/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
* published by the Free Software Foundation, either version 2 of the
* License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public
* License along with this program. If not, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.FileNotFoundException;
import java.io.IOException;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;
import ome.xml.model.primitives.PositiveFloat;
import ome.units.quantity.Length;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* NiftiReader is the file format reader for NIfTI files.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class NiftiReader extends FormatReader {
// -- Constants --
/** Code for meters. */
private static final int UNITS_METER = 1;
/** Code for millimeters. */
private static final int UNITS_MM = 2;
/** Code for milliseconds. */
private static final int UNITS_MSEC = 16;
/** Code for microseconds. */
private static final int UNITS_USEC = 24;
// -- Fields --
/** Offset to the pixel data in the .img file. */
private int pixelOffset;
/** File containing the pixel data. */
private transient RandomAccessInputStream pixelFile;
private String pixelsFilename;
private short nDimensions;
private String description;
private double voxelWidth, voxelHeight, sliceThickness, deltaT;
// -- Constructor --
/** Constructs a new NIfTI reader. */
public NiftiReader() {
super("NIfTI", new String[] {"nii", "img", "hdr"});
suffixSufficient = false;
domains = new String[] {FormatTools.MEDICAL_DOMAIN,
FormatTools.UNKNOWN_DOMAIN};
hasCompanionFiles = true;
datasetDescription = "A single .nii file or one .img file and a " +
"similarly-named .hdr file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isSingleFile(String) */
@Override
public boolean isSingleFile(String id) throws FormatException, IOException {
return checkSuffix(id, "nii");
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (checkSuffix(name, "nii")) return true;
int dot = name.lastIndexOf(".");
if (dot == 0) dot = name.length() - 1;
if (dot < 0) return false;
if (!open) return false;
String headerFile = name.substring(0, dot) + ".hdr";
try {
RandomAccessInputStream header = new RandomAccessInputStream(headerFile);
boolean isValid = isThisType(header);
header.close();
return isValid;
}
catch (FileNotFoundException e) { } // NB: No output for missing header.
catch (IOException e) { LOGGER.debug("", e); }
return false;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 348;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
stream.seek(344);
String magic = stream.readString(3);
return magic.equals("ni1") || magic.equals("n+1");
}
/* @see loci.formats.IFormatReader#getDomains() */
@Override
public String[] getDomains() {
FormatTools.assertId(currentId, true, 1);
String[] domain = new String[1];
domain[0] = nDimensions <= 3 ?
FormatTools.UNKNOWN_DOMAIN : FormatTools.MEDICAL_DOMAIN;
return domain;
}
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException
{
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int planeSize = FormatTools.getPlaneSize(this);
pixelFile.seek(pixelOffset + no * planeSize);
readPlane(pixelFile, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (pixelsFilename.equals(currentId) && noPixels) return null;
if (!noPixels && !pixelsFilename.equals(currentId)) {
return new String[] {currentId, pixelsFilename};
}
return new String[] {currentId};
}
/* @see loci.formats.IFormatReader#fileGroupOption(String) */
@Override
public int fileGroupOption(String id) throws FormatException, IOException {
return FormatTools.MUST_GROUP;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (pixelFile != null) pixelFile.close();
if (!fileOnly) {
pixelOffset = 0;
pixelFile = null;
pixelsFilename = null;
nDimensions = 0;
description = null;
voxelWidth = voxelHeight = sliceThickness = deltaT = 0d;
}
}
/* @see loci.formats.IFormatReader#reopenFile() */
@Override
public void reopenFile() throws IOException {
super.reopenFile();
if (pixelFile == null) {
pixelFile = new RandomAccessInputStream(pixelsFilename);
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
// the dataset has two files - we want the one ending in '.hdr'
if (id.endsWith(".img")) {
LOGGER.info("Looking for header file");
String header = id.substring(0, id.lastIndexOf(".")) + ".hdr";
if (new Location(header).exists()) {
setId(header);
return;
}
else throw new FormatException("Header file not found.");
}
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata m = core.get(0);
in.seek(40);
short check = in.readShort();
boolean little = check < 1 || check > 7;
in.seek(40);
if (id.endsWith(".hdr")) {
pixelsFilename = id.substring(0, id.lastIndexOf(".")) + ".img";
pixelFile = new RandomAccessInputStream(pixelsFilename);
}
else if (id.endsWith(".nii")) {
pixelsFilename = id;
pixelFile = in;
}
in.order(little);
pixelFile.order(little);
m.littleEndian = little;
LOGGER.info("Reading header");
nDimensions = in.readShort();
m.sizeX = in.readShort();
m.sizeY = in.readShort();
m.sizeZ = in.readShort();
m.sizeT = in.readShort();
in.skipBytes(20);
short dataType = in.readShort();
in.skipBytes(36);
pixelOffset = (int) in.readFloat();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
populateExtendedMetadata();
}
LOGGER.info("Populating core metadata");
m.sizeC = 1;
if (getSizeZ() == 0) m.sizeZ = 1;
if (getSizeT() == 0) m.sizeT = 1;
m.imageCount = getSizeZ() * getSizeT();
m.indexed = false;
m.dimensionOrder = "XYCZT";
populatePixelType(dataType);
m.rgb = getSizeC() > 1;
m.interleaved = isRGB();
LOGGER.info("Populating MetadataStore");
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(description, 0);
Length sizeX =
FormatTools.getPhysicalSizeX(new Double(voxelWidth));
Length sizeY =
FormatTools.getPhysicalSizeY(new Double(voxelHeight));
Length sizeZ =
FormatTools.getPhysicalSizeZ(new Double(sliceThickness));
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, 0);
}
store.setPixelsTimeIncrement(new Time(new Double(deltaT), UNITS.S), 0);
}
}
// -- Helper methods --
private void populatePixelType(int dataType) throws FormatException {
CoreMetadata m = core.get(0);
switch (dataType) {
case 1:
case 2:
m.pixelType = FormatTools.UINT8;
break;
case 4:
m.pixelType = FormatTools.INT16;
break;
case 8:
m.pixelType = FormatTools.INT32;
break;
case 16:
m.pixelType = FormatTools.FLOAT;
break;
case 64:
m.pixelType = FormatTools.DOUBLE;
break;
case 128:
m.pixelType = FormatTools.UINT8;
m.sizeC = 3;
case 256:
m.pixelType = FormatTools.INT8;
break;
case 512:
m.pixelType = FormatTools.UINT16;
break;
case 768:
m.pixelType = FormatTools.UINT32;
break;
case 2304:
m.pixelType = FormatTools.UINT8;
m.sizeC = 4;
default:
throw new FormatException("Unsupported data type: " + dataType);
}
}
private void populateExtendedMetadata() throws IOException {
in.seek(40);
char sliceOrdering = in.readChar();
in.skipBytes(8);
short dim5 = in.readShort();
short dim6 = in.readShort();
short dim7 = in.readShort();
float intent1 = in.readFloat();
float intent2 = in.readFloat();
float intent3 = in.readFloat();
short intentCode = in.readShort();
short dataType = in.readShort();
short bitpix = in.readShort();
short sliceStart = in.readShort();
in.skipBytes(4);
voxelWidth = in.readFloat();
voxelHeight = in.readFloat();
sliceThickness = in.readFloat();
deltaT = in.readFloat();
in.skipBytes(16);
float scaleSlope = in.readFloat();
float scaleIntercept = in.readFloat();
short sliceEnd = in.readShort();
char sliceCode = in.readChar();
char units = in.readChar();
int spatialUnits = (units & 7);
int timeUnits = (units & 0x38);
// correct physical dimensions according to spatial and time units
int spatialCorrection = 1;
switch (spatialUnits) {
case UNITS_METER:
spatialCorrection = 1000000;
break;
case UNITS_MM:
spatialCorrection = 1000;
break;
}
voxelWidth *= spatialCorrection;
voxelHeight *= spatialCorrection;
sliceThickness *= spatialCorrection;
int timeCorrection = 1;
switch (timeUnits) {
case UNITS_MSEC:
timeCorrection = 1000;
break;
case UNITS_USEC:
timeCorrection = 1000000;
break;
}
deltaT /= timeCorrection;
float calMax = in.readFloat();
float calMin = in.readFloat();
float sliceDuration = in.readFloat();
float toffset = in.readFloat();
in.skipBytes(8);
description = in.readString(80);
in.skipBytes(24);
short qformCode = in.readShort();
short sformCode = in.readShort();
float quaternionB = in.readFloat();
float quaternionC = in.readFloat();
float quaternionD = in.readFloat();
float quaternionX = in.readFloat();
float quaternionY = in.readFloat();
float quaternionZ = in.readFloat();
float[][] transform = new float[3][4];
for (int i=0; i<transform.length; i++) {
for (int j=0; j<transform[i].length; j++) {
transform[i][j] = in.readFloat();
}
}
String intentName = in.readString(16);
if (in.getFilePointer() + 4 < in.length()) {
in.skipBytes(4);
byte extension = in.readByte();
in.skipBytes(3);
if (extension != 0) {
long max = in.equals(pixelFile) ? pixelOffset : in.length();
while (in.getFilePointer() < max) {
long fp = in.getFilePointer();
int esize = in.readInt();
int ecode = in.readInt();
// TODO : parse key/value pairs from header extensions
if (ecode == 2) {
// DICOM format - attribute tag and value
}
else if (ecode == 4) {
// AFNI format - XML-style elements
}
in.seek(fp + esize);
}
}
}
LOGGER.info("Populating metadata table");
for (int i=0; i<transform.length; i++) {
String axis = i == 0 ? "X" : i == 1 ? "Y" : "Z";
for (int j=0; j<transform[i].length; j++) {
addGlobalMeta("Affine transform " + axis + "[" + j + "]",
transform[i][j]);
}
}
addGlobalMeta("Intent name", intentName);
addGlobalMeta("Slice Ordering", sliceOrdering);
addGlobalMeta("Number of dimensions", nDimensions);
addGlobalMeta("Width", getSizeX());
addGlobalMeta("Height", getSizeY());
addGlobalMeta("Number of Z slices", getSizeZ());
addGlobalMeta("Number of time points", getSizeT());
addGlobalMeta("Dimension 5", dim5);
addGlobalMeta("Dimension 6", dim6);
addGlobalMeta("Dimension 7", dim7);
addGlobalMeta("Intent #1", intent1);
addGlobalMeta("Intent #2", intent2);
addGlobalMeta("Intent #3", intent3);
addGlobalMeta("Intent code", intentCode);
addGlobalMeta("Data type", dataType);
addGlobalMeta("Bits per pixel", bitpix);
addGlobalMeta("Slice start", sliceStart);
addGlobalMeta("Voxel width", voxelWidth);
addGlobalMeta("Voxel height", voxelHeight);
addGlobalMeta("Slice thickness", sliceThickness);
addGlobalMeta("Time increment", deltaT);
addGlobalMeta("Scale slope", scaleSlope);
addGlobalMeta("Scale intercept", scaleIntercept);
addGlobalMeta("Slice end", sliceEnd);
addGlobalMeta("Calibrated maximum", calMax);
addGlobalMeta("Calibrated minimum", calMin);
addGlobalMeta("Slice duration", sliceDuration);
addGlobalMeta("Time offset", toffset);
addGlobalMeta("Description", description);
addGlobalMeta("Q-form Code", qformCode);
addGlobalMeta("S-form Code", sformCode);
addGlobalMeta("Quaternion b parameter", quaternionB);
addGlobalMeta("Quaternion c parameter", quaternionC);
addGlobalMeta("Quaternion d parameter", quaternionD);
addGlobalMeta("Quaternion x parameter", quaternionX);
addGlobalMeta("Quaternion y parameter", quaternionY);
addGlobalMeta("Quaternion z parameter", quaternionZ);
}
}