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Merge pull request qupath#862 from petebankhead/tile-requests
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Reduce unnecessary tile reads in AbstractImageServer
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@petebankhead
petebankhead authored Dec 14, 2021
2 parents 603e00c + f0a7628 commit 48dfb82
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Showing 7 changed files with 240 additions and 82 deletions.
3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,7 +5,9 @@ This is a *minor release* that aims to be fully compatible with v0.3.0 while fix

List of bugs fixed:
* 'Add intensity features' does not reinitialize options (including channels) when new images are opened (https://github.com/qupath/qupath/issues/836)
* Reading images with ImageJ is too slow and memory-hungry (https://github.com/qupath/qupath/issues/860)
* 'Keep settings' in Brightness/Contrast dialog does not always retain channel colors (https://github.com/qupath/qupath/issues/843)
* ImageServers can request the same tile in multiple threads simultaneously (https://github.com/qupath/qupath/issues/861)
* Up arrow can cause viewer to move beyond nSlices for Z-stack (https://github.com/qupath/qupath/issues/821)
* Location text does not update when navigating with keyboard (https://github.com/qupath/qupath/issues/819)
* Multichannel .tif output is broken in TileExporter (https://github.com/qupath/qupath/issues/838)
Expand All @@ -15,6 +17,7 @@ List of bugs fixed:
* 'Automate -> Show workflow command history' displays empty workflow (https://github.com/qupath/qupath/pull/851)
* Extensions are sometimes loaded too late when running command line scripts (https://github.com/qupath/qupath/issues/852)
* ICC Profiles could not be set in the viewer (unused preview feature, https://github.com/qupath/qupath/pull/850)
* convert-ome command doesn't report when it is finished (https://github.com/qupath/qupath/issues/859)

### Dependency updates
* JavaFX 17.0.1
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2 changes: 1 addition & 1 deletion qupath-app/src/main/java/qupath/QuPath.java
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Expand Up @@ -388,7 +388,7 @@ private void createTileCache() {
percentage = 10;
} else if (percentage > 90) {
logger.warn("No more than 90% of available memory can be used for tile caching (you requested {}%)", percentage);
percentage = 00;
percentage = 90;
}
long tileCacheSize = Math.round(maxAvailable * (percentage / 100.0));
logger.info(String.format("Setting tile cache size to %.2f MB (%.1f%% max memory)", tileCacheSize/(1024.*1024.), percentage));
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163 changes: 101 additions & 62 deletions qupath-core-processing/src/main/java/qupath/imagej/images/servers/ImageJServer.java
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Expand Up @@ -4,7 +4,7 @@
* %%
* Copyright (C) 2014 - 2016 The Queen's University of Belfast, Northern Ireland
* Contact: IP Management (ipmanagement@qub.ac.uk)
* Copyright (C) 2018 - 2020 QuPath developers, The University of Edinburgh
* Copyright (C) 2018 - 2021 QuPath developers, The University of Edinburgh
* %%
* QuPath is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as
Expand Down Expand Up @@ -33,7 +33,6 @@
import java.awt.image.DataBufferUShort;
import java.awt.image.Raster;
import java.awt.image.SampleModel;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
Expand All @@ -52,6 +51,7 @@
import ij.ImagePlus;
import ij.ImageStack;
import ij.gui.Roi;
import ij.io.Opener;
import ij.measure.Calibration;
import ij.plugin.Duplicator;
import ij.plugin.ImageInfo;
Expand Down Expand Up @@ -89,7 +89,7 @@ public class ImageJServer extends AbstractImageServer<BufferedImage> implements

private URI uri;
private String[] args;

private ImagePlus imp;

private ColorModel colorModel;
Expand All @@ -103,33 +103,42 @@ public class ImageJServer extends AbstractImageServer<BufferedImage> implements
public ImageJServer(final URI uri, final String...args) throws IOException {
super(BufferedImage.class);
this.uri = uri;
File file = GeneralTools.toPath(uri).toFile();
String path = file.getAbsolutePath();
if (path.toLowerCase().endsWith(".tif") || path.toLowerCase().endsWith(".tiff")) {
imp = IJ.openVirtual(path);
// We only want a virtual stack if we have a large z-stack or time series
long bpp = imp.getBitDepth() / 8;
if (bpp == 3)
bpp = 4; // ImageJ uses 4 bytes for an RGB image, but reports 24-bit
long nBytes = (long)imp.getWidth() * imp.getHeight() * imp.getStackSize() * bpp;
long maxMemory = Runtime.getRuntime().maxMemory();
long allowedMemory;
if (maxMemory == Long.MAX_VALUE)
allowedMemory = 1024L * 1024L * 1024L;
else
allowedMemory = maxMemory / 8;
if ((imp.getNFrames() == 1 && imp.getNSlices() == 1) || nBytes < allowedMemory) {
logger.debug("Opening {} fully, estimated {} MB (max memory {} MB)", uri, nBytes / (1024L * 1024L), maxMemory / (1024L * 1024L));
imp = IJ.openImage(path);
} else {
logger.debug("Opening {} as virtual stack, estimated {} MB (max memory {} MB)", uri, nBytes / (1024L * 1024L), maxMemory / (1024L * 1024L));
var filePath = GeneralTools.toPath(uri);
var file = filePath != null ? filePath.toFile() : null;
String path = file == null ? uri.toString() : file.getAbsolutePath();

// Open as a virtual stack if we have 1) a TIFF, with 2) multiple slices and 3) a large file size -
// otherwise try to open directly (which is much faster if memory permits)
long maxMemory = Runtime.getRuntime().maxMemory();
if (file != null && path.toLowerCase().endsWith(".tif") || path.toLowerCase().endsWith(".tiff")) {
// Because ImageJ only supports uncompressed TIFFs, we simply use the file size
long fileLength = file == null ? Long.MAX_VALUE : file.length();
long maxFileLength = Math.max(1024*1024*10, maxMemory / 8);
if (fileLength > maxFileLength) {
var info = Opener.getTiffFileInfo(path);
if (info != null && info.length > 1) {
logger.debug("Opening {} as virtual stack", uri);
imp = IJ.openVirtual(path);
}
}
}
if (imp == null)
if (imp == null) {
logger.debug("Opening {} as ImagePlus", uri);
imp = IJ.openImage(path);
}
if (imp == null)
throw new IOException("Could not open " + path + " with ImageJ");

// Log a warning if the image is very large
double sizeBytes = imp.getSizeInBytes();
if (!imp.getStack().isVirtual() && sizeBytes > maxMemory / 16) {
logger.warn("The image is very large relative to the available memory ({} MB / {} MB, {} %)",
GeneralTools.formatNumber(sizeBytes / (1024.0 * 1024.0), 1),
GeneralTools.formatNumber(maxMemory / (1024.0 * 1024.0), 1),
GeneralTools.formatNumber(sizeBytes / maxMemory * 100.0, 1));
logger.warn("Consider saving the image in a pyramidal format, e.g. using 'QuPath convert-ome' from the command line to create a pyramidal OME-TIFF.");
}

Calibration cal = imp.getCalibration();
double xMicrons = IJTools.tryToParseMicrons(cal.pixelWidth, cal.getXUnit());
double yMicrons = IJTools.tryToParseMicrons(cal.pixelHeight, cal.getYUnit());
Expand Down Expand Up @@ -295,63 +304,71 @@ protected String createID() {
}

@Override
public synchronized BufferedImage readBufferedImage(RegionRequest request) {
// Deal with any cropping
// ImagePlus imp2 = this.imp;
public BufferedImage readBufferedImage(RegionRequest request) {

// long startTime = System.nanoTime();

int z = request.getZ()+1;
int t = request.getT()+1;
int nChannels = nChannels();

// // There would be a possibility to intercept these calls and perform a z-projection...
// if (nZSlices() > 1) {
// imp.setT(t);
// ZProjector zProjector = new ZProjector(imp);
// zProjector.setMethod(ZProjector.MAX_METHOD);
// zProjector.setStartSlice(1);
// zProjector.setStopSlice(nZSlices());
// zProjector.doHyperStackProjection(false);
// imp = zProjector.getProjection();
// z = 1;
// t = 1;
// }
// In ImageJ's world, RGB effectively should be treated as 1 channel
if (imp.getType() == ImagePlus.COLOR_RGB)
nChannels = 1;

double downsample = request.getDownsample();
int w = (int)Math.max(1, Math.round(imp.getWidth() / downsample));
int h = (int)Math.max(1, Math.round(imp.getHeight() / downsample));

ImagePlus imp2;
Rectangle roi = null;
if (!(request.getX() == 0 && request.getY() == 0 && request.getWidth() == this.imp.getWidth() && request.getHeight() == this.imp.getHeight())) {
// Synchronization introduced because of concurrency issues around here!
this.imp.setRoi(request.getX(), request.getY(), request.getWidth(), request.getHeight());
// Crop for required z and time
Duplicator duplicator = new Duplicator();
imp2 = duplicator.run(this.imp, 1, nChannels, z, z, t, t);
this.imp.killRoi();
roi = new Rectangle(request.getX(), request.getY(), request.getWidth(), request.getHeight());
// Synchronization introduced because of concurrency issues when cropping!
synchronized (imp) {
if (nChannels == 1) {
int ind = imp.getStackIndex(1, z, t);
var ip = imp.getStack().getProcessor(ind);
ip.setRoi(roi);
ip = ip.crop();
imp2 = imp.createImagePlus();
imp2.setProcessor(ip);
ip.resetRoi();
} else {
this.imp.setRoi(roi);
// Crop for required z and time
Duplicator duplicator = new Duplicator();
imp2 = duplicator.run(this.imp, 1, nChannels, z, z, t, t);
this.imp.killRoi();
}
}
if (imp2.getHeight() != request.getHeight()||
imp2.getWidth() != request.getWidth())
logger.warn("Unexpected image size {}x{} for request {}", imp.getWidth(), imp.getHeight(), request);
z = 1;
t = 1;
// imp = imp.duplicate();
imp2.killRoi();
} else
imp2 = this.imp;

// Deal with any downsampling
if (request.getDownsample() != 1) {
ImageStack stackNew = null;
Rectangle roi = imp2.getProcessor().getRoi();
int w = (int)Math.max(1, Math.round(imp.getWidth() / request.getDownsample()));
int h = (int)Math.max(1, Math.round(imp.getHeight() / request.getDownsample()));
if (downsample != 1) {
if (roi != null) {
w = (int)Math.max(1, Math.round(roi.getWidth() / request.getDownsample()));
h = (int)Math.max(1, Math.round(roi.getHeight() / request.getDownsample()));
w = (int)Math.max(1, Math.round(roi.getWidth() / downsample));
h = (int)Math.max(1, Math.round(roi.getHeight() / downsample));
}
for (int i = 1; i <= nChannels; i++) {
int ind = imp2.getStackIndex(i, z, t);
ImageProcessor ip = imp2.getStack().getProcessor(ind);
ip.setInterpolationMethod(ImageProcessor.BILINEAR);
ip = ip.resize(w, h, true);
if (stackNew == null)
stackNew = new ImageStack(ip.getWidth(), ip.getHeight());
stackNew.addSlice("Channel " + i, ip);
ImageStack stackNew = null;
// We synchronize on imp2 because it might be the same as imp - and 'resize' respects any crop ROI
synchronized (imp2) {
for (int i = 1; i <= nChannels; i++) {
int ind = imp2.getStackIndex(i, z, t);
ImageProcessor ip = imp2.getStack().getProcessor(ind);
ip.setInterpolationMethod(ImageProcessor.BILINEAR);
ip = ip.resize(w, h, true);
if (stackNew == null)
stackNew = new ImageStack(ip.getWidth(), ip.getHeight());
stackNew.addSlice("Channel " + i, ip);
}
}
imp2 = new ImagePlus(imp2.getTitle(), stackNew);
imp2.setDimensions(nChannels, 1, 1);
Expand All @@ -361,9 +378,21 @@ public synchronized BufferedImage readBufferedImage(RegionRequest request) {
}

// If we don't have a color model yet, reuse this one
var img = convertToBufferedImage(imp2, z, t, colorModel);
BufferedImage img;
synchronized (imp2) {
img = convertToBufferedImage(imp2, z, t, colorModel);
}
if (imp != imp2) {
imp2.changes = false;
imp2.close();
}

if (colorModel == null)
colorModel = img.getColorModel();

// long endTime = System.nanoTime();
// System.err.println("Duration: " + GeneralTools.formatNumber((endTime - startTime)/1000000.0, 1));

return img;
}

Expand Down Expand Up @@ -470,4 +499,14 @@ protected ServerBuilder<BufferedImage> createServerBuilder() {
args);
}

@Override
public void close() throws Exception {
super.close();
if (imp != null) {
imp.changes = false;
imp.close();
imp = null;
}
}

}
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