MarsOpenN5asImagePlusCommand: WIP creation commit

src/main/java/de/mpg/biochem/mars/n5/commands/MarsOpenN5asImagePlusCommand.java

@@ -0,0 +1,178 @@
+/*-
+ * #%L
+ * Molecule Archive Suite (Mars) - core data storage and processing algorithms.
+ * %%
+ * Copyright (C) 2018 - 2023 Karl Duderstadt
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package de.mpg.biochem.mars.n5.commands;
+
+import com.amazonaws.services.s3.AmazonS3;
+import ij.*;
+import ij.io.FileInfo;
+import net.imagej.DatasetService;
+import org.janelia.saalfeldlab.n5.ij.N5Importer;
+import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
+import org.scijava.ItemIO;
+import org.scijava.app.StatusService;
+import org.scijava.command.Command;
+import org.scijava.command.DynamicCommand;
+import org.scijava.convert.ConvertService;
+import org.scijava.log.LogService;
+import org.scijava.menu.MenuConstants;
+import org.scijava.plugin.Menu;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Arrays;
+import java.util.concurrent.ExecutorService;
+import java.util.function.Consumer;
+import java.util.stream.Collectors;
+import java.util.concurrent.ExecutorService;
+import java.util.concurrent.Executors;
+
+import net.imagej.Dataset;
+import ij.ImagePlus;
+import net.imagej.DatasetService;
+import net.imglib2.RandomAccessibleInterval;
+import net.imglib2.img.ImagePlusAdapter;
+import net.imglib2.img.Img;
+import net.imglib2.img.display.imagej.ImageJFunctions;
+import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory;
+import net.imglib2.realtransform.AffineTransform2D;
+import net.imglib2.realtransform.RealViews;
+import net.imglib2.type.NativeType;
+import net.imglib2.type.numeric.RealType;
+import net.imglib2.view.Views;
+
+import de.mpg.biochem.mars.n5.*;
+import org.janelia.saalfeldlab.n5.DatasetAttributes;
+import org.janelia.saalfeldlab.n5.N5Reader;
+import org.janelia.saalfeldlab.n5.ij.N5Importer.N5BasePathFun;
+import org.janelia.saalfeldlab.n5.metadata.*;
+import org.janelia.saalfeldlab.n5.metadata.canonical.CanonicalMetadataParser;
+import org.janelia.saalfeldlab.n5.metadata.imagej.ImagePlusLegacyMetadataParser;
+import org.janelia.saalfeldlab.n5.ui.DataSelection;
+import org.janelia.saalfeldlab.n5.ui.DatasetSelectorDialog;
+import org.janelia.saalfeldlab.n5.ui.N5DatasetTreeCellRenderer;
+//import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata;
+//import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
+
+@Plugin(type = Command.class, label = "Open N5 as ImagePlus", menu = { @Menu(
+        label = MenuConstants.PLUGINS_LABEL, weight = MenuConstants.PLUGINS_WEIGHT,
+        mnemonic = MenuConstants.PLUGINS_MNEMONIC), @Menu(label = "Mars",
+        weight = MenuConstants.PLUGINS_WEIGHT, mnemonic = 'm'), @Menu(
+        label = "Image", weight = 1, mnemonic = 'i'), @Menu(label = "Util",
+        weight = 7, mnemonic = 'u'), @Menu(label = "Open N5 as ImagePlus",
+        weight = 11, mnemonic = 'o') })
+public class MarsOpenN5asImagePlusCommand extends DynamicCommand implements Command {
+    /**
+     * SERVICES
+     */
+    @Parameter
+    private LogService logService;
+
+    @Parameter
+    private StatusService statusService;
+
+    @Parameter
+    private ConvertService convertService;
+
+    @Parameter
+    private DatasetService datasetService;
+
+    @Parameter(label = "image", type = ItemIO.OUTPUT)
+    private Dataset dataset;
+
+    @Override
+    public void run() {
+        DatasetSelectorDialog selectionDialog = new DatasetSelectorDialog(
+                new MarsN5ViewerReaderFun(), new N5BasePathFun(),
+                "", new N5MetadataParser[] {},
+                new N5MetadataParser[] { new ImagePlusLegacyMetadataParser(),
+                        new N5CosemMetadataParser(),
+                        new N5SingleScaleMetadataParser(),
+                        new CanonicalMetadataParser(),
+                        new N5GenericSingleScaleMetadataParser() });
+
+        selectionDialog.setVirtualOption(true);
+        selectionDialog.setCropOption(false);
+
+        selectionDialog.setTreeRenderer(new N5DatasetTreeCellRenderer(
+                true));
+
+        // Prevents NullPointerException
+        selectionDialog.setContainerPathUpdateCallback(x -> {});
+
+        final Consumer<DataSelection> callback = (
+                DataSelection dataSelection) -> {
+                    //Read metadata file
+                    //MarsMicromanagerFormat.Parser
+
+                    //parsePositionMV2(final String jsonData, final Metadata meta,
+                    //final int posIndex)
+
+
+
+                    String rootPath = selectionDialog.getN5RootPath();
+                    String datasetPath = dataSelection.metadata.get(0).getPath();
+                    N5DatasetMetadata datasetMeta = (N5DatasetMetadata) dataSelection.metadata.get(0);
+
+                    //Build n5 reader
+                    N5Reader n5 = new MarsN5ViewerReaderFun().apply(rootPath);
+                    ExecutorService exec = Executors.newFixedThreadPool(8);
+
+                    //System.out.println(((N5AmazonS3Reader) n5).getKeyValueAccess().lockForReading(datasetPath + "/metadata.txt").newInputStream());
+
+                    System.out.println("datasetMeta " + dataSelection.metadata.get(0));
+
+                    //if (datasetMeta != null && datasetMeta instanceof AxisMetadata) {
+                    //    System.out.println("AxisMetadata " + (AxisMetadata) datasetMeta));
+                    //}
+
+                    ImagePlus imp;
+                    try {
+                        imp = N5Importer.read(n5, exec, datasetMeta, null, selectionDialog.isVirtual(), null);
+
+                        FileInfo fileInfo = imp.getOriginalFileInfo();
+                        if (fileInfo == null)
+                            fileInfo = new FileInfo();
+
+                        fileInfo.url = rootPath + "?" + datasetMeta.getPath();
+                        imp.setFileInfo(fileInfo);
+                        imp.show();
+                    } catch (final IOException e) {
+                        IJ.error("failed to read n5");
+                    }
+            };
+
+        selectionDialog.run(callback);
+    }
+
+    private String getMetadataString(String url) {
+        return "";
+    }
+}