Epidemic plugin error

Image Analysis
#1

Hi,
I tried tu run the EpiDemic plugin and I got this error:
“An error occured while plugin ‘EpiDEMIC’ was running :
java.lang.NullPointerException
at plugins.ferreol.demics.EpiDEMIC.buildpupil(EpiDEMIC.java:985)
at plugins.ferreol.demics.EpiDEMIC.access$2200(EpiDEMIC.java:72)
at plugins.ferreol.demics.EpiDEMIC$20.run(EpiDEMIC.java:1001)”

Here the history output:

OpenJDK Runtime Environment 11.0.9+11 (64 bit)
Running on Windows 10 10.0 (amd64)
Number of processors : 8
System total memory : 18.9 GB
System available memory : 9.7 GB
Max java memory : 14.7 GB
Image cache initialized (reserved memory = 8640 MB, disk cache location = C:/WINDOWS/TMP)

java.lang.NoClassDefFoundError: com/xuggle/xuggler/Global
Caused by :
java.lang.ClassNotFoundException: com.xuggle.xuggler.Global
Class ‘plugins.lagache.colocalizationstudio.function_fit’ cannot be loaded :
Required class ‘flanagan.analysis.RegressionFunction’ not found.
VTK 6.3.0 library successfully loaded…
Icy Version 2.1.0.1 started !
The following plugin(s) has been correctly installed:
Parallel Colt library for Icy 0.9.5.0
JavaCL library for Icy 1.0.6.1
Class ‘plugins.lagache.colocalizationstudio.function_fit’ cannot be loaded :
Required class ‘flanagan.analysis.RegressionFunction’ not found.

The following plugin(s) has been correctly installed:
JFree Chart library for Icy 1.0.17.0
Particles animation 1.2.1.0
NHerve ImageAnalysis Toolbox 1.2.1.0
JFree Common library for Icy 1.0.0.0
Java 3D library for Icy 1.6.0.0
Xuggler Video Importer 1.1.2.1
Xuggler library for Icy 5.5.1.0
EJML (Efficient Java Matrix Library) for Icy 0.17.0.0
Flanagan scientific library for Icy 1.1.1.0
ROI Intensity Evolution 2.0.1.0
Color Picker Threshold 1.2.1.0
HK-Means 2.9.1.0
Rigid registration 1.3.0.0
Protocols 3.0.12.1
Mice Profiler Tracker 7.1.1.0
Texture Segmentation 1.2.1.0
ROI to detection 1.0.2.0
NHerve Toolbox 1.3.1.0

*** One or more readers is misbehaving. See the debug output for more information. e.g.:
loci.formats.in.APLReader@21b31e1a -> java.lang.NullP

How I can correct this problem?
Thank you very much in advance.
Best regards,
Michel

#2

Dear Michel Kress,

Could you upload a test image and the parameters you used in EpiDEMIC in order to allow other users to reproduce this error?

Could you also give the version of EpiDEMIC you used?

To do so, go to the preferences window:
Preferences_button
In the preferences window, go to Plugin -> Local Plugin and search for EpiDEMIC

Preferences
Preferences864×538 29.9 KB

EpiDEMIC_plugin_version
EpiDEMIC_plugin_version868×543 29.5 KB

Many thanks in advance!
Best regards,
Marion

#3

Hi Michel,
Can you reproduce this bug? Can you explain how it happens? If I’m able to reproduce this bug, I will correct it.
I usually answer to bug reports, when the email is set and the context explained.
Regards,

Ferréol

1 Like
#4

Hi Marion and Ferréol,
I am using epidemic 1.2.1.0 and Icy 2.1.0.1.
When I click on “show PSF” or “Start deconvolution”, I got these errors:
“java.lang.NullPointerException
at plugins.ferreol.demics.EpiDEMIC.buildpupil(EpiDEMIC.java:985)
at plugins.ferreol.demics.EpiDEMIC.launch(EpiDEMIC.java:786)
at plugins.ferreol.demics.EpiDEMIC.access$1800(EpiDEMIC.java:72)
at plugins.ferreol.demics.EpiDEMIC$18.run(EpiDEMIC.java:676)”
I used default parameters
Yes I reproduced these errors on two different computers.
My file is a multi-tif, I crop of Zeiss czi file, it is a three channels but I tried also with one channel.
I reproduced this bugs with two different files but always zeiss czi.
I send a test image.
Thank you very much.
Regards,
MichelExperiment-639 (crop) (crop).rar (7.6 MB)

1 Like
#5

Welcome on the image.sc forum, @FerreolS!
Thank you for the test image @M_Kress.

I can also reproduce this bug (same Icy and plugin versions): I open the image, open the EpiDEMIC plugin, select a Data source and click on Show PSF and it gives me this

java.lang.NullPointerException
	at plugins.ferreol.demics.EpiDEMIC.buildpupil(EpiDEMIC.java:985)
	at plugins.ferreol.demics.EpiDEMIC.access$2200(EpiDEMIC.java:72)
	at plugins.ferreol.demics.EpiDEMIC$20.run(EpiDEMIC.java:1001)

if I now click on Start deconvolution, it gives me this

java.lang.NullPointerException
	at plugins.ferreol.demics.EpiDEMIC.buildpupil(EpiDEMIC.java:985)
	at plugins.ferreol.demics.EpiDEMIC.launch(EpiDEMIC.java:786)
	at plugins.ferreol.demics.EpiDEMIC.access$1800(EpiDEMIC.java:72)
	at plugins.ferreol.demics.EpiDEMIC$18.run(EpiDEMIC.java:676)
#6

Thanks for the bug report. It is fixed now. This was due to wrongly set refractive index in the file metadata.
Cheers
Ferréol

2 Likes