Mailman 3 July 2013 - scikit-image

Re: Welcome to the core team, @jni!
by Johannes Schönberger 26 Jul '13

26 Jul '13

Hi, Sorry for the delayed welcome from my side... Great to have you in the team! Johannes Schönberger Am 23.07.2013 um 13:29 schrieb "Stéfan van der Walt" <stefan(a)sun.ac.za>: > Dear all, > > It gives me great pleasure to welcome Juan Nunez-Iglesias to the core > skimage team! Juan certainly earned his way by suffering through many > of our most nit picky reviews, and through his excellent > contributions, including the recent N-d extension to SLIC > segmentation. > > Juan, it's great to have you on board. > > Stéfan > > -- > You received this message because you are subscribed to the Google Groups "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > >

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Re: Welcome to the core team, @jni!
by Tony Yu 23 Jul '13

23 Jul '13

Congratulations, Juan. It's great to have you on the team! On Tue, Jul 23, 2013 at 8:00 AM, Juan Nunez-Iglesias <jni.soma(a)gmail.com>wrote: > Woot! Thank you. It's great to be here. I love the project and the team. > > > On Tue, Jul 23, 2013 at 9:29 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Dear all, >> >> It gives me great pleasure to welcome Juan Nunez-Iglesias to the core >> skimage team! Juan certainly earned his way by suffering through many >> of our most nit picky reviews, and through his excellent >> contributions, including the recent N-d extension to SLIC >> segmentation. >> >> Juan, it's great to have you on board. >> >> Stéfan >> >> -- >> You received this message because you are subscribed to the Google Groups >> "scikit-image" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to scikit-image+unsubscribe(a)googlegroups.com. >> For more options, visit https://groups.google.com/groups/opt_out. >> >> >> > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > >

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Re: Welcome to the core team, @jni!
by Juan Nunez-Iglesias 23 Jul '13

23 Jul '13

Woot! Thank you. It's great to be here. I love the project and the team. On Tue, Jul 23, 2013 at 9:29 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > Dear all, > > It gives me great pleasure to welcome Juan Nunez-Iglesias to the core > skimage team! Juan certainly earned his way by suffering through many > of our most nit picky reviews, and through his excellent > contributions, including the recent N-d extension to SLIC > segmentation. > > Juan, it's great to have you on board. > > Stéfan > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > >

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Welcome to the core team, @jni!
by Stéfan van der Walt 23 Jul '13

23 Jul '13

Dear all, It gives me great pleasure to welcome Juan Nunez-Iglesias to the core skimage team! Juan certainly earned his way by suffering through many of our most nit picky reviews, and through his excellent contributions, including the recent N-d extension to SLIC segmentation. Juan, it's great to have you on board. Stéfan

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Issue with skimage.transform.warp - 'numpy.float64' object cannot be interpreted as an index
by Alistair Muldal 22 Jul '13

22 Jul '13

Hi all, I've been using skimage.transform.warp to apply affine transformations to a series of movie frames, using this wrapper function: def applytform(img,tmat,**kwargs): """ A wrapper to call skimage.transform.warp for fast similarity transformations. Also returns the mask of the transformed image (a boolean array, True only in pixels containing the transformed image). All keyword arguments are passed directly to warp. """ # warp needs floating point images -1.0 <= I <= 1.0 origtype, imin, imax = img.dtype, img.min(), img.max() tmpimg = (np.float64(img) - imin) / (imax-imin) # tmpimg = np.require(tmpimg,np.float32,'CAOW') # tmat = np.require(tmat,np.float32,'CAOW') # construct a callable transform object, apply it using warp s = SimilarityTransform(matrix=tmat) # import ipdb;ipdb.set_trace() tmpimg = warp(tmpimg,s.inverse,mode='constant',cval=np.nan,**kwargs) mask = ~np.isnan(tmpimg) tmpimg[~mask] = 0. # convert back to original scaling and type img = tmpimg*imax + imin img = img.astype(origtype) return img,mask I've had no problems using skimage v0.7.1, but I've recently tried updating to v0.8.2 and now the same code gives me this error: /home/alistair/src/python/ca_tadpoles2/opt/d/imtransform3.pyc in applytform(img, tmat, **kwar gs) 50 s = SimilarityTransform(matrix=tmat) 51 # import ipdb;ipdb.set_trace() ---> 52 tmpimg = warp(tmpimg,s.inverse,mode='constant',cval=np.nan,**kwargs) 53 mask = ~np.isnan(tmpimg) 54 tmpimg[~mask] = 0. /home/alistair/.venvs/newskimage/lib/python2.7/site-packages/skimage/transform/_geometric.pyc in warp(image, inverse_map, map_args, output_shape, order, mode, cval, reverse_map) 989 dims.append(_warp_fast(image[..., dim], matrix, 990 output_shape=output_shape, --> 991 order=order, mode=mode, cval=cval)) 992 out = np.dstack(dims) 993 if orig_ndim == 2: /home/alistair/.venvs/newskimage/lib/python2.7/site-packages/skimage/transform/_warps_cy.so i n skimage.transform._warps_cy._warp_fast (skimage/transform/_warps_cy.c:1636)() TypeError: 'numpy.float64' object cannot be interpreted as an index I've tried casting the image and the transformation matrix to np.float32, but this gave me a different error: /home/alistair/src/python/ca_tadpoles2/opt/d/imtransform3.pyc in applytform(img, tmat, **kwargs) 50 s = SimilarityTransform(matrix=tmat) 51 # import ipdb;ipdb.set_trace() ---> 52 tmpimg = warp(tmpimg,s.inverse,mode='constant',cval=np.nan,**kwargs) 53 mask = ~np.isnan(tmpimg) 54 tmpimg[~mask] = 0. /home/alistair/.venvs/newskimage/lib/python2.7/site-packages/skimage/transform/_geometric.pyc in warp(image, inverse_map, map_args, output_shape, order, mode, cval, reverse_map) 989 dims.append(_warp_fast(image[..., dim], matrix, 990 output_shape=output_shape, --> 991 order=order, mode=mode, cval=cval)) 992 out = np.dstack(dims) 993 if orig_ndim == 2: /home/alistair/.venvs/newskimage/lib/python2.7/site-packages/skimage/transform/_warps_cy.so in skimage.transform._warps_cy._warp_fast (skimage/transform/_warps_cy.c:1505)() ValueError: Buffer dtype mismatch, expected 'double_t' but got 'float' Any idea what's going on here?

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Re: How to get a region chain code?
by Marianne Corvellec 21 Jul '13

21 Jul '13

Hello, On Tuesday, July 16, 2013 4:46:28 AM UTC-4, Stefan van der Walt wrote: > > This is the third time in about a month that we have the need to determine > geometric properties of regions. The right solution here is to build a > region graph, like I described in the ticket (sorry, I can't check the > number from my phone right now). > I guess this one: https://github.com/scikit-image/scikit-image/issues/622 Marianne

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Re: Cython help: Time taken to execute a function (profiling) changes drastically depending on image size
by Tony Yu 21 Jul '13

21 Jul '13

On Sun, Jul 21, 2013 at 4:45 AM, Chintak Sheth <chintaksheth(a)gmail.com>wrote: > Hi, > > I am writing the code for Image inpainting using Fast Marching Method. > After writing the initial implementation in Python, I am now cythonising > parts of the code [1]. After profiling, the majority of the time is taken > by the 3 function in [2]. In particular, even after cythonizing, > `inpaint_point` takes the majority of the time. > > The results of profiling for 2 different image sizes are here > http://pastebin.com/aTY1bbn6. The first result is for image size of > 100X100 and the second one for 512X512. The mask size which I use is > constant for both cases. So, the number of function calls to > `inpaint_point` for both are the same as can be seem in the profiling > result. > > Still why do I get such a drastic time difference in the 2 cases ? Any > ideas, what I am missing here or doing inefficiently ? > Having different Cython functions using different copies of your data (i.e. one version as uint8, one as float) seems like a bad idea. And making that copy inside of a loop is probably killing performance: https://github.com/chintak/scikit-image/blob/inpaint/skimage/inpaint/_inpai… > Chintak > > [1] https://github.com/chintak/scikit-image/tree/inpaint/skimage/inpaint > > [2] > https://github.com/chintak/scikit-image/blob/inpaint/skimage/inpaint/_inpai… > > -- > You received this message because you are subscribed to the Google Groups > "scikit-image" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to scikit-image+unsubscribe(a)googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. > > >

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Cython help: Time taken to execute a function (profiling) changes drastically depending on image size
by Chintak Sheth 21 Jul '13

21 Jul '13

Hi, I am writing the code for Image inpainting using Fast Marching Method. After writing the initial implementation in Python, I am now cythonising parts of the code [1]. After profiling, the majority of the time is taken by the 3 function in [2]. In particular, even after cythonizing, `inpaint_point` takes the majority of the time. The results of profiling for 2 different image sizes are here http://pastebin.com/aTY1bbn6. The first result is for image size of 100X100 and the second one for 512X512. The mask size which I use is constant for both cases. So, the number of function calls to `inpaint_point` for both are the same as can be seem in the profiling result. Still why do I get such a drastic time difference in the 2 cases ? Any ideas, what I am missing here or doing inefficiently ? Chintak [1] https://github.com/chintak/scikit-image/tree/inpaint/skimage/inpaint [2] https://github.com/chintak/scikit-image/blob/inpaint/skimage/inpaint/_inpai…

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Re: Contiguous Array
by Chintak Sheth 21 Jul '13

21 Jul '13

Hi Ronnie, On Jul 21, 2013 10:00 AM, "Ronnie Ghose" <ronnie.ghose(a)gmail.com> wrote: > > So in skimage/colors why does it matter if the array is contiguous? Is this for Cython operations later? > Yeah it is mainly for using memory views in Cython which is initialized as C contiguous. `cdef some_type[:. ::1] var_name` In thus case ::1 is for C contiguous. Chintak

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Contiguous Array
by Ronnie Ghose 21 Jul '13

21 Jul '13

So in skimage/colors why does it matter if the array is contiguous? Is this for Cython operations later? Thanks, Ronnie

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