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Add test for image names when resolutions are not flattened #4114

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merged 4 commits into from
Jan 10, 2024
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Add test for image names when resolutions are not flattened #4114

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2de6968
Add a test for the image names reported when resolutions are not flat…
melissalinkert Nov 7, 2023
6959661
Only set the alternate (unflattened) image name if it is different
melissalinkert Nov 10, 2023
7ed65ec
Rename unflattened image name attribute
melissalinkert Dec 15, 2023
46a435f
Fix unflattened name configuration for single-series datasets
melissalinkert Dec 24, 2023
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17 changes: 15 additions & 2 deletions components/test-suite/src/loci/tests/testng/Configuration.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,8 +42,9 @@
import loci.formats.FormatTools;
import loci.formats.IFormatReader;
import loci.formats.ImageReader;
import loci.formats.in.DynamicMetadataOptions;
import loci.formats.MetadataTools;
import loci.formats.ReaderWrapper;
import loci.formats.in.DynamicMetadataOptions;
import loci.formats.meta.IMetadata;

import ome.xml.model.primitives.PositiveInteger;
Expand Down Expand Up @@ -108,6 +109,7 @@ public class Configuration {
private static final String EXCITATION_WAVELENGTH_UNIT = "ExcitationWavelengthUnit_";
private static final String DETECTOR = "Detector_";
private static final String NAME = "Name";
private static final String UNFLATTENED_NAME = "Alternate_Name";
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private static final String DESCRIPTION = "Description";
private static final String SERIES_COUNT = "series_count";
private static final String RESOLUTION_COUNT = "resolution_count";
Expand Down Expand Up @@ -418,6 +420,10 @@ public String getImageName() {
return currentTable.get(NAME);
}

public String getUnflattenedImageName() {
return currentTable.get(UNFLATTENED_NAME);
}

public boolean hasImageDescription() {
return currentTable.containsKey(DESCRIPTION);
}
Expand Down Expand Up @@ -551,6 +557,7 @@ private void populateINI(IFormatReader reader) {
IFormatReader unflattenedReader = reader;
if (seriesCount > 1) {
unflattenedReader = new ImageReader();
unflattenedReader.setMetadataStore(MetadataTools.createOMEXMLMetadata());
unflattenedReader.setFlattenedResolutions(false);
unflattenedReader.setMetadataOptions(new DynamicMetadataOptions());
try {
Expand All @@ -559,6 +566,7 @@ private void populateINI(IFormatReader reader) {
catch (FormatException | IOException e) { }
seriesCount = unflattenedReader.getSeriesCount();
}
IMetadata unflattenedRetrieve = (IMetadata) unflattenedReader.getMetadataStore();

globalTable.put(SERIES_COUNT, String.valueOf(seriesCount));

Expand Down Expand Up @@ -649,7 +657,12 @@ else if (r instanceof ReaderWrapper) {
// TODO
}

seriesTable.put(NAME, retrieve.getImageName(index));
String flattenedName = retrieve.getImageName(index);
seriesTable.put(NAME, flattenedName);
String unflattenedName = unflattenedRetrieve.getImageName(series);
if ((flattenedName == null && unflattenedName != null) || !flattenedName.equals(unflattenedName)) {
seriesTable.put(UNFLATTENED_NAME, unflattenedName);
}
seriesTable.put(DESCRIPTION, retrieve.getImageDescription(index));

Length physicalX = retrieve.getPixelsPhysicalSizeX(index);
Expand Down
47 changes: 46 additions & 1 deletion components/test-suite/src/loci/tests/testng/FormatReaderTest.java
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Expand Up @@ -963,7 +963,7 @@ private boolean isEqual(String expected, String real) {

if (expected == null && real == null) {
return true;
} else if (expected.equals("null") && real == null) {
} else if ("null".equals(expected) && real == null) {
return true;
} else if (expected == null) {
return false;
Expand Down Expand Up @@ -1421,6 +1421,51 @@ public void testImageNames() {
result(testName, true);
}

@Test(groups = {"all", "fast", "automated"})
public void testUnflattenedImageNames() {
if (config == null) throw new SkipException("No config tree");
String testName = "testUnflattenedImageNames";
if (!initFile()) result(testName, false, "initFile");

boolean success = true;
String msg = null;
IFormatReader resolutionReader = setupReader(false, true);
try {
IMetadata retrieve = (IMetadata) resolutionReader.getMetadataStore();

if (resolutionReader.getSeriesCount() != config.getSeriesCount(false)) {
success = false;
msg = "incorrect unflattened series count";
}

for (int i=0; i<resolutionReader.getSeriesCount() && success; i++) {
config.setSeries(i, false);

String realName = retrieve.getImageName(i);
String expectedName = config.getImageName();

if (!isEqual(expectedName, realName)) {
String unflattenedName = config.getUnflattenedImageName();
if (!isEqual(unflattenedName, realName)) {
msg = "Series " + i + " (got '" + realName +
"', expected '" + expectedName + "' or '" + unflattenedName + "')";
success = false;
}
}
}
}
finally {
try {
resolutionReader.close();
}
catch (IOException e) {
success = false;
msg = "Could not close reader";
}
}
result(testName, success, msg);
}

@Test(groups = {"all", "fast", "automated"})
public void testImageDescriptions() {
if (config == null) throw new SkipException("No config tree");
Expand Down