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MarsMicromanager support metadata.txt only reading
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When populating metadata directly using only the metadata.txt file and images can not be located there is an NPE. This begins to address this issue.
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@karlduderstadt
karlduderstadt committed Nov 2, 2023
1 parent 9546589 commit 2688b26
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Showing 2 changed files with 33 additions and 34 deletions.
23 changes: 11 additions & 12 deletions src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerFormat.java
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Original file line number Diff line number Diff line change
Expand Up @@ -606,12 +606,11 @@ else if (key.equals("Time")) {
else if (key.equals("Comment")) {
p.comment = value;
}
else if (key.equals("FileName")) {
else if (key.equals("FileName") && metadataFile != null) {
final Location file = metadataFile.sibling(value);
p.locationMap.put(new Index(slice), file);
if (p.baseTiff == null) {
p.baseTiff = file;
System.out.println("p.baseTiff " + p.baseTiff);
}
}
else if (key.equals("Width")) {
Expand Down Expand Up @@ -764,7 +763,7 @@ else if (key.equals(p.cameraRef + "-Exposure")) {
else if (key.startsWith("DAC-") && key.endsWith("-Volts")) {
p.voltage.add(new Double(value));
}
else if (key.equals("FileName")) {
else if (key.equals("FileName") && metadataFile != null) {
final Location file = metadataFile.sibling(value);
p.locationMap.put(new Index(slice), file);
if (p.baseTiff == null) {
Expand All @@ -782,15 +781,15 @@ else if (key.equals("FileName")) {

p.timestamps = stamps.toArray(new Double[stamps.size()]);
Arrays.sort(p.timestamps);
ms.setName(p.metadataFile.parent().parent().getName() + " (Pos" + p.positionIndex + ")");

ms.setName(ms.getName() + " (Pos" + p.positionIndex + ")");

// look for the optional companion XML file

p.xmlFile = p.metadataFile.sibling(XML);
if (dataHandleService.exists(p.xmlFile)) {
parseXMLFile(meta, posIndex);
}
//p.xmlFile = p.metadataFile.sibling(XML);
//if (dataHandleService.exists(p.xmlFile)) {
// parseXMLFile(meta, posIndex);
//}
}

private void parsePositionMV2(final String jsonData, final Metadata meta,
Expand Down Expand Up @@ -882,7 +881,7 @@ else if (key.equals("Time")) {
else if (key.equals("Comment")) {
p.comment = value;
}
else if (key.equals("FileName")) {
else if (key.equals("FileName") && metadataFile != null) {
final Location file = metadataFile.sibling(value);
p.locationMap.put(new Index(slice), file);
if (p.baseTiff == null) {
Expand Down Expand Up @@ -1084,7 +1083,7 @@ else if (key.equals("ElapsedTime-ms")) {
final double t = Double.parseDouble(value);
stamps.add(new Double(t / 1000));
}
else if (key.equals("FileName")) {
else if (key.equals("FileName") && metadataFile != null) {
final Location file = metadataFile.sibling(value);
p.locationMap.put(new Index(slice), file);
if (p.baseTiff == null) {
Expand Down Expand Up @@ -1118,7 +1117,6 @@ else if (key.equals("UUID") && p.UUID == null) {
ms.setName(ms.getName() + " (Pos" + p.positionIndex + ")");

// look for the optional companion XML file

//p.xmlFile = p.metadataFile.sibling(XML);
//if (dataHandleService.exists(p.xmlFile)) {
// parseXMLFile(meta, posIndex);
Expand Down Expand Up @@ -1487,6 +1485,7 @@ public Location getLocation(final Metadata meta, final int imageIndex,
}
}
}
if (tiffs == null) return null;
return locationMap.size() == 0 ? tiffs.get((int) planeIndex) : null;
}

Expand Down
44 changes: 22 additions & 22 deletions src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerTranslator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -183,36 +183,36 @@ private void populateMetadata(final Metadata meta,
store.setPlaneExposureTime(new Time(p.exposureTime, UNITS.SECOND), i,
q);

final Location tiff = positions.get(i).getLocation(meta, i, q);

//Check if the tiff file exists. If a sparse collection was performed some planes
//may not have been collected. In that case, add empty placeholder plane data
if (tiff != null && dataHandleService.exists(tiff))
{
boolean fullPlane = true;
if (positions.get(i).tiffs != null) {
//Check if the tiff file exists. If a sparse collection was performed some planes
//may not have been collected. In that case, add empty placeholder plane data
final Location tiff = positions.get(i).getLocation(meta, i, q);
if (tiff != null && dataHandleService.exists(tiff)) fullPlane = true;
else fullPlane = false;
}
//If tiffs is null, there was no access to the original files when processing the metadata.txt
//In this case, full plane information is included for all possible planes.

ArrayList<MapPair> planeParameterList = new ArrayList<MapPair>();
if (fullPlane) {
if (nextStamp < p.timestamps.length)
store.setPlaneDeltaT(new Time(p.timestamps[nextStamp++],
UNITS.SECOND), i, q);

store.setPlaneTheC(p.getTheC(meta, i, q), i, q);
store.setPlaneTheZ(p.getTheZ(meta, i, q), i, q);
store.setPlaneTheT(p.getTheT(meta, i, q), i, q);

Map<String, String> planeMetaTable = p.getPlaneMap(meta, i, q);

ArrayList<MapPair> planeParameterList = new ArrayList<MapPair>();
for (String planeParameterKey : planeMetaTable.keySet())
planeParameterList.add(new MapPair(planeParameterKey, planeMetaTable.get(planeParameterKey)));

store.setMapAnnotationValue(planeParameterList, q);
store.setMapAnnotationID("MPlane-" + i + "-" + q, q);
store.setPlaneAnnotationRef("MPlane-" + i + "-" + q, i, q, 0);
} else {
ArrayList<MapPair> planeParameterList = new ArrayList<MapPair>();

store.setMapAnnotationValue(planeParameterList, q);
store.setMapAnnotationID("MPlane-" + i + "-" + q, q);
store.setPlaneAnnotationRef("MPlane-" + i + "-" + q, i, q, 0);

for (String planeParameterKey : planeMetaTable.keySet())
planeParameterList.add(new MapPair(planeParameterKey, planeMetaTable.get(planeParameterKey)));
}

store.setMapAnnotationValue(planeParameterList, q);
store.setMapAnnotationID("MPlane-" + i + "-" + q, q);
store.setPlaneAnnotationRef("MPlane-" + i + "-" + q, i, q, 0);
}

final String serialNumber = p.detectorID;
Expand Down

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