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*------------------------------------------------------------------------------
* Copyright (C) 2006-2015 University of Dundee. All rights reserved.
*
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License along
* with this program; if not, write to the Free Software Foundation, Inc.,
* 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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*/
package omero.gateway.model;
import java.sql.Timestamp;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static omero.rtypes.rstring;
import omero.RInt;
import omero.RTime;
import omero.model.Annotation;
import omero.model.CommentAnnotation;
import omero.model.DatasetImageLink;
import omero.model.Fileset;
import omero.model.Format;
import omero.model.Image;
import omero.model.ImageAnnotationLink;
import omero.model.ImageI;
import omero.model.Instrument;
import omero.model.LongAnnotation;
import omero.model.OriginalFile;
import omero.model.Pixels;
/**
* The data that makes up an <i>OME</i> Image along with links to its Pixels,
* enclosing Datasets, and the Experimenter that owns this Image.
*
* @author Jean-Marie Burel <a
* href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @author <br>
* Andrea Falconi <a
* href="mailto:a.falconi@dundee.ac.uk"> a.falconi@dundee.ac.uk</a>
* @version 2.2
* @since OME2.2
*/
public class ImageData extends DataObject {
/** Identifies the {@link ImageI#NAME} field. */
public final static String NAME = ImageI.NAME;
/** Identifies the {@link ImageI#DESCRIPTION} field. */
public final static String DESCRIPTION = ImageI.DESCRIPTION;
/** Identifies the {@link ImageI#PIXELS} field. */
public final static String PIXELS = ImageI.PIXELS;
/** Identifies the {@link ImageI#ANNOTATIONLINKS} field. */
public final static String ANNOTATIONS = ImageI.ANNOTATIONLINKS;
/** Identifies the {@link ImageI#DATASETLINKS} field. */
public final static String DATASET_LINKS = ImageI.DATASETLINKS;
/**
* All the Pixels that belong to this Image. The elements of this set are
* {@link PixelsData} objects. This field may not be <code>null</code> nor
* empty. As a minimum, it will contain the {@link #defaultPixels default}
* Pixels.
*
* An <i>OME</i> Image can be associated to more than one 5D pixels set
* (that is, the raw image data) if all those sets are derived from an
* initial image file. An example is a deconvolved image and the original
* file: those two pixels sets would be represented by the same <i>OME</i>
* Image. In the case there's more than one pixels set, the first pixels
* identifies the pixels that are used by default for analysis and
* visualization.
*/
private List<PixelsData> allPixels;
/**
* All the Datasets that contain this Image. The elements of this set are
* {@link DatasetData} objects. If this Image is not contained in any
* Dataset, then this set will be empty — but never <code>null</code>.
*/
private Set<DatasetData> datasets;
/**
* All the annotations related to this Image. The elements of the set are
* {@link AnnotationData} objects. If this Image hasn't been annotated, then
* this set will be empty — but never <code>null</code>.
*/
private Set<AnnotationData> annotations;
/**
* The number of annotations attached to this Image. This field may be
* <code>null</code> meaning no count retrieved, and it may be less than
* the actual number if filtered by user.
*/
private Long annotationCount;
/** The path to the image file, for a single image. */
private String pathToFile;
/** The index of the image if the image belongs to a multi-images file. */
private int index;
/** The path to the multi-images file. */
private String parentFilePath;
/** Reference to the original file when the image is not registered. */
private OriginalFile reference;
/** Creates a new instance. */
public ImageData() {
setDirty(true);
setValue(new ImageI());
index = -1;
}
/**
* Creates a new instance.
*
* @param image
* Back pointer to the {@link Image} model object. Mustn't be
* <code>null</code>.
* @throws IllegalArgumentException
* If the object is <code>null</code>.
*/
public ImageData(Image image) {
if (image == null) {
throw new IllegalArgumentException("Object cannot null.");
}
setValue(image);
index = -1;
}
/**
* Sets the path to the file.
*
* @param path The value to set.
*/
public void setPathToFile(String path)
{
if (path == null) pathToFile = getName();
else pathToFile = path;
}
/**
* Sets the reference to the file to register.
*
* @param reference The value to set.
*/
public void setReference(OriginalFile reference)
{
this.reference = reference;
}
/**
* Returns the reference to the file to register.
*
* @return See above.
*/
public OriginalFile getReference() { return reference; }
/**
* Returns the path to the file.
*
* @return See above.
*/
public String getPathToFile() { return pathToFile ;}
/**
* Sets the path to the file hosting the image. This should only
* be used to handle multi-images file e.g. some <code>Leica</code> files.
* Sets the index of the image within that file.
*
* @param path The path to set.
* @param index The index to set.
*/
public void setParentFilePath(String path, int index)
{
parentFilePath = path;
this.index = index;
}
/**
* Returns the path to the file hosting the image. This should only
* be used to handle multi-images file e.g. some <code>Leica</code> files.
*
* @return See above.
*/
public String getParentFilePath() { return parentFilePath; }
/**
* Returns the index of the image within the multi-images file.
*
* @return See above.
*/
public int getIndex() { return index; }
/**
* Returns the series.
*
* @return See above.
*/
public int getSeries()
{
Image image = asImage();
RInt value = image.getSeries();
if (value == null) return 0;
return value.getValue();
}
/**
* Returns the format of the image.
*
* @return See above.
*/
public String getFormat()
{
Image image = asImage();
Format format = image.getFormat();
if (format == null) return null;
return format.getValue().getValue();
}
/**
* Sets the registered file.
*
* @param object The object to store.
*/
public void setRegisteredFile(Image object)
{
if (object == null) return;
if (!(object instanceof Image))
throw new IllegalArgumentException("Image not supported.");
Image img = asImage();
img.setId(object.getId());
}
// Immutables
/**
* Sets the name of the image.
*
* @param name
* The name of the image. Mustn't be <code>null</code>.
* @throws IllegalArgumentException
* If the name is <code>null</code>.
*/
public void setName(String name) {
if (name == null) {
throw new IllegalArgumentException("The name cannot be null.");
}
setDirty(true);
asImage().setName(rstring(name));
}
/**
* Returns the name of the image.
*
* @return See above.
*/
public String getName() {
omero.RString n = asImage().getName();
if (n == null || n.getValue() == null) {
throw new IllegalStateException(
"The name should never have been null");
}
return n.getValue();
}
/**
* Sets the description of the image.
*
* @param description
* The description of the image.
*/
public void setDescription(String description) {
setDirty(true);
asImage().setDescription(
description == null ? null : rstring(description));
}
/**
* Returns the description of the image.
*
* @return See above.
*/
public String getDescription() {
omero.RString d = asImage().getDescription();
return d == null ? null : d.getValue();
}
/**
* Returns <code>true</code> if the image has been archived,
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean isArchived() {
omero.RBool value = asImage().getArchived();
if (value == null) {
//Add FS check
Fileset fs = asImage().getFileset();
return (fs != null);
}
return value.getValue();
}
/**
* Returns the number of annotations linked to the object, key: id of the
* user, value: number of annotation. The map may be <code>null</code> if
* no annotation.
*
* @return See above.
*/
public Map<Long, Long> getAnnotationsCounts() {
return asImage().getAnnotationLinksCountPerOwner();
}
/**
* Returns the insertion time of the image.
*
* @return See above.
*/
public Timestamp getInserted() {
return timeOfEvent(asImage().getDetails().getCreationEvent());
}
/**
* Returns the acquisition date.
*
* @return See above.
*/
public Timestamp getAcquisitionDate()
{
RTime time = asImage().getAcquisitionDate();
if (time == null) return null;
return new Timestamp(time.getValue());
}
// Single-valued objects.
/**
* Returns the default set of pixels.
*
* @return See above.
*/
public PixelsData getDefaultPixels() {
List<PixelsData> list = getAllPixels();
if (list == null || list.size() == 0) return null;
return list.get(0);
}
/**
* Sets the default set of pixels.
*
* @param defaultPixels
* The default set of pixels.
*/
public void setDefaultPixels(PixelsData defaultPixels) {
if (getDefaultPixels() == defaultPixels) {
return;
}
setDirty(true);
allPixels = null; // Invalidated
asImage().setPrimaryPixels(defaultPixels.asPixels());
}
// Sets
/**
* Returns all the sets of pixels related to this image.
*
* @return See above.
*/
@SuppressWarnings("unchecked")
public List<PixelsData> getAllPixels() {
if (allPixels == null && asImage().sizeOfPixels() >= 0) {
allPixels = new ArrayList<PixelsData>();
List<Pixels> pixels = asImage().copyPixels();
for (Pixels p : pixels) {
allPixels.add(new PixelsData(p));
}
}
return allPixels == null ? null : new ArrayList<PixelsData>(allPixels);
}
/**
* Sets the set of pixels related to this image.
*
* @param newValue
* The set of pixels' set.
*/
public void setAllPixels(List<PixelsData> newValue) {
List<PixelsData> currentValue = getAllPixels();
SetMutator<PixelsData> m = new SetMutator<PixelsData>(currentValue,
newValue);
while (m.moreDeletions()) {
setDirty(true);
asImage().removePixels(m.nextDeletion().asPixels());
}
while (m.moreAdditions()) {
setDirty(true);
asImage().addPixels(m.nextAddition().asPixels());
}
allPixels = m.result();
}
/**
* Returns the datasets containing this image.
*
* @return See above.
*/
public Set getDatasets() {
if (datasets == null && asImage().sizeOfDatasetLinks() >= 0) {
datasets = new HashSet<DatasetData>();
List<DatasetImageLink> links = asImage().copyDatasetLinks();
for (DatasetImageLink link : links) {
datasets.add(new DatasetData(link.getParent()));
}
}
return datasets == null ? null : new HashSet(datasets);
}
/**
* Sets the datasets containing the image.
*
* @param newValue
* The set of datasets.
*/
public void setDatasets(Set newValue) {
Set<DatasetData> currentValue = getDatasets();
SetMutator<DatasetData> m = new SetMutator<DatasetData>(currentValue,
newValue);
while (m.moreDeletions()) {
setDirty(true);
asImage().unlinkDataset(m.nextDeletion().asDataset());
}
while (m.moreAdditions()) {
setDirty(true);
asImage().linkDataset(m.nextAddition().asDataset());
}
datasets = new HashSet<DatasetData>(m.result());
}
/**
* Returns the annotations
*
* @return See above.
*/
public Set getAnnotations() {
if (annotations == null) {
int size = asImage().sizeOfAnnotationLinks();
if (size >= 0) {
annotations = new HashSet<AnnotationData>(size);
List<ImageAnnotationLink> links = asImage()
.copyAnnotationLinks();
for (ImageAnnotationLink link : links) {
Annotation a = link.getChild();
if (a instanceof CommentAnnotation) {
annotations.add(new TextualAnnotationData(
(CommentAnnotation) a));
} else if (a instanceof LongAnnotation) {
annotations.add(new RatingAnnotationData(
(LongAnnotation) a));
}
}
}
}
return annotations == null ? null : new HashSet<AnnotationData>(
annotations);
}
/**
* Sets the image's annotations.
*
* @param newValue
* The set of annotations.
*/
public void setAnnotations(Set newValue) {
Set<AnnotationData> currentValue = getAnnotations();
SetMutator<AnnotationData> m = new SetMutator<AnnotationData>(
currentValue, newValue);
while (m.moreDeletions()) {
setDirty(true);
asImage().unlinkAnnotation(m.nextDeletion().asAnnotation());
annotationCount = annotationCount == null ? null : new Long(
annotationCount.longValue() - 1);
}
while (m.moreAdditions()) {
setDirty(true);
asImage().linkAnnotation(m.nextAddition().asAnnotation());
annotationCount = annotationCount == null ? null : new Long(
annotationCount.longValue() + 1);
}
annotations = new HashSet<AnnotationData>(m.result());
}
/**
* Returns <code>true</code> if the image is a lifetime image,
* <code>false</code> otherwise.
*
* @return See above.
*/
public boolean isLifetime()
{
String name = getName();
return (name != null && name.endsWith(".sdt"));
}
/**
* Returns the id of the instrument if any.
*
* @return See above.
*/
public long getInstrumentId()
{
Instrument instrument = asImage().getInstrument();
if (instrument == null) return -1;
return instrument.getId().getValue();
}
/**
* Returns <code>true</code> is the image has been imported the new
* import strategy known as FS import, <code>false</code> if imported
* using the previous import approach (data duplication).
*
* @return See above.
*/
public boolean isFSImage()
{
return asImage().getFileset() != null;
}
/**
* Returns the ID of the fileset to which this image belongs. Similar to
* {@link ImageData#isFSImage()}, for images imported pre-FS (data
* duplication) <code>-1</code> will be returned. Else - the <code>long
* </code> value of the fileset ID.
*
* @return See above.
*/
public long getFilesetId()
{
long id = -1;
if (isFSImage()) {
id = asImage().getFileset().getId().getValue();
}
return id;
}
}