package org.janelia.saalfeldlab.paintera.ui.dialogs.create;
import bdv.util.volatiles.SharedQueue;
import bdv.viewer.Source;
import com.sun.javafx.application.PlatformImpl;
import javafx.application.Platform;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.IntegerProperty;
import javafx.beans.property.LongProperty;
import javafx.beans.property.StringProperty;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.event.ActionEvent;
import javafx.scene.Node;
import javafx.scene.Scene;
import javafx.scene.control.Alert;
import javafx.scene.control.Button;
import javafx.scene.control.ButtonType;
import javafx.scene.control.Menu;
import javafx.scene.control.MenuButton;
import javafx.scene.control.MenuItem;
import javafx.scene.control.TextField;
import javafx.scene.control.TitledPane;
import javafx.scene.layout.HBox;
import javafx.scene.layout.Priority;
import javafx.scene.layout.Region;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;
import javafx.util.Pair;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.img.cell.AbstractCellImg;
import net.imglib2.img.cell.CellGrid;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.volatiles.VolatileUnsignedByteType;
import org.janelia.saalfeldlab.fx.ui.DirectoryField;
import org.janelia.saalfeldlab.fx.ui.Exceptions;
import org.janelia.saalfeldlab.fx.ui.NamedNode;
import org.janelia.saalfeldlab.fx.ui.ObjectField;
import org.janelia.saalfeldlab.fx.ui.SpatialField;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.paintera.Paintera;
import org.janelia.saalfeldlab.paintera.data.DataSource;
import org.janelia.saalfeldlab.paintera.data.n5.N5DataSource;
import org.janelia.saalfeldlab.paintera.data.n5.N5FSMeta;
import org.janelia.saalfeldlab.paintera.data.n5.ReflectionException;
import org.janelia.saalfeldlab.paintera.state.SourceState;
import org.janelia.saalfeldlab.paintera.ui.PainteraAlerts;
import org.janelia.saalfeldlab.util.n5.N5Data;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.lang.invoke.MethodHandles;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
public class CreateDataset
{
private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
private static final double NAME_WIDTH = 150;
private final Source<?> currentSource;
private final List<SourceState<?, ?>> allSources;
private final ObservableList<MipMapLevel> mipmapLevels = FXCollections.observableArrayList();
private final Node mipmapLevelsNode = MipMapLevel.makeNode(
mipmapLevels,
100,
NAME_WIDTH,
30,
ObjectField.SubmitOn.values());
private final MenuItem populateFromCurrentSource = new MenuItem("_From Current Source");
private final Menu populateFromSource = new Menu("_Select Source");
private final MenuButton setFromButton = new MenuButton("_Populate", null, populateFromSource, populateFromCurrentSource);
private final HBox setFromCurrentBox = new HBox(new Region(), setFromButton);
{
HBox.setHgrow(setFromCurrentBox.getChildren().get(0), Priority.ALWAYS);
populateFromCurrentSource.setOnAction(e -> {
e.consume();
this.populateFrom(currentSource());
});
}
private final TextField name = new TextField();
{
name.setMaxWidth(Double.MAX_VALUE);
}
private final DirectoryField n5Container = new DirectoryField(System.getProperty("user.home"), 100);
private final ObjectField<String, StringProperty> dataset = ObjectField.stringField(
"",
ObjectField.SubmitOn.values());
{
dataset.valueProperty().addListener((obs, oldv, newv) -> {
if (newv != null && Optional.ofNullable(name.textProperty().get()).orElse("").equals(""))
{
final String[] split = newv.split("/");
name.setText(split[split.length - 1]);
}
});
}
private final SpatialField<LongProperty> dimensions = SpatialField.longField(
1,
d -> d > 0,
100,
ObjectField.SubmitOn.values());
private final SpatialField<IntegerProperty> blockSize = SpatialField.intField(
1,
d -> d > 0,
100,
ObjectField.SubmitOn.values());
private final SpatialField<DoubleProperty> resolution = SpatialField.doubleField(
1.0,
r -> r > 0,
100,
ObjectField.SubmitOn.values());
private final SpatialField<DoubleProperty> offset = SpatialField.doubleField(
0.0,
o -> true,
100,
ObjectField.SubmitOn.values());
private final TitledPane scaleLevels = new TitledPane("Scale Levels", mipmapLevelsNode);
private final VBox pane = new VBox(
NamedNode.nameIt("Name", NAME_WIDTH, true, name),
NamedNode.nameIt("N5", NAME_WIDTH, true, n5Container.asNode()),
NamedNode.nameIt("Dataset", NAME_WIDTH, true, dataset.textField()),
NamedNode.nameIt("Dimensions", NAME_WIDTH, false, NamedNode.bufferNode(new Region()),
dimensions.getNode()
),
NamedNode.nameIt("Block Size", NAME_WIDTH, false, NamedNode.bufferNode(new Region()), blockSize.getNode()),
NamedNode.nameIt("Resolution", NAME_WIDTH, false, NamedNode.bufferNode(new Region()),
resolution.getNode()
),
NamedNode.nameIt("Offset", NAME_WIDTH, false, NamedNode.bufferNode(new Region()), offset.getNode()),
setFromCurrentBox,
scaleLevels
);
public CreateDataset(
Source<?> currentSource,
SourceState<?, ?>... allSources)
{
this(currentSource, Arrays.asList(allSources));
}
public CreateDataset(
Source<?> currentSource,
Collection<SourceState<?, ?>> allSources)
{
this.currentSource = currentSource;
this.allSources = new ArrayList<>(allSources);
this.allSources.forEach(s -> {
final MenuItem mi = new MenuItem(s.nameProperty().get());
mi.setOnAction(e -> this.populateFrom(s.getDataSource()));
mi.setMnemonicParsing(false);
this.populateFromSource.getItems().add(mi);
});
this.populateFromSource.setVisible(this.allSources.size() > 0);
Optional.ofNullable(currentSource).ifPresent(this::populateFrom);
}
public Optional<Pair<N5FSMeta, String>> showDialog()
{
final Alert alert = PainteraAlerts.confirmation("C_reate", "_Cancel", true);
alert.setHeaderText("Create new Label dataset");
alert.getDialogPane().setContent(this.pane);
alert.getDialogPane().lookupButton(ButtonType.OK).addEventFilter(
ActionEvent.ACTION,
e -> {
final String container = this.n5Container.directoryProperty().getValue().getAbsolutePath();
final String dataset = this.dataset.valueProperty().get();
final String name = this.name.getText();
try
{
LOG.debug("Trying to create empty label dataset `{}' in container `{}'", dataset, container);
if (dataset == null || dataset.equals(""))
throw new IOException("Dataset not specified!");
if (name == null || name.equals(""))
throw new IOException("Name not specified!");
N5Data.createEmptyLabelDataset(
container,
dataset,
dimensions.getAs(new long[3]),
blockSize.getAs(new int[3]),
resolution.getAs(new double[3]),
offset.getAs(new double[3]),
mipmapLevels.stream().map(MipMapLevel::downsamplingFactors).toArray(double[][]::new),
mipmapLevels.stream().mapToInt(MipMapLevel::maxNumEntries).toArray()
);
} catch (IOException ex)
{
LOG.error("Unable to create empty dataset", ex);
e.consume();
Alert exceptionAlert = Exceptions.exceptionAlert(
Paintera.Constants.NAME,
"Unable to create new dataset: " + ex.getMessage(),
ex
);
exceptionAlert.show();
}
});
final Optional<ButtonType> button = alert.showAndWait();
final String container = this.n5Container.directoryProperty().getValue().getAbsolutePath();
final String dataset = this.dataset.valueProperty().get();
final String name = this.name.getText();
return button.filter( ButtonType.OK::equals ).map( bt -> new Pair<>(new N5FSMeta(container, dataset), name));
}
private Source<?> currentSource()
{
return this.currentSource;
}
private void populateFrom(Source<?> source)
{
if (source == null)
return;
if (source instanceof N5DataSource<?, ?>)
{
N5DataSource<?, ?> n5s = (N5DataSource<?, ?>) source;
if (n5s.meta() instanceof N5FSMeta)
{
n5Container.directoryProperty().setValue(new File(((N5FSMeta) n5s.meta()).basePath()));
}
}
final RandomAccessibleInterval<?> data = source.getSource(0, 0);
this.dimensions.getX().valueProperty().set(data.dimension(0));
this.dimensions.getY().valueProperty().set(data.dimension(1));
this.dimensions.getZ().valueProperty().set(data.dimension(2));
if (data instanceof AbstractCellImg<?, ?, ?, ?>)
{
final CellGrid grid = ((AbstractCellImg<?, ?, ?, ?>) data).getCellGrid();
this.blockSize.getX().valueProperty().set(grid.cellDimension(0));
this.blockSize.getY().valueProperty().set(grid.cellDimension(1));
this.blockSize.getZ().valueProperty().set(grid.cellDimension(2));
}
AffineTransform3D transform = new AffineTransform3D();
source.getSourceTransform(0, 0, transform);
this.resolution.getX().valueProperty().set(transform.get(0, 0));
this.resolution.getY().valueProperty().set(transform.get(1, 1));
this.resolution.getZ().valueProperty().set(transform.get(2, 2));
this.offset.getX().valueProperty().set(transform.get(0, 3));
this.offset.getY().valueProperty().set(transform.get(1, 3));
this.offset.getZ().valueProperty().set(transform.get(2, 3));
}
public static void main(String[] args) throws IOException, ReflectionException {
PlatformImpl.startup(() -> {
});
final AffineTransform3D tf = new AffineTransform3D();
tf.set(
4.0, 0.0, 0.0, 1.0,
0.0, 5.0, 0.0, 5.0,
0.0, 0.0, 40., -1.
);
final N5Reader reader = new N5FSReader(
"/home/phil/local/tmp/sample_a_padded_20160501.n5");
final DataSource<UnsignedByteType, VolatileUnsignedByteType> raw = N5Data.openRawAsSource(
reader,
"volumes/raw/data/s0",
tf,
new SharedQueue(1, 20),
1,
"NAME"
);
final CreateDataset cd = new CreateDataset(raw);
Platform.runLater(() -> {
final Button b = new Button("BUTTON");
b.setOnAction(e -> LOG.info( "Got new dataset meta: {}", cd.showDialog()));
final Scene scene = new Scene(b);
final Stage stage = new Stage();
stage.setScene(scene);
stage.show();
});
}
}
