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ZarrReader: Use chunk API #20

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ZarrReader: Use chunk API #20

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52 changes: 22 additions & 30 deletions src/loci/formats/in/ZarrReader.java
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Original file line number Diff line number Diff line change
Expand Up @@ -134,6 +134,14 @@ public int getOptimalTileWidth() {
return zarrService.getChunkSize()[0];
}

/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
//TODO: Re-add @Override
//@Override
public int[] getOptimalChunkSize() {
FormatTools.assertId(currentId, true, 1);
return zarrService.getChunkSize();
}

/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
Expand Down Expand Up @@ -399,58 +407,42 @@ public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws F
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int[] coordinates = getZCTCoords(no);
int [] shape = {1, 1, 1, h, w};
int [] offsets = {coordinates[2], coordinates[1], coordinates[0], y, x};
return openBytes(buf, shape, offsets);
}

//TODO: Re-add @Override
//@Override
public byte[] openBytes(byte[] buf, int[] shape, int[] offsets) throws FormatException, IOException {
//TODO: checkPlaneParameters to be re-added once FormatTools updated
//FormatTools.checkParameters(this, buf.length, shape, offsets);

int zarrArrayShapeSize = zarrService.getShape().length;
if (zarrArrayShapeSize < 5) {
shape = getOriginalShape(shape, zarrArrayShapeSize);
}
int [] offsets = {coordinates[2], coordinates[1], coordinates[0], y, x};
if (zarrArrayShapeSize < 5) {
offsets = getOriginalShape(offsets, zarrArrayShapeSize);
}
Object image = zarrService.readBytes(shape, offsets);

boolean little = zarrService.isLittleEndian();
int bpp = FormatTools.getBytesPerPixel(zarrService.getPixelType());
if (image instanceof byte[]) {
buf = (byte []) image;
}
else if (image instanceof short[]) {
short[] data = (short[]) image;
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
DataTools.unpackBytes(data[(row * w) + i], buf, base + 2 * i, 2, little);
}
}
buf = DataTools.shortsToBytes(data, little);
}
else if (image instanceof int[]) {
int[] data = (int[]) image;
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
DataTools.unpackBytes(data[(row * w) + i], buf, base + 4 * i, 4, little);
}
}
buf = DataTools.intsToBytes(data, little);
}
else if (image instanceof float[]) {
float[] data = (float[]) image;
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
int value = Float.floatToIntBits(data[(row * w) + i]);
DataTools.unpackBytes(value, buf, base + 4 * i, 4, little);
}
}
buf = DataTools.floatsToBytes(data, little);
}
else if (image instanceof double[]) {
double[] data = (double[]) image;
for (int row = 0; row < h; row++) {
int base = row * w * bpp;
for (int i = 0; i < w; i++) {
long value = Double.doubleToLongBits(data[(row * w) + i]);
DataTools.unpackBytes(value, buf, base + 8 * i, 8, little);
}
}
buf = DataTools.doublesToBytes(data, little);
}
return buf;
}
Expand Down