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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 @@ -1220,7 +1220,8 @@ public void saveResolutions(int series)
.nested(nested)
.compressor(CompressorFactory.create(
compressionType.toString(), compressionProperties));
ZarrArray.create(getRootPath().resolve(resolutionString), arrayParams);
ZarrArray.create(getRootPath().resolve(resolutionString),
arrayParams, getArrayAttributes());

nTile = new AtomicInteger(0);
tileCount = (int) Math.ceil((double) scaledWidth / tileWidth)
Expand Down Expand Up @@ -1514,6 +1515,27 @@ private void setSeriesLevelMetadata(int series, int resolutions)
datasets.add(Collections.singletonMap("path", lastPath));
}
multiscale.put("datasets", datasets);

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.

List<Map<String, String>> axes = new ArrayList<Map<String, String>>();
String axisOrder = dimensionOrder.toString();
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 Expand Up @@ -1761,6 +1783,16 @@ private Class<?> getBaseReaderClass() throws FormatException, IOException {
}
}

private Map<String, Object> getArrayAttributes() {
Map<String, Object> attrs = new HashMap<String, Object>();
if (dimensionOrder != null) {
String order = dimensionOrder.toString().toLowerCase();
String[] axes = new StringBuilder(order).reverse().toString().split("");
attrs.put("_ARRAY_DIMENSIONS", axes);
}
return attrs;
}

/**
* Check if the given metadata object contains at least one plate
* with at least one well that links to an image.
Expand Down
22 changes: 22 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 Down Expand Up @@ -1413,6 +1426,15 @@ 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