Mailman 3 December 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,

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Problems with coordinate ranges when doing conversion from LCH to LAB to RGB
by Matteo Nov. 16, 2015

Nov. 16, 2015

A while ago I wrote a post on my blog with code on how to import in Python a colour palette in an ASCII file and convert it to a Matplotlib colormap: mycarta.wordpress.com/2014/04/25/convert-color-palettes-to-python-matplotli… Following that post I wrote a tutorial on a geoscience magazine on how to evaluate and compare colormaps using Python: wiki.seg.org/wiki/How_to_evaluate_and_compare_color_maps In the accompanying notebook I show how to convert a 256x3 RGB colormap to a 256x256x3 RGB image, then convert it to CIELAB using scikit-image's rgb2lab, then plot the 256x1 lightness (L) array to evaluate the colormaps perceptually. You can read the relevant extract of the notebook using this nbviewer link: http://nbviewer.ipython.org/urls/dl.dropbox.com/s/54zoax2qesb71wn/evaluate_… In that case scikit-image worked really well for me. Now I am trying to follow up with a new tutorial and I run into problems with the color space conversions. You can follow what I am trying to do in this other notebook extract: http://nbviewer.ipython.org/urls/dl.dropbox.com/s/noli66nzrlk0676/make_colo… The goal of this new tutorial is to show how to build colormaps from scratch using perceptual principles. I design a color palette in LCH (polar version of CIELAB) by keeping Chroma and Lightness fixed and interpolating Hue around the circle, then convert to LAB, then to RGB. As far as I know the code I wrote should work, but the result is a black colormap. I am thinking I got wrong one or more of the ranges for the LCH coordinates. I assumed L between (0,1), Ch between (0,1), and H between (0, 2*pi). Is that wrong, and if that's the case, what are the ranges? Many of them are not stated clearly in the documentation in here: http://scikit-image.org/docs/dev/api/skimage.color.html Is it possible to update the documentation to clearly state all ranges for all colour spaces. Thanks for your help. Matteo

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Pattern and object recognition with COSFIRE
by Almar Klein July 6, 2015

July 6, 2015

Hi all, Just wanted to mention an algorithm which I was very impressed by and which might be an awesome addition to scikit-image. The algorithm is called COSFIRE (Combination of Shifted Filter Responses). I saw a talk by Geore Azzopardi, who presented the use of the algorithm for object and patter recognition. I was very impressed with the quality of segmentation of the shown examples, but also with the wide variety of image data (e.g. retina images, traffic signs, hand-written characters, and more). The filter is inspired by how the brain processes visual information, and according to the author the algorithm is actually quite simple. The algorithm was the topic of his PhD and he's going to continue working on it in his new job. The code (in Matlab) is available, so it might be worth a shot to try and port it to Python. Some links: - PhD thesis: http://www.cs.rug.nl/~george/phd-thesis/ - Matlab code: nl.mathworks.com/matlabcentral/fileexchange/37395 - Paper in MIA: http://www.medicalimageanalysisjournal.com/article/S1361-8415%2814%2900136-… - Almar

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ANN: imageio v1.0
by Almar Klein July 3, 2015

July 3, 2015

Hi all, I'm pleased to announce version 1.0 of imageio - a library for reading and writing images. This library started as a spin-off of the freeimage plugin in skimage, and is now a fully-fledged library with unit tests and all. Imageio provides an easy interface to read and write a wide range of image data, including animated images, volumetric data, and scientific formats. It is cross-platform, runs on Python 2.x and 3.x, and is easy to install. Imageio is plugin-based, making it easy to extend. It could probably use more scientific formats. I welcome anyone who's interested to contribute! install: pip install imageio website: http://imageio.github.io release notes: http://imageio.readthedocs.org/en/latest/releasenotes.html Regards, Almar

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Re: Pattern and object recognition with COSFIRE
by George Azzopardi June 26, 2015

June 26, 2015

Dear all, I am pleased to see interest in the COSFIRE approach that I started during my PhD studies. The COSFIRE approach is a trainable pattern recognition approach which can be applied to several applications, including feature detection, object recognition and localization, image classification, contour detection and vessel segmentation. The selectively for a pattern of interest is automatically configured in a training process. The method involves several computations that are independent of each other, and thus it can be easily implemented using parallel programming (e.g. on a GPU). The original paper (http://www.cs.rug.nl/~george/articles/PAMI2013.pdf) combines information about the contours of the concerned pattern. We now have another paper which is currently being reviewed for CVPR2015 where we show that by adding colour information COSFIRE filters become even more robust. Please feel free to send me other ideas on how this work can be developed further. I would be very happy and available to work with an undergraduate or a postgraduate student (or any other person) to have this parallel implementation in Python. I see that you already added it to the Requested-features page. You can also add my contact details (geazzo@gmail) there for the interested readers. All my papers can be freely downloaded from my website: http://www.cs.rug.nl/~george/research-activities/ regards, George On Tuesday, 16 December 2014 15:22:45 UTC+1, Stefan van der Walt wrote: > > On Tue, Dec 16, 2014 at 1:57 PM, Pratap Vardhan <prat...(a)gmail.com > <javascript:>> wrote: > > I found few copies of the paper hosted by universities. I haven't > checked if > > these are the actual pre-prints - However, by the citation it looks like > it. > > Thanks! I've added it to the list: > > https://github.com/scikit-image/scikit-image/wiki/Requested-features > > Stéfan >

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Example: Scikit-image and trackpy (bubble tracking in foams)
by François Boulogne March 25, 2015

March 25, 2015

Hi, Just for your information, I wrote an example based on my research to show the use of scikit-image with trackpy for feature detection and tracking. http://nbviewer.ipython.org/github/soft-matter/trackpy-examples/blob/master… Hopefully, this might be helpful for future workshops or presentations. Best, -- François Boulogne. http://www.sciunto.org GPG: 32D5F22F

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Hi, I would like to offer my help in the next GSoC
by Ma ChienLi Jan. 8, 2015

Jan. 8, 2015

Hi, everybody~ I am Ma Chienli, an undergraduate from China, majoring in electronic and information engineering. I have beed using python for scientific computation for a year and now I am learning cython. I would like to offer my for your next (possible) GSoC project of writting the scipy.ndimage in cython :) So, at first, from where should I start? Cheers Ma P.S. I just created another thread which did not show up. If this thread conflicts with it, please delete one of them .

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Fwd: [Numpy-discussion] numpy dev-version-string change
by Stéfan van der Walt Dec. 28, 2014

Dec. 28, 2014

---------- Forwarded message ---------- From: "Ralf Gommers" <ralf.gommers(a)gmail.com> Date: Dec 28, 2014 10:43 AM Subject: [Numpy-discussion] numpy dev-version-string change To: "Discussion of Numerical Python" <numpy-discussion(a)scipy.org> Cc: Hi all, This is a heads up that the numpy version string for development versions is changing from x.y.z.dev-githash to x.y.z.dev+githash (note the +). This is due to PEP 440 [1], which specifies local (i.e. non-released) versions have to use a "+". Pip 6.0, released a few days ago, enforces this so we noticed immediately that without this version string change pip sorted the latest dev wheel build from master below any released version. Change in numpy at [2]; identical change in scipy at [3]. Note that this is unlikely but not impossible to break custom version string parsers (like [4]). Cheers, Ralf [1] https://www.python.org/dev/peps/pep-0440/ [2] https://github.com/numpy/numpy/pull/5387 [3] https://github.com/scipy/scipy/pull/4307 [4] https://github.com/scipy/scipy/blob/master/scipy/lib/_version.py _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion(a)scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

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Re: How do you keep documentation so nice?
by Adam Hughes Dec. 21, 2014

Dec. 21, 2014

Hey Thomas, Sorry for late reply. Can you expand on this a little bit? Benjamin Root said to ask you about how the docs work. Essentially, how do you host them on the master branch under the docs folder and still have them hosted at matplotlib.org? Instead of hosting them on gh-pages and having them show up as github.com/matplotlib? I'm having the hardest time finding info on this. On Thursday, December 11, 2014 12:58:00 PM UTC-5, Thomas Caswell wrote: > > matplotlib uses the organization-level gh-pages to host the documentation > which seems to work pretty well. > > On Thu Dec 11 2014 at 12:45:30 PM Adam Hughes <hughes...(a)gmail.com > <javascript:>> wrote: > >> Thanks, that's great advice. Also, do you guys pay to host your site? >> Can you recommend a low-cost, or free, static-website hosting vendor? We >> are currently using gh-pages branch on github to host our site, and I >> really hate having this secondary branch. Especially when I need the >> documentation to have access to the source code modules or setup.py file >> (as it's on a second branch). >> >> On Thu, Dec 11, 2014 at 6:56 AM, Juan Nunez-Iglesias <jni....(a)gmail.com >> <javascript:>> wrote: >>> >>> Adam, just fyi, we are considering moving away from GoogleGroups... (See >>> a separate discussion on this list). Since you are on the ground floor, you >>> might want to reconsider your choice. I've been using Nabble for my (very >>> low volume!) gala list and it's been really good. >>> >>> >>> >>> >>> On Thu, Dec 11, 2014 at 12:01 PM, Adam Hughes <hughes...(a)gmail.com >>> <javascript:>> wrote: >>> >>>> Thanks Michael. >>>> >>>> Be warned, only about 3 people are using the library at the moment, so >>>> it's quite likely that you'll encounter some bugs just by virtue of using a >>>> new dataset that probably will bring to light some considerations that we >>>> overlooked. In addition, I only support pandas 0.14 right now (0.15 has a >>>> lot of private API changes that directly affect us). But we did feel like >>>> the library was close enough to ready to share it, and I hope you can try >>>> it out. If you do want to give it a whirl sometime soon, please feel free >>>> to contact us at sks...(a)googlegroups.com <javascript:> (or me >>>> personally) and we will at least make sure to help get you up and running. >>>> Let us know what kind of data you're working on and what type of analysis >>>> you're doing. We've spend a lot of time putting out datastructures >>>> together, but we haven't put a great deal of thought into the actual >>>> spectral utilitiles, workflows and analysis that we should host, other than >>>> correlation spectroscopy and base things like dynamic baseline fitting. >>>> >>>> >>>> >>>> On Wed, Dec 10, 2014 at 6:14 PM, Michael Aye <kmicha...(a)gmail.com >>>> <javascript:>> wrote: >>>> >>>>> On 2014-12-10 02:43:46, Adam Hughes <hughes...(a)gmail.com> wrote: >>>>> >>>>>> > http://hugadams.github.io/scikit-spectra/ >>>>>>>> >>>>>>>> That is a very impressive notebook widget shown in the video! I >>>>>>>> love >>>>>>>> how it interacts with mpl3d. >>>>>>>> >>>>>>>> >>>>>>>> Ditto! Man, can't wait to play with this! Very happy that there's >>>>> finally a package focusing on spectral analysis! It also just comes at the >>>>> right time, just started in my new job working on data from an imaging >>>>> spectrometer for the first time. ;) >>>>> >>>>> Michael >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to a topic in the >>>>> Google Groups "scikit-image" group. >>>>> To unsubscribe from this topic, visit >>>>> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe >>>>> . >>>>> To unsubscribe from this group and all its topics, send an email to >>>>> scikit-image...(a)googlegroups.com <javascript:>. >>>>> 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...(a)googlegroups.com <javascript:>. >>>> For more options, visit https://groups.google.com/d/optout. >>>> >>> >>> -- >>> You received this message because you are subscribed to a topic in the >>> Google Groups "scikit-image" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/scikit-image/k5K6_vanZVI/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> scikit-image...(a)googlegroups.com <javascript:>. >>> 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...(a)googlegroups.com <javascript:>. >> For more options, visit https://groups.google.com/d/optout. >> >

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User Interaction with RectangleTool
by Salvatore Scaramuzzino Dec. 19, 2014

Dec. 19, 2014

Hi to all I'm new in scikit-image, and i develop algorithms for medical applications. Sometimes is very very useful to have user interaction, in particular Region of Interest (ROI) selection over an image. I found in skimage the RectangleTool and i'm trying to write a simple ROI selector in order to use the rectangle coords in successive computations. unfortunately i can't be able to handle mouse events: for example if i've: #import import skimage as sk from skimage import data import matplotlib.pyplot as plt from skimage.viewer.canvastools import RectangleTool import numpy as np from skimage.draw import polygon from skimage.draw import line im = data.lena() f, ax = plt.subplots() plt.imshow(im) def cable(img): # is here usable "extents?" rect_tool = RectangleTool(ax,on_enter=cable(im)) i simply want to see "extents" which is the attribute that store coords for user-selected rectangle according to http://scikit-image.org/docs/dev/api/skimage.viewer.canvastools.html?highli… i hope this is clear and if it's possible i think is useful to embed this example in docs. thanks in advance

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