[SCIFIO] T1dSavingImagePlanes breaks when changing from PNG to TIFF

[Michael Ellis]

Curtis, many thanks.

Whilst I’m on the subject of TIFF I experimented with using the TIFF specific reader/parser.

Our TIFF files use the PAGE_NAME TIFF TIFF tag to give a name to each of the channel names. Is this information accessible through the SCIFIO?

Many thanks — Michael Ellis

On 3 Dec 2014, at 18:26, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Michael,
> 
> > I’m curious though because I didn’t think PNG files could handle
> > anything other than 2D images.
> 
> SCIFIO writes the APNG format [1] when there are multiple planes.
> 
> > So I try to open the SCIFIOTutorial.png in ImageJ and I see only a
> > single plane image.
> 
> Standard PNG readers (including ImageJ 1.x's built-in PNG reader) will read only the first plane. Did you try with File > Import > Image... which uses SCIFIO when opening?
> 
> > I change SCIFIOTutorial.png to SCIFIOTutorial.tif and run the program.
> > I get the following exception:
> > 
> > Exception in thread "main" io.scif.FormatException: Buffer too small
> > (got 2500, expected 12500).
> 
> Thanks for the report. I can confirm this bug. I filed an issue for it:
>     https://github.com/scifio/scifio/issues/236
> 
> > So how do I save a X,Y,Channels image in TIFF format with SCIFIO?
> 
> Once that issue is resolved, things should work!
> 
> Regards,
> Curtis
> 
> [1] https://en.wikipedia.org/wiki/APNG
> 
> On Wed, Dec 3, 2014 at 5:20 AM, Michael Ellis <michael.ellis at dsuk.biz> wrote:
> T1dSavingImagePlanes saves a fake image “8bit-signed&pixelType=int8&lengths=50,50,3,5,7&axes=X,Y,Z,Channel,Time.fake” as a png file.
> 
> I run the program and it completes without errors.
> 
> I’m curious though because I didn’t think PNG files could handle anything other than 2D images. So I try to open the SCIFIOTutorial.png
> in ImageJ and I see only a single plane image. There are no warnings or errors when saving the file to suggest that there is any loss of fidelity. Is
> that the intention?
> 
> Anyway, I know TIFF files can support multiple channels, so I change SCIFIOTutorial.png to SCIFIOTutorial.tif and run the program. I get the following exception:
> 
> Exception in thread "main" io.scif.FormatException: Buffer too small (got 2500, expected 12500).
>         at io.scif.util.FormatTools.checkBufferSize(FormatTools.java:665)
>         at io.scif.util.FormatTools.checkPlaneForWriting(FormatTools.java:610)
>         at io.scif.AbstractWriter.checkParams(AbstractWriter.java:121)
>         at io.scif.formats.TIFFFormat$Writer.savePlane(TIFFFormat.java:1291)
>         at io.scif.formats.TIFFFormat$Writer.writePlane(TIFFFormat.java:1399)
>         at io.scif.AbstractWriter.savePlane(AbstractWriter.java:168)
>         at io.scif.AbstractWriter.savePlane(AbstractWriter.java:159)
>         at io.scif.tutorials.core.T1dSavingImagePlanes.main(T1dSavingImagePlanes.java:75)
> 
> Now this is most unexpected, because I would have assumed the TIFF format was able to store the images with at least the same fidelity as PNG.
> 
> OK I know TIFF can save files of 3 dimensions, so I change the fake images to “8bit-signed&pixelType=int8&lengths=50,50,7&axes=X,Y,Channel.fake”
> 
> Again I get and exception.
> 
> OK, how about a 2D image, “8bit-signed&pixelType=int8&lengths=50,50&axes=X,Y.fake”?
> 
> And that finally works.
> 
> So how do I save a X,Y,Channels image in TIFF format with SCIFIO?
> 
> Thanks for any help.
> 
> — Michael Ellis
> Digital Scientific UK Ltd.
> 
> 
> 
> 
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