Timing comparisons between mahotas & scikits-image

[Luis Pedro Coelho]

Great!

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.

Best,
Luis

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 
>>
>> https://groups.google.com/d/topic/pythonvision/SSCF4LUlRKQ/discussion 
>>
>> 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
>
>
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