All Classes and Interfaces
Class
Description
This class provides a skeletal implementation of the
SpatialFilter interface,
for complex data to minimize the effort required to implement this interface.A Model that can be fitted to dynamic data where contrast agent is injected, and
the tissue response to an input function is measured.
Superclass for the results of dynamic contrast analysis.
AbstractDynamicFrame - a GUI for performing general image dynamic analysis.
MonitorWorker for running dynamic contrast analysis.
This class provides a skeletal implementation of the
SpatialFilter interface,
to minimize the effort required to implement this interface.Program to add a Checksum to an ROI file.
The
AffineTransform3D class represents a 3D affine transform
that performs a linear mapping from 3D coordinates to other 3D
coordinates that preserves the "straightness" and
"parallelness" of lines.This abstract class handles the NIFTI 1.1 extended data.
Class for writing and reading arterial input function data (graphs).
This class represents a multi-dimensional Analyze 7.5 image header file.
This class is a representation of a multi-dimensional image in the Analyze 7.5 format.
A file filter for Analyze header files.
A Class representing a Handle at the negative end of axis A on an EllipticalROI.
Class to handle Analyze lookup files (colour mapping files).
Enables and disables debugging messages for the Analyze package.
Signals that an error in the Analyze package has occurred.
An abstract Analyze header representation.
This is an abstract class that is the superclass of a multi-dimensional image in the
Analyze 7.5 format or the NIFTI format.
This class represents the pixel formats (data types) that can be used in Analyze, and NIFTI
(extended Analyze) images.
A Class representing a Handle at the positive end of axis A on an EllipticalROI.
Class to estimate the auto-correlation of a time-series by examining the residuals of a GLM fit.
A Class representing a Handle at the end of an axis on an EllipticalROI.
A class representing an array of binary (1-bit) values in a more compact way than
does a boolean[].
A Class representing a Handle at the negative end of axis B on an EllipticalROI.
An enumeration of possible boundary conditions when applying, for example, spatial filters and
interpolators.
A Class representing a Handle at the positive end of axis B on an EllipticalROI.
Abstract class to provide byte swapping facilities, allowing correct interpretation
of multi-byte numbers on machines of different byte orders.
A class to implement a cancellable Thread.
A flag that can be set to indicate that a cancellation has taken place.
Thrown when an action is cancelled by the user.
An interface implemented by classes that can perform cardiac analysis.
A JPanel that can be used to specify cardiac analysis parameters.
A Class representing a Handle at the centre of an ROI.
A SpatialFilter for altering the colour components of a colour image.
A FilterSpecifierPanel for a colour image filter.
The
ColourMapping class represents a mapping from pixel presentation values (PPVs)
to colours that are shown on a display device, such as a computer monitor.An interpolator for a 3- (or fewer) dimensional array of pixels in a Colour image.
An enumeration of possible ROI combination operations that can be
be applied to a set of ROIs to create a single resulting ROI.
A JPanel for selecting a
CombineMode.This class handles the NIFTI 1.1 non-NUL ASCII text extended data.
A complex (real, imaginary) number.
An enumeration of the possible display/calculation modes for complex numbers.
An enumeration of the modes of operation of intensity level contour generation.
A JComboBox for selecting a ContourMode.
A class for edge detection and contour following.
A MonitorWorker for performing edge detection and contouring from a seed point.
Signals that an iterative procedure has failed to converge.
An abstract Class representing a Handle at one of the four corners of an ROI.
A cubic spline interpolator for tabulated values of (x,y).
A represention of a planar curved line on an image.
The superclass of models that can be fitted to DCE-MRI data.
A class for calculating Dice similarity scores between two sets of ROIs.
This class handles NIFTI 1.1 DICOM extended data.
Class for deallocating memory associated with
DirectByteBuffer.A complex (real, imaginary) number, with double precision.
A representation of an array of double-precision pixels.
Signals the attempted creation and addition of an identical duplicate ROI to an image.
An interface implemented by classes that can fit to dynamic signals that vary as a function of
time.
A JPanel that can be used to specify dynamic model parameters.
An abstract result of a computation from a dynamic signal change.
A Class representing a Handle on the East edge of an ROI.
An abstract Class representing a Handle at one of the four edges of an ROI.
An interface that ROIs implement if they have an editable outline shape with handles
at each vertex.
A Class representing an elliptical region of an image.
A dialog used to create Elliptical ROIs.
A Class representing a Handle at one of the two ends of a LineROI.
Exit status codes on program termination.
A Class describing the minimum and maximum Feret's diameter.
A convolution filter that uses the Fast Fourier Transform to perform the convolution
in Fourier space.
A class for selecting a SpatialFilter.
A JPanel that contains a JTabbedPane that can be used to select one of the
known SpatialFilters.
A class for performing filtering of complex images based on a moving kernel of pixels
with fixed complex weights within the kernel.
A class for performing filtering of images based on a moving kernel of pixels with fixed weights
within the kernel.
A complex (real, imaginary) number, with single precision.
A
FixedWeightsKernelFilter for performing a Gaussian blurring of an image.A FilterSpecifierPanel for a Gaussian blur filter.
A Class representing an ROI Handle, used for changing the shape of an ROI.
Access to the built-in and head template images.
A class for creating histograms and finding statistics about arrays of values
(normally pixel intensities).
A specification for Histogram bins.
A JDialog that is used to display ROI audit-trail information as a table.
A Class representing an item in the life and history of an ROI.
An enumeration of the types of HistoryItem that are associated with ROIs.
A Class representing an irregularly-shaped region but with one or more holes.
Class for handling the ICBM atlas labels.
Contains settings that are common across all images, together with some utilities for images.
Enables and disables debugging messages for the image package.
Abstract
Class for File Choosers for opening ReadableImages, and saving
WritableImages,
Includes appropriate file filters, titles and button labels.ImageFileChooser suitable for selecting a ReadableImage
file for loading.ImageFileChooser suitable for selecting a WritableImage
file for saving.A file filter for all images that can be loaded directly into Jim.
An
ImageGrid allows the selection of a 2-D 'matrix' of
ReadableImages and contains the mechanism for adding images to the matrix,
removing images from the matrix, etc.A FileFilter for ImageJ region of interest files.
Calculation of factors derived from the moments of an image.
Class to add extensions, prefixes and suffices to image file and URL names.
JComponent that is used to preview an image file.
Signals that an error has occurred when trying to save an image.
An
ImageSelectionGroupPanel allows the selection of a group of
ReadableImages and contains the mechanism for adding images to the group,
removing images from the group, etc.An interface implemented by classes that want to be able to generate user components
to put into an
ImageSelectionGroupPanel.An
ImageSelectionPanel is a JPanel that can be used to
select an image, either for reading or for writing.Contains various image utility static methods.
Contains static methods for writing images.
A JDialog for showing progress through an operation that will take an indeterminate
number of steps, or an unknown time to complete.
NIFTI 1.1 extended data that allows artibrary text to be associated with an image.
An image information item key-value pair.
Representation of a list of information to be
associated either with an image as a whole, or with a particular element
of a particular dimension of an image.
Signals that an error has occurred while creating or handling an
InfoList.Signals that information about an
InfoStorer has not been found.An interface that classes implement to indicate that they can store
arbitrary textual information.
Abstract class providing methods to read primitve data values from input sources.
The types of input image configuration: either a single input image, or multiple input images.
A component that can be used to select a
ReadableImage for input.A Handle to indicate and move the insertion point for a RadialDivider.
An intensity preset, particularly for CT images.
A
JMenu containing a list of IntensityPresets and allied operations.An enumeration of possible intensity relationships.
A Button for setting an intensity relation.
Class for generating JPanels for selecting an IntensityRelation.
A JPanel for selecting an IntensityRelation.
An enumeration of the different ways in which a user can interact with an ROI.
An enumeration of the types of interpolation that can be used for resampling images.
Signals that an invalid parameter has been passed to a constructor or method, and
that error must be handled by the caller.
Signals that an error has occurred while trying to read or generate a colour
mapping.
Signals that an error has occurred when performing an operation on an image.
A Class representing an irregularly-shaped closed region on an image.
A Class representing an IrregularROI being drawn on an image.
A
FixedWeightsKernelFilter for performing a Laplacian filtering of an image.A FilterSpecifierPanel for a Laplacian edge-detection filter.
Interface that ROIs having the property of linearity implement.
A Class representing a straight line on an image.
A dialog used to create Line ROIs.
This SwingWorker is used to perform logical operations (AND, AND NOT, UNION, INTERSECTION, XOR)
on ROIs.
An enumeration of logical operation on ROIs.
A Class representing a point on an image.
A dialog used to create Marker ROIs.
An enumeration of possible masking operation actions that can
be applied to an ROI to mask out some of an image's pixels.
An enumeration of possible masking mode.
A JPanel for selecting a
MaskMode.A
SpatialFilter for performing median filtering of an image.A FilterSpecifierPanel for a median filter.
An interface for showing messages to the user.
An enumeration of the known imaging and other modalities.
A javax.swing.JComboBox that is used for selecting a Modality.
A class to implement a
SwingWorker that can pop up a ProgressMonitor
to allow user cancellation.This SwingWorker is used to perform morphological operations (dilation and erosion) on ROIs.
A
SpatialFilter for performing a morphological operation on an image.A FilterSpecifierPanel for a moprphological operation filter.
An enumeration of the possible morphological operations on an image.
The radiological planes that can be used to describe the approximate orientation of
a scan plane.
A
JFrame for performing an analysis of images where the contrast changes from
one image to the next.A
MultipleImageSelectionPanel shows a list of images,
and contains the mechanism for selecting a new list of images, adding images to the list,
removing images from the list, and changing the order of images in the list.An abstract representation of a multi-dimensional image.
Enables and disables debugging messages for the MultiSliceImage package.
This class represents a multi-dimensional NIFTI-2 image header file.
This class is a representation of a multi-dimensional image in the NIFTI-2 format,
the updated NIFTI format.
A file filter for NIFTI images.
This class represents a multi-dimensional NIFTI-1 image header file.
This class is a representation of a multi-dimensional image in the NIFTI-1 format
(see
The Neuroimaging Informatics Technology Initiative),
an extension of the original Analyze 7.5 format
(see The Biomedical Imaging Resource).
This class represents the NIFTI intents.
This class represents the NIFTI qforms and sforms.
A Class representing a Handle at of the North East corner of an ROI.
A Class representing a Handle on the North edge of an ROI.
A Class representing a Handle at of the North West corner of an ROI.
Signals that an error has occurred when performing a numerical operation.
A Class representing a curved line on an image, represented by
a set of knots, with spline interpolators between the knots to define the shape of the curve.
Abstract class providing methods to write primitve data values to output files and streams.
An
OutputImageSelectionPanel is a JPanel that can be used to
select an image name for output.Indicates that a parameter is not stored in an image.
Noise reduction filter based in averaging pixel intensities based on the similarity of
patches that are not necessarily local to the pixel.
A FilterSpecifierPanel for a patch similarity noise reduction filter.
An enumeration of the possible positions in which a patient may be lying in
the scanning equipment (e.g, head-first, supine).
A javax.swing.JComboBox that is used for selecting a PatientPosition.
A JPanel that can be used to select the size of a "pen" used to erase parts of IrregularROIs.
A Class for converting an image where the intensity values represent phase, to phase
values in the range -pi ..
An abstract representation of an array of pixels of varying type.
An enumeration of the pixel formats (data types) that can be used in images.
An Enumeration of the two types of operation for pixel accessor methods.
A 3-D polynomial used to represent a set of image intensities.
An interface that is implemented by components that can save their settings to
user preferences.
An Icon that is used to preview an image (UNC, Analyze, NIFTI, DICOM).
An enumeration of DICOM pulse sequence types.
A javax.swing.JComboBox that is used for selecting a PulseSequenceType.
An enumeration of recognised DICOM pulse sequence variants.
A radial divider, for cardiac segental analysis.
Interface implemented by classes that ensure an image of that class can be read.
A Comparable point in space that can be used to sort positions.
An Class representing a rectangular region of an image.
A dialog used to create Rectangular ROIs.
Interface that regularly-shaped ROIs implement.
An Enumeration of the types rendering interpolation when drawing pixel values to screen.
A javax.swing.JComboBox that is used for selecting a RenderingInterpolationType.
A JButton for setting the RenderingInterpolationType.
Abstract Class to generate reports.
An enumration of the types of report that can be generated.
A
Class representing a region of interest.An interface implemented by classes that can perform analysis on propagated ROIs.
A JPanel that can be used to specify ROI calculation parameters.
An abstract class of dialogs use to create ROIs.
An enumeration of the different types of (undoable) actions that can be performed on an ROI.
Signals that an error has occurred while handling an ROI.
A JFileChooser for choosing region of interest files (files with extension ".roi", or
".zip" for ImageJ ROI files).
A FileFilter for region of interest files.
A
FileSelectionPanel for selecting an ROI file.A JFileChooser for choosing a file (a file with extension ".txt") into which
region of interest intensities will be written.
A javax.swing.JDialog used to set the user Preferences related to ROIs.
An enumeration of the different states in which an ROI can be.
A Class containing the statistics that are computed for an ROI.
A JFileChooser for choosing region of interest statistics files (files with extension ".txt")
into which ROI stats will be written.
An ROIStreamTokenizer used to parse ROIs from an input stream.
Interface that rotatable ROIs implement.
The rotation angles that can be used to rotate an image in steps of 90 degrees.
A JPanel for selecting an image rotation angle in steps of 90 degrees.
A JPanel for showing the details of a
ReadableImage.An interface implemented by classes that can perform cardiac analysis.
An interface implemented by classes that can perform calculations on propagated ROIs.
An
SelectedImagePanel is a JPanel that shows a
selected image.A
FixedWeightsKernelFilter for performing a sharpen filtering operation on an image.A FilterSpecifierPanel for a sharpening filter.
A JPanel for selecting a single or multiple input images, depending on a user-selection.
This class represents the timing pattern of the slice acquisition.
This
SwingWorker is used to smooth IrregularROIs.A
FixedWeightsKernelFilter for performing a Sobel filtering of an image.A {
SpatialFilter for producing the magnitude of the gradient of an image.A FilterSpecifierPanel for a Sobel edge-detection filter.
An enumeration of the types of Sobel filter.
A Class representing a Handle at of the South East corner of an ROI.
A Class representing a Handle on the South edge of an ROI.
A Class representing a Handle at of the South West corner of an ROI.
Interface implemented by classes that can spatially filter images.
A JPanel that can be used to specify spatial filter parameters.
A Class representing a curved line on an image, either open or closed, represented by
a set of knots, with spline interpolators between the knots to define the shape of the curve.
A Comparator used in sorting operations for ROIs based on their statistics.
An enumeration of the types of statistic that are computed for ROIs.
Interface that stretchable ROIs implement.
An enumeration of the types of sub-sampling to be used for resampling images.
A class for testing the autoCrop method in ImageUtils.
A Class for putting text on an image.
A dialog used to create Text ROIs.
A class for normalising image intensities.
This class represents the NIFTI units of time.
Class to show a twiddly rotating line to indicate that some action is being performed
in text-mode applications.
Enables and disables debugging messages for the UNC package.
Signals that a constructor or method in the UNC package has failed.
A file filter for UNC images.
This class is a representation of a multi-dimensional image in the
University of North Carolina (UNC) format.
This class represents the pixel formats (data types) that can be used in UNC images.
This class handles private (unknown-format) NIFTI 1.1 extended data.
Thrown when a file that should be set, has not been set by a user in a Component used to
select a file.
Thrown when an image that should be set, has not been set by a user in a Component used to
select an image.
A Class representing a Handle at one of the vertices of an EditableOutlineROI.
Enumeration of the possible spacing factors for VertexHandles when displayed on an ROI,
to prevent then being shown too close together.
A JPanel for selecting the vertex handle spacing.
A volume-of-interest, which is a stack of ROIs that connect in 3-D across slices.
A Class containing the statistics that are computed for a Volume-of-Interest (VOI).
An interpolator for a 3- (or fewer) dimensional array of pixels.
An enumeration of MR image intensity weighting types.
A JPanel for selecting a WeightingType.
A Class representing a Handle on the West edge of an ROI.
Interface implemented by classes that ensure an image of that class can be written.
This class handles NIFTI 1.1 XCEDE extended data.
This abstract class handles NIFTI 1.1 XML extended data.
This class represents the NIFTI units of length.