[MINC-users] Usage of mincconcat

[Jason Lerch]

This sounds like a fairly easy roll-your-own task, especially if your tiles are not overlapping and you don't have to figure out how they stitch together.

Some pseudo python code:

from pyminc.volumes.factory import *
from optparse import OptionParser, OptionGroup

if __name__ == "__main__":
    # argument parsing bits as needed, but I'm feeling lazy
    (options, args) = parser.parse_args()
    # construct volume
    # need to know the number of slices
    output_filename = args.pop()
    n_slices = len(args)
    vol = volumeFromDescription(output_filename, 
                                options.dimorder,
                                sizes=(n_slices,output_size[0],output_size[1]),
                                starts=(0,0,0),
                                steps=(options.slice_gap, 
                                       options.output_resolution,    # specify as options - I'm too lazy to add the opt parse bits above :)
                                       options.output_resolution), 
                                volumeType='ushort')
    for i in range(n_slices):
        # assuming that it's one slice per tile - modify as necessary
        inslice = volumeFromFile(args[i])
        vol.data[i,:,:] = inslice.data
    vol.writeFile()
    vol.closeVolume()
	
Jason

On 2013-09-05, at 8:50 AM, Andrew Wood <andrew at biospective.com> wrote:

> Hi Andrew,
> 
> 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?
> 
> Thanks,
> Andrew
> 
> 
> On Wed, Sep 4, 2013 at 11:02 PM, Andrew Janke <a.janke at gmail.com> wrote:
> 
>> Hi Andrew,
>> 
>>> I'm trying to use mincconcat to stitch some images together.
>>> 
>>> For example, I have A.mnc:
>>> 
>>>    dimension name         length         step        start
>>>    --------------         ------         ----        -----
>>>    yspace                      1          0.1         -5.7
>>>    zspace                    750   0.00295238      15.5531
>>>    xspace                    750  -0.00295238      33.3619
>>> 
>>> and B.mnc:
>>>    dimension name         length         step        start
>>>    --------------         ------         ----        -----
>>>    yspace                      1          0.1         -5.7
>>>    zspace                    750   0.00295238      15.5531
>>>    xspace                    750  -0.00295238      31.1476
>>> 
>>> I've tried concating them along x with something like this:
>>> 
>>> mincconcat -concat_dimension xspace A.mnc B.mnc C.mnc
>>> 
>>> This comes back with an error:
>>> "Don't use an image dimension as a loop dimension."
>>> 
>>> Is there a way to concat these images to make one image with
>>> xspace:length=1500?
>> 
>> Indeed there is. mincconcat in general will only work if you are
>> concat'ing on the slowest varying dimension of a file. Thus before you
>> concat do this:
>> 
>>   mincreshape -dimorder xspace,yspace,zspace A.mnc A_res.mnc
>>   mincreshape -dimorder xspace,yspace,zspace B.mnc B_res.mnc
>> 
>> At which point:
>> 
>>   mincconcat -concat_dimension xspace A_res.mnc B_res.mnc C.mnc
>> 
>> Should get you what you are after.
>> 
>> 
>> 
>> a
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>> 
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