Java (ImageJ/Fiji) software package for 3D deconvolution microscopy
Home Page: http://bigwww.epfl.ch/deconvolution/deconvolutionlab2/
License: GNU General Public License v3.0
I'm using DL2 v2.1.2 to process a batch of images and there's a memory leak somewhere. Other people have had this issue and, based on the below Image.sc thread, it seems that the issue was resolved with the release of v2.1.1. Could the issue have been reintroduced with the release of v2.1.2?
https://forum.image.sc/t/deconvolutionlab2-filling-up-heap-space/8881
Hello,
Is there a way to batch the java application using command line in headless mode?
I tried an example like this to run RL decon with 15 iterations
java -jar $HOME/Fiji.app/plugins/DeconvolutionLab_2.jar Run -image $PWD/somefile.tif -psf $PWD/PSF.tif -algorithm RL 15 -out $PWD/1.tif -path $PWD
It did not work. What is the correct command to run the RL decon using batch command line?
Thank you.
I cannot figure out which java wrapper for fftw is being used here and how to compile it. I would like to recompile the JNI wrapper around a native arm_64 (apple silicon) to improve performance on M1 mac.
Hi everyone.
Just installed fiji app and have been using youtube videos to follow up to the use of this app with stacked confocal imagens.
Was learning about deconvolution. Added the DeconvolutionLab_2.jar file to the fiji's pluggin folder. During my first trials it seemed to work fine, but it wont open/run.
Any suggestions as to how overcome this?
Thank you in advance.
H, I am running the demo code in Matlab:
result = DL2.RIF(rand(40, 40, 30), rand(30, 30, 30), 0.125, '-out mip rand');
Error take places, looks like a problem in path.
The path was a not writable path:
C:\Program Files\MATLAB\R2016a\bin\win64\rand.tif
result = DL2.RIF(rand(40, 40, 30), rand(30, 30, 30), 0.125, '-out mip rand');
Log 685.80 us 373.6Mb DeconvolutionLab2 2.1.2 (27.06.2018) on Matlab
Log 2407.77 us 381.0Mb AcademicFFT Added
Log 4.55 ms 381.0Mb JTransforms not found
Log 6.69 ms 381.0Mb FFTW Widsom not found in : D:\FFTW\
Log 7.04 ms 381.0Mb FFTW Widsom not found in : D:\
Log 7.49 ms 381.0Mb FFTW Widsom not found in : C:\Users\rmd\FFTW\
Log 8.14 ms 381.0Mb FFTW Widsom not found in : C:\Users\rmd\
Log 8.51 ms 381.0Mb FFTW not found
Log 12.60 us 384.6Mb Create Live Real Signal
Log 253.19 ms 400.4Mb Image: 40x40x30
Log 255.41 ms 400.4Mb PSF: 30x30x30
Log 256.23 ms 400.4Mb Impossible to load the reference image
Log 258.07 ms 400.4Mb Path: C:\Program Files\MATLAB\R2016a\bin\win64\ (writable)
Log 259.06 ms 400.4Mb Algorithm: Regularized Inverse Filter
Log 263.68 ms 400.4Mb Input: 40x40x30
Log 278.48 ms 400.8Mb PSF: 40x40x30 normalized 1.0
Log 279.62 ms 400.8Mb RIF is starting (direct)
Log 301.67 ms 401.2Mb AcademicFFT initialized for [40x40x30]
Log 364.07 ms 409.6Mb RIF data ready
Log 365.00 ms 409.6Mb RIF(0.1250)
Log 571.21 ms 431.3Mb Show Real Signal rand
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at ij.gui.ImageWindow.windowActivated(ImageWindow.java:555)
at java.awt.Window.processWindowEvent(Unknown Source)
at java.awt.Window.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.KeyboardFocusManager.redispatchEvent(Unknown Source)
at java.awt.DefaultKeyboardFocusManager.typeAheadAssertions(Unknown Source)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SentEvent.dispatch(Unknown Source)
at java.awt.DefaultKeyboardFocusManager$DefaultKeyboardFocusManagerSentEvent.dispatch(Unknown Source)
at java.awt.DefaultKeyboardFocusManager.sendMessage(Unknown Source)
at java.awt.DefaultKeyboardFocusManager.dispatchEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Window.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.SequencedEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$500(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
File saving error (IOException):
"C:\Program Files\MATLAB\R2016a\bin\win64\rand.tif (refuse to visit。)"
C:\Program Files\MATLAB\R2016a\bin\win64\\rand.tif
Log 779.57 ms 440.6Mb Save Real Signal C:\Program Files\MATLAB\R2016a\bin\win64\\rand.tif
Log 780.36 ms 440.6Mb Time: 0.5 s Peak:37.8 Mb
Log 780.72 ms 440.6Mb Regularized Inverse Filter is finished
Log 781.85 ms 440.6Mb End of RIF in 0.5 s and 37.8 Mb
Hi @dasv74. Would you consider a pull request that adds GPU support to DL2?
From https://github.com/hadim/DeconvolutionLab2/tree/jcufft/src/main/java/fft/jcufft
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