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Bug 219 - Error Image Stack is empty when presing 'Hessian based analysis'
Error Image Stack is empty when presing 'Hessian based analysis'
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Mac OS
: P2 normal
Assigned To: Mark Longair
Depends on:
Blocks:
 
Reported: 2010-08-17 03:33 CDT by Yihwa Kim
Modified: 2010-08-23 05:46 CDT
0 users

See Also:


Attachments
the screen capture of the neurite tracer window (119.64 KB, image/png)
2010-08-18 11:00 CDT, Yihwa Kim
screen capture of the current status (915.90 KB, image/png)
2010-08-20 03:38 CDT, Yihwa Kim

Description Yihwa Kim 2010-08-17 03:33:55 CDT
Hi 
I am using Simple Neurite Tracer, and when I press Hessian-based analysis, I get an error saying 'Image Stack is empty' and the Hessian based analysis button becomes inactivated (it cannot be selected anymore).

Best wishes

Yihwa
Comment 1 Yihwa Kim 2010-08-17 03:37:53 CDT
Sorry I thought it was an error, but it seems to be doing something.. 
It now says Calculating Gaussian.. 
So probably Gaussian is being done.
However the status bar is not moving and it doesn't show intermediate results or so as was in the tutorial video.
Best wishes

Yihwa 
Comment 2 Yihwa Kim 2010-08-17 03:44:22 CDT
Now there is an error. 
-------------------------------------------------------------
There was an exception in the search thread:

java.lang.NullPointerException
	at features.ComputeCurvatures.hessianEigenvaluesAtPoint3D(ComputeCurvatures.java:726)
	at tracing.TracerThread.costMovingTo(TracerThread.java:239)
	at tracing.SearchThread.run(SearchThread.java:533)

-------------------------------------------------------------

Most of the buttons are now deactivated still.. 
Comment 3 Johannes Schindelin 2010-08-17 10:32:34 CDT
Please take the time to make a coherent bug report where you say _exactly_ how to reproduce the issue, and what exactly the issue is. Preferably all of this in the initial report.
Comment 4 Yihwa Kim 2010-08-17 11:02:04 CDT
Sorry about spurios mails that I have created.
It seems 'Hessian-based analysis' takes quite much time. 
When I first opened it I wasn't quite sure what the error 'image stack is empty' meant in the context of 'hessian-based analysis'. Especially since already an image was loaded which I had been tracing. (I had searched for this phrase in the error search database, but didn't find anything).
The last error seemed to arise when I cancled the process of 'hessain-based analysis' and I might have pressed somewhere on the actual image stack. 

So far, I haven't got Hessian-based analysis working, I wonder if it just takes quite much time (I have waited for about 1/2 hour, didn't finish), or it crashed due to big file size.. 
It would be nice to know what is actually happening, and if there is anything I should be keeping in mind when I use that.

Thanks again for developing this software. It is very nice to use, and also for the quick help. 
Next time I create a report, I would try to be more succint and follow the instructions that you suggested. 


Comment 5 Mark Longair 2010-08-17 11:24:41 CDT
(In reply to comment #3)
> Please take the time to make a coherent bug report where you say _exactly_ how
> to reproduce the issue, and what exactly the issue is. Preferably all of this
> in the initial report.

Indeed - in addition to a recipe for reproducing the problem, as Johannes asks
for, could you also let me know:

 - Does this problem happen every time now, or was it a one-off?

 - Is this a 2D image or 3D image stack?

 - What are the dimensions of the image you are tracing?

 - I see that you've marked your platform as Mac OS - could you let me know
which version of Mac OS you are using?

 - Did you have any other images or windows opened in ImageJ when you started
tracing your image?

I'm afraid I haven't managed to reproduce this bug yet, but with some of the
above details, perhaps we can.

When there's a (hopefully rare) error like this some buttons may be left
disabled, I'm afraid.  I will improve this in a future version.

regards,
mark
Comment 6 Mark Longair 2010-08-17 11:34:21 CDT
(In reply to comment #4)
[..] 
> So far, I haven't got Hessian-based analysis working, I wonder if it just takes
> quite much time (I have waited for about 1/2 hour, didn't finish), or it
> crashed due to big file size.. 
> It would be nice to know what is actually happening, and if there is anything I
> should be keeping in mind when I use that.
[..]

It may take a very long time depending on the image size (as I mentioned in the previous comment), the value of sigma that you are choosing and (of course) the specification of the computer you're using.  So if you can supply those details maybe we can rule that out or investigate further.

Another thing to check is to run the system monitor - if the CPU is at 100% then that's a strong indication that it's just taking a long time.

regards,
mark
Comment 7 Yihwa Kim 2010-08-18 10:56:57 CDT
- Does this problem happen every time now, or was it a one-off?
I am using the same image, and it seems to happen each time. 

 - Is this a 2D image or 3D image stack?
It was a 3D image stack
size was 116 MB.

 - What are the dimensions of the image you are tracing?
3D

 - I see that you've marked your platform as Mac OS - could you let me know
which version of Mac OS you are using?

Version 10.5.8

 - Did you have any other images or windows opened in ImageJ when you started
tracing your image?


No only one image was open. 

I'm afraid I haven't managed to reproduce this bug yet, but with some of the
above details, perhaps we can.
Comment 8 Yihwa Kim 2010-08-18 11:00:19 CDT
Created attachment 23
the screen capture of the neurite tracer window

Hi 
The CPU usage is only about 10 - 15 % and the one used by fiji is only .1 % .

For the value of sigma, I had used the default value.
best wishes

Yihwa
Comment 9 Mark Longair 2010-08-18 18:58:36 CDT
Since I still can't see how this is happening with any of the test images I've tried, would you be prepared to upload this file so that I can try to reproduce the problem with the same file that you're using?  (It can be any image file that causes this problem for you in Simple Neurite Tracer.)

Of course, I will only use this image to try to fix the problem.  If you would be happy with that, then you can use the "Help > Upload Sample Image" menu option, which will upload the file so that myself and the other Fiji developers can look at it.

many thanks,
mark
Comment 10 Yihwa Kim 2010-08-19 10:44:57 CDT
Hi 
Even when I cancel it it just says Cancelling Gaussian generation and nothing seems to happen. 
I will upload the file on the next report. 
Comment 11 Yihwa Kim 2010-08-19 10:55:55 CDT
I have uploaded the sample image under the name testimage.tif.

This file is 15 MB. The files I had been using were about 50 MB. 

Bes wishes

Yihwa
Comment 12 Mark Longair 2010-08-19 19:04:28 CDT
(In reply to comment #11)
> I have uploaded the sample image under the name testimage.tif.
> 
> This file is 15 MB. The files I had been using were about 50 MB. 
> 
> Bes wishes
> 
> Yihwa

Yihwa,

Thank you for uploading that.  However, I don't have any problem turning on Hessian-based analysis for that image.  Could you possible describe exactly what you do, with that precise image, from starting Fiji until you get the exception?  For example, that should include how you open the file (which exact menu option), which options you select at each stage, and so on.

I hope this isn't too much trouble to go to, but this is one of those cases where it seems that a really detailed bug report will be necessary.

many thanks,
mark
Comment 13 Yihwa Kim 2010-08-20 03:38:18 CDT
Created attachment 25
screen capture of the current status

1. Starting Fiji
2. File -> Import -> TIFF Virtual Stack 
3. Plugin -> Segmentation -> Simple Neurite Tracer 
4. Pressing OK when Simple Neurite Tracer appears 
5. From the Neurite Tracer window, Pressing Hessian-based analysis 
(without changing any of the default values of sigma and multiplier)
6. A window appears that says 'Image Stack is empty' and I press OK
7. From the Neurite Tracer Window , Under Instructions appears 'Calculating  Gaussian ... ' 

Nothing seems to happen...
Comment 14 Mark Longair 2010-08-20 08:23:09 CDT
(In reply to comment #13)
> Created an attachment (id=25) [details]
> screen capture of the current status
> 
> 1. Starting Fiji
> 2. File -> Import -> TIFF Virtual Stack 
> 3. Plugin -> Segmentation -> Simple Neurite Tracer 
> 4. Pressing OK when Simple Neurite Tracer appears 
> 5. From the Neurite Tracer window, Pressing Hessian-based analysis 
> (without changing any of the default values of sigma and multiplier)
> 6. A window appears that says 'Image Stack is empty' and I press OK
> 7. From the Neurite Tracer Window , Under Instructions appears 'Calculating 
> Gaussian ... ' 
> 
> Nothing seems to happen... 

A-ha!  I think the problem is that you're opening the image as a virtual stack.  Try opening it just normally (e.g. with File > Open ...) and see if that works better.  In any case, I'll add a helpful error if people try to use a virtual stack for something that's not supported.

regards,
mark
Comment 15 Yihwa Kim 2010-08-20 09:57:47 CDT
Yes Indeed!!!
It works now! :) 
Thanks!

Uhm I didn't know it was different, loading the file via 'open' option and the import 'open virtual stack'. 
What are the differences? 

With regards to the 'Hessian based analysis' itself, I don't see so much difference in the quality of the image itself before and after. 
What should I be expecting to see?

Best wishes

Yihwa
Comment 16 Mark Longair 2010-08-20 12:15:13 CDT
(In reply to comment #15)
> Yes Indeed!!!
> It works now! :) 
> Thanks!
> 
> Uhm I didn't know it was different, loading the file via 'open' option and the
> import 'open virtual stack'. 
> What are the differences? 
> 
> With regards to the 'Hessian based analysis' itself, I don't see so much
> difference in the quality of the image itself before and after. 
> What should I be expecting to see?
> 
> Best wishes
> 
> Yihwa

I have released a change that means that this option should work even if you do open the stack as a virtual stack.  If you go to "Help > Update Fiji" you should be offered the uption to update jars/VIB-lib.jar - this should fix the problem.

In answer to your question, the results of the filtering aren't shown in the image, but will affect the search between points and paths found.  (If you turn it on and off you should see a difference in the character of the search progress shown on the image in cyan.)

If you want to see the results on your image, you can run the "Plugins > Analyze > Tubeness".  For a small region and a limited number of different values of sigma, the "Pick Sigma Visually" option will show you a preview of the "tubeness" filtering on the small region you select.

I hope that's of some help.

regards,
mark
Comment 17 Yihwa Kim 2010-08-23 05:46:37 CDT

> If you want to see the results on your image, you can run the "Plugins >
Analyze > Tubeness".  For a small region and a limited number of different
values of sigma, the "Pick Sigma Visually" option will show you a preview of
the "tubeness" filtering on the small region you select.



Hi I have tried "Plugins > Analyze > Tubeness" option, however I got the error that it is out of memory. 
I tried to increase the memory but it was already set to 2.7 GB (which was more than the 2GB I had). 
Does this function require a lot of memory? ?

Best wishes

Yihwa