Code cleanup

src/main/java/sc/fiji/snt/gui/DemoRunner.java

@@ -240,8 +240,8 @@ public ImagePlus getImage() {
 			public void load() {
 				super.load();
 				// apply tags
-				ui.getPathManager().runCommand("Traced Channel");
-				ui.getPathManager().runCommand("Traced Frame");
+				ui.getPathManager().applyDefaultTags("Traced Channel");
+				ui.getPathManager().applyDefaultTags("Traced Frame");
 			}
 		};
 		entry.summary = "Downloads a Drosophila S2 cell undergoing mitosis in which K-fibers were traced during anaphase.";

src/main/java/sc/fiji/snt/gui/FileChooser.java

@@ -0,0 +1,302 @@
+/*-
+ * #%L
+ * Fiji distribution of ImageJ for the life sciences.
+ * %%
+ * Copyright (C) 2010 - 2023 Fiji developers.
+ * %%
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public
+ * License along with this program.  If not, see
+ * <http://www.gnu.org/licenses/gpl-3.0.html>.
+ * #L%
+ */
+
+package sc.fiji.snt.gui;
+
+import java.awt.BasicStroke;
+import java.awt.Component;
+import java.awt.Desktop;
+import java.awt.Graphics2D;
+import java.awt.Insets;
+import java.awt.RenderingHints;
+import java.awt.geom.Area;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Line2D;
+import java.awt.geom.Path2D;
+import java.awt.geom.Rectangle2D;
+import java.awt.geom.RoundRectangle2D;
+import java.io.File;
+import java.io.IOException;
+
+import javax.swing.AbstractButton;
+import javax.swing.BoxLayout;
+import javax.swing.JButton;
+import javax.swing.JFileChooser;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JToggleButton;
+import javax.swing.UIManager;
+import javax.swing.filechooser.FileFilter;
+
+import com.formdev.flatlaf.FlatClientProperties;
+import com.formdev.flatlaf.icons.FlatAbstractIcon;
+import com.formdev.flatlaf.ui.FlatUIUtils;
+import com.formdev.flatlaf.util.SystemInfo;
+
+/**
+ * Improvements to JFileChooser, namely:
+ * <ul>
+ * <li>Confirmation dialog when overriding files</li>
+ * <li>Accessory panel with FlatLaf buttons to:</li>
+ * <ul>
+ * <li>Toggle visibility of hidden files</li>
+ * <li>Filter file list by custom pattern</li>
+ * <li>Reveal contents in native file explorer</li>
+ * </ul>
+ * </ul>
+ * Other fixes (current directory always the root folder on linux) and tweaks
+ * (drag & drop, etc.) are provided by GuiUtils to keep dependencies to a
+ * minimum. TODO: submit this upstream porting to SciJava
+ */
+public class FileChooser extends JFileChooser {
+
+	private static final long serialVersionUID = 9398079702362074L;
+	private JToggleButton toggleHiddenFilesButton;
+	private String userFilterPattern;
+
+	public FileChooser() {
+		setAcceptAllFileFilterUsed(true);
+		attachAccessoryPanel();
+	}
+
+	@Override
+	public void setFileHidingEnabled(final boolean b) {
+		if (toggleHiddenFilesButton != null)
+			toggleHiddenFilesButton.setSelected(!b);
+		super.setFileHidingEnabled(b);
+	}
+
+	@Override
+	public void approveSelection() {
+		final File f = getSelectedFile();
+		if (f.exists() && getDialogType() == SAVE_DIALOG) {
+			final int result = JOptionPane.showConfirmDialog(this,
+					String.format("%s already exists.%nOverwrite?", f.getName()), "Override File?",
+					JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE);
+			switch (result) {
+			case JOptionPane.YES_OPTION:
+				super.approveSelection();
+				return;
+			case JOptionPane.CANCEL_OPTION:
+				cancelSelection();
+				return;
+			default:
+				return;
+			}
+		}
+		super.approveSelection();
+	}
+
+	private void attachAccessoryPanel() {
+		final JPanel panel = new JPanel();
+		panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
+		toggleHiddenFilesButton = new JToggleButton(new HiddenFilesIcon());
+		toggleHiddenFilesButton.setToolTipText("Toggle visibility of hidden files");
+		panel.add(toggleHiddenFilesButton);
+		toggleHiddenFilesButton.addItemListener(e -> setFileHidingEnabled(!toggleHiddenFilesButton.isSelected()));
+		final JButton rescanButton = new JButton(new ReloadFilesIcon());
+		rescanButton.setToolTipText("Refresh contents");
+		rescanButton.addActionListener(e -> rescanCurrentDirectory());
+		panel.add(rescanButton);
+		final JButton filterButton = new JButton(new FilterFilesIcon());
+		filterButton.setToolTipText("Filter current file list");
+		filterButton.addActionListener(e -> applyFilterPattern());
+		panel.add(filterButton);
+		final JButton revealButton = new JButton(new RevealFilesIcon());
+		revealButton.setToolTipText("Show current directory in native file explorer");
+		revealButton.addActionListener(e -> {
+			final File f = (getSelectedFile() == null || isMultiSelectionEnabled()) ? getCurrentDirectory()
+					: getSelectedFile();
+			reveal(f);
+		});
+		panel.add(revealButton);
+		mod(toggleHiddenFilesButton, rescanButton, filterButton, revealButton);
+		setAccessory(panel);
+	}
+
+	private void mod(final AbstractButton... buttons) {
+		// as per FlatFileChooser.* icons
+		final Insets margin = UIManager.getInsets("Button.margin");
+		for (final AbstractButton b : buttons) {
+			b.putClientProperty(FlatClientProperties.BUTTON_TYPE, FlatClientProperties.BUTTON_TYPE_TOOLBAR_BUTTON);
+			b.setMargin(margin);
+			b.setFocusable(false);
+		}
+	}
+
+	private void applyFilterPattern() {
+		if (userFilterPattern == null)
+			userFilterPattern = "";
+		final String result = (String) JOptionPane.showInputDialog(this, "Only show filenames containing:",
+				"Filter by Pattern", JOptionPane.PLAIN_MESSAGE, null, null, userFilterPattern);
+		if (result != null && !result.isEmpty()) {
+			userFilterPattern = result;
+			final FileFilter filter = new FileNamePatternFilter(userFilterPattern);
+			addChoosableFileFilter(filter);
+			setFileFilter(filter);
+		}
+	}
+
+	private void error(final String msg) {
+		JOptionPane.showMessageDialog(this, msg, "Error", JOptionPane.ERROR_MESSAGE);
+	}
+
+	private void fileNotAccessibleError(final File dir) {
+		if (dir == null)
+			error("Directory does not seem to be accessible.");
+		else
+			error("Could not access\n" + dir.getAbsolutePath());
+	}
+
+	protected void reveal(final File file) {
+		if (file == null) {
+			fileNotAccessibleError(file);
+			return;
+		}
+		final File dir = (file.isDirectory()) ? file : file.getParentFile();
+		try {
+			Desktop.getDesktop().open(dir); // TODO: Move to java9: Desktop.getDesktop().browseFileDirectory(file);
+		} catch (final UnsupportedOperationException ue) {
+			if (SystemInfo.isLinux)
+				try {
+					Runtime.getRuntime().exec(new String[] { "xdg-open", dir.getAbsolutePath() });
+				} catch (final Exception ignored) {
+					fileNotAccessibleError(dir);
+				}
+		} catch (final NullPointerException | IllegalArgumentException | IOException iae) {
+			fileNotAccessibleError(dir);
+		}
+	}
+
+	private static class FileNamePatternFilter extends FileFilter {
+		final String pattern;
+
+		FileNamePatternFilter(final String pattern) {
+			this.pattern = pattern;
+		}
+
+		@Override
+		public boolean accept(final File f) {
+			return f.getName().contains(pattern);
+		}
+
+		@Override
+		public String getDescription() {
+			return "Files and Folders containing '" + pattern + "'";
+		}
+
+	}
+
+	/* Icon definitions, mostly duplicated from FlatLaf */
+	private static class RevealFilesIcon extends FlatAbstractIcon {
+
+		public RevealFilesIcon() {
+			// from FlatFileChooser.* icons
+			super(16, 16, UIManager.getColor("Actions.Grey"));
+		}
+
+		void prepGraphics(final Graphics2D g) {
+			// from FlatFileViewComputerIcon
+			g.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, RenderingHints.VALUE_STROKE_PURE);
+			g.setStroke(new BasicStroke(1, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
+		}
+
+		@Override
+		protected void paintIcon(final Component c, final Graphics2D g) {
+			prepGraphics(g);
+			// from FlatFileViewComputerIcon
+			g.draw(new RoundRectangle2D.Float(2.5f, 3.5f, 11, 7, 2, 2));
+			g.drawLine(8, 11, 8, 12);
+			g.draw(new Line2D.Float(4.5f, 12.5f, 11.5f, 12.5f));
+		}
+	}
+
+	private static class HiddenFilesIcon extends RevealFilesIcon {
+
+		@Override
+		protected void paintIcon(final Component c, final Graphics2D g) {
+			prepGraphics(g);
+			// from FlatRevealIcon
+			final Path2D path = new Path2D.Float(Path2D.WIND_EVEN_ODD);
+			path.append(new Ellipse2D.Float(5.15f, 6.15f, 5.7f, 5.7f), false);
+			path.append(new Ellipse2D.Float(6, 7, 4, 4), false);
+			g.fill(path);
+			final Path2D path2 = new Path2D.Float(Path2D.WIND_EVEN_ODD);
+			path2.append(new Ellipse2D.Float(2.15f, 4.15f, 11.7f, 11.7f), false);
+			path2.append(new Ellipse2D.Float(3, 5, 10, 10), false);
+			final Area area = new Area(path2);
+			area.subtract(new Area(new Rectangle2D.Float(0, 9.5f, 16, 16)));
+			g.fill(area);
+		}
+	}
+
+	private static class FilterFilesIcon extends RevealFilesIcon {
+		private Area area;
+
+		@Override
+		protected void paintIcon(final Component c, final Graphics2D g) {
+			prepGraphics(g);
+			// from FlatSearchIcon
+			if (area == null) {
+				area = new Area(new Ellipse2D.Float(2, 2, 10, 10));
+				area.subtract(new Area(new Ellipse2D.Float(3, 3, 8, 8)));
+				area.add(new Area(FlatUIUtils.createPath(10.813, 9.75, 14, 12.938, 12.938, 14, 9.75, 10.813)));
+			}
+			g.fill(area);
+		}
+	}
+
+	private static class ReloadFilesIcon extends RevealFilesIcon {
+
+		@Override
+		protected void paintIcon(final Component c, final Graphics2D g) {
+			g.setRenderingHint(RenderingHints.KEY_STROKE_CONTROL, RenderingHints.VALUE_STROKE_PURE);
+			g.setStroke(new BasicStroke(0f, BasicStroke.CAP_ROUND, BasicStroke.JOIN_ROUND));
+			// converted from FlatLaf /demo/icons/refresh.svg (16px viewBox) scaled to 14px
+			final Path2D p = new Path2D.Float();
+			p.moveTo(10.820312, 10.605469);
+			p.curveTo(9.796875, 11.6875, 8.328125, 12.332031, 6.722656, 12.246094);
+			p.curveTo(4.136719, 12.109375, 2.085938, 10.125, 1.785156, 7.640625);
+			p.lineTo(3.410156, 7.78125);
+			p.curveTo(3.75, 9.363281, 5.117188, 10.582031, 6.808594, 10.671875);
+			p.curveTo(7.945312, 10.730469, 8.988281, 10.265625, 9.703125, 9.488281);
+			p.lineTo(7.886719, 7.667969);
+			p.lineTo(12.261719, 7.667969);
+			p.lineTo(12.261719, 12.042969);
+			p.closePath();
+			g.fill(p);
+			p.moveTo(3.183594, 3.398438);
+			p.curveTo(4.203125, 2.320312, 5.671875, 1.675781, 7.273438, 1.761719);
+			p.curveTo(9.824219, 1.894531, 11.855469, 3.828125, 12.199219, 6.265625);
+			p.lineTo(10.570312, 6.125);
+			p.curveTo(10.195312, 4.589844, 8.851562, 3.417969, 7.191406, 3.328125);
+			p.curveTo(6.054688, 3.269531, 5.011719, 3.734375, 4.296875, 4.511719);
+			p.lineTo(6.121094, 6.335938);
+			p.lineTo(1.746094, 6.335938);
+			p.lineTo(1.746094, 1.960938);
+			p.lineTo(3.183594, 3.398438);
+			p.closePath();
+			g.fill(p);
+		}
+	}
+
+}