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Add group path to series index mapping in root attributes #157

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Sep 23, 2022
Merged

Add group path to series index mapping in root attributes #157

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11581a5
Add group path to series index mapping in root attributes
melissalinkert Jun 4, 2022
beb41fa
Move group map to `OME/.zattrs` and update attribute name
melissalinkert Jun 7, 2022
508c9bb
Switch `series` attribute from map to list
melissalinkert Jun 7, 2022
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41 changes: 33 additions & 8 deletions src/main/java/com/glencoesoftware/bioformats2raw/Converter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -665,6 +665,39 @@ public void convert()
scaleFormatString = "%s/%s/%d/%d";
}

// fileset level metadata
if (!noRootGroup) {
final ZarrGroup root = ZarrGroup.create(getRootPath());
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put("bioformats2raw.layout", LAYOUT);

root.writeAttributes(attributes);
}
if (!noOMEMeta) {
Path metadataPath = getRootPath().resolve("OME");
final ZarrGroup root = ZarrGroup.create(metadataPath);
Map<String, Object> attributes = new HashMap<String, Object>();

// record the path to each series (multiscales) and the corresponding
// series (OME-XML Image) index
// using the index as the key would mean that the index is stored
// as a string instead of an integer
List<String> groups = new ArrayList<String>();
for (Integer index : seriesList) {
String resolutionString = String.format(
scaleFormatString, getScaleFormatStringArgs(index, 0));
String seriesString = "";
if (resolutionString.indexOf('/') >= 0) {
seriesString = resolutionString.substring(0,
resolutionString.lastIndexOf('/'));
}
groups.add(seriesString);
}
attributes.put("series", groups);

root.writeAttributes(attributes);
}

for (Integer index : seriesList) {
try {
write(index);
Expand Down Expand Up @@ -1215,14 +1248,6 @@ public void saveResolutions(int series)
sizeX, tileWidth, sizeY, tileHeight, sizeZ, chunkDepth, imageCount
);

// fileset level metadata
if (!noRootGroup) {
final ZarrGroup root = ZarrGroup.create(getRootPath());
Map<String, Object> attributes = new HashMap<String, Object>();
attributes.put("bioformats2raw.layout", LAYOUT);
root.writeAttributes(attributes);
}

// series level metadata
setSeriesLevelMetadata(series, resolutions);

Expand Down
83 changes: 82 additions & 1 deletion src/test/java/com/glencoesoftware/bioformats2raw/test/ZarrTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,13 @@ public void testAdditionalScaleFormatStringArgs() throws Exception {
series0.openArray("0");
series0 = ZarrGroup.open(output.resolve("ghi/999/1").toString());
series0.openArray("0");

Path omePath = output.resolve("OME");
ZarrGroup z = ZarrGroup.open(omePath.toString());
List<String> groupMap = (List<String>) z.getAttributes().get("series");
assertEquals(groupMap.size(), 2);
assertEquals(groupMap.get(0), "abc/888/0");
assertEquals(groupMap.get(1), "ghi/999/1");
}

/**
Expand Down Expand Up @@ -240,6 +247,14 @@ public void testDefaultLayoutIsSetAndIsNested() throws Exception {
ZarrGroup z = ZarrGroup.open(output.toString());
Integer layout = (Integer)
z.getAttributes().get("bioformats2raw.layout");

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 1);
assertEquals(groupMap.get(0), "0");

ZarrArray series0 = ZarrGroup.open(output.resolve("0")).openArray("0");

// no getter for DimensionSeparator in ZarrArray
Expand Down Expand Up @@ -428,6 +443,14 @@ public void testMultiSeries() throws Exception {
assertTool();
ZarrGroup z = ZarrGroup.open(output.toString());

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 2);
assertEquals(groupMap.get(0), "0");
assertEquals(groupMap.get(1), "1");

// Check series 0 dimensions and special pixels
ZarrArray series0 = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
Expand Down Expand Up @@ -462,6 +485,16 @@ public void testSingleBeginningSeries() throws Exception {
assertTool("-s", "0");
ZarrGroup z = ZarrGroup.open(output.toString());

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 1);
assertEquals(groupMap.get(0), "0");

OME ome = getOMEMetadata();
assertEquals(1, ome.sizeOfImageList());

// Check series 0 dimensions and special pixels
ZarrArray series0 = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
Expand Down Expand Up @@ -489,6 +522,16 @@ public void testSingleEndSeries() throws Exception {
assertTool("-s", "1");
ZarrGroup z = ZarrGroup.open(output.toString());

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 1);
assertEquals(groupMap.get(0), "0");

OME ome = getOMEMetadata();
assertEquals(1, ome.sizeOfImageList());

// Check series 1 dimensions and special pixels
ZarrArray series0 = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
Expand Down Expand Up @@ -516,6 +559,16 @@ public void testSingleMiddleSeries() throws Exception {
assertTool("-s", "1");
ZarrGroup z = ZarrGroup.open(output.toString());

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 1);
assertEquals(groupMap.get(0), "0");

OME ome = getOMEMetadata();
assertEquals(1, ome.sizeOfImageList());

// Check series 1 dimensions and special pixels
ZarrArray series0 = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
Expand Down Expand Up @@ -912,11 +965,21 @@ public void testNoHCSOption() throws Exception {

ZarrGroup z = ZarrGroup.open(output);

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 12);
for (int i=0; i<12; i++) {
assertEquals(groupMap.get(i), String.valueOf(i));
}

// Check dimensions and block size
ZarrArray series0 = z.openArray("0/0");
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getShape());
assertArrayEquals(new int[] {1, 1, 1, 512, 512}, series0.getChunks());
assertEquals(12, z.getGroupKeys().size());
// 12 series + OME group
assertEquals(13, z.getGroupKeys().size());

// Check OME metadata
OME ome = getOMEMetadata();
Expand Down Expand Up @@ -952,6 +1015,22 @@ public void testHCSMetadata() throws Exception {
int rowCount = 2;
int colCount = 3;
int fieldCount = 2;

Path omePath = output.resolve("OME");
ZarrGroup omeGroup = ZarrGroup.open(omePath.toString());
List<String> groupMap =
(List<String>) omeGroup.getAttributes().get("series");
assertEquals(groupMap.size(), 12);
int index = 0;
for (int r=0; r<rowCount; r++) {
for (int c=0; c<colCount; c++) {
for (int f=0; f<fieldCount; f++) {
String groupPath = (char) (r + 'A') + "/" + (c + 1) + "/" + f;
assertEquals(groupMap.get(index++), groupPath);
}
}
}

Map<String, List<String>> plateMap = new HashMap<String, List<String>>();
plateMap.put("A", Arrays.asList("1", "2", "3"));
plateMap.put("B", Arrays.asList("1", "2", "3"));
Expand Down Expand Up @@ -1390,6 +1469,8 @@ public void testNoOmeMetaExportOption() throws Exception {

assertTrue(!Files.exists(
output.resolve("OME").resolve("METADATA.ome.xml")));
assertTrue(!Files.exists(
output.resolve("OME").resolve(".zattrs")));
}

/**
Expand Down