[ImageJ-devel] [ImgLib2] The img-metadata branch

Brian Northan bnorthan at gmail.com
Mon Dec 16 11:23:55 CST 2013 

Hi Mark

My code is here: https://github.com/bnorthan/projects -- be warned it is in
need of some refactoring which I plan to do as ImageJ2 scripting becomes
available.

A simple example of running my custom commands is in
"SimpleCreatePhantoms.sh"  (the other scripts will not work because of
references to things on my own machine).

The code is for a project I did earlier in the year (
http://spie.org/x648.xml?product_id=2002974).

The main program is called DeconvolutionTest.java... which has ended up
evolving into a command parser.  I never really polished it though because
I am going to throw it away and use ImageJ2 scripting as that develops.
A lot of things in the code base fall into that category, things I put
together quickly but are meant to be replaced with the "proper" imagej2
component.

SimpleCreatePhantoms.sh just calls a command to create a blank phantom,
then a second command to place a sphere in it.


On Mon, Dec 16, 2013 at 9:09 AM, Mark Hiner <hinerm at gmail.com> wrote:

> P.S. please feel free to send your commands via private e-mail, if you
> don't want them to be public.
>
> Similarly, if you can share the dataset you're using that would be
> ideal... but no worries if it's proprietary or anything.
>
>
> On Mon, Dec 16, 2013 at 8:07 AM, Mark Hiner <hiner at wisc.edu> wrote:
>
>> Hi Brian,
>>
>>  Ahhh.. I'm sorry! I misunderstood. If that's the actual stack trace then
>> no, I don't think you are having any problems with the dependency tree, and
>> all your pom settings should be fine given that stack trace.
>>
>>  Sidetrack: the pom-scijava doesn't actually have snapshot versions. It's
>> basically just versioning glue - it defines a version properties to help
>> ensure consistent versions of the various SciJava libraries (like SCIFIO)
>> are consumed. Using 1.111 is fine, as we want to use the latest version of
>> everything since SCIFIO-0.7.4/0.7.5 are quite new. Let me know if that's
>> not clear...
>>
>>   Anyway, since we know it worked in 0.7.3, I would like to bisect<https://www.kernel.org/pub/software/scm/git/docs/git-bisect.html>and figure out what happened. However, I currently can't reproduce the
>> issue. When I open a float dataset with SCIFIO 0.7.5 in IJ2 I'm able to
>> write it as a .tif. So you're probably exposing a bug with other commands
>> interacting with SCIFIO.
>>
>>  Can you share your custom commands? If not, could you let me know which
>> commands you're calling?
>>
>> Thanks,
>> - Mark
>>
>>
>>
>>
>> On Fri, Dec 13, 2013 at 1:49 PM, Brian Northan <bnorthan at gmail.com>wrote:
>>
>>> Hi Mark
>>>
>>> I am using IJ2 in headless mode with some custom commands I wrote.  So
>>> it is always possible that I still have old references somewhere.  However
>>> that stack trace was actually generated with 0.7.4.  When I had noted that
>>> 0.7.5-SNAPSHOT threw an exception, I went back to 0.7.4 to make sure that
>>> worked but it also had the same exception.  Then I went back to 0.7.3 which
>>> worked (other than the floating point problem).
>>>
>>> Below is the stack trace using 0.7.5-SNAPSHOT.   (btw since I am using
>>> IJ2 maybe there is something else wrong in the dependency tree??  One of
>>> the IJ2 components??  Should I set the sci-java version to a SNAPSHOT
>>> version too??  It is 1.111 right now.
>>>
>>>      at org.scijava.Context.inject(Context.java:273)
>>>     at
>>> org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:241)
>>>     at
>>> org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:229)
>>>     at
>>> org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:220)
>>>     at
>>> org.scijava.plugin.AbstractSingletonService.createInstances(AbstractSingletonService.java:95)
>>>     at
>>> org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:73)
>>>     at
>>> org.scijava.plugin.AbstractSingletonService$1.get(AbstractSingletonService.java:87)
>>>     at
>>> org.scijava.plugin.AbstractSingletonService$1.get(AbstractSingletonService.java:83)
>>>     at
>>> org.scijava.object.ObjectIndex.resolvePending(ObjectIndex.java:391)
>>>     at org.scijava.object.ObjectIndex.get(ObjectIndex.java:136)
>>>     at
>>> org.scijava.object.DefaultObjectService.getObjects(DefaultObjectService.java:89)
>>>     at
>>> io.scif.codec.DefaultCodecService.getCodec(DefaultCodecService.java:65)
>>>     at
>>> io.scif.formats.tiff.TiffCompression.compress(TiffCompression.java:330)
>>>     at io.scif.formats.tiff.TiffSaver.writeImage(TiffSaver.java:391)
>>>     at io.scif.formats.tiff.TiffSaver.writeImage(TiffSaver.java:279)
>>>      at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1250)
>>>     at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1290)
>>>
>>>     at io.scif.AbstractWriter.savePlane(AbstractWriter.java:107)
>>>     at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:532)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:380)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:133)
>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:114)
>>>
>>>
>>>
>>> On Fri, Dec 13, 2013 at 1:40 PM, Mark Hiner <hinerm at gmail.com> wrote:
>>>
>>>>
>>>> Hi Brian,
>>>>
>>>>
>>>>>  I referenced the scifio 0.7.5-SNAPSHOT (would that be correct to get
>>>>> the absolute latest??)
>>>>>
>>>>
>>>> Yep this should be the latest snapshot.
>>>>
>>>>  in my POM and ran into an exception when executing my code.
>>>>>
>>>>
>>>> ...
>>>>
>>>>
>>>>>      at
>>>>> io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1255)
>>>>>     at
>>>>> io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1295)
>>>>>     at io.scif.AbstractWriter.savePlane(AbstractWriter.java:107)
>>>>>     at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:532)
>>>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:380)
>>>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:133)
>>>>>     at io.scif.img.ImgSaver.saveImg(ImgSaver.java:114)
>>>>>
>>>>
>>>> That stack trace suggests that an older version of the TIFFFormat is
>>>> being used. It must be from prior commit 37953<https://github.com/scifio/scifio/commit/379530aab9a9848e59363d87dcbdb79c4842bfc3>(because the TiffSaver.writeImage call is now on line 1250, not 1255). I'm
>>>> assuming it's from the 0.7.4 release.
>>>>
>>>>  Are you just running the code snippet that Curtis posted a while back
>>>> (or your own similar snippet)? Or are you using SCIFIO in IJ2, or another
>>>> application?
>>>>
>>>>  Could you run "mvn dependency:tree", or check the "Maven Dependencies"
>>>> tab if you're using Eclipse? I'm assuming something must still have a 0.7.4
>>>> SCIFIO reference, which is being pulled in instead of 0.7.5...
>>>>
>>>> Sorry for the inconvenience.. let me know what you find!
>>>>
>>>> Thanks,
>>>> Mark
>>>>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://imagej.net/pipermail/imagej-devel/attachments/20131216/ae2577f2/attachment-0001.html>

More information about the ImageJ-devel mailing list