From 87f7e29763044939c20e06eec4e7666ad04fd83a Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Tue, 23 Mar 2021 17:17:14 -0500
Subject: [PATCH] Use well row_index and column_index if available

---
 .../pyramid/PyramidFromDirectoryWriter.java     | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
index 9b7fdb6..2f1a8f0 100755
--- a/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
+++ b/src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
@@ -382,13 +382,22 @@ private void populateMetadata() throws IOException {
       int wsIndex = 0;
       for (int i=0; i<wells.size(); i++) {
         String well = (String) wells.get(i).get("path");
+        Integer rowIndex = (Integer) wells.get(i).get("row_index");
+        Integer colIndex = (Integer) wells.get(i).get("column_index");
         String[] path = well.split("/");
 
+        if (rowIndex == null) {
+          LOG.warn("Well {} row_index missing; attempting to calculate", i);
+          rowIndex = rowLookup.get(path[path.length - 2]);
+        }
+        if (colIndex == null) {
+          LOG.warn("Well {} column_index missing; attempting to calculate", i);
+          colIndex = colLookup.get(path[path.length - 1]);
+        }
+
         metadata.setWellID(MetadataTools.createLSID("Well", 0, i), 0, i);
-        metadata.setWellColumn(
-          new NonNegativeInteger(colLookup.get(path[path.length - 1])), 0, i);
-        metadata.setWellRow(
-          new NonNegativeInteger(rowLookup.get(path[path.length - 2])), 0, i);
+        metadata.setWellColumn(new NonNegativeInteger(colIndex), 0, i);
+        metadata.setWellRow(new NonNegativeInteger(rowIndex), 0, i);
 
         ZarrGroup wellGroup = getZarrGroup(well);