org.hkijena.jipipe.extensions.ij3d.datatypes

Class ROI3DListData

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractList<E>

java.util.ArrayList<ROI3D>

org.hkijena.jipipe.extensions.ij3d.datatypes.ROI3DListData

All Implemented Interfaces:

Closeable, Serializable, AutoCloseable, Cloneable, Iterable<ROI3D>, Collection<ROI3D>, List<ROI3D>, RandomAccess, JIPipeData

public class ROI3DListData
extends ArrayList<ROI3D>
implements JIPipeData

See Also:

Serialized Form

Field Summary

Fields inherited from class java.util.AbstractList

modCount

Constructor Summary

Constructors

Constructor and Description
ROI3DListData()
ROI3DListData(ROI3DListData other)

Method Summary

Modifier and Type	Method and Description
List<ROI3D>	addFromPopulation(mcib3d.geom.Objects3DPopulation population, int channel, int frame) Adds ROI from a population
ij.ImagePlus	createBlankCanvas(String title, BitDepth bitDepth)
ij.ImagePlus	createBlankCanvas(String title, int bitDepth)
void	display(String displayName, JIPipeWorkbench workbench, JIPipeDataSource source) This function should display the data in the GUI.
JIPipeData	duplicate(JIPipeProgressInfo progressInfo) Duplicates the data
void	exportData(JIPipeWriteDataStorage storage, String name, boolean forceName, JIPipeProgressInfo progressInfo) Saves the data to a folder
ROI3DListData	filteredForFrameAndChannel(int channel, int frame)
mcib3d.geom.Vector3D[]	getBounds() Gets the bounds of the 3D ROI
Map<ImageSliceIndex,List<ROI3D>>	groupByPosition(boolean perChannel, boolean perFrame) Groups the ROI by their image positions
static ROI3DListData	importData(JIPipeReadDataStorage storage, JIPipeProgressInfo progressInfo)
static ROI3DListData	importData(Path zipFile, JIPipeProgressInfo progressInfo)
void	loadObjectsFromStream(InputStream inputStream, JIPipeProgressInfo progressInfo) Copy of the original loadObjects() method adapted to loading from streams
void	logicalAnd()
void	logicalOr()
void	logicalXor()
ResultsTableData	measure(mcib3d.image3d.ImageHandler referenceImage, int measurements, boolean physicalUnits, String columnPrefix, JIPipeProgressInfo progressInfo)
void	outline(ROI3DOutline outline, boolean ignoreErrors, JIPipeProgressInfo progressInfo)
void	save(Path path)
void	saveObjectsToStream(OutputStream stream, JIPipeProgressInfo progressInfo)
ROI3DListData	shallowCopy()
ij.ImagePlus	toLabels(ij.ImagePlus referenceImage, JIPipeProgressInfo progressInfo)
ij.ImagePlus	toMask(ij.ImagePlus referenceImage, JIPipeProgressInfo progressInfo)
mcib3d.geom.Objects3DPopulation	toPopulation()
mcib3d.geom.Objects3DPopulation	toPopulation(int channel, int frame)
ROIListData	toRoi2D(JIPipeProgressInfo progressInfo)
String	toString()

Methods inherited from class java.util.ArrayList

add, add, addAll, addAll, clear, clone, contains, ensureCapacity, forEach, get, indexOf, isEmpty, iterator, lastIndexOf, listIterator, listIterator, remove, remove, removeAll, removeIf, removeRange, replaceAll, retainAll, set, size, sort, spliterator, subList, toArray, toArray, trimToSize

Methods inherited from class java.util.AbstractList

equals, hashCode

Methods inherited from class java.util.AbstractCollection

containsAll

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.hkijena.jipipe.api.data.JIPipeData

close, createThumbnail, exportThumbnails, getDescriptionOf, getMenuPathOf, getNameOf, getSortedList, getStorageDocumentation, getStorageSchema, groupByMenuPath, isCommon, isHeavy, isHidden, preview, toDetailedString

Methods inherited from interface java.util.List

containsAll, equals, hashCode

Methods inherited from interface java.util.Collection

parallelStream, stream

Constructor Detail

ROI3DListData

public ROI3DListData()

ROI3DListData

public ROI3DListData(ROI3DListData other)

Method Detail

importData

public static ROI3DListData importData(JIPipeReadDataStorage storage,
                                       JIPipeProgressInfo progressInfo)

importData

public static ROI3DListData importData(Path zipFile,
                                       JIPipeProgressInfo progressInfo)

exportData

public void exportData(JIPipeWriteDataStorage storage,
                       String name,
                       boolean forceName,
                       JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeData

Saves the data to a folder

Specified by:

exportData in interface JIPipeData

Parameters:

storage - The storage where the data should be written

name - A name reference that can be used to generate filename(s)

forceName - If enabled, the data is saved potentially destructively. Generated files must always contain the name parameter. This is used to collect results for humans or other algorithms.

progressInfo - the progress

save

public void save(Path path)

duplicate

public JIPipeData duplicate(JIPipeProgressInfo progressInfo)

Description copied from interface: JIPipeData

Duplicates the data

Specified by:

duplicate in interface JIPipeData

Parameters:

progressInfo - the progress of duplicating the data

Returns:

a deep copy of the data

display

public void display(String displayName,
                    JIPipeWorkbench workbench,
                    JIPipeDataSource source)

Description copied from interface: JIPipeData

This function should display the data in the GUI. The UI can handle multiple of such operations via JIPipeDataDisplayOperation that can be registered separately. This item will always be shown as "Default" in the list of operations.

Specified by:

display in interface JIPipeData

Parameters:

displayName - a name that can be used

workbench - the workbench

source - optional source of the data. Can be null or any kind of data type (e.g. JIPipeDataSlot)

toString

public String toString()

Overrides:

toString in class AbstractCollection<ROI3D>

groupByPosition

public Map<ImageSliceIndex,List<ROI3D>> groupByPosition(boolean perChannel,
                                                        boolean perFrame)

Groups the ROI by their image positions

Parameters:

perChannel - group per channel

perFrame - group per frame

Returns:

groups (grouped by zero-index positions)

loadObjectsFromStream

public void loadObjectsFromStream(InputStream inputStream,
                                  JIPipeProgressInfo progressInfo)

Copy of the original loadObjects() method adapted to loading from streams

Parameters:

inputStream - the input stream

progressInfo - the progress info

saveObjectsToStream

public void saveObjectsToStream(OutputStream stream,
                                JIPipeProgressInfo progressInfo)

measure

public ResultsTableData measure(mcib3d.image3d.ImageHandler referenceImage,
                                int measurements,
                                boolean physicalUnits,
                                String columnPrefix,
                                JIPipeProgressInfo progressInfo)

getBounds

public mcib3d.geom.Vector3D[] getBounds()

Gets the bounds of the 3D ROI

Returns:

array with two 3D vectors, the first one being the location and the other one containing the width, height, and depth

toPopulation

public mcib3d.geom.Objects3DPopulation toPopulation()

toPopulation

public mcib3d.geom.Objects3DPopulation toPopulation(int channel,
                                                    int frame)

filteredForFrameAndChannel

public ROI3DListData filteredForFrameAndChannel(int channel,
                                                int frame)

addFromPopulation

public List<ROI3D> addFromPopulation(mcib3d.geom.Objects3DPopulation population,
                                     int channel,
                                     int frame)

Adds ROI from a population

Parameters:

population - the population

channel - the channel (one-based)

frame - the frame (one-based)

Returns:

added ROI3D

logicalAnd

public void logicalAnd()

logicalOr

public void logicalOr()

logicalXor

public void logicalXor()

createBlankCanvas

public ij.ImagePlus createBlankCanvas(String title,
                                      BitDepth bitDepth)

createBlankCanvas

public ij.ImagePlus createBlankCanvas(String title,
                                      int bitDepth)

toMask

public ij.ImagePlus toMask(ij.ImagePlus referenceImage,
                           JIPipeProgressInfo progressInfo)

toLabels

public ij.ImagePlus toLabels(ij.ImagePlus referenceImage,
                             JIPipeProgressInfo progressInfo)

toRoi2D

public ROIListData toRoi2D(JIPipeProgressInfo progressInfo)

outline

public void outline(ROI3DOutline outline,
                    boolean ignoreErrors,
                    JIPipeProgressInfo progressInfo)

shallowCopy

public ROI3DListData shallowCopy()