Package | Description |
---|---|
org.nanes.slideset |
Slide Set tables and the ImageJ plugin
|
org.nanes.slideset.dm |
Classes implementing the data model
|
org.nanes.slideset.dm.read |
Readers for converting "underlying" data to "processed" data
|
org.nanes.slideset.dm.write |
Writers for converting "processed" data to "underlying" data
|
org.nanes.slideset.ex |
Error handling
|
org.nanes.slideset.io |
Read and write data files
|
org.nanes.slideset.pi |
Slide Set commands and plugin management
|
org.nanes.slideset.ui |
The Slide Set user interface
|
Modifier and Type | Method and Description |
---|---|
int |
SlideSet.addColumn(LinkedHashMap<String,String> properties)
Add an empty column
|
int |
SlideSet.addColumn(LinkedHashMap<String,String> properties)
Add an empty column
|
int |
SlideSet.addColumn(LinkedHashMap<String,String> properties,
ArrayList<DataElement<?>> data)
Add a column with data
|
int |
SlideSet.addColumn(LinkedHashMap<String,String> properties,
ArrayList<DataElement<?>> data)
Add a column with data
|
int |
SlideSet.addColumn(String name,
Class<? extends DataElement> elementClass)
Add an empty column with no (
null ) MIME type. |
int |
SlideSet.addColumn(String name,
Class<? extends DataElement> elementClass)
Add an empty column with no (
null ) MIME type. |
int |
SlideSet.addColumn(String name,
Class<? extends DataElement> elementClass,
String mimeType)
Add an empty column.
|
int |
SlideSet.addColumn(String name,
Class<? extends DataElement> elementClass,
String mimeType)
Add an empty column.
|
int |
SlideSet.addColumn(String name,
String elementClass)
Add an empty column with no (
null ) MIME type. |
int |
SlideSet.addColumn(String name,
String elementClass)
Add an empty column with no (
null ) MIME type. |
int |
SlideSet.addColumn(String name,
String elementClass,
String mimeType)
Add an empty column.
|
int |
SlideSet.addColumn(String name,
String elementClass,
String mimeType)
Add an empty column.
|
int |
SlideSet.addRow()
Add a row with default values
|
int |
SlideSet.addRow()
Add a row with default values
|
int |
SlideSet.addRow(List<DataElement> data)
Add a row from a
List of DataElement s. |
int |
SlideSet.addRow(List<DataElement> data)
Add a row from a
List of DataElement s. |
private boolean |
SlideSet.checkColumnElementConsistency(int column)
Check if all the
DataElement s in this column
are of the same type and have the same MIME type set. |
private boolean |
SlideSet.checkColumnElementConsistency(int column)
Check if all the
DataElement s in this column
are of the same type and have the same MIME type set. |
private boolean |
SlideSet.checkDataElementCompatibility(int column,
DataElement<?> element)
Check if the class and MIME type of a
DataElement
match those of a column in this table. |
private boolean |
SlideSet.checkDataElementCompatibility(int column,
DataElement<?> element)
Check if the class and MIME type of a
DataElement
match those of a column in this table. |
private boolean |
SlideSet.checkUnderlyingCompatability(int column,
Object underlying)
Check if an object may be stored in a column directly
using a
setUnderlying() method (i.e. |
private boolean |
SlideSet.checkUnderlyingCompatability(int column,
Object underlying)
Check if an object may be stored in a column directly
using a
setUnderlying() method (i.e. |
void |
SlideSet.convertColumn(int index,
Class<? extends DataElement<?>> elementType,
String mimeType)
Convert the data type stored in a column.
|
void |
SlideSet.convertColumn(int index,
Class<? extends DataElement<?>> elementType,
String mimeType)
Convert the data type stored in a column.
|
private Class<? extends DataElement<?>> |
SlideSet.getColumnElementClass(int index) |
private Class<? extends DataElement<?>> |
SlideSet.getColumnElementClass(int index) |
Class<? extends DataElement> |
SlideSet.getColumnElementType(int index)
Get the
DataElement type used in a column. |
Class<? extends DataElement> |
SlideSet.getColumnElementType(int index)
Get the
DataElement type used in a column. |
Class<?> |
SlideSet.getColumnUnderlyingType(int index)
Get the underlying type used to store data in a column.
|
Class<?> |
SlideSet.getColumnUnderlyingType(int index)
Get the underlying type used to store data in a column.
|
private DataElement<?> |
SlideSet.getNewColumnElement(int index)
Generate a new
DataElement appropriate
for the selected column. |
private DataElement<?> |
SlideSet.getNewColumnElement(int index)
Generate a new
DataElement appropriate
for the selected column. |
void |
SlideSet.makeDefaultLink(int column,
int row)
Set a cell to an auto-generated link
|
void |
SlideSet.makeDefaultLink(int column,
int row)
Set a cell to an auto-generated link
|
void |
SlideSet.removeChild(SlideSet child)
Remove a
SlideSet as a child of this SlideSet |
void |
SlideSet.removeChild(SlideSet child)
Remove a
SlideSet as a child of this SlideSet |
void |
SlideSet.setUnderlying(int column,
int row,
Object underlying)
Change the underlying table-stored value of an item.
|
void |
SlideSet.setUnderlying(int column,
int row,
Object underlying)
Change the underlying table-stored value of an item.
|
Modifier and Type | Method and Description |
---|---|
void |
DataTypeIDService.getColumnReadWritePairs(Class<?> type,
SlideSet data,
ArrayList<ColumnBoundReader> readers,
ArrayList<ColumnBoundWriter> writers)
Get
ColumnBoundReader —ColumnBoundWriter pairs
that can be used to read and write the specified type to a column
in the provided SlideSet table. |
void |
DataTypeIDService.getColumnReadWritePairs(Class<?> type,
SlideSet data,
ArrayList<ColumnBoundReader> readers,
ArrayList<ColumnBoundWriter> writers)
Get
ColumnBoundReader —ColumnBoundWriter pairs
that can be used to read and write the specified type to a column
in the provided SlideSet table. |
ArrayList<ColumnBoundReader> |
DataTypeIDService.getCompatableColumnReaders(Class<?> type,
SlideSet data)
Get a list of
ColumnBoundReader s that will read
data from the given table that are assignment-compatible with
the specified class. |
ArrayList<ColumnBoundReader> |
DataTypeIDService.getCompatableColumnReaders(Class<?> type,
SlideSet data)
Get a list of
ColumnBoundReader s that will read
data from the given table that are assignment-compatible with
the specified class. |
Class<? extends DataElement> |
DataTypeIDService.getReaderElementType(Class<? extends ElementReader> reader)
Get the
DataElement type read by an ElementReader type. |
Class<? extends DataElement> |
DataTypeIDService.getReaderElementType(Class<? extends ElementReader> reader)
Get the
DataElement type read by an ElementReader type. |
ArrayList<String> |
DataTypeIDService.getReaderMimeTypes(Class<? extends ElementReader> reader)
Get the list of MIME types that can be read by
an
ElementReader type. |
ArrayList<String> |
DataTypeIDService.getReaderMimeTypes(Class<? extends ElementReader> reader)
Get the list of MIME types that can be read by
an
ElementReader type. |
Class<?> |
DataTypeIDService.getReaderUnderlyingType(Class<? extends ElementReader> reader)
Get the underlying type read by an
ElementReader type. |
Class<?> |
DataTypeIDService.getReaderUnderlyingType(Class<? extends ElementReader> reader)
Get the underlying type read by an
ElementReader type. |
void |
DataTypeIDService.getTableForWriters(ArrayList<String> columnNames,
ArrayList<Class<? extends ElementWriter>> writerTypes,
SlideSet table,
ArrayList<ColumnBoundWriter> writers)
Create a table with column types matching the specified list
of
ElementWriter classes. |
void |
DataTypeIDService.getTableForWriters(ArrayList<String> columnNames,
ArrayList<Class<? extends ElementWriter>> writerTypes,
SlideSet table,
ArrayList<ColumnBoundWriter> writers)
Create a table with column types matching the specified list
of
ElementWriter classes. |
Class<? extends DataElement> |
DataTypeIDService.getWriterElementType(Class<? extends ElementWriter> writer)
Get the
DataElement type written by an ElementWriter type. |
Class<? extends DataElement> |
DataTypeIDService.getWriterElementType(Class<? extends ElementWriter> writer)
Get the
DataElement type written by an ElementWriter type. |
ColumnBoundReader<?,?> |
DataTypeIDService.makeColumnBoundConstantReader(Class<? extends ElementReader> readerType,
Object data,
SlideSet table)
Create a
ColumnBoundReader that will always read from
a constant DataElement . |
ColumnBoundReader<?,?> |
DataTypeIDService.makeColumnBoundConstantReader(Class<? extends ElementReader> readerType,
Object data,
SlideSet table)
Create a
ColumnBoundReader that will always read from
a constant DataElement . |
P |
ColumnBoundReader.read(int row)
Read data from the specified row
|
P |
ColumnBoundReader.read(int row)
Read data from the specified row
|
void |
CommandTemplate.readXML(XMLStreamReader xsr)
Populate these properties from an XML stream.
|
void |
CommandTemplate.readXML(XMLStreamReader xsr)
Populate these properties from an XML stream.
|
void |
CommandTemplate.setInputChoices(ArrayList<Integer> ics,
ArrayList<Object> cs)
Set the command input choice parameters.
|
void |
CommandTemplate.setInputChoices(ArrayList<Integer> ics,
ArrayList<Object> cs)
Set the command input choice parameters.
|
void |
CommandTemplate.setOutputChoices(ArrayList<Integer> ocs,
ArrayList<Integer> spfs,
ArrayList<String> lds,
ArrayList<String> lps,
ArrayList<String> les)
Set the command output choices.
|
void |
CommandTemplate.setOutputChoices(ArrayList<Integer> ocs,
ArrayList<Integer> spfs,
ArrayList<String> lds,
ArrayList<String> lps,
ArrayList<String> les)
Set the command output choices.
|
void |
BooleanElement.setUnderlyingText(String text) |
abstract void |
DataElement.setUnderlyingText(String text)
Set this element's "underlying" value based on a
String |
void |
DoubleElement.setUnderlyingText(String text) |
void |
IntegerElement.setUnderlyingText(String text) |
void |
IntegerElement.setUnderlyingText(String text) |
void |
DoubleElement.setUnderlyingText(String text) |
abstract void |
DataElement.setUnderlyingText(String text)
Set this element's "underlying" value based on a
String |
void |
BooleanElement.setUnderlyingText(String text) |
void |
ColumnBoundWriter.write(P item,
int row)
Write data to the table
|
void |
ColumnBoundWriter.write(P item,
int row)
Write data to the table
|
Constructor and Description |
---|
CommandTemplate(XMLStreamReader xsr) |
CommandTemplate(XMLStreamReader xsr) |
Modifier and Type | Method and Description |
---|---|
private Document |
SVGFileToAbstractOverlayReader.loadDocument(File file)
Load the DOM from an SVG file
|
private Document |
SVGFileToIJ1ROIReader.loadDocument(File file)
Load the DOM from an SVG file
|
private Document |
SVGFileToIJ1ROIReader.loadDocument(File file)
Load the DOM from an SVG file
|
private Document |
SVGFileToAbstractOverlayReader.loadDocument(File file)
Load the DOM from an SVG file
|
Boolean |
BooleanToBooleanReader.read(BooleanElement elementToRead) |
Byte |
BooleanToByteReader.read(BooleanElement elementToRead) |
Integer |
BooleanToIntReader.read(BooleanElement elementToRead) |
Short |
BooleanToShortReader.read(BooleanElement elementToRead) |
Short |
BooleanToShortReader.read(BooleanElement elementToRead) |
Integer |
BooleanToIntReader.read(BooleanElement elementToRead) |
Byte |
BooleanToByteReader.read(BooleanElement elementToRead) |
Boolean |
BooleanToBooleanReader.read(BooleanElement elementToRead) |
Double |
DoubleToDoubleReader.read(DoubleElement elementToRead) |
Float |
DoubleToFloatReader.read(DoubleElement elementToRead) |
Float |
DoubleToFloatReader.read(DoubleElement elementToRead) |
Double |
DoubleToDoubleReader.read(DoubleElement elementToRead) |
P |
ElementReader.read(E elementToRead)
Convert "underlying" data to "processed" data.
|
P |
ElementReader.read(E elementToRead)
Convert "underlying" data to "processed" data.
|
net.imagej.Dataset |
ImageFileToDatasetReader.read(FileLinkElement elementToRead) |
net.imagej.display.ImageDisplay |
ImageFileToImageDisplayReader.read(FileLinkElement elementToRead) |
ij.ImagePlus |
ImageFileToImagePlusReader.read(FileLinkElement elementToRead) |
ij.gui.ImageWindow |
ImageFileToImageWindowReader.read(FileLinkElement elementToRead) |
net.imagej.overlay.AbstractOverlay[] |
RoisetFileToAbstractOverlayReader.read(FileLinkElement elementToRead) |
net.imagej.overlay.AbstractOverlay[] |
SVGFileToAbstractOverlayReader.read(FileLinkElement elementToRead) |
ij.gui.Roi[] |
SVGFileToIJ1ROIReader.read(FileLinkElement elementToRead) |
WekaClassifierFile |
WekaClassifierReader.read(FileLinkElement elementToRead) |
WekaClassifierFile |
WekaClassifierReader.read(FileLinkElement elementToRead) |
ij.gui.Roi[] |
SVGFileToIJ1ROIReader.read(FileLinkElement elementToRead) |
net.imagej.overlay.AbstractOverlay[] |
SVGFileToAbstractOverlayReader.read(FileLinkElement elementToRead) |
net.imagej.overlay.AbstractOverlay[] |
RoisetFileToAbstractOverlayReader.read(FileLinkElement elementToRead) |
ij.gui.ImageWindow |
ImageFileToImageWindowReader.read(FileLinkElement elementToRead) |
ij.ImagePlus |
ImageFileToImagePlusReader.read(FileLinkElement elementToRead) |
net.imagej.display.ImageDisplay |
ImageFileToImageDisplayReader.read(FileLinkElement elementToRead) |
net.imagej.Dataset |
ImageFileToDatasetReader.read(FileLinkElement elementToRead) |
Byte |
IntToByteReader.read(IntegerElement elementToRead) |
Double |
IntToDoubleReader.read(IntegerElement elementToRead) |
Float |
IntToFloatReader.read(IntegerElement elementToRead) |
Integer |
IntToIntReader.read(IntegerElement elementToRead) |
Long |
IntToLongReader.read(IntegerElement elementToRead) |
Short |
IntToShortReader.read(IntegerElement elementToRead) |
Short |
IntToShortReader.read(IntegerElement elementToRead) |
Long |
IntToLongReader.read(IntegerElement elementToRead) |
Integer |
IntToIntReader.read(IntegerElement elementToRead) |
Float |
IntToFloatReader.read(IntegerElement elementToRead) |
Double |
IntToDoubleReader.read(IntegerElement elementToRead) |
Byte |
IntToByteReader.read(IntegerElement elementToRead) |
String |
StringToStringReader.read(StringElement elementToRead) |
String |
StringToStringReader.read(StringElement elementToRead) |
Modifier and Type | Method and Description |
---|---|
private void |
AbstractOverlaysToSVGFileWriter.applyDefaultStyles(XMLStreamWriter xsw)
Default SVG styling attributes for overlays
|
private void |
IJ1ROIsToSVGFileWriter.applyDefaultStyles(XMLStreamWriter xsw)
Default SVG styling attributes for overlays
|
private void |
IJ1ROIsToSVGFileWriter.applyDefaultStyles(XMLStreamWriter xsw)
Default SVG styling attributes for overlays
|
private void |
AbstractOverlaysToSVGFileWriter.applyDefaultStyles(XMLStreamWriter xsw)
Default SVG styling attributes for overlays
|
private void |
AbstractOverlaysToSVGFileWriter.closeFile(XMLStreamWriter xsw)
End the SVG file and do cleanup
|
private void |
IJ1ROIsToSVGFileWriter.closeFile(XMLStreamWriter xsw)
End the SVG file and do cleanup
|
private void |
IJ1ROIsToSVGFileWriter.closeFile(XMLStreamWriter xsw)
End the SVG file and do cleanup
|
private void |
AbstractOverlaysToSVGFileWriter.closeFile(XMLStreamWriter xsw)
End the SVG file and do cleanup
|
private void |
AbstractOverlaysToSVGFileWriter.getPlanarAxes(net.imagej.overlay.AbstractOverlay overlay,
int[] axes)
Get the X and Y axis indeces for an overlay
|
private void |
AbstractOverlaysToSVGFileWriter.getPlanarAxes(net.imagej.overlay.AbstractOverlay overlay,
int[] axes)
Get the X and Y axis indeces for an overlay
|
private XMLStreamWriter |
AbstractOverlaysToSVGFileWriter.setupFile(String path,
int width,
int height,
String img)
Start the SVG file
|
private XMLStreamWriter |
IJ1ROIsToSVGFileWriter.setupFile(String path,
int width,
int height,
String img)
Start the SVG file
|
private XMLStreamWriter |
IJ1ROIsToSVGFileWriter.setupFile(String path,
int width,
int height,
String img)
Start the SVG file
|
private XMLStreamWriter |
AbstractOverlaysToSVGFileWriter.setupFile(String path,
int width,
int height,
String img)
Start the SVG file
|
void |
AbstractOverlaysToRoisetFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
FileLinkElement elementToWrite) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
FileLinkElement elementToWrite) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
FileLinkElement elementToWrite) |
void |
AbstractOverlaysToRoisetFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
FileLinkElement elementToWrite) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path,
int width,
int height) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path,
int width,
int height) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path,
int width,
int height,
String imgPath) |
void |
AbstractOverlaysToSVGFileWriter.write(net.imagej.overlay.AbstractOverlay[] data,
String path,
int width,
int height,
String imgPath) |
void |
DatasetToImageFileWriter.write(net.imagej.Dataset data,
FileLinkElement elementToWrite) |
void |
DatasetToPngFileWriter.write(net.imagej.Dataset data,
FileLinkElement elementToWrite) |
void |
DatasetToPngFileWriter.write(net.imagej.Dataset data,
FileLinkElement elementToWrite) |
void |
DatasetToImageFileWriter.write(net.imagej.Dataset data,
FileLinkElement elementToWrite) |
void |
ImageDisplayToImageFileWriter.write(net.imagej.display.ImageDisplay data,
FileLinkElement elementToWrite) |
void |
ImageDisplayToImageFileWriter.write(net.imagej.display.ImageDisplay data,
FileLinkElement elementToWrite) |
void |
ImagePlusToImageFileWriter.write(ij.ImagePlus data,
FileLinkElement elementToWrite) |
void |
ImagePlusToPngFileWriter.write(ij.ImagePlus data,
FileLinkElement elementToWrite) |
void |
ImagePlusToPngFileWriter.write(ij.ImagePlus data,
FileLinkElement elementToWrite) |
void |
ImagePlusToImageFileWriter.write(ij.ImagePlus data,
FileLinkElement elementToWrite) |
void |
ElementWriter.write(P data,
E elementToWrite)
Convert "processed" data to "underlying" data.
|
void |
ElementWriter.write(P data,
E elementToWrite)
Convert "processed" data to "underlying" data.
|
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
FileLinkElement elementToWrite) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
FileLinkElement elementToWrite) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path,
int width,
int height) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path,
int width,
int height) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path,
int width,
int height,
String imgPath) |
void |
IJ1ROIsToSVGFileWriter.write(ij.gui.Roi[] data,
String path,
int width,
int height,
String imgPath) |
private void |
AbstractOverlaysToSVGFileWriter.writeEllipseOverlay(XMLStreamWriter xsw,
net.imagej.overlay.EllipseOverlay overlay)
Write an ellipse overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writeEllipseOverlay(XMLStreamWriter xsw,
net.imagej.overlay.EllipseOverlay overlay)
Write an ellipse overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writeFile(String path,
net.imagej.overlay.AbstractOverlay[] overlays,
int width,
int height,
String img)
Write the SVG file to
path |
private void |
AbstractOverlaysToSVGFileWriter.writeFile(String path,
net.imagej.overlay.AbstractOverlay[] overlays,
int width,
int height,
String img)
Write the SVG file to
path |
private void |
IJ1ROIsToSVGFileWriter.writeFile(String path,
ij.gui.Roi[] rois,
int width,
int height,
String img)
Write the SVG file to
path |
private void |
IJ1ROIsToSVGFileWriter.writeFile(String path,
ij.gui.Roi[] rois,
int width,
int height,
String img)
Write the SVG file to
path |
private void |
AbstractOverlaysToSVGFileWriter.writeGeneralPathOverlay(XMLStreamWriter xsw,
net.imagej.overlay.GeneralPathOverlay overlay)
Write a general path overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writeGeneralPathOverlay(XMLStreamWriter xsw,
net.imagej.overlay.GeneralPathOverlay overlay)
Write a general path overlay
|
private void |
IJ1ROIsToSVGFileWriter.writeLine(XMLStreamWriter xsw,
ij.gui.Line roi)
Write a Line ROI
|
private void |
IJ1ROIsToSVGFileWriter.writeLine(XMLStreamWriter xsw,
ij.gui.Line roi)
Write a Line ROI
|
private void |
AbstractOverlaysToSVGFileWriter.writeLineOverlay(XMLStreamWriter xsw,
net.imagej.overlay.LineOverlay overlay)
Write a line overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writeLineOverlay(XMLStreamWriter xsw,
net.imagej.overlay.LineOverlay overlay)
Write a line overlay
|
private void |
IJ1ROIsToSVGFileWriter.writeOvalRoi(XMLStreamWriter xsw,
ij.gui.OvalRoi roi)
Write an OvalRoi
|
private void |
IJ1ROIsToSVGFileWriter.writeOvalRoi(XMLStreamWriter xsw,
ij.gui.OvalRoi roi)
Write an OvalRoi
|
private void |
AbstractOverlaysToSVGFileWriter.writeOverlay(XMLStreamWriter xsw,
net.imagej.overlay.AbstractOverlay overlay)
Write an overlay, if supported
|
private void |
AbstractOverlaysToSVGFileWriter.writeOverlay(XMLStreamWriter xsw,
net.imagej.overlay.AbstractOverlay overlay)
Write an overlay, if supported
|
private void |
IJ1ROIsToSVGFileWriter.writeOverlay(XMLStreamWriter xsw,
ij.gui.Roi roi)
Write an overlay, if supported
|
private void |
IJ1ROIsToSVGFileWriter.writeOverlay(XMLStreamWriter xsw,
ij.gui.Roi roi)
Write an overlay, if supported
|
private void |
AbstractOverlaysToSVGFileWriter.writePointOverlay(XMLStreamWriter xsw,
net.imagej.overlay.PointOverlay overlay)
Write a point overlay.
|
private void |
AbstractOverlaysToSVGFileWriter.writePointOverlay(XMLStreamWriter xsw,
net.imagej.overlay.PointOverlay overlay)
Write a point overlay.
|
private void |
IJ1ROIsToSVGFileWriter.writePointRoi(XMLStreamWriter xsw,
ij.gui.PointRoi roi)
Write a PointRoi
|
private void |
IJ1ROIsToSVGFileWriter.writePointRoi(XMLStreamWriter xsw,
ij.gui.PointRoi roi)
Write a PointRoi
|
private void |
AbstractOverlaysToSVGFileWriter.writePolygonOverlay(XMLStreamWriter xsw,
net.imagej.overlay.PolygonOverlay overlay)
Write a polygon overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writePolygonOverlay(XMLStreamWriter xsw,
net.imagej.overlay.PolygonOverlay overlay)
Write a polygon overlay
|
private void |
IJ1ROIsToSVGFileWriter.writePolygonRoi(XMLStreamWriter xsw,
ij.gui.PolygonRoi roi)
Write a PolygonRoi
|
private void |
IJ1ROIsToSVGFileWriter.writePolygonRoi(XMLStreamWriter xsw,
ij.gui.PolygonRoi roi)
Write a PolygonRoi
|
private void |
IJ1ROIsToSVGFileWriter.writeRectangle(XMLStreamWriter xsw,
ij.gui.Roi roi)
Write a rectangular Roi
|
private void |
IJ1ROIsToSVGFileWriter.writeRectangle(XMLStreamWriter xsw,
ij.gui.Roi roi)
Write a rectangular Roi
|
private void |
AbstractOverlaysToSVGFileWriter.writeRectangleOverlay(XMLStreamWriter xsw,
net.imagej.overlay.RectangleOverlay overlay)
Write a rectangle overlay
|
private void |
AbstractOverlaysToSVGFileWriter.writeRectangleOverlay(XMLStreamWriter xsw,
net.imagej.overlay.RectangleOverlay overlay)
Write a rectangle overlay
|
private void |
IJ1ROIsToSVGFileWriter.writeShapeRoi(XMLStreamWriter xsw,
ij.gui.ShapeRoi roi)
Write a ShapeRoi
|
private void |
IJ1ROIsToSVGFileWriter.writeShapeRoi(XMLStreamWriter xsw,
ij.gui.ShapeRoi roi)
Write a ShapeRoi
|
Modifier and Type | Class and Description |
---|---|
class |
ColumnTypeException
Signals the column types of a table do not match the expected types.
|
class |
DefaultPathNotSetException
Indicates that a new link cannot be generated because the default link
path is not set in the
column properties |
class |
ImgLinkException
Signals a problem with a link to an image.
|
class |
LinkException
Signals a problem with a data table file reference
|
class |
LinkNotFoundException
Indicates a link points to a file that does not exist.
|
class |
NoPluginInputSourceException
Signals that a command cannot be run on a table
one of the plugin inputs requires a type which
cannot be read from the table or entered as a constant.
|
class |
OperationCanceledException
Thrown when a SlideSet operation has been canceled.
|
class |
RoiLinkException
Signals a problem with a link to an ROI set.
|
class |
SVGParseException
Signals an error parsing an SVG file
|
class |
UnsupportedOverlayException
Signal that an
Overlay type is not supported. |
Modifier and Type | Method and Description |
---|---|
SlideSet |
XMLService.read(File file)
Read
SlideSet data from an XML file |
SlideSet |
XMLService.read(File file)
Read
SlideSet data from an XML file |
void |
CommandSkeletonService.read(File file,
ArrayList<CommandTemplate> cts,
ArrayList<String> rootColumnTypes)
Read a command skeleton from an XML file.
|
void |
CommandSkeletonService.read(File file,
ArrayList<CommandTemplate> cts,
ArrayList<String> rootColumnTypes)
Read a command skeleton from an XML file.
|
private SlideSet |
XMLService.readTable()
Nestable utility function to read one SlideSet
|
private SlideSet |
XMLService.readTable()
Nestable utility function to read one SlideSet
|
void |
CommandSkeletonService.runSkeleton(List<CommandTemplate> cts,
List<String> rootColTypes,
SlideSet root,
SlideSetPluginLoader sspl,
boolean overrideRootWarning)
Run a command skeleton on a data table.
|
void |
CommandSkeletonService.runSkeleton(List<CommandTemplate> cts,
List<String> rootColTypes,
SlideSet root,
SlideSetPluginLoader sspl,
boolean overrideRootWarning)
Run a command skeleton on a data table.
|
void |
CommandSkeletonService.write(SlideSet data,
File file)
Write a command skeleton to an XML file.
|
void |
CommandSkeletonService.write(SlideSet data,
File file)
Write a command skeleton to an XML file.
|
Modifier and Type | Method and Description |
---|---|
private void |
SlideSetPluginLoader.addColumnsForParentFields(ArrayList<Integer> includedFields,
SlideSet parent,
SlideSet results)
Add columns to the results table for included fields from
the input table
|
private void |
SlideSetPluginLoader.addColumnsForParentFields(ArrayList<Integer> includedFields,
SlideSet parent,
SlideSet results)
Add columns to the results table for included fields from
the input table
|
private void |
SlideSetPluginLoader.fillServices(org.scijava.module.Module module,
Iterable<org.scijava.module.ModuleItem<?>> inputs)
Prefill service inputs
|
private void |
SlideSetPluginLoader.fillServices(org.scijava.module.Module module,
Iterable<org.scijava.module.ModuleItem<?>> inputs)
Prefill service inputs
|
private ArrayList<ColumnBoundReader> |
SlideSetPluginLoader.getReaders(Iterable<org.scijava.module.ModuleItem<?>> inputs,
SlideSet data,
PluginInputPicker pip,
String docPath,
CommandTemplate ct)
Create a list of
ColumnBoundReader s for each input |
private ArrayList<ColumnBoundReader> |
SlideSetPluginLoader.getReaders(Iterable<org.scijava.module.ModuleItem<?>> inputs,
SlideSet data,
PluginInputPicker pip,
String docPath,
CommandTemplate ct)
Create a list of
ColumnBoundReader s for each input |
static double |
ROILengths.getRoiLenth(net.imagej.overlay.AbstractOverlay overlay)
Calculate the length, in pixels, of an
AbstractOverlay border. |
static double |
ROILengths.getRoiLenth(net.imagej.overlay.AbstractOverlay overlay)
Calculate the length, in pixels, of an
AbstractOverlay border. |
private void |
SlideSetPluginLoader.getWriters(ArrayList<org.scijava.module.ModuleItem<?>> outputs,
boolean reduce,
PluginOutputPicker pop,
ArrayList<ColumnBoundWriter> writers,
SlideSet resultsTable,
String[] parentLabels,
ArrayList<Integer> parentFields,
ArrayList<String> linkDir,
ArrayList<String> linkPre,
ArrayList<String> linkExt,
CommandTemplate ct)
Prepare for plugin results be creating a results table
and appropriate
ColumnBoundWriter s to write the
results to it |
private void |
SlideSetPluginLoader.getWriters(ArrayList<org.scijava.module.ModuleItem<?>> outputs,
boolean reduce,
PluginOutputPicker pop,
ArrayList<ColumnBoundWriter> writers,
SlideSet resultsTable,
String[] parentLabels,
ArrayList<Integer> parentFields,
ArrayList<String> linkDir,
ArrayList<String> linkPre,
ArrayList<String> linkExt,
CommandTemplate ct)
Prepare for plugin results be creating a results table
and appropriate
ColumnBoundWriter s to write the
results to it |
static boolean |
RoiUtils.isNearBorder(double[] P,
net.imagej.overlay.AbstractOverlay overlay,
double radius)
Determine if a point is near a border defined by an set of vertices.
|
static boolean |
RoiUtils.isNearBorder(double[] P,
net.imagej.overlay.AbstractOverlay overlay,
double radius)
Determine if a point is near a border defined by an set of vertices.
|
SlideSet |
SlideSetPluginLoader.runPlugin(org.scijava.command.CommandInfo plugin,
SlideSet data,
PluginInputPicker pip,
PluginOutputPicker pop)
Run a
SlideSetPlugin |
SlideSet |
SlideSetPluginLoader.runPlugin(org.scijava.command.CommandInfo plugin,
SlideSet data,
PluginInputPicker pip,
PluginOutputPicker pop)
Run a
SlideSetPlugin |
SlideSet |
SlideSetPluginLoader.runPlugin(String className,
SlideSet data,
PluginInputPicker pip,
PluginOutputPicker pop)
Run a
SlideSetPlugin |
SlideSet |
SlideSetPluginLoader.runPlugin(String className,
SlideSet data,
PluginInputPicker pip,
PluginOutputPicker pop)
Run a
SlideSetPlugin |
private void |
SlideSetPluginLoader.saveResults(org.scijava.module.Module m,
ArrayList<org.scijava.module.ModuleItem<?>> outputs,
boolean reduce,
ArrayList<ColumnBoundWriter> writers,
ArrayList<Integer> parentFields,
SlideSet resultsTable,
SlideSet parentTable,
int parentRow)
Save results from a command execution
|
private void |
SlideSetPluginLoader.saveResults(org.scijava.module.Module m,
ArrayList<org.scijava.module.ModuleItem<?>> outputs,
boolean reduce,
ArrayList<ColumnBoundWriter> writers,
ArrayList<Integer> parentFields,
SlideSet resultsTable,
SlideSet parentTable,
int parentRow)
Save results from a command execution
|
private void |
SlideSetPluginLoader.setupFileLinkColumns(SlideSet table,
ArrayList<String> linkDir,
ArrayList<String> linkPre,
ArrayList<String> linkExt)
Generate default path links as needed
|
private void |
SlideSetPluginLoader.setupFileLinkColumns(SlideSet table,
ArrayList<String> linkDir,
ArrayList<String> linkPre,
ArrayList<String> linkExt)
Generate default path links as needed
|
ij.ImagePlus |
SilentSlicer.sliceSilently(ij.ImagePlus imp) |
ij.ImagePlus |
SilentSlicer.sliceSilently(ij.ImagePlus imp) |
net.imagej.Dataset[] |
UnmixAbsorbance.unmix(net.imagej.Dataset input,
double[] absOne,
double[] absTwo)
Separate an RGB image into two absorbance components.
|
net.imagej.Dataset[] |
UnmixAbsorbance.unmix(net.imagej.Dataset input,
double[] absOne,
double[] absTwo)
Separate an RGB image into two absorbance components.
|
Modifier and Type | Method and Description |
---|---|
void |
HelpLoader.getHelp() |
void |
HttpHelpLoader.getHelp() |
void |
HttpHelpLoader.getHelp() |
void |
HelpLoader.getHelp() |
void |
HelpLoader.getHelp(String pageKey) |
void |
HttpHelpLoader.getHelp(String pageKey)
Open a documentation page.
|
void |
HttpHelpLoader.getHelp(String pageKey)
Open a documentation page.
|
void |
HelpLoader.getHelp(String pageKey) |
private void |
RoiEditor.loadData()
Load the internal data
|
private void |
RoiEditor.loadData()
Load the internal data
|
private void |
RoiEditorIJ1.loadImageData()
Load the index of images
|
private void |
RoiEditorIJ1.loadImageData()
Load the index of images
|
private void |
RoiEditor.loadOverlays()
Load overlay data from disk
|
private void |
RoiEditor.loadOverlays()
Load overlay data from disk
|
private void |
RoiEditorIJ1.loadRois()
Load the ROI data
|
private void |
RoiEditorIJ1.loadRois()
Load the ROI data
|
private void |
HttpHelpLoader.start() |
private void |
HttpHelpLoader.start() |
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