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read the acquisition settings from one snapshot per run #496

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Merged
bls337 merged 1 commit into from
Sep 26, 2026
Merged

read the acquisition settings from one snapshot per run #496

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45 changes: 30 additions & 15 deletions src/main/java/org/micromanager/lightsheetmanager/model/acquisitions/AcquisitionEngine.java
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@
import mmcorej.org.json.JSONArray;
import mmcorej.org.json.JSONException;
import mmcorej.org.json.JSONObject;
import org.micromanager.PositionList;
import org.micromanager.Studio;
import org.micromanager.acqj.main.Acquisition;
import org.micromanager.acquisition.internal.MMAcquistionControlCallbacks;
Expand Down Expand Up @@ -459,20 +460,34 @@ public void requestResume() {
* This function adds in its fields in order to achieve compatibility.
*/
protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata) {
return addMMSummaryMetadata(summaryMetadata, acqSettings_,
studio_.positions().getPositionList());
}

/**
* As above, but from a run snapshot, so the summary describes the run even if the settings
* or the position list are edited while it is in flight.
*
* @param summaryMetadata the acquisition's own summary metadata, mutated in place
* @param settings the run snapshot
* @param positionList the run's position list snapshot
*/
protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata,
final ScapeAcquisitionSettings settings, final PositionList positionList) {
try {
// These are the ones from the clojure engine that may yet need to be translated
// "Channels" -> {Long@25854} 2

summaryMetadata.put(PropertyKey.CHANNEL_GROUP.key(), acqSettings_.channels().group());
summaryMetadata.put(PropertyKey.CHANNEL_GROUP.key(), settings.channels().group());

// one name per position on the store's channel axis; with simultaneous cameras the
// channel index varies fastest, so walk cameras outermost and repeat the whole channel
// list per camera. This loop order is the slot order: reverse one and every image gets
// the wrong name.
final List<String> channelNames = new ArrayList<>();
final List<String> baseChannelNames = new ArrayList<>();
if (acqSettings_.channels().enabled() && acqSettings_.channels().count() > 0) {
for (ChannelSpec c : acqSettings_.channels().used()) {
if (settings.channels().enabled() && settings.channels().count() > 0) {
for (ChannelSpec c : settings.channels().used()) {
baseChannelNames.add(c.getName());
}
} else {
Expand All @@ -481,7 +496,7 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata
if (model_.devices().adapter().numSimultaneousCameras() > 1) {
for (CameraBase camera : model_.devices().imagingCameras()) {
for (String channelName : baseChannelNames) {
channelNames.add(acqSettings_.channels().enabled()
channelNames.add(settings.channels().enabled()
? channelName + "-" + camera.getDeviceName()
: camera.getDeviceName());
}
Expand All @@ -501,17 +516,17 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata

// MM MDA acquisitions have a defined number of
// frames/slices/channels/positions at the outset
summaryMetadata.put(PropertyKey.FRAMES.key(), acqSettings_.isUsingTimePoints() ? acqSettings_.numTimePoints() : 1);
summaryMetadata.put(PropertyKey.FRAMES.key(), settings.isUsingTimePoints() ? settings.numTimePoints() : 1);

summaryMetadata.put(PropertyKey.SLICES.key(), acqSettings_.volume().slicesPerView());
summaryMetadata.put(PropertyKey.SLICES.key(), settings.volume().slicesPerView());

summaryMetadata.put(PropertyKey.CHANNELS.key(), channelNames.size());
summaryMetadata.put(PropertyKey.POSITIONS.key(), acqSettings_.isUsingMultiplePositions() ?
studio_.positions().getPositionList().getNumberOfPositions() : 1);
summaryMetadata.put(PropertyKey.POSITIONS.key(), settings.isUsingMultiplePositions() ?
positionList.getNumberOfPositions() : 1);

// MM MDA acquisitions have a defined order
summaryMetadata.put(PropertyKey.SLICES_FIRST.key(),
acqSettings_.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED);
settings.acquisitionMode() == AcquisitionMode.STAGE_SCAN_INTERLEAVED);
summaryMetadata.put(PropertyKey.TIME_FIRST.key(),
false); // currently only position, time ordering

Expand All @@ -526,14 +541,14 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata
}
summaryMetadata.put(PropertyKey.AXIS_ORDER.key(), axes);

final int numPositions = studio_.positions().getPositionList().getNumberOfPositions();
final int numPositions = positionList.getNumberOfPositions();

// channelNames.size() already includes the simultaneous-camera factor
final Coords dims = studio_.data().coordsBuilder()
.channel(channelNames.size())
.z(acqSettings_.volume().slicesPerView())
.timePoint(acqSettings_.isUsingTimePoints() ? acqSettings_.numTimePoints() : 1)
.stagePosition(acqSettings_.isUsingMultiplePositions() ? numPositions : 1)
.z(settings.volume().slicesPerView())
.timePoint(settings.isUsingTimePoints() ? settings.numTimePoints() : 1)
.stagePosition(settings.isUsingMultiplePositions() ? numPositions : 1)
.build();

final List<String> axisOrder = new ArrayList<>();
Expand All @@ -546,11 +561,11 @@ protected DefaultSummaryMetadata addMMSummaryMetadata(JSONObject summaryMetadata
final DefaultSummaryMetadata dsmd = (DefaultSummaryMetadata) dsmb
.prefix("")
.axisOrder(axisOrder)
.channelGroup(model_.acquisitions().settings().channels().group())
.channelGroup(settings.channels().group())
.channelNames(channelNames)
.imageWidth((int)core_.getImageWidth())
.imageHeight((int)core_.getImageHeight())
.zStepUm(acqSettings_.volume().sliceStepSize())
.zStepUm(settings.volume().sliceStepSize())
.intendedDimensions(dims)
.build();

Expand Down
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