[SCIFIO] ImgOpener - ImgOptions - SubRegions

[Michael Zinsmaier]

Hi Mark,

I get the error for a dataset with axes > 2. I perpared some sample code 
(maybe something is wrong here) and I'll send you the file in a seperate 
mail.

Regards Michael

----------------------------------------------------------------

     public static void main(String[] args) throws FormatException, 
IOException, ImgIOException, InstantiableException {
             String imgRef = 
"C:/Users/zinsmaie/Desktop/bilder/5d/2chZT.lsm";

             Context c = new Context(SciJavaService.class, 
SCIFIOService.class);
             SCIFIO sci = new SCIFIO(c);

             Reader reader = sci.initializer()
                     .initializeReader(imgRef, true);

             ImgOptions options = new ImgOptions();

//WORKS
//                DimRange[] ranges = new DimRange[] {new DimRange("0")};
//                AxisType[] axes = new AxisType[] {Axes.CHANNEL};
//EXCEPTION
                 DimRange[] ranges = new DimRange[] {new DimRange("0-10")};
                 AxisType[] axes = new AxisType[] {Axes.Z};
//WORKS
//                    DimRange[] ranges = new DimRange[] {new 
DimRange("0"), new DimRange("0-10")};
//                    AxisType[] axes = new AxisType[] {Axes.CHANNEL, 
Axes.Z};


                 options.setRegion(new SubRegion(axes, ranges));

         ImgPlus<RealType> ret = new ImgOpener().openImg(reader,
                     new UnsignedByteType(), new ArrayImgFactory(), 
options);

         System.out.println(ret.getName());
     }
> Hi Michael,
>
>  I was only able to reproduce this when trying to create a SubRegion 
> for Axes that weren't present.
>
>  In the case of ImgOpener, Axes of length 1 are discarded... so they 
> effectively "aren't present" and can't have a SubRegion applied to 
> them (since they are implicitly included anyway in the image).
>
>  Unfortunately, I'm not sure how to make the error reporting better, 
> in general, on this issue.. since, when constructing a SubRegion, 
> there's no way to know what dataset(s) it will be applied to... it's 
> up to the consuming software to use the SubRegion information when 
> reading the dataset.
>
>  I could add some defensive checks to verify that axes are present.. 
> but this whole system is going to be reworked in 0.7.0 for 
> N-dimensionality. So I'm going to add a comment to our N-dim ticket 
> <https://github.com/scifio/scifio/issues/19> to test this.
>
>  For now, in your code, can you check if an axis length is < 2 before 
> creating the SubRegion, and if so - don't add it to the SubRegion 
> specification?
>
>  Oh - if you are getting this issue for Axes you know have a length > 
> 1, send me the dataset, because something else is going on there. :)
>
> Thanks,
> Mark
>
>
>
>
> On Fri, Aug 23, 2013 at 2:55 AM, Michael Zinsmaier 
> <michael.zinsmaier at gmx.de <mailto:michael.zinsmaier at gmx.de>> wrote:
>
>     Hi together,
>
>     defining intervals via the ImgOptions mechanism seems not to work
>     if you define an Interval only for one Axes (except for Channel).
>     E.g. consider that you want to select only time=0 from a 5dim
>     Image (x,y,Channel,z,Time) and define the SubRegion as follows
>     new SubRegion(new AxesType[]{Time}, new Range[]{0}). An array
>     index out of bounds exception is thrown.
>
>     It does however work if you do the same thing with Channel and it
>     works also if you specify Ranges for Channel, Z and Time.
>
>     The API of SubRegion (Map Constructor) gives me the feeling that
>     is should not be necessary to specify Axes that I want to include
>     completly.
>     I hope thats correct if not I would like to suggest to change it.
>
>     Best regards
>     Michael
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://scif.io/pipermail/scifio/attachments/20130826/182c451d/attachment-0002.html>