[MITgcm-support] identifying connected regions

[Daniel Goldberg]

Thanks Samar! The two problems do seem as though they might be similar
(they are both image processing problems..) I will have a look at the
references you sent and have a think if this could be done some other way
than serially.

Thanks
Dan

On Wed, Feb 9, 2022 at 9:49 PM Samar Khatiwala <
samar.khatiwala at earth.ox.ac.uk> wrote:

> Hi Dan,
>
> I don’t know if it is relevant to your problem but have you looked into
> the flood-fill algorithm? I haven’t used a parallel version as canned
> serial ones
> (e.g., imfill in Matlab and flood_fill in python) were more than
> sufficient for the fairly large satellite images I was analyzing (and there
> are even more
> efficient implementations available
> <https://gmd.copernicus.org/articles/9/4451/2016/>). But if you really
> need to do this on-the-fly in MITgcm, rather than offline, I know that
> parallel implementations do
> exist (e.g., this
> <https://www.sciencedirect.com/science/article/pii/S0021999118306557> and
> this
> <https://deepai.org/publication/scan-flood-fill-scaff-an-efficient-automatic-precise-region-filling-algorithm-for-complicated-regions>
> ).
>
> Best,
>
> Samar
>
> On Feb 9, 2022, at 3:16 PM, Daniel Goldberg <dan.goldberg at ed.ac.uk> wrote:
>
> thanks JM! i have talked to others who have tackled this issue as you
> describe.. but I do struggle to think through how to transform the simplest
> algorithm i know of
> <https://people.sc.fsu.edu/~jburkardt/f77_src/image_components/components.f> into
> one that would work with EXCH, so i will proceed with gathering first and
> broadcasting, which might be very slow -- i will see!
>
>
> On Wed, Feb 9, 2022 at 3:03 PM Jean-Michel Campin <jmc at mit.edu> wrote:
>
>> This email was sent to you by someone outside the University.
>> You should only click on links or attachments if you are certain that the
>> email is genuine and the content is safe.
>>
>> Hi Dan,
>>
>> I think you could collect the full (global) 2-D field on 1 proc and work
>> with
>> this. But you should be able also to design the algorithm that works on
>> each tile
>> and then, with a couple of EXCH calls, finish the work at the global
>> level.
>> But this second solution probably requires more careful coding.
>>
>> On the side (I don't think it's that relevant here), in term of global
>> communication, I added (~ 10.y ago) a function to do a cummulative sum
>> (cumulsum_z_tile.F).
>> in case there is some similarity with your problem.
>>
>> Cheers,
>> Jean-Michel
>>
>> On Wed, Feb 09, 2022 at 09:11:11AM +0000, Daniel Goldberg wrote:
>> > thanks very much martin. this should be possible to use directly.
>> >
>> > best
>> > dan
>> >
>> > On Wed, Feb 9, 2022 at 8:01 AM Martin Losch <Martin.Losch at awi.de>
>> wrote:
>> > >
>> > > Hi Dan,
>> > >
>> > > I am not aware of any implementation of that within the MITgcm.
>> > >
>> > > There are gather and scatter routines in eesupp/src, e.g.
>> gather_2d_r8.F
>> > >
>> > > Martin
>> > >
>> > > > On 7. Feb 2022, at 14:25, Daniel Goldberg <dan.goldberg at ed.ac.uk>
>> wrote:
>> > > >
>> > > > Hello -
>> > > >
>> > > > I am curious if any part of model/src or a package implements an
>> > > > algorithm to identify connected regions of a 2D (or 3D) array?
>> > > >
>> > > > If not, i feel this might be best solved in serial, and am wondering
>> > > > if there are utilities to gather processor tiles to a single 2D
>> array
>> > > > (and broadcast such an array to tiles) that should be used or are
>> > > > ideal to use. I am aware that something like this must be done with
>> > > > useSingleCpuIO but am not sure if this is the best template to
>> follow.
>> > > >
>> > > > Many thanks
>> > > > Dan
>> > > >
>> > > > --
>> > > > Daniel Goldberg, PhD (he/him)
>> > > > Reader in Glaciology
>> > > > School of Geosciences, University of Edinburgh
>> > > > Geography Building, Drummond Street, Edinburgh EH8 9XP
>> > > >
>> > > >
>> > > > em: dan.goldberg at ed.ac.uk
>> > > > web: https://www.geos.ed.ac.uk/homes/dgoldber
>> > > > The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336. Is e buidheann carthannais a
>> th??? ann an Oilthigh Dhùn Èideann, clàraichte an Alba, àireamh clàraidh
>> SC005336.
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