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ciliaq_preparator's Issues

java.lang.NullPointerException - CiliaQPrepMain.java:273

When running an image that is not saved, CiliaQ Preparator crashes with the error message:

 
java.lang.NullPointerException
	at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:273)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:750)

TODO:
Catch the error and output an interpretable message to the user explaining how the user can avoid this issue.

After processed with CANNY 3D through CiliaQ Preparator, the cilia from the new generated 2D Picture showed loss of pixels

Hello Hansen,

Thank you for providing us this powerful plugin! After processing my 2D pictures with CANNY 3D through CiliaQ Preparator, I found that some cilia from the segmented channel showed a loss of pixels, but not all the cilia. It looks like the ciliaQ won't pick these missing pixels finally when we quantify the cilia intensity. Would you have any good suggestions? Thanks!

2021-03-26_175805
2021-03-26_175853
2021-03-26_180242
2021-03-26_180356

Errors with Hysteresis and Canny 3D segmentation

Recently errors occur when applying "HYSTERESIS threshold" or "CANNY3D" as the "Segmentation method", but only when the image was loaded through the multi-task manager processing option ( ).

For CANNY 3D, two error messages appear:
Message 1:

java.lang.NullPointerException
	at ciliaQ_Prep_jnh.canny3d_thresholder.Processing.doProcessing(Processing.java:52)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingCanny3D(CiliaQPrepMain.java:1437)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:567)
	at ij.IJ.runUserPlugIn(IJ.java:244)
	at ij.IJ.runPlugIn(IJ.java:210)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:750)

Message 2:

java.lang.NullPointerException
	at mcib_plugins.Hysteresis_Thresholding.run(Hysteresis_Thresholding.java:43)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:246)
	at ij.IJ.runPlugIn(IJ.java:210)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at ij.IJ.run(IJ.java:326)
	at ij.IJ.run(IJ.java:416)
	at ciliaQ_Prep_jnh.canny3d_thresholder.Processing.doProcessing(Processing.java:50)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingCanny3D(CiliaQPrepMain.java:1437)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:567)
	at ij.IJ.runUserPlugIn(IJ.java:244)
	at ij.IJ.runPlugIn(IJ.java:210)
	at ij.Executer.runCommand(Executer.java:152)
	at ij.Executer.run(Executer.java:70)
	at java.lang.Thread.run(Thread.java:750)

For applying the HYSTERESIS threshold, one error messages appears:

java.lang.NullPointerException
	at ciliaQ_Prep_jnh.CiliaQPrepMain.doHysteresisThreshold(CiliaQPrepMain.java:1523)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.segmentUsingHysteresis(CiliaQPrepMain.java:1486)
	at ciliaQ_Prep_jnh.CiliaQPrepMain.run(CiliaQPrepMain.java:580)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:750)

The errors must relate to changes in the 3DSuite library that CiliaQ Preparator uses for performing operations in the segmentation workflows for "HYSTERESIS threshold" or "CANNY3D" since these errors only emerge recently.

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