Mailman 3 November 2013 - scikit-image

Re: Kakadu JP2000 reader
by Stuart Mumford Nov. 17, 2013

Nov. 17, 2013

You might want to checkout the glymur project. https://github.com/quintusdias/glymur Stuart On 18 Nov 2013 06:57, "Stéfan van der Walt" <stefan(a)sun.ac.za> wrote: > Dear Michael > > On Tue, Oct 29, 2013 at 12:59 AM, Michael Aye <kmichael.aye(a)gmail.com> > wrote: > > I was wondering if it would be possible to implement the Kakadu JP2000 > > reader into scikit-image? I believe but am not sure that the reader only > > could be used without licensing fees? At least it's worth investigating > > because that reader is really the most powerful JP2000 reader out there > and > > the only one that can deal with the large HiRISE images of the MRO > > spacecraft. > > Does FreeImage then fail on these images? Do you have an example > image for us to test on? > > Thanks > 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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scikit-image paper
by Juan Nunez-Iglesias Nov. 17, 2013

Nov. 17, 2013

Hi All, I'm moving the discussion of the paper to the mailing list, as requested by Stefan. Here's a summary of the points so far: * Josh brought up a Computational Science and Discovery special issue as not only a possible venue for the paper but a general renewed call to action about this paper. * I vetoed the CSD special issue, despite having no formal power of veto =P, and suggested we opt instead for a fully open access journal, such as F1000Research. * This and Johannes's email sparked a discussion about possible homes for it. Current suggestions: - F1000 Research - JMLR MLOSS [sklearn published here] - Journal of Open Research Software [mahotas published here] - Image Processing On Line (ipol.im) - Journal on Image and Video Processing (jivp.eurasipjournals.com) * Stefan suggested as the author list, "currently active core contributors", but would certainly add more authors that have "made a substantial contribution to the package." I feel the same way and I imagine other current core devs would not object to this either. (?) * There is a markdown template PR here: https://github.com/scikit-image/scikit-image-paper/pull/2 Johannes gave a +1 to merging that, and I give another, so that makes +2, I'll merge following this email. =) (I have a question about this point: for managing LaTeX papers on git, I have usually stuck to the convention of "1 sentence: 1 line". Do we want this for this paper, or wrap at 72 characters, or something else?) I think that's everything, though I'm sure the discussion will continue! Stefan asked me to elaborate on my suggestion of F1000. I must admit I don't know much about the other journals on the list, and would need to look into them. Things that I *expect* from our eventual home are: - open access. - CC or similar licensing that allows text mining applications. Further niceties offered by F1000Res: - papers published immediately as preprint. - open peer review - once two reviewers have signed off on the paper, it is considered "peer reviewed". Reviewers can request modifications, and full paper and revision history is maintained. - peer reviewed articles are indexed by PubMed. Essentially, the review model is quite similar to the GitHub PR process, which sounds great to me. PeerJ offers a similar (identical?) model, but is currently not LaTeX friendly, which pretty much rules it out for this. Juan.

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Re: template matching example with a color image leads to Value Error.
by Raphael Ackermann Nov. 17, 2013

Nov. 17, 2013

On Sun, Nov 17, 2013 at 10:20 AM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > On Sun, Nov 17, 2013 at 10:46 AM, Johannes Schönberger <jsch(a)demuc.de> > wrote: > > We can consider this as a bug. It must be mentioned in the doc string. > > > > But I don’t see a reason why we shouldn’t support N-D or at least 3- and > 4-D (3-D plus channels) images… ? > > I agree -- let's file a ticket to track this issue. > > Done: https://github.com/scikit-image/scikit-image/issues/818

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Advice on improving a analysis on images of nanoparticles
by Adam Hughes Nov. 17, 2013

Nov. 17, 2013

Dear Scikit-Image (SKI) team, I have over a hundred scanning electron microscope (SEM) images of gold nanoparticles on glass surfaces, and I've generated several scripts in ImageJ/Python to batch analyze them. The analysis is fairly crude, and consists mostly of users manually thresholding to make a binary image, applying a simple noise filter and performing ImageJ's particle counting routine. Afterwards, my scripts use Python to do plotting, statistics and then output .txt, excel and .tex files. Eventually, I'd like to remove the ImageJ portion altogether and refactor the code to use SKI exclusively; however, for now, I am mainly interested in improving the results with some features of SKI. The images are in a .pdf can be downloaded directly here<http://www.4shared.com/office/xX37rOfh/SCIKIT_TEST_Notable.html>. (Just a hair too big to attach) What I'd like to do is to look at a subset of our images and see if SKI can enhance the image/remove defects. I've chosen 10 images to represent various cases and attached a summary via googledrive. The images are categorized as follows (preliminary questions are in blue): *NICE* - Image is about as good as we can get, and shouldn't have many artifacts. Can these be further enhanced? *LOWCONTRAST *- Can the contrast in these images be enhanced automatically in SKI? *NONCIRC* - Particles appear non-circular due to stigmation offset in microscope. Is it possible to reshape them/make them more circular? *WARPED* - Images that have artifacts, or uneven contrast, due to aberrations in SEM beam during imaging. * I'm especially interested in removing uneven contrast.* *WATERSHED* - These images have overlapping AuNPs, and I had hoped that SKI's watershedding routines might help disentangle them. The *watershed segmentation guide*<http://scikit-image.org/docs/dev/auto_examples/plot_watershed.html>indicates that there are several ways to approach this problem. On the attached PDF, each page shows the original SEM image (converted from highres.tiff to png), a binary image, our manually chosen adjustment threshold, and two estimates of the particle diameter distribution (don't worry about details of this). I was really hoping that some SKI experts would examine these images and suggest some algorithms or insights to address the aforementioned concerns. *The overall goal is to survey the most common problems in SEM imaging of nanoparticles, give examples of each, and demonstrate how SKI can improve the particle counting.* Thanks for you time, and for making a really nice open-source package.

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template matching example with a color image leads to Value Error.
by Raphael Ackermann Nov. 17, 2013

Nov. 17, 2013

Hi I am trying to do template matching. Running http://scikit-image.org/docs/0.9.x/auto_examples/plot_template.html#example… works perfectly fine. But when I change image = data.coins() --> image = data.lena() to have a non b/w image I get the following error. Traceback (most recent call last): File "/..../template_matching.py", line 11, in <module> result = match_template(image, coin) File "/usr/local/lib/python2.7/dist-packages/scikit_image-0.9.3-py2.7-linux-x86_64.egg/skimage/feature/template.py", line 80, in match_template result = _template.match_template(image, template) File "_template.pyx", line 50, in skimage.feature._template.match_template (skimage/feature/_template.c:1967) ValueError: Buffer has wrong number of dimensions (expected 2, got 3) Is it not possible to call match_template() with a color image? Or what am I doing wrong? I can't find anything in the documentation or the code that this should only work for black and white images. When I replace the scikit-image algorith with one from cv2 result = match_template(image, coin) --> result = cv2.matchTemplate(image, coin, cv2.TM_CCOEFF_NORMED) I can at least continue further in the example and it finds the coordinates where the template matches. Is this a bug? If not the documentation/example should be updated to make it clear that this only works for b/w images. Thanks Raphael

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weird behaviour of skimage.transform.rotate()
by Sigmund Nov. 13, 2013

Nov. 13, 2013

Moin moin! (Enthought Canopy Python 2.7.3 | 64-bit | (default, Aug 8 2013, 05:30:12) [MSC v.1500 64 bit (AMD64)] on win32) I noticed that the rotate function is not working correct for me or at least not in the way I expect it to function. Could someone check this or tell me what I'm doing wrong. I would like to rotate a image/array for some degrees. import numpy as np import matplotlib.pyplot as plt import skimage.transform as sk_trans im_array = np.ones((30,30)) im_array[12,:]=2 im_array[13,:]=3 im_array[14,:]=4 im_array[15,:]=5 im_array[16,:]=4 im_array[17,:]=3 im_array[18,:]=2 img_rot = sk_trans.rotate(im_array,45) plt.imshow(im_array,interpolation='none') plt.show() plt.imshow(img_rot,interpolation='none') plt.show() Thanks Siggi

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Re: What's 'stable' version currently?
by Johannes Schönberger Nov. 12, 2013

Nov. 12, 2013

Sorry, I didn’t see that you were asking for a review, so I just merged. See https://github.com/scikit-image/scikit-image-web/pull/14 for a slightly modified layout and automatic release date insertion. Am 12.11.2013 um 16:31 schrieb Stéfan van der Walt <stefan(a)sun.ac.za>: > Here's a start--this PR grabs it directly from PyPi: > > https://github.com/scikit-image/scikit-image-web/pull/13 > > Some spacing issues etc., so some suggestions on how to tweak welcome. > > On Tue, Nov 12, 2013 at 4:55 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> Easiest way to do that is to just grab it from docversions.js. >> >> On 12 Nov 2013 20:20, "Johannes Schönberger" <jsch(a)demuc.de> wrote: >>> >>> Yes, but only in the documentation section and not on the home page in the >>> sidebar on the top left. >>> >>> We should change this to automatically update the version number, because >>> building the docs and uploading it every time is a pain... >>> >>> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma(a)gmail.com>: >>> >>> I thought we had changed the site version string to read "0.9.x"??? >>> >>> >>> On Tue, Nov 12, 2013 at 8:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za> >>> wrote: >>>> >>>> Those are all bug fix releases, but yes: the website needs an update. In >>>> fact, why don't we have the website builder just query pipy? >>>> >>>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: >>>>> >>>>> I am asking because the website says 0.9.0, but pip just brought me >>>>> 0.9.3? >>>>> So either 0.9.3 is stable, and the website needs an update, or pip >>>>> provides unstable versions, which would not be in line with what is written >>>>> on skimage's Download page? >>>>> >>>>> Cheers, >>>>> Michael >>>>> >>>>> >>>>> -- >>>>> 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. >>> >>> >>> -- >>> 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. > > -- > 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: What's 'stable' version currently?
by Stéfan van der Walt Nov. 12, 2013

Nov. 12, 2013

Here's a start--this PR grabs it directly from PyPi: https://github.com/scikit-image/scikit-image-web/pull/13 Some spacing issues etc., so some suggestions on how to tweak welcome. On Tue, Nov 12, 2013 at 4:55 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: > Easiest way to do that is to just grab it from docversions.js. > > On 12 Nov 2013 20:20, "Johannes Schönberger" <jsch(a)demuc.de> wrote: >> >> Yes, but only in the documentation section and not on the home page in the >> sidebar on the top left. >> >> We should change this to automatically update the version number, because >> building the docs and uploading it every time is a pain... >> >> Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma(a)gmail.com>: >> >> I thought we had changed the site version string to read "0.9.x"??? >> >> >> On Tue, Nov 12, 2013 at 8:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za> >> wrote: >>> >>> Those are all bug fix releases, but yes: the website needs an update. In >>> fact, why don't we have the website builder just query pipy? >>> >>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: >>>> >>>> I am asking because the website says 0.9.0, but pip just brought me >>>> 0.9.3? >>>> So either 0.9.3 is stable, and the website needs an update, or pip >>>> provides unstable versions, which would not be in line with what is written >>>> on skimage's Download page? >>>> >>>> Cheers, >>>> Michael >>>> >>>> >>>> -- >>>> 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. >> >> >> -- >> 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: What's 'stable' version currently?
by Stéfan van der Walt Nov. 12, 2013

Nov. 12, 2013

Easiest way to do that is to just grab it from docversions.js. On 12 Nov 2013 20:20, "Johannes Schönberger" <jsch(a)demuc.de> wrote: > Yes, but only in the documentation section and not on the home page in the > sidebar on the top left. > > We should change this to automatically update the version number, because > building the docs and uploading it every time is a pain... > > Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma(a)gmail.com>: > > I thought we had changed the site version string to read "0.9.x"??? > > > On Tue, Nov 12, 2013 at 8:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za>wrote: > >> Those are all bug fix releases, but yes: the website needs an update. In >> fact, why don't we have the website builder just query pipy? >> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: >> >>> I am asking because the website says 0.9.0, but pip just brought me >>> 0.9.3? >>> So either 0.9.3 is stable, and the website needs an update, or pip >>> provides unstable versions, which would not be in line with what is written >>> on skimage's Download page? >>> >>> Cheers, >>> Michael >>> >>> >>> -- >>> 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. >> > > -- > 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: What's 'stable' version currently?
by Johannes Schönberger Nov. 12, 2013

Nov. 12, 2013

Yes, but only in the documentation section and not on the home page in the sidebar on the top left. We should change this to automatically update the version number, because building the docs and uploading it every time is a pain... > Am 12.11.2013 um 12:53 schrieb "Juan Nunez-Iglesias" <jni.soma(a)gmail.com>: > > I thought we had changed the site version string to read "0.9.x"??? > > >> On Tue, Nov 12, 2013 at 8:40 PM, Stéfan van der Walt <stefan(a)sun.ac.za> wrote: >> Those are all bug fix releases, but yes: the website needs an update. In fact, why don't we have the website builder just query pipy? >> >>> On 12 Nov 2013 14:40, "Michael Aye" <kmichael.aye(a)gmail.com> wrote: >>> I am asking because the website says 0.9.0, but pip just brought me 0.9.3? >>> So either 0.9.3 is stable, and the website needs an update, or pip provides unstable versions, which would not be in line with what is written on skimage's Download page? >>> >>> Cheers, >>> Michael >>> >>> >>> -- >>> 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. > > -- > 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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