From 30089a0ccb0a82aa8226098fb323deaba1cfe7ab Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Tue, 4 Dec 2012 12:58:13 +0000
Subject: [PATCH] SP-366 BIS-254: SOB-6: Allow setting rescaling parameters per
user per plate (implementation)
SVN: 27850
---
.../etl/dto/ImageTransfomationFactories.java | 31 ++++
.../client/web/client/application/Dict.java | 27 ++--
.../ScreeningDisplaySettingsManager.java | 20 ++-
.../detailviewers/ChannelChooser.java | 28 +++-
.../detailviewers/ChannelChooserPanel.java | 115 +++++++++++---
.../ChannelWidgetWithListener.java | 12 +-
.../detailviewers/DefaultChannelState.java | 17 ++
.../detailviewers/IDefaultChannelState.java | 4 +
.../MaterialReplicaSummaryComponent.java | 10 +-
.../UserDefinedRescalingSettingsDialog.java | 147 ++++++++++++++++++
.../detailviewers/WellContentDialog.java | 5 +-
.../detailviewers/WellSearchGrid.java | 9 +-
.../dto/LogicalImageChannelsReference.java | 17 +-
.../detailviewers/image/Image.java | 15 +-
.../client/web/public/screening-dictionary.js | 4 +
.../basic/dto/ImageDatasetParameters.java | 12 +-
.../shared/basic/dto/IntensityRange.java | 80 ++++++++++
.../shared/basic/dto/ScreeningConstants.java | 1 +
.../basic/dto/ScreeningDisplaySettings.java | 23 ++-
19 files changed, 516 insertions(+), 61 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/IntensityRange.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
index b47fa281993..bfd6e221852 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/ImageTransfomationFactories.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.openbis.dss.etl.dto;
import java.util.Map;
import ch.systemsx.cisd.base.image.IImageTransformerFactory;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.transformations.IntensityRangeImageTransformerFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
* Stores transformations defined for the image on different levels.
@@ -48,6 +50,12 @@ public class ImageTransfomationFactories
{
return defaultTransformationOrNull;
}
+ if (transformationCodeOrNull.toLowerCase().startsWith(
+ ScreeningConstants.USER_DEFINED_RESCALING_CODE.toLowerCase()))
+ {
+ return getUserDefinedTransformationOrDefault(transformationCodeOrNull);
+ }
+
return singleChannelMap.get(transformationCodeOrNull);
}
@@ -88,4 +96,27 @@ public class ImageTransfomationFactories
{
return defaultTransformationCodeOrNull;
}
+
+ private IImageTransformerFactory getUserDefinedTransformationOrDefault(
+ String userDefinedTransformation)
+ {
+ String[] parameters =
+ userDefinedTransformation.replaceAll(
+ "^.*\\(\\s*([0-9]+)\\s*,\\s*([0-9]+)\\s*\\)\\s*$", "$1,$2").split(",");
+
+ if (parameters.length == 2)
+ {
+ try
+ {
+ int blackPoint = Integer.parseInt(parameters[0]);
+ int whitePoint = Integer.parseInt(parameters[1]);
+
+ return new IntensityRangeImageTransformerFactory(blackPoint, whitePoint);
+ } catch (NumberFormatException ex)
+ {
+ }
+ }
+
+ return defaultTransformationOrNull;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
index 196843adc4b..3d493f813c9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/Dict.java
@@ -132,31 +132,36 @@ public final class Dict extends ch.systemsx.cisd.openbis.generic.client.web.clie
public static final String RESOLUTION_CHOOSER_DEFAULT = "RESOLUTION_CHOOSER_DEFAULT";
public static final String RESOLUTION_CHOOSER_RESOLUTION = "RESOLUTION_CHOOSER_RESOLUTION";
-
- public static final String HEAT_MAP_RANGE_CHOOSER_BUTTON =
- "heat_map_range_chooser_button";
- public static final String HEAT_MAP_RANGE_CHOOSER_TITLE =
- "heat_map_range_chooser_title";
-
+ public static final String HEAT_MAP_RANGE_CHOOSER_BUTTON = "heat_map_range_chooser_button";
+
+ public static final String TITLE_USER_DEFINED_RESCALING_DIALOG =
+ "TITLE_USER_DEFINED_RESCALING_DIALOG";
+
+ public static final String RESCALING_DIALOG_MIN = "RESCALING_DIALOG_MIN";
+
+ public static final String RESCALING_DIALOG_MAX = "RESCALING_DIALOG_MAX";
+
+ public static final String HEAT_MAP_RANGE_CHOOSER_TITLE = "heat_map_range_chooser_title";
+
public static final String HEAT_MAP_RANGE_CHOOSER_TYPE_LABEL_PREFIX =
"heat_map_range_chooser_type_label_";
-
+
public static final String HEAT_MAP_RANGE_CHOOSER_TYPE_TOOLTIP_PREFIX =
"heat_map_range_chooser_type_tooltip_";
public static final String HEAT_MAP_RANGE_CHOOSER_FIXED_TYPE_LABEL =
"heat_map_range_chooser_type_fixed_type_label";
-
+
public static final String HEAT_MAP_RANGE_CHOOSER_FIXED_TYPE_LOWEST_SCALE_LABEL =
"heat_map_range_chooser_type_fixed_type_lowest_scale_label";
-
+
public static final String HEAT_MAP_RANGE_CHOOSER_FIXED_TYPE_HIGHEST_SCALE_LABEL =
"heat_map_range_chooser_type_fixed_type_highest_scale_label";
-
+
public static final String HEAT_MAP_RANGE_CHOOSER_FIXED_TYPE_SAME_VALUE_VALIDATION_MSG =
"heat_map_range_chooser_type_fixed_type_same_value_validation_message";
-
+
private Dict()
{
// Can not be instantiated.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplaySettingsManager.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplaySettingsManager.java
index 15bc186be88..83d772e583a 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplaySettingsManager.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/ScreeningDisplaySettingsManager.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewConte
import ch.systemsx.cisd.openbis.generic.client.web.client.application.framework.DisplaySettingsManager;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.IRangeType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.RangeType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningDisplaySettings;
@@ -148,7 +149,7 @@ public class ScreeningDisplaySettingsManager
}
delays.put(displayTypeId, delay);
}
-
+
public IRangeType getHeatMapRangeType(String featureCode)
{
Map<String, IRangeType> featureRangeTypes = screeningSettings.getDefaultFeatureRangeTypes();
@@ -162,7 +163,7 @@ public class ScreeningDisplaySettingsManager
}
return RangeType.MIN_MAX;
}
-
+
public void setHeatMapRangeType(String featureCode, IRangeType rangeType)
{
Map<String, IRangeType> featureRangeTypes = screeningSettings.getDefaultFeatureRangeTypes();
@@ -174,4 +175,19 @@ public class ScreeningDisplaySettingsManager
featureRangeTypes.put(featureCode, rangeType);
}
+ @SuppressWarnings("deprecation")
+ public Map<String, IntensityRange> getIntensityRangesForChannels(String displayTypeId)
+ {
+ Map<String, IntensityRange> intensityRangesForChannels =
+ screeningSettings.getIntensityRangesForChannels().get(displayTypeId);
+
+ if (intensityRangesForChannels == null)
+ {
+ intensityRangesForChannels = new HashMap<String, IntensityRange>();
+ screeningSettings.getIntensityRangesForChannels().put(displayTypeId,
+ intensityRangesForChannels);
+ }
+
+ return intensityRangesForChannels;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
index af0014311fd..849d86e9916 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooser.java
@@ -50,6 +50,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesR
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetOverlayImagesReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
@@ -94,6 +95,8 @@ class ChannelChooser
private String imageTransformationCodeOrNull;
+ private IntensityRange rangeOrNull;
+
public ChannelChooser(LogicalImageReference basicImage, IChanneledViewerFactory viewerFactory,
IDefaultChannelState defaultChannelState)
{
@@ -106,6 +109,7 @@ class ChannelChooser
this.imageTransformationCodeOrNull =
tryGetInitialImageTransformationCode(defaultChannelState, basicChannelCodes,
basicImage.getImagetParameters());
+ this.rangeOrNull = tryGetInitialIntensityRange(defaultChannelState, basicChannelCodes);
this.defaultChannelState = defaultChannelState;
this.selectedOverlayChannels = new HashSet<ImageDatasetChannel>();
}
@@ -122,7 +126,7 @@ class ChannelChooser
{
LogicalImageChannelsReference state =
new LogicalImageChannelsReference(basicImage, basicChannelCodes,
- imageTransformationCodeOrNull, selectedOverlayChannels);
+ imageTransformationCodeOrNull, rangeOrNull, selectedOverlayChannels);
LayoutContainer view =
viewerFactory.create(state,
@@ -137,7 +141,9 @@ class ChannelChooser
final IViewContext<IScreeningClientServiceAsync> context,
final AsyncCallback<Void> callback)
{
- final Widget loading = new Text(context.getMessage(ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict.LOAD_IN_PROGRESS));
+ final Widget loading =
+ new Text(
+ context.getMessage(ch.systemsx.cisd.openbis.generic.client.web.client.application.Dict.LOAD_IN_PROGRESS));
container.add(loading);
context.getService().getImageDatasetResolutions(basicImage.getDatasetCode(),
@@ -330,11 +336,13 @@ class ChannelChooser
@Override
public void selectionChanged(List<String> newlySelectedChannels,
@SuppressWarnings("hiding")
- String imageTransformationCodeOrNull)
+ String imageTransformationCodeOrNull, @SuppressWarnings("hiding")
+ IntensityRange rangeOrNull)
{
basicChannelCodes = newlySelectedChannels;
ChannelChooser.this.imageTransformationCodeOrNull =
imageTransformationCodeOrNull;
+ ChannelChooser.this.rangeOrNull = rangeOrNull;
refresh();
}
});
@@ -408,4 +416,18 @@ class ChannelChooser
return null;
}
+
+ private static IntensityRange tryGetInitialIntensityRange(
+ IDefaultChannelState defaultChannelState, List<String> channels)
+ {
+ if (channels.size() == 1)
+ {
+ String channel = channels.get(0);
+ IntensityRange rangeOrNull = defaultChannelState.tryGetIntensityRange(channel);
+
+ return rangeOrNull;
+ }
+
+ return null;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
index d95b597b95e..d04fad25187 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelChooserPanel.java
@@ -27,9 +27,13 @@ import java.util.Map;
import java.util.Set;
import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.ButtonEvent;
import com.extjs.gxt.ui.client.event.Events;
import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.event.SelectionListener;
import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.extjs.gxt.ui.client.widget.form.AdapterField;
import com.extjs.gxt.ui.client.widget.form.CheckBox;
import com.extjs.gxt.ui.client.widget.form.CheckBoxGroup;
import com.extjs.gxt.ui.client.widget.form.Field;
@@ -43,6 +47,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.SimpleModelComboBox;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -68,7 +73,8 @@ public class ChannelChooserPanel extends LayoutContainer
*/
public static interface ChannelSelectionListener
{
- void selectionChanged(List<String> channels, String imageTransformationCodeOrNull);
+ void selectionChanged(List<String> channels, String imageTransformationCodeOrNull,
+ IntensityRange rangeOrNull);
}
public static final String DEFAULT_TRANSFORMATION_CODE = "$DEFAULT$";
@@ -80,6 +86,11 @@ public class ChannelChooserPanel extends LayoutContainer
"Grayscale images with color depth higher then 8 bits are transformed in the optimal way for a single image. Otherwise no filter is applied.",
"", false));
+ public static final LabeledItem<InternalImageTransformationInfo> USER_DEFINED_RESCALING_TRANSFORMATION =
+ convertToLabeledItem(new InternalImageTransformationInfo(
+ ScreeningConstants.USER_DEFINED_RESCALING_CODE, "User defined",
+ "User defined intensity rescaling", "", false));
+
private final IMessageProvider messageProvider;
private IDefaultChannelState defaultChannelState;
@@ -92,6 +103,11 @@ public class ChannelChooserPanel extends LayoutContainer
private LabelField adjustLabel = new LabelField("Filter:");
+ private Button userDefinedTransformationSettingsButton = new Button("Settings");
+
+ private AdapterField userDefinedTransformationSettingsButtonField = new AdapterField(
+ userDefinedTransformationSettingsButton);
+
private Map<String, Set<InternalImageTransformationInfo>> transformationsForChannels =
new HashMap<String, Set<InternalImageTransformationInfo>>();
@@ -105,7 +121,6 @@ public class ChannelChooserPanel extends LayoutContainer
{
selectionChanged();
}
-
};
private final Listener<BaseEvent> transformationSelection = new Listener<BaseEvent>()
@@ -113,11 +128,15 @@ public class ChannelChooserPanel extends LayoutContainer
@Override
public void handleEvent(BaseEvent be)
{
+ String transformationCode =
+ transformationsComboBox.getSimpleValue().getItem().getCode();
defaultChannelState.setDefaultTransformation(getSelectedValues().get(0),
- transformationsComboBox.getSimpleValue().getItem().getCode());
- notifySelectionListeners(getSelectedValues(), tryGetSelectedTransformationCode());
+ transformationCode);
+ changeTransformationSettingsButtonVisibility(true, false);
+ notifySelectionListeners(getSelectedValues(),
+ tryGetSelectedTransformationCode(false),
+ defaultChannelState.tryGetIntensityRange(getSelectedValues().get(0)));
}
-
};
public ChannelChooserPanel(IMessageProvider messageProvider,
@@ -126,7 +145,7 @@ public class ChannelChooserPanel extends LayoutContainer
this(messageProvider, defChannelState, Collections.<String> emptyList(), null);
}
- public ChannelChooserPanel(IMessageProvider messageProvider,
+ public ChannelChooserPanel(final IMessageProvider messageProvider,
IDefaultChannelState defChannelState, List<String> selectedChannelsOrNull,
ImageDatasetParameters imageDatasetParameters)
{
@@ -147,6 +166,21 @@ public class ChannelChooserPanel extends LayoutContainer
group.add(channelsComboBox);
group.add(adjustLabel);
group.add(transformationsComboBox);
+ group.add(userDefinedTransformationSettingsButtonField);
+
+ userDefinedTransformationSettingsButton
+ .addSelectionListener(new SelectionListener<ButtonEvent>()
+ {
+ @Override
+ public void componentSelected(ButtonEvent ce)
+ {
+ UserDefinedRescalingSettingsDialog dialog =
+ new UserDefinedRescalingSettingsDialog(messageProvider,
+ defaultChannelState, getSelectedValues().get(0));
+ dialog.addListener(Events.Hide, transformationSelection);
+ dialog.show();
+ }
+ });
add(group);
@@ -357,34 +391,49 @@ public class ChannelChooserPanel extends LayoutContainer
ensureAtLeastOneCheckboxChecked();
updateTransformationComboBox();
- notifySelectionListeners(selection, tryGetSelectedTransformationCode());
+ notifySelectionListeners(selection, tryGetSelectedTransformationCode(false),
+ defaultChannelState.tryGetIntensityRange(selectedComboValue));
}
- public String tryGetSelectedTransformationCode()
+ public String tryGetSelectedTransformationCode(boolean force)
{
- if (transformationsComboBox.isVisible())
- {
- String code =
- transformationsComboBox.getSelection().get(0).getValue().getItem().getCode();
+ String code = null;
- if (DEFAULT_TRANSFORMATION_CODE.equals(code))
- {
- return null;
- } else
- {
- return code;
- }
+ if (force || transformationsComboBox.isVisible(false))
+ {
+ code = transformationsComboBox.getSelection().get(0).getValue().getItem().getCode();
+ } else if (transformationsComboBox.getStore().getModels().size() == 1)
+ {
+ code =
+ transformationsComboBox.getStore().getModels().get(0).getValue().getItem()
+ .getCode();
}
- return null;
+ return transformCode(code);
+ }
+
+ public IntensityRange tryGetSelectedIntensityRange()
+ {
+ return defaultChannelState.tryGetIntensityRange(getSelectedValues().get(0));
+ }
+
+ private static String transformCode(String code)
+ {
+ if (code == null || DEFAULT_TRANSFORMATION_CODE.equals(code))
+ {
+ return null;
+ } else
+ {
+ return code;
+ }
}
private void notifySelectionListeners(List<String> selection,
- String imageTransformationCodeOrNull)
+ String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
{
for (ChannelSelectionListener listener : channelSelectionListeners)
{
- listener.selectionChanged(selection, imageTransformationCodeOrNull);
+ listener.selectionChanged(selection, imageTransformationCodeOrNull, rangeOrNull);
}
}
@@ -490,10 +539,10 @@ public class ChannelChooserPanel extends LayoutContainer
{
transformationsComboBox.setVisible(false);
adjustLabel.setVisible(false);
+ userDefinedTransformationSettingsButtonField.setVisible(false);
return;
}
transformationsComboBox.add(model);
- setTransformationsVisible(true);
selectTransformation(selectedValues.get(0));
} else
@@ -502,6 +551,19 @@ public class ChannelChooserPanel extends LayoutContainer
}
}
+ private void changeTransformationSettingsButtonVisibility(boolean visible, boolean force)
+ {
+ if (visible
+ && ScreeningConstants.USER_DEFINED_RESCALING_CODE
+ .equals(tryGetSelectedTransformationCode(force)))
+ {
+ userDefinedTransformationSettingsButtonField.setVisible(true);
+ } else
+ {
+ userDefinedTransformationSettingsButtonField.setVisible(false);
+ }
+ }
+
private static boolean isDefaultTransformationDefined(Set<InternalImageTransformationInfo> infos)
{
for (InternalImageTransformationInfo imageTransformationInfo : infos)
@@ -518,6 +580,7 @@ public class ChannelChooserPanel extends LayoutContainer
{
transformationsComboBox.setVisible(visible);
adjustLabel.setVisible(visible);
+ changeTransformationSettingsButtonVisibility(visible, false);
}
private void selectTransformation(String channelCode)
@@ -546,6 +609,8 @@ public class ChannelChooserPanel extends LayoutContainer
transformationsComboBox.setSelection(Collections.singletonList(transformationsComboBox
.getStore().getModels().get(0)));
}
+
+ changeTransformationSettingsButtonVisibility(true, true);
}
private boolean setSelectedValue(String code,
@@ -553,8 +618,8 @@ public class ChannelChooserPanel extends LayoutContainer
{
if (code != null)
{
- for (SimpleComboValue<LabeledItem<InternalImageTransformationInfo>> info : combobox.getStore()
- .getModels())
+ for (SimpleComboValue<LabeledItem<InternalImageTransformationInfo>> info : combobox
+ .getStore().getModels())
{
if (info.getValue().getItem().getCode().equals(code))
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
index 2bc0f4a8558..0e83909df37 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ChannelWidgetWithListener.java
@@ -22,10 +22,12 @@ import com.extjs.gxt.ui.client.widget.LayoutContainer;
import com.google.gwt.user.client.ui.Widget;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.utils.GuiUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
/**
* Allows to create a {@link Widget} ({@link #asWidget()}) containing channel view and allows to
- * manually update visible channel via the ({@link #selectionChanged(List, String)}) method.
+ * manually update visible channel via the ({@link #selectionChanged(List, String, IntensityRange)})
+ * method.
*
* @author Izabela Adamczyk
*/
@@ -37,7 +39,8 @@ public class ChannelWidgetWithListener implements ChannelChooserPanel.ChannelSel
interface ISimpleChanneledViewerFactory
{
- Widget create(List<String> channelCodes, String imageTransformationCodeOrNull);
+ Widget create(List<String> channelCodes, String imageTransformationCodeOrNull,
+ IntensityRange rangeOrNull);
}
public ChannelWidgetWithListener(final ISimpleChanneledViewerFactory viewerFactory)
@@ -52,12 +55,13 @@ public class ChannelWidgetWithListener implements ChannelChooserPanel.ChannelSel
}
@Override
- public void selectionChanged(List<String> channelNames, String imageTransformationCodeOrNull)
+ public void selectionChanged(List<String> channelNames, String imageTransformationCodeOrNull,
+ IntensityRange rangeOrNull)
{
if (channelNames != null)
{
GuiUtils.replaceLastItem(container,
- viewerFactory.create(channelNames, imageTransformationCodeOrNull));
+ viewerFactory.create(channelNames, imageTransformationCodeOrNull, rangeOrNull));
}
}
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/DefaultChannelState.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/DefaultChannelState.java
index c118f892a83..921561aebd4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/DefaultChannelState.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/DefaultChannelState.java
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewConte
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningDisplaySettingsManager;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.ScreeningViewContext;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
/**
* @author Kaloyan Enimanev
@@ -85,4 +86,20 @@ public class DefaultChannelState implements IDefaultChannelState
getDisplaySettingManager().setDefaultResolution(displayTypeId, resolution);
}
+ @Override
+ public void setIntensityRange(String channel, IntensityRange intensityRange)
+ {
+ getIntensityRange().put(channel, intensityRange);
+ }
+
+ @Override
+ public IntensityRange tryGetIntensityRange(String channel)
+ {
+ return getIntensityRange().get(channel);
+ }
+
+ private Map<String, IntensityRange> getIntensityRange()
+ {
+ return getDisplaySettingManager().getIntensityRangesForChannels(displayTypeId);
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/IDefaultChannelState.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/IDefaultChannelState.java
index 90d3182c1bf..d91f1ed3401 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/IDefaultChannelState.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/IDefaultChannelState.java
@@ -3,6 +3,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.
import java.util.List;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
/**
* Allows to get and set the channels chosen by default when images are shown in a specific context.
@@ -23,4 +24,7 @@ public interface IDefaultChannelState
public void setDefaultResolution(ImageResolution resolution);
+ public void setIntensityRange(String channel, IntensityRange intensityRange);
+
+ public IntensityRange tryGetIntensityRange(String channel);
}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
index 1da95be910a..fc2bcda9326 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/MaterialReplicaSummaryComponent.java
@@ -63,6 +63,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReplicaImage;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.ExperimentSearchCriteria;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
/**
* Component which for a specified material and experiment presents 1. feature vectors (detailed and
@@ -345,15 +346,18 @@ public class MaterialReplicaSummaryComponent
final ISimpleChanneledViewerFactory viewerFactory = new ISimpleChanneledViewerFactory()
{
@Override
- public Widget create(List<String> channels, String imageTransformationCodeOrNull)
+ public Widget create(List<String> channels, String imageTransformationCodeOrNull,
+ IntensityRange rangeOrNull)
{
return WellContentDialog.createImageViewerForChannel(screeningViewContext,
- image, oneImageSizeFactorPx, channels, imageTransformationCodeOrNull);
+ image, oneImageSizeFactorPx, channels, imageTransformationCodeOrNull,
+ rangeOrNull);
}
};
ChannelWidgetWithListener widgetWithListener = new ChannelWidgetWithListener(viewerFactory);
widgetWithListener.selectionChanged(channelChooser.getSelectedValues(),
- channelChooser.tryGetSelectedTransformationCode());
+ channelChooser.tryGetSelectedTransformationCode(false),
+ channelChooser.tryGetSelectedIntensityRange());
ImageDatasetParameters imageParameters = image.tryGetImageDataset().getImageParameters();
channelChooser.addSelectionChangedListener(widgetWithListener);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
new file mode 100644
index 00000000000..e05c6767bb5
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/UserDefinedRescalingSettingsDialog.java
@@ -0,0 +1,147 @@
+/*
+ * Copyright 2012 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.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.widget.Dialog;
+import com.extjs.gxt.ui.client.widget.Label;
+import com.extjs.gxt.ui.client.widget.button.Button;
+import com.google.gwt.user.client.ui.Grid;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.IntegerField;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class UserDefinedRescalingSettingsDialog extends Dialog
+{
+ private final Label labelMin;
+
+ private final Label labelMax;
+
+ private final IntegerField minTextField;
+
+ private final IntegerField maxTextField;
+
+ private final IMessageProvider messageProvider;
+
+ private final IDefaultChannelState defaultChannelState;
+
+ private final String channelCode;
+
+ public UserDefinedRescalingSettingsDialog(IMessageProvider messageProvider,
+ IDefaultChannelState defaultChannelState, String channelCode)
+ {
+ super();
+
+ this.messageProvider = messageProvider;
+ this.defaultChannelState = defaultChannelState;
+ this.channelCode = channelCode;
+
+ setHeading(this.messageProvider.getMessage(Dict.TITLE_USER_DEFINED_RESCALING_DIALOG));
+ setButtons(Dialog.OKCANCEL);
+ labelMin = new Label(this.messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN));
+ labelMax = new Label(this.messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX));
+ minTextField =
+ new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MIN), true);
+ maxTextField =
+ new IntegerField(messageProvider.getMessage(Dict.RESCALING_DIALOG_MAX), true);
+
+ setInitialValues();
+
+ Grid grid = new Grid(2, 2);
+ grid.setWidget(0, 0, labelMin);
+ grid.setWidget(0, 1, minTextField);
+ grid.setWidget(1, 0, labelMax);
+ grid.setWidget(1, 1, maxTextField);
+
+ add(grid);
+
+ setAutoWidth(true);
+ setAutoHeight(true);
+
+ addListener(Events.Show, new Listener<BaseEvent>()
+ {
+ @Override
+ public void handleEvent(BaseEvent be)
+ {
+ center();
+ }
+ });
+ }
+
+ private void setInitialValues()
+ {
+ minTextField.setValue(0);
+ maxTextField.setValue(255);
+
+ IntensityRange range = defaultChannelState.tryGetIntensityRange(channelCode);
+ if (range != null)
+ {
+ minTextField.setValue(range.getBlackPoint());
+ maxTextField.setValue(range.getWhitePoint());
+ }
+ }
+
+ @Override
+ protected final void onButtonPressed(final Button button)
+ {
+ if (button.getItemId().equals(Dialog.OK))
+ {
+ button.disable();
+ if (minTextField.isValid() && maxTextField.isValid())
+ {
+ super.onButtonPressed(button);
+ updateIntensityRescaling();
+
+ hide();
+ } else
+ {
+ button.enable();
+ }
+ } else
+ {
+ super.onButtonPressed(button);
+ hide();
+ }
+ }
+
+ public void updateIntensityRescaling()
+ {
+ IntensityRange result = null;
+
+ try
+ {
+ int min = Integer.parseInt(minTextField.getValue().toString());
+ int max = Integer.parseInt(maxTextField.getValue().toString());
+
+ result = new IntensityRange(min, max);
+ } catch (NumberFormatException e)
+ {
+ }
+
+ if (result != null)
+ {
+ defaultChannelState.setIntensityRange(channelCode, result);
+ }
+ }
+}
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 4976fa4114e..f86322e8d6c 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
@@ -63,6 +63,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.TileLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
@@ -170,7 +171,7 @@ public class WellContentDialog extends ImageDialog
public static Widget createImageViewerForChannel(
final IViewContext<IScreeningClientServiceAsync> viewContext,
final WellContent wellImage, int imageSizePx, List<String> channels,
- String imageTransformationCodeOrNull)
+ String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
{
final ImageDatasetEnrichedReference imageDataset = tryGetImageDataset(wellImage);
if (imageDataset == null)
@@ -208,7 +209,7 @@ public class WellContentDialog extends ImageDialog
new LogicalImageReference(imageDataset, locationOrNull);
LogicalImageChannelsReference channelReferences =
LogicalImageChannelsReference.createWithoutOverlays(wellImages, channels,
- imageTransformationCodeOrNull);
+ imageTransformationCodeOrNull, rangeOrNull);
LayoutContainer staticTilesGrid =
LogicalImageViewer.createTilesGrid(channelReferences, sessionId, imageSizePx,
clickHandler, null);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
index 8fd690102eb..76abc4000ed 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellSearchGrid.java
@@ -72,6 +72,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.u
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.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellSearchCriteria.AnalysisProcedureCriteria;
@@ -637,17 +638,19 @@ public class WellSearchGrid extends TypedTableGrid<WellContent> implements
{
@Override
public Widget create(List<String> channels,
- String imageTransformationCodeOrNull)
+ String imageTransformationCodeOrNull,
+ IntensityRange rangeOrNull)
{
return WellContentDialog.createImageViewerForChannel(
getViewContext(), entity, IMAGE_SIZE_PX, channels,
- imageTransformationCodeOrNull);
+ imageTransformationCodeOrNull, rangeOrNull);
}
};
ChannelWidgetWithListener widgetWithListener =
new ChannelWidgetWithListener(viewerFactory);
widgetWithListener.selectionChanged(channelChooser.getSelectedValues(),
- channelChooser.tryGetSelectedTransformationCode());
+ channelChooser.tryGetSelectedTransformationCode(false),
+ channelChooser.tryGetSelectedIntensityRange());
ImageDatasetParameters imageParameters = images.getImageParameters();
channelChooser.addSelectionChangedListener(widgetWithListener);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
index 2929a72282e..87034aefc2d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/dto/LogicalImageChannelsReference.java
@@ -20,6 +20,8 @@ import java.util.HashSet;
import java.util.List;
import java.util.Set;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
+
/**
* Channels of the basic images and overlay images.
*
@@ -29,10 +31,10 @@ public class LogicalImageChannelsReference
{
public static LogicalImageChannelsReference createWithoutOverlays(
LogicalImageReference basicImage, List<String> channels,
- String imageTransformationCodeOrNull)
+ String imageTransformationCodeOrNull, IntensityRange rangeOrNull)
{
return new LogicalImageChannelsReference(basicImage, channels,
- imageTransformationCodeOrNull, new HashSet<ImageDatasetChannel>());
+ imageTransformationCodeOrNull, rangeOrNull, new HashSet<ImageDatasetChannel>());
}
// ----
@@ -43,14 +45,18 @@ public class LogicalImageChannelsReference
private final String imageTransformationCodeOrNull;
+ private final IntensityRange rangeOrNull;
+
private final Set<ImageDatasetChannel> overlayChannels;
public LogicalImageChannelsReference(LogicalImageReference basicImage, List<String> channels,
- String imageTransformationCodeOrNull, Set<ImageDatasetChannel> overlayChannels)
+ String imageTransformationCodeOrNull, IntensityRange rangeOrNull,
+ Set<ImageDatasetChannel> overlayChannels)
{
this.basicImage = basicImage;
this.channels = channels;
this.imageTransformationCodeOrNull = imageTransformationCodeOrNull;
+ this.rangeOrNull = rangeOrNull;
this.overlayChannels = overlayChannels;
}
@@ -73,4 +79,9 @@ public class LogicalImageChannelsReference
{
return imageTransformationCodeOrNull;
}
+
+ public IntensityRange tryGetIntensityRange()
+ {
+ return rangeOrNull;
+ }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
index 9645a47fc94..27b95c867b8 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/image/Image.java
@@ -32,6 +32,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.d
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.ImageDatasetChannel;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageChannelsReference;
import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.dto.LogicalImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.IntensityRange;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ImageServletUrlParameters;
@@ -61,8 +62,20 @@ public class Image extends LayoutContainer
if (getInitializer().getChannelReferences().tryGetImageTransformationCode() != null)
{
+ String suffix = "";
+ if (ScreeningConstants.USER_DEFINED_RESCALING_CODE.equalsIgnoreCase(getInitializer()
+ .getChannelReferences().tryGetImageTransformationCode()))
+ {
+ IntensityRange range =
+ getInitializer().getChannelReferences().tryGetIntensityRange();
+ if (range != null)
+ {
+ suffix = "(" + range.getBlackPoint() + "," + range.getWhitePoint() + ")";
+ }
+ }
url.addParameter(ImageServletUrlParameters.SINGLE_CHANNEL_TRANSFORMATION_CODE_PARAM,
- getInitializer().getChannelReferences().tryGetImageTransformationCode());
+ getInitializer().getChannelReferences().tryGetImageTransformationCode()
+ + suffix);
}
addImageTransformerSignature(url, getInitializer().getChannelReferences());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
index 8816bbc4497..b47d96e6c8f 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/screening-dictionary.js
@@ -141,6 +141,10 @@ RESOLUTION_CHOOSER_LABEL: "Resolution:",
RESOLUTION_CHOOSER_DEFAULT: "Default",
RESOLUTION_CHOOSER_RESOLUTION: "{0}x{1}",
+TITLE_USER_DEFINED_RESCALING_DIALOG: "Set rescaling parameters",
+RESCALING_DIALOG_MIN: "black point: ",
+RESCALING_DIALOG_MAX: "white point: ",
+
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
};
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
index e185875d656..a5bce90cfc0 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
@@ -21,6 +21,7 @@ import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.application.detailviewers.ChannelChooserPanel;
/**
* Describes the images in the dataset: tiles geometry, channels, dataset code and plate geometry if
@@ -49,7 +50,7 @@ public class ImageDatasetParameters implements Serializable
private boolean isMultidimensional;
private String mergedChannelTransformerFactorySignatureOrNull;
-
+
public Integer tryGetRowsNum()
{
return rowsNumOrNull;
@@ -129,14 +130,19 @@ public class ImageDatasetParameters implements Serializable
public List<InternalImageTransformationInfo> getAvailableImageTransformationsFor(
String channelCode)
{
+ List<InternalImageTransformationInfo> result =
+ new ArrayList<InternalImageTransformationInfo>();
+ result.add(ChannelChooserPanel.USER_DEFINED_RESCALING_TRANSFORMATION.getItem());
+
for (InternalImageChannel channel : channels)
{
if (channel.getCode().equalsIgnoreCase(channelCode))
{
- return channel.getAvailableImageTransformations();
+ result.addAll(channel.getAvailableImageTransformations());
+ return result;
}
}
- return new ArrayList<InternalImageTransformationInfo>();
+ return result;
}
public boolean isMultidimensional()
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/IntensityRange.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/IntensityRange.java
new file mode 100644
index 00000000000..655e7da495a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/IntensityRange.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright 2012 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.shared.basic.dto;
+
+import java.io.Serializable;
+
+/**
+ * The intensity range in a distribution of pixel values for a given symmetric quantile value.
+ *
+ * @author Pawel Glyzewski
+ */
+public class IntensityRange implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private int blackPoint;
+
+ private int whitePoint;
+
+ @SuppressWarnings("unused")
+ private IntensityRange()
+ {
+ }
+
+ public IntensityRange(int blackPoint, int whitePoint)
+ {
+ this.blackPoint = blackPoint;
+ this.whitePoint = whitePoint;
+ }
+
+ /**
+ * The minimal level (black point).
+ */
+ public int getBlackPoint()
+ {
+ return blackPoint;
+ }
+
+ /**
+ * The maximal level (white point).
+ */
+ public int getWhitePoint()
+ {
+ return whitePoint;
+ }
+
+ @SuppressWarnings("unused")
+ private void setBlackPoint(int blackPoint)
+ {
+ this.blackPoint = blackPoint;
+ }
+
+ @SuppressWarnings("unused")
+ private void setWhitePoint(int whitePoint)
+ {
+ this.whitePoint = whitePoint;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "MinMax [minLevel=" + blackPoint + ", maxLevel=" + whitePoint + "]";
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
index 933e4f98033..f1e1e87242e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningConstants.java
@@ -257,4 +257,5 @@ public class ScreeningConstants
public final static String TILE_COL_PARAM = "tileCol";
}
+ public static final String USER_DEFINED_RESCALING_CODE = "$USER_DEFINED_RESCALING$";
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningDisplaySettings.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningDisplaySettings.java
index 4a54e287b10..08e17004823 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningDisplaySettings.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ScreeningDisplaySettings.java
@@ -40,11 +40,14 @@ public class ScreeningDisplaySettings implements Serializable
private Map<String, ImageResolution> defaultResolutions;
private Map<String, Integer> defaultMovieDelays;
-
+
private Map<String, IRangeType> defaultFeatureRangeTypes;
private String defaultAnalysisProcedure;
+ private Map<String, Map<String, IntensityRange>> intensityRangesForChannels =
+ new HashMap<String, Map<String, IntensityRange>>();
+
/** @deprecated Should be used only by ScreeningDisplaySettingsManager. */
@Deprecated
public Map<String, String> getDefaultChannels()
@@ -118,6 +121,24 @@ public class ScreeningDisplaySettings implements Serializable
this.defaultMovieDelays = defaultMovieDelays;
}
+ /** @deprecated Should be used only by ScreeningDisplaySettingsManager. */
+ @Deprecated
+ public Map<String, Map<String, IntensityRange>> getIntensityRangesForChannels()
+ {
+ if (intensityRangesForChannels == null)
+ {
+ intensityRangesForChannels = new HashMap<String, Map<String, IntensityRange>>();
+ }
+ return intensityRangesForChannels;
+ }
+
+ @SuppressWarnings("unused")
+ private void setIntensityRangesForChannels(
+ Map<String, Map<String, IntensityRange>> intensityRangesForChannels)
+ {
+ this.intensityRangesForChannels = intensityRangesForChannels;
+ }
+
public Map<String, IRangeType> getDefaultFeatureRangeTypes()
{
return defaultFeatureRangeTypes;
--
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