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Merge pull request #100 from saalfeldlab/ngff-export-axis-order
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Ngff export axis order
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@bogovicj
bogovicj authored Dec 4, 2024
2 parents d9b8ec2 + d103418 commit 73f11e8
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Showing 2 changed files with 158 additions and 32 deletions.
74 changes: 57 additions & 17 deletions src/main/java/org/janelia/saalfeldlab/n5/ij/N5ScalePyramidExporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -532,12 +532,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
// get the image to save
final RandomAccessibleInterval<T> baseImg = getBaseImage();

final M baseMetadata;
if (impMeta != null)
baseMetadata = (M)impMeta.readMetadata(image);
else
baseMetadata = null;

final M baseMetadata = initializeBaseMetadata();
currentChannelMetadata = copyMetadata(baseMetadata);
M currentMetadata;

Expand All @@ -561,6 +556,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
final double[] currentResolution = new double[nd];
System.arraycopy(baseResolution, 0, currentResolution, 0, nd);

// TODO here
final N multiscaleMetadata = initializeMultiscaleMetadata((M)currentMetadata, channelDataset);
currentTranslation = new double[nd];

Expand Down Expand Up @@ -629,6 +625,53 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
n5.close();
}

@SuppressWarnings("unchecked")
protected <M extends N5DatasetMetadata> M initializeBaseMetadata() {

M baseMetadata = null;
if (impMeta != null) {
try {
baseMetadata = (M) impMeta.readMetadata(image);
} catch (IOException e) {
}
}

if (impMeta instanceof NgffToImagePlus) {

/*
* ImagePlus axes need to be permuted before conversion to ngff (i.e. from XYCZT
* to XYZCT) The data are permuted elsewhere, here we ensure the metadata
* reflect that chagnge
*/
final NgffSingleScaleAxesMetadata ngffMeta = (NgffSingleScaleAxesMetadata) baseMetadata;
baseMetadata = (M) new NgffSingleScaleAxesMetadata(ngffMeta.getPath(), ngffMeta.getScale(),
ngffMeta.getTranslation(), permuteAxesForNgff(ngffMeta.getAxes()), ngffMeta.getAttributes());
}

return baseMetadata;
}

protected Axis[] permuteAxesForNgff(final Axis[] axes) {

boolean hasC = false;
boolean hasZ = false;
boolean hasT = false;
for (int i = 0; i < axes.length; i++) {
hasC = hasC || axes[i].getName().equals("c");
hasZ = hasZ || axes[i].getName().equals("z");
hasT = hasT || axes[i].getName().equals("t");
}

if (hasC && hasZ) {
if (hasT)
return new Axis[] { axes[0], axes[1], axes[3], axes[2], axes[4] };
else
return new Axis[] { axes[0], axes[1], axes[3], axes[2] };
}

return axes;
}

protected void initializeDataset() {

dataset = image.getShortTitle();
Expand Down Expand Up @@ -936,10 +979,16 @@ protected <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata> L
// some metadata styles never split channels, return input image in that
// case
if (metadataStyle.equals(NONE) || metadataStyle.equals(N5Importer.MetadataCustomKey) ||
metadataStyle.equals(N5Importer.MetadataOmeZarrKey) ||
metadataStyle.equals(N5Importer.MetadataImageJKey)) {
return Collections.singletonList(img);
}
else if (metadataStyle.equals(N5Importer.MetadataOmeZarrKey)) {

if (image.getNChannels() > 1 && image.getNSlices() > 1)
return Collections.singletonList(Views.permute(img, 2, 3));
else
return Collections.singletonList(img);
}

// otherwise, split channels
final ArrayList<RandomAccessibleInterval<T>> channels = new ArrayList<>();
Expand All @@ -962,6 +1011,7 @@ protected <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata> L
// make a 4d image in order XYZT
channelImg = Views.permute(Views.addDimension(channelImg, 0, 0), 2, 3);
}

channels.add(channelImg);
}

Expand Down Expand Up @@ -1311,16 +1361,6 @@ private static <T extends NativeType<T>> RandomAccessibleInterval<T> downsampleA
return BlockAlgoUtils.cellImg(blocks, dimensions, cellDimensions);
}

private int[] sliceBlockSize(final int exclude) {

return removeElement(chunkSize, exclude);
}

private long[] sliceDownsamplingFactors(final int exclude) {

return removeElement(currentAbsoluteDownsampling, exclude);
}

private static int[] removeElement(final int[] arr, final int excludeIndex) {

final int[] out = new int[arr.length - 1];
Expand Down
116 changes: 101 additions & 15 deletions src/test/java/org/janelia/saalfeldlab/n5/metadata/NgffTests.java
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Original file line number Diff line number Diff line change
@@ -1,36 +1,61 @@
package org.janelia.saalfeldlab.n5.metadata;

import static org.junit.Assert.assertArrayEquals;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;

import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
import java.util.Arrays;

import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5Exception;
import org.janelia.saalfeldlab.n5.N5FSReader;
import org.janelia.saalfeldlab.n5.N5Reader;
import org.janelia.saalfeldlab.n5.ij.N5Importer;
import org.janelia.saalfeldlab.n5.ij.N5ScalePyramidExporter;
import org.janelia.saalfeldlab.n5.universe.N5Factory;
import org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes;
import org.janelia.saalfeldlab.n5.universe.metadata.NgffMultiScaleGroupAttributes.MultiscaleDataset;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
import org.junit.Assert;
import org.junit.Before;
import org.junit.BeforeClass;
import org.junit.Test;


import ij.ImagePlus;
import ij.gui.NewImage;

public class NgffTests {

private N5FSReader n5;

@Before
public void setUp() throws IOException {
private final String n5Root = "src/test/resources/ngff.n5";

private static File baseDir;

@BeforeClass
public static void setup() {

try {
baseDir = Files.createTempDirectory("ngff-tests-").toFile();
baseDir.deleteOnExit();

} catch (IOException e) {
e.printStackTrace();
}
}

final String n5Root = "src/test/resources/ngff.n5";
n5 = new N5FSReader(n5Root);
}
@Test
public void testNgffGroupAttributeParsing() {

@Test
public void testNgffGroupAttributeParsing() {
final double eps = 1e-9;
try( final N5FSReader n5 = new N5FSReader(n5Root) ) {

final double eps = 1e-9;
try {
NgffMultiScaleGroupAttributes[] multiscales = n5.getAttribute("ngff_grpAttributes", "multiscales", NgffMultiScaleGroupAttributes[].class );
NgffMultiScaleGroupAttributes[] multiscales = n5.getAttribute("ngff_grpAttributes", "multiscales",
NgffMultiScaleGroupAttributes[].class);
Assert.assertEquals("one set of multiscales", 1, multiscales.length);

MultiscaleDataset[] datasets = multiscales[0].datasets;
Assert.assertEquals("num levels", 6, datasets.length);

Expand All @@ -48,6 +73,67 @@ public void testNgffGroupAttributeParsing() {
fail("Ngff parsing failed");
e.printStackTrace();
}
}
}

@Test
public void testNgffExportAxisOrder() {

testNgfffAxisOrder("xyczt", new int[] { 10, 8, 6, 4, 2 });

testNgfffAxisOrder("xyzt", new int[] { 10, 8, 1, 4, 2 });
testNgfffAxisOrder("xyct", new int[] { 10, 8, 6, 1, 2 });
testNgfffAxisOrder("xycz", new int[] { 10, 8, 6, 4, 1 });

testNgfffAxisOrder("xyc", new int[] { 10, 8, 6, 1, 1 });
testNgfffAxisOrder("xyz", new int[] { 10, 8, 1, 4, 1 });
testNgfffAxisOrder("xyt", new int[] { 10, 8, 1, 1, 2 });
}

public void testNgfffAxisOrder(final String dataset, int[] size) {

final int nx = size[0];
final int ny = size[1];
final int nc = size[2];
final int nz = size[3];
final int nt = size[4];

final String metadataType = N5Importer.MetadataOmeZarrKey;
final String compressionType = N5ScalePyramidExporter.RAW_COMPRESSION;

final ImagePlus imp = NewImage.createImage("test", nx, ny, nz * nc * nt, 8, NewImage.FILL_BLACK);
imp.setDimensions(nc, nz, nt);

final N5ScalePyramidExporter writer = new N5ScalePyramidExporter();
writer.setOptions(imp, baseDir.getAbsolutePath(), dataset, N5ScalePyramidExporter.ZARR_FORMAT, "64", false,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionType);
writer.run();

final long[] expectedDims = Arrays.stream(new long[] { nx, ny, nz, nc, nt }).filter(x -> x > 1).toArray();

try (final N5Reader n5 = new N5Factory().openReader(baseDir.getAbsolutePath())) {

assertTrue(n5.exists(dataset));
assertTrue(n5.datasetExists(dataset + "/s0"));

final DatasetAttributes dsetAttrs = n5.getDatasetAttributes(dataset + "/s0");
assertArrayEquals("dimensions", expectedDims, dsetAttrs.getDimensions());

int i = 0;
final Axis[] axes = n5.getAttribute(dataset, "multiscales[0]/axes", Axis[].class);

if (nt > 1)
assertEquals("t", axes[i++].getName());

if (nc > 1)
assertEquals("c", axes[i++].getName());

if (nz > 1)
assertEquals("z", axes[i++].getName());

assertEquals("y", axes[i++].getName());
assertEquals("x", axes[i++].getName());
}

}

}

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