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Merge pull request #90 from melissalinkert/multi-plane-rgb
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Expand support for `--rgb`
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@chris-allan
chris-allan authored Dec 6, 2022
2 parents 4e7dbf9 + f914084 commit a3960fd
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Showing 2 changed files with 148 additions and 79 deletions.
202 changes: 123 additions & 79 deletions src/main/java/com/glencoesoftware/pyramid/PyramidFromDirectoryWriter.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,8 @@ public class PyramidFromDirectoryWriter implements Callable<Void> {

@Option(
names = "--rgb",
description = "Attempt to write channels as RGB; channel count must be 3"
description = "Attempt to write channels as RGB; " +
"channel count must be a multiple of 3"
)
boolean rgb = false;

Expand Down Expand Up @@ -679,20 +680,51 @@ else if (layoutVersion != 3) {
s.dimensionLengths[s.dimensionOrder.indexOf("T") - 2] = s.t;
s.dimensionLengths[s.dimensionOrder.indexOf("C") - 2] = s.c;

s.rgb = rgb && (s.c == 3) && (s.z * s.t == 1);
if (!s.rgb) {
s.planeCount *= s.c;
}
else {
int rgbChannels = 1;
int effectiveChannels = s.c;

// --rgb flag only respected if the number of channels in the source data
// is a multiple of 3
// this assumes that channels should be grouped by 3s (not 2s or 4s)
// into RGB planes
// this could be made configurable later?
s.rgb = rgb && (s.c % 3 == 0);
if (s.rgb) {
rgbChannels = 3;
effectiveChannels = s.c / rgbChannels;
LOG.debug("Merging {} original channels into {} RGB channels",
s.c, effectiveChannels);

OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) metadata.getRoot();
Pixels pixels = root.getImage(seriesIndex).getPixels();
while (pixels.sizeOfChannelList() > 1) {
Channel ch = pixels.getChannel(pixels.sizeOfChannelList() - 1);
for (int index=pixels.sizeOfChannelList()-1; index>0; index--) {
if (index % rgbChannels == 0) {
continue;
}
Channel ch = pixels.getChannel(index);
pixels.removeChannel(ch);
}
Channel onlyChannel = pixels.getChannel(0);
onlyChannel.setSamplesPerPixel(new PositiveInteger(s.c));
for (int index=0; index<pixels.sizeOfChannelList(); index++) {
Channel channel = pixels.getChannel(index);
channel.setSamplesPerPixel(new PositiveInteger(rgbChannels));
}

// RGB data needs to have XYC* dimension order
if (!s.dimensionOrder.startsWith("XYC")) {
if (s.dimensionOrder.indexOf("Z") < s.dimensionOrder.indexOf("T")) {
s.dimensionOrder = "XYCZT";
}
else {
s.dimensionOrder = "XYCTZ";
}
}
}
else if (rgb) {
LOG.warn(
"Ignoring --rgb flag; channel count {} is not a multiple of 3", s.c);
}

s.planeCount *= effectiveChannels;

s.describePyramid(reader, metadata);

Expand All @@ -708,15 +740,16 @@ else if (layoutVersion != 3) {
MetadataTools.populateMetadata(
this.metadata, seriesIndex, null, s.littleEndian, s.dimensionOrder,
FormatTools.getPixelTypeString(s.pixelType),
descriptor.sizeX, descriptor.sizeY, s.z, s.c, s.t, s.rgb ? s.c : 1);
descriptor.sizeX, descriptor.sizeY, s.z, s.c, s.t,
rgbChannels);
}
else {
if (legacy) {
MetadataTools.populateMetadata(this.metadata,
descriptor.resolutionNumber, null, s.littleEndian,
s.dimensionOrder, FormatTools.getPixelTypeString(s.pixelType),
descriptor.sizeX, descriptor.sizeY,
s.z, s.c, s.t, s.rgb ? s.c : 1);
s.z, s.c, s.t, rgbChannels);
}
else {
metadata.setResolutionSizeX(new PositiveInteger(
Expand Down Expand Up @@ -776,7 +809,7 @@ private void convertPyramid(PyramidSeries s)
}
}

int rgbChannels = s.rgb ? s.c : 1;
int rgbChannels = s.rgb ? 3 : 1;
int bytesPerPixel = FormatTools.getBytesPerPixel(s.pixelType);
try {
for (int resolution=0; resolution<s.numberOfResolutions; resolution++) {
Expand All @@ -803,77 +836,88 @@ private void convertPyramid(PyramidSeries s)
pb = null;
}

for (int plane=0; plane<s.planeCount; plane++) {
int tileIndex = 0;
// if the resolution has already been calculated,
// just read each tile from disk and store in the OME-TIFF
for (int y = 0; y < descriptor.numberOfTilesY; y++) {
for (int x = 0; x < descriptor.numberOfTilesX; x++, tileIndex++) {
Region region = new Region(
x * descriptor.tileSizeX,
y * descriptor.tileSizeY, 0, 0);
region.width = (int) Math.min(
descriptor.tileSizeX, descriptor.sizeX - region.x);
region.height = (int) Math.min(
descriptor.tileSizeY, descriptor.sizeY - region.y);

if (region.width <= 0 || region.height <= 0) {
continue;
}
int plane = 0;
for (int t=0; t<s.t; t++) {
for (int c=0; c<(s.c / rgbChannels); c++) {
for (int z=0; z<s.z; z++, plane++) {
int tileIndex = 0;
// if the resolution has already been calculated,
// just read each tile from disk and store in the OME-TIFF
for (int y=0; y<descriptor.numberOfTilesY; y++) {
for (int x=0; x<descriptor.numberOfTilesX; x++, tileIndex++) {
Region region = new Region(
x * descriptor.tileSizeX,
y * descriptor.tileSizeY, 0, 0);
region.width = (int) Math.min(
descriptor.tileSizeX, descriptor.sizeX - region.x);
region.height = (int) Math.min(
descriptor.tileSizeY, descriptor.sizeY - region.y);

if (region.width <= 0 || region.height <= 0) {
continue;
}

for (int ch=0; ch<rgbChannels; ch++) {
StopWatch t0 = new Slf4JStopWatch("getInputTileBytes");
byte[] tileBytes;
try {
int planeIndex = plane * rgbChannels + ch;
tileBytes =
getInputTileBytes(s, resolution, planeIndex, x, y, region);
}
finally {
t0.stop();
}
for (int ch=0; ch<rgbChannels; ch++) {
StopWatch t0 = new Slf4JStopWatch("getInputTileBytes");
byte[] tileBytes;
try {
// assumes TCZYX order consistent with bioformats2raw
int planeIndex = FormatTools.positionToRaster(
s.dimensionLengths,
new int[] {z, c * rgbChannels + ch, t});
tileBytes =
getInputTileBytes(s, resolution, planeIndex,
x, y, region);
}
finally {
t0.stop();
}

final int currentIndex = tileCount * ch + tileIndex;
final int currentPlane = plane;
final int currentResolution = resolution;
executor.execute(() -> {
Slf4JStopWatch t1 = new Slf4JStopWatch("writeTile");
try {
if (tileBytes != null) {
if (region.width == descriptor.tileSizeX &&
region.height == descriptor.tileSizeY)
{
writeTile(s, currentPlane, tileBytes,
currentIndex, currentResolution);
final int currentIndex = tileCount * ch + tileIndex;
final int currentPlane = plane;
final int currentResolution = resolution;
executor.execute(() -> {
Slf4JStopWatch t1 = new Slf4JStopWatch("writeTile");
try {
if (tileBytes != null) {
if (region.width == descriptor.tileSizeX &&
region.height == descriptor.tileSizeY)
{
writeTile(s, currentPlane, tileBytes,
currentIndex, currentResolution);
}
else {
// padded tile, use descriptor X and Y tile size
int tileX = descriptor.tileSizeX;
int tileY = descriptor.tileSizeY;
byte[] realTile =
new byte[tileX * tileY * bytesPerPixel];
int totalRows = region.height;
int inRowLen = region.width * bytesPerPixel;
int outRowLen = tileX * bytesPerPixel;
for (int row=0; row<totalRows; row++) {
System.arraycopy(tileBytes, row * inRowLen,
realTile, row * outRowLen, inRowLen);
}
writeTile(s, currentPlane, realTile,
currentIndex, currentResolution);
}
}
}
else {
// padded tile, use descriptor X and Y tile size
byte[] realTile =
new byte[descriptor.tileSizeX * descriptor.tileSizeY
* bytesPerPixel];
int totalRows = region.height;
int inRowLen = region.width * bytesPerPixel;
int outRowLen = descriptor.tileSizeX * bytesPerPixel;
for (int row=0; row<totalRows; row++) {
System.arraycopy(tileBytes, row * inRowLen,
realTile, row * outRowLen, inRowLen);
catch (FormatException|IOException e) {
LOG.error(
"Failed to write tile in series {} resolution {}",
s.index, currentResolution, e);
}
finally {
t1.stop();
if (pb != null) {
pb.step();
}
writeTile(s, currentPlane, realTile,
currentIndex, currentResolution);
}
}
}
catch (FormatException|IOException e) {
LOG.error("Failed to write tile in series {} resolution {}",
s.index, currentResolution, e);
});
}
finally {
t1.stop();
if (pb != null) {
pb.step();
}
}
});
}
}
}
}
Expand Down Expand Up @@ -996,7 +1040,7 @@ else if (FormatTools.isSigned(s.pixelType)) {

ifd.put(IFD.SAMPLE_FORMAT, sampleFormat);

int[] bps = new int[s.rgb ? s.c : 1];
int[] bps = new int[s.rgb ? 3 : 1];
Arrays.fill(bps, FormatTools.getBytesPerPixel(s.pixelType) * 8);
ifd.put(IFD.BITS_PER_SAMPLE, bps);

Expand Down
25 changes: 25 additions & 0 deletions src/test/java/com/glencoesoftware/raw2ometiff/test/ConversionTest.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,9 @@ void iteratePixels() throws Exception {
inputReader.setSeries(series);
outputReader.setSeries(series);

Assert.assertEquals(
inputReader.getImageCount(), outputReader.getImageCount());
Assert.assertEquals(inputReader.getSizeC(), outputReader.getSizeC());
for (int plane=0; plane<inputReader.getImageCount(); plane++) {
Object inputPlane = getPlane(inputReader, plane);
Object outputPlane = getPlane(outputReader, plane);
Expand Down Expand Up @@ -409,6 +412,28 @@ public void testOddImageSize() throws Exception {
iteratePixels();
}

/**
* Test RGB with multiple timepoints.
*/
@Test
public void testRGBMultiT() throws Exception {
input = fake("sizeC", "3", "sizeT", "5", "rgb", "3");
assertBioFormats2Raw();
assertTool("--rgb");
iteratePixels();
}

/**
* Test RGB with multiple channels.
*/
@Test
public void testRGBMultiC() throws Exception {
input = fake("sizeC", "12", "rgb", "3");
assertBioFormats2Raw();
assertTool("--rgb");
iteratePixels();
}

/**
* Test TIFF metadata.
*/
Expand Down

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