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fix: metadata parameters for n5-viewer metadata dialect
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* use downsamplingFactors with average downsampling
* set downsamplingFactors to ones with sample downsampling
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@bogovicj
bogovicj committed Apr 15, 2024
1 parent c70dea5 commit 441813c
Showing 1 changed file with 189 additions and 34 deletions.
223 changes: 189 additions & 34 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 @@ -67,14 +67,15 @@
import org.janelia.saalfeldlab.n5.universe.metadata.AbstractN5DatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.MetadataUtils;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadata.CosemTransform;
import org.janelia.saalfeldlab.n5.universe.metadata.N5CosemMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5DatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5Metadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataWriter;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.SpatialMetadataGroup;
import org.janelia.saalfeldlab.n5.universe.metadata.SpatialModifiable;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.Axis;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.axes.AxisUtils;
Expand All @@ -101,6 +102,8 @@
import net.imglib2.RealRandomAccessible;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.interpolation.randomaccess.NLinearInterpolatorFactory;
import net.imglib2.realtransform.AffineGet;
import net.imglib2.realtransform.AffineTransform3D;
import net.imglib2.realtransform.RealViews;
import net.imglib2.realtransform.ScaleAndTranslation;
import net.imglib2.type.NativeType;
Expand Down Expand Up @@ -393,13 +396,6 @@ public void parseBlockSize() {
parseBlockSize(Intervals.dimensionsAsLongArray(ImageJFunctions.wrap(image)));
}

protected boolean metadataSupportsScales() {

return metadataStyle.equals(N5Importer.MetadataN5ViewerKey) ||
metadataStyle.equals(N5Importer.MetadataN5CosemKey) ||
metadataStyle.equals(N5Importer.MetadataOmeZarrKey);
}

/**
* Returns the container path with an additional storage prefix if the
* format is defined by the plugin parameter. or null if the passed uri and
Expand Down Expand Up @@ -489,16 +485,18 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
currentMetadata = copyMetadata((M)currentChannelMetadata);
final String channelDataset = getChannelDatasetName(c);
RandomAccessibleInterval<T> currentChannelImg = channelImgs.get(c);
final int nd = currentChannelImg.numDimensions();

final double[] relativeTranslation = new double[nd];
final int nd = currentChannelImg.numDimensions();
final double[] baseResolution = new double[nd];
fillResolution(baseMetadata, baseResolution);

// every channel starts at the original scale level reset downsampling factors to 1
// every channel starts at the original scale level reset
// downsampling factors to 1
currentAbsoluteDownsampling = new long[nd];
Arrays.fill(currentAbsoluteDownsampling, 1);

final double[] baseResolution = new double[nd];
Arrays.fill(baseResolution, 1);
final double[] currentResolution = new double[nd];
System.arraycopy(baseResolution, 0, currentResolution, 0, nd);

final N multiscaleMetadata = initializeMultiscaleMetadata((M)currentMetadata, channelDataset);
currentTranslation = new double[nd];
Expand All @@ -513,6 +511,7 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
// downsample when relevant
long[] relativeFactors = new long[nd];
Arrays.fill(relativeFactors, 1);

if (s > 0) {
relativeFactors = getRelativeDownsampleFactors(currentMetadata, currentChannelImg.numDimensions(), s, currentAbsoluteDownsampling);

Expand All @@ -522,28 +521,33 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex

currentChannelImg = downsampleMethod((RandomAccessibleInterval<T>)getPreviousScaleImage(c, s), relativeFactors);

// update resolution
Arrays.setAll(currentResolution, i -> {
return currentAbsoluteDownsampling[i] * baseResolution[i];
});

if (downsampleMethod.equals(DOWN_AVERAGE))
Arrays.setAll(currentTranslation, i -> {
if (currentAbsoluteDownsampling[i] > 1)
return 0.5 * currentAbsoluteDownsampling[i] - 0.5;
return baseResolution[i] * (0.5 * currentAbsoluteDownsampling[i] - 0.5);
else
return 0.0;
});

if (downsampleMethod.equals(DOWN_AVERAGE))
Arrays.fill(relativeTranslation, 0.5);
}

// update metadata to reflect this scale level, returns new metadata instance
currentMetadata = (M)metadataForThisScale(dset, currentMetadata, downsampleMethod, relativeFactors, relativeTranslation);
currentMetadata = (M)metadataForThisScale(dset, currentMetadata, downsampleMethod,
baseResolution,
currentAbsoluteDownsampling,
currentResolution,
currentTranslation);

// write to the appropriate dataset
// if dataset exists and not overwritten, don't write metadata
if (!write(currentChannelImg, n5, dset, compression, currentMetadata))
continue;

storeScaleReference(c, s, currentChannelImg);

updateMultiscaleMetadata(multiscaleMetadata, currentMetadata);
anyScalesWritten = true;

Expand All @@ -562,6 +566,25 @@ public <T extends RealType<T> & NativeType<T>, M extends N5DatasetMetadata, N ex
n5.close();
}

protected int numNonChannelDimensions(final ImagePlus imp) {

int nd = 2;
if (imp.getNSlices() > 1)
nd++;

if (imp.getNFrames() > 1)
nd++;

return nd;
}

protected boolean metadataSupportsScales() {

return metadataStyle.equals(N5Importer.MetadataN5ViewerKey) ||
metadataStyle.equals(N5Importer.MetadataN5CosemKey) ||
metadataStyle.equals(N5Importer.MetadataOmeZarrKey);
}

@SuppressWarnings("unchecked")
protected <M extends N5DatasetMetadata> M defaultMetadata(final ImagePlus imp) {

Expand Down Expand Up @@ -632,32 +655,75 @@ protected boolean lastScale(final int[] chunkSize, final Interval imageDimension
return false;
}

protected <M extends N5DatasetMetadata> M metadataForThisScale(final String newPath, final M baseMetadata,
protected <M extends N5DatasetMetadata> void fillResolution(final M baseMetadata, final double[] resolution) {

if (baseMetadata == null) {
Arrays.fill(resolution, 1);
return;
}

if (baseMetadata.getClass().equals(N5SingleScaleMetadata.class)) {
final double[] res = ((N5SingleScaleMetadata)baseMetadata).getPixelResolution();
final int nd = res.length < resolution.length ? res.length : resolution.length;
System.arraycopy(res, 0, resolution, 0, nd);
} else if (baseMetadata instanceof N5CosemMetadata) {
final double[] res = ((N5CosemMetadata)baseMetadata).getCosemTransform().scale;
final int nd = res.length < resolution.length ? res.length : resolution.length;
System.arraycopy(res, 0, resolution, 0, nd);
} else if (baseMetadata instanceof NgffSingleScaleAxesMetadata) {
final double[] res = ((NgffSingleScaleAxesMetadata)baseMetadata).getScale();
final int nd = res.length < resolution.length ? res.length : resolution.length;
System.arraycopy(res, 0, resolution, 0, nd);

} else if (baseMetadata instanceof SpatialMetadata) {
final AffineGet affine = ((SpatialMetadata)baseMetadata).spatialTransform();
final int nd = affine.numTargetDimensions();
for (int i = 0; i < nd; i++)
resolution[i] = affine.get(i, i);
} else
Arrays.fill(resolution, 1);
}

protected <M extends N5DatasetMetadata> M metadataForThisScale(final String newPath,
final M baseMetadata,
final String downsampleMethod,
final long[] downsamplingFactors,
final double[] baseResolution,
final long[] absoluteDownsamplingFactors,
final double[] scale,
final double[] translation) {

return metadataForThisScale(newPath, baseMetadata, downsampleMethod,
Arrays.stream(downsamplingFactors).mapToDouble(x -> (double)x).toArray(),
baseResolution,
Arrays.stream(absoluteDownsamplingFactors).mapToDouble(x -> (double)x).toArray(),
scale,
translation);
}

@SuppressWarnings("unchecked")
protected <M extends N5DatasetMetadata> M metadataForThisScale(final String newPath, final M baseMetadata,
protected <M extends N5DatasetMetadata> M metadataForThisScale(final String newPath,
final M baseMetadata,
final String downsampleMethod,
final double[] relativeFactor,
final double[] relativeTranslation) {

final double[] baseResolution,
final double[] absoluteDownsamplingFactors,
final double[] absoluteScale,
final double[] absoluteTranslation) {

if (baseMetadata instanceof SpatialModifiable) {
return (M)(((SpatialModifiable<?>)baseMetadata).modifySpatialTransform(
newPath,
relativeFactor,
relativeTranslation));
}
if (baseMetadata == null)
return null;

// System.err.println("WARNING: metadata not spatial modifiable");
return baseMetadata;
/**
* if metadata is N5SingleScaleMetadata and not a subclass of it then
* this is using N5Viewer metadata which does not have an offset
*/
if (baseMetadata.getClass().equals(N5SingleScaleMetadata.class)) {
return (M)buildN5VMetadata(newPath, (N5SingleScaleMetadata)baseMetadata, downsampleMethod, baseResolution, absoluteDownsamplingFactors);
} else if (baseMetadata instanceof N5CosemMetadata) {
return (M)buildCosemMetadata(newPath, (N5CosemMetadata)baseMetadata, absoluteScale, absoluteTranslation);

} else if (baseMetadata instanceof NgffSingleScaleAxesMetadata) {
return (M)buildNgffMetadata(newPath, (NgffSingleScaleAxesMetadata)baseMetadata, absoluteScale, absoluteTranslation);
} else
return baseMetadata;
}

protected <T extends RealType<T> & NativeType<T>> RandomAccessibleInterval<T> downsampleMethod(final RandomAccessibleInterval<T> img,
Expand Down Expand Up @@ -909,6 +975,95 @@ protected <M extends N5Metadata> void writeMetadata(final M metadata, final N5Wr
});
}

protected N5SingleScaleMetadata buildN5VMetadata(
final String path,
final N5SingleScaleMetadata baseMetadata,
final String downsampleMethod,
final double[] baseResolution,
final double[] downsamplingFactors) {

/**
* N5Viewer metadata doesn't have a way to directly represent offset.
* Rather, the half-pixel offsets that averaging downsampling introduces
* are assumed when downsampling factors are not equal to ones.
*
* As a result, we use downsampling factors with average downsampling,
* but set the factors to one otherwise.
*/
final int nd = baseResolution.length > 3 ? 3 : baseResolution.length;
final double[] resolution = new double[nd];
final double[] factors = new double[nd];

if (downsampleMethod.equals(N5ScalePyramidExporter.DOWN_AVERAGE)) {
System.arraycopy(baseResolution, 0, resolution, 0, nd);
System.arraycopy(downsamplingFactors, 0, factors, 0, nd);
} else {
for (int i = 0; i < nd; i++)
resolution[i] = baseResolution[i] * downsamplingFactors[i];

Arrays.fill(factors, 1);
}

final AffineTransform3D transform = new AffineTransform3D();
for (int i = 0; i < nd; i++)
transform.set(resolution[i], i, i);

return new N5SingleScaleMetadata(
path,
transform,
factors,
resolution,
baseMetadata.getOffset(),
baseMetadata.unit(),
baseMetadata.getAttributes(),
baseMetadata.minIntensity(),
baseMetadata.maxIntensity(),
baseMetadata.isLabelMultiset());

}

protected N5CosemMetadata buildCosemMetadata(
final String path,
final N5CosemMetadata baseMetadata,
final double[] absoluteResolution,
final double[] absoluteTranslation) {

final double[] resolution = new double[absoluteResolution.length];
System.arraycopy(absoluteResolution, 0, resolution, 0, absoluteResolution.length);

final double[] translation = new double[absoluteTranslation.length];
System.arraycopy(absoluteTranslation, 0, translation, 0, absoluteTranslation.length);

return new N5CosemMetadata(
path,
new CosemTransform(
baseMetadata.getCosemTransform().axes,
resolution,
translation,
baseMetadata.getCosemTransform().units),
baseMetadata.getAttributes());
}

protected NgffSingleScaleAxesMetadata buildNgffMetadata(
final String path,
final NgffSingleScaleAxesMetadata baseMetadata,
final double[] absoluteResolution,
final double[] absoluteTranslation) {

final double[] resolution = new double[absoluteResolution.length];
System.arraycopy(absoluteResolution, 0, resolution, 0, absoluteResolution.length);

final double[] translation = new double[absoluteTranslation.length];
System.arraycopy(absoluteTranslation, 0, translation, 0, absoluteTranslation.length);

return new NgffSingleScaleAxesMetadata(
path,
resolution,
translation,
baseMetadata.getAxes(),
baseMetadata.getAttributes());
}

@SuppressWarnings({"rawtypes", "unchecked"})
private <T extends RealType & NativeType, M extends N5Metadata> boolean write(
final RandomAccessibleInterval<T> image,
Expand Down

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