[ome-devel] calling getImageCount or getPlaneCount from matlab returns wrong values

[Grabmayr, Heinrich]

Thanks Josh,

Curtis' post was actually the one I was building on - I just started a new thread because I think my problem is matlab-related (see my description)


--Heinrich

-----Ursprüngliche Nachricht-----
Von: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] Im Auftrag von Josh Moore
Gesendet: Montag, 23. Januar 2012 09:28
An: Heinrich Grabmayr
Cc: ome-devel at lists.openmicroscopy.org.uk
Betreff: Re: [ome-devel] calling getImageCount or getPlaneCount from matlab returns wrong values

Replied to by Curtis on the ImageJ list: http://comments.gmane.org/gmane.comp.java.imagej/23522

> I know it's been awhile since this thread, but I wanted to clarify 
> that Bio-Formats does support parsing of variable time stamps, 
> converted from any supported format. And as Janne suggests, there are 
> some examples that demonstrate how to do it.
> 
> For an ImageJ macro, see planeTimings.txt, linked from:
>   
> http://loci.wisc.edu/bio-formats/imagej
> 
> 
> For Java code, see PrintTimestamps.java, linked from:
>   
> http://loci.wisc.edu/bio-formats/bio-formats-java-library
> 
> 
> HTH,
> Curtis

Cheers,
~Josh


On Jan 21, 2012, at 7:40 PM, Heinrich Grabmayr wrote:

> Hello everyone,
> 
> 
> 
> I just tried to get the total number of planes in an image in matlab.
> 
> So I opened the file using bfopen.m from the loci website and get the 
> image cell; metadata is stored in the second entry, so trying r = 
> bfopen(..); meta = r{2}; a = meta.getImageCount() b = 
> meta.getPlaneCount(0)
> 
> 
> 
> returns a==b==0.
> 
> However, running the command line script  showinf with the same 
> versions of loci_tools and bio_formats (4.3.3), the correct value is given in line 475:
> 
> int imageCount = reader.getImageCount();
> 
> Also, when I query
> 
> getPixelsSizeT(0)
> 
> getPixelsSizeC(0)
> 
> in matlab, the correct values are returned, and all the rest of 
> metadata not concerned with planes is returned correctly.
> 
> meta.getPlaneDeltaT(0,0)
> 
> returns empy.
> 
> 
> 
> I cannot think of any reason for this but the initialization of 
> metadata in bfopen might be different than that in showinf? But then, 
> why should querying it work with anything but planes?
> 
> 
> 
> Does any of you have an idea about that?
> 
> 
> 
> Cheers
> 
> --Heinrich
> 

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