@Override
public List<NemaData> readFile(File theFile)
throws IllegalArgumentException, FileNotFoundException, IOException {
HashMap<String, HashMap<String, Double>> pathsToAffinityMap =
new HashMap<String, HashMap<String, Double>>();
HashSet<String> allTags = new HashSet<String>();
double minAffinity = Double.POSITIVE_INFINITY;
double maxAffinity = Double.NEGATIVE_INFINITY;
String[][] tagData =
DeliminatedTextFileUtilities.loadDelimTextData(theFile, READ_DELIMITER, -1);
int nrows = tagData.length;
for (int r = 0; r < nrows; r++) {
String aPath = tagData[r][0].trim();
if (aPath.equals("")) {
throw new IllegalArgumentException(
"Error: an empty track name was read from file: " + theFile.getAbsolutePath());
}
String tagName = PathAndTagCleaner.cleanTag(tagData[r][1].trim());
if (tagName.equals("")) {
throw new IllegalArgumentException(
"Error: an empty class name was read from file: " + theFile.getAbsolutePath());
}
allTags.add(tagName);
Double value = Double.valueOf(tagData[r][2].trim());
if ((value != Double.NaN)
&& (value != Double.NEGATIVE_INFINITY)
&& (value != Double.POSITIVE_INFINITY)) {
if (value > maxAffinity) {
maxAffinity = value;
} else if (value < minAffinity) {
minAffinity = value;
}
}
HashMap<String, Double> tagMap = pathsToAffinityMap.get(aPath);
if (tagMap == null) {
tagMap = new HashMap<String, Double>();
pathsToAffinityMap.put(aPath, tagMap);
}
tagMap.put(tagName, value);
}
getLogger()
.fine(
"Read tag affinity sets for "
+ pathsToAffinityMap.size()
+ " paths from "
+ theFile.getAbsolutePath());
// normalise affinity values
double affRange = maxAffinity - minAffinity;
getLogger()
.fine(
"Normalising affinity scores:\n"
+ "\tMin affinity: "
+ minAffinity
+ "\n"
+ "\tMax affinity: "
+ maxAffinity
+ "\n"
+ "\tRange: "
+ affRange);
String aTag;
double normval;
for (Iterator<HashMap<String, Double>> it = pathsToAffinityMap.values().iterator();
it.hasNext(); ) {
HashMap<String, Double> aMap = it.next();
for (Iterator<String> it1 = aMap.keySet().iterator(); it1.hasNext(); ) {
aTag = it1.next();
normval = (aMap.get(aTag) - minAffinity) / affRange;
aMap.put(aTag, normval);
}
}
List<NemaData> examples = new ArrayList<NemaData>(pathsToAffinityMap.size());
NemaData obj;
File path;
String trackID;
for (Iterator<String> it = pathsToAffinityMap.keySet().iterator(); it.hasNext(); ) {
String pathStr = it.next();
path = new File(pathStr);
trackID = PathAndTagCleaner.convertFileToMIREX_ID(path);
obj = new NemaData(trackID);
obj.setMetadata(NemaDataConstants.TAG_AFFINITY_MAP, pathsToAffinityMap.get(pathStr));
obj.setMetadata(NemaDataConstants.TAG_EXPERIMENT_CLASSNAMES, allTags);
obj.setMetadata(NemaDataConstants.PROP_FILE_LOCATION, path.getAbsolutePath());
examples.add(obj);
}
getLogger()
.info(
examples.size()
+ " examples with "
+ NemaDataConstants.TAG_AFFINITY_MAP
+ " metadata read from file: "
+ theFile.getAbsolutePath());
return examples;
}
@SuppressWarnings("unchecked")
@Override
public void writeFile(File theFile, List<NemaData> data)
throws IllegalArgumentException, FileNotFoundException, IOException {
BufferedWriter writer = null;
try {
writer = new BufferedWriter(new FileWriter(theFile));
NemaData obj;
String identifier;
String tag;
HashMap<String, Double> tagAffinities = null;
int noFileLocation = 0;
for (Iterator<NemaData> it = data.iterator(); it.hasNext(); ) {
obj = it.next();
try {
identifier = obj.getStringMetadata(NemaDataConstants.PROP_FILE_LOCATION);
} catch (IllegalArgumentException e) {
identifier = obj.getId();
noFileLocation++;
}
tagAffinities =
(HashMap<String, Double>) obj.getMetadata(NemaDataConstants.TAG_AFFINITY_MAP);
// write a line per tag
for (Iterator<String> tagIt = tagAffinities.keySet().iterator(); tagIt.hasNext(); ) {
tag = tagIt.next();
writer.write(
identifier + WRITE_DELIMITER + tag + WRITE_DELIMITER + tagAffinities.get(tag));
writer.newLine();
}
}
if (noFileLocation == 0) {
getLogger()
.info(
data.size()
+ " examples with "
+ NemaDataConstants.TAG_AFFINITY_MAP
+ " metadata written to file: "
+ theFile.getAbsolutePath());
} else {
getLogger()
.warning(
noFileLocation
+ " of "
+ data.size()
+ " examples (with "
+ NemaDataConstants.TAG_AFFINITY_MAP
+ " metadata) did not have file locations, hence they will have be written out with the trackID only.\nFile written: "
+ theFile.getAbsolutePath());
}
} finally {
if (writer != null) {
try {
writer.flush();
writer.close();
} catch (IOException ex) {
getLogger().log(Level.SEVERE, null, ex);
}
}
}
}
