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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