OBF: add FLIM support

See https://trac.openmicroscopy.org/ome/ticket/13196

components/formats-bsd/src/loci/formats/in/OBFReader.java

@@ -221,7 +221,7 @@ protected void initFile(String id) throws FormatException, IOException {
  CoreMetadata meta_data = core.get(image);
 
  final String name = meta_data.seriesMetadata.get("Name").toString();
- metadataStore.setImageName(name, image);
+ metadataStore.setImageName(name.trim(), image);
 
  @SuppressWarnings("unchecked")
  final List<Double> lengths = (List<Double>) meta_data.seriesMetadata.get("Lengths");
@@ -449,6 +449,22 @@ private long initStack(long current) throws FormatException, IOException {
  final int length = in.readInt();
  final String label = in.readString(length);
  labels.add(label);
+
+ if (label.endsWith("X") || (dimension == 1 && isFLIMLabel(labels.get(0)))) {
+ meta_data.sizeX = sizes[dimension];
+ }
+ else if (label.endsWith("Y") || (dimension == 2 && isFLIMLabel(labels.get(0)))) {
+ meta_data.sizeY = sizes[dimension];
+ }
+ else if (isFLIMLabel(label)) {
+ meta_data.sizeZ = sizes[dimension];
+ meta_data.moduloZ.type = FormatTools.LIFETIME;
+ meta_data.moduloZ.typeDescription = label;
+ meta_data.moduloZ.start = 0;
+ meta_data.moduloZ.step = 1;
+ meta_data.moduloZ.end = meta_data.sizeZ - 1;
+ meta_data.imageCount = meta_data.sizeZ * meta_data.sizeC * meta_data.sizeT;
+ }
  }
  meta_data.seriesMetadata.put("Labels", labels);
 
@@ -486,6 +502,10 @@ private long initStack(long current) throws FormatException, IOException {
  }
  }
 
+ private boolean isFLIMLabel(String label) {
+ return label.startsWith("SPCM");
+ }
+
  private int getPixelType(int type) throws FormatException {
  switch (type) {
  case 0x01: return FormatTools.UINT8;
@@ -551,11 +571,17 @@ public byte[] openBytes(int no, byte[] buffer, int x, int y, int w, int h)
  final int columns = getSizeX();
  final int bytesPerPixel = getBitsPerPixel() / 8;
 
+ boolean isFLIM = FormatTools.LIFETIME.equals(getModuloZ().type);
+
  final int series = getSeries();
  final Stack stack = stacks.get(series);
  if (stack.compression) {
  if (series != currentInflatedFrame.series) {
- currentInflatedFrame.bytes = new byte[rows * columns * bytesPerPixel];
+ int bufferSize = rows * columns * bytesPerPixel;
+ if (isFLIM) {
+ bufferSize *= getSizeZ();
+ }
+ currentInflatedFrame.bytes = new byte[bufferSize];
  currentInflatedFrame.series = series;
  currentInflatedFrame.number = - 1;
  }
@@ -566,7 +592,7 @@ public byte[] openBytes(int no, byte[] buffer, int x, int y, int w, int h)
 
  byte[] bytes = currentInflatedFrame.bytes;
  if (no != currentInflatedFrame.number) {
- if (no < currentInflatedFrame.number) {
+ if (no < currentInflatedFrame.number && !isFLIM) {
  currentInflatedFrame.number = - 1;
  }
  if (currentInflatedFrame.number == - 1) {
@@ -575,7 +601,9 @@ public byte[] openBytes(int no, byte[] buffer, int x, int y, int w, int h)
  }
 
  byte[] input = new byte[8192];
- while (no != currentInflatedFrame.number) {
+ int end = isFLIM ? getSizeZ() - 1 : no;
+
+ while (currentInflatedFrame.number != end) {
  int offset = 0;
  while (offset != bytes.length) {
  if (inflater.needsInput()) {
@@ -586,6 +614,10 @@ public byte[] openBytes(int no, byte[] buffer, int x, int y, int w, int h)
  in.read(input, 0, length);
  inflater.setInput(input, 0, length);
  }
+ else if (isFLIM && remainder == 0 && currentInflatedFrame.number >= 0) {
+ offset = bytes.length;
+ continue;
+ }
  else {
  throw new FormatException("Corrupted zlib compression");
  }
@@ -603,14 +635,37 @@ else if (inflater.needsDictionary()) {
  ++ currentInflatedFrame.number;
  }
  }
- for (int row = 0; row != h; ++ row) {
- System.arraycopy(bytes, ((row + y) * columns + x) * bytesPerPixel, buffer, row * w * bytesPerPixel, w * bytesPerPixel);
+ if (isFLIM) {
+ for (int yy=y; yy<y+h; yy++) {
+ for (int xx=x; xx<x+w; xx++) {
+ int src = getSizeZ() * bytesPerPixel * ((yy * getSizeX()) + xx) + no * bytesPerPixel;
+ int dest = ((yy - y) * w * bytesPerPixel) + ((xx - x) * bytesPerPixel);
+ System.arraycopy(bytes, src, buffer, dest, bytesPerPixel);
+ }
+ }
+ }
+ else {
+ for (int row = 0; row != h; ++ row) {
+ System.arraycopy(bytes, ((row + y) * columns + x) * bytesPerPixel, buffer, row * w * bytesPerPixel, w * bytesPerPixel);
+ }
  }
  }
  else {
- for (int row = 0; row != h; ++ row) {
- in.seek(stack.position + ((no * rows + row + y) * columns + x) * bytesPerPixel);
- in.read(buffer, row * w * bytesPerPixel, w * bytesPerPixel);
+ if (isFLIM) {
+ for (int yy=y; yy<y+h; yy++) {
+ for (int xx=x; xx<x+w; xx++) {
+ long src = stack.position + getSizeZ() * bytesPerPixel * ((yy * getSizeX()) + xx) + no * bytesPerPixel;
+ int dest = ((yy - y) * w * bytesPerPixel) + ((xx - x) * bytesPerPixel);
+ in.seek(src);
+ in.read(buffer, dest, bytesPerPixel);
+ }
+ }
+ }
+ else {
+ for (int row = 0; row != h; ++ row) {
+ in.seek(stack.position + ((no * rows + row + y) * columns + x) * bytesPerPixel);
+ in.read(buffer, row * w * bytesPerPixel, w * bytesPerPixel);
+ }
  }
  }