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2023-03-24 11:22:00 | |
Full thread dump OpenJDK 64-Bit Server VM (25.332-b09 mixed mode): | |
"RMI TCP Connection(2)-192.168.68.53" #66 daemon prio=5 os_prio=0 tid=0x00000173573c2800 nid=0x55a8 runnable [0x000000648192d000] | |
java.lang.Thread.State: RUNNABLE | |
at java.net.SocketInputStream.socketRead0(Native Method) | |
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) | |
at java.net.SocketInputStream.read(SocketInputStream.java:171) | |
at java.net.SocketInputStream.read(SocketInputStream.java:141) |
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#@ OpService ops | |
#@ ImgPlus image | |
#@OUTPUT ImgPlus copy | |
#@OUTPUT Integer a | |
a = 21 | |
copy = ops.copy().img(image.getImg()) | |
c = copy.cursor() | |
c.fwd() | |
v = c.get().copy() |
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package test; | |
import java.util.StringJoiner; | |
import java.util.concurrent.ExecutorService; | |
import java.util.concurrent.Executors; | |
import java.util.concurrent.TimeUnit; | |
import java.util.regex.Matcher; | |
import java.util.regex.Pattern; | |
public class Sandbox { |
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package test; | |
import java.util.StringJoiner; | |
import java.util.concurrent.ExecutorService; | |
import java.util.concurrent.Executors; | |
import java.util.concurrent.TimeUnit; | |
import java.util.regex.Matcher; | |
import java.util.regex.Pattern; | |
public class Sandbox { |
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https://docs.google.com/presentation/d/1E_sYCh00fSGYmSue_PRifqaGJ61RnstMdcX5c_c1jWM/edit?usp=sharing |
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The following images show memory leaks due to mapped images not being cleaned up. | |
The MemoryOverview shows two hard reference paths keeping byte[] instances alive (blue and green). They both go through python classes to a HashMap. | |
The Objects1 and Objects2 images show these two paths expanded and reveals that we likely have two paths to the same map, and thus to the same set of objects. | |
Persumably our Python code is making these mappings but not cleaning up after them. Persumably there is also a hard reference to these images in ImageJ itself, so it would make sense on the Python side to cache WeakReferences to the images - or add some callback that ensures these mappings are eventually removed (or manually clean the maps at the end of the script). | |
To find the problematic python code we can look for the relevant variable names (snapshotPixels, rLUT1, bLUT1, gLUT1, etc...) |
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// search for TODO sections to see parameters that still need tuning | |
//This macro takes a 3-channel 16 bit immunofluorescance image as input. | |
// channel 1 (red): SC | |
// channel 2 (green): foci | |
// channel 3 (blue): centromeres | |
//The primary goal of this macro is to identify rois covering main cell features, | |
//measure the total distance of skeletonized SC, number of foci on each SC and distance from foci to the centromere on the same skeleton | |
// Requirements: |
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package org.scijava; | |
import java.io.FileOutputStream; | |
import java.io.IOException; | |
public class Main { | |
public static void main(String... args) throws IOException { | |
//FIXME: set this path to the location of the jar containing this main class. | |
String url = "C:/Users/Johannes/loci/test/target/scijava-tests-2.43.1-SNAPSHOT.jar"; |
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import java.io.BufferedReader; | |
import java.io.IOException; | |
import java.io.InputStreamReader; | |
import java.lang.reflect.InvocationTargetException; | |
import java.lang.reflect.Method; | |
import java.net.URL; | |
import java.net.URLClassLoader; | |
public class Main { |
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<?xml version="1.0" encoding="UTF-8"?> | |
<?JvmMonitor version="3.8.1"?> | |
<cpu-profile date="2015/01/25 12:09:02" runtime="8608@localhost" mainClass="org.eclipse.jdt.internal.junit.runner.RemoteTestRunner" arguments="-Dscijava.log.level=error -Dfile.encoding=UTF-8"> | |
<thread name="main"> | |
<frame name="io.scif.services.SCIFIODatasetService.create(net.imagej.ImgPlus)" cnt="1" time="0"> | |
<frame name="io.scif.services.SCIFIODatasetService.datasetService()" cnt="1" time="0"/> | |
</frame> | |
<frame name="io.scif.services.DefaultDatasetIOService.open(java.lang.String)" cnt="7676" time="175061"> | |
<frame name="io.scif.config.SCIFIOConfig.imgOpenerSetIndex(int)" cnt="7676" time="0"> | |
<frame name="io.scif.config.SCIFIOConfig.imgOpenerSetRange(io.scif.img.Range)" cnt="7676" time="0"/> |
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