I've pushed the suggested changes : https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca... Thanks, Dan 2011/3/31 Dan Farmer <dfarmernv@gmail.com>:

I will try to address your comments tonight and also see about removing smooth.py and just incorporating the one function we're using into canny.py for now as Thouis suggested. Thanks to both of you for looking at it. I'll message back when I've pushed the changes.

-Dan

2011/3/31 Stéfan van der Walt <stefan@sun.ac.za>:

...

Hi Dan

On Thu, Mar 31, 2011 at 1:02 AM, Dan Farmer <dfarmernv@gmail.com> wrote:

...

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

I read through your patch and made some preliminary comments.

...

Mostly just trying to follow procedure. I already mentioned my concerns in the previous thread. I made one stab at introduced a "None" default for the mask, but I got hung up and reverted it. The default I was going to propose was np.ones(img.shape,bool) (and after the fact I even noticed that's how it is used in one of the unit tests). But I started thinking that that could be quite wasteful of memory if you were working with large images (on my test use case with ~512x512 images it's about 300 KB for the "fake" mask).

It seems as though this specific implementation of the algorithms relies on creating the mask, so I don't think you can get away from it.  The typical way to do it would be:

def canny(..., mask=None, ...):    if mask is None:        mask = np.ones(x.shape, dtype=bool)

...

The problem I had was that if I don't allocate the emask array I get run-time errors starting at line 129 (in the diff of canny.py) because the arrays all have different lengths if they aren't logical_and'd with emask above.

Yes, I think the only way to avoid allocating the mask explicitly is to rewrite the algorithm in Cython, where you can modify behaviour inside the for-loop.

Regards Stéfan

Hey Dan, I just had a look at this code, and there are some things I would do before pulling in the changes: - Document which dtype is expected of the input image. It appears to work for floats, int, uint8 etc, but each gives a different output result. Since the tests are using floats, I assume a floating point image is expected. This should be documented in the docstring along with the expected range of the image. i.e. is it a 0.0 - 1.0 float image or a 0.0 - 255.0 float image. Also, the docs should state it only works on 2D grayscale images, so the user needs to convert their color image beforehand. - Document the valid ranges of values for the low threshold, and high threshold. - There is a lot of use of np.logical_* functions. These are around 20% slower than numpy's overloaded bitwise & and | operators. It seems these logical_* functions are being applied to boolean images so the two operations (logical and bitwise) are equivalent. I would use the faster of the two. It's faster and easier to read. - ndimage has a sobel function, was there a particular reason you chose to do a 2d convolution instead? 2 separable 1d convolutions as done by ndimage.sobel should be faster than a 2d convolution (especially since ndimage does optimizing cache manipulations under the covers). - Does the mask operate over any generic area, or is the mask expected to be rectangular? If it's a rectangular mask, is there really a need for it when the user could just pass in a slice to their image instead. - A minor pedantic gripe; I like to have spaces after commas in array indices and tuples. i.e. this: (1, 2), arr[:, 5:6], instead of: (1,2), arr[:,5:6]. A space immediately after a comma is recommended in PEP8. - Variable naming. Lots of single and two letter variables like 'c', 'c1, 'c2', 'w', 'm', 'cc', etc... Let's give these descriptive names. - For computing magntitude, use np.hypot(isobel, jsobel), instead of the manual computation you use. np.hypot is 2x faster on a 1000x1000 image since it doesn't create any temporaries. - inline the smoothing the function, unless you're using it elsewhere. Lastly, thanks for working and spending time on this code! Cheers! Chris 2011/4/2 Dan Farmer <dfarmernv@gmail.com>

I've pushed the suggested changes :

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

Thanks, Dan

2011/3/31 Dan Farmer <dfarmernv@gmail.com>:

...

I will try to address your comments tonight and also see about removing smooth.py and just incorporating the one function we're using into canny.py for now as Thouis suggested. Thanks to both of you for looking at it. I'll message back when I've pushed the changes.

-Dan

2011/3/31 Stéfan van der Walt <stefan@sun.ac.za>:

...

Hi Dan

On Thu, Mar 31, 2011 at 1:02 AM, Dan Farmer <dfarmernv@gmail.com> wrote:

...

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

I read through your patch and made some preliminary comments.

...

Mostly just trying to follow procedure. I already mentioned my concerns in the previous thread. I made one stab at introduced a "None" default for the mask, but I got hung up and reverted it. The default I was going to propose was np.ones(img.shape,bool) (and after the fact I even noticed that's how it is used in one of the unit tests). But I started thinking that that could be quite wasteful of memory if you were working with large images (on my test use case with ~512x512 images it's about 300 KB for the "fake" mask).

It seems as though this specific implementation of the algorithms relies on creating the mask, so I don't think you can get away from it. The typical way to do it would be:

def canny(..., mask=None, ...): if mask is None: mask = np.ones(x.shape, dtype=bool)

...

The problem I had was that if I don't allocate the emask array I get run-time errors starting at line 129 (in the diff of canny.py) because the arrays all have different lengths if they aren't logical_and'd with emask above.

Yes, I think the only way to avoid allocating the mask explicitly is to rewrite the algorithm in Cython, where you can modify behaviour inside the for-loop.

Regards Stéfan

Thanks for the detailed feedback. I've pushed some more changes that I think cover everything. I left the mask and smoothing function for the moment based on Thouis feedback. https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca... -Dan On Mon, Apr 4, 2011 at 7:56 PM, Chris Colbert <sccolbert@gmail.com> wrote:

Hey Dan, I just had a look at this code, and there are some things I would do before pulling in the changes:

Document which dtype is expected of the input image. It appears to work for floats, int, uint8 etc, but each gives a different output result. Since the tests are using floats, I assume a floating point image is expected. This should be documented in the docstring along with the expected range of the image. i.e. is it a 0.0 - 1.0 float image or a 0.0 - 255.0 float image. Also, the docs should state it only works on 2D grayscale images, so the user needs to convert their color image beforehand. Document the valid ranges of values for the low threshold, and high threshold. There is a lot of use of np.logical_* functions. These are around 20% slower than numpy's overloaded bitwise & and | operators. It seems these logical_* functions are being applied to boolean images so the two operations (logical and bitwise) are equivalent. I would use the faster of the two. It's faster and easier to read. ndimage has a sobel function, was there a particular reason you chose to do a 2d convolution instead? 2 separable 1d convolutions as done by ndimage.sobel should be faster than a 2d convolution (especially since ndimage does optimizing cache manipulations under the covers). Does the mask operate over any generic area, or is the mask expected to be rectangular? If it's a rectangular mask, is there really a need for it when the user could just pass in a slice to their image instead. A minor pedantic gripe; I like to have spaces after commas in array indices and tuples. i.e. this: (1, 2), arr[:, 5:6], instead of: (1,2), arr[:,5:6]. A space immediately after a comma is recommended in PEP8. Variable naming. Lots of single and two letter variables like 'c', 'c1, 'c2', 'w', 'm', 'cc', etc... Let's give these descriptive names. For computing magntitude, use np.hypot(isobel, jsobel), instead of the manual computation you use. np.hypot is 2x faster on a 1000x1000 image since it doesn't create any temporaries. inline the smoothing the function, unless you're using it elsewhere.

Lastly, thanks for working and spending time on this code! Cheers! Chris

2011/4/2 Dan Farmer <dfarmernv@gmail.com>

...

I've pushed the suggested changes :

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

Thanks, Dan

2011/3/31 Dan Farmer <dfarmernv@gmail.com>:

...

I will try to address your comments tonight and also see about removing smooth.py and just incorporating the one function we're using into canny.py for now as Thouis suggested. Thanks to both of you for looking at it. I'll message back when I've pushed the changes.

-Dan

2011/3/31 Stéfan van der Walt <stefan@sun.ac.za>:

...

Hi Dan

On Thu, Mar 31, 2011 at 1:02 AM, Dan Farmer <dfarmernv@gmail.com> wrote:

...

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

I read through your patch and made some preliminary comments.

...

Mostly just trying to follow procedure. I already mentioned my concerns in the previous thread. I made one stab at introduced a "None" default for the mask, but I got hung up and reverted it. The default I was going to propose was np.ones(img.shape,bool) (and after the fact I even noticed that's how it is used in one of the unit tests). But I started thinking that that could be quite wasteful of memory if you were working with large images (on my test use case with ~512x512 images it's about 300 KB for the "fake" mask).

It seems as though this specific implementation of the algorithms relies on creating the mask, so I don't think you can get away from it.  The typical way to do it would be:

def canny(..., mask=None, ...):    if mask is None:        mask = np.ones(x.shape, dtype=bool)

...

The problem I had was that if I don't allocate the emask array I get run-time errors starting at line 129 (in the diff of canny.py) because the arrays all have different lengths if they aren't logical_and'd with emask above.

Yes, I think the only way to avoid allocating the mask explicitly is to rewrite the algorithm in Cython, where you can modify behaviour inside the for-loop.

Regards Stéfan

Ok, I've pushed those changes. Thanks, Dan 2011/4/5 Stéfan van der Walt <stefan@sun.ac.za>:

Hi Dan

On Tue, Apr 5, 2011 at 7:51 AM, Dan Farmer <dfarmernv@gmail.com> wrote:

...

Thanks for the detailed feedback. I've pushed some more changes that I think cover everything. I left the mask and smoothing function for the moment based on Thouis feedback.

https://github.com/dfarmer/scikits.image/compare/master...dfarmer-filters-ca...

I think we're almost ready to pull!

Some last nitpicks:

- The docstring format requires indentation of items, e.g.

   image : array        The image to smooth

- PEP8 suggests not indenting equal signs to be aligned:

   not_mask               = np.logical_not(mask)    bleed_over             = function(mask.astype(float))    ...

With these and Chris's changes, I think we're good to go!

Thanks a lot for your effort.

Cheers Stéfan