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 <bnort...@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 <hi...@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 <bnort...@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 <hin...@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 <hi...@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 <bnort...@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$Writer.savePlane(TIFFFormat.java:1290) >>>>>> >>>>>> at io.scif.AbstractWriter.savePlane(AbstractWriter.java:107) >>>>>> at io.scif.img.ImgSaver.writePlanes(ImgSaver.java:532) >>>>>> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:380) >>>>>> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:133) >>>>>> at io.scif.img.ImgSaver.saveImg(ImgSaver.java:114) >>>>>> >>>>>> >>>>>> >>>>>> On Fri, Dec 13, 2013 at 1:40 PM, Mark Hiner <hin...@gmail.com> wrote: >>>>>> >>>>>>> >>>>>>> Hi Brian, >>>>>>> >>>>>>> >>>>>>>> I referenced the scifio 0.7.5-SNAPSHOT (would that be correct to >>>>>>>> get the absolute latest??) >>>>>>>> >>>>>>> >>>>>>> Yep this should be the latest snapshot. >>>>>>> >>>>>>> in my POM and ran into an exception when executing my code. >>>>>>>> >>>>>>> >>>>>>> ... >>>>>>> >>>>>>> >>>>>>>> at >>>>>>>> io.scif.formats.TIFFFormat$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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