I made a timing comparison between mahotas & scikits-image.
operation | mahotas | pymorph | skimage
------------+----------+----------+---------
erode | 10.80 | 14.33 | 80.17
dilate | 11.44 | 8.93 | 41.59
open | 22.45 | 23.20 | 80.18
center mass | 7.05 | NA | NA
sobel | 75.03 | NA | 105.72
cwatershed | 201.03 | 56586.50 | 290.41
daubechies | 19.05 | NA | NA
haralick | 306.48 | NA | 7391.37
(Best viewed with fixed-width fonts)
The unit of measurement is the time it takes to run ``numpy.max(image)`` Mahotas is always faster than skimage (although pymorph is better for certain morphological basic operations). I used GCLM in skimage to stand for Haralick, which is a rough approximation.
I attach the script that generates these (against github skimage). If you think that I have used skimage incorrectly, please let me know.
Best,
-- Luis Pedro Coelho | Institute for Molecular Medicine | http://luispedro.org
Very impressive. Would it be possible to integrate numba as well with
mahotas? I haven't tested it much but seems to get quite a bit of speed up
using it.
> Very impressive. Would it be possible to integrate numba as well with
> mahotas? I haven't tested it much but seems to get quite a bit of speed up
> using it.
>> I made a timing comparison between mahotas & scikits-image.
>> operation | mahotas | pymorph | skimage
>> ------------+----------+----------+---------
>> erode | 10.80 | 14.33 | 80.17
>> dilate | 11.44 | 8.93 | 41.59
>> open | 22.45 | 23.20 | 80.18
>> center mass | 7.05 | NA | NA
>> sobel | 75.03 | NA | 105.72
>> cwatershed | 201.03 | 56586.50 | 290.41
>> daubechies | 19.05 | NA | NA
>> haralick | 306.48 | NA | 7391.37
>> (Best viewed with fixed-width fonts)
>> The unit of measurement is the time it takes to run ``numpy.max(image)``
>> Mahotas is always faster than skimage (although pymorph is better for
>> certain
>> morphological basic operations). I used GCLM in skimage to stand for
>> Haralick,
>> which is a rough approximation.
>> I attach the script that generates these (against github skimage). If you
>> think that I have used skimage incorrectly, please let me know.
>> Best,
>> --
>> Luis Pedro Coelho | Institute for Molecular Medicine |
>> http://luispedro.org
I have not yet tried numba. I tend to be a bit behind the curve on these things.
I updated the table with openCV, which is ridiculously fast, but only supports C-Arrays (otherwise, you get an interpreter crash). Check Table 1 on page 7 on the new version of the paper (attached).
Stéfan: I have not yet fixed your reference, but I will have to redo all of the references for the final manuscript.
Best,
Luis
PS: Since updating that server, I have had problems with configuration on pythonvision.org. I will figure it out when I decide to lose a few hours on nginx/apache configuration.
> Very impressive. Would it be possible to integrate numba as well with
> mahotas? I haven't tested it much but seems to get quite a bit of speed
> up using it.
> You should put the speed test results on a website or blog somewhere. I
> checked pythonvision.org <http://pythonvision.org/> but it looks like it
> is broken at the moment.
> On Thu, Aug 30, 2012 at 1:44 PM, Anthony Oliver
> <anth...@sightmachine.com <mailto:anth...@sightmachine.com>> wrote:
> Very impressive. Would it be possible to integrate numba as well
> with mahotas? I haven't tested it much but seems to get quite a bit
> of speed up using it.
> You should put the speed test results on a website or blog
> somewhere. I checked pythonvision.org <http://pythonvision.org> but
> it looks like it is broken at the moment.
> I made a timing comparison between mahotas & scikits-image.
> operation | mahotas | pymorph | skimage
> ------------+----------+----------+---------
> erode | 10.80 | 14.33 | 80.17
> dilate | 11.44 | 8.93 | 41.59
> open | 22.45 | 23.20 | 80.18
> center mass | 7.05 | NA | NA
> sobel | 75.03 | NA | 105.72
> cwatershed | 201.03 | 56586.50 | 290.41
> daubechies | 19.05 | NA | NA
> haralick | 306.48 | NA | 7391.37
> (Best viewed with fixed-width fonts)
> The unit of measurement is the time it takes to run
> ``numpy.max(image)``
> Mahotas is always faster than skimage (although pymorph is
> better for certain
> morphological basic operations). I used GCLM in skimage to stand
> for Haralick,
> which is a rough approximation.
> I attach the script that generates these (against github
> skimage). If you
> think that I have used skimage incorrectly, please let me know.
> Best,
> --
> Luis Pedro Coelho | Institute for Molecular Medicine |
> http://luispedro.org
I will redo the timings in the next round of manuscript corrections (I already submitted last weeks results yesterday) for the mahotas paper. I might try to speed up things on mahotas' side too :)
A little friendly competition always gets users better software.
Best,
Luis
On 09/02/2012 03:41 PM, Stéfan van der Walt wrote:
> On Thu, Aug 30, 2012 at 9:46 AM, Luis Pedro Coelho <l...@luispedro.org
> <mailto:l...@luispedro.org>> wrote:
> > I made a timing comparison between mahotas & scikits-image.
Now that I look at this, I realise that the comparison is not fair to mahotas because it includes a thresholding step. The correct comparison would run mahotas.sobel(f, just_filter=True) which runs in almost the exact same time as skimage because it is almost the exact same code ;-)
mahotas.center_of_mass also handles labeled images; btw.
On Tuesday, September 4, 2012 4:22:54 PM UTC+1, Johannes Schönberger wrote:
> After another round of performance improvements for the sobel filter, I > get:
> erode & 9.03 & 13.67 & 13.31 & \\
>> dilate & 12.45 & 9.40 & 6.60 & \\
>> open & 21.99 & 22.70 & 13.25 & \\
>> center mass & 6.63 & NA & NA & \\
>> sobel & 74.66 & NA & 43.72 & \\
> Note, that there also exists a possibility to calculate the center of mass > using the `regionprops` function and the properties "Centroid" and > "WeightedCentroid". But due to the label overhead this is probably a lot > slower than your implementation.
> Am Donnerstag, 30. August 2012 18:52:59 UTC+2 schrieb Luis Pedro Coelho:
>> Hello,
>> In the context of my previous email to pythonvision
>> I made a timing comparison between mahotas & scikits-image.
>> operation | mahotas | pymorph | skimage >> ------------+----------+----------+--------- >> erode | 10.80 | 14.33 | 80.17 >> dilate | 11.44 | 8.93 | 41.59 >> open | 22.45 | 23.20 | 80.18 >> center mass | 7.05 | NA | NA >> sobel | 75.03 | NA | 105.72 >> cwatershed | 201.03 | 56586.50 | 290.41 >> daubechies | 19.05 | NA | NA >> haralick | 306.48 | NA | 7391.37
>> (Best viewed with fixed-width fonts)
>> The unit of measurement is the time it takes to run ``numpy.max(image)`` >> Mahotas is always faster than skimage (although pymorph is better for >> certain >> morphological basic operations). I used GCLM in skimage to stand for >> Haralick, >> which is a rough approximation.
>> I attach the script that generates these (against github skimage). If you >> think that I have used skimage incorrectly, please let me know.
>> Best, >> -- >> Luis Pedro Coelho | Institute for Molecular Medicine | >> http://luispedro.org
