imodpasteur / imodpasteur/ZOLA-3D

Error when using sCMOS corrections

Open
#7 3 comments 0 reactions 0 assignees View on GitHub
Dominant language
Java
Stars
19
Forks
3
PR merge metrics
No merged PRs in 30d

Description

Thanks for all of the hard work on ZOLA! We have a question because we are running into an error when using sCMOS correction.

We are running ZOLA-3D on Windows 7 Pro 64-bit, ImageJ 1.52n, and Java 8.

Using a stack of PSFs we are able to successfully run Calibration: PSF modeling, using the GPU/CUDA 10, if we choose the Camera setup: EMCCD option for the camera. However, when we choose Camera setup:sCMOS and provide ZOLA-3D with the file paths for three needed files (16-bit TIFFs for offset, variance, and gain) that we normally utilize for fitting with the Huang et al algorithm in MATLAB, we get the following error:

> (Fiji Is Just) ImageJ 2.0.0-rc-69/1.52n; Java 1.8.0_131 [64-bit]; Windows 7 6.1; 1272MB of 96000MB (1%)
>
> java.util.regex.PatternSyntaxException: Unexpected internal error near index 1
> \\
> ^
> at java.util.regex.Pattern.error(Pattern.java:1955)
> at java.util.regex.Pattern.compile(Pattern.java:1702)
> at java.util.regex.Pattern.(Pattern.java:1351)
> at java.util.regex.Pattern.compile(Pattern.java:1028)
> at java.lang.String.split(String.java:2380)
> at java.lang.String.split(String.java:2422)
> at org.pasteur.imagej.ZOLA.calibration(ZOLA.java:1862)
> at org.pasteur.imagej.ZOLA.run(ZOLA.java:340)
> at ij.IJ.runUserPlugIn(IJ.java:229)
> at ij.IJ.runPlugIn(IJ.java:193)
> at ij.Executer.runCommand(Executer.java:137)
> at ij.Executer.run(Executer.java:66)
> at java.lang.Thread.run(Thread.java:748)

I have tried to change the file delimiter to '\', \\', '\\\\', and '/' with no success. Any suggestions?

Thanks!

Contributor guide

No contributing guide indexed for this repository

Research direction

Start in ZOLA.java at the calibration entry point and the reported line 1862, then inspect the path parsing involved in the sCMOS setup. Reproduce the Windows configuration with the three TIFF paths and verify that calibration no longer raises the PatternSyntaxException and proceeds past this step.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
computer-vision
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
28/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.