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MarsOpenN5asImagePlusCommand: default to local image copy
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Here we add the LoopBuilder support to create a local copy of the image by default unless as virtual is selected.
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@karlduderstadt
karlduderstadt committed Nov 2, 2023
1 parent 2343385 commit fa5964a
Showing 1 changed file with 17 additions and 70 deletions.
87 changes: 17 additions & 70 deletions src/main/java/de/mpg/biochem/mars/n5/commands/MarsOpenN5asImagePlusCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,12 +36,16 @@
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;
Expand Down Expand Up @@ -128,9 +132,8 @@
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') })
label = "Import", weight = 1, mnemonic = 'i'), @Menu(label = "Open N5 as ImagePlus (minio)",
weight = 20, mnemonic = 'o') })
public class MarsOpenN5asImagePlusCommand extends DynamicCommand implements Command {
/**
* SERVICES
Expand Down Expand Up @@ -201,32 +204,11 @@ public void run() {
positions.add(p);
source.setPositions(positions);

//meta.setFiltered(config.parserIsFiltered());

//meta.setDatasetName(handle.get().getName());
//meta.setSource(handle);
//meta.setSourceLocation(handle.get());

parser.populateMetadata(jsonData, source, source, false);
source.populateImageMetadata();

Dataset dataset = getImage(n5, datasetMeta, source);

//System.out.println("dataset " + dataset.numDimensions() + " " + dataset.getImgPlus().dimensionsAsLongArray());

//dataset.getProperties().put("scifio.metadata.global", source);
Dataset dataset = getImage(n5, datasetMeta, source, selectionDialog.isVirtual());
uiService.show(dataset);


//System.out.println(result);

//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");
} catch (FormatException e) {
Expand All @@ -236,37 +218,12 @@ public void run() {

selectionDialog.run(callback);
}
@SuppressWarnings({"rawtypes", "unchecked"})
private <T extends NumericType<T> & NativeType<T>> Dataset getImage(final N5Reader n5, final N5DatasetMetadata datasetMeta, final boolean asVirtual) {
ExecutorService exec = Executors.newFixedThreadPool(8);

final CachedCellImg imgRaw = N5Utils.open(n5, datasetMeta.getPath());

//Images are stored as XYZCT and we permute to XYCZT which is ImagePlus axis order
final RandomAccessibleInterval<T> imgView = Views.permute( imgRaw, 2, 3 );

ImagePlus imp;
if (asVirtual) {
imp = ImageJFunctions.wrap(imgView, datasetMeta.getName(), exec);
} else {
final ImagePlusImg<T, ?> ipImg = new ImagePlusImgFactory<>(Util.getTypeFromInterval(imgView)).create(imgView);
LoopBuilder.setImages(imgView, ipImg)
.multiThreaded(new DefaultTaskExecutor(exec))
.forEachPixel((x, y) -> y.set(x));

imp = ipImg.getImagePlus();
}

return convertService.convert(imp, Dataset.class);
}

@SuppressWarnings({"rawtypes", "unchecked"})
private <T extends NumericType<T> & NativeType<T>> Dataset getImage(final N5Reader n5, final N5DatasetMetadata datasetMeta, final Metadata metadata) {
private <T extends NumericType<T> & NativeType<T>> Dataset getImage(final N5Reader n5, final N5DatasetMetadata datasetMeta, final Metadata metadata, final boolean asVirtual) {
ExecutorService exec = Executors.newFixedThreadPool(8);

final CachedCellImg imgRaw = N5Utils.open(n5, datasetMeta.getPath());
//Images are stored as XYZCT and we permute to XYCZT which is ImagePlus axis order
//final RandomAccessibleInterval<T> imgView = Views.permute( imgRaw, 2, 3 );

AxisType[] axes = new AxisType[5];
axes[0] = Axes.X;
Expand All @@ -275,32 +232,22 @@ private <T extends NumericType<T> & NativeType<T>> Dataset getImage(final N5Read
axes[3] = Axes.CHANNEL;
axes[4] = Axes.TIME;

final SCIFIOImgPlus<T> imgPlus = new SCIFIOImgPlus(imgRaw, datasetMeta.getName(), axes);
imgPlus.setMetadata(metadata);
imgPlus.setImageMetadata(metadata.get(0));

final Dataset dataset = datasetService.create((ImgPlus) imgPlus);

return dataset;


/*ImagePlus imp;
Img<T> img;
if (asVirtual) {
imp = ImageJFunctions.wrap(imgView, datasetMeta.getName(), exec);
img = imgRaw;
} else {
final ImagePlusImg<T, ?> ipImg = new ImagePlusImgFactory<>(Util.getTypeFromInterval(imgView)).create(imgView);
LoopBuilder.setImages(imgView, ipImg)
final PlanarImg<T, ?> planarImg = new PlanarImgFactory<>(Util.getTypeFromInterval((RandomAccessibleInterval<T>) imgRaw)).create(imgRaw);
LoopBuilder.setImages((RandomAccessibleInterval<T>) imgRaw, planarImg)
.multiThreaded(new DefaultTaskExecutor(exec))
.forEachPixel((x, y) -> y.set(x));

imp = ipImg.getImagePlus();
img = planarImg;
}

return convertService.convert(imp, Dataset.class);
*/
}
final SCIFIOImgPlus<T> imgPlus = new SCIFIOImgPlus(img, datasetMeta.getName(), axes);
imgPlus.setMetadata(metadata);
imgPlus.setImageMetadata(metadata.get(0));

private String getMetadataString(String url) {
return "";
return datasetService.create((ImgPlus) imgPlus);
}
}

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