eguvep / jpiv Goto Github PK

Hi there,

It's my first day using JPIV and somehow manged to break it :')

I've tried a few datasets of mine and the same synt0-4 sequence, both with some reasonable results, until I've came accross two issues:

(1) Exception in thread "Thread-5" java.lang.IllegalArgumentException: Crop The rectangular crop area must not be outside the image.
crop.txt

which I'm not entirely sure what it indicates since the same parameters worked fine before. So decided to start fresh and try synt dataset which led me to error (2)
(2) the scripts are gone from their menu- which even when the path is adjusted form 'preference -> path' still doesn’t fix it. So i tried running one from 'scripts->open' which basically resulted in nothing.
synt 2d data gen.txt

Would really appreciate all the help I can get.
Kind regards. 

Anyone willing to help a biologist? I opened & selected my 650 image sequence, set settings to analyze sequential files (1-2, 2-3, 3-4, etc) then ran PIV image analysis. No output but I have this error. Sorry, but the code is all greek to me. Should I retreat, or might there be some simple fix?

JPIV 2020.04.26
Copyright (C) 2020 Peter Vennemann
JPIV is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
See http://www.gnu.org/licenses/ for details.
Can not find a user settings file.
You are probably using JPIV the first time.
A default settings file is created in your home directory.
Session started by jamesmurray on 10.4.2021 at 15:56
No files selected.
JPiv PIV evaluation started.
Available cores: 8
Using 2 cores.
Processing: t-tetra-pt67x-r-higher 001
Exception in thread "Thread-3" java.lang.IllegalAccessError: class javax.media.jai.RasterAccessor (in unnamed module @0x4ccc0db7) cannot access class sun.awt.image.BytePackedRaster (in module java.desktop) because module java.desktop does not export sun.awt.image to unnamed module @0x4ccc0db7
at javax.media.jai.RasterAccessor.(RasterAccessor.java:802)
at com.sun.media.jai.opimage.CopyOpImage.computeRect(CopyOpImage.java:68)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:969)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.opimage.CropOpImage.getTile(CropOpImage.java:122)
at com.sun.media.jai.opimage.TranslateIntOpImage.getTile(TranslateIntOpImage.java:132)
at javax.media.jai.PlanarImage.cobbleUShort(PlanarImage.java:3052)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2175)
at javax.media.jai.UntiledOpImage.computeTile(UntiledOpImage.java:212)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:750)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:750)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at javax.media.jai.UntiledOpImage.computeTile(UntiledOpImage.java:212)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.opimage.TranslateIntOpImage.getTile(TranslateIntOpImage.java:132)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at com.sun.media.jai.opimage.PeriodicShiftOpImage.computeTile(PeriodicShiftOpImage.java:118)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:911)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.copyData(PlanarImage.java:2343)
at javax.media.jai.RenderedOp.copyData(RenderedOp.java:2299)
at javax.media.jai.PlanarImage.getAsBufferedImage(PlanarImage.java:2525)
at javax.media.jai.PlanarImage.getAsBufferedImage(PlanarImage.java:2546)
at jpiv2.PivEvaluation$AddCorrelation.run(PivEvaluation.java:450)
Exception in thread "Thread-2" java.lang.IllegalAccessError: class javax.media.jai.RasterAccessor (in unnamed module @0x4ccc0db7) cannot access class sun.awt.image.BytePackedRaster (in module java.desktop) because module java.desktop does not export sun.awt.image to unnamed module @0x4ccc0db7
at javax.media.jai.RasterAccessor.(RasterAccessor.java:802)
at com.sun.media.jai.opimage.CopyOpImage.computeRect(CopyOpImage.java:68)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:969)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.opimage.CropOpImage.getTile(CropOpImage.java:122)
at com.sun.media.jai.opimage.TranslateIntOpImage.getTile(TranslateIntOpImage.java:132)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at javax.media.jai.UntiledOpImage.computeTile(UntiledOpImage.java:212)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:750)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:750)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at javax.media.jai.UntiledOpImage.computeTile(UntiledOpImage.java:212)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.opimage.TranslateIntOpImage.getTile(TranslateIntOpImage.java:132)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at com.sun.media.jai.opimage.PeriodicShiftOpImage.computeTile(PeriodicShiftOpImage.java:118)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PointOpImage.computeTile(PointOpImage.java:911)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.copyData(PlanarImage.java:2343)
at javax.media.jai.RenderedOp.copyData(RenderedOp.java:2299)
at javax.media.jai.PlanarImage.getAsBufferedImage(PlanarImage.java:2525)
at javax.media.jai.PlanarImage.getAsBufferedImage(PlanarImage.java:2546)
at jpiv2.PivEvaluation$AddCorrelation.run(PivEvaluation.java:450)

Is there any chance that SIMD can be used to accelerate the algorithms for long evaluations?

According to the documentation there is an option to process files from the command line e.g.:

Some people prefer jpiv to accept a list of images on the command line. The images should be evaluated immediately. The executable jpivc.jar can do that. Launch a PIV evaluation via command line by executing java -jar -Xmx4G jpivc.jar *.tiff, for example. The files *.tiff are your PIV images.

However I can't find the suggested file jpivc.jar anywhere.
Further when using the command line, how would I set settings like "General > consecutive" or "Interrogation Window" parameters

Cheers