/*
*------------------------------------------------------------------------------
* 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.ArrayList;
import java.util.List;
import omero.api.RawPixelsStorePrx;
import omero.gateway.Gateway;
import omero.gateway.LoginCredentials;
import omero.gateway.SecurityContext;
import omero.gateway.facility.BrowseFacility;
import omero.gateway.facility.RawDataFacility;
import omero.gateway.rnd.Plane2D;
import omero.log.SimpleLogger;
import omero.gateway.model.ExperimenterData;
import omero.gateway.model.ImageData;
import omero.gateway.model.PixelsData;
/**
* Sample code showing how to access raw data.
*
* @author Jean-Marie Burel
* <a href="mailto:j.burel@dundee.ac.uk">j.burel@dundee.ac.uk</a>
* @since Beta4.3.2
*/
public class RawDataAccess
{
//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";
private static long imageId = 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
{
BrowseFacility browse = gateway.getFacility(BrowseFacility.class);
return browse.getImage(ctx, imageID);
}
// Retrieve plane
// ==============
/**
* Retrieve a given plane.
* This is useful when you need the pixels intensity.
*/
private void retrievePlane()
throws Exception
{
RawDataFacility rdf = gateway.getFacility(RawDataFacility.class);
//To retrieve the image, see above.
PixelsData pixels = image.getDefaultPixels();
int sizeZ = pixels.getSizeZ();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
try {
Plane2D p;
for (int z = 0; z < sizeZ; z++)
for (int t = 0; t < sizeT; t++)
for (int c = 0; c < sizeC; c++)
p = rdf.getPlane(ctx, pixels, z, t, c);
} catch (Exception e) {
throw new Exception("Cannot read the plane", e);
}
}
// Retrieve tile
// =============
/**
* Retrieve a given tile.
* This is useful when you need the pixels intensity.
*/
private void retrieveTile()
throws Exception
{
RawDataFacility rdf = gateway.getFacility(RawDataFacility.class);
//To retrieve the image, see above.
PixelsData pixels = image.getDefaultPixels();
int sizeZ = pixels.getSizeZ();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
try {
//tile = (50, 50, 10, 10) x, y, width, height of tile
int x = 0;
int y = 0;
int width = pixels.getSizeX()/2;
int height = pixels.getSizeY()/2;
Plane2D p;
for (int z = 0; z < sizeZ; z++) {
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
p = rdf.getTile(ctx, pixels, z, t, c, x, y, width,
height);
}
}
}
} catch (Exception e) {
throw new Exception("Cannot read the tiles", e);
}
}
// Retrieve stack
// ==============
/**
* Retrieve a given stack.
* This is useful when you need the pixels intensity.
*/
private void retrieveStack()
throws Exception
{
// TODO: Add method to RawDataFacility !
//To retrieve the image, see above.
PixelsData pixels = image.getDefaultPixels();
int sizeT = pixels.getSizeT();
int sizeC = pixels.getSizeC();
long pixelsId = pixels.getId();
RawPixelsStorePrx store = null;
try {
store = gateway.getPixelsStore(ctx);
store.setPixelsId(pixelsId, false);
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
byte[] plane = store.getStack(c, t);
}
}
} catch (Exception e) {
throw new Exception("Cannot read the stack", e);
} finally {
if (store != null) store.close();
}
}
// Retrieve hypercube
// ==================
/**
* Retrieve a given hypercube.
* This is useful when you need the pixels intensity.
*/
private void retrieveHypercube()
throws Exception
{
// TODO: Add method to RawDataFacility !
//To retrieve the image, see above.
PixelsData pixels = image.getDefaultPixels();
long pixelsId = pixels.getId();
// offset values in each dimension XYZCT
List<Integer> offset = new ArrayList<Integer>();
int n = 5;
for (int i = 0; i < n; i++) {
offset.add(i, 0);
}
List<Integer> size = new ArrayList<Integer>();
size.add(pixels.getSizeX());
size.add(pixels.getSizeY());
size.add(pixels.getSizeZ());
size.add(pixels.getSizeC());
size.add(pixels.getSizeT());
// indicate the step in each direction, step = 1,
//will return values at index 0, 1, 2.
//step = 2, values at index 0, 2, 4 etc.
List<Integer> step = new ArrayList<Integer>();
for (int i = 0; i < n; i++) {
step.add(i, 1);
}
RawPixelsStorePrx store = null;
try {
store = gateway.getPixelsStore(ctx);
store.setPixelsId(pixelsId, false);
byte[] values = store.getHypercube(offset, size, step);
} catch (Exception e) {
throw new Exception("Cannot read the hypercube", e);
} finally {
if (store != null) store.close();
}
}
/**
* end-code
*/
/**
* Connects and invokes the various methods.
* @param args The login credentials.
* @param imageId The image id.
*/
RawDataAccess(String[] args, long imageId)
{
LoginCredentials cred = new LoginCredentials(args);
gateway = new Gateway(new SimpleLogger());
try {
ExperimenterData user = gateway.connect(cred);
ctx = new SecurityContext(user.getGroupId());
image = loadImage(imageId);
retrievePlane();
retrieveTile();
retrieveStack();
retrieveHypercube();
} 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 RawDataAccess(args, imageId);
System.exit(0);
}
}