Package com.xinapse.multisliceimage.roi

The package com.xinapse.multisliceimage.roi is used to create and manipulate 2-dimensional regions of interest (ROIs).

See:
Description

Interface Summary

CanAddROIToFrame	An interface to indicate that a javax.swing.JFrame can receive ROIs.
EditableOutlineROI	An interface that ROIs implement if they have an editable outline with handles at each vertex.
LinearROI	Interface that ROIs having the property of linearity implement.
RegularROI	Interface that regularly-shaped ROIs implement.
RotatableROI	Interface that rotatable ROIs implement.
StretchableROI	Interface that stretchable ROIs implement.

Class Summary

AddChecksum	Program to add a Checksum to an ROI file.
ANegativeHandle	A Class representing a Handle at the negative end of axis A on an EllipticalROI.
APositiveHandle	A Class representing a Handle at the positive end of axis A on an EllipticalROI.
AxisHandle	A Class representing a Handle at the end of an axis on an EllipticalROI.
BNegativeHandle	A Class representing a Handle at the negative end of axis B on an EllipticalROI.
BPositiveHandle	A Class representing a Handle at the positive end of axis B on an EllipticalROI.
CentreHandle	A Class representing a Handle at the centre of an ROI.
CombineMode.Panel	A JPanel for selecting a CombineMode.
ContourMode.ComboBox
ContourROI	A class for edge detection and contour following.
ContourWorker	A MonitorWorker for performing edge detection and contouring from a seed point.
CornerHandle	An abstract Class representing a Handle at one of the four corners of an ROI.
CurvedLineROI	A Class representing a curved line on an image.
EastHandle	A Class representing a Handle on the East edge of an ROI.
EdgeHandle	An abstract Class representing a Handle at one of the four edges of an ROI.
EllipticalROI	A Class representing an elliptical region of an image.
EllipticalROICreateDialog	A dialog used to create Elliptical ROIs.
EndHandle	A Class representing a Handle at one of the two ends of a LineROI.
Feret	A Class describing the minimum and maximum Feret's diameter.
Handle	A Class representing an ROI Handle, used for changing the shape of an ROI.
HistoryDialog	A JDialog that is used to display ROI audit-trail information.
HistoryItem	A Class representing an item in the life and history of an ROI.
HollowROI	A Class representing an irregularly-shaped, region but with one or more hollows.
ImageJROIFileFilter	A FileFilter for ImageJ region of interest files.
IrregularROI	A Class representing an irregularly-shaped closed region on an image.
IrregularROIInProgress	A Class representing an IrregularROI being drawn on an image.
LineROI	A Class representing a straight line on an image.
LineROICreateDialog	A dialog used to create Line ROIs.
Marker	A Class representing a point on an image.
MarkerCreateDialog	A dialog used to create Marker ROIs.
MaskMode.Panel	A JPanel for selecting a MaskMode.
MorphologicalOperationWorker	This SwingWorker is used to perform morphological operations (dilation and erosion) on ROIs.
NorthEastHandle	A Class representing a Handle at of the North East corner of an ROI.
NorthHandle	A Class representing a Handle on the North edge of an ROI.
NorthWestHandle	A Class representing a Handle at of the North West corner of an ROI.
PenSizePanel	A JPanel that can be used to select the size of a "pen" used to erase parts of IrregularROIs.
RectangularROI	An Class representing a rectangular region of an image.
RectangularROICreateDialog	A dialog used to create Rectangular ROIs.
ROI	A Class representing a region of interest.
ROICreateDialog	An abstract class of dialogs use to create ROIs.
ROIFileChooser	A JFileChooser for choosing region of interest files (files with extension ".roi", or ".zip" for ImageJ ROI files).
ROIFileFilter	A FileFilter for region of interest files.
ROIFileSelectionPanel	A FileSelectionPanel for selecting an ROI file.
ROIIntensitiesFileChooser	A JFileChooser for choosing a file (a file with extension ".txt") into which region of interest intensities will be written.
ROIPreferencesDialog	A javax.swing.JDialog used to set the user Preferences related to ROIs.
ROIStats	A Class containing the statistics that are computed for an ROI.
ROIStatsFileChooser	A JFileChooser for choosing region of interest statistics files (files with extension ".txt") into which ROI stats will be written.
SmootherWorker	This SwingWorker is used to smooth IrregularROIs.
SouthEastHandle	A Class representing a Handle at of the South East corner of an ROI.
SouthHandle	A Class representing a Handle on the South edge of an ROI.
SouthWestHandle	A Class representing a Handle at of the South West corner of an ROI.
StatsComparator	A Comparator used in sorting operations for ROIs based on their statistics.
Text	A Class for putting text on an image.
TextCreateDialog	A dialog used to create Text ROIs.
VertexHandle	A Class representing a Handle at one of the vertices of an EditableOutlineROI.
WestHandle	A Class representing a Handle on the West edge of an ROI.

Enum Summary

CombineMode	An enumeration of possible ROI combination operations that can be be applied to a set of ROIs to create a single resulting ROI.
ContourMode	An enumeration of the modes of operation of intensity level contour generation.
HistoryType	An enumeration of the types of HistoryItem that are associated with ROIs.
InteractionType	An enumeration of the different ways in which a user can interact with an ROI.
MaskAction	An enumeration of possible masking operation actions that can be applied to an ROI to mask out some of an image's pixels.
MaskMode	An enumeration of possible masking mode.
ROIEditAction	An enumeration of the different types of (undoable) actions that can be performed on an ROI.
ROIState	An enumeration of the different states in which an ROI can be.
StatsType	An enumeration of the types of statistic that are computed for ROIs.

Exception Summary

DuplicateROIException	Signals the attempted creation and addition of an identical duplicate ROI to an image.
ROIException	Signals that an error has occurred while handling an ROI.

Package com.xinapse.multisliceimage.roi Description

The package com.xinapse.multisliceimage.roi is used to create and manipulate 2-dimensional regions of interest (ROIs).

The following ROIs can be handled:

• Marker. A point marker.
• Text. A text annotation marker.
• LineROI. A straight line.
• CurvedLineROI. A curved line.
• RectangularROI. A rectangular ROI with sides parallel to the horizontal and vertical.
• EllipticalROI. A elliptical ROI, with rotatable axes.
• IrregularROI. A irregular-shaped ROI with a closed outline.
• ContourROI. A irregular-shaped ROI with a closed outline, formed by contouring from a single point in the image.

Statistics can be computed about the ROIs, such as area, mean intensity, standard deviation in intensity, minimum and maximum intensity. In addition, the LineROI and CurvedLineROIs have a length statistic.

ROIs can be manipulated by intersecting them, and can be used as masks for an image to select pixels inside or outside the ROIs.