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OMEXMLReader: Handle BinData in non-Pixels elements such as Mask #2682

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merged 2 commits into from Dec 6, 2016
Merged

OMEXMLReader: Handle BinData in non-Pixels elements such as Mask #2682

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OMEXMLReader: Handle BinData in non-Pixels elements such as Mask
Dec 2, 2016
458b407
OMEXMLReader: Simplify conditionals
Dec 5, 2016
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51 changes: 30 additions & 21 deletions components/formats-bsd/src/loci/formats/in/OMEXMLReader.java
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Expand Up @@ -338,67 +338,76 @@ 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) {
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!inPixels?

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if fiddling anyway then maybe put it first given shortcut logic

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Pushed fixes for these, thanks.

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) {
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Just inPixels instead of 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("=\"");
xmlBuffer.append(value);
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("=\"");
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