From 5de98043113904470edef1b97884040d386928a9 Mon Sep 17 00:00:00 2001
From: karlduderstadt <duderstadt@biochem.mpg.de>
Date: Thu, 2 Nov 2023 15:16:17 +0100
Subject: [PATCH] MarsMicromanagerFormat: add hasPlane position method

This changes translation so the local file locations are not used. Instead, planes are determined by what is in the metadata.txt file.
---
 .../mars/scifio/MarsMicromanagerFormat.java      |  9 +++++++++
 .../mars/scifio/MarsMicromanagerTranslator.java  | 16 ++++------------
 2 files changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerFormat.java b/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerFormat.java
index 5083e9b..aa717fe 100644
--- a/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerFormat.java
+++ b/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerFormat.java
@@ -1490,6 +1490,15 @@ public Location getLocation(final Metadata meta, final int imageIndex,
 			}
 		
 		//DROP-IN
+		public boolean hasPlane(final Metadata meta, final int imageIndex,
+											   final long planeIndex)
+		{
+			final long[] zct = FormatTools.rasterToPosition(imageIndex, planeIndex,
+					meta, Index.expectedAxes);
+
+			return planeToMetaTable.containsKey("MPlane-" + imageIndex + "-" + zct[0] + "-" + zct[1] + "-" + zct[2]);
+		}
+
 		public Map<String, String> getPlaneMap(final Metadata meta, final int imageIndex,
 			final long planeIndex)
 		{
diff --git a/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerTranslator.java b/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerTranslator.java
index c17668e..9f2bf68 100644
--- a/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerTranslator.java
+++ b/src/main/java/de/mpg/biochem/mars/scifio/MarsMicromanagerTranslator.java
@@ -183,19 +183,11 @@ private void populateMetadata(final Metadata meta,
 						store.setPlaneExposureTime(new Time(p.exposureTime, UNITS.SECOND), i,
 							q);
 
-					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) {
+
+					//Check if the plane exists. If a sparse collection was performed some planes
+					//may not have been collected.
+					if (positions.get(i).hasPlane(meta, i, q)) {
 						if (nextStamp < p.timestamps.length)
 							store.setPlaneDeltaT(new Time(p.timestamps[nextStamp++],
 									UNITS.SECOND), i, q);