/**
* Get the values of this attribute as multiple short arrays, one per frame.
*
* <p>Caller needs to supply the number for frames so that pixel data can be split across
* per-frame arrays (since not necessarily known when this attribute was created or read.
*
* <p>This allocates new arrays of sufficient length, which may fail if they are too large, and
* defeats the point of leaving the values on disk in the first place. However, it is a fallback
* for when the caller does not want to go to the trouble of creating a {@link
* java.nio.MappedByteBuffer MappedByteBuffer} from which to get a {@link java.nio.ShortBuffer
* ShortBuffer} from the file, or more likely is not even aware that the attribute values have
* been left on disk.
*
* @param numberOfFrames the number of frames
* @return the values as an array of arrays of bytes
* @throws DicomException thrown if values cannot be read
*/
public short[][] getShortValuesPerFrame(int numberOfFrames) throws DicomException {
// System.err.println("OtherWordAttributeOnDisk.getShortValuesPerFrame(): lazy read of of all
// frames into heap allocated memory as per-frame arrays, rather than using memory mapped buffer
// :(");
short[][] v = null;
if (valueLength > 0) {
long bytesperframe = valueLength / numberOfFrames;
int len = (int) (bytesperframe / 2);
v = new short[numberOfFrames][];
try {
BinaryInputStream i =
new BinaryInputStream(
new FileInputStream(file), false /*bigEndian - byte order is irrelevant*/);
i.skipInsistently(byteOffset);
for (int f = 0; f < numberOfFrames; ++f) {
short[] buffer = new short[len];
v[f] = buffer;
i.readUnsigned16(buffer, 0, len);
}
i.close();
} catch (IOException e) {
e.printStackTrace(System.err);
throw new DicomException(
"Failed to read value (length "
+ valueLength
+ " dec) in delayed read of "
+ ValueRepresentation.getAsString(getVR())
+ " attribute "
+ getTag());
}
}
return v;
}
/**
* Get the value of this attribute as a short array for one selected frame.
*
* <p>This allocates a new array of sufficient length, which may fail if it is too large, and
* defeats the point of leaving the values on disk in the first place. However, it is a fallback
* for when the caller does not want to go to the trouble of creating a {@link
* java.nio.MappedByteBuffer MappedByteBuffer} from which to get a {@link java.nio.ShortBuffer
* ShortBuffer} from the file, or more likely is not even aware that the attribute values have
* been left on disk, because {@link com.pixelmed.dicom.AttributeFactory AttributeFactory}
* silently created an instance of this class rather than an in-memory {@link
* com.pixelmed.dicom.OtherWordAttribute OtherWordAttribute}.
*
* @param frameNumber from 0
* @param numberOfFrames the number of frames
* @return the values as an array of short
* @throws DicomException thrown if values cannot be read
*/
public short[] getShortValuesForSelectedFrame(int frameNumber, int numberOfFrames)
throws DicomException {
// System.err.println("OtherWordAttributeOnDisk.getShortValuesForSelectedFrame(): lazy read of
// selected frame "+frameNumber+" into heap allocated memory, rather than using memory mapped
// buffer :(");
short[] buffer = null;
long bytesperframe = valueLength / numberOfFrames;
long byteoffsetfromstartofattributevalue = bytesperframe * frameNumber;
if (byteoffsetfromstartofattributevalue + bytesperframe <= valueLength) {
int len = (int) (bytesperframe / 2);
buffer = new short[len];
try {
BinaryInputStream i = new BinaryInputStream(new FileInputStream(file), bigEndian);
i.skipInsistently(byteOffset + byteoffsetfromstartofattributevalue);
i.readUnsigned16(buffer, 0, len);
i.close();
} catch (IOException e) {
throw new DicomException(
"Failed to read frame "
+ frameNumber
+ " of "
+ numberOfFrames
+ " frames, size "
+ bytesperframe
+ " dec and offset "
+ byteoffsetfromstartofattributevalue
+ " dec bytes in delayed read of "
+ ValueRepresentation.getAsString(getVR())
+ " attribute "
+ getTag());
}
} else {
throw new DicomException(
"Requested frame "
+ frameNumber
+ " of "
+ numberOfFrames
+ " frames, size "
+ bytesperframe
+ " dec and offset "
+ byteoffsetfromstartofattributevalue
+ " dec bytes to read value exceeds length "
+ valueLength
+ " dec in delayed read of "
+ ValueRepresentation.getAsString(getVR())
+ " attribute "
+ getTag());
}
return buffer;
}
/**
* Construct a byte ordered stream from the supplied stream.
*
* <p>The byte order may be changed later.
*
* @param i the input stream to read from
*/
public EncapsulatedInputStream(BinaryInputStream i) {
this.i = i;
bigEndian = i.isBigEndian();
buffer = new byte[8];
fragment = null;
firstTime = true;
sequenceDelimiterEncountered = false;
endOfFrameEncountered = false;
}
/**
* Get the values of this attribute as a short array.
*
* <p>This allocates a new array of sufficient length, which may fail if it is too large, and
* defeats the point of leaving the values on disk in the first place. However, it is a fallback
* for when the caller does not want to go to the trouble of creating a {@link
* java.nio.MappedByteBuffer MappedByteBuffer} from which to get a {@link java.nio.ShortBuffer
* ShortBuffer} from the file, or more likely is not even aware that the attribute values have
* been left on disk, because {@link com.pixelmed.dicom.AttributeFactory AttributeFactory}
* silently created an instance of this class rather than an in-memory {@link
* com.pixelmed.dicom.OtherWordAttribute OtherWordAttribute}.
*
* @return the values as an array of short
* @throws DicomException thrown if values cannot be read
*/
public short[] getShortValues() throws DicomException {
// System.err.println("OtherWordAttributeOnDisk.getShortValues(): lazy read into heap allocated
// memory, rather than using memory mapped buffer :(");
short[] buffer = null;
if (valueLength > 0) {
int len = (int) (valueLength / 2);
buffer = new short[len];
try {
BinaryInputStream i = new BinaryInputStream(new FileInputStream(file), bigEndian);
i.skipInsistently(byteOffset);
i.readUnsigned16(buffer, 0, len);
i.close();
} catch (IOException e) {
throw new DicomException(
"Failed to read value (length "
+ valueLength
+ " dec) in delayed read of "
+ ValueRepresentation.getAsString(getVR())
+ " attribute "
+ getTag());
}
}
return buffer;
}
private long readItemTag() throws IOException {
AttributeTag tag = readAttributeTag();
// System.err.println("EncapsulatedInputStream.readItemTag: tag="+tag);
long vl = i.readUnsigned32(); // always implicit VR form for items and delimiters
bytesRead += 4;
if (tag.equals(TagFromName.SequenceDelimitationItem)) {
// System.err.println("EncapsulatedInputStream.readItemTag: SequenceDelimitationItem");
vl = 0; // regardless of what was read
sequenceDelimiterEncountered = true;
} else if (!tag.equals(TagFromName.Item)) {
throw new IOException(
"Unexpected DICOM tag "
+ tag
+ " (vl="
+ vl
+ ") in encapsulated data whilst expecting Item or SequenceDelimitationItem");
}
// System.err.println("EncapsulatedInputStream.readItemTag: length="+vl);
return vl;
}
/**
* @param i
* @exception IOException
*/
private AttributeTag readAttributeTag() throws IOException {
int group = i.readUnsigned16();
int element = i.readUnsigned16();
bytesRead += 4;
return new AttributeTag(group, element);
}
/**
* Extracts <code>len</code> bytes of data from the current or subsequent fragments.
*
* @param b the buffer into which the data is read.
* @param off the start offset of the data.
* @param len the number of bytes read.
* @return the total number of bytes read into the buffer (always whatever was asked for), or -1
* if there is no more data because the end of a frame has been reached.
* @exception IOException if an I/O error occurs.
*/
public final int read(byte b[], int off, int len) throws IOException {
// System.err.println("EncapsulatedInputStream.read(byte [],"+off+","+len+")");
// System.err.println("EncapsulatedInputStream.read() at start,
// fragmentRemaining="+fragmentRemaining);
// System.err.println("EncapsulatedInputStream.read() at start,
// endOfFrameEncountered="+endOfFrameEncountered);
// System.err.println("EncapsulatedInputStream.read() at start,
// currentFragmentContainsEndOfFrame="+currentFragmentContainsEndOfFrame);
if (endOfFrameEncountered) {
// System.err.println("EncapsulatedInputStream.read() returning -1 since
// endOfFrameEncountered");
return -1; // i.e., won't advance until nextFrame() is called to reset this state
}
int count = 0;
int remainingToDo = len;
while (remainingToDo > 0 && !sequenceDelimiterEncountered && !endOfFrameEncountered) {
// System.err.println("EncapsulatedInputStream.read() remainingToDo="+remainingToDo);
if (fragment == null) {
if (firstTime) {
// System.err.println("EncapsulatedInputStream.read() firstTime");
// first time ... skip offset table ...
long offsetTableLength = readItemTag();
if (sequenceDelimiterEncountered) {
throw new IOException("Expected offset table item tag; got sequence delimiter");
}
// System.err.println("EncapsulatedInputStream.read() skipping
// offsetTableLength="+offsetTableLength);
i.skipInsistently(offsetTableLength);
bytesRead += offsetTableLength;
firstTime = false;
}
// load a new fragment ...
// System.err.println("EncapsulatedInputStream.read() loading a new fragment");
long vl =
readItemTag(); // if sequenceDelimiterEncountered, vl will be zero and no more will be
// done
if (vl != 0) {
currentFragmentContainsEndOfFrame = false;
fragmentRemaining = fragmentSize = (int) vl;
fragment = new byte[fragmentSize];
i.readInsistently(fragment, 0, fragmentSize);
bytesRead += fragmentSize;
fragmentOffset = 0;
// System.err.println("EncapsulatedInputStream.read() fragmentRemaining
// initially="+fragmentRemaining);
// System.err.println("EncapsulatedInputStream.read() fragment =
// "+com.pixelmed.utils.HexDump.dump(fragment));
// Ignore everything between (the last) EOI marker and the end of the fragment
int positionOfEOI = fragmentRemaining - 1;
while (--positionOfEOI > 0) {
int firstMarkerByte = fragment[positionOfEOI] & 0xff;
int secondMarkerByte = fragment[positionOfEOI + 1] & 0xff;
// System.err.println("EncapsulatedInputStream.read() fragment
// fragment["+positionOfEOI+"] = 0x"+Integer.toHexString(firstMarkerByte));
// System.err.println("EncapsulatedInputStream.read() fragment
// fragment["+(positionOfEOI+1)+"] = 0x"+Integer.toHexString(secondMarkerByte));
if (firstMarkerByte == 0xff && secondMarkerByte == 0xd9) {
currentFragmentContainsEndOfFrame = true;
break;
}
}
// System.err.println("EncapsulatedInputStream.read() positionOfEOI="+positionOfEOI);
if (positionOfEOI > 0) { // will be zero if we did not find one
fragmentRemaining =
positionOfEOI + 2; // effectively skips all (hopefully padding) bytes after the EOI
}
// System.err.println("EncapsulatedInputStream.read() fragmentRemaining after removing
// trailing padding="+fragmentRemaining);
}
}
int amountToCopyFromThisFragment =
remainingToDo < fragmentRemaining ? remainingToDo : fragmentRemaining;
// System.err.println("EncapsulatedInputStream.read()
// amountToCopyFromThisFragment="+amountToCopyFromThisFragment);
if (amountToCopyFromThisFragment > 0) {
System.arraycopy(fragment, fragmentOffset, b, off, amountToCopyFromThisFragment);
off += amountToCopyFromThisFragment;
fragmentOffset += amountToCopyFromThisFragment;
fragmentRemaining -= amountToCopyFromThisFragment;
remainingToDo -= amountToCopyFromThisFragment;
count += amountToCopyFromThisFragment;
}
if (fragmentRemaining <= 0) {
fragment = null;
if (currentFragmentContainsEndOfFrame) {
endOfFrameEncountered =
true; // once EOI has been seen in a fragment, use the rest of the fragment including
// the EOI, but no further
}
}
}
// System.err.println("EncapsulatedInputStream.read() returning count="+count);
// System.err.println("EncapsulatedInputStream.read()
// returning="+com.pixelmed.utils.HexDump.dump(fragment,off,count));
return count == 0
? -1
: count; // always returns more than 0 unless end, which is signalled by -1
}