Bug 106 – [NeuriteSimpleTracer reports traces on the 3D viewer with wrong coodinates]

Bug 106 - [NeuriteSimpleTracer reports traces on the 3D viewer with wrong coodinates]


Summary:	[NeuriteSimpleTracer reports traces on the 3D viewer with wrong coodinates]

Status:	RESOLVED WORKSFORME

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2009-11-23 19:36 CST by Giorgio G.
Modified:	2010-03-17 13:15 CDT
CC List:	1 user (show)

See Also:

Description Giorgio G. 2009-11-23 19:36:12 CST

[NeuriteSimpleTracer reports traces on the 3D viewer with wrong coodinates. The trace on the 3D viewer is thus not in the right place]

Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_16
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_16-b01
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 14.2-b01
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

Comment 1 Mark Longair 2009-11-23 19:47:17 CST

Thanks for your bug report.  Could you clarify what you mean in more detail?  e.g. do you mean that when you import an SWC file, the traces appear in the wrong place?  If that's the case, please could you point me to the SWC file that is causing the problems, and I'll look into it further.

If it's a different problem, could you explain in more detail how to reproduce the bug?

many thanks
mark

Comment 2 Giorgio G. 2009-11-23 20:18:17 CST

Hi Mark,
thank you for replying.

I'm just new with the simple neurite tracer.
I've started making some tracers by this plug in cheking the option to have the 3D viewer applied at the same time to my stak. I noticed that the traces are reported on the 3D viewer...which is great! But in a worng place. Maybe it is just a matter of resizing their coordinates in the same way the stack is resized in the 3D viewer.

I hope to be clear. I am sorry in the opposite case, I would try to explain better.

Best regards,
Giorgio

(In reply to comment #1)
> Thanks for your bug report.  Could you clarify what you mean in more detail? 
> e.g. do you mean that when you import an SWC file, the traces appear in the
> wrong place?  If that's the case, please could you point me to the SWC file
> that is causing the problems, and I'll look into it further.
> 
> If it's a different problem, could you explain in more detail how to reproduce
> the bug?
> 
> many thanks
> mark
> 

(In reply to comment #0)
> [NeuriteSimpleTracer reports traces on the 3D viewer with wrong coodinates. The
> trace on the 3D viewer is thus not in the right place]
> 
> Information about your version of Java - this information is useful for the
> Fiji developers:
>   os.arch => x86
>   os.name => Windows XP
>   os.version => 5.1
>   java.version => 1.6.0_16
>   java.vendor => Sun Microsystems Inc.
>   java.runtime.name => Java(TM) SE Runtime Environment
>   java.runtime.version => 1.6.0_16-b01
>   java.vm.name => Java HotSpot(TM) Client VM
>   java.vm.version => 14.2-b01
>   java.vm.vendor => Sun Microsystems Inc.
>   java.vm.info => mixed mode
>   java.awt.graphicsenv => sun.awt.Win32GraphicsEnvironment
>   java.specification.name => Java Platform API Specification
>   java.specification.version => 1.6
>   sun.cpu.endian => little
>   sun.desktop => windows
>   file.separator => \
>

Comment 3 Mark Longair 2010-03-17 13:15:38 CDT

There's nothing I can really do about this bug without an example SWC file that displays the problem, as I asked for in comment #1, and ideally a companion image.

So, I'm closing this for the moment with WORKSFORME - if you do supply those files I'm happy to reopen it.

(I will also note that there are many broken SWC files out in the wild, and automatically guessing which particular problems a given file has is difficult to do well.)