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Merged
bls337 merged 2 commits into from
Sep 28, 2026
Merged

remove series.json #503

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59e2c97
remove series.json and the extra time point metadata
Sep 27, 2026
f7b3683
Merge branch 'micro-manager:main' into separate-timepoints
bls337 Sep 28, 2026
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52 changes: 6 additions & 46 deletions ...in/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngineScape.java
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Original file line number Diff line number Diff line change
Expand Up @@ -73,8 +73,6 @@ public class AcquisitionEngineScape extends AcquisitionEngine {
PLogicScape controller_;
ArrayList<Double> savedExposures_ = new ArrayList<>();
Point2D.Double xyPosUm_;
// wall clock start of the series, which relates one dataset's elapsed times to another's
private long seriesStartEpochMs_;
// Snapshot taken when the run is armed. The position list is user-editable at any time, so
// a live read can give different answers to different parts of one run: the saved
// position_list.pos, the generated events, and the per-arm stage scan setup must agree.
Expand Down Expand Up @@ -527,22 +525,16 @@ private boolean startTimePointAcquisition(final ScapeAcquisitionSettings setting
SummaryMetadata dsmd = addMMSummaryMetadata(summaryMetadata, settings, positionList_,
numTimePoints);
if (separate) {
// Series identity, since every dataset holds time index 0. The start time is the
// actual one, taken as the dataset opens: a late time point starts after its slot.
final long startEpochMs = System.currentTimeMillis();
// Every dataset holds time index 0, so record which time point this is. The start
// time is the actual one, taken as the dataset opens: a late time point starts after
// its slot.
dsmd = dsmd.copyBuilder()
// Micro-Manager's own start time key and format
.startDate(new SimpleDateFormat("yyyy-MM-dd HH:mm:ss.SSS Z", Locale.ROOT)
.format(new Date(startEpochMs)))
.format(new Date()))
.userData(PropertyMaps.builder()
.putBoolean("SeparateTimePoints", true)
.putInteger("TimePointIndex", datasetTimeIndex)
.putInteger("NumTimePoints", settings.numTimePoints())
.putLong("IntervalMs",
Math.round(settings.timePointIntervalSec() * 1000.0))
.putString("SeriesName", new File(root).getName())
.putLong("SeriesStartEpochMs", seriesStartEpochMs_)
.putLong("TimePointStartEpochMs", startEpochMs)
.build())
.build();
}
Expand Down Expand Up @@ -1032,14 +1024,9 @@ private boolean runSeparateTimePoints(final ScapeAcquisitionSettings settings,
return false; // early exit => nowhere to write
}

// differs from saveName when a folder with that name already existed
final String seriesName = new File(seriesDir).getName();
seriesStartEpochMs_ = System.currentTimeMillis();
final long seriesStartNs = System.nanoTime();
// directory names of the completed datasets
final List<String> datasetNames = new ArrayList<>();
writeSeriesManifest(seriesDir, seriesName, numTimePoints, intervalMs, datasetNames,
"running");

// the last dataset's window stays open until the next time point starts, so a series
// that stops in the wait still shows it
Expand Down Expand Up @@ -1073,9 +1060,6 @@ private boolean runSeparateTimePoints(final ScapeAcquisitionSettings settings,
final boolean keepGoing =
finishTimePoint(settings, timeIndex, datasetDir, datasetNames);
inFlightIndex = -1; // accounted for by finishTimePoint
// after every time point, so a series that dies still lists what it completed
writeSeriesManifest(seriesDir, seriesName, numTimePoints, intervalMs, datasetNames,
"running");
if (!keepGoing) {
break;
}
Expand All @@ -1087,9 +1071,6 @@ private boolean runSeparateTimePoints(final ScapeAcquisitionSettings settings,
writeIncompleteMarker(inFlightDir, inFlightIndex, "failed");
}
final int completed = datasetNames.size();
final String status = completed == numTimePoints ? "complete" : "ended early";
writeSeriesManifest(seriesDir, seriesName, numTimePoints, intervalMs, datasetNames,
status);
studio_.logs().logMessage("separate time points: " + completed + " of " + numTimePoints
+ " datasets complete in " + seriesDir);
}
Expand Down Expand Up @@ -1186,26 +1167,6 @@ private String createSeriesDirectory(final String saveDir, final String saveName
return seriesDir;
}

/**
* Writes series.json into the series folder: before the first time point, after each one,
* and at the end with the final status. Datasets are listed by directory name, so the
* manifest still holds when the series folder is moved.
*/
private void writeSeriesManifest(final String seriesDir, final String seriesName,
final int numTimePoints, final long intervalMs, final List<String> datasetNames,
final String status) {
final Map<String, Object> manifest = new LinkedHashMap<>();
manifest.put("seriesName", seriesName);
manifest.put("status", status);
manifest.put("numTimePoints", numTimePoints);
manifest.put("completedTimePoints", datasetNames.size());
manifest.put("intervalMs", intervalMs);
manifest.put("seriesStartEpochMs", seriesStartEpochMs_);
manifest.put("datasets", new ArrayList<>(datasetNames));
FileUtils.writeStringToFile(seriesDir + File.separator + "series.json",
new GsonBuilder().setPrettyPrinting().create().toJson(manifest));
}

/**
* Ends one time point of a series, after waitForCompletion(), and says whether the series
* should go on. Records the dataset as complete or marks it incomplete, and leaves its window
Expand All @@ -1214,7 +1175,7 @@ private void writeSeriesManifest(final String seriesDir, final String seriesName
* @param settings the run snapshot
* @param timeIndex the time point that just ended
* @param datasetDir where this time point was written
* @param datasetNames the series manifest's completed list, appended to when this one is whole
* @param datasetNames the completed datasets, appended to when this one is whole
* @return true if the next time point should run
*/
private boolean finishTimePoint(final ScapeAcquisitionSettings settings, final int timeIndex,
Expand All @@ -1240,8 +1201,7 @@ private boolean finishTimePoint(final ScapeAcquisitionSettings settings, final i
keepGoing = false;
}

// an incomplete dataset is also marked inside its folder, for anything that reads the
// folder rather than the manifest
// an incomplete dataset is marked inside its folder, so it is not mistaken for a whole one
if (incompleteReason == null) {
datasetNames.add(new File(datasetDir).getName());
} else {
Expand Down
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