private void analyzeEdfFile() {
if (!analyzed) {
if (referenceFile != null) {
HashMap<String, String> headerMap = new HashMap<String, String>();
try {
FileInputStream fis = new FileInputStream(referenceFile.getAbsolutePath());
DataInputStream dis = new DataInputStream(fis);
int character = -1;
StringBuffer headerBuffer = new StringBuffer();
boolean newLine = false;
while (true) {
try {
character = dis.read();
if (character == -1) {
break;
}
headerBuffer.append((char) character);
if (character == '\n') {
newLine = true;
} else {
if ((character == '}') && newLine) {
character = dis.read();
break;
}
newLine = false;
}
} catch (IOException e) {
character = -1;
break;
}
}
if (character != -1) {
char toCheck = headerBuffer.charAt(0);
while (Character.isWhitespace(toCheck) || (toCheck == '{')) {
headerBuffer.delete(0, 1);
toCheck = headerBuffer.charAt(0);
}
toCheck = headerBuffer.charAt(headerBuffer.length() - 1);
while (Character.isWhitespace(toCheck) || (toCheck == '}')) {
headerBuffer.delete(headerBuffer.length() - 1, headerBuffer.length());
toCheck = headerBuffer.charAt(headerBuffer.length() - 1);
}
String[] lines = headerBuffer.toString().split(";");
for (String line : lines) {
int separatorIndex = line.lastIndexOf('=');
if (separatorIndex > -1) {
headerMap.put(
line.substring(0, separatorIndex).trim(),
line.substring(separatorIndex + 1).trim());
}
}
readImageFromFile(headerMap, dis);
// Cleaning keys bound to image
headerMap.remove("ByteOrder");
headerMap.remove("Dim_1");
headerMap.remove("Dim_2");
headerMap.remove("DataType");
// Avoid having another item with the same name as image item
headerMap.remove("Image");
// Other DataItems
HashMap<String, EdfGroup> subGroupMap = new HashMap<String, EdfGroup>();
for (String key : headerMap.keySet()) {
int openIndex = key.lastIndexOf('(');
int closeIndex = key.lastIndexOf(')');
if ((openIndex > -1) && (closeIndex > openIndex)) {
// Group items by name
String groupName = key.substring(openIndex + 1, closeIndex);
EdfGroup subGroup = subGroupMap.get(groupName);
if (subGroup == null) {
subGroup = new EdfGroup(null);
subGroup.setName(groupName);
subGroup.setShortName(groupName);
subGroup.setAnalyzed(true);
addSubgroup(subGroup);
subGroupMap.put(groupName, subGroup);
}
String itemName = key.substring(0, openIndex).replaceAll("=", "").trim();
subGroup.addDataItem(buildDataItem(itemName, headerMap.get(key)));
} else {
// Build simple dataItem
addDataItem(buildDataItem(key, headerMap.get(key)));
}
}
subGroupMap.clear();
headerMap.clear();
dis.close();
}
} catch (FileNotFoundException e) {
// Just ignore this case
} catch (IOException e) {
// Just ignore this case
}
}
}
analyzed = true;
}
private void readImageFromFile(HashMap<String, String> headerMap, DataInputStream dis) {
// Image Recovery
try {
boolean littleEndian = "LowByteFirst".equals(headerMap.get("ByteOrder"));
int dimX = Integer.valueOf(headerMap.get("Dim_1"));
int dimY = Integer.valueOf(headerMap.get("Dim_2"));
String dataType = headerMap.get("DataType");
int y = 0, x = 0;
Object imageValue = null;
boolean unsigned = dataType.startsWith("Unsigned");
if ("SignedByte".equals(dataType)) {
imageValue = new byte[dimY][dimX];
byte[][] arrayImageValue = (byte[][]) imageValue;
while (y < dimY) {
int read = dis.read();
if (read == -1) {
imageValue = null;
break;
} else {
arrayImageValue[y][x] = (byte) read;
x++;
if (x >= dimX) {
x = 0;
y++;
}
}
}
} else if ("UnsignedByte".equals(dataType)) {
imageValue = new short[dimY][dimX];
short[][] arrayImageValue = (short[][]) imageValue;
while (y < dimY) {
int read = dis.read();
if (read == -1) {
imageValue = null;
break;
} else {
arrayImageValue[y][x] = (short) read;
x++;
if (x >= dimX) {
x = 0;
y++;
}
}
}
} else if ("UnsignedShort".equals(dataType) || "SignedInteger".equals(dataType)) {
// Specific
imageValue = new int[dimY][dimX];
// short = 2 bytes
// int = 4 bytes
int factor = (unsigned) ? 2 : 4;
int sizeToRead = factor * dimY * dimX;
// Global
Object flatImageValue = null;
ByteBuffer byteBuffer = EdfFileReader.readAsBytes(sizeToRead, littleEndian, dis);
// Specific
if ("UnsignedShort".equals(dataType)) {
flatImageValue = new short[dimY * dimX];
ShortBuffer shortBuffer = byteBuffer.asShortBuffer();
shortBuffer.get((short[]) flatImageValue);
} else {
flatImageValue = new int[dimY * dimX];
IntBuffer integerBuffer = byteBuffer.asIntBuffer();
integerBuffer.get((int[]) flatImageValue);
}
int globalIndex = 0;
for (int yIndex = 0; yIndex < dimY; yIndex++) {
for (int xIndex = 0; xIndex < dimX; xIndex++) {
int value = Array.getInt(flatImageValue, globalIndex);
value = (unsigned) ? value & 0xffff : value;
((int[][]) imageValue)[yIndex][xIndex] = value;
globalIndex++;
}
}
} else if ("SignedLong".equals(dataType) || "UnsignedInteger".equals(dataType)) {
// Specific
imageValue = new long[dimY][dimX];
// long = 8 bytes
// int = 4 bytes
int factor = (unsigned) ? 4 : 8;
int sizeToRead = factor * dimY * dimX;
// Global
Object flatImageValue = null;
ByteBuffer byteBuffer = EdfFileReader.readAsBytes(sizeToRead, littleEndian, dis);
// Specific
if ("UnsignedInteger".equals(dataType)) {
flatImageValue = new int[dimY * dimX];
IntBuffer integerBuffer = byteBuffer.asIntBuffer();
integerBuffer.get((int[]) flatImageValue);
} else {
flatImageValue = new long[dimY * dimX];
LongBuffer longBuffer = byteBuffer.asLongBuffer();
longBuffer.get((long[]) flatImageValue);
}
int globalIndex = 0;
for (int yIndex = 0; yIndex < dimY; yIndex++) {
for (int xIndex = 0; xIndex < dimX; xIndex++) {
long value = Array.getLong(flatImageValue, globalIndex);
value = (unsigned) ? value & 0xFFFFFFFFL : value;
((long[][]) imageValue)[yIndex][xIndex] = value;
globalIndex++;
}
}
} else if ("Signed64".equals(dataType)) {
throw new NotImplementedException();
} else if ("Unsigned64".equals(dataType)) {
unsigned = true;
throw new NotImplementedException();
} else if ("FloatValue".equals(dataType)) {
throw new NotImplementedException();
} else if ("DoubleValue".equals(dataType)) {
throw new NotImplementedException();
}
if (imageValue != null) {
EdfDataItem imageDataItem =
new EdfDataItem("Image", new DefaultArrayMatrix(EdfFactory.NAME, imageValue), unsigned);
addDataItem(imageDataItem);
}
} catch (Exception e) {
e.printStackTrace();
// ignore exceptions for Image Recovery
}
}
