Parse .vsi timestamps similar to Z positions

Author: melissalinkert

components/formats-gpl/src/loci/formats/in/CellSensReader.java

@@ -912,6 +912,7 @@ else if (zCount > 0) {
       if (pyramid != null) {
         int nextPlane = 0;
         int effectiveSizeC = core.get(i).rgb ? 1 : core.get(i).sizeC;
+        int[] tzc = new int[] {core.get(i).sizeT, core.get(i).sizeZ, core.get(i).sizeC};
         for (int c=0; c<effectiveSizeC; c++) {
           store.setDetectorSettingsID(
             MetadataTools.createLSID("Detector", 0, nextPyramid - 1), ii, c);
@@ -971,6 +972,24 @@ else if (pyramid.zStart != null && pyramid.zIncrement != null) {
                   UNITS.MICROMETER), ii, nextPlane);
               }
               store.setPixelsPhysicalSizeZ(FormatTools.getPhysicalSizeZ(pyramid.zIncrement), ii);
+
+              // calculate index into timestamp list using TZC order
+              // that matches the plane iteration order here, and seems to work
+              // on the limited data we have that is fully 5D
+              // this approach may need to be re-evaluated for new data though
+              int reorderedPlane = FormatTools.positionToRaster(tzc, new int[] {t, z, c});
+              if (reorderedPlane < pyramid.tValues.size()) {
+                store.setPlaneDeltaT(
+                  FormatTools.createTime(pyramid.tValues.get(reorderedPlane),
+                  UNITS.MILLISECOND), ii, nextPlane);
+              }
+              else if (pyramid.tStart != null && pyramid.tIncrement != null) {
+                store.setPlaneDeltaT(
+                  FormatTools.createTime(pyramid.tStart + (t * pyramid.tIncrement),
+                  UNITS.MILLISECOND), ii, nextPlane);
+              }
+              store.setPixelsTimeIncrement(
+                FormatTools.createTime(pyramid.tIncrement, UNITS.MILLISECOND), ii);
             }
           }
         }
@@ -1960,6 +1979,15 @@ else if (tagPrefix.equals("Z increment")) {
                 else if (tagPrefix.equals("Z value")) {
                   pyramid.zValues.add(DataTools.parseDouble(value));
                 }
+                else if (tagPrefix.equals("Timelapse start")) {
+                  pyramid.tStart = DataTools.parseDouble(value);
+                }
+                else if (tagPrefix.equals("Timelapse increment")) {
+                  pyramid.tIncrement = DataTools.parseDouble(value);
+                }
+                else if (tagPrefix.equals("Timestamp ")) {
+                  pyramid.tValues.add(DataTools.parseDouble(value));
+                }
               }
             }
             catch (NumberFormatException e) {
@@ -2082,6 +2110,8 @@ private String getVolumeName(int tag) {
         return "Channel Wavelength ";
       case WORKING_DISTANCE:
         return "Objective Working Distance ";
+      case TIME_VALUE:
+        return "Timestamp ";
     }
     LOGGER.debug("Unhandled volume {}", tag);
     return "";
@@ -2668,6 +2698,11 @@ class Pyramid {
     public transient Double zStart;
     public transient Double zIncrement;
     public transient ArrayList<Double> zValues = new ArrayList<Double>();
+
+    public transient Double tStart;
+    public transient Double tIncrement;
+    public transient ArrayList<Double> tValues = new ArrayList<Double>();
+
     public boolean   HasAssociatedEtsFile = false;
   }