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

Brian Northan bnorthan at gmail.com
Wed Jan 8 16:39:33 CST 2014 

Hi Mark

Thanks for the fix.  And thanks for the example code for making the command
discoverable.

Brian


On Wed, Jan 8, 2014 at 4:52 PM, Mark Hiner <hiner at wisc.edu> wrote:

> Ahh.. looks like this was just a general bug in opening TIFF data. Sorry
> that wasn't clear to me.
>
> Anyway, it's fixed now locally. I'll release SCIFIO 0.8.2 tonight or
> tomorrow which will include the fix (you'll just have to update your
> pom-scijava to the latest version at that point).
>
> Side note: you may want to define your CreatePhantomCommand (and other
> commands?) as discoverable IJ2 commands..
>
> For example:
>
> @Plugin(type=Command.class, menu = {
>     @Menu(label = MenuConstants.PLUGINS_LABEL,
>             weight = MenuConstants.PLUGINS_WEIGHT,
>             mnemonic = MenuConstants.PLUGINS_MNEMONIC),
>         @Menu(label = "Truenorth", mnemonic = 't'), @Menu(label = "Create
> Phantom", weight = 1) })
> public class CreatePhantomCommand  implements Command
> {
> ...
> }
>
> Would make the CreatePhantomCommand discoverable by searching commands, or
> via the Plugin menu. Made testing in IJ2 a little easier for me..
>
> Anyway, thanks again!
> - Mark
>
>
> On Wed, Jan 8, 2014 at 3:01 PM, Brian Northan <bnorthan at gmail.com> wrote:
>
>> Hi Mark
>>
>> To clarify I was only changing the spacings to 0 as a hack to get around
>> the error I was seeing.  The code I was wondering about (around line 975 of
>> TIFFFormat.java) is only called for spacing > 0.0.
>>
>> You can repeat the error by running the CreatePhantomCommand we discussed
>> a couple weeks ago.  (I believe you retrieved the code and got it running
>> but let me know if you need the instructions again).
>>
>> The error can be repeated by running the CreatePhantomCommand to create a
>> blank image and then trying to load the output into ImageJ2.  The stack
>> trace that I get from ImageJ2 is then as follows...
>>
>> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>>     at java.util.ArrayList.rangeCheck(ArrayList.java:604)
>>     at java.util.ArrayList.get(ArrayList.java:382)
>>     at io.scif.AbstractMetadata.get(AbstractMetadata.java:138)
>>     at
>> io.scif.formats.TIFFFormat$BaseTIFFParser.initMetadata(TIFFFormat.java:975)
>>     at io.scif.formats.TIFFFormat$Parser.initMetadata(TIFFFormat.java:375)
>>     at
>> io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:645)
>>     at
>> io.scif.formats.TIFFFormat$BaseTIFFParser.typedParse(TIFFFormat.java:627)
>>     at io.scif.AbstractParser.parse(AbstractParser.java:326)
>>     at io.scif.AbstractParser.parse(AbstractParser.java:105)
>>     at io.scif.AbstractParser.parse(AbstractParser.java:59)
>>     at io.scif.AbstractReader.setSource(AbstractReader.java:217)
>>     at
>> io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:96)
>>     at io.scif.img.ImgOpener.createReader(ImgOpener.java:365)
>>     at io.scif.img.ImgOpener.openImg(ImgOpener.java:147)
>>     at
>> imagej.data.DefaultDatasetService.open(DefaultDatasetService.java:254)
>>     at imagej.data.io.DatasetIOPlugin.open(DatasetIOPlugin.java:82)
>>     at imagej.data.io.DatasetIOPlugin.open(DatasetIOPlugin.java:54)
>>     at imagej.io.DefaultIOService.open(DefaultIOService.java:87)
>>     at imagej.plugins.commands.io.OpenFile.run(OpenFile.java:85)
>>     at imagej.command.CommandModule.run(CommandModule.java:196)
>>     at imagej.module.ModuleRunner.run(ModuleRunner.java:170)
>>     at imagej.module.ModuleRunner.call(ModuleRunner.java:131)
>>     at imagej.module.ModuleRunner.call(ModuleRunner.java:70)
>>     at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
>>     at java.util.concurrent.FutureTask.run(FutureTask.java:166)
>>     at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
>>     at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
>>     at java.lang.Thread.run(Thread.java:724)
>>
>>
>> On Wed, Jan 8, 2014 at 3:40 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>
>>> Hi Brian,
>>>
>>>  Sorry to hear that some tests are failing for you now.
>>>
>>>  It does sound like there could be a bug here, but I will need more
>>> information to track it down.
>>>
>>>  Which tests are you running exactly, and what's the stack trace you
>>> get? If you could provide a minimal set of steps to reproduce the error,
>>> that would be great. Also, where are you setting the pixel size to be 0?
>>> (as a side note, a value of 1.0 might be safer.. which is what these axes
>>> are supposed to default to)
>>>
>>> Thanks!
>>> Mark
>>>
>>>
>>> On Wed, Jan 8, 2014 at 9:57 AM, Brian Northan <bnorthan at gmail.com>wrote:
>>>
>>>> Hi Mark
>>>>
>>>> Hope you had a good holiday.   I noticed some tests of mine failing
>>>> just after Christmas. I think the failure possibly has something to do with
>>>> a change in setting pixel size when loading.  Right around line 1000 in
>>>> this commit.
>>>>
>>>>
>>>> https://github.com/scifio/scifio/commit/232261b978cbaeb42eb28c67cdddb7aca1acb1b6
>>>>
>>>> If you remember I have a script SimpleCreatePhantoms.sh which creates a
>>>> blank image then places a sphere in it.  It now fails in the second step
>>>> because it cannot reload the blank image.  I also cannot reload the newly
>>>> created blank image into the latest build of ImageJ.
>>>>
>>>> I have a workaround (set pixel size to zero since I am not actually
>>>> using it right now) so it isn't critical but thought I'd let you know about
>>>> a potential bug.
>>>>
>>>> Brian
>>>>
>>>>
>>>> On Mon, Dec 16, 2013 at 3:32 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>>>
>>>>> No problem. That "error" message when failing to create services is
>>>>> confusing.
>>>>>
>>>>> Glad it's working, let us know if you have any more problems!
>>>>>
>>>>> - Mark
>>>>>
>>>>>
>>>>> On Mon, Dec 16, 2013 at 2:19 PM, Brian Northan <bnorthan at gmail.com>wrote:
>>>>>
>>>>>> Hi Mark
>>>>>>
>>>>>> I just checked and It did work after all...  I actually never checked
>>>>>> to see if the final output was created.  I just saw the exception and
>>>>>> assumed it had stopped.
>>>>>>
>>>>>> So everything appears great now,.  Looks like the floating point
>>>>>> numbers are being saved correctly.
>>>>>>
>>>>>> Thanks for the fix
>>>>>>
>>>>>> Brian
>>>>>>
>>>>>>
>>>>>> On Mon, Dec 16, 2013 at 2:46 PM, Mark Hiner <hiner at wisc.edu> wrote:
>>>>>>
>>>>>>> Hi Brian,
>>>>>>>
>>>>>>>  So, running your CreatePhantomCommand via the DeconvolutionTest
>>>>>>> class actually creates a blank image for me... I ran it from Eclipse
>>>>>>> directly though.
>>>>>>>
>>>>>>>  Also, I did observe the same error message that you saw, but the
>>>>>>> message was just logged and execution continued (because the services that
>>>>>>> failed to instantiate weren't necessary for execution.. so the "error"
>>>>>>> nature of the message is a bit of an overstatement in this case).
>>>>>>>
>>>>>>>  It is possible that some classes in SCIFIO erroneously have
>>>>>>> required services that aren't available in headless mode, but nothing stood
>>>>>>> out to me as suspicious.
>>>>>>>
>>>>>>> Could you do two more things for me:
>>>>>>>
>>>>>>> 1) Try running your scripts without using a headless IJ2 to verify
>>>>>>> this works on your end.
>>>>>>>
>>>>>>> 2) Set the Java system property: "scijava.log.level=4" and re-paste
>>>>>>> the error output. This will turn full debugging on.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Mark
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Dec 16, 2013 at 11:23 AM, Brian Northan <bnorthan at gmail.com>wrote:
>>>>>>>
>>>>>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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