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Add dataset source url
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karlduderstadt committed Nov 2, 2023
1 parent fa5964a commit d2bd994
Showing 1 changed file with 1 addition and 37 deletions.
Original file line number Diff line number Diff line change
@@ -28,26 +28,20 @@
*/
package de.mpg.biochem.mars.n5.commands;

import com.amazonaws.services.s3.AmazonS3;
import ij.*;
import ij.io.FileInfo;
import io.scif.FormatException;
import io.scif.img.SCIFIOImgPlus;
import net.imagej.DatasetService;
import net.imagej.ImgPlus;
import net.imagej.axis.AxisType;
import net.imglib2.img.cell.CellImg;
import net.imglib2.img.planar.PlanarImg;
import net.imglib2.img.planar.PlanarImgFactory;
import org.apache.commons.io.IOUtils;
import org.janelia.saalfeldlab.n5.ij.N5Importer;
import org.janelia.saalfeldlab.n5.imglib2.N5Utils;
import org.janelia.saalfeldlab.n5.s3.N5AmazonS3Reader;
import org.janelia.saalfeldlab.n5.universe.metadata.N5DatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadataParser;
import net.imglib2.img.cell.CellImgFactory;
import org.scijava.Context;
import org.scijava.ItemIO;
import org.scijava.app.StatusService;
import org.scijava.command.Command;
import org.scijava.command.DynamicCommand;
@@ -58,74 +52,43 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;

import net.imagej.axis.Axis;
import net.imagej.axis.Axes;

import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
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.imglib2.cache.img.CachedCellImg;
import net.imglib2.type.numeric.NumericType;
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.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.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMultiScaleMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5DatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5GenericSingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5ViewerMultiscaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalDatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.canonical.CanonicalSpatialDatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.OmeNgffMetadataParser;

import net.imglib2.img.imageplus.ImagePlusImg;
import net.imglib2.img.imageplus.ImagePlusImgFactory;
import net.imglib2.loops.LoopBuilder;
import net.imglib2.util.Util;
import net.imglib2.view.Views;
import net.imglib2.parallel.DefaultTaskExecutor;
import org.scijava.ui.UIService;
import io.scif.Metadata;

import de.mpg.biochem.mars.scifio.MarsMicromanagerFormat;

@Plugin(type = Command.class, label = "Open N5 as ImagePlus", menu = { @Menu(
@@ -208,6 +171,7 @@ public void run() {
source.populateImageMetadata();

Dataset dataset = getImage(n5, datasetMeta, source, selectionDialog.isVirtual());
dataset.setSource(rootPath + datasetPath);
uiService.show(dataset);
} catch (final IOException e) {
IJ.error("failed to read n5");

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