proposed
```
boolean proposed
```
    - changedMarkIDArr
```
int[] changedMarkIDArr
```
    - executionTime
```
long executionTime
```
    - iter
```
int iter
```
Package org.anchoranalysis.plugin.mpp.bean.contour
- Class TraverseContourException extends AnchorCheckedException implements Serializable
  
  serialVersionUID:
  
  4293810593116687378L
Package org.anchoranalysis.spatial.axis
- Class AxisConversionException extends AnchorFriendlyCheckedException implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.spatial.box
- Class BoundingBox extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - cornerMin
```
Point3i cornerMin
```
      The bottom-left corner of the bounding box.
      This the minimum point in all dimensions for the bounding-box.
    - cornerMaxInclusive
```
Point3i cornerMaxInclusive
```
      The top-right corner of the bounding box (inclusive).
      This the maximum valid point in all dimensions for the bounding-box.
      It is calculated lazily when first needed by BoundingBox.calculateCornerMaxInclusive().
    - cornerMaxExclusive
```
Point3i cornerMaxExclusive
```
      The top-right corner of the bounding box (exclusive).
      This is cornerMaxInclusive with 1 added in each dimension.
      It is calculated lazily when first needed by BoundingBox.calculateCornerMaxExclusive().
    - extent
```
Extent extent
```
      Dimensions in pixels needed to represent the bounding box.
      This emanates in a positive direction from cornerMin to define the complete box.
- Class Extent extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - size
```
ReadableTuple3i size
```
      Sizes in each dimension.
    - areaXY
```
int areaXY
```
      Size in X multiplied by size in Y.
      This may be convenient for calculating offsets and for iterations.
      Note if the area is too large to be stored as an int, a -1 is stored instead. This should be checked for, with an appropriate error message, or alternative behavior occurring in these instances.
      We avoid storing the area as a long, as it would create computational overhead in the vast bulk of cases where an int is sufficient, especially for operations like calculating offsets that may occur repeatedly in a loop. It is preferable to handle the outlier cases of very large areas separately.
Package org.anchoranalysis.spatial.orientation
- Class Orientation extends Object implements Serializable
  
  serialVersionUID:
  
  1L
- Class Orientation2D extends Orientation implements Serializable
  
  serialVersionUID:
  
  1528190376087281572L
  - Serialized Fields
    - angleRadians
```
double angleRadians
```
      The angle of the rotation in the 2D plane anti-clockwise, in radians.
- Class Orientation3DEulerAngles extends Orientation implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - rotationX
```
double rotationX
```
      Rotation around X-dimension (in radians) anti-clockwise.
      This is the alpha parameter.
    - rotationY
```
double rotationY
```
      Rotation around Y-dimension (in radians) anti-clockwise.
      This is the beta parameter.
    - rotationZ
```
double rotationZ
```
      Rotation around Z-dimension (in radians) anti-clockwise.
      This is the gamma parameter.
- Class OrientationAxisAngle extends Orientation implements Serializable
  
  serialVersionUID:
  
  -2592680414423106545L
  - Serialized Fields
    - axis
```
Vector3d axis
```
      Axis part of axis-angle orientation (should be normalized). Once this is passed here, it is consumed, and must not be changed elsewhere.
    - angle
```
double angle
```
      Angle part of axis-angle orientation (anti-clock in radians).
- Class OrientationRotationMatrix extends Orientation implements Serializable
  
  serialVersionUID:
  
  -496736778234811706L
  - Serialized Fields
    - rotationMatrix
```
RotationMatrix rotationMatrix
```
      The rotation-matrix. Once used here, it must be treated as immutable, and its state may not be changed elsewhere.
- Class RotationMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - delegate
```
cern.colt.matrix.DoubleMatrix2D delegate
```
      The underlying matrix implementing the rotation.
      This name is deliberately kept as delegate to avoid breaking serialized objects.
    - singlePoint
```
cern.colt.matrix.DoubleMatrix2D singlePoint
```
      Used temporarily to store the value of a single-point, to avoid unnecessary heap allocation.
Package org.anchoranalysis.spatial.point
- Class Point2d extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
      X-axis component of point.
    - y
```
double y
```
      Y-axis component of point.
- Class Point2f extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
float x
```
      X-axis component of point.
    - y
```
float y
```
      Y-axis component of point.
- Class Point2i extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
int x
```
      X-axis component of point.
    - y
```
int y
```
      Y-axis component of point.
- Class Point3d extends Tuple3d implements Serializable
  
  serialVersionUID:
  
  1L
- Class Point3f extends Tuple3f implements Serializable
  
  serialVersionUID:
  
  1L
- Class Point3i extends Tuple3i implements Serializable
  
  serialVersionUID:
  
  1L
- Class Tuple3d extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
double x
```
      X-axis component of the tuple.
    - y
```
double y
```
      Y-axis component of the tuple.
    - z
```
double z
```
      Z-axis component of the tuple.
- Class Tuple3f extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
float x
```
      X-axis component of the tuple.
    - y
```
float y
```
      Y-axis component of the tuple.
    - z
```
float z
```
      Z-axis component of the tuple.
- Class Tuple3i extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    - x
```
int x
```
      X-axis component of the tuple.
    - y
```
int y
```
      Y-axis component of the tuple.
    - z
```
int z
```
      Z-axis component of the tuple.
- Class Vector3d extends Tuple3d implements Serializable
  
  serialVersionUID:
  
  1L
Package org.anchoranalysis.test
- Class TestDataInitializeException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L
- Class TestDataLoadException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1L

Serialized Form

Package org.anchoranalysis.bean.define

Class DefineAddException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.bean.exception

Class BeanDuplicateException extends AnchorFriendlyRuntimeException implements Serializable

Class BeanMisconfiguredException extends AnchorFriendlyCheckedException implements Serializable

Class BeanStrangeException extends AnchorFriendlyRuntimeException implements Serializable

Package org.anchoranalysis.bean.permute.assign

Class AssignPermutationException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.bean.xml.exception

Class BeanMisconfiguredXMLException extends AnchorCombinableException implements Serializable

Class BeanXMLException extends AnchorFriendlyCheckedException implements Serializable

Class LocalisedBeanException extends AnchorCombinableException implements Serializable

Class ProvisionFailedException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.bean.xml.factory

Class HelperDescribeXMLNode extends Object implements Serializable

Package org.anchoranalysis.core.exception

Class AnchorCheckedException extends Exception implements Serializable

Class AnchorNeverOccursException extends AnchorRuntimeException implements Serializable

Class AnchorRuntimeException extends RuntimeException implements Serializable

Class CheckedUnsupportedOperationException extends AnchorCheckedException implements Serializable

Class CreateException extends AnchorFriendlyCheckedException implements Serializable

Class InitializeException extends AnchorFriendlyCheckedException implements Serializable

Class OperationFailedException extends AnchorFriendlyCheckedException implements Serializable

Class OperationFailedRuntimeException extends AnchorRuntimeException implements Serializable

Package org.anchoranalysis.core.exception.combinable

Class AnchorCombinableException extends AnchorCheckedException implements Serializable

Serialized Fields

description

Class SummaryException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.core.exception.friendly

Class AnchorFriendlyCheckedException extends AnchorCheckedException implements Serializable

Class AnchorFriendlyRuntimeException extends AnchorRuntimeException implements Serializable

Class AnchorImpossibleSituationException extends AnchorFriendlyRuntimeException implements Serializable

Package org.anchoranalysis.core.functional

Class CheckedStream.ConvertedToRuntimeException extends AnchorFriendlyRuntimeException implements Serializable

Serialized Fields

exception

Package org.anchoranalysis.core.identifier.provider

Class NamedProviderGetException extends AnchorCombinableException implements Serializable

Package org.anchoranalysis.core.index

Class GetOperationFailedException extends AnchorFriendlyCheckedException implements Serializable

Serialized Fields

key

message

Class SetOperationFailedException extends AnchorCheckedException implements Serializable

Package org.anchoranalysis.core.serialize

Class DeserializationFailedException extends AnchorCheckedException implements Serializable

Package org.anchoranalysis.core.system.path

Class PathDifferenceException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.experiment

Class ExperimentExecutionException extends AnchorFriendlyCheckedException implements Serializable

Class JobExecutionException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.feature.calculate

Class FeatureCalculationException extends AnchorCheckedException implements Serializable

Class NamedFeatureCalculateException extends AnchorFriendlyCheckedException implements Serializable

Serialized Fields

messageWithoutKey

Package org.anchoranalysis.image.bean.nonbean

Class UnitValueException extends AnchorCheckedException implements Serializable

Package org.anchoranalysis.image.bean.nonbean.segment

Class SegmentationFailedException extends AnchorFriendlyCheckedException implements Serializable

Package org.anchoranalysis.image.bean.nonbean.spatial.arrange

Class ArrangeStackException extends AnchorCheckedException implements Serializable

Package org.anchoranalysis.image.bean.unitvalue.distance

Class DistancePhysical extends UnitValueDistance implements Serializable

Serialized Fields

value

unitType

Class DistanceVoxels extends UnitValueDistance implements Serializable

Serialized Fields

value

Class UnitValueDistance extends AnchorBean<UnitValueDistance> implements Serializable

Package org.anchoranalysis.image.core.dimensions

Class IncorrectImageSizeException extends AnchorFriendlyCheckedException implements Serializable

Class Resolution extends Object implements Serializable

Serialized Fields

res

Package org.anchoranalysis.image.core.dimensions.size.suggestion

Class SuggestionFormatException extends AnchorFriendlyCheckedException implements Serializable