[GRASS-user] Does v.kernel have to take 16+ hours?

Wed Dec 5 18:58:07 PST 2012

It's gotten slow again. This run will probably take more than 10 hours.
However, I am using a standard deviation of 1000. Is that what could be
causing this?

*v.kernel input=tickets at PERMANENT output=tickets_new_heatmap_1000
stddeviation=1000*
*STDDEV: 1000.000000*
*RES: 18.290457 ROWS: 2370 COLS: 2650*
*
*
*Writing output raster map using smooth parameter=1000.000000.*
*
*
*Normalising factor=6482635.018778.*

On Sat, Nov 24, 2012 at 9:03 PM, Aren Cambre <aren at arencambre.com> wrote:

> I installed r53983. The v.kernel execution that took almost a day now
> executes in 25.5 minutes. Thank you!
>
> Aren
>
>
> On Fri, Nov 23, 2012 at 12:51 PM, Markus Metz <
> markus.metz.giswork at gmail.com> wrote:
>
>> On Fri, Nov 23, 2012 at 5:35 PM, Aren Cambre <aren at arencambre.com> wrote:
>> > Thanks!
>> >
>> > I am not familiar with GRASS's release customs. Will this become part
>> of a
>> > binary release soon, or should I just pull down the latest release in
>> the
>> > 6.4.2 trunk? I'm assuming this has been merged into the trunk...
>>
>> It should be available as a binary for Windows by tomorrow in the
>> nightly builds [0].
>>
>> Markus M
>>
>> [0] http://wingrass.fsv.cvut.cz/grass64/
>>
>> >
>> > Aren
>> >
>> >
>> > On Fri, Nov 23, 2012 at 7:32 AM, Markus Metz <
>> markus.metz.giswork at gmail.com>
>> > wrote:
>> >>
>> >> On Fri, Nov 23, 2012 at 2:07 PM, Aren Cambre <aren at arencambre.com>
>> wrote:
>> >> > Isn't taking about 10,000% too much time considered a bug? :-)
>> >>
>> >> Hmm, yes. v.kernel is fixed in devbr6 and relbr6 with r53982 and
>> >> r53983, respectively.
>> >>
>> >> Markus M
>> >>
>> >> >
>> >> > On Nov 23, 2012 5:11 AM, "Markus Metz" <
>> markus.metz.giswork at gmail.com>
>> >> > wrote:
>> >> >>
>> >> >> On Fri, Nov 23, 2012 at 4:14 AM, Aren Cambre <aren at arencambre.com>
>> >> >> wrote:
>> >> >> > I'm able to reproduce reliably here. I'll email you details
>> >> >> > privately.
>> >> >>
>> >> >> Thanks. I can confirm that v.kernel takes a long time in GRASS 6
>> with
>> >> >> the settings provided by you. It does not crash, however.
>> >> >>
>> >> >> I can speed up v.kernel in GRASS 6 to complete in 10 minutes instead
>> >> >> of 16+ hours, but I am not sure if this fix can/will go into GRASS
>> 6.4
>> >> >> because by now only bugs should be fixed.
>> >> >>
>> >> >> Markus M
>> >> >>
>> >> >> >
>> >> >> > Aren
>> >> >> >
>> >> >> >
>> >> >> > On Thu, Nov 22, 2012 at 9:02 AM, Markus Metz
>> >> >> > <markus.metz.giswork at gmail.com>
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> On Sat, Nov 17, 2012 at 4:06 PM, Aren Cambre <
>> aren at arencambre.com>
>> >> >> >> wrote:
>> >> >> >> > I have a dataset of just over 700,000 incidents that happened
>> in
>> >> >> >> > square-ish
>> >> >> >> > Texas county that's about 30 miles on each side.
>> >> >> >> >
>> >> >> >> > Here's the parameters reported by v.kernel as it's executing:
>> >> >> >> >
>> >> >> >> > STDDEV: 1000.000000
>> >> >> >> > RES: 111.419043 ROWS: 458   COLS: 447
>> >> >> >> >
>> >> >> >> > Writing output raster map using smooth parameter=1000.000000.
>> >> >> >> >
>> >> >> >> > Normalising factor=6482635.018778.
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > I am running this on a Windows 7 x64 machine with 8 GB RAM and
>> an
>> >> >> >> > Intel
>> >> >> >> > Core
>> >> >> >> > i7 Q720 1.6 GHz with 4 physical cores. I notice that it's not
>> >> >> >> > multithreaded,
>> >> >> >> > only using 1 core.
>> >> >> >> >
>> >> >> >> > It takes about 16 hours to complete. Is this correct? I'd like
>> to
>> >> >> >> > use
>> >> >> >> > this
>> >> >> >> > on a dataset with closer to 5 million records, and I'm really
>> >> >> >> > concerned
>> >> >> >> > how
>> >> >> >> > long it may take.
>> >> >> >>
>> >> >> >> The time required by v.kernel is a function of the number of
>> cells
>> >> >> >> and
>> >> >> >> the input parameter stddeviation. The larger any of these values
>> is,
>> >> >> >> the more time v.kernel will need. Nevertheless, I think that the
>> 16+
>> >> >> >> hours are not correct. I tested with a vector with 3 million
>> points
>> >> >> >> for a grid with 2700 rows and 1087 columns, magnitudes larger
>> than
>> >> >> >> the
>> >> >> >> grid used by you. v.kernel completes in just over one minute.
>> >> >> >>
>> >> >> >> >
>> >> >> >> > I posted my question about the 16+ hours at
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> http://gis.stackexchange.com/questions/41058/how-do-i-compute-v-kernel-maps-in-less-than-16-hours/
>> .
>> >> >> >> > Bill Huber, who si apparently knowledgeable about kernel
>> density
>> >> >> >> > calculations in general, posted a response, and he felt like a
>> >> >> >> > kernel
>> >> >> >> > density map shouldn't take much time at all. But digging more
>> >> >> >> > deeply,
>> >> >> >> > turns
>> >> >> >> > out he had come up with a kernel density calculation method
>> over a
>> >> >> >> > decade
>> >> >> >> > ago using Fourier transforms. See
>> >> >> >> > http://www.directionsmag.com/features/convolution/129753 and
>> the
>> >> >> >> > next
>> >> >> >> > two
>> >> >> >> > articles linked to it (they are short articles). Apparently
>> this
>> >> >> >> > transforms
>> >> >> >> > it from an O(n^2) problem to an O(n ln n) complexity problem.
>> >> >> >>
>> >> >> >> The approach of Bill Huber is raster-based, not vector based,
>> making
>> >> >> >> some things easier, at the cost of precision. The coordinate
>> >> >> >> precision, however, is only needed for kernel functions other
>> than
>> >> >> >> uniform. In GRASS, you could get something like a raster-based
>> >> >> >> density
>> >> >> >> map by
>> >> >> >>
>> >> >> >> - exporting the points with v.out.ascii
>> >> >> >> - re-importing the points with r.in.xyz method=n to get the
>> number
>> >> >> >> of
>> >> >> >> points per cell
>> >> >> >> - running a neighborhood analysis using a circular window with
>> >> >> >> r.neighbors method=sum -c
>> >> >> >>
>> >> >> >> Optionally you could use the gauss option of r.neighbors to get
>> an
>> >> >> >> equivalent to v.kernel kernel=gaussian
>> >> >> >>
>> >> >> >> HTH,
>> >> >> >>
>> >> >> >> Markus M
>> >> >> >>
>> >> >> >> >
>> >> >> >> > I inspected v.kernel's main.c
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > (
>> http://trac.osgeo.org/grass/browser/grass/trunk/vector/v.kernel/main.c),
>> >> >> >> > and looks like v.kernel uses an output-centric method (using
>> >> >> >> > Bill's
>> >> >> >> > wording)
>> >> >> >> > of calculating the output, which seems like O(n^2) complexity.
>> >> >> >> >
>> >> >> >> > So I guess what I'm getting at is it appears to me that the
>> >> >> >> > algorithm
>> >> >> >> > behind
>> >> >> >> > GRASS GIS's v.kernel is straightforward but is a greedy
>> algorithm
>> >> >> >> > (http://en.wikipedia.org/wiki/Greedy_algorithm), which is
>> fine,
>> >> >> >> > but
>> >> >> >> > it
>> >> >> >> > make
>> >> >> >> > take a while to execute. Is this true?
>> >> >> >> >
>> >> >> >> > Is there not spatial indexing I could add to the dataset? I've
>> >> >> >> > done
>> >> >> >> > various
>> >> >> >> > Google searches on that and can't come up with anything clear.
>> >> >> >> >
>> >> >> >> > Aren
>> >> >> >> >
>> >> >> >> > _______________________________________________
>> >> >> >> > grass-user mailing list
>> >> >> >> > grass-user at lists.osgeo.org
>> >> >> >> > http://lists.osgeo.org/mailman/listinfo/grass-user
>> >> >> >> >
>> >> >> >
>> >> >> >
>> >
>> >
>>
>
>
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