Issues with scaling images for canny edge detection

[Josh Warner]

I can‘t duplicate this, but I may know what's going on.

img_as_float converts non-float datatypes into floating-point images on the 
range [0, 1]. The traceback you note shows that a floating point array was 
passed to img_as_float, but the image had values outside [0, 1]. Try 
checking hot.dtype before running img_as_float; if it's an (unsigned) 
integer, everything should work fine. 

>From the operation you listed, abs_hot = hot + abs(np.min(hot)), it seems 
like hot should still be an integer, but that traceback code path is only 
active for inputs where arr.dtype.kind == 'f' so abs_hot got converted to 
float at some point. Check abs_hot.dtype right prior to running img_as_float; 
is it an integer or a float?

My intuition for a blank canny result is that your division operation abs_hot 
/ np.max(abs_hot) may have been between two integer types, resulting in a 
boolean array which would have almost no edges. Try assigning normhot = 
abs_hot / np.max(abs_hot) and checking the dtype; if it's boolean, cast one 
or both to float before the division and re-run. The other possibility is 
the canny parameters are pretty far off.

I‘m not sure what’s going on with the raw result, but check the above and 
get back with us! Hopefully that helps to get things moving.

Josh

On Tuesday, June 25, 2013 10:37:20 AM UTC-5, Robin Wilson wrote:

Hi,
>
> *Summary: *I'm fairly new to skimage, and I'm trying to replicate some 
> work I've done in IDL using the Canny edge detector. I've imported the same 
> image into skimage and tried running the Canny function with the same 
> parameters, but I either get a blank image, or very different results to 
> IDL which don't change regardless of the parameters I use. I suspect my 
> problems may be related to how I am scaling my image to make it between 0 
> and 1, as the documentation for the skimage Canny function requires.
>
> *More details:*
> The input image I used in both IDL and skimage is available at 
> https://www.dropbox.com/s/xaiq9kitrf1b4cf/HOT_sub.tif.
>
> In IDL I called the CANNY function (documentation available at 
> http://www.exelisvis.com/docs/CANNY.html) as follows:
>
> result = CANNY(image, HIGH=0.95, LOW=0.3, SIGMA=2)
>
> and got the following image:
>
>
>
> <https://lh3.googleusercontent.com/-xwuyuH_mxEA/Ucm2Y2m2EyI/AAAAAAAAEnw/46OmI8iuf0Q/s1600/IDL_Output.png>
> I loaded the image into skimage as follows:
>
> hot = skimage.io.imread("HOT_sub.tif")
>
> And removed all negative values by adding the absolute value of the 
> minimum:
>
> abs_hot = hot + abs(np.min(hot))
>
> From what I'd read in the documentation, the function img_as_float would 
> then scale this between 0 and 1 in a sensible way, but it gave an error:
>
> C:\Python27\lib\site-packages\skimage\util\dtype.pyc in convert(image, 
> dtype)
>      73     if kind_in == 'f':
>      74         if np.min(image) < 0 or np.max(image) > 1:
> ---> 75             raise ValueError("Images of type float must be between 
> 0 and 1")
>      76         if kind == 'f':
>      77             # floating point -> floating point
>
> ValueError: Images of type float must be between 0 and 1
>
> So I did it myself by simply dividing by the maximum value:
>
> im_hot = img_as_float(abs_hot/np.max(abs_hot)
>
> However, running the Canny edge detector on this image produces an 
> entirely blank edge image:
>
> edges = canny(im_hot, sigma=2, low_threshold=0.3, high_threshold=0.90)
> np.sum(edges) # Gives 0 showing there are no edges found
>
> Regardless how I play with the parameters, I can't seem to get it to give 
> me any edges.
>
> Interestingly, if I ignore the instructions to make sure that my input 
> image is between 0 and 1, and just use the raw image:
>
> edges = canny(hot, sigma=2, low_threshold=0.3, high_threshold=0.90)
>
> I get a more sensible result (well, at least it isn't blank!):
>
>
> <https://lh5.googleusercontent.com/-Ta33pkF-pIY/Ucm4abti3lI/AAAAAAAAEoA/iyX6FSKSPF4/s1600/skimage.png>
> But this is very different to the result given by IDL - and furthermore, 
> adjusting the parameters doesn't seem to change the output at all.
>
> What am I doing wrong here? I suspect it is something to do with the image 
> scaling, but I'm not sure - it could be a conceptual problem with my image 
> processing knowledge, or I could be using skimage improperly. Does anyone 
> have any ideas or suggestions as to where to go from here? If I manage to 
> solve this I will, of course, write up the solution on my blog so that 
> others can benefit too.
>
> Best regards,
>
> Robin
> University of Southampton, UK
>
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