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zitmen / thunderstorm

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging
http://zitmen.github.io/thunderstorm/
GNU General Public License v3.0
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no data table output in Fiji 1.49o29 #20

Closed zitmen closed 9 years ago

zitmen commented 9 years ago 
What steps will reproduce the problem?
1.data are originally collected with Leica software from GSD 3D 'scope
2.with fiji, open movie (as virtual stack) of blinking images from lif file
3.save movie as tiff file in fiji
4.run ThunderSTORM plugin

What is the expected output? What do you see instead?
32-bit tiff stack comes out fine, but no data table. 

What version of the product are you using? On what operating system?
I hope this is a minor bug because I was getting data tables with Fiji last Thursday.

Please provide any additional information below.

This is the error message I get from Fiji:

(Fiji Is Just) ImageJ 2.0.0-rc-19/1.49o29; Java 1.8.0_25 [64-bit]; Windows 7 6.1; 843MB
of 12191MB (6%)

org.apache.commons.math3.exception.ConvergenceException: illegal state: unable to perform
Q.R decomposition on the 121x11 jacobian matrix
    at org.apache.commons.math3.optim.nonlinear.vector.jacobian.LevenbergMarquardtOptimizer.qrDecomposition(LevenbergMarquardtOptimizer.java:884)
    at org.apache.commons.math3.optim.nonlinear.vector.jacobian.LevenbergMarquardtOptimizer.doOptimize(LevenbergMarquardtOptimizer.java:331)
    at org.apache.commons.math3.optim.nonlinear.vector.jacobian.LevenbergMarquardtOptimizer.doOptimize(LevenbergMarquardtOptimizer.java:113)
    at org.apache.commons.math3.optim.BaseOptimizer.optimize(BaseOptimizer.java:143)
    at org.apache.commons.math3.optim.BaseMultivariateOptimizer.optimize(BaseMultivariateOptimizer.java:66)
    at org.apache.commons.math3.optim.nonlinear.vector.MultivariateVectorOptimizer.optimize(MultivariateVectorOptimizer.java:87)
    at org.apache.commons.math3.optim.nonlinear.vector.JacobianMultivariateVectorOptimizer.optimize(JacobianMultivariateVectorOptimizer.java:83)
    at org.apache.commons.math3.optim.nonlinear.vector.jacobian.AbstractLeastSquaresOptimizer.optimize(AbstractLeastSquaresOptimizer.java:197)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.LSQFitter.fit(LSQFitter.java:59)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.MultipleLocationsImageFitting.run(MultipleLocationsImageFitting.java:83)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.MultipleLocationsImageFitting.estimateParameters(MultipleLocationsImageFitting.java:134)
    at cz.cuni.lf1.lge.ThunderSTORM.estimators.CylindricalLensZEstimator.estimateParameters(CylindricalLensZEstimator.java:25)
    at cz.cuni.lf1.lge.ThunderSTORM.AnalysisPlugIn.run(AnalysisPlugIn.java:250)
    at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:263)
    at ij.plugin.filter.PlugInFilterRunner.processStack(PlugInFilterRunner.java:194)
    at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:145)
    at ij.IJ.runUserPlugIn(IJ.java:201)
    at ij.IJ.runPlugIn(IJ.java:163)
    at ij.Executer.runCommand(Executer.java:131)
    at ij.Executer.run(Executer.java:64)
    at java.lang.Thread.run(Unknown Source)

Original issue reported on code.google.com by maryebrown1 on 2015-01-20 20:41:28

zitmen commented 9 years ago 
Hi, what do you mean by it worked last Thursday? Did you make an update? What version
were you using before and what version you use now?
Also, this looks like calibration, is it?
Could you attach a tiff stack that causes the error? It can be just a small cropped
area.

My first thought is that the calibration curve cannot be fitted for some reason...maybe
there are too many beads and some don't look alike (for example if there was couple
of them overlapping each other). Or maybe width of your PSF (in pixels) is too big
for the current size of fitting window.

I might be able to tell you more when I see the data.

Original issue reported on code.google.com by zitmen on 2015-01-21 15:30:48

zitmen commented 9 years ago 
After showing my data to a colleague, it looks like I had a bad data set. I
had to run the data in blocks and I used the good blocks of data.

Sorry to have inconvenienced you.

Original issue reported on code.google.com by maryebrown1 on 2015-01-22 16:32:32

zitmen commented 9 years ago 
Ok, no worries. I am changing this to Done. If something else occurs, let me know. I'll
be glad to help you.

Original issue reported on code.google.com by zitmen on 2015-01-22 16:35:21

zitmen commented 9 years ago 
Thank you!

Original issue reported on code.google.com by maryebrown1 on 2015-01-22 16:40:33