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Store dimension order using new "axes" spec #121

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merged 6 commits into from
Mar 1, 2022
Merged

Store dimension order using new "axes" spec #121

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475a9aa
Store dimension order using new "axes" spec
melissalinkert Dec 13, 2021
990b688
Check "axes" metadata in existing multiscales/dimension order tests
melissalinkert Dec 14, 2021
2dc3d70
Merge branch 'master' of github.com:glencoesoftware/bioformats2raw in…
melissalinkert Jan 26, 2022
7595d77
Fix axes metadata when dimensionOrder is null
melissalinkert Feb 2, 2022
fa6dd05
Add test for axes metadata when using "--dimension-order original"
melissalinkert Feb 4, 2022
8f430e2
Don't set _ARRAY_DIMENSIONS attribute
melissalinkert Feb 8, 2022
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34 changes: 33 additions & 1 deletion src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1472,9 +1472,10 @@ private void saveHCSMetadata(IMetadata meta) throws IOException {
* @param resolutions Total number of resolutions from which
* names will be generated.
* @throws IOException
* @throws InterruptedException
*/
private void setSeriesLevelMetadata(int series, int resolutions)
throws IOException
throws IOException, InterruptedException
{
LOGGER.debug("setSeriesLevelMetadata({}, {})", series, resolutions);
String resolutionString = String.format(
Expand Down Expand Up @@ -1514,6 +1515,37 @@ private void setSeriesLevelMetadata(int series, int resolutions)
datasets.add(Collections.singletonMap("path", lastPath));
}
multiscale.put("datasets", datasets);

String axisOrder = null;
if (dimensionOrder != null) {
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Under which case would dimensionOrder be null? In this scenario, the multi-scale would contain no axes and be invalid or can we infer a default value?

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I think I originally assumed here that dimensionOrder can't really be null, and this is just being extra safe. Going back and looking at the history of the --dimension-order option though, dimensionOrder can be null if --dimension-order original is used. In that case, you're correct that the axes metadata is missing, so I need to fix that here.

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7595d77 should fix this so that axes is populated for any value of dimensionOrder.

axisOrder = dimensionOrder.toString();
}
else {
IFormatReader reader = readers.take();
try {
axisOrder = reader.getDimensionOrder();
}
finally {
readers.put(reader);
}
}
List<Map<String, String>> axes = new ArrayList<Map<String, String>>();
for (int i=axisOrder.length()-1; i>=0; i--) {
String axis = axisOrder.substring(i, i + 1).toLowerCase();
String type = "space";
if (axis.equals("t")) {
type = "time";
}
else if (axis.equals("c")) {
type = "channel";
}
Map<String, String> thisAxis = new HashMap<String, String>();
thisAxis.put("name", axis);
thisAxis.put("type", type);
axes.add(thisAxis);
}
multiscale.put("axes", axes);

Path subGroupPath = getRootPath().resolve(seriesString);
LOGGER.debug(" creating subgroup {}", subGroupPath);
ZarrGroup subGroup = ZarrGroup.create(subGroupPath);
Expand Down
31 changes: 31 additions & 0 deletions src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Expand Up @@ -260,6 +260,10 @@ public void testMultiscalesMetadata() throws Exception {
(List<Map<String, Object>>) multiscale.get("datasets");
assertTrue(datasets.size() > 0);
assertEquals("0", datasets.get(0).get("path"));

List<Map<String, Object>> axes =
(List<Map<String, Object>>) multiscale.get("axes");
checkAxes(axes, "TCZYX");
}

/**
Expand All @@ -284,6 +288,15 @@ public void testSetXYCZTDimensionOrder() throws Exception {
ZarrGroup z = ZarrGroup.open(output.toString());
ZarrArray array = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 2, 512, 512}, array.getShape());

z = ZarrGroup.open(output.resolve("0").toString());
List<Map<String, Object>> multiscales = (List<Map<String, Object>>)
z.getAttributes().get("multiscales");
assertEquals(1, multiscales.size());
Map<String, Object> multiscale = multiscales.get(0);
List<Map<String, Object>> axes =
(List<Map<String, Object>>) multiscale.get("axes");
checkAxes(axes, "TZCYX");
}

/**
Expand All @@ -296,6 +309,15 @@ public void testSetOriginalDimensionOrder() throws Exception {
ZarrGroup z = ZarrGroup.open(output.toString());
ZarrArray array = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 2, 512, 512}, array.getShape());

z = ZarrGroup.open(output.resolve("0").toString());
List<Map<String, Object>> multiscales = (List<Map<String, Object>>)
z.getAttributes().get("multiscales");
assertEquals(1, multiscales.size());
Map<String, Object> multiscale = multiscales.get(0);
List<Map<String, Object>> axes =
(List<Map<String, Object>>) multiscale.get("axes");
checkAxes(axes, "TZCYX");
}

/**
Expand Down Expand Up @@ -1413,6 +1435,15 @@ private void checkWell(ZarrGroup wellGroup, int fieldCount)
}
}

private void checkAxes(List<Map<String, Object>> axes, String order) {
assertEquals(axes.size(), order.length());
for (int i=0; i<axes.size(); i++) {
String name = axes.get(i).get("name").toString();
assertEquals(name, order.toLowerCase().substring(i, i + 1));
assertTrue(axes.get(i).containsKey("type"));
}
}

private Path getTestFile(String resourceName) throws IOException {
try {
return Paths.get(this.getClass().getResource(resourceName).toURI());
Expand Down