Merge pull request #106 from melissalinkert/mrxs-position-metadata

mrxs: store tile position adjustment values as Plane.PositionX and Plane.PositionY

src/main/java/com/glencoesoftware/bioformats2raw/MiraxReader.java

@@ -525,6 +525,8 @@ protected void initFile(String id) throws FormatException, IOException {
 
     int nonHierCount = Integer.parseInt(hierarchy.get("NONHIER_COUNT"));
     int totalCount = 0;
+    int originX = 0;
+    int originY = 0;
     int metadataWidth = 0;
     int metadataHeight = 0;
     for (int i=0; i<nonHierCount; i++) {
@@ -619,12 +621,12 @@ else if (name.equals("StitchingIntensityLayer")) {
               }
             }
 
-            minX -= (minX % 256);
-            minY -= (minY % 256);
+            originX = minX - (minX % 256);
+            originY = minY - (minY % 256);
 
             for (int t=0; t<nTiles; t++) {
-              tilePositions[t][0] -= minX;
-              tilePositions[t][1] -= minY;
+              tilePositions[t][0] -= originX;
+              tilePositions[t][1] -= originY;
             }
 
             stream.close();
@@ -942,6 +944,9 @@ else if (name.equals("VIMSLIDE_POSITION_BUFFER")) {
         }
       }
 
+      store.setPlanePositionX(new Length(originX, UNITS.PIXEL), 0, 0);
+      store.setPlanePositionY(new Length(originY, UNITS.PIXEL), 0, 0);
+
       // parse channel data
 
       for (int c=0; c<getSizeC(); c++) {