[SCIFIO] Block-wise writer

[Burkhard Hoeckendorf]

Dear Mark,

If I understand correctly, setting the planar axis count to 3, for a 3D 
image, results in a single call of writePlane(...) for the entire image. 
Because there is only a single 3D "plane". This is exactly what I want, 
because my writer can not write a series of 2D planes.

Still, ImageJ won't let the writer actually handle the 3D plane. 
Instead, it complains about the image having n planes, while it really 
should have only 1, because the planar axis count in the metadata is set 
to 3.

I managed to read 3D planes/blocks using this strategy (up to 2GB, see 
earlier topic entitled "Block-wise reader"), and would be very happy if 
I could do the same for writing files, at least until you have sorted 
out the sub-region caching, which would overcome the size restriction. 
Please advise if I am still missing something, or if this is not the 
right way of doing this for now.

Cheers,
Burkhard


On 1/30/2015 1:00 PM, scifio-request at scif.io wrote:
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>     1. Block-wise writer (Burkhard Hoeckendorf)
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> Message: 1
> Date: Thu, 29 Jan 2015 16:57:02 -0500
> From: Burkhard Hoeckendorf <burkhard.hoeckendorf at web.de>
> To: scifio at scif.io
> Subject: [SCIFIO] Block-wise writer
> Message-ID: <54CAACAE.5060301 at web.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Mark,
>
> Its me again, this time I have a quick question about writing >2D
> blocks. For the format I mentioned in my previous mail, I have a
> metadata translator that sets the planar axis count to 3-5. I know that
> my writer implementation can handle that, but ImageJ won't let it.
> Instead, I get a message box saying "Source dataset contains: n planes,
> but writer format only supports: 1". Is there an easy way around this?
>
> Thanks,
> Burkhard
>
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 30 Jan 2015 10:53:00 -0600
> From: Mark Hiner <hiner at wisc.edu>
> To: Burkhard Hoeckendorf <burkhard.hoeckendorf at web.de>
> Cc: "scifio at scif.io" <scifio at scif.io>
> Subject: Re: [SCIFIO] Block-wise writer
> Message-ID:
> 	<CA+B=mGoZvHugf_H3tAhvCCY0cTB+PV=z7gSJFvCG+u_decPeYA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Burkhard,
>
> Argh, I think you are getting bit by a confusing naming choice in SCIFIO. A
> "planar axis" in SCIFIO means its value contributes to the size of a plane,
> not the number of planes. See the ImageMetadata javadoc[1] for a better
> explanation.
>
> So, if you have an XYZT dataset for example, and you set your planar axis
> count to 4, the writer thinks it has one plane of size X * Y * Z * T (which
> is why the warning says it only supports 1 plane in your case).
>
> If you set the planar axis count to 2 in this case, you would have Z * T
> number of planes, each of size X * Y.
>
> If anything is still unclear about planar axes, just let me know. I'm happy
> to look over code examples for your translator/writer, as well, and will
> try to create better documentation on this subject[2].
>
> Best,
> Mark
>
> [1]
> http://javadoc.imagej.net/SCIFIO/io/scif/ImageMetadata.html#setPlanarAxisCount(int)
> [2] https://github.com/scifio/scifio-tutorials/issues/2
>
> On Thu, Jan 29, 2015 at 3:57 PM, Burkhard Hoeckendorf <
> burkhard.hoeckendorf at web.de> wrote:
>
>> Dear Mark,
>>
>> Its me again, this time I have a quick question about writing >2D blocks.
>> For the format I mentioned in my previous mail, I have a metadata
>> translator that sets the planar axis count to 3-5. I know that my writer
>> implementation can handle that, but ImageJ won't let it. Instead, I get a
>> message box saying "Source dataset contains: n planes, but writer format
>> only supports: 1". Is there an easy way around this?
>>
>> Thanks,
>> Burkhard
>>
>> _______________________________________________
>> SCIFIO mailing list
>> SCIFIO at scif.io
>> http://scif.io/mailman/listinfo/scifio
>>
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