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fix Nd2 wellinfo missing #4448

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fix Nd2 wellinfo missing #4448

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76fb178
fix well info in ND2 viewer
maartenpaul Feb 20, 2026
340de95
Fix position name extraction for nested loop ND2 files
maartenpaul May 8, 2026
377816f
Expose ND2 position name via OME StageLabel and series metadata
maartenpaul May 11, 2026
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6 changes: 3 additions & 3 deletions components/formats-gpl/src/loci/formats/in/ND2Handler.java
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Original file line number Diff line number Diff line change
Expand Up @@ -513,17 +513,17 @@ else if (qName.equals("uiWidthBytes") || qName.startsWith("uiBpcInMemory") || qN
else if ("dPosX".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posX.add(new Length(number, UNITS.MICROMETER));
metadata.put("X position for position #" + posX.size(), value);
}
else if ("dPosY".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posY.add(new Length(number, UNITS.MICROMETER));
metadata.put("Y position for position #" + posY.size(), value);
}
else if ("dPosZ".equals(prevElement) && qName.startsWith("item_")) {
final Double number = DataTools.parseDouble(value);
posZ.add(new Length(number, UNITS.MICROMETER));
metadata.put("Z position for position #" + posZ.size(), value);
}
else if (qName.equals("dPosName") && value != null && !value.isEmpty()) {
posNames.add(value);
}
else if (qName.startsWith("item_")) {
int v = Integer.parseInt(qName.substring(qName.indexOf('_') + 1));
Expand Down
28 changes: 24 additions & 4 deletions components/formats-gpl/src/loci/formats/in/ND2Reader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -113,6 +113,7 @@ public class ND2Reader extends SubResolutionFormatReader {
private ArrayList<Length> posX;
private ArrayList<Length> posY;
private ArrayList<Length> posZ;
private ArrayList<String> posNames = new ArrayList<String>();
private ArrayList<Double> exposureTime = new ArrayList<Double>();

private Map<String, Integer> channelColors;
Expand Down Expand Up @@ -380,6 +381,7 @@ public void close(boolean fileOnly) throws IOException {
objectiveMag = null;
objectiveModel = null;
exposureTime.clear();
posNames.clear();
positionCount = 0;
}
}
Expand Down Expand Up @@ -2233,6 +2235,11 @@ else if (name.equals("dObjectiveMag")) {
else if (name.equals("sObjective")) {
objectiveModel = value.toString();
}
else if (name.equals("pPosName") || name.equals("sPosition") || name.equals("dPosName")) {
if (!value.toString().isEmpty()) {
posNames.add(value.toString());
}
}

if (type != 11 && type != 10 && type != 9) { // if not level add global meta
addGlobalMeta(name, value);
Expand All @@ -2257,14 +2264,19 @@ private void populateMetadataStore(ND2Handler handler) throws FormatException

String filename = new Location(getCurrentFile()).getName();
if (handler != null) {
ArrayList<String> posNames = handler.getPositionNames();
ArrayList<String> handlerPosNames = handler.getPositionNames();
ArrayList<String> effectivePosNames = handlerPosNames.size() > 0 ? handlerPosNames : this.posNames;
int nameWidth = String.valueOf(getSeriesCount()).length();
for (int i=0; i<getSeriesCount(); i++) {
String seriesSuffix = String.format("(series %0" + nameWidth + "d)", i + 1);
String suffix = (i < posNames.size() && !posNames.get(i).equals("")) ?
posNames.get(i) : seriesSuffix;
boolean hasPosName =
i < effectivePosNames.size() && !effectivePosNames.get(i).equals("");
String suffix = hasPosName ? effectivePosNames.get(i) : seriesSuffix;
String name = filename + " " + suffix;
store.setImageName(name.trim(), i);
if (hasPosName) {
store.setStageLabelName(effectivePosNames.get(i), i);
}
}
}

Expand Down Expand Up @@ -2393,8 +2405,8 @@ else if (backupHandler != null && backupHandler.getExposureTimes().size() == exp
}
int zcPlanes = getImageCount() / ((split ? getSizeC() : 1) * getSizeT());
for (int i=0; i<getSeriesCount(); i++) {
setSeries(i);
if (tsT.size() > 0) {
setSeries(i);
for (int n=0; n<getImageCount(); n++) {
int[] coords = getZCTCoords(n);
int stampIndex = coords[0];
Expand Down Expand Up @@ -2435,6 +2447,14 @@ else if (exposureTime.size() == 1) {
if (posX == null) posX = handler.getXPositions();
if (posY == null) posY = handler.getYPositions();
if (posZ == null) posZ = handler.getZPositions();
ArrayList<String> handlerPosNames = handler.getPositionNames();
ArrayList<String> seriesPosNames = handlerPosNames.size() > 0 ? handlerPosNames : this.posNames;
if (i < seriesPosNames.size() && !seriesPosNames.get(i).equals("")) {
addSeriesMeta("Position name", seriesPosNames.get(i));
}
}
else if (i < this.posNames.size() && !this.posNames.get(i).equals("")) {
addSeriesMeta("Position name", this.posNames.get(i));
}

String pos = "for position";
Expand Down
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