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test: pyramid writing
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@bogovicj
bogovicj committed Apr 24, 2024
1 parent 8479488 commit e498db1
Showing 1 changed file with 101 additions and 42 deletions.
143 changes: 101 additions & 42 deletions src/test/java/org/janelia/saalfeldlab/n5/TestExportImports.java
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Original file line number Diff line number Diff line change
Expand Up @@ -12,13 +12,19 @@
import java.net.URL;
import java.util.HashMap;
import java.util.List;
import java.util.Optional;
import java.util.function.Function;

import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Reader;
import org.janelia.saalfeldlab.n5.hdf5.N5HDF5Writer;
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.N5CosemMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5MetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.universe.metadata.N5SpatialDatasetMetadata;
import org.janelia.saalfeldlab.n5.universe.metadata.ome.ngff.v04.NgffSingleScaleMetadataParser;
import org.janelia.saalfeldlab.n5.zarr.N5ZarrReader;
import org.janelia.saalfeldlab.n5.zarr.N5ZarrWriter;
import org.junit.Assert;
Expand All @@ -31,6 +37,7 @@
import net.imglib2.RandomAccess;
import net.imglib2.img.Img;
import net.imglib2.img.display.imagej.ImageJFunctions;
import net.imglib2.realtransform.AffineTransform;
import net.imglib2.type.NativeType;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.RealType;
Expand Down Expand Up @@ -108,6 +115,7 @@ public void testReadWriteParse()
final String compressionString = N5ScalePyramidExporter.GZIP_COMPRESSION;
final String[] containerTypes = new String[] { "FILESYSTEM", "ZARR", "HDF5" };
final String[] metadataTypes = new String[]{
N5Importer.MetadataOmeZarrKey,
N5Importer.MetadataImageJKey,
N5Importer.MetadataN5CosemKey,
N5Importer.MetadataN5ViewerKey
Expand All @@ -131,6 +139,8 @@ public void testReadWriteParse()
}
}



public static < T extends RealType< T > & NativeType< T > > boolean equal( final ImagePlus a, final ImagePlus b )
{
try {
Expand Down Expand Up @@ -252,14 +262,13 @@ else if (metadataType.equals(N5Importer.MetadataOmeZarrKey) || metadataType.equa

assertEquals( String.format( "%s %s one image opened ", outputPath, dataset ), 1, impList.size() );

final double EPS = 1e-9;
final ImagePlus impRead = impList.get( 0 );
if( testMeta )
{
final boolean resEqual = impRead.getCalibration().pixelWidth == imp.getCalibration().pixelWidth &&
impRead.getCalibration().pixelHeight == imp.getCalibration().pixelHeight
&& impRead.getCalibration().pixelDepth == imp.getCalibration().pixelDepth;

assertTrue( String.format( "%s resolutions ", dataset ), resEqual );
assertEquals( String.format( "%s resolutions x", dataset ), imp.getCalibration().pixelWidth, impRead.getCalibration().pixelWidth, EPS );
assertEquals( String.format( "%s resolutions y", dataset ), imp.getCalibration().pixelHeight, impRead.getCalibration().pixelHeight, EPS );
assertEquals( String.format( "%s resolutions z", dataset ), imp.getCalibration().pixelDepth, impRead.getCalibration().pixelDepth, EPS );

final boolean unitsEqual = impRead.getCalibration().getUnit().equals( imp.getCalibration().getUnit() );
assertTrue( String.format( "%s units ", dataset ), unitsEqual );
Expand Down Expand Up @@ -563,7 +572,48 @@ public void testMultiChannelHelper( final String metatype, final String suffix )
singleReadWriteParseTest( imp, n5RootPath, dataset, blockSizeString, metatype, compressionString, true, nc == 1 );
}
}
}
}

@Test
public void testReadWriteParsePyramid()
{
final HashMap<String,String> typeToExtension = new HashMap<>();
typeToExtension.put( "FILESYSTEM", "n5" );
typeToExtension.put( "ZARR", "zarr" );
typeToExtension.put( "HDF5", "h5" );

final String blockSizeString = "2,2,2";
final String compressionString = N5ScalePyramidExporter.GZIP_COMPRESSION;

final String[] containerTypes = new String[] { "FILESYSTEM", "ZARR", "HDF5" };
final String[] metadataTypes = new String[]{
N5Importer.MetadataN5CosemKey,
N5Importer.MetadataN5ViewerKey,
N5Importer.MetadataOmeZarrKey
};

final String[] downsampleTypes = new String[]{
N5ScalePyramidExporter.DOWN_AVERAGE,
N5ScalePyramidExporter.DOWN_SAMPLE
};

final int bitDepth = 16;
final ImagePlus imp = NewImage.createImage("test", 16, 16, 16, bitDepth, NewImage.FILL_NOISE);
imp.setDimensions( 1, 4, 1 );
for( final String containerType : containerTypes )
{
for( final String downsampleMethod : downsampleTypes )
{
for( final String metatype : metadataTypes )
{
final String n5RootPath = baseDir + "/test." + typeToExtension.get( containerType );
final String datasetBase = "/test_"+metatype+"_"+downsampleMethod+"_"+bitDepth;
final String dataset = datasetBase;

pyramidReadWriteParseTest( imp, n5RootPath, dataset, blockSizeString, downsampleMethod, metatype, compressionString, true, true );
}
}
}
}

Expand All @@ -578,62 +628,71 @@ public void pyramidReadWriteParseTest(
final boolean testMeta,
final boolean testData )
{
final double EPS = 1e-6;
final N5ScalePyramidExporter writer = new N5ScalePyramidExporter();
writer.setOptions( imp, outputPath, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, true, downsampleMethod, metadataType, compressionType);
writer.run(); // run() closes the n5 writer

final String readerDataset;
if( metadataType.equals( N5Importer.MetadataN5ViewerKey ))
readerDataset = dataset + "/c0/s0";
else if( metadataType.equals( N5Importer.MetadataN5CosemKey ) && imp.getNChannels() > 1 )
readerDataset = dataset + "/c0";
else
readerDataset = dataset;

final String n5PathAndDataset = outputPath + readerDataset;

final N5Importer reader = new N5Importer();
reader.setShow( false );
final List< ImagePlus > impList = reader.process( n5PathAndDataset, false );

assertEquals( String.format( "%s %s one image opened ", outputPath, dataset ), 1, impList.size() );

final ImagePlus impRead = impList.get( 0 );

if( testMeta )
final N5Reader n5r = new N5Factory()
.openReader(outputPath);
String[] dsetList = n5r.list(readerDataset);
for( String d : dsetList )
{
final boolean resEqual = impRead.getCalibration().pixelWidth == imp.getCalibration().pixelWidth &&
impRead.getCalibration().pixelHeight == imp.getCalibration().pixelHeight
&& impRead.getCalibration().pixelDepth == imp.getCalibration().pixelDepth;

assertTrue( String.format( "%s resolutions ", dataset ), resEqual );

final boolean unitsEqual = impRead.getCalibration().getUnit().equals( imp.getCalibration().getUnit() );
assertTrue( String.format( "%s units ", dataset ), unitsEqual );
}

if( testData )
{
boolean imagesEqual;
if( imp.getType() == ImagePlus.COLOR_RGB )
{
imagesEqual = equalRGB( imp, impRead );
assertEquals( String.format( "%s as rgb ", dataset ), ImagePlus.COLOR_RGB, impRead.getType() );
}
else
imagesEqual = equal( imp, impRead );

assertTrue( String.format( "%s data ", dataset ), imagesEqual );
final String dsetPath = readerDataset + "/" + d;
assertTrue("dataset does not exist at: " + d , n5r.datasetExists(readerDataset+ "/" + d));

final int nd = n5r.getDatasetAttributes(dsetPath).getNumDimensions();
final int level = Integer.parseInt( d.replaceFirst("^s", ""));
final double factor = Math.pow(2, level);
final double[] flatAffine = downsamplingAffineFlat( nd, factor, downsampleMethod );

final N5MetadataParser<?> parser = getParser(metadataType);
@SuppressWarnings("unchecked")
final Optional<N5SpatialDatasetMetadata> meta = (Optional<N5SpatialDatasetMetadata>)parser.parseMetadata(n5r,dsetPath);
assertTrue("metadata does not exist or not parsable", meta.isPresent());
assertArrayEquals("affine", flatAffine, meta.get().spatialTransform().getRowPackedCopy(), EPS);
}

n5r.close();
try {
final N5Writer n5w = new N5Factory().openWriter(outputPath);
n5w.remove();
} catch (final N5Exception e) {
e.printStackTrace();
n5w.close();
} catch (final N5Exception e) { }
}

private double[] downsamplingAffineFlat( final int nd, final double factor, final String downsampleMethod ) {

final AffineTransform out = new AffineTransform(nd);
for (int i = 0; i < nd; i++) {
out.set(factor, i, i);
if (downsampleMethod.equals(N5ScalePyramidExporter.DOWN_AVERAGE)) {
out.set( 0.5 * factor - 0.5, i, nd);
}
}
return out.getRowPackedCopy();
}

impRead.close();
@SuppressWarnings("unchecked")
private <T extends N5SpatialDatasetMetadata> N5MetadataParser<T> getParser(final String metadataType) {

switch (metadataType) {
case N5Importer.MetadataN5CosemKey:
return (N5MetadataParser<T>)new N5CosemMetadataParser();
case N5Importer.MetadataN5ViewerKey:
return (N5MetadataParser<T>)new N5SingleScaleMetadataParser();
case N5Importer.MetadataOmeZarrKey:
return (N5MetadataParser<T>)new NgffSingleScaleMetadataParser();
default:
return null;
}
}

public void testPyramidHelper( final String metatype, final String suffix )
Expand Down

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