/*
*------------------------------------------------------------------------------
* Copyright (C) 2006-2016 University of Dundee & Open Microscopy Environment.
* 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.
*
*------------------------------------------------------------------------------
*/
package training;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import omero.RLong;
import omero.api.IContainerPrx;
import omero.api.IPixelsPrx;
import omero.api.RawPixelsStorePrx;
import omero.gateway.Gateway;
import omero.gateway.LoginCredentials;
import omero.gateway.SecurityContext;
import omero.log.SimpleLogger;
import omero.model.DatasetI;
import omero.model.DatasetImageLink;
import omero.model.DatasetImageLinkI;
import omero.model.IObject;
import omero.model.Image;
import omero.model.ImageI;
import omero.model.LengthI;
import omero.model.PixelsType;
import ome.model.enums.UnitsLength;
import omero.sys.ParametersI;
import omero.gateway.model.ExperimenterData;
import omero.gateway.model.ImageData;
import omero.gateway.model.PixelsData;
/**
* Sample code showing how to create new image.
*
* @author Jean-Marie Burel
* <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @since Beta4.3.2
*/
public class CreateImage
{
//The value used if the configuration file is not used. To edit*/
/** The server address.*/
private static String hostName = "serverName";
/** The username.*/
private static String userName = "userName";
/** The password.*/
private static String password = "password";
/** The id of an image.*/
private static long imageId = 1;
/** Id of the dataset hosting the image of reference.*/
private static long datasetId = 1;
//end edit
/** The image.*/
private ImageData image;
private Gateway gateway;
private SecurityContext ctx;
/**
* start-code
*/
/**
* Loads the image.
* @param imageID The id of the image to load.
* @return See above.
*/
private ImageData loadImage(long imageID)
throws Exception
{
IContainerPrx proxy = gateway.getPojosService(ctx);
List<Image> results = proxy.getImages(Image.class.getName(),
Arrays.asList(imageId), new ParametersI());
//You can directly interact with the IObject or the Pojos object.
//Follow interaction with the Pojos.
if (results.size() == 0)
throw new Exception("Image does not exist. Check ID.");
return new ImageData(results.get(0));
}
/**
* Returns a linearized version of the plane.
* @param z The selected z-section.
* @param c The selected wavelength.
* @param t The selected timepoint.
* @param sizeZ The number of z-sections.
* @param sizeZ The number of wavelengths.
* @return See above.
*/
private Integer linearize(int z, int c, int t, int sizeZ, int sizeC)
{
if (z < 0 || sizeZ <= z)
throw new IllegalArgumentException(
"z out of range [0, "+sizeZ+"]: "+z+".");
if (c < 0 || sizeC <= c)
throw new IllegalArgumentException(
"c out of range [0, "+sizeC+"]: "+c+".");
return Integer.valueOf(sizeZ*sizeC*t + sizeZ*c + z);
}
// Create Image
// ============
/**
* Creates a new image with one channel from a source image.
* @param datasetID The dataset's id to link the new image to.
*/
private void CreateNewImage(long datasetID)
throws Exception
{
PixelsData pixels = image.getDefaultPixels();
int sizeZ = pixels.getSizeZ();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
int sizeX = pixels.getSizeX();
int sizeY = pixels.getSizeY();
long pixelsId = pixels.getId();
//Sets the pixel size using units (new in 5.1.0)
LengthI units = new LengthI(9.8, UnitsLength.ANGSTROM);
pixels.setPixelSizeX(units);
pixels.setPixelSizeY(units);
if (sizeC <= 1)
throw new Exception("The image must have at least 2 channels.");
RawPixelsStorePrx store = null;
//Create a new image.
Map<Integer, byte[]> map = new LinkedHashMap<Integer, byte[]>();
try {
store = gateway.getPixelsStore(ctx);
store.setPixelsId(pixelsId, false);
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
for (int z = 0; z < sizeZ; z++) {
byte[] plane = store.getPlane(z, c, t);
map.put(linearize(z, c, t, sizeZ, sizeC), plane);
}
}
}
} catch (Exception e) {
throw new Exception("Cannot retrieve the plane", e);
} finally {
if (store != null) store.close();
}
//Now we are going to create the new image.
IPixelsPrx proxy = gateway.getPixelsService(ctx);
List<IObject> l = proxy.getAllEnumerations(PixelsType.class.getName());
Iterator<IObject> i = l.iterator();
PixelsType type = null;
String original = pixels.getPixelType();
while (i.hasNext()) {
PixelsType o = (PixelsType) i.next();
String value = o.getValue().getValue();
if (value.equals(original)) {
type = o;
break;
}
}
if (type == null)
throw new Exception("Pixels Type not valid.");
String name = "newImageFrom"+image.getId();
List<Integer> channels = new ArrayList<Integer>();
for (int c = 0; c < sizeC; c++) {
channels.add(c);
}
RLong idNew = proxy.createImage(sizeX, sizeY, sizeZ, sizeT,
channels, type, name, "From Image ID: "+image.getId());
if (idNew == null)
throw new Exception("New image could not be created.");
ImageData newImage = loadImage(idNew.getValue());
//link the new image and the dataset hosting the source image.
DatasetImageLink link = new DatasetImageLinkI();
link.setParent(new DatasetI(datasetID, false));
link.setChild(new ImageI(newImage.getId(), false));
gateway.getUpdateService(ctx).saveAndReturnObject(link);
//Write the data.
try {
store = gateway.getPixelsStore(ctx);
store.setPixelsId(newImage.getDefaultPixels().getId(), false);
int index = 0;
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
for (int z = 0; z < sizeZ; z++) {
index = linearize(z, c, t, sizeZ, sizeC);
store.setPlane(map.get(index), z, c, t);
}
}
}
store.save();
} catch (Exception e) {
throw new Exception("Cannot set the plane", e);
} finally {
if (store != null) store.close();
}
}
/**
* end-code
*/
/**
* Connects and invokes the various methods.
* @param args The login credentials
* @param imageId The image's id
* @param datasetId The dataset's id
*/
CreateImage(String[] args, long imageId, long datasetId)
{
LoginCredentials cred = new LoginCredentials(args);
gateway = new Gateway(new SimpleLogger());
try {
ExperimenterData user = gateway.connect(cred);
ctx = new SecurityContext(user.getGroupId());
image = loadImage(imageId);
CreateNewImage(datasetId);
} catch (Exception e) {
e.printStackTrace();
} finally {
try {
gateway.disconnect(); // Be sure to disconnect
} catch (Exception e) {
e.printStackTrace();
}
}
}
/**
* Runs the script without configuration options.
*
* @param args The login credentials.
*/
public static void main(String[] args)
{
if (args == null || args.length == 0)
args = new String[] { "--omero.host=" + hostName,
"--omero.user=" + userName, "--omero.pass=" + password };
new CreateImage(args, imageId, datasetId);
System.exit(0);
}
}