[MINC-users] Usage of mincconcat

[Jason Lerch]

On 2013-09-05, at 12:04 PM, Andrew Wood <andrew at biospective.com> wrote:

> Jason's Python solution is quite attractive to me, because my "processing
> step" is a Python script. I should be able to adapt that and embed it right
> in the processing routine. My motivation for tiling/concating was driven by
> having images that are too big to fit in memory, so I don't think the issue
> is completely solved. I can extract the tiles as pyminc hyperslabs, but am
> I able to write back the processed hyperslabs without loading the entire
> destination image?
> 
> That is, am I right that this loads vol's entire data block, despite only
> needing to modify part of it?:
>    vol.data[i,:,:] = myslab

You are right. In pyminc the data is not loaded upon opening the volume, but is loaded the first time the .data element is accessed. The way to work around that is to create the volumes as before, but never directly access the .data bit and instead use the getHyperslab and setHyperslab methods. That should do the trick for you, I think.

Jason


> 
> Thanks,
> Andrew
> 
> 
> On Thu, Sep 5, 2013 at 8:58 AM, Andrew Janke <a.janke at gmail.com> wrote:
> 
>> On 5 September 2013 22:50, Andrew Wood <andrew at biospective.com> wrote:
>>> Thanks for that. What I've actually done is split a large image into
>> tiles
>>> or cubes for processing. Now that I've got processed hyperslabs, I'm
>>> stitching them back together. From what you described, I'll have to
>> reshape
>>> the slabs for concatting into rows, then reshape the rows for concatting
>>> into slices, then reshape the slices for concatting back to the full
>> volume.
>>> 
>>> I suppose there's no way to stitch them without taking a big reshaping
>> I/O
>>> hit?
>> 
>> This is only the case if you are concatenating along a dimension that
>> is already in the file(s). If when you reshape you do this:
>> 
>>   mincreshape -dimrange yspace=100,0  3d.mnc y-100.mnc
>> 
>> to pull out y slice #100 you will remove the y dimension.
>> 
>> Then you can concat with:
>> 
>>   mincconcat -concay_dimension yspace y-100.mnc ....  3d.mnc
>> 
>> Note that in the above you will have to manually store the starts,
>> steps and direction cosines.
>> 
>> Or, just bash the volume back together ignoring start/step/etc and use
>> minccopy to overwrite the data in a copy of the original file.
>> 
>> 
>> a
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