package org.janelia.saalfeldlab.paintera.ui.opendialog.menu.n5;
import com.pivovarit.function.ThrowingFunction;
import javafx.beans.binding.Bindings;
import javafx.beans.binding.BooleanBinding;
import javafx.beans.binding.ObjectBinding;
import javafx.beans.binding.StringBinding;
import javafx.beans.property.DoubleProperty;
import javafx.beans.property.ObjectProperty;
import javafx.beans.property.SimpleObjectProperty;
import javafx.beans.value.ObservableObjectValue;
import javafx.beans.value.ObservableValue;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.geometry.Insets;
import javafx.scene.control.Button;
import javafx.scene.control.ButtonType;
import javafx.scene.control.CustomMenuItem;
import javafx.scene.control.Dialog;
import javafx.scene.control.Label;
import javafx.scene.control.MenuButton;
import javafx.scene.control.TitledPane;
import javafx.scene.control.Tooltip;
import javafx.scene.effect.InnerShadow;
import javafx.scene.layout.GridPane;
import javafx.scene.layout.Priority;
import javafx.scene.layout.VBox;
import javafx.scene.paint.Color;
import net.imglib2.Volatile;
import net.imglib2.img.cell.CellGrid;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.IntegerType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.volatiles.AbstractVolatileRealType;
import net.imglib2.view.composite.RealComposite;
import org.janelia.saalfeldlab.fx.ui.Exceptions;
import org.janelia.saalfeldlab.fx.ui.MatchSelection;
import org.janelia.saalfeldlab.fx.util.InvokeOnJavaFXApplicationThread;
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.paintera.Paintera;
import org.janelia.saalfeldlab.paintera.PainteraBaseView;
import org.janelia.saalfeldlab.paintera.data.n5.VolatileWithSet;
import org.janelia.saalfeldlab.paintera.state.SourceState;
import org.janelia.saalfeldlab.paintera.ui.opendialog.CombinesErrorMessages;
import org.janelia.saalfeldlab.paintera.ui.opendialog.NameField;
import org.janelia.saalfeldlab.paintera.ui.opendialog.menu.OpenDialogMenuEntry;
import org.janelia.saalfeldlab.paintera.ui.opendialog.meta.MetaPanel;
import org.scijava.plugin.Plugin;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.lang.invoke.MethodHandles;
import java.util.Arrays;
import java.util.Collection;
import java.util.List;
import java.util.Optional;
import java.util.concurrent.ExecutorService;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
import java.util.function.Supplier;
import java.util.stream.Collectors;
public class N5OpenSourceDialog extends Dialog<GenericBackendDialogN5> implements CombinesErrorMessages {
private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
@Plugin(type = OpenDialogMenuEntry.class, menuPath = "_N5", priority = Double.MAX_VALUE)
public static class N5FSOpener implements OpenDialogMenuEntry {
private static final FileSystem fs = new FileSystem();
@Override
public BiConsumer<PainteraBaseView, Supplier<String>> onAction() {
return (pbv, projectDirectory) -> {
try (final GenericBackendDialogN5 dialog = fs.backendDialog(pbv.getPropagationQueue())) {
N5OpenSourceDialog osDialog = new N5OpenSourceDialog(pbv, dialog);
osDialog.setHeaderFromBackendType("N5");
Optional<GenericBackendDialogN5> backend = osDialog.showAndWait();
if (backend == null || !backend.isPresent())
return;
N5OpenSourceDialog.addSource(osDialog.getName(), osDialog.getType(), dialog, osDialog.getChannelSelection(), pbv, projectDirectory);
fs.containerAccepted();
} catch (Exception e1) {
LOG.debug("Unable to open n5 dataset", e1);
Exceptions.exceptionAlert(Paintera.Constants.NAME, "Unable to open N5 data set", e1).show();
}
};
}
}
@Plugin(type = OpenDialogMenuEntry.class, menuPath = "_HDF5", priority = Double.MAX_VALUE / 2.0)
public static class N5HDFOpener implements OpenDialogMenuEntry {
private static final HDF5 hdf5 = new HDF5();
@Override
public BiConsumer<PainteraBaseView, Supplier<String>> onAction() {
return (pbv, projectDirectory) -> {
try (final GenericBackendDialogN5 dialog = hdf5.backendDialog(pbv.getPropagationQueue())) {
N5OpenSourceDialog osDialog = new N5OpenSourceDialog(pbv, dialog);
osDialog.setHeaderFromBackendType("HDF5");
Optional<GenericBackendDialogN5> backend = osDialog.showAndWait();
if (backend == null || !backend.isPresent())
return;
N5OpenSourceDialog.addSource(osDialog.getName(), osDialog.getType(), dialog, osDialog.getChannelSelection(), pbv, projectDirectory);
hdf5.containerAccepted();
} catch (Exception e1) {
LOG.debug("Unable to open hdf5 dataset", e1);
Exceptions.exceptionAlert(Paintera.Constants.NAME, "Unable to open HDF5 data set", e1).show();
}
};
}
}
@Plugin(type = OpenDialogMenuEntry.class, menuPath= "_Google Cloud", priority = Double.MAX_VALUE / 4.0)
public static class GoogleCloudOpener implements OpenDialogMenuEntry {
@Override
public BiConsumer<PainteraBaseView, Supplier<String>> onAction() {
return (pbv, projectDirectory) -> {
try {
final GoogleCloud googleCloud = new GoogleCloud();
try (final GenericBackendDialogN5 dialog = googleCloud.backendDialog(pbv.getPropagationQueue())) {
final N5OpenSourceDialog osDialog = new N5OpenSourceDialog(pbv, dialog);
osDialog.setHeaderFromBackendType("Google Cloud");
Optional<GenericBackendDialogN5> backend = osDialog.showAndWait();
if (backend == null || !backend.isPresent())
return;
N5OpenSourceDialog.addSource(osDialog.getName(), osDialog.getType(), dialog, osDialog.getChannelSelection(), pbv, projectDirectory);
}
} catch (Exception e1) {
LOG.debug("Unable to open google cloud dataset", e1);
Exceptions.exceptionAlert(Paintera.Constants.NAME, "Unable to open Google Cloud data set", e1).show();
}
};
}
}
private final VBox dialogContent;
private final GridPane grid;
private final MenuButton typeChoiceButton;
private final ObjectProperty<MetaPanel.TYPE> typeChoice = new SimpleObjectProperty<>(MetaPanel.TYPE.LABEL);
private final Label errorMessage;
private final TitledPane errorInfo;
private final ObservableList<MetaPanel.TYPE> typeChoices = FXCollections.observableArrayList(MetaPanel.TYPE.values());
private final NameField nameField = new NameField(
"Source name",
"Specify source name (required)",
new InnerShadow(10, Color.ORANGE)
);
private final BooleanBinding isError;
private final ExecutorService propagationExecutor;
private final GenericBackendDialogN5 backendDialog;
private final MetaPanel metaPanel = new MetaPanel();
public N5OpenSourceDialog(final PainteraBaseView viewer, final GenericBackendDialogN5 backendDialog) {
super();
this.backendDialog = backendDialog;
this.metaPanel.listenOnDimensions(backendDialog.dimensionsProperty());
this.propagationExecutor = viewer.getPropagationQueue();
this.setTitle("Open data set");
this.getDialogPane().getButtonTypes().addAll(ButtonType.CANCEL, ButtonType.OK);
((Button)this.getDialogPane().lookupButton(ButtonType.CANCEL)).setText("_Cancel");
((Button)this.getDialogPane().lookupButton(ButtonType.OK)).setText("_OK");
this.errorMessage = new Label("");
this.errorInfo = new TitledPane("", errorMessage);
this.isError = Bindings.createBooleanBinding(() -> Optional.ofNullable(this.errorMessage.textProperty().get())
.orElse(
"").length() > 0, this.errorMessage.textProperty());
errorInfo.textProperty().bind(Bindings.createStringBinding(
() -> this.isError.get() ? "ERROR" : "",
this.isError
));
this.getDialogPane().lookupButton(ButtonType.OK).disableProperty().bind(this.isError);
this.errorInfo.visibleProperty().bind(this.isError);
final Tooltip revertAxisTooltip = new Tooltip("If you data is using `zyx` you should revert it.");
this.grid = new GridPane();
this.nameField.errorMessageProperty().addListener((obs, oldv, newv) -> combineErrorMessages());
this.dialogContent = new VBox(10, nameField.textField(), grid, metaPanel.getPane(), errorInfo);
this.setResizable(true);
GridPane.setMargin(this.backendDialog.getDialogNode(), new Insets(0, 0, 0, 30));
this.grid.add(this.backendDialog.getDialogNode(), 1, 0);
GridPane.setHgrow(this.backendDialog.getDialogNode(), Priority.ALWAYS);
this.getDialogPane().setContent(dialogContent);
final VBox choices = new VBox();
this.typeChoiceButton = new MenuButton("_Type");
List<String> typeChoicesString = typeChoices.stream().map(Enum::name).collect(Collectors.toList());
final StringBinding typeChoiceButtonText = Bindings.createStringBinding(() -> typeChoice.get() == null ? "_Type" : "_Type: " + typeChoice.get(), typeChoice);
final ObjectBinding<Tooltip> datasetDropDownTooltip = Bindings.createObjectBinding(() -> Optional.ofNullable(typeChoice.get()).map(t -> "Type of the dataset: " + t).map(Tooltip::new).orElse(null), typeChoice);
typeChoiceButton.tooltipProperty().bind(datasetDropDownTooltip);
typeChoiceButton.textProperty().bind(typeChoiceButtonText);
final MatchSelection matcher = MatchSelection.fuzzySorted(typeChoicesString, s -> {
typeChoice.set(MetaPanel.TYPE.valueOf(s));
typeChoiceButton.hide();
});
// clear style to avoid weird blue highlight
final CustomMenuItem cmi = new CustomMenuItem(matcher, false);
cmi.getStyleClass().clear();
typeChoiceButton.getItems().setAll(cmi);
typeChoiceButton.setOnAction(e -> {typeChoiceButton.show(); matcher.requestFocus();});
this.metaPanel.bindDataTypeTo(this.typeChoice);
backendDialog.datsetAttributesProperty().addListener((obs, oldv, newv) -> Optional
.ofNullable(newv)
.map(ThrowingFunction.unchecked(this::updateType))
.ifPresent(this.typeChoice::set));
final ObservableObjectValue<DatasetAttributes> attributesProperty = backendDialog.datsetAttributesProperty();
final ObjectBinding<long[]> dimensionsProperty = Bindings.createObjectBinding(() -> attributesProperty.get().getDimensions().clone(), attributesProperty);
final DoubleProperty[] res = backendDialog.resolution();
final DoubleProperty[] off = backendDialog.offset();
this.metaPanel.listenOnResolution(res[0], res[1], res[2]);
this.metaPanel.listenOnOffset(off[0], off[1], off[2]);
this.metaPanel.listenOnMinMax(backendDialog.min(), backendDialog.max());
backendDialog.errorMessage().addListener((obs, oldErr, newErr) -> combineErrorMessages());
backendDialog.nameProperty().addListener((obs, oldName, newName) -> Optional.ofNullable(newName).ifPresent(nameField.textField().textProperty()::set));
combineErrorMessages();
Optional.ofNullable(backendDialog.nameProperty().get()).ifPresent(nameField.textField()::setText);
metaPanel.listenOnResolution(backendDialog.resolution()[0], backendDialog.resolution()[1], backendDialog.resolution()[2]);
metaPanel.getRevertButton().setOnAction(event -> {
backendDialog.setResolution(revert(metaPanel.getResolution()));
backendDialog.setOffset(revert(metaPanel.getOffset()));
});
this.typeChoice.setValue(typeChoices.get(0));
this.typeChoiceButton.setMinWidth(100);
choices.getChildren().addAll(this.typeChoiceButton);
this.grid.add(choices, 0, 0);
this.setResultConverter(button -> button.equals(ButtonType.OK) ? backendDialog : null);
combineErrorMessages();
setTitle(Paintera.Constants.NAME);
}
public MetaPanel.TYPE getType() {
return typeChoice.getValue();
}
public int[] getChannelSelection() { return metaPanel.channelInformation().getChannelSelectionCopy(); }
public String getName() {
return nameField.getText();
}
public MetaPanel getMeta() {
return this.metaPanel;
}
@Override
public Collection<ObservableValue<String>> errorMessages() {
return Arrays.asList(this.nameField.errorMessageProperty(), getBackend().errorMessage());
}
@Override
public Consumer<Collection<String>> combiner() {
return strings -> InvokeOnJavaFXApplicationThread.invoke(() -> this.errorMessage.setText(String.join(
"\n",
strings
)));
}
private GenericBackendDialogN5 getBackend() {
return this.backendDialog;
}
private static final double[] revert(final double[] array) {
final double[] reverted = new double[array.length];
for (int i = 0; i < array.length; ++i) {
reverted[i] = array[array.length - 1 - i];
}
return reverted;
}
private static void addSource(
final String name,
final MetaPanel.TYPE type,
final GenericBackendDialogN5 dataset,
final int[] channelSelection,
final PainteraBaseView viewer,
final Supplier<String> projectDirectory) throws Exception {
LOG.debug("Type={}", type);
switch (type) {
case RAW:
LOG.trace("Adding raw data");
addRaw(name, channelSelection, dataset, viewer);
break;
case LABEL:
addLabel(name, dataset, viewer, projectDirectory);
break;
default:
break;
}
}
private static <T extends RealType<T> & NativeType<T>, V extends AbstractVolatileRealType<T, V> & NativeType<V>> void
addRaw(
final String name,
final int[] channelSelection,
final GenericBackendDialogN5 dataset,
PainteraBaseView viewer) throws Exception {
final DatasetAttributes attributes = dataset.getAttributes();
if (attributes.getNumDimensions() == 4)
{
LOG.debug("4-dimensional data, assuming channel index at {}", 3);
final List<? extends SourceState<RealComposite<T>, VolatileWithSet<RealComposite<V>>>> channels = dataset.getChannels(
name,
channelSelection,
viewer.getQueue(),
viewer.getQueue().getNumPriorities() - 1);
LOG.debug("Got {} channel sources", channels.size());
InvokeOnJavaFXApplicationThread.invoke(() -> channels.forEach(viewer::addState));
LOG.debug("Added {} channel sources", channels.size());
}
else {
final SourceState<T, V> raw = dataset.getRaw(name, viewer.getQueue(), viewer.getQueue().getNumPriorities() - 1);
LOG.debug("Got raw: {}", raw);
InvokeOnJavaFXApplicationThread.invoke(() -> viewer.addState(raw));
}
}
private static <D extends NativeType<D> & IntegerType<D>, T extends Volatile<D> & NativeType<T>> void addLabel(
final String name,
final GenericBackendDialogN5 dataset,
final PainteraBaseView viewer,
final Supplier<String> projectDirectory) throws Exception {
final DatasetAttributes attributes = dataset.getAttributes();
if (attributes.getNumDimensions() > 3)
throw new Exception("Only 3D label data supported but got " + attributes.getNumDimensions() + " dimensions.");
final SourceState<D, T> rep = dataset.getLabels(
name,
viewer.getQueue(),
viewer.getQueue().getNumPriorities() - 1,
viewer.viewer3D().meshesGroup(),
viewer.viewer3D().viewFrustumProperty(),
viewer.viewer3D().eyeToWorldTransformProperty(),
viewer.getMeshManagerExecutorService(),
viewer.getMeshWorkerExecutorService(),
viewer.getPropagationQueue(),
projectDirectory
);
InvokeOnJavaFXApplicationThread.invoke(() -> viewer.addState(rep));
}
private static int[] blockSize(final CellGrid grid) {
final int[] blockSize = new int[grid.numDimensions()];
Arrays.setAll(blockSize, grid::cellDimension);
return blockSize;
}
public void setHeaderFromBackendType(String backendType)
{
this.setHeaderText(String.format("Open %s dataset", backendType));
}
private MetaPanel.TYPE updateType(final DatasetAttributes attributes) throws Exception {
if (attributes == null)
return null;
if (this.backendDialog.isLabelMultisetType()) {
return MetaPanel.TYPE.LABEL;
}
switch (attributes.getDataType()) {
case UINT64:
case UINT32:
case INT64:
return MetaPanel.TYPE.LABEL;
default:
return MetaPanel.TYPE.RAW;
}
}
}
