Mailman 3 March 2014 - scikit-image

Re: skimage and opencv
by Emmanuelle Gouillart Sept. 22, 2016

Sept. 22, 2016

Hi FranÃ¯Â¿Â½ois, that's an excellent question, and not a troll :-). Opencv is a very powerful library, but it focuses primarily on computer vision (feature detection and extraction, classification, ...), as opposed to image processing in general (with other tasks such as denoising, segmentation, ...). The other big difference is that skimage builds on numpy ndarrays, and uses the full power of the numpy API (including of course the basic facilities for processing arrays as images that come with numpy), as well as some of scipy functions (you could have added scipy.ndimage to your list -- a few functions in skimage are wrappers around scipy.ndimage, that exist for the sake of completeneness). One important consequence is that algorithms working for 3-d or even n-d images can be easily implemented in 3-d/n-d in skimage, whereas opencv is restricted to 2-D images (as far as I know). Thanks to the use of numpy arrays, the API of skimage is also quite pleasant for a numpy user, more than the API of opencv. A related difference is that skimage is written in python and cython, whereas opencv is a C++ library. The two libraries attract a different crowd of developers, and a Python/Cython toolkit based on numpy arrays is easier to develop and maintain inside the Scientific Python ecosystem. I'm sure that other devs/users will have things to add to this discussion! Cheers, Emmanuelle On Thu, Dec 27, 2012 at 02:06:08PM -0800, FranÃ¯Â¿Â½ois wrote: > Hi users and devs, > It came to my knowledge that another python library (based on C++ and C > codes) for image processing exists too : opencv > I understand that numpy intregrates some basic features and we need some > advanced features but I have the feeling that skimages is redoundant with > opencv in some ways. > What's the position of skimage about that? (Don't read this question as a > troll but like a real question). > I mean that similar features exist in both. Would not be possible to > reuse/integrate opencv or merge? what's the reason for keeping them apart? > My observation is there is 4 libraries to manipulate images: > * PIL > * numpy > * skimages > * opencv > That's a lot. > Cheers,

3 2

Re: Contribution: circles and hough transform
by François June 18, 2014

June 18, 2014

Hi, FYI, I plan to work on the detection of ellipses quite soon. Stefan indicated to me a reference which seems fairly simple to implement. Cheers, François.

3 3

Re: "Cythonize" not working on OSX?
by Stéfan van der Walt June 5, 2014

June 5, 2014

On Mon, 03 Feb 2014 16:44:07 +1100, Juan Nunez-Iglesias wrote: > I didn't know this was a possible course of action! =) I have no idea how > many people are affected, or how quick a fix can be... Is it worth > exploring a bit more before reversing it? I actually have very little idea > about the entire build process so I can't offer much insight here... It broke the build on my system too (perhaps it does not check correctly for old versions), so my preference is to revert and have another look at it. StÃ©fan

3 2

Color rotation (hue)
by Jean-Patrick Pommier March 27, 2014

March 27, 2014

Hi, I 'd like to modify continuously a pure red image to get an orange, yellow, green, light blue, blue, purple image. The idea is to convert a rgb image, to convert it into hsv color space, to modify the hue value then to back convert into rgb color space. The problem is that only green and blue can be obtained but no intermediate color: <https://lh4.googleusercontent.com/-s_Acsx0EmRY/UylefCuSGnI/AAAAAAAABsQ/T7pA…> According to adobe<http://dba.med.sc.edu/price/irf/Adobe_tg/models/hsb.html>, adding a hue equal to 36 should yield a yellow image. *Here's the code:* from skimage import io from skimage import color from scipy import ndimage as nd import numpy as np from matplotlib import pyplot as plt import os cy55 = io.imread('/home/jeanpat/MFISH/PSI/P07/01/Cy5/P070109C.tif') zero = np.zeros(cy55.shape,dtype=np.uint8) rgb0 = np.dstack([cy55, zero,zero]) hue_rotations = [18, 36,72,90,108] images = {} images[0] = rgb0 hsv0 = color.rgb2hsv(rgb0) for hue in hue_rotations: hsv = np.copy(hsv0) hsv[:,:,0] = hsv[:,:,0]+ hue rgb = color.hsv2rgb(hsv) images[hue] = rgb Any greyscaled image should be ok but the image used here is: <https://lh5.googleusercontent.com/-whwEGZWWhIE/UylgLDhf0VI/AAAAAAAABsc/02kl…>

3 6

Fwd: skimage.novice
by Stéfan van der Walt March 25, 2014

March 25, 2014

Hi everyone I am traveling at the moment, so if someone could please have a look at the issue outlined below. Stéfan ---------- Forwarded message ---------- From: Michael Hansen Date: Mon, Mar 24, 2014 at 3:08 PM Subject: Re: skimage.novice [...] It looks like we're close. There's an odd bug showing up in the scikit-image tests [0] that I'm not sure is related to novice (described here [1]). My hands are tied for now, as I can no longer build scikit-image on my machine -- cython 0.17.4 gives me a "NotImplementedError: New relative imports." when running "make". Can you comment Stefan? - Mike [0] https://travis-ci.org/scikit-image/scikit-image/builds/21143584 [1] https://github.com/scikit-image/scikit-image/pull/946#issuecomment-38158266

1 0

Re: Desired Image Compression algorithms in scikit-image
by Ankit Agrawal March 21, 2014

March 21, 2014

Hi all, I have chosen a highly cited(>6400) paper<http://www.stanford.edu/class/ee398a/handouts/papers/Shapiro%20-%20EZT.pdf>`Embedded Image Coding using ZeroTrees of Wavelet Coefficients` as an image compression algorithm to implement in my proposal for now. A short tutorial in the form of slides on the same can be found here<http://www.ws.binghamton.edu/fowler/fowler%20personal%20page/EE523_files/Ch…> . Regards, Ankit Agrawal, Communication and Signal Processing, IIT Bombay. On Thu, Mar 20, 2014 at 12:26 AM, Ronnie Ghose <ronnie.ghose(a)gmail.com>wrote: > also another problem is the many different ways you can do image > compression, if you look at the second paper of the paper ankit linked, > there are no few options - and those are only the ones they explicitly > cited > > > On Wed, Mar 19, 2014 at 2:35 PM, Ankit Agrawal <aaaagrawal(a)gmail.com>wrote: > >> >> >> On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: >> >>> >>> >>> >>> On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >>> >>>> As point of note, if you are looking into doing Python based JPEG200 >>>> you should look over the glymur project ( >>>> https://github.com/quintusdias/glymur) which is Python wrappers around >>>> the OpenJPEG C lib. If you can code the compression algorithm in Python, >>>> that library might provide you some framework for dealing with the meta >>>> data and other things(which are in Python in glymur), save you re-inventing >>>> the wheel. >>>> >>> >>> I just had a look at Glymur, and that's the kind of code that's useful >>> but you really don't want to write. I suggested JPEG 2000 simply because >>> it's a well-known wavelet based algorithm. The scope of Ankit's GSoC should >>> be *algorithms* imho; dealing with file formats, metatdata, etc. would be a >>> huge time sink and out of scope for both scipy and scikit-image I'd think. >>> >> >> I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not >> something I can manage completely in two and a half weeks. Meanwhile, I am >> going through the most cited paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that I got in this area 'Image Compression Through Wavelet Transform >> Coding', which seems big too. I think maybe Josh has knowledge about >> wavelet based compression techniques? >> >> >>> >>> >>>> SunPy has had a lot of contact from the Glymur dev he is a helpful guy. >>>> >>>> Stuart >>>> >>>> >>>> On 18 March 2014 16:16, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >>>> >>>>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf >>>>> >>>>> -- >>>>> 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/d/optout. >>>>> >>>> >>>> -- >>>> 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/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

1 0

color detection and change color
by Aswani Kumar March 20, 2014

March 20, 2014

Hi, i am a python/django developer. i am looking for a solution to replace fabric in an image, So the solution should detect shirt and change color based on choice. Is it possible to do that using scikit? if yes, please give me any little idea to help straight to the point.

2 3

skimage.graph module
by Siva Prasad Varma March 20, 2014

March 20, 2014

Hi, Can anyone help me understand what is skimage.graph module is intended for ? the API Reference page<http://scikit-image.org/docs/dev/api/skimage.graph.html> for graph module does not include any description about the module. just a single line about the module would suffice like done in sklearn documentation<http://scikit-learn.org/stable/modules/classes.html#module-sklearn.cluster> . Currently the module has Minimum Cost Path algorithms and Shortest Path. What I'm trying to figure out is why they are being kept in a separate module, as in what general context are they useful. Thanks, Regards, Siva Prasad Varma.

3 2

Unreal Engine open source (offtopic)
by Adam Hughes March 20, 2014

March 20, 2014

Hey guys, This is a bit off topic, but I thought anyone interested in image processing and, particularly, texture/color and other material descriptors might find this really interested. Check out Materials - 5 for a really cook interface for desiging materials. http://www.youtube.com/watch?v=lngF4VVNER4&list=PLZlv_N0_O1gaCL2XjKluO7N2Pm… Hope this is cool.

1 0

Re: Desired Image Compression algorithms in scikit-image
by Ronnie Ghose March 19, 2014

March 19, 2014

also another problem is the many different ways you can do image compression, if you look at the second paper of the paper ankit linked, there are no few options - and those are only the ones they explicitly cited On Wed, Mar 19, 2014 at 2:35 PM, Ankit Agrawal <aaaagrawal(a)gmail.com> wrote: > > > On Wed, Mar 19, 2014 at 4:41 AM, Ralf Gommers <ralf.gommers(a)gmail.com>wrote: > >> >> >> >> On Tue, Mar 18, 2014 at 5:20 PM, Stuart Mumford <stuart(a)mumford.me.uk>wrote: >> >>> As point of note, if you are looking into doing Python based JPEG200 you >>> should look over the glymur project ( >>> https://github.com/quintusdias/glymur) which is Python wrappers around >>> the OpenJPEG C lib. If you can code the compression algorithm in Python, >>> that library might provide you some framework for dealing with the meta >>> data and other things(which are in Python in glymur), save you re-inventing >>> the wheel. >>> >> >> I just had a look at Glymur, and that's the kind of code that's useful >> but you really don't want to write. I suggested JPEG 2000 simply because >> it's a well-known wavelet based algorithm. The scope of Ankit's GSoC should >> be *algorithms* imho; dealing with file formats, metatdata, etc. would be a >> huge time sink and out of scope for both scipy and scikit-image I'd think. >> > > I concur with Ralf. IMHO, the complete implementation of JPEG 2000 is not > something I can manage completely in two and a half weeks. Meanwhile, I am > going through the most cited paper<https://www.math.purdue.edu/~lucier/692/DJL-image-compression.pdf>that I got in this area 'Image Compression Through Wavelet Transform > Coding', which seems big too. I think maybe Josh has knowledge about > wavelet based compression techniques? > > >> >> >>> SunPy has had a lot of contact from the Glymur dev he is a helpful guy. >>> >>> Stuart >>> >>> >>> On 18 March 2014 16:16, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >>> >>>> www.jpeg.org/jpeg2000guide/papers/madamsjp2k.pdf >>>> >>>> -- >>>> 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/d/optout. >>>> >>> >>> -- >>> 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/d/optout. >>> >> >> -- >> 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/d/optout. >> > > -- > 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/d/optout. >

1 0