| Package | Description |
|---|---|
| loci.visbio.data | |
| loci.visbio.ext | |
| loci.visbio.overlays | |
| loci.visbio.view |
| Modifier and Type | Class and Description |
|---|---|
class |
ArbitrarySlice
A transform for slicing a stack of images in 3D.
|
class |
CollapseTransform
CollapseTransform converts a dimensional axis into a series of range
components.
|
class |
DataSampling
DataSampling is a resampling of another transform.
|
class |
Dataset
A Dataset object encompasses a multidimensional biological image series.
|
class |
ImageTransform
ImageTransform is a DataTransform superclass that provides image data.
|
class |
ProjectionTransform
ProjectionTransform performs a maximum intensity projection across a given
dimensional axis.
|
class |
SpectralTransform
SpectralTransform is a mapping of spectral bands onto an RGB or grayscale
color space, as specified by the user with weighted sliders.
|
| Modifier and Type | Field and Description |
|---|---|
protected DataTransform |
ThumbnailHandler.data
Data transform on which this thumbnail handler operates.
|
protected DataTransform |
DataTransform.parent
Parent transform from which this transform obtains its data.
|
| Modifier and Type | Method and Description |
|---|---|
DataTransform |
DataManager.getDataById(int id)
Gets the data transform with the associated ID.
|
DataTransform |
DataTransform.getParent()
Gets the parent of this transform.
|
DataTransform |
DataManager.getSelectedData()
Gets the currently selected data object.
|
DataTransform |
DataControls.getSelectedData()
Gets the currently selected data object.
|
static DataTransform |
SpectralTransform.makeTransform(DataManager dm)
Creates a new spectral mapping, with user interaction.
|
static DataTransform |
ProjectionTransform.makeTransform(DataManager dm)
Creates a new maximum intensity projection, with user interaction.
|
static DataTransform |
Dataset.makeTransform(DataManager dm)
Creates a new dataset, with user interaction.
|
static DataTransform |
DataSampling.makeTransform(DataManager dm)
Creates a new data sampling, with user interaction.
|
static DataTransform |
CollapseTransform.makeTransform(DataManager dm)
Creates a new dimensional collapse, with user interaction.
|
static DataTransform |
ArbitrarySlice.makeTransform(DataManager dm)
Creates a new set of overlays, with user interaction.
|
static DataTransform |
Dataset.makeTransform(DataManager dm,
File file,
Component parent)
Creates a new dataset, with user interaction, with the given default file.
|
| Modifier and Type | Method and Description |
|---|---|
Vector<DataTransform> |
DataManager.getDataList()
Gets a list of data transforms present in the tree.
|
| Modifier and Type | Method and Description |
|---|---|
void |
DataManager.addData(DataTransform data)
Adds a data object to the list.
|
void |
DataControls.addData(DataTransform data)
Adds a data object to the data object tree.
|
protected void |
DataControls.doDataInfo(DataTransform data)
Updates data information panel, and toggles button availability.
|
void |
DataCache.dump(DataTransform trans,
int[] pos,
String append)
Removes the data object at the specified dimensional position from the
cache.
|
void |
DataCache.dump(DataTransform trans,
String append)
Removes from the cache data objects at all dimensional positions for the
given data object.
|
protected DefaultMutableTreeNode |
DataControls.findNode(DataTransform data)
Finds the tree node representing this data object.
|
Data |
DataCache.getData(DataTransform trans,
int[] pos,
String append,
int dim)
Gets the data object from the cache, computing it if the cache misses.
|
protected String |
DataCache.getKey(DataTransform trans,
int[] pos,
String append)
Gets a key string suitable for hashing for the given transform at the
specified position.
|
boolean |
DataCache.hasData(DataTransform trans,
int[] pos,
String append)
Gets whether the cache has data for the given transform at the specified
dimensional position.
|
void |
DataControls.hideControls(DataTransform data)
Hides frame containing controls for the given data object.
|
static boolean |
SpectralTransform.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
ProjectionTransform.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
Dataset.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
DataSampling.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
CollapseTransform.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
ArbitrarySlice.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
void |
DataCache.putData(DataTransform trans,
int[] pos,
String append,
Data d)
Puts the given data object into the cache for the specified transform at
the given dimensional position.
|
void |
DataManager.removeData(DataTransform data)
Removes a data object from the list.
|
boolean |
DataControls.removeData(DataTransform data)
Removes a data object from the data object tree.
|
void |
DataManager.removeData(DataTransform data,
boolean confirm)
Removes a data object from the list.
|
boolean |
DataControls.removeData(DataTransform data,
boolean confirm)
Removes a data object from the data object tree, confirming with the user
first if confirm flag is set and the object has derivative objects.
|
void |
DataControls.setSelectedData(DataTransform data)
Selects the given data object in the tree.
|
void |
DataManager.showControls(DataTransform data)
Shows dialog containing controls for the given data object.
|
void |
DataControls.showControls(DataTransform data)
Shows frame containing controls for the given data object.
|
| Constructor and Description |
|---|
ArbitrarySlice(DataTransform parent,
String name)
Creates an overlay object for the given transform.
|
CollapseTransform(DataTransform parent,
String name,
int axis)
Creates a dimensional collapse from the given transform.
|
DataSampling(DataTransform parent,
String name,
int[] min,
int[] max,
int[] step,
int resX,
int resY,
boolean[] range)
Creates a data sampling from the given transform.
|
DataTransform(DataTransform parent,
String name)
Creates a data transform with the given transform as its parent.
|
ImageTransform(DataTransform parent,
String name)
Creates an image transform with the given transform as its parent.
|
ImageTransform(DataTransform parent,
String name,
double width,
double height,
double step)
Creates an image transform with the given transform as its parent, that is
dimensioned according to the specified values in microns.
|
ProjectionTransform(DataTransform parent,
String name,
int axis)
Creates a maximum intensity projection from the given transform.
|
SamplingThumbHandler(DataTransform data,
String filename)
Creates a thumbnail handler.
|
SpectralTransform(DataTransform parent,
String name,
int numRange)
Creates a spectral mapping from the given transform.
|
ThumbnailHandler(DataTransform data,
String filename)
Creates a thumbnail handler.
|
| Modifier and Type | Class and Description |
|---|---|
class |
ExternalFunction
ExternalFunction is an abstract transform that calls some form of external
function.
|
class |
ExternalProgram
ExternalProgram is a transform that uses system calls to an external program
to evaluate a function, using stdin and stdout for binary data transfer.
|
class |
MatlabFunction
MatlabFunction executes a MATLAB script or function on a data object.
|
| Modifier and Type | Method and Description |
|---|---|
static DataTransform |
MatlabFunction.makeTransform(DataManager dm)
Creates a new MATLAB transform, with user interaction.
|
static DataTransform |
ExternalProgram.makeTransform(DataManager dm)
Creates a new external program, with user interaction.
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
MatlabFunction.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
static boolean |
ExternalProgram.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
| Constructor and Description |
|---|
ExternalFunction(DataTransform parent,
String name,
String function)
Creates an external function transform from the given transform.
|
ExternalProgram(DataTransform parent,
String name,
String function)
Creates an external program transform from the given transform.
|
MatlabFunction(DataTransform parent,
String name,
String function)
Creates a MATLAB transform from the given transform.
|
| Modifier and Type | Class and Description |
|---|---|
class |
OverlayTransform
A set of overlays on top another transform.
|
| Modifier and Type | Method and Description |
|---|---|
static DataTransform |
OverlayTransform.makeTransform(DataManager dm)
Creates a new set of overlays, with user interaction.
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
OverlayTransform.isValidParent(DataTransform data)
Indicates whether this transform type would accept the given transform as
its parent transform.
|
| Constructor and Description |
|---|
OverlayTransform(DataTransform parent,
String name)
Creates an overlay object for the given transform.
|
| Modifier and Type | Field and Description |
|---|---|
protected DataTransform |
TransformLink.trans
Data transform linked to the display.
|
protected DataTransform |
SliceToggler.transform
Data transform upon which this slice toggler operates.
|
| Modifier and Type | Method and Description |
|---|---|
DataTransform |
TransformLink.getTransform()
Gets the link's data transform.
|
DataTransform[] |
TransformHandler.getTransforms()
Gets data transforms linked to the display.
|
DataTransform[] |
BioSlideWidget.getTransforms()
Gets transforms affected by this slider.
|
| Modifier and Type | Method and Description |
|---|---|
void |
TransformPanel.addTransform(DataTransform trans)
Adds the given data transform to the list.
|
void |
TransformHandler.addTransform(DataTransform trans)
Links the given data transform to the display.
|
void |
StackHandler.addTransform(DataTransform trans)
Links the given data transform to the display.
|
void |
DisplayWindow.addTransform(DataTransform trans)
Links the given data transform to the display.
|
boolean |
BioSlideWidget.addTransform(DataTransform trans,
int ndx)
Adds a transform to the list affected by this slider.
|
int |
TransformHandler.getAxis(DataTransform trans,
int axis)
Identifies the dimensional axis of the given transform to which the
specified slider axis corresponds, or -1 if none.
|
TransformLink |
TransformHandler.getLink(DataTransform trans)
Gets the transform link object for the given data transform.
|
int |
TransformHandler.getLinkIndex(DataTransform trans)
Gets the transform link index for the given data transform.
|
int[] |
TransformHandler.getPos(DataTransform trans)
Gets the dimensional position specified by the given transform's slider
widgets.
|
boolean |
TransformPanel.hasTransform(DataTransform trans)
Gets whether the given transform is currently linked to the display.
|
boolean |
TransformHandler.hasTransform(DataTransform trans)
Gets whether the given transform is currently linked to the display.
|
boolean |
DisplayWindow.hasTransform(DataTransform trans)
Gets whether the given transform is currently linked to the display.
|
void |
TransformPanel.moveTransformDown(DataTransform trans)
Moves the given transform down in the list.
|
void |
TransformHandler.moveTransformDown(DataTransform trans)
Moves the given transform down in the Z-order.
|
void |
TransformPanel.moveTransformUp(DataTransform trans)
Moves the given transform up in the list.
|
void |
TransformHandler.moveTransformUp(DataTransform trans)
Moves the given transform up in the Z-order.
|
void |
TransformPanel.removeTransform(DataTransform trans)
Removes the given data transform from the list.
|
void |
TransformHandler.removeTransform(DataTransform trans)
Removes the given data transform from the display.
|
void |
DisplayWindow.removeTransform(DataTransform trans)
Removes the given data transform from the display.
|
void |
SliceToggler.setTransform(DataTransform trans)
Sets the transform affected by this slice toggler.
|
| Constructor and Description |
|---|
BioSlideWidget(DataTransform trans,
int ndx)
Constructs a new slider widget from the given transform and index.
|
StackLink(StackHandler h,
DataTransform t)
Creates a link between the given data transform and the specified stack
handler's display.
|
TransformLink(TransformHandler h,
DataTransform t)
Creates a link between the given data transform and the specified transform
handler's display.
|
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