missing kernel or block size in equalize_adapthist

[Steven Silvester]

Hi Kai,

The limits were set based on the original implementation, but there is no
reason they need to stay at 16.  Using an arbitrary size tile is what would
take a substantial rewrite.  Looking at your numbers, it looks like a 13x10
block size will get you ~150x150 tile size.  At the full 16x16, you'd have
120x90 pixels.


Regards,

Steve

On Thu, May 28, 2015 at 1:35 PM, Kai Wiechen <kwiechen1 at gmail.com> wrote:

> Hi Steve,
>
> yes, I would like to have finer control of block/kernel size to obtain
> similar results if I apply this to small test patches or the larger
> complete image. Is there any reason to limit ntiles_x/y to 16?
>
> Regards,
>
> Kai
>
> Am Mittwoch, 27. Mai 2015 03:17:01 UTC+2 schrieb Steven Silvester:
>>
>> Hi Kai,
>>
>> Is the issue that you want finer grain control of the block size?  If so,
>> that would require a substantial rewrite.
>>
>> Please feel free to open an issue on Github if that is the case.
>>
>>
>> Regards,
>>
>> Steve
>>
>>
>> On May 26, 2015, at 1:58 AM, Kai Wiechen <kwie... at gmail.com> wrote:
>>
>> Hi Steve,
>>
>> but these parameters are limited to the range 1..16. The small test
>> patches are 150x150 pixels, the complete images have 1920x1448 pixels. I
>> have applied equalize_adapthist here with default parameters (n_tiles=8).
>>
>> Best regards,
>>
>> Kai
>>
>> On Tuesday, May 26, 2015 at 12:54:34 AM UTC+2, Steven Silvester wrote:
>>>
>>> Hi Kai,
>>>
>>> Do the `n_tiles*` arguments not meet your needs?  By defining the number
>>> of tiles in X and Y, you are equivalently setting a block size.
>>>
>>>
>>> http://scikit-image.org/docs/stable/api/skimage.exposure.html#equalize-adapthist
>>>
>>>
>>> Regards,
>>>
>>> Steve
>>>
>>> On Monday, May 25, 2015 at 1:49:53 PM UTC-5, Kai Wiechen wrote:
>>>>
>>>>
>>>> <https://lh3.googleusercontent.com/-0jVbtyT6ArM/VWNtiWHECgI/AAAAAAAABOg/AKpRcr4fKHU/s1600/nuclei_equalize_adapthist.jpg>
>>>> Hello,
>>>>
>>>> I am using equalize_adapthist after color deconvolution and some
>>>> morphological operations to enhance local contrast of nuclei in
>>>> histological images. There are different results when applying
>>>> equalize_adapthist when using small patches and larger size whole images
>>>> (left small patch, right large size whole image). The CLAHE implementation
>>>> in ImageJ has a 'block size' parameter and the implementation in Pixinsight
>>>> has a 'Kernel size' parameter to get results depending on the local
>>>> context. Is it possible to 'simulate' this behaviour with scikit-image?
>>>>
>>>> Best regards,
>>>>
>>>> Kai
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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