Mark Hiner hinerm
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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) |
hinerm
/ ij_test.py
Created
April 19, 2021 18:14
A trivial python script that takes an input image and outputs a "copy", with all values set to the first pixel value.
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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 { |
hinerm
/ link to presentation
Created
May 19, 2016 16:02
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| https://docs.google.com/presentation/d/1E_sYCh00fSGYmSue_PRifqaGJ61RnstMdcX5c_c1jWM/edit?usp=sharing |
hinerm
/ scifio javadoc warnings
Last active
December 25, 2015 04:38
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| [WARNING] Javadoc Warnings | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/java/io/scif/formats/TIFFFormat.java:990: warning - Tag @link: can't find initStandardMetadata(Metadata) in io.scif.formats.TIFFFormat.BaseTIFFParser | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/package-info.java:347: warning - Tag @link: reference not found: Plane | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/package-info.java:347: warning - Tag @link: reference not found: RandomAccessInputStream | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: net.imglib2.img.ImgPlus | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: net.imglib2.img.ImgPlus | |
| [WARNING] /Users/mhiner/loci/scifio/scifio/src/main/javadoc/io/scif/img/package-info.java:51: warning - Tag @link: reference not found: io.scif.io.img.ImgOpener | |
| [WARNING] /Users/m |
hinerm
/ FollowedClasses
Last active
December 15, 2015 11:49
FollowedClasses - a list of classes that have SCIFIO equivalents. git log --follow should work for these.
NewClasses - a parallel list of the modern classes
follow.sh - a script that will compare the log --follow results of FollowedClasses and NewClasses and log the results.
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| components/loci-legacy/src/loci/common/AbstractNIOHandle.java | |
| components/loci-legacy/src/loci/common/BZip2Handle.java | |
| components/loci-legacy/src/loci/common/ByteArrayHandle.java | |
| components/loci-legacy/src/loci/common/CBZip2InputStream.java | |
| components/loci-legacy/src/loci/common/CRC.java | |
| components/loci-legacy/src/loci/common/CaseInsensitiveLocation.java | |
| components/loci-legacy/src/loci/common/Constants.java | |
| components/loci-legacy/src/loci/common/DataTools.java | |
| components/loci-legacy/src/loci/common/DateTools.java | |
| components/loci-legacy/src/loci/common/DebugTools.java |
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| #!/bin/bash | |
| # | |
| # History checking script | |
| # | |
| # This script checks out each commit that | |
| # exists on a dev_branch but not a base_branch. | |
| # "ant clean tools" is run on that branch, | |
| # and a log file is written with the results | |
| # of the build to | |
| # <log_dir>/<PASSED/FAILED><commit hash><commit message>.log |
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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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