Mailman 3 October 2014 - scikit-image

Re: skimage and opencv
by Emmanuelle Gouillart 22 Sep '16

22 Sep '16

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 16 Nov '15

16 Nov '15

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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some broken links in example notebooks
by Michael Aye 12 Nov '14

12 Nov '14

I guess you create the example notebooks somehow automatically with sphinx? Because the descriptive text is written in html which mostly shows up well in the notebook, but the links to other skimage functions do show up weird/broken. I even don't know if it's possible or reasonable to fix that somehow for a locally downloaded notebook, but I just wanted to inform you in case you were not aware. My example is for http://scikit-image.org/docs/dev/auto_examples/plot_blob.html The way it's shown in my notebook (ipython 2.3) can be seen here: https://www.dropbox.com/s/ptzoqfx22yhn5vu/Screenshot%202014-10-08%2017.54.4… If you think it's worth a GH issue, just say the word and I create one. Regards, Michael

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The Gray Level Difference Vector (GLDV)
by Artur Bercik 31 Oct '14

31 Oct '14

Dear scikit-image Users: It is so nice to find The Gray Level Co-occurrence Matrix (GLCM) in scikit-image. http://scikit-image.org/docs/dev/auto_examples/plot_glcm.html However, I am interested in using The Gray Level Difference Vector (GLDV). Is not it available in scikit-image? Can someone guide me how to calculate it? Thanks in the advance. Artur Bercik

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scikit-image paper: please cite and distribute
by Stefan van der Walt 30 Oct '14

30 Oct '14

Hi everyone Whether we like it or not, the academic world runs on the currency of citations. Our scikit-image paper is performing OK (10 citations so far), but I know for a fact that there are many more projects using it, and that the package is not necessarily cited in their publications. I'm therefore asking that, for the benefit of the project, you distribute the paper as widely as possible and encourage those who use the software to cite it. As long as the citations roll in, the devs (many of whom are at academic institutions) can justify spending their time fixing issues and producing newly designed functionality. Thanks and regards, Stéfan Stéfan van der Walt, Johannes L. Schönberger, Juan Nunez-Iglesias, François Boulogne, Joshua D. Warner, Neil Yager, Emmanuelle Gouillart, Tony Yu and the scikit-image contributors. scikit-image: Image processing in Python. PeerJ 2:e453 (2014) http://dx.doi.org/10.7717/peerj.453 @article{scikit-image, title = {scikit-image: image processing in {P}ython}, author = {van der Walt, {S}téfan and {S}chönberger, {J}ohannes {L}. and {N}unez-{I}glesias, {J}uan and {B}oulogne, {F}rançois and {W}arner, {J}oshua {D}. and {Y}ager, {N}eil and {G}ouillart, {E}mmanuelle and {Y}u, {T}ony and the scikit-image contributors}, year = {2014}, month = {6}, keywords = {Image processing, Reproducible research, Education, Visualization, Open source, Python, Scientific programming}, volume = {2}, pages = {e453}, journal = {PeerJ}, issn = {2167-8359}, url = {http://dx.doi.org/10.7717/peerj.453}, doi = {10.7717/peerj.453} }

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issue with skimage at anaconda
by Jaime Lopez Carvajal 29 Oct '14

29 Oct '14

Hi all, I am having problems installing scikit-image into Anaconda suite, although it comes with a prebuilt, i erased this skimage version to replace it github clone version. When I try to upgrade the skimage by console command it says this requeriment is already up to date (see attached image). but it doesnt appear at directory, as you can see (see attached image) How can I fix this issue? thanks in advance, Jaime

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Postdoc position on image analysis - Max Planck Institute of Biochemistry
by Ruben Fernandez 28 Oct '14

28 Oct '14

A postdoc position for an image analysis specialist is available at the Department of Molecular Structural Biology <http://www.biochem.mpg.de/en/rd/baumeister> at the Max Planck Institute (MPI) of Biochemistry (Martinsried, Germany). The project aims to develop data processing and segmentation techniques to analyze the structures found in cryo-electron tomograms of cells containing toxic protein aggregates in the context of neurodegenerative disease. The position can be funded for up to 5 years by an ERC Synergy Grant awarded to the ToPAG (Toxic Protein AGgregation in neurodegeneration) consortium formed by four MPI-Martinsried departments. The goal of this multidisciplinary initiative is to investigate the mechanisms by which protein misfolding leads to neurodegeneration in diseases such as Alzheimer’s or Parkinson’s. The MPI of Biochemistry hosts a world-class cryo-electron microscopy center with multiple high end transmission electron microscopes (including Titan Krios, Tecnai Polara, Tecnai F20), several of which are equipped with energy filters, direct electron detectors and phase plates. The Institute also houses advanced equipment for sample preparation and ample computational resources. Applicants should hold a Ph.D. degree in Computer Science or related disciplines and experience in 3D data processing, preferably cryo-electron tomography. To apply, please send a motivation letter, CV and contact information of two referees to Wolfgang Baumeister (baumeist(a)biochem.mpg.de) or Rubén Fernández-Busnadiego (ruben(a)biochem.mpg.de). Ruben Fernandez-Busnadiego, Ph. D. Project Group Leader Max Planck Institute of Biochemistry Dept. Molecular Structural Biology Am Klopferspitz 18 82152 Martinsried Germany

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scikit-image fft
by Christopher 17 Oct '14

17 Oct '14

Hi all, Discovered sci-image recently, and I like it so far. Right now I am basically trying to do an fft, filter out certain frequencies, and then back transform it to an image. My first thought was to use fft, but I can't find an fft function in the docs. I see that numpy has an fft function, but running that on a sci-kit image gives unpleasant errors. Is there perhaps a better method for this than fft? Any suggestions? chris

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Python book on computer vision
by Simon 16 Oct '14

16 Oct '14

Hi All, I am looking for a book on computer vision in python. I am relatively new to computer vision but have some experience in AI. I have learnt a fair amount form scikit-image documentation and trying things out, but need some more overview. Most of the books I have found are related to opencv. Does anyone have a book that they can recommend. I am more interested in getting an overview of the different techniques of object recognition and categorisation then code examples. Thanks Simon

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Build error
by Georges H 13 Oct '14

13 Oct '14

Hi all, I'm encountering a problem with the installation from source for scikit-image-master sudo python setup.py install Output is : creating build/temp.macosx-10.9-intel-2.7 compile options: '-I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c' cc: geometry.c clang: error: no such file or directory: 'geometry.c' clang: error: no input files clang: error: no such file or directory: 'geometry.c' clang: error: no input files error: Command "cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c geometry.c -o build/temp.macosx-10.9-intel-2.7/geometry.o" failed with exit status 1 All requirements are installed and running under osx I also did a clean : clean sudo python setup.py clean --all and retried same result any insight is greatly appreciated. Thanks.

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