From 8a368ab0ceba5f29632281122ba7212798b7b5e1 Mon Sep 17 00:00:00 2001
From: Roger Leigh <rleigh@dundee.ac.uk>
Date: Fri, 2 Dec 2016 14:23:33 +0000
Subject: [PATCH 1/2] OMEXMLReader: Handle BinData in non-Pixels elements such
 as Mask

The reader made the assumption that BinData was only found inside
Pixels.  However, it's also contained within Mask, and the reader
was stripping out all BinData content when initially reading the
OME-XML (it pre-processes it with a custom SAX parser before
creating the MetadataStore).  This change makes the stripping
selective, so it only occurs for BinData elements contained
within Pixels.
---
 .../src/loci/formats/in/OMEXMLReader.java     | 51 +++++++++++--------
 1 file changed, 30 insertions(+), 21 deletions(-)

diff --git a/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java b/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
index 46b179fea6e..0bd6669dbe3 100644
--- a/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
+++ b/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
@@ -338,47 +338,53 @@ class OMEXMLHandler extends BaseHandler {
     private final StringBuilder xmlBuffer;
     private String currentQName;
     private Locator locator;
+    private boolean inPixels;
 
     public OMEXMLHandler() {
       xmlBuffer = new StringBuilder();
+      inPixels = false;
     }
 
     @Override
     public void characters(char[] ch, int start, int length) {
-      if (currentQName.indexOf("BinData") < 0) {
+      if (currentQName.indexOf("BinData") < 0 || inPixels == false) {
         xmlBuffer.append(new String(ch, start, length));
       }
     }
 
     @Override
     public void endElement(String uri, String localName, String qName) {
+      if (qName.indexOf("Pixels") != -1) {
+        inPixels = false;
+      }
+
       xmlBuffer.append("</");
       xmlBuffer.append(qName);
       xmlBuffer.append(">");
     }
 
     @Override
-    public void startElement(String ur, String localName, String qName,
+    public void startElement(String uri, String localName, String qName,
       Attributes attributes)
     {
       currentQName = qName;
 
-      if (qName.indexOf("BinData") == -1) {
+      if (qName.indexOf("Pixels") != -1) {
+        inPixels = true;
+      }
+
+      if (qName.indexOf("BinData") != -1 && inPixels == true) {
+        binData.add(
+          new BinData(locator.getLineNumber(), locator.getColumnNumber()));
+        String compress = attributes.getValue("Compression");
+        compression.add(compress == null ? "" : compress);
+
         xmlBuffer.append("<");
         xmlBuffer.append(qName);
         for (int i=0; i<attributes.getLength(); i++) {
           String key = XMLTools.escapeXML(attributes.getQName(i));
           String value = XMLTools.escapeXML(attributes.getValue(i));
-          if (key.equals("BigEndian")) {
-            String endian = value.toLowerCase();
-            if (!endian.equals("true") && !endian.equals("false")) {
-              // hack for files that specify 't' or 'f' instead of
-              // 'true' or 'false'
-              if (endian.startsWith("t")) endian = "true";
-              else if (endian.startsWith("f")) endian = "false";
-            }
-            value = endian;
-          }
+          if (key.equals("Length")) value = "0";
           xmlBuffer.append(" ");
           xmlBuffer.append(key);
           xmlBuffer.append("=\"");
@@ -386,19 +392,22 @@ public void startElement(String ur, String localName, String qName,
           xmlBuffer.append("\"");
         }
         xmlBuffer.append(">");
-      }
-      else {
-        binData.add(
-          new BinData(locator.getLineNumber(), locator.getColumnNumber()));
-        String compress = attributes.getValue("Compression");
-        compression.add(compress == null ? "" : compress);
-
+      } else {
         xmlBuffer.append("<");
         xmlBuffer.append(qName);
         for (int i=0; i<attributes.getLength(); i++) {
           String key = XMLTools.escapeXML(attributes.getQName(i));
           String value = XMLTools.escapeXML(attributes.getValue(i));
-          if (key.equals("Length")) value = "0";
+          if (key.equals("BigEndian")) {
+            String endian = value.toLowerCase();
+            if (!endian.equals("true") && !endian.equals("false")) {
+              // hack for files that specify 't' or 'f' instead of
+              // 'true' or 'false'
+              if (endian.startsWith("t")) endian = "true";
+              else if (endian.startsWith("f")) endian = "false";
+            }
+            value = endian;
+          }
           xmlBuffer.append(" ");
           xmlBuffer.append(key);
           xmlBuffer.append("=\"");

From 458b407b05fd259aa01de7977613df1aa8b9080a Mon Sep 17 00:00:00 2001
From: Roger Leigh <rleigh@dundee.ac.uk>
Date: Mon, 5 Dec 2016 16:11:21 +0000
Subject: [PATCH 2/2] OMEXMLReader: Simplify conditionals

---
 components/formats-bsd/src/loci/formats/in/OMEXMLReader.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java b/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
index 0bd6669dbe3..8151f264561 100644
--- a/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
+++ b/components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
@@ -347,7 +347,7 @@ public OMEXMLHandler() {
 
     @Override
     public void characters(char[] ch, int start, int length) {
-      if (currentQName.indexOf("BinData") < 0 || inPixels == false) {
+      if (!inPixels || currentQName.indexOf("BinData") < 0) {
         xmlBuffer.append(new String(ch, start, length));
       }
     }
@@ -373,7 +373,7 @@ public void startElement(String uri, String localName, String qName,
         inPixels = true;
       }
 
-      if (qName.indexOf("BinData") != -1 && inPixels == true) {
+      if (inPixels && qName.indexOf("BinData") != -1) {
         binData.add(
           new BinData(locator.getLineNumber(), locator.getColumnNumber()));
         String compress = attributes.getValue("Compression");