private void findTIFFs() throws IOException {
Location baseFile = new Location(currentId).getAbsoluteFile();
Location parent = baseFile.getParentFile();
FilePattern pattern = new FilePattern(baseFile);
String[] tiffs = pattern.getFiles();
NumericComparator comparator = new NumericComparator();
Arrays.sort(tiffs, comparator);
Vector<String> validTIFFs = new Vector<String>();
for (String tiff : tiffs) {
if (!new Location(tiff).exists()) {
String base = tiff.substring(tiff.lastIndexOf(File.separator) + 1);
base = base.substring(0, base.indexOf("."));
String suffix = tiff.substring(tiff.lastIndexOf("."));
while (base.length() < 3) {
base = "0" + base;
}
Location test = new Location(parent, base + suffix);
if (test.exists()) {
tiff = test.getAbsolutePath();
} else continue;
}
validTIFFs.add(tiff);
}
files = validTIFFs.toArray(new String[validTIFFs.size()]);
}
/* @see loci.formats.FormatReader#initFile(String) */
public void initFile(String id) throws FormatException, IOException {
super.initFile(id);
tiffReader = new MinimalTiffReader();
positions = new Vector<Position>();
LOGGER.info("Reading metadata file");
// find metadata.txt
Location file = new Location(currentId).getAbsoluteFile();
Location parentFile = file.getParentFile();
String metadataFile = METADATA;
if (file.exists()) {
metadataFile = new Location(parentFile, METADATA).getAbsolutePath();
// look for other positions
if (parentFile.getName().indexOf("Pos_") >= 0) {
parentFile = parentFile.getParentFile();
String[] dirs = parentFile.list(true);
Arrays.sort(dirs);
for (String dir : dirs) {
if (dir.indexOf("Pos_") >= 0) {
Position pos = new Position();
Location posDir = new Location(parentFile, dir);
pos.metadataFile = new Location(posDir, METADATA).getAbsolutePath();
positions.add(pos);
}
}
} else {
Position pos = new Position();
pos.metadataFile = metadataFile;
positions.add(pos);
}
}
core = new CoreMetadata[positions.size()];
for (int i = 0; i < positions.size(); i++) {
core[i] = new CoreMetadata();
setSeries(i);
parsePosition(i);
}
setSeries(0);
populateMetadata();
}
/* Locate the experiment file given any file in set */
private String locateExperimentFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "exp")) {
Location parent = new Location(id).getAbsoluteFile().getParentFile();
if (checkSuffix(id, "tif")) parent = parent.getParentFile();
Location expFile = new Location(parent, EXPERIMENT_FILE);
if (expFile.exists()) {
return expFile.getAbsolutePath();
}
throw new FormatException(
"Could not find " + EXPERIMENT_FILE + " in " + parent.getAbsolutePath());
}
return id;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String name, boolean open) {
if (super.isThisType(name, open)) return true;
if (!checkSuffix(name, "tif") && open) {
Location current = new Location(name).getAbsoluteFile();
Location parent = current.getParentFile();
String tiff = current.getName();
int index = tiff.lastIndexOf(".");
if (index >= 0) {
tiff = tiff.substring(0, index);
}
tiff += ".tif";
Location tiffFile = new Location(parent, tiff);
return tiffFile.exists() && isThisType(tiffFile.getAbsolutePath(), open);
}
return false;
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
if (!checkSuffix(id, "vsi")) {
Location current = new Location(id).getAbsoluteFile();
Location parent = current.getParentFile();
parent = parent.getParentFile();
Location grandparent = parent.getParentFile();
String vsi = parent.getName();
vsi = vsi.substring(1, vsi.length() - 1) + ".vsi";
Location vsiFile = new Location(grandparent, vsi);
if (!vsiFile.exists()) {
throw new FormatException("Could not find .vsi file.");
} else {
id = vsiFile.getAbsolutePath();
}
}
parser = new TiffParser(id);
ifds = parser.getIFDs();
RandomAccessInputStream vsi = new RandomAccessInputStream(id);
vsi.order(parser.getStream().isLittleEndian());
vsi.seek(8);
readTags(vsi);
vsi.seek(parser.getStream().getFilePointer());
vsi.skipBytes(273);
ArrayList<String> files = new ArrayList<String>();
Location file = new Location(id).getAbsoluteFile();
Location dir = file.getParentFile();
String name = file.getName();
name = name.substring(0, name.lastIndexOf("."));
Location pixelsDir = new Location(dir, "_" + name + "_");
String[] stackDirs = pixelsDir.list(true);
if (stackDirs != null) {
for (String f : stackDirs) {
Location stackDir = new Location(pixelsDir, f);
String[] pixelsFiles = stackDir.list(true);
if (pixelsFiles != null) {
for (String pixelsFile : pixelsFiles) {
if (checkSuffix(pixelsFile, "ets")) {
files.add(new Location(stackDir, pixelsFile).getAbsolutePath());
}
}
}
}
}
files.add(file.getAbsolutePath());
usedFiles = files.toArray(new String[files.size()]);
core = new CoreMetadata[files.size() - 1 + ifds.size()];
tileOffsets = new Long[files.size() - 1][];
rows = new int[files.size() - 1];
cols = new int[files.size() - 1];
nDimensions = new int[core.length];
IFDList exifs = parser.getExifIFDs();
compressionType = new int[core.length];
tileX = new int[core.length];
tileY = new int[core.length];
tileMap = new HashMap[core.length];
for (int s = 0; s < core.length; s++) {
core[s] = new CoreMetadata();
}
for (int s = 0; s < core.length; s++) {
tileMap[s] = new HashMap<TileCoordinate, Integer>();
if (s == 0 && !hasFlattenedResolutions()) {
core[s].resolutionCount = ifds.size() + (files.size() == 1 ? 0 : 1);
}
if (s < files.size() - 1) {
setSeries(s);
parseETSFile(files.get(s), s);
core[s].littleEndian = compressionType[s] == RAW;
core[s].interleaved = core[s].rgb;
if (s == 0 && exifs.size() > 0) {
IFD exif = exifs.get(0);
int newX = exif.getIFDIntValue(IFD.PIXEL_X_DIMENSION);
int newY = exif.getIFDIntValue(IFD.PIXEL_Y_DIMENSION);
if (getSizeX() > newX || getSizeY() > newY) {
core[s].sizeX = newX;
core[s].sizeY = newY;
}
}
setSeries(0);
} else {
IFD ifd = ifds.get(s - files.size() + 1);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
core[s].sizeX = (int) ifd.getImageWidth();
core[s].sizeY = (int) ifd.getImageLength();
core[s].sizeZ = 1;
core[s].sizeT = 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed =
p == PhotoInterp.RGB_PALETTE
&& (get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = 1;
core[s].pixelType = ifd.getPixelType();
core[s].interleaved = false;
core[s].falseColor = false;
core[s].thumbnail = s != 0;
}
core[s].metadataComplete = true;
core[s].dimensionOrder = "XYCZT";
}
vsi.close();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
/* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
for (IFD ifd : ifds) {
tiffParser.fillInIFD(ifd);
}
String comment = ifds.get(0).getComment();
String[] values = comment.split(";");
for (String v : values) {
int eq = v.indexOf("=");
if (eq < 0) continue;
String key = v.substring(0, eq).trim();
String value = v.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("OverlapsXY")) {
String[] overlapValues = value.split(" ");
overlaps = new int[ifds.size() * 2];
for (int i = 0; i < overlapValues.length; i++) {
overlaps[i] = Integer.parseInt(overlapValues[i]);
}
}
}
core = new CoreMetadata[ifds.size()];
for (int i = 0; i < core.length; i++) {
setSeries(i);
core[i] = new CoreMetadata();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {}
}
setSeries(0);
// repopulate core metadata
for (int s = 0; s < core.length; s++) {
IFD ifd = ifds.get(s);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
long numTileRows = ifd.getTilesPerColumn() - 1;
long numTileCols = ifd.getTilesPerRow() - 1;
int overlapX = overlaps[s * 2];
int overlapY = overlaps[s * 2 + 1];
core[s].sizeX = (int) (ifd.getImageWidth() - (numTileCols * overlapX));
core[s].sizeY = (int) (ifd.getImageLength() - (numTileRows * overlapY));
core[s].sizeZ = 1;
core[s].sizeT = 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed =
p == PhotoInterp.RGB_PALETTE
&& (get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = 1;
core[s].pixelType = ifd.getPixelType();
core[s].metadataComplete = true;
core[s].interleaved = false;
core[s].falseColor = false;
core[s].dimensionOrder = "XYCZT";
core[s].thumbnail = s > 0;
}
// look for all of the other associated metadata files
files = new ArrayList<String>();
Location baseFile = new Location(currentId).getAbsoluteFile();
Location parent = baseFile.getParentFile();
String name = baseFile.getName();
if (name.indexOf(".") >= 0) {
name = name.substring(0, name.indexOf(".") + 1);
}
roiFile = new Location(parent, name + "ROI").getAbsolutePath();
roiDrawFile = new Location(parent, name + "ROI-draw").getAbsolutePath();
String[] list = parent.list(true);
for (String f : list) {
if (!f.equals(baseFile.getName())) {
files.add(new Location(parent, f).getAbsolutePath());
}
}
}