diff --git a/pom.xml b/pom.xml
index 5453b265..16941696 100644
--- a/pom.xml
+++ b/pom.xml
@@ -7,7 +7,7 @@
org.openspimuOpenSPIM
- 1.0.4-SNAPSHOT
+ 1.0.5-SNAPSHOTjarµOpenSPIM
diff --git a/src/main/java/spim/algorithm/DefaultAntiDrift.java b/src/main/java/spim/algorithm/DefaultAntiDrift.java
index 476d0fad..bf984d53 100644
--- a/src/main/java/spim/algorithm/DefaultAntiDrift.java
+++ b/src/main/java/spim/algorithm/DefaultAntiDrift.java
@@ -1,6 +1,9 @@
package spim.algorithm;
import ij.ImageStack;
+import ij.plugin.filter.Convolver;
+import ij.plugin.filter.GaussianBlur;
+import ij.plugin.filter.RankFilters;
import ij.process.*;
import org.apache.commons.math3.geometry.euclidean.threed.Vector3D;
@@ -18,6 +21,14 @@ public class DefaultAntiDrift extends AbstractAntiDrift
*/
private final double sigma;
private final AntiDrift.Type type;
+ private final GaussianBlur gaussianBlur = new GaussianBlur();
+ private final Convolver convolver = new Convolver();
+ private final RankFilters filters = new RankFilters();
+ private final float[] kernel = new float[]{-1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1,
+ -1, -1, 24, -1, -1,
+ -1, -1, -1, -1, -1,
+ -1, -1, -1, -1, -1,};
public DefaultAntiDrift(double sigmaValue)
{
@@ -49,6 +60,9 @@ public void reset()
@Override public void addXYSlice( ImageProcessor ip )
{
ImageProcessor copy = ip.duplicate();
+ gaussianBlur.blurGaussian( copy, sigma );
+ convolver.convolve( copy, kernel, 5, 5 );
+ filters.rank( copy, 2, 2 );
switch (type) {
case CenterOfMass:
@@ -56,7 +70,6 @@ public void reset()
stack.addSlice( copy );
break;
case PhaseCorrelation:
- copy.blurGaussian( sigma );
latest.addXYSlice( copy );
break;
}
diff --git a/src/main/java/spim/mm/MicroManager.java b/src/main/java/spim/mm/MicroManager.java
index a91e29c8..508b6bb6 100644
--- a/src/main/java/spim/mm/MicroManager.java
+++ b/src/main/java/spim/mm/MicroManager.java
@@ -1331,14 +1331,14 @@ public static void shutdown()
@Subscribe
public void onAcquisitionStart( AcquisitionStartedEvent ae) {
- System.out.println("Acquisition started");
+// System.out.println("Acquisition started");
// store_ = ae.getDatastore();
}
@Subscribe
public void onAcquisitionEnd( AcquisitionEndedEvent ae) {
- System.out.println("Acquisition stopped");
+// System.out.println("Acquisition stopped");
// store_ = null;
}
@@ -1349,7 +1349,7 @@ public void onSystemConfigurationLoaded(SystemConfigurationLoadedEvent event) {
@Subscribe
public void onStagePositionChanged(StagePositionChangedEvent event) {
- System.out.println("Stage changed");
+// System.out.println("Stage changed");
}
@Subscribe
diff --git a/src/main/java/spim/model/data/PositionItem.java b/src/main/java/spim/model/data/PositionItem.java
index 599eb234..aa1af6e6 100644
--- a/src/main/java/spim/model/data/PositionItem.java
+++ b/src/main/java/spim/model/data/PositionItem.java
@@ -1,5 +1,11 @@
package spim.model.data;
+import javafx.beans.InvalidationListener;
+import javafx.beans.property.BooleanProperty;
+import javafx.beans.property.SimpleBooleanProperty;
+import javafx.beans.property.SimpleStringProperty;
+import javafx.beans.property.StringProperty;
+
/**
* Description: PositionItem is used for position table.
*
@@ -15,12 +21,14 @@ public class PositionItem
private double zStart;
private double zEnd;
private double zStep;
+ private final BooleanProperty selected = new SimpleBooleanProperty();
+ private final StringProperty name = new SimpleStringProperty();
public PositionItem()
{
}
- public PositionItem( double x, double y, double r, double zStart, double zEnd, double zStep )
+ public PositionItem( double x, double y, double r, double zStart, double zEnd, double zStep, InvalidationListener invalidationListener )
{
this.x = x;
this.y = y;
@@ -28,6 +36,8 @@ public PositionItem( double x, double y, double r, double zStart, double zEnd, d
this.zStart = zStart;
this.zEnd = zEnd;
this.zStep = zStep;
+ this.name.set("");
+ selectedProperty().addListener( observable -> invalidationListener.invalidated( observable ) );
}
public double getX()
@@ -74,6 +84,12 @@ public String getPosZString() {
return String.format( "%.0f", zStart );
}
+ public String getName() {
+ return name.getValue();
+ }
+
+ public StringProperty getNameProperty() { return name; }
+
public void setX( double x )
{
this.x = x;
@@ -105,7 +121,21 @@ public void setZStep( double zStep )
}
public int getNumberOfSlices() {
- return (int) ((int) (getZEnd() - getZStart() + getZStep()) / getZStep());
+ return (int) ((int) (getZEnd() - getZStart() + getZStep()) / getZStep() + 1);
+ }
+
+ public BooleanProperty selectedProperty() { return selected; }
+
+ public boolean getSelected() {
+ return selected.get();
+ }
+
+ public void setSelected(boolean selected) {
+ this.selected.set( selected );
+ }
+
+ public void setName(String name) {
+ this.name.set(name);
}
@Override public String toString()
diff --git a/src/main/java/spim/ui/view/component/AcquisitionPanel.java b/src/main/java/spim/ui/view/component/AcquisitionPanel.java
index d4a33bd7..d776fa1f 100644
--- a/src/main/java/spim/ui/view/component/AcquisitionPanel.java
+++ b/src/main/java/spim/ui/view/component/AcquisitionPanel.java
@@ -389,6 +389,7 @@ public AcquisitionPanel(SPIMSetup setup, Studio studio, StagePanel stagePanel, T
{
@Override public void changed( ObservableValue< ? extends Number > observable, Number oldValue, Number newValue )
{
+// System.out.println(String.format("%f / %d", newValue.doubleValue(), totalImages.getValue()));
pi.setProgress( newValue.doubleValue() / totalImages.getValue() );
}
} );
@@ -1207,6 +1208,13 @@ private void updateUI ( AcquisitionSetting setting ) {
positionItems = setting.getPositionItems();
positionItemTableView.getItems().setAll( positionItems );
+ InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+ for(int i = 0; i < positionItems.size(); i++) {
+// positionItems.get( i ).setValue( positionItems.get(i).getValue() );
+// positionItems.get( i ).setSelected( positionItems.get(i).getSelected() );
+ positionItems.get( i ).selectedProperty().addListener( observable -> invalidationListener.invalidated( observable ) );
+ }
+
// 3. Z-Stack panel
enabledZStacks.set( setting.getEnabledZStacks() );
@@ -1353,7 +1361,7 @@ public boolean startAcquisition( Button acquireButton )
if ( enabledSaveImages.get() )
{
if(null != folder.listFiles()) {
- boolean found = folder.exists();
+ boolean found = folder.exists() && folder.listFiles().length > 1;
if(found) {
Optional< ButtonType > results = new Alert( Alert.AlertType.WARNING, "The filename already exists. All files with the same name will be replaced. Do you want to proceed?\nPress No to create another folder and keep all files.",
@@ -1462,7 +1470,7 @@ public boolean startAcquisition( Button acquireButton )
engine.performAcquisition( getStudio(), getSpimSetup(), stagePanel, ( java.awt.Rectangle) roiRectangle.get(), tp,
timePointItemTableView.getItems(), currentTP, waitSeconds,
arduinoSelected, finalFolder, filename.getValue(),
- positionItemTableView.getItems(), channelItemList, processedImages,
+ positionItemTableView.getItems().filtered(p -> p.getSelected()), channelItemList, processedImages,
enabledSaveImages.get(), savingFormat.getValue(), saveMIP.getValue(), antiDrift.getValue(), experimentNote.getValue(),
antiDriftLog, antiDriftRefCh.get(), antiDriftTypeToggle, onTheFly.getValue() );
@@ -1515,6 +1523,8 @@ static double getUnit(String unitString) {
private Node createPositionListPane( TableView< PositionItem > positionItemTableView ) {
positionItemTableView.setEditable( true );
+ InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+
EventHandler newEventHandler = ( EventHandler< ActionEvent > ) event -> {
SPIMSetup spimSetup = getSpimSetup();
if(spimSetup != null ) {
@@ -1522,10 +1532,10 @@ private Node createPositionListPane( TableView< PositionItem > positionItemTable
double x = spimSetup.getXStage().getPosition();
double y = spimSetup.getYStage().getPosition();
double z = spimSetup.getZStage().getPosition();
- positionItemTableView.getItems().add( new PositionItem( x, y, r, z, z, zStackStepSize ) );
+ positionItemTableView.getItems().add( new PositionItem( x, y, r, z, z, zStackStepSize, invalidationListener ) );
}
else {
- positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, 20, 50, 10 ) );
+ positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, 20, 50, 10, invalidationListener ) );
}
};
@@ -1610,12 +1620,12 @@ public void computeTotalPositionImages() {
long totalImages = 0;
for(PositionItem item : positionItemTableView.getItems())
{
- if(item.getZEnd() > item.getZStart()) {
+ if(item.getSelected() && item.getZEnd() > item.getZStart()) {
totalImages += item.getNumberOfSlices();
}
}
- propertyMap.get("positions").setValue( positionItemTableView.getItems().size() + "" );
+ propertyMap.get("positions").setValue( positionItemTableView.getItems().filtered(p -> p.getSelected()).size() + "" );
propertyMap.get("slices").setValue( totalImages + "" );
}
@@ -1853,6 +1863,8 @@ private LabeledPane createSummaryPane() {
label.textProperty().bind( propertyMap.get("positions") );
label.textProperty().addListener( observable -> computeTotal() );
+ propertyMap.get("slices").addListener( observable -> computeTotal() );
+
Label label2 = new Label();
label2.textProperty().bind( propertyMap.get("totalImages") );
gridpane.addRow( 0, new Label("No. of positions: "), label, new Label("Total images: "), label2 );
@@ -2097,7 +2109,8 @@ public void changed(ObservableValue observable, String oldValu
// }
// } );
- Button clearButton = new Button( "New Z-stack" );
+ Button clearButton = new Button( "Define new Z-stack" );
+ clearButton.setStyle("-fx-base: #ffbec4;");
clearButton.setOnAction(new EventHandler() {
@Override
public void handle(ActionEvent event) {
@@ -2134,7 +2147,7 @@ public void handle(ActionEvent event) {
}
} );
- zStackGridPane.addRow( 3, new HBox( newButton, clearButton ) );
+ zStackGridPane.addRow( 3, new VBox( newButton, clearButton ) );
// create a group
HBox b = new HBox(new Label("Stage"));
@@ -2148,13 +2161,15 @@ public void handle(ActionEvent event) {
Button helpButton = createHelpButton();
helpButton.setOnAction( event -> new HelpWindow().show(HelpType.ZSTACK));
- CheckboxPane pane = new CheckboxPane( "Define Z-stacks", zStackGroup, helpButton );
+ CheckboxPane pane = new CheckboxPane( "Z-stacks", zStackGroup, helpButton );
enabledZStacks = pane.selectedProperty();
return pane;
}
private void addNewPosition( int zStart, int zEnd, double zStep ) {
SPIMSetup spimSetup = getSpimSetup();
+ InvalidationListener invalidationListener = observable -> computeTotalPositionImages();
+
if(spimSetup != null ) {
double r = spimSetup.getThetaStage().getPosition();
double x = spimSetup.getXStage().getPosition();
@@ -2164,13 +2179,13 @@ private void addNewPosition( int zStart, int zEnd, double zStep ) {
if( zStart < 0 && zEnd < 0 ) {
double z = spimSetup.getZStage().getPosition();
- positionItemTableView.getItems().add(new PositionItem(x, y, r, z, z, zStep));
+ positionItemTableView.getItems().add(new PositionItem(x, y, r, z, z, zStep, invalidationListener));
} else {
- positionItemTableView.getItems().add(new PositionItem(x, y, r, zStart, zEnd, zStep));
+ positionItemTableView.getItems().add(new PositionItem(x, y, r, zStart, zEnd, zStep, invalidationListener));
}
}
else {
- positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, zStart, zEnd, zStep ) );
+ positionItemTableView.getItems().add( new PositionItem( 10, 20, 30, zStart, zEnd, zStep, invalidationListener ) );
}
}
diff --git a/src/main/java/spim/ui/view/component/MMAcquisitionEngine.java b/src/main/java/spim/ui/view/component/MMAcquisitionEngine.java
index 7111cf26..0fe4b6ff 100644
--- a/src/main/java/spim/ui/view/component/MMAcquisitionEngine.java
+++ b/src/main/java/spim/ui/view/component/MMAcquisitionEngine.java
@@ -380,13 +380,15 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
if(toogleGroupValue.equals("Centre of mass")) {
driftCompMap.put(positionItem, new DefaultAntiDrift());
} else if(toogleGroupValue.equals("Phase correlation")) {
- driftCompMap.put(positionItem, new DefaultAntiDrift(10));
+ driftCompMap.put(positionItem, new DefaultAntiDrift(2));
}
}
}
AcqWrapperEngine engine = new AcqWrapperEngine( setup, frame, store, currentCamera, cameras, outFolder, acqFilenamePrefix, channelItems, arduinoSelected, processedImages, driftCompMap, adReferenceChannel, onTheFly);
+ SystemInfo.dumpMemoryStatusToLog(core);
+
mainLoop:
for(TimePointItem tpItem : timePointItems ) {
if(tpItem.getType().equals( TimePointItem.Type.Acq ))
@@ -398,8 +400,6 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
int step = 0;
- SystemInfo.dumpMemoryStatusToLog(core);
-
for ( PositionItem positionItem : positionItems )
{
final int tp = timePoints;
@@ -482,7 +482,7 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
}
core.logMessage("MMAcquisition started");
- System.out.println("MMAcquisition started");
+// System.out.println("MMAcquisition started");
engine.startAcquire( timePoints, step, positionItem );
while(engine.isAcquisitionRunning()) {
@@ -498,7 +498,7 @@ private void runNormalSmartImagingMMAcq(SPIMSetup setup, final Studio frame, Dat
}
core.logMessage("MMAcquisition finished");
- System.out.println("MMAcquisition finished");
+// System.out.println("MMAcquisition finished");
if(setup.getArduino1() != null)
setup.getArduino1().setSwitchState( "0" );
@@ -594,6 +594,8 @@ else if(tpItem.getType().equals( TimePointItem.Type.Wait ))
}
}
+ SystemInfo.dumpMemoryStatusToLog(core);
+
engine.exit();
store.freeze();
System.err.println("AcquisitionEngine exited.");
diff --git a/src/main/java/spim/ui/view/component/StagePanel.java b/src/main/java/spim/ui/view/component/StagePanel.java
index 141a57d5..5e7b951c 100644
--- a/src/main/java/spim/ui/view/component/StagePanel.java
+++ b/src/main/java/spim/ui/view/component/StagePanel.java
@@ -39,6 +39,7 @@
import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashMap;
+import java.util.Optional;
import java.util.concurrent.Executors;
import java.util.concurrent.ScheduledExecutorService;
import java.util.concurrent.TimeUnit;
@@ -431,10 +432,20 @@ private VBox createControls()
for(String str : stack.getList()) {
MenuItem newItem = new MenuItem( str );
String[] tokens = str.split( ":" );
- double r = Double.parseDouble( tokens[0] );
- double x = Double.parseDouble( tokens[1] );
- double y = Double.parseDouble( tokens[2] );
- double z = Double.parseDouble( tokens[3] );
+
+ double r, x, y, z;
+
+ if(tokens.length == 5) {
+ r = Double.parseDouble( tokens[1] );
+ x = Double.parseDouble( tokens[2] );
+ y = Double.parseDouble( tokens[3] );
+ z = Double.parseDouble( tokens[4] );
+ } else {
+ r = Double.parseDouble( tokens[0] );
+ x = Double.parseDouble( tokens[1] );
+ y = Double.parseDouble( tokens[2] );
+ z = Double.parseDouble( tokens[3] );
+ }
newItem.setOnAction( event -> {
stageUnitR.setCurrentPos(r);
@@ -473,11 +484,24 @@ private VBox createControls()
double y = stageUnitY.getCurrentValue();
double z = stageUnitZ.getCurrentValue();
- System.out.println(String.format( "Saved location - R: %.1f, X: %.1f, Y: %.1f, Z: %.1f",
- r, x, y, z));
+ // create a text input dialog
+ TextInputDialog td = new TextInputDialog("Enter name for position");
+ String returnedName = "";
+
+ // setHeaderText
+ td.setHeaderText("Enter the position name");
+
+ // show the dialog and wait for the name
+ Optional result = td.showAndWait();
+ if (result.isPresent()) {
+ returnedName = td.getEditor().getText().replace(":", "");
+ }
+
+ System.out.println(String.format( "Saved location - Name: %s, R: %.1f, X: %.1f, Y: %.1f, Z: %.1f",
+ returnedName, r, x, y, z));
- String newLocation = String.format( "%.1f:%.1f:%.1f:%.1f",
- r, x, y, z);
+ String newLocation = String.format( "%s:%.1f:%.1f:%.1f:%.1f",
+ returnedName, r, x, y, z);
stack.add( newLocation );
}
diff --git a/src/main/java/spim/ui/view/component/acquisition/AcqWrapperEngine.java b/src/main/java/spim/ui/view/component/acquisition/AcqWrapperEngine.java
index 022945df..8f0d2ef9 100644
--- a/src/main/java/spim/ui/view/component/acquisition/AcqWrapperEngine.java
+++ b/src/main/java/spim/ui/view/component/acquisition/AcqWrapperEngine.java
@@ -228,7 +228,7 @@ public AcqWrapperEngine(SPIMSetup setup, final Studio frame, Datastore store,
channels_ = channels;
setChannelGroup( channelGroupName );
- if ( outFolder != null ) {
+ if ( outFolder != null && acqFilenamePrefix != null ) {
File saveDir = new File(outFolder, acqFilenamePrefix + "-MIP");
if (!outFolder.exists() && !outFolder.mkdirs()) {
diff --git a/src/main/java/spim/ui/view/component/acquisition/TaggedImageSink.java b/src/main/java/spim/ui/view/component/acquisition/TaggedImageSink.java
index b47ce3e3..b2a5674b 100644
--- a/src/main/java/spim/ui/view/component/acquisition/TaggedImageSink.java
+++ b/src/main/java/spim/ui/view/component/acquisition/TaggedImageSink.java
@@ -134,7 +134,7 @@ public void run() {
if (tagged != null) {
if ( TaggedImageQueue.isPoison(tagged)) {
// Acquisition has ended. Clean up under "finally"
- System.out.println("IsPoison");
+// System.out.println("IsPoison");
break;
}
try {
diff --git a/src/main/java/spim/ui/view/component/util/StackPositionTableCell.java b/src/main/java/spim/ui/view/component/util/StackPositionTableCell.java
new file mode 100644
index 00000000..5e9a69fb
--- /dev/null
+++ b/src/main/java/spim/ui/view/component/util/StackPositionTableCell.java
@@ -0,0 +1,106 @@
+package spim.ui.view.component.util;
+
+import javafx.event.EventHandler;
+import javafx.scene.Node;
+import javafx.scene.control.Cell;
+import javafx.scene.control.TableCell;
+import javafx.scene.control.TableColumn;
+import javafx.scene.control.TableRow;
+import javafx.scene.control.cell.TextFieldTableCell;
+import javafx.scene.input.MouseEvent;
+import javafx.util.Callback;
+import javafx.util.StringConverter;
+import javafx.util.converter.DefaultStringConverter;
+import spim.model.data.PositionItem;
+
+/**
+ * Description: To render different color for "Position" type and "Stack" type for Position Item
+ *
+ * Author: HongKee Moon (moon@mpi-cbg.de), Scientific Computing Facility
+ * Organization: MPI-CBG Dresden
+ * Date: March 2022
+ */
+public class StackPositionTableCell extends TextFieldTableCell
+{
+ public static Callback, TableCell> forTableColumn() {
+ return forTableColumn(new DefaultStringConverter());
+ }
+
+ public static Callback, TableCell> forTableColumn(
+ final StringConverter converter) {
+ return list -> new StackPositionTableCell(converter);
+ }
+
+ static StackPositionTableCell lastCell;
+
+ StackPositionTableCell(StringConverter converter) {
+ super(converter);
+ this.addEventFilter( MouseEvent.MOUSE_CLICKED, new EventHandler() {
+ @Override
+ public void handle(MouseEvent event) {
+ if (event.getClickCount() > 1) {
+ StackPositionTableCell c = (StackPositionTableCell) event.getSource();
+ lastCell = c;
+ lastCell.startSuperStartEdit();
+ } else {
+ if (lastCell != null && !lastCell.equals(event.getSource())) {
+ lastCell.cancelEdit();
+ lastCell = null;
+ }
+ }
+ }
+ });
+ }
+
+ @Override public void startEdit() {
+ if (! isEditable()
+ || ! getTableView().isEditable()
+ || ! getTableColumn().isEditable()) {
+ return;
+ }
+ }
+
+ /** {@inheritDoc} */
+ @Override public void updateItem(T item, boolean empty) {
+ super.updateItem(item, empty);
+ this.updateItem(this, getConverter(), null);
+ }
+
+ void updateItem(final Cell cell,
+ final StringConverter converter,
+ final Node graphic) {
+ if (cell.isEmpty()) {
+ cell.setText(null);
+ cell.setGraphic(null);
+ setStyle( "" );
+ } else {
+ if (cell.isEditing()) {
+ cell.setText(null);
+ } else {
+ TableRow row = getTableRow();
+ T item = row.getItem();
+ if( item instanceof PositionItem) {
+ PositionItem tItem = ( PositionItem ) item;
+
+ if(tItem.getZStart() == tItem.getZEnd())
+ cell.setStyle( "-fx-background-color: -fx-background; -fx-background: #ffecea;" );
+ else
+ cell.setStyle( "-fx-background-color: -fx-background; -fx-background: #e0ffe4;" );
+ }
+
+ cell.setText(getItemText(cell, converter));
+ cell.setGraphic(graphic);
+ }
+ }
+ }
+
+ private String getItemText(Cell cell, StringConverter converter) {
+ return converter == null ?
+ cell.getItem() == null ? "" : cell.getItem().toString() :
+ converter.toString(cell.getItem());
+ }
+
+ void startSuperStartEdit() {
+ super.startEdit();
+ }
+}
\ No newline at end of file
diff --git a/src/main/java/spim/ui/view/component/util/TableViewUtil.java b/src/main/java/spim/ui/view/component/util/TableViewUtil.java
index 50c3fc4d..d6052fbf 100644
--- a/src/main/java/spim/ui/view/component/util/TableViewUtil.java
+++ b/src/main/java/spim/ui/view/component/util/TableViewUtil.java
@@ -2,9 +2,11 @@
import de.jensd.fx.glyphs.fontawesome.FontAwesomeIcon;
import de.jensd.fx.glyphs.fontawesome.FontAwesomeIconView;
+import javafx.beans.binding.Bindings;
import javafx.beans.property.ReadOnlyDoubleWrapper;
import javafx.beans.property.ReadOnlyIntegerWrapper;
import javafx.beans.property.ReadOnlyStringWrapper;
+import javafx.beans.value.ChangeListener;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
@@ -13,6 +15,7 @@
import javafx.event.EventHandler;
import javafx.geometry.Pos;
+import javafx.scene.Node;
import javafx.scene.control.Button;
import javafx.scene.control.ComboBox;
import javafx.scene.control.ContentDisplay;
@@ -26,6 +29,7 @@
import javafx.scene.control.cell.CheckBoxTableCell;
import javafx.scene.control.cell.ChoiceBoxTableCell;
import javafx.scene.control.cell.PropertyValueFactory;
+import javafx.scene.control.cell.TextFieldTableCell;
import javafx.scene.input.ClipboardContent;
import javafx.scene.input.DataFormat;
import javafx.scene.input.Dragboard;
@@ -118,6 +122,12 @@ public void handle(MouseEvent event) {
return cell;
}
};
+ TableColumn booleanColumn = new TableColumn<>("");
+ booleanColumn.setPrefWidth( 20 );
+ booleanColumn.setCellValueFactory( new PropertyValueFactory<>( "selected" ) );
+ booleanColumn.setCellFactory( tc -> new CheckBoxTableCell<>() );
+ booleanColumn.setOnEditCommit( event -> event.getRowValue().setSelected( event.getNewValue() ) );
+ tv.getColumns().add( booleanColumn );
TableColumn numberColumn = new TableColumn<>( "#" );
numberColumn.setPrefWidth( 20 );
@@ -150,7 +160,7 @@ public void handle(MouseEvent event) {
column.setCellValueFactory( (param) ->
new ReadOnlyStringWrapper( param.getValue().getZString() )
);
- column.setCellFactory( NumberFieldTableCell.forTableColumn() );
+ column.setCellFactory( StackPositionTableCell.forTableColumn() );
column.setOnEditCommit( event -> {
String zString = event.getNewValue();
String[] tokens = zString.split( "-" );
@@ -158,11 +168,14 @@ public void handle(MouseEvent event) {
if(tokens.length == 2) {
event.getRowValue().setZStart( Double.parseDouble( tokens[0] ) );
event.getRowValue().setZEnd( Double.parseDouble( tokens[1] ) );
+// event.getTableColumn().setStyle( "-fx-background-color: -fx-background; -fx-background: #e0ffe4;" );
} else if(tokens.length == 1) {
event.getRowValue().setZStart( Double.parseDouble( tokens[0] ) );
event.getRowValue().setZStep( 1 );
event.getRowValue().setZEnd( Double.parseDouble( tokens[0] ) );
+// event.getTableColumn().setStyle( "-fx-background-color: -fx-background; -fx-background: #ffecea;" );
}
+ event.getTableView().refresh();
// invoke selected item changed!
cascadeUpdatedValues( acquisitionPanel, tv );
@@ -193,6 +206,13 @@ public void handle(MouseEvent event) {
numberColumn.setEditable( true );
tv.getColumns().add(numberColumn);
+ TableColumn textColumn = new TableColumn<>("Name");
+ textColumn.setPrefWidth(100);
+ textColumn.setCellValueFactory( param -> param.getValue().getNameProperty() );
+ textColumn.setCellFactory( TextFieldTableCell.forTableColumn() );
+ textColumn.setOnEditCommit( event -> event.getRowValue().setName( event.getNewValue() ) );
+ tv.getColumns().add(textColumn);
+
TableColumn btnColumn = new TableColumn<>("");
btnColumn.setPrefWidth(130);
Callback, TableCell> cellFactory = new Callback, TableCell>() {
diff --git a/src/main/resource/spim/help/DefineZStacks.html b/src/main/resource/spim/help/DefineZStacks.html
index 0386e27b..f48b23a6 100644
--- a/src/main/resource/spim/help/DefineZStacks.html
+++ b/src/main/resource/spim/help/DefineZStacks.html
@@ -33,7 +33,7 @@
-
Define Z-stacks
+
Z-stacks
Here the beginning and the end of a new stack together with its Z step size can be specified using the Z stage. One has to first find the sample and a centre it in the field of view. By navigating through the sample along the z-axis the beginning and end of a z-stack is specified.
@@ -55,7 +55,7 @@
Define Z-stacks
It is possible to manually change any positional values by double-clicking on one of the positional entries. Note that this can be done during an ongoing imaging session.
-
New Z-stack
+
Define new Z-stack
Clicking this button will clear all previously locked Z-stack values in order to define a new Z-stack.
It is possible to manually change any positional values by double-clicking on one of the positional entries. Note that this can be done during an ongoing imaging session.