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First pass particle labelling runs out of label space on huge images on big machines #276

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mdoube opened this issue Nov 17, 2020 · 0 comments
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mdoube commented Nov 17, 2020

Describe the bug
Particle Analyser fails to complete properly, complaining for the last thread:

Exception in thread "Thread-132" java.lang.ArrayIndexOutOfBoundsException: 2016
	at org.bonej.plugins.ConnectedComponents.lambda$firstIDAttribution$1(ConnectedComponents.java:264)
	at java.lang.Thread.run(Thread.java:748)

and for many threads:

Exception in thread "Thread-126" java.lang.IllegalArgumentException: ID 7602176 is greater than the allowed range (max 7602175)
	at org.bonej.plugins.ConnectedComponents.expandMap(ConnectedComponents.java:998)
	at org.bonej.plugins.ConnectedComponents.lambda$firstIDAttribution$1(ConnectedComponents.java:323)
	at java.lang.Thread.run(Thread.java:748)

To Reproduce
Steps to reproduce the behavior:

  1. Open a huge image, e.g. 150 GB with 3 million particle on a big machine e.g. 132 CPU threads
  2. Run Particle Analyser

Expected behavior
Particle Analyser completes successfully

Environment

  • OS: Windows 10
  • Java version ??
  • 64 Intel Xeon Gold 6142M processors @2.60 GHz base speed. Nvidia Quadro RTX 8000 GPU, and 2 TB RAM

Additional context
First reported here:
https://forum.image.sc/t/bonej-analyse-particles-file-size-limitation/45137/7

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