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style(test): BdvMetadataIoTests cleanup
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@bogovicj
bogovicj committed Mar 6, 2024
1 parent 1e3afd3 commit b8349b8
Showing 1 changed file with 52 additions and 55 deletions.
107 changes: 52 additions & 55 deletions src/test/java/org/janelia/saalfeldlab/n5/bdv/BdvMetadataIoTests.java
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Original file line number Diff line number Diff line change
Expand Up @@ -52,10 +52,10 @@ public class BdvMetadataIoTests {
private File baseDir;

@Before
public void before()
{
final URL configUrl = BdvMetadataIoTests.class.getResource( "/plugins.config" );
baseDir = new File( configUrl.getFile()).getParentFile();
public void before() {

final URL configUrl = BdvMetadataIoTests.class.getResource("/plugins.config");
baseDir = new File(configUrl.getFile()).getParentFile();
}

public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & NumericType<V>> void readWriteParseTest(
Expand All @@ -66,23 +66,25 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
final String metadataType,
final String compressionType,
final boolean testMeta,
final boolean testData ) throws IOException
{
final boolean testData) throws IOException {

final N5ScalePyramidExporter writer = new N5ScalePyramidExporter();
writer.setOptions( imp, outputPath, dataset, blockSizeString, true,
writer.setOptions(imp, outputPath, dataset, N5ScalePyramidExporter.AUTO_FORMAT, blockSizeString, true,
N5ScalePyramidExporter.DOWN_SAMPLE, metadataType, compressionType);
writer.run(); // run() closes the n5 writer

writer.setOverwrite(true); // overwrite on for this test
writer.run(); // run() closes the n5 writer

final String readerDataset = dataset;

final N5Reader n5 = new N5Factory().openReader(outputPath);
final N5DatasetDiscoverer datasetDiscoverer = new N5DatasetDiscoverer(n5, Executors.newSingleThreadExecutor(), (x) -> true,
Arrays.asList( N5ViewerCreator.n5vParsers ),
Arrays.asList( N5ViewerCreator.n5vGroupParsers ));
Arrays.asList(N5ViewerCreator.n5vParsers),
Arrays.asList(N5ViewerCreator.n5vGroupParsers));

final N5TreeNode root = datasetDiscoverer.discoverAndParseRecursive("");
final Optional<N5TreeNode> metaOpt = root.getDescendant(readerDataset);
if( !metaOpt.isPresent())
if (!metaOpt.isPresent())
fail("could not find metadata at: " + readerDataset);

final List<ConverterSetup> converterSetups = new ArrayList<>();
Expand All @@ -99,11 +101,11 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
sourcesAndConverters,
options);

assertEquals( String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size() );
assertEquals( String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints );
assertEquals(String.format("channels for %s", dataset), imp.getNChannels(), sourcesAndConverters.size());
assertEquals(String.format("time points for %s", dataset), imp.getNFrames(), numTimepoints);

final Source<T> src0 = sourcesAndConverters.get(0).getSpimSource();
assertEquals( String.format("slices for %s", dataset), imp.getNSlices(),
assertEquals(String.format("slices for %s", dataset), imp.getNSlices(),
src0.getSource(0, 0).dimension(2));

final AffineTransform3D tform = new AffineTransform3D();
Expand All @@ -113,24 +115,22 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
final double rz = tform.get(2, 2);
final String unit = src0.getVoxelDimensions().unit();

if( testMeta )
{
final boolean resEqual =
rx == imp.getCalibration().pixelWidth &&
if (testMeta) {
final boolean resEqual = rx == imp.getCalibration().pixelWidth &&
ry == imp.getCalibration().pixelHeight &&
rz == imp.getCalibration().pixelDepth;

assertTrue( String.format( "%s resolutions ", dataset ), resEqual );
assertTrue( String.format( "%s units ", dataset ),
unit.equals( imp.getCalibration().getUnit()));
assertTrue(String.format("%s resolutions ", dataset), resEqual);
assertTrue(String.format("%s units ", dataset),
unit.equals(imp.getCalibration().getUnit()));

}

if( testData )
{
if (testData) {
final List<Source<T>> srcList = sourcesAndConverters.stream().map(sac -> sac.getSpimSource()).collect(Collectors.toList());
assertTrue(String.format("%s data ", dataset), sourceDataIdentical(imp, srcList));
}
n5.close();

// remove
final N5Writer n5w = new N5Factory().openWriter(outputPath);
Expand All @@ -142,56 +142,55 @@ public <T extends NumericType<T> & NativeType<T>, V extends Volatile<T> & Numeri
* and ensure bdv sources are correctly read.
*/
@Test
public void testMultiChannel() throws IOException
{
for( final String suffix : new String[] { ".h5", ".n5", ".zarr" })
{
public void testMultiChannel() throws IOException {

for (final String suffix : new String[]{".h5", ".n5", ".zarr"}) {
testMultiChannelHelper(N5Importer.MetadataN5ViewerKey, suffix);
testMultiChannelHelper(N5Importer.MetadataN5CosemKey, suffix);
testMultiChannelHelper(N5Importer.MetadataOmeZarrKey, suffix);
testMultiChannelHelper(N5Importer.MetadataImageJKey, suffix);
}
}

public void testMultiChannelHelper( final String metatype, final String suffix ) throws IOException
{
public void testMultiChannelHelper(final String metatype, final String suffix) throws IOException {

final int bitDepth = 8;

final String n5RootPath = baseDir + "/test_"+ metatype+"_dimCombos" + suffix;
final String n5RootPath = baseDir + "/test_" + metatype + "_dimCombos" + suffix;
final String blockSizeString = "16";
final String compressionString = "raw";

// add zero to avoid eclipse making these final
int nc = 1; nc += 0;
int nz = 4; nz += 0;
int nt = 5; nt += 0;

for( nc = 1; nc <= 3; nc += 2)
{
for( nz = 1; nz <= 4; nz += 3)
{
for( nt = 1; nt <= 5; nt += 4)
{
int nc = 1;
nc += 0;
int nz = 4;
nz += 0;
int nt = 5;
nt += 0;

for (nc = 1; nc <= 3; nc += 2) {
for (nz = 1; nz <= 4; nz += 3) {
for (nt = 1; nt <= 5; nt += 4) {
final int N = nc * nz * nt;
final ImagePlus imp = NewImage.createImage("test", 8, 6, N, bitDepth, NewImage.FILL_NOISE);
imp.setDimensions( nc, nz, nt );
imp.setDimensions(nc, nz, nt);
imp.getCalibration().pixelWidth = 0.5;
imp.getCalibration().pixelHeight = 0.6;

if( nz > 1 )
if (nz > 1)
imp.getCalibration().pixelDepth = 0.7;

imp.getCalibration().setUnit("mm");

final String dataset = String.format("/c%dz%dt%d", nc, nz, nt);
readWriteParseTest( imp, n5RootPath, dataset, blockSizeString, metatype, compressionString, true, true );
readWriteParseTest(imp, n5RootPath, dataset, blockSizeString, metatype, compressionString, true, true);
}
}
}
}

private static <T extends NumericType<T> & NativeType<T>> boolean sourceDataIdentical( final ImagePlus gt, final List<Source<T>> source )
{
private static <T extends NumericType<T> & NativeType<T>> boolean sourceDataIdentical(final ImagePlus gt, final List<Source<T>> source) {

@SuppressWarnings("unchecked")
final Img<T> imgRaw = (Img<T>)ImageJFunctions.wrap(gt);
final ImagePlusLegacyMetadataParser parser = new ImagePlusLegacyMetadataParser();
Expand All @@ -218,22 +217,20 @@ private static <T extends NumericType<T> & NativeType<T>> boolean sourceDataIden
return true;
}

public static < T extends NumericType< T > & NativeType< T > > boolean equal( final RandomAccessibleInterval<T> imgA, final RandomAccessibleInterval<T> imgB )
{
public static <T extends NumericType<T> & NativeType<T>> boolean equal(final RandomAccessibleInterval<T> imgA, final RandomAccessibleInterval<T> imgB) {

try {
final Cursor< T > c = Views.flatIterable(imgA).cursor();
final RandomAccess< T > r = imgB.randomAccess();
while( c.hasNext() )
{
final Cursor<T> c = Views.flatIterable(imgA).cursor();
final RandomAccess<T> r = imgB.randomAccess();
while (c.hasNext()) {
c.fwd();
r.setPosition( c );
r.setPosition(c);

if( !c.get().valueEquals(r.get()))
if (!c.get().valueEquals(r.get()))
return false;
}
return true;
}catch( final Exception e )
{
} catch (final Exception e) {
return false;
}
}
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