From 68b8e170817f45d3dcdc10c85c51e845cee51ad3 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Tue, 10 Dec 2024 15:46:51 -0600
Subject: [PATCH 1/2] OIR: parse time step from TIMELAPSE axis when possible

---
 .../src/loci/formats/in/OIRReader.java            | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/OIRReader.java b/components/formats-gpl/src/loci/formats/in/OIRReader.java
index 447ae76aa70..cf175479402 100644
--- a/components/formats-gpl/src/loci/formats/in/OIRReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OIRReader.java
@@ -92,6 +92,7 @@ public class OIRReader extends FormatReader {
 
   private transient Double zStart;
   private transient Double zStep;
+  private transient Double tStart;
   private transient Double tStep;
   private transient HashMap<Integer, Double> timestampAdjustments = new HashMap<Integer, Double>();
 
@@ -277,6 +278,7 @@ public void close(boolean fileOnly) throws IOException {
       minT = Integer.MAX_VALUE;
       zStart = null;
       zStep = null;
+      tStart = null;
       tStep = null;
     }
   }
@@ -603,6 +605,9 @@ else if (!checkSuffix(id, "oir")) {
       for (int i=0; i<getImageCount(); i++) {
         int t = getZCTCoords(i)[2];
         double deltaT = t * tStep;
+        if (tStart != null) {
+          deltaT += tStart;
+        }
         for (Integer frame : timestampAdjustments.keySet()) {
           if (t >= frame) {
             deltaT += (timestampAdjustments.get(frame) - tStep);
@@ -1189,8 +1194,12 @@ private void parseImageProperties(Element root) throws FormatException {
               Element speed = getFirstChild(getFirstChild(scanner, "lsmimage:param"), "lsmparam:speed");
               speed = getFirstChild(speed, "commonparam:speedInformation");
               Element seriesInterval = getFirstChild(speed, "commonparam:seriesInterval");
-              if (seriesInterval != null) {
-                tStep = DataTools.parseDouble(seriesInterval.getTextContent());
+
+              // prefer setting tStep from the TIMELAPSE axis,
+              // but fall back to this if needed
+              if (seriesInterval != null && tStep == null) {
+                // units are seconds, so multiply to get milliseconds
+                tStep = DataTools.parseDouble(seriesInterval.getTextContent()) * 1000;
               }
             }
           }
@@ -1358,6 +1367,8 @@ private void parseAxis(Element dimensionAxis) {
       else if (name.equals("TIMELAPSE")) {
         if (m.sizeT <= 1) {
           m.sizeT = Integer.parseInt(size.getTextContent());
+          tStart = DataTools.parseDouble(start.getTextContent());
+          tStep = DataTools.parseDouble(step.getTextContent());
         }
       }
       else if (name.equals("LAMBDA")) {

From a0b60c99672bf67b85cb1bfa718166b54e07149d Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 11 Dec 2024 14:15:20 -0600
Subject: [PATCH 2/2] Fix time step units, and ignore 0 values

---
 .../formats-gpl/src/loci/formats/in/OIRReader.java  | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/components/formats-gpl/src/loci/formats/in/OIRReader.java b/components/formats-gpl/src/loci/formats/in/OIRReader.java
index cf175479402..cda84e60ab0 100644
--- a/components/formats-gpl/src/loci/formats/in/OIRReader.java
+++ b/components/formats-gpl/src/loci/formats/in/OIRReader.java
@@ -36,6 +36,7 @@
 import java.util.Objects;
 import javax.xml.parsers.ParserConfigurationException;
 
+import loci.common.Constants;
 import loci.common.DataTools;
 import loci.common.DateTools;
 import loci.common.Location;
@@ -1198,8 +1199,8 @@ private void parseImageProperties(Element root) throws FormatException {
               // prefer setting tStep from the TIMELAPSE axis,
               // but fall back to this if needed
               if (seriesInterval != null && tStep == null) {
-                // units are seconds, so multiply to get milliseconds
-                tStep = DataTools.parseDouble(seriesInterval.getTextContent()) * 1000;
+                // units are expected to be milliseconds
+                tStep = DataTools.parseDouble(seriesInterval.getTextContent());
               }
             }
           }
@@ -1367,8 +1368,12 @@ private void parseAxis(Element dimensionAxis) {
       else if (name.equals("TIMELAPSE")) {
         if (m.sizeT <= 1) {
           m.sizeT = Integer.parseInt(size.getTextContent());
-          tStart = DataTools.parseDouble(start.getTextContent());
-          tStep = DataTools.parseDouble(step.getTextContent());
+          // units are expected to be seconds, multiply to get milliseconds
+          tStart = DataTools.parseDouble(start.getTextContent()) * 1000;
+          double stepValue = DataTools.parseDouble(step.getTextContent());
+          if (stepValue > Constants.EPSILON) {
+            tStep = stepValue * 1000;
+          }
         }
       }
       else if (name.equals("LAMBDA")) {