diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
index 20d46f6f18af940d10248e032b3b7b99b0da1738..b2691bee8a6fca5fae8581306ab19062c2606723 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java
@@ -122,7 +122,11 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
private static Integer tryGetIntParam(HttpServletRequest request, String paramName)
{
- String value = getParam(request, paramName);
+ String value = request.getParameter(paramName);
+ if (value == null)
+ {
+ return null;
+ }
try
{
return Integer.valueOf(value);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
index d9e8ebd3a3e6ebc132f4b5add99a133197314f45..b480205be9ebb191186c105f55421591192feeb2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -103,7 +103,7 @@ public interface IScreeningClientService extends IClientService
throws UserFailureException;
/** Lists all images for a given well in the given dataset */
- public List<ChannelStackImageReference> listImageChannelStacks(String datasetCode,
+ public List<ImageChannelStackReference> listImageChannelStacks(String datasetCode,
String datastoreCode, WellLocation wellLocation);
/**
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
index 1f2f678291b251ee95ac0423d47dfd36175c9bd0..ced06948de770a2198498b77f2492192550575d4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -92,7 +92,7 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
*/
public void listImageChannelStacks(String datasetCode, String datastoreCode,
WellLocation wellLocation,
- AsyncCallback<List<ChannelStackImageReference>> abstractAsyncCallback);
+ AsyncCallback<List<ImageChannelStackReference>> abstractAsyncCallback);
/**
* @see IScreeningClientService#registerLibrary(LibraryRegistrationInfo)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageUrlUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageUrlUtils.java
new file mode 100644
index 0000000000000000000000000000000000000000..199e3682f3f085372a3e6aa112ea9af7e01a4ab8
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageUrlUtils.java
@@ -0,0 +1,120 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+
+import com.extjs.gxt.ui.client.widget.Component;
+import com.extjs.gxt.ui.client.widget.Html;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.renderers.SimpleImageHtmlRenderer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Generates URLs pointing to the images on Data Store server.
+ *
+ * @author Tomasz Pylak
+ */
+public class ImageUrlUtils
+{
+ /**
+ * Creates a widget which displays the URL to the specified image on DSS and adds it to the
+ * container.
+ */
+ public static void addImageUrlWidget(LayoutContainer container, String sessionId,
+ WellImages images, String channel, int row, int col, int imageWidth, int imageHeight)
+ {
+ String imageURL =
+ createDatastoreImageUrl(sessionId, images, channel, row, col, imageWidth,
+ imageHeight);
+ addUrlWidget(container, imageURL, imageHeight);
+ }
+
+ /**
+ * Creates a widget which displays the URL to the specified image on DSS and adds it to the
+ * container.
+ */
+ public static void addImageUrlWidget(LayoutContainer container, String sessionId,
+ WellImages images, String channel, ImageChannelStackReference channelStackRef,
+ int imageWidth, int imageHeight)
+ {
+ String imageURL =
+ createDatastoreImageUrl(sessionId, images, channel, channelStackRef, imageWidth,
+ imageHeight);
+ addUrlWidget(container, imageURL, imageHeight);
+ }
+
+ /** generates URL of an image on Data Store server */
+ private static String createDatastoreImageUrl(String sessionID, WellImages images,
+ String channel, ImageChannelStackReference channelStackRef, int width, int height)
+ {
+ URLMethodWithParameters methodWithParameters =
+ createBasicImageURL(sessionID, images, channel);
+
+ methodWithParameters
+ .addParameter("channelStackId", channelStackRef.getChannelStackTechId());
+ String linkURL = methodWithParameters.toString();
+ methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
+
+ String imageURL = methodWithParameters.toString();
+ return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
+ }
+
+ /** creates a widget which displays the specified URL and adds it to the container */
+ private static void addUrlWidget(LayoutContainer container, String url, int height)
+ {
+ Component tileContent = new Html(url);
+ tileContent.setHeight("" + height);
+ PlateStyleSetter.setPointerCursor(tileContent);
+ container.add(tileContent);
+ }
+
+ /** generates URL of an image on Data Store server */
+ private static String createDatastoreImageUrl(String sessionID, WellImages images,
+ String channel, int tileRow, int tileCol, int width, int height)
+ {
+ URLMethodWithParameters methodWithParameters =
+ createBasicImageURL(sessionID, images, channel);
+
+ methodWithParameters.addParameter("wellRow", images.getWellLocation().getRow());
+ methodWithParameters.addParameter("wellCol", images.getWellLocation().getColumn());
+ methodWithParameters.addParameter("tileRow", tileRow);
+ methodWithParameters.addParameter("tileCol", tileCol);
+ String linkURL = methodWithParameters.toString();
+ methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
+
+ String imageURL = methodWithParameters.toString();
+ return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
+ }
+
+ private static URLMethodWithParameters createBasicImageURL(String sessionID, WellImages images,
+ String channel)
+ {
+ URLMethodWithParameters methodWithParameters =
+ new URLMethodWithParameters(images.getDownloadUrl() + "/"
+ + ScreeningConstants.DATASTORE_SCREENING_SERVLET_URL);
+ methodWithParameters.addParameter("sessionID", sessionID);
+ methodWithParameters.addParameter("dataset", images.getDatasetCode());
+ methodWithParameters.addParameter("channel", channel);
+ if (channel.equals(ScreeningConstants.MERGED_CHANNELS))
+ {
+ methodWithParameters.addParameter("mergeChannels", "true");
+ }
+ return methodWithParameters;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
index 18f83c1663e571c27c8723a918fc3f271ffbba32..c826f64c66976b749eaa2f4950b3b6b43465d7b9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java
@@ -16,23 +16,12 @@
package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
-import java.util.ArrayList;
-import java.util.Collections;
import java.util.List;
-import java.util.Map;
-import java.util.TreeMap;
-import java.util.Map.Entry;
import com.extjs.gxt.ui.client.Style.Scroll;
-import com.extjs.gxt.ui.client.event.Events;
-import com.extjs.gxt.ui.client.event.Listener;
-import com.extjs.gxt.ui.client.event.SliderEvent;
-import com.extjs.gxt.ui.client.widget.Component;
import com.extjs.gxt.ui.client.widget.Dialog;
import com.extjs.gxt.ui.client.widget.Html;
-import com.extjs.gxt.ui.client.widget.Label;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
-import com.extjs.gxt.ui.client.widget.Slider;
import com.extjs.gxt.ui.client.widget.Text;
import com.extjs.gxt.ui.client.widget.layout.FitLayout;
import com.extjs.gxt.ui.client.widget.layout.RowLayout;
@@ -45,18 +34,16 @@ import com.google.gwt.user.client.ui.Widget;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.renderer.LinkRenderer;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.renderers.SimpleImageHtmlRenderer;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.listener.OpenEntityDetailsTabClickListener;
import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooser.DefaultChannelState;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooser.IChanneledViewerFactory;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
@@ -65,7 +52,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterials
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria.SingleExperimentSearchCriteria;
/**
- * A dialog which shows the content of the well.
+ * A dialog which shows the content of the well (static or a timepoints movie).
*
* @author Tomasz Pylak
*/
@@ -79,6 +66,9 @@ public class WellContentDialog extends Dialog
private static final int NO_IMAGES_DIALOG_HEIGHT_PX = 160;
+ /**
+ * A dialog which shows the content of the well (static or a timepoints movie).
+ */
public static void showContentDialog(final WellData wellData, DefaultChannelState channelState,
final ScreeningViewContext viewContext)
{
@@ -90,30 +80,100 @@ public class WellContentDialog extends Dialog
final WellImages imagesOrNull = wellData.tryGetImages();
if (imagesOrNull != null && imagesOrNull.isMultidimensional())
{
- showTimepointImageViewer(contentDialog, wellData, imagesOrNull, channelState,
+ showTimepointImageDialog(contentDialog, wellData, imagesOrNull, channelState,
viewContext);
} else
{
- if (imagesOrNull != null)
+ showStaticImageDialog(contentDialog, wellData, imagesOrNull, channelState, viewContext);
+ }
+ }
+
+ /**
+ * Creates a view for the specified channel.
+ *
+ * @param channel Channel numbers start with 1. Channel 0 consists of all other channels merged.
+ */
+ public static Widget createImageViewerForChannel(IViewContext<?> viewContext,
+ WellContent wellContent, int imageWidthPx, int imageHeightPx, String channel)
+ {
+ DatasetImagesReference images = wellContent.tryGetImages();
+ if (images == null)
+ {
+ return new Text("Images not acquired.");
+ }
+ WellLocation locationOrNull = wellContent.tryGetLocation();
+ if (locationOrNull == null)
+ {
+ return new Text("Incorrect well code.");
+ }
+ if (images.getImageParameters().getChannelsNames().contains(channel) == false
+ && channel.equals(ScreeningConstants.MERGED_CHANNELS) == false)
+ {
+ return new Text("No images available for this channel.");
+ }
+ WellImages wellImages = new WellImages(images, locationOrNull);
+ String sessionId = getSessionId(viewContext);
+ return createTilesGrid(wellImages, channel, sessionId, imageWidthPx, imageHeightPx);
+ }
+
+ // --------------- STATIC IMAGES VIEWER
+
+ private static void showStaticImageDialog(final WellContentDialog contentDialog,
+ final WellData wellData, final WellImages imagesOrNull,
+ DefaultChannelState channelState, final ScreeningViewContext viewContext)
+ {
+ if (imagesOrNull != null)
+ {
+ LayoutContainer imageViewer =
+ createStaticImageViewer(imagesOrNull, channelState, viewContext);
+ contentDialog.addComponent(imageViewer);
+ }
+ contentDialog.setupContentAndShow(wellData);
+ }
+
+ private static LayoutContainer createStaticImageViewer(final WellImages images,
+ DefaultChannelState channelState, final IViewContext<?> viewContext)
+ {
+ final IChanneledViewerFactory viewerFactory = new IChanneledViewerFactory()
+ {
+ public LayoutContainer create(String channel)
+ {
+ String sessionId = getSessionId(viewContext);
+ return createTilesGrid(images, channel, sessionId, getImageWidth(images),
+ getImageHeight(images));
+ }
+ };
+ return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
+ .getChannelsNames());
+ }
+
+ private static LayoutContainer createTilesGrid(WellImages images, String channel,
+ String sessionId, int imageWidth, int imageHeight)
+ {
+ LayoutContainer container = new LayoutContainer(new TableLayout(images.getTileColsNum()));
+ for (int row = 1; row <= images.getTileRowsNum(); row++)
+ {
+ for (int col = 1; col <= images.getTileColsNum(); col++)
{
- LayoutContainer imageViewer =
- createImageViewer(imagesOrNull, channelState, viewContext);
- contentDialog.addComponent(imageViewer);
+ ImageUrlUtils.addImageUrlWidget(container, sessionId, images, channel, row, col,
+ imageWidth, imageHeight);
}
- contentDialog.setupContentAndShow(wellData);
}
+ return container;
}
- private static void showTimepointImageViewer(final WellContentDialog contentDialog,
+ // --------------- TIMEPOINT IMAGES PLAYER
+
+ private static void showTimepointImageDialog(final WellContentDialog contentDialog,
final WellData wellData, final WellImages images,
final DefaultChannelState channelState, final ScreeningViewContext viewContext)
{
viewContext.getService().listImageChannelStacks(images.getDatasetCode(),
images.getDatastoreCode(), images.getWellLocation(),
- new AbstractAsyncCallback<List<ChannelStackImageReference>>(viewContext)
+ new AbstractAsyncCallback<List<ImageChannelStackReference>>(viewContext)
{
@Override
- protected void process(List<ChannelStackImageReference> channelStackImages)
+ protected void process(List<ImageChannelStackReference> channelStackImages)
{
LayoutContainer imageViewer =
createTimepointImageViewer(channelStackImages, images,
@@ -125,32 +185,50 @@ public class WellContentDialog extends Dialog
}
private static LayoutContainer createTimepointImageViewer(
- List<ChannelStackImageReference> channelStackImages, WellImages images,
- DefaultChannelState channelState, IViewContext<?> viewContext)
+ final List<ImageChannelStackReference> channelStackImages, final WellImages images,
+ final DefaultChannelState channelState, IViewContext<?> viewContext)
{
- System.out.println("result: " + channelStackImages);
- float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
- String sessionId = getSessionId(viewContext);
-
- return createTilesGridForStack(channelStackImages, images, channelState.getDefaultChannel(images
- .getChannelsNames()), sessionId,
- (int) (ONE_IMAGE_WIDTH_PX * imageSizeMultiplyFactor),
- (int) (ONE_IMAGE_HEIGHT_PX * imageSizeMultiplyFactor));
+ final String sessionId = getSessionId(viewContext);
+ final IChanneledViewerFactory viewerFactory = new IChanneledViewerFactory()
+ {
+ public LayoutContainer create(String channel)
+ {
+ return WellContentTimepointsViewer.createTilesGrid(sessionId,
+ channelStackImages, images, channel, getImageWidth(images),
+ getImageHeight(images));
+ }
+ };
+ return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
+ .getChannelsNames());
}
- private static int getDialogWidth(final WellImages images)
+ // ---------------- STATIC METHODS -------------------
+
+ private static int getDialogWidth(WellImages images)
{
float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
return (int) (ONE_IMAGE_WIDTH_PX * imageSizeMultiplyFactor) * images.getTileColsNum() + 100;
}
- private static int getDialogHeight(final WellImages images)
+ private static int getDialogHeight(WellImages images)
{
float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
return Math.max((int) (ONE_IMAGE_HEIGHT_PX * imageSizeMultiplyFactor)
* images.getTileRowsNum() + 100, 300);
}
+ private static int getImageHeight(WellImages images)
+ {
+ float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
+ return (int) (ONE_IMAGE_HEIGHT_PX * imageSizeMultiplyFactor);
+ }
+
+ private static int getImageWidth(WellImages images)
+ {
+ float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
+ return (int) (ONE_IMAGE_WIDTH_PX * imageSizeMultiplyFactor);
+ }
+
private static SingleExperimentSearchCriteria getExperiment(WellData wellData)
{
return new SingleExperimentSearchCriteria(wellData.getExperimentId().getId(), wellData
@@ -164,7 +242,12 @@ public class WellContentDialog extends Dialog
return 3.0F / dim;
}
- // ----------------
+ private static String getSessionId(IViewContext<?> viewContext)
+ {
+ return viewContext.getModel().getSessionContext().getSessionID();
+ }
+
+ // ---------- DIALOG CLASS TO DISPLAY WELL PROPERTIES ------
private final WellMetadata metadataOrNull;
@@ -190,7 +273,7 @@ public class WellContentDialog extends Dialog
}
- public void addComponent(LayoutContainer component)
+ private void addComponent(LayoutContainer component)
{
dialogContent.add(component);
}
@@ -299,281 +382,4 @@ public class WellContentDialog extends Dialog
return LinkRenderer.getLinkWidget(entity.getCode(), listener);
}
- // -------------
-
- private static LayoutContainer createImageViewer(final WellImages images,
- DefaultChannelState channelState, final IViewContext<?> viewContext)
- {
- final float imageSizeMultiplyFactor = getImageSizeMultiplyFactor(images);
- final IChanneledViewerFactory viewerFactory = new IChanneledViewerFactory()
- {
- public LayoutContainer create(String channel)
- {
- String sessionId = getSessionId(viewContext);
- return createTilesGridWithSlider(images, channel, sessionId,
- (int) (ONE_IMAGE_WIDTH_PX * imageSizeMultiplyFactor),
- (int) (ONE_IMAGE_HEIGHT_PX * imageSizeMultiplyFactor));
- }
- };
- return ChannelChooser.createViewerWithChannelChooser(viewerFactory, channelState, images
- .getChannelsNames());
- }
-
- /**
- * Creates a view for the specified channel.
- *
- * @param channel Channel numbers start with 1. Channel 0 consists of all other channels merged.
- */
- public static Widget createImageViewerForChannel(IViewContext<?> viewContext,
- WellContent wellContent, int imageWidthPx, int imageHeightPx, String channel)
- {
- DatasetImagesReference images = wellContent.tryGetImages();
- if (images == null)
- {
- return new Text("Images not acquired.");
- }
- WellLocation locationOrNull = wellContent.tryGetLocation();
- if (locationOrNull == null)
- {
- return new Text("Incorrect well code.");
- }
- if (images.getImageParameters().getChannelsNames().contains(channel) == false
- && channel.equals(ScreeningConstants.MERGED_CHANNELS) == false)
- {
- return new Text("No images available for this channel.");
- }
- WellImages wellImages = new WellImages(images, locationOrNull);
- String sessionId = getSessionId(viewContext);
- return WellContentDialog.createTilesGrid(wellImages, channel, sessionId, imageWidthPx,
- imageHeightPx);
- }
-
- private static LayoutContainer createTilesGrid(WellImages images, String channel,
- String sessionId, int imageWidth, int imageHeight)
- {
- LayoutContainer container = new LayoutContainer(new TableLayout(images.getTileColsNum()));
- for (int row = 1; row <= images.getTileRowsNum(); row++)
- {
- for (int col = 1; col <= images.getTileColsNum(); col++)
- {
- Component tileContent;
- String imageURL =
- createDatastoreImageUrl(images, channel, row, col, imageWidth, imageHeight,
- sessionId);
- tileContent = new Html(imageURL);
- tileContent.setHeight("" + imageHeight);
- PlateStyleSetter.setPointerCursor(tileContent);
- container.add(tileContent);
- }
- }
- return container;
- }
-
- private static LayoutContainer createTilesGridForStack(
- List<ChannelStackImageReference> channelStackImages, WellImages images, String channel,
- String sessionId, int imageWidth, int imageHeight)
- {
- final LayoutContainer mainContainer = new LayoutContainer();
-
- final List<LayoutContainer> frames = new ArrayList<LayoutContainer>();
- Map<Float, List<ChannelStackImageReference>> channelStackImagesByTimepoint =
- groupImagesByTimepoint(channelStackImages);
-
- int counter = 0;
- for (Entry<Float, List<ChannelStackImageReference>> entry : channelStackImagesByTimepoint
- .entrySet())
- {
- List<ChannelStackImageReference> imageReferences = entry.getValue();
- Collections.sort(imageReferences); // TODO needed? were data already sorted?
- final LayoutContainer container =
- new LayoutContainer(new TableLayout(images.getTileColsNum()));
- frames.add(container);
- for (ChannelStackImageReference imageReference : imageReferences)
- {
- Component tileContent;
- String imageURL =
- createDatastoreImageUrl(images, channel, imageReference, imageWidth,
- imageHeight, sessionId);
- tileContent = new Html(imageURL);
- tileContent.setHeight("" + imageHeight);
- PlateStyleSetter.setPointerCursor(tileContent);
- container.add(tileContent);
- }
- mainContainer.add(container);
- if (counter > 0)
- {
- container.setVisible(false);
- }
- counter++;
- }
-
- final Float[] timepoints = channelStackImagesByTimepoint.keySet().toArray(new Float[0]);
- final Slider slider = createTimepointsSlider(frames.size() - 1, new Listener<SliderEvent>()
- {
- public void handleEvent(SliderEvent e)
- {
- int oldValue = e.getOldValue();
- int newValue = e.getNewValue();
- frames.get(oldValue).hide();
- frames.get(newValue).show();
- mainContainer.remove(mainContainer.getItem(0));
- mainContainer.insert(new Label(createTimepointLabel(timepoints, newValue)), 0);
- mainContainer.layout();
- }
- });
- mainContainer.insert(slider, 0);
- mainContainer.insert(new Label(createTimepointLabel(timepoints, 0)), 0);
- slider.setValue(0);
-
- return mainContainer;
- }
-
- private static String createTimepointLabel(Float[] timepoints, int value)
- {
- return "Timepoint: " + timepoints[value] + "sec (" + value + "/" + (timepoints.length - 1)
- + ")";
- }
-
- private static Map<Float, List<ChannelStackImageReference>> groupImagesByTimepoint(
- List<ChannelStackImageReference> channelStackImages)
- {
- Map<Float, List<ChannelStackImageReference>> result =
- new TreeMap<Float, List<ChannelStackImageReference>>();
- for (ChannelStackImageReference ref : channelStackImages)
- {
- Float t = ref.tryGetTimepoint();
- List<ChannelStackImageReference> imageReferences = result.get(t);
- if (imageReferences == null)
- {
- imageReferences = new ArrayList<ChannelStackImageReference>();
- result.put(t, imageReferences);
- }
- imageReferences.add(ref);
- }
- return result;
- }
-
- // TODO 2010-08-16, Piotr Buczek: remove this code - this is just to demo slider behaviour
- private static LayoutContainer createTilesGridWithSlider(WellImages images, String channel,
- String sessionId, int imageWidth, int imageHeight)
- {
- final LayoutContainer mainContainer = new LayoutContainer();
-
- final List<LayoutContainer> frames = new ArrayList<LayoutContainer>();
- final List<String> channelNames = images.getChannelsNames();
- final int channels = channelNames.size() - 1;
-
- int counter = 0;
- for (String channelName : channelNames)
- {
- final LayoutContainer container =
- new LayoutContainer(new TableLayout(images.getTileColsNum()));
- frames.add(container);
- for (int row = 1; row <= images.getTileRowsNum(); row++)
- {
- for (int col = 1; col <= images.getTileColsNum(); col++)
- {
- Component tileContent;
- String imageURL =
- createDatastoreImageUrl(images, channelName, row, col, imageWidth,
- imageHeight, sessionId);
- tileContent = new Html(imageURL);
- tileContent.setHeight("" + imageHeight);
- PlateStyleSetter.setPointerCursor(tileContent);
- container.add(tileContent);
- }
- }
- mainContainer.add(container);
- if (counter > 0)
- {
- container.setVisible(false);
- }
- counter++;
- }
-
- final Slider slider = createTimepointsSlider(frames.size() - 1, new Listener<SliderEvent>()
- {
- public void handleEvent(SliderEvent e)
- {
- int oldValue = e.getOldValue();
- int newValue = e.getNewValue();
- frames.get(oldValue).hide();
- frames.get(newValue).show();
- mainContainer.remove(mainContainer.getItem(0));
- mainContainer.insert(new Label("Timepoint: " + newValue + "/" + channels), 0);
- mainContainer.layout();
- }
- });
- mainContainer.insert(slider, 0);
- mainContainer.insert(new Label("Timepoint: 0/" + channels), 0);
- slider.setValue(0);
-
- return mainContainer;
- }
-
- private static final Slider createTimepointsSlider(int maxValue, Listener<SliderEvent> listener)
- {
- final Slider slider = new Slider();
- slider.setWidth(230);
- slider.setIncrement(1);
- slider.setMaxValue(maxValue);
- slider.setClickToChange(true);
- slider.addListener(Events.Change, listener);
- return slider;
- }
-
- /** generates URL of an image on Data Store server */
- private static String createDatastoreImageUrl(WellImages images, String channel,
- ChannelStackImageReference channelStackRef, int width, int height, String sessionID)
- {
- URLMethodWithParameters methodWithParameters =
- createBasicImageURL(images, channel, sessionID);
-
- methodWithParameters
- .addParameter("channelStackId", channelStackRef.getChannelStackTechId());
- String linkURL = methodWithParameters.toString();
- methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
-
- String imageURL = methodWithParameters.toString();
- return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
- }
-
- /** generates URL of an image on Data Store server */
- private static String createDatastoreImageUrl(WellImages images, String channel, int tileRow,
- int tileCol, int width, int height, String sessionID)
- {
- URLMethodWithParameters methodWithParameters =
- createBasicImageURL(images, channel, sessionID);
-
- methodWithParameters.addParameter("wellRow", images.getWellLocation().getRow());
- methodWithParameters.addParameter("wellCol", images.getWellLocation().getColumn());
- methodWithParameters.addParameter("tileRow", tileRow);
- methodWithParameters.addParameter("tileCol", tileCol);
- String linkURL = methodWithParameters.toString();
- methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
-
- String imageURL = methodWithParameters.toString();
- return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
- }
-
- private static URLMethodWithParameters createBasicImageURL(WellImages images, String channel,
- String sessionID)
- {
- URLMethodWithParameters methodWithParameters =
- new URLMethodWithParameters(images.getDownloadUrl() + "/"
- + ScreeningConstants.DATASTORE_SCREENING_SERVLET_URL);
- methodWithParameters.addParameter("sessionID", sessionID);
- methodWithParameters.addParameter("dataset", images.getDatasetCode());
- methodWithParameters.addParameter("channel", channel);
- if (channel.equals(ScreeningConstants.MERGED_CHANNELS))
- {
- methodWithParameters.addParameter("mergeChannels", "true");
- }
- return methodWithParameters;
- }
-
- private static String getSessionId(IViewContext<?> viewContext)
- {
- return viewContext.getModel().getSessionContext().getSessionID();
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentTimepointsViewer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentTimepointsViewer.java
new file mode 100644
index 0000000000000000000000000000000000000000..1e584ed3d8168e0aeaf393ef94254b4a6a761382
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentTimepointsViewer.java
@@ -0,0 +1,199 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Map.Entry;
+
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.event.SliderEvent;
+import com.extjs.gxt.ui.client.widget.Label;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.Slider;
+import com.extjs.gxt.ui.client.widget.layout.TableLayout;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
+
+/**
+ * Allows to view timepoint images of the well.
+ *
+ * @author Tomasz Pylak
+ */
+class WellContentTimepointsViewer
+{
+
+ public static LayoutContainer createTilesGrid(String sessionId,
+ List<ImageChannelStackReference> channelStackImages, WellImages images, String channel,
+ int imageWidth, int imageHeight)
+ {
+ Map<Float, List<ImageChannelStackReference>> channelStackImagesByTimepoint =
+ groupImagesByTimepoint(channelStackImages);
+
+ List<LayoutContainer> frames =
+ createTimepointFrames(channelStackImagesByTimepoint, images, channel, sessionId,
+ imageWidth, imageHeight);
+
+ Float[] timepoints = channelStackImagesByTimepoint.keySet().toArray(new Float[0]);
+ return createMoviePlayer(frames, timepoints);
+ }
+
+ private static LayoutContainer createMoviePlayer(final List<LayoutContainer> frames,
+ final Float[] timepoints)
+ {
+ final LayoutContainer mainContainer = new LayoutContainer();
+ addAll(mainContainer, frames);
+
+ final Slider slider = createTimepointsSlider(frames.size() - 1, new Listener<SliderEvent>()
+ {
+ public void handleEvent(SliderEvent e)
+ {
+ int oldValue = e.getOldValue();
+ int newValue = e.getNewValue();
+ frames.get(oldValue).hide();
+ frames.get(newValue).show();
+ mainContainer.remove(mainContainer.getItem(0));
+ mainContainer.insert(new Label(createTimepointLabel(timepoints, newValue)), 0);
+ mainContainer.layout();
+ }
+ });
+ mainContainer.insert(slider, 0);
+ mainContainer.insert(new Label(createTimepointLabel(timepoints, 0)), 0);
+ slider.setValue(0);
+
+ return mainContainer;
+ }
+
+ private static List<LayoutContainer> createTimepointFrames(
+ Map<Float, List<ImageChannelStackReference>> channelStackImagesByTimepoint,
+ WellImages images, String channel, String sessionId, int imageWidth, int imageHeight)
+ {
+ final List<LayoutContainer> frames = new ArrayList<LayoutContainer>();
+ int counter = 0;
+ for (Entry<Float, List<ImageChannelStackReference>> entry : channelStackImagesByTimepoint
+ .entrySet())
+ {
+ List<ImageChannelStackReference> imageReferences = entry.getValue();
+ final LayoutContainer container =
+ createTilesGridForTimepoint(imageReferences, images, channel, sessionId,
+ imageWidth, imageHeight);
+ frames.add(container);
+ if (counter > 0)
+ {
+ container.setVisible(false);
+ }
+ counter++;
+ }
+ return frames;
+ }
+
+ private static void addAll(LayoutContainer container, List<LayoutContainer> frames)
+ {
+ for (LayoutContainer frame : frames)
+ {
+ container.add(frame);
+ }
+ }
+
+ private static LayoutContainer createTilesGridForTimepoint(
+ List<ImageChannelStackReference> channelStackReferences, WellImages images,
+ String channel, String sessionId, int imageWidth, int imageHeight)
+ {
+ final LayoutContainer container =
+ new LayoutContainer(new TableLayout(images.getTileColsNum()));
+
+ ImageChannelStackReference[/* tileRow */][/* tileCol */] tilesMap =
+ createTilesMap(channelStackReferences, images);
+ for (int row = 1; row <= images.getTileRowsNum(); row++)
+ {
+ for (int col = 1; col <= images.getTileColsNum(); col++)
+ {
+ ImageChannelStackReference stackRef = tilesMap[row - 1][col - 1];
+ if (stackRef != null)
+ {
+ ImageUrlUtils.addImageUrlWidget(container, sessionId, images, channel,
+ stackRef, imageWidth, imageHeight);
+ } else
+ {
+ addDummyImage(container, imageWidth, imageHeight);
+ }
+ }
+ }
+ return container;
+ }
+
+ private static ImageChannelStackReference[][] createTilesMap(
+ List<ImageChannelStackReference> stackReferences, WellImages images)
+ {
+ int rows = images.getTileRowsNum();
+ int cols = images.getTileColsNum();
+ ImageChannelStackReference[][] map = new ImageChannelStackReference[rows][cols];
+ for (ImageChannelStackReference stackRef : stackReferences)
+ {
+ map[stackRef.getTileRow() - 1][stackRef.getTileCol() - 1] = stackRef;
+ }
+ return map;
+ }
+
+ private static void addDummyImage(LayoutContainer container, int imageWidth, int imageHeight)
+ {
+ Label dummy = new Label();
+ dummy.setWidth(imageWidth);
+ dummy.setHeight(imageHeight);
+ container.add(dummy);
+ }
+
+ private static String createTimepointLabel(Float[] timepoints, int sequenceNumber)
+ {
+ Float timepoint = timepoints[sequenceNumber];
+ int numberOfSequences = timepoints.length - 1;
+ return "Timepoint: " + timepoint + "sec (" + sequenceNumber + "/" + numberOfSequences + ")";
+ }
+
+ private static Map<Float, List<ImageChannelStackReference>> groupImagesByTimepoint(
+ List<ImageChannelStackReference> channelStackImages)
+ {
+ Map<Float, List<ImageChannelStackReference>> result =
+ new TreeMap<Float, List<ImageChannelStackReference>>();
+ for (ImageChannelStackReference ref : channelStackImages)
+ {
+ Float t = ref.tryGetTimepoint();
+ List<ImageChannelStackReference> imageReferences = result.get(t);
+ if (imageReferences == null)
+ {
+ imageReferences = new ArrayList<ImageChannelStackReference>();
+ result.put(t, imageReferences);
+ }
+ imageReferences.add(ref);
+ }
+ return result;
+ }
+
+ private static final Slider createTimepointsSlider(int maxValue, Listener<SliderEvent> listener)
+ {
+ final Slider slider = new Slider();
+ slider.setWidth(230);
+ slider.setIncrement(1);
+ slider.setMaxValue(maxValue);
+ slider.setClickToChange(true);
+ slider.addListener(Events.Change, listener);
+ return slider;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
index a65574ac2c2bd00bfb397cdf2459e0dd39fd101d..d8e5fb01d87ce403b65c86649246115970e58c5a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java
@@ -57,7 +57,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.BuildAndEnvironmentInfo;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -283,7 +283,7 @@ public final class ScreeningClientService extends AbstractClientService implemen
return server.getVocabulary(sessionToken, ScreeningConstants.PLATE_GEOMETRY);
}
- public List<ChannelStackImageReference> listImageChannelStacks(String datasetCode,
+ public List<ImageChannelStackReference> listImageChannelStacks(String datasetCode,
String datastoreCode, WellLocation wellLocation)
{
final String sessionToken = getSessionToken();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index b550a89a021d88e5515d4df4aa78fbbf474c6d58..a578f567ab885c539d43d2d3508cc6035ffec744 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -59,7 +59,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
@@ -148,7 +148,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
materialCriteria, true);
}
- public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+ public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
String datasetCode, String datastoreCode, WellLocation wellLocation)
{
Session session = getSession(sessionToken);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index c0868ed59a1584c27851175fd326febe4e2704c3..c56f526cdb82f54cea81ede18a2ba0bc3870d72c 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -42,7 +42,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
@@ -96,7 +96,7 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
- public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+ public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
String datasetCode, String datastoreCode, WellLocation wellLocation)
{
logAccess(sessionToken, "listImageChannelStacks", "dataset(%s) well(%s)", datasetCode,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
index f47bcc96a8498d6e00639a04b749ab706a0682fc..57cba039aa6389efa4dfadd2f8390048138f312f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java
@@ -40,7 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
@@ -96,7 +96,7 @@ public class PlateContentLoader
/**
* Loads information about all channels stacks of a given well in a given dataset.
*/
- public static List<ChannelStackImageReference> loadImageChannelStacks(Session session,
+ public static List<ImageChannelStackReference> loadImageChannelStacks(Session session,
IScreeningBusinessObjectFactory businessObjectFactory, String datasetCode,
String datastoreCode, WellLocation wellLocation)
{
@@ -325,7 +325,7 @@ public class PlateContentLoader
.createForContainer(plateId));
}
- private List<ChannelStackImageReference> loadImageChannelStacks(String datasetCode,
+ private List<ImageChannelStackReference> loadImageChannelStacks(String datasetCode,
String datastoreCode, WellLocation wellLocation)
{
IHCSDatasetLoader datasetLoader =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
index dd04e5ace82cda2f4eedab0a1e5fe7d34ed692a5..6b72c3c9680d86bf9575984e94f3db3d751eee3e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.PlateMaterialsSearchCriteriaPredicate;
import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
@@ -79,7 +79,7 @@ public interface IScreeningServer extends IServer
@Transactional
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
- public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+ public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
@AuthorizationGuard(guardClass = DataSetCodePredicate.class) String datasetCode,
String datastoreCode, WellLocation wellLocation);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelStackImageReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStackReference.java
similarity index 79%
rename from screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelStackImageReference.java
rename to screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStackReference.java
index d600d4d70bf49bb2dcd53a03c474b09614dd949d..f993c24131d0906cdc8162111ef4c90d1ac5970b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelStackImageReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageChannelStackReference.java
@@ -24,8 +24,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
*
* @author Tomasz Pylak
*/
-public class ChannelStackImageReference implements IsSerializable,
- Comparable<ChannelStackImageReference>
+public class ImageChannelStackReference implements IsSerializable
{
// technical id in the imaging db
private long channelStackTechId;
@@ -36,11 +35,11 @@ public class ChannelStackImageReference implements IsSerializable,
// GWT only
@SuppressWarnings("unused")
- private ChannelStackImageReference()
+ private ImageChannelStackReference()
{
}
- public ChannelStackImageReference(long channelStackTechId, int tileRow, int tileCol,
+ public ImageChannelStackReference(long channelStackTechId, int tileRow, int tileCol,
Float tOrNull, Float zOrNull)
{
this.channelStackTechId = channelStackTechId;
@@ -91,16 +90,4 @@ public class ChannelStackImageReference implements IsSerializable,
return "channelStack=" + channelStackTechId + ", tile[" + tileRow + "," + tileCol + "]"
+ desc;
}
-
- public int compareTo(ChannelStackImageReference other)
- {
- if (this.tileRow == other.tileRow)
- {
- return this.tileCol < other.tileCol ? -1 : (this.tileCol == other.tileCol ? 0 : 1);
- } else
- {
- return this.tileRow < other.tileRow ? -1 : 1;
- }
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
index 14ec2678eec9a92673f5d9e59b88eba24520c1a6..498fd5cffb08c4dd4b62d863c13e54f676e04fa2 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java
@@ -21,7 +21,7 @@ import java.util.Arrays;
import java.util.List;
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelStackDTO;
@@ -119,7 +119,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
return dataset.getIsMultidimensional();
}
- public List<ChannelStackImageReference> listImageChannelStacks(WellLocation wellLocation)
+ public List<ImageChannelStackReference> listImageChannelStacks(WellLocation wellLocation)
{
int spotYRow = wellLocation.getRow();
int spotXColumn = wellLocation.getColumn();
@@ -128,9 +128,9 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
return convert(stacks);
}
- private static List<ChannelStackImageReference> convert(List<ImgChannelStackDTO> stacks)
+ private static List<ImageChannelStackReference> convert(List<ImgChannelStackDTO> stacks)
{
- List<ChannelStackImageReference> result = new ArrayList<ChannelStackImageReference>();
+ List<ImageChannelStackReference> result = new ArrayList<ImageChannelStackReference>();
for (ImgChannelStackDTO stack : stacks)
{
result.add(convert(stack));
@@ -138,9 +138,9 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
return result;
}
- private static ChannelStackImageReference convert(ImgChannelStackDTO stack)
+ private static ImageChannelStackReference convert(ImgChannelStackDTO stack)
{
- return new ChannelStackImageReference(stack.getId(), stack.getRow(), stack.getColumn(),
+ return new ImageChannelStackReference(stack.getId(), stack.getRow(), stack.getColumn(),
stack.getT(), stack.getZ());
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
index a2c6bbd0b31db7f1222719dbb2e5874d595148a8..cdddd3a5e6bb8804ba6134810ae69849376812de 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/IHCSDatasetLoader.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
import java.util.List;
import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
/**
@@ -44,5 +44,5 @@ public interface IHCSDatasetLoader
/**
* Loads information about all channels stacks of a given well.
*/
- List<ChannelStackImageReference> listImageChannelStacks(WellLocation wellLocation);
+ List<ImageChannelStackReference> listImageChannelStacks(WellLocation wellLocation);
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
index 59d357e52a20c146e801f9992aa6a71890ed7ad5..4c57b86fcfa0c394b3fcc83599a79922017812ea 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/dataaccess/IImagingQueryDAO.java
@@ -98,7 +98,7 @@ public interface IImagingQueryDAO extends TransactionQuery
@Select("select * from CONTAINERS where ID = ?{1}")
public ImgContainerDTO getContainerById(long containerId);
- @Select("select * from CHANNEL_STACKS cs join SPOTS s on s.id = cs.spot_id where "
+ @Select("select cs.* from CHANNEL_STACKS cs join SPOTS s on s.id = cs.spot_id where "
+ "cs.ds_id = ?{1} and s.x = ?{2} and s.y = ?{3}")
public List<ImgChannelStackDTO> listChannelStacks(long datasetId, int spotX, int spotY);