Mailman 3 April 2019 - scikit-image

Scikit Blob detection, Not properly working on 3D image
by Francesco Alemanno 15 May '19

15 May '19

Hello everyone, recently (and for the first time) i had to deal with image processing, my problem is detecting sferical blobs in a 3D grayscale image shaped like this (20,1000,1000). So i looked inside scikit, and i found the function blob_dog&log&doh (the three main algorithms), the procedure is working perfectly for the X and Y coordinates (x,y in [0,1000]x[0,1000]) but failing miserably at identifying the correct Z coord (Z in [0,20]). I think this has to do with: the blobs occupy rougly 30x30 pixels in X,Y, but only 3/4 pixels in Z (since my 3D images have to be taken with a lower resolution in Z). Moreover the algorithms apparently use isotropic gaussian filtering so the variance is the same in all directions (at a given sigma scale) according to the algorithm (Unfortunately not according to my data). Is there any reasonable/sane way to fix for this? What do you guys suggest?

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2019 John Hunter Excellence in Plotting Contest Reminder
by Nelle Varoquaux 26 Apr '19

26 Apr '19

Hi everybody, My apologies to those of you getting this on multiple lists. In memory of John Hunter, we are pleased to be announce the SciPy John Hunter Excellence in Plotting Competition for 2019. This open competition aims to highlight the importance of data visualization to scientific progress and showcase the capabilities of open source software. Participants are invited to submit scientific plots to be judged by a panel. The winning entries will be announced and displayed at the conference. John Hunter’s family and NumFocus are graciously sponsoring cash prizes for the winners in the following amounts: - 1st prize: $1000 - 2nd prize: $750 - 3rd prize: $500 - Entries must be submitted by June, 8th to the form at https://goo.gl/forms/cFTB3FUBrMPfQ7Vz1 - Winners will be announced at Scipy 2019 in Austin, TX. - Participants do not need to attend the Scipy conference. - Entries may take the definition of “visualization” rather broadly. Entries may be, for example, a traditional printed plot, an interactive visualization for the web, or an animation. - Source code for the plot must be provided, in the form of Python code and/or a Jupyter notebook, along with a rendering of the plot in a widely used format. This may be, for example, PDF for print, standalone HTML and Javascript for an interactive plot, or MPEG-4 for a video. If the original data can not be shared for reasons of size or licensing, "fake" data may be substituted, along with an image of the plot using real data. - Each entry must include a 300-500 word abstract describing the plot and its importance for a general scientific audience. - Entries will be judged on their clarity, innovation and aesthetics, but most importantly for their effectiveness in communicating a real-world problem. Entrants are encouraged to submit plots that were used during the course of research or work, rather than merely being hypothetical. - SciPy reserves the right to display any and all entries, whether prize-winning or not, at the conference, use in any materials or on its website, with attribution to the original author(s). SciPy John Hunter Excellence in Plotting Competition Co-Chairs Hannah Aizenman Thomas Caswell Madicken Munk Nelle Varoquaux

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Announcing dash-canvas: interactive annotations & image
by Emmanuelle Gouillart 09 Apr '19

09 Apr '19

processing Reply-To: Dear list, it is my pleasure to advertise here dash-canvas, a new open-source (MIT) package for interactive annotations and image processing. dash-canvas is based on Dash, a web application framework by Plotly, the Javascript library react-sketch providing drawing capabilities, and scikit-image for processing annotations drawn by users. I hope it can be a useful tool for interactive and semi-supervized image processing workflows. The development of dash-canvas has been funded by Plotly. A gallery of examples is available on https://dash-canvas.plotly.host/Portal/. For documentation on dash-canvas, please see https://dash.plot.ly/canvas. The package is very new and still alpha. Bug reports, comments, issues and pull requests are very welcome on https://github.com/plotly/dash-canvas for the package itself or https://github.com/plotly/canvas-portal for the gallery. Suggestions for examples, demos and feature requests would be particularly appreciated. Cheers Emma

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strange style in regionprops
by richard＠rdg.cc 09 Apr '19

09 Apr '19

Hi, I am planning on contributing some changes to measure.regionprops, mainly for reducing memory usage. I have noticed a couple of really odd things with respect to coding style in this code. I am tempted to just refactor this to a more conventional style in the course of making my changes, but it looks like someone went to quite some trouble to do it this way, so I thought I would ask here first in case there is some reason for doing it like this. Firstly, the way the methods are made into property methods (i.e. what would normally be simply declared with the @property decorator) is strange. This is currently done by running through the class dir and adding the properties; more strangely the code to do this is burred in a method which also programmatically re-factors the doc strings. This method is set to run only when __debug__ is defined, which means that if python happens to be run with the -O flag, then any code which uses regionprops in the conventional manner (including all unit tests) will fail in a very confusing way. The doc string thing is also strange. All the methods in the _RegionProperties class don't actually have docstrings. The actual attribute documentation is instead in some notes inside the regionprops function. The docstring for this is programmatically pasted into the appropriate __doc__ attributes on module import with a complicated regex. -- Richard

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Re: Starting to contribute
by Genevieve Buckley 08 Apr '19

08 Apr '19

Heitor, I think these links are the astropy docs Juan referred to (the ones in the previous email took me to a "Sorry, this page does not exist" message): http://docs.astropy.org/en/stable/development/workflow/development_workflow… http://docs.astropy.org/en/stable/development/workflow/git_edit_workflow_ex… There is also a "good first issue" tag in the scikit-image issues: https://github.com/scikit-image/scikit-image/labels/good%20first%20issue Hope that helps some! On Mon, 8 Apr 2019 at 02:00, <scikit-image-request(a)python.org> wrote: > Send scikit-image mailing list submissions to > scikit-image(a)python.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.python.org/mailman3/lists/scikit-image.python.org/ > or, via email, send a message with subject or body 'help' to > scikit-image-request(a)python.org > > You can reach the person managing the list at > scikit-image-owner(a)python.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of scikit-image digest..." > > Today's Topics: > > 1. Re: Starting to contribute (Juan Nunez-Iglesias) > > > ---------------------------------------------------------------------- > > Date: Sat, 6 Apr 2019 23:38:51 -0400 > From: Juan Nunez-Iglesias <jni(a)fastmail.com> > Subject: [scikit-image] Re: Starting to contribute > To: "Mailing list for scikit-image (http://scikit-image.org)" > <scikit-image(a)python.org> > Message-ID: <84BD86AF-0ADC-4D9B-887A-32D25F669258(a)fastmail.com> > Content-Type: multipart/alternative; > boundary="Apple-Mail=_E545562F-EEA5-47A4-AB1A-E38BE531237D" > > > --Apple-Mail=_E545562F-EEA5-47A4-AB1A-E38BE531237D > Content-Transfer-Encoding: quoted-printable > Content-Type: text/plain; > charset=utf-8 > > Hi Heitor, > > We have a contributing guide here: > > http://scikit-image.org/docs/stable/contribute.html = > <http://scikit-image.org/docs/stable/contribute.html> > > If you have never contributed to open source, though, someone recently = > pointed me to the Astropy contributor guide as the gold standard, and I = > have to agree. I highly recommend reading through the whole thing. The = > process is very similar across the whole ecosystem. > > = > http://docs.astropy.org/en/stable/development/workflow/development_workflo= > w.html > <http://docs.astropy.org/en/stable/development/workflow/development_workflo=…> > = > < > http://docs.astropy.org/en/stable/development/workflow/development_workfl= > ow.html > <http://docs.astropy.org/en/stable/development/workflow/development_workfl=o…> > > > > specifically the worked example: > > = > http://docs.astropy.org/en/stable/development/workflow/git_edit_workflow_e= > xamples.html#astropy-fix-example > <http://docs.astropy.org/en/stable/development/workflow/git_edit_workflow_e=…> > = > < > http://docs.astropy.org/en/stable/development/workflow/git_edit_workflow_= > examples.html#astropy-fix-example > <http://docs.astropy.org/en/stable/development/workflow/git_edit_workflow_=e…> > > > > Juan. > > > On 6 Apr 2019, at 8:43 am, Heitor Boschirolli = > <heitor.boschirolli(a)gmail.com> wrote: > >=20 > > meant* > >=20 > > Em s=C3=A1b, 6 de abr de 2019 =C3=A0s 09:30, Heitor Boschirolli = > <heitor.boschirolli(a)gmail.com <mailto:heitor.boschirolli@gmail.com>> = > escreveu: > > I'm really sorry (I sent both emails), I meat scikit-image... = > (reaaaaly sorry) > >=20 > > Em s=C3=A1b, 6 de abr de 2019 =C3=A0s 09:28, Emmanuelle Gouillart = > <emmanuelle.gouillart(a)normalesup.org = > <mailto:emmanuelle.gouillart@normalesup.org>> escreveu: > > Hi Heitor, > >=20 > > you mention scikit-learn and this is the mailing-list for = > scikit-image, > > which package would you like to contribute to, scikit-learn or > > scikit-image? The mailing list for scikit-learn is > > scikit-learn(a)python.org <mailto:scikit-learn@python.org>. > >=20 > > Best > > Emma > >=20 > > On Sat, Apr 06, 2019 at 09:04:26AM -0300, Heitor Boschirolli wrote: > > > Hello! > >=20 > > > I would like to start to contribute to scikit-learn, I never = > contributed to > > > open-source code before, and I'm not sure if that's a problem. > >=20 > > > I'm reeealy sorry if that the wrong address to contact you for = > contributions > > > btw. > >=20 > > > Best regards, Heitor Boschirolli c: > >=20 > > > _______________________________________________ > > > scikit-image mailing list -- scikit-image(a)python.org = > <mailto:scikit-image@python.org> > > > To unsubscribe send an email to scikit-image-leave(a)python.org = > <mailto:scikit-image-leave@python.org> > > _______________________________________________ > > scikit-image mailing list -- scikit-image(a)python.org = > <mailto:scikit-image@python.org> > > To unsubscribe send an email to scikit-image-leave(a)python.org = > <mailto:scikit-image-leave@python.org> > > _______________________________________________ > > scikit-image mailing list -- scikit-image(a)python.org > > To unsubscribe send an email to scikit-image-leave(a)python.org > > > --Apple-Mail=_E545562F-EEA5-47A4-AB1A-E38BE531237D > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; > charset=utf-8 > > <html><head><meta http-equiv=3D"Content-Type" content=3D"text/html; = > charset=3Dutf-8"></head><body style=3D"word-wrap: break-word; = > -webkit-nbsp-mode: space; line-break: after-white-space;" class=3D"">Hi = > Heitor,<div class=3D""><br class=3D""></div><div class=3D"">We have a = > contributing guide here:</div><div class=3D""><br class=3D""></div><div = > class=3D""><a href=3D"http://scikit-image.org/docs/stable/contribute.html > "= > = > class=3D"">http://scikit-image.org/docs/stable/contribute.html > </a></div><d= > iv class=3D""><br class=3D""></div><div class=3D"">If you have never = > contributed to open source, though, someone recently pointed me to the = > Astropy contributor guide as the gold standard, and I have to agree. I = > highly recommend reading through the whole thing. The process is very = > similar across the whole ecosystem.</div><div class=3D""><br = > class=3D""></div><div class=3D""><a = > href=3D" > http://docs.astropy.org/en/stable/development/workflow/development= > _workflow.html > <http://docs.astropy.org/en/stable/development/workflow/development=_workflo…>" > = > class=3D""> > http://docs.astropy.org/en/stable/development/workflow/developm= > ent_workflow.html > <http://docs.astropy.org/en/stable/development/workflow/developm=ent_workflo…></a></div><div > class=3D""><br class=3D""></div><div = > class=3D"">specifically the worked example:</div><div class=3D""><br = > class=3D""></div><div class=3D""><a = > href=3D" > http://docs.astropy.org/en/stable/development/workflow/git_edit_wo= > rkflow_examples.html#astropy-fix-example > <http://docs.astropy.org/en/stable/development/workflow/git_edit_wo=rkflow_e…>" > = > class=3D""> > http://docs.astropy.org/en/stable/development/workflow/git_edit= > _workflow_examples.html#astropy-fix-example > <http://docs.astropy.org/en/stable/development/workflow/git_edit=_workflow_e…></a></div><div > class=3D""><br = > class=3D""></div><div class=3D"">Juan.<br class=3D""><div><br = > class=3D""><blockquote type=3D"cite" class=3D""><div class=3D"">On 6 Apr = > 2019, at 8:43 am, Heitor Boschirolli <<a = > href=3D"mailto:heitor.boschirolli@gmail.com" = > class=3D"">heitor.boschirolli(a)gmail.com</a>> wrote:</div><br = > class=3D"Apple-interchange-newline"><div class=3D""><div dir=3D"ltr" = > class=3D"">meant*</div><br class=3D""><div class=3D"gmail_quote"><div = > dir=3D"ltr" class=3D"gmail_attr">Em s=C3=A1b, 6 de abr de 2019 =C3=A0s = > 09:30, Heitor Boschirolli <<a = > href=3D"mailto:heitor.boschirolli@gmail.com" = > class=3D"">heitor.boschirolli(a)gmail.com</a>> escreveu:<br = > class=3D""></div><blockquote class=3D"gmail_quote" style=3D"margin:0px = > 0px 0px 0.8ex;border-left:1px solid = > rgb(204,204,204);padding-left:1ex"><div dir=3D"ltr" class=3D"">I'm = > really sorry (I sent both emails), I meat scikit-image... (reaaaaly = > sorry)</div><br class=3D""><div class=3D"gmail_quote"><div dir=3D"ltr" = > class=3D"gmail_attr">Em s=C3=A1b, 6 de abr de 2019 =C3=A0s 09:28, = > Emmanuelle Gouillart <<a = > href=3D"mailto:emmanuelle.gouillart@normalesup.org" target=3D"_blank" = > class=3D"">emmanuelle.gouillart(a)normalesup.org</a>> escreveu:<br = > class=3D""></div><blockquote class=3D"gmail_quote" style=3D"margin:0px = > 0px 0px 0.8ex;border-left:1px solid = > rgb(204,204,204);padding-left:1ex">Hi Heitor,<br class=3D""> > <br class=3D""> > you mention scikit-learn and this is the mailing-list for = > scikit-image,<br class=3D""> > which package would you like to contribute to, scikit-learn or<br = > class=3D""> > scikit-image? The mailing list for scikit-learn is<br class=3D""> > <a href=3D"mailto:scikit-learn@python.org" target=3D"_blank" = > class=3D"">scikit-learn(a)python.org</a>.<br class=3D""> > <br class=3D""> > Best<br class=3D""> > Emma<br class=3D""> > <br class=3D""> > On Sat, Apr 06, 2019 at 09:04:26AM -0300, Heitor Boschirolli wrote:<br = > class=3D""> > > Hello!<br class=3D""> > <br class=3D""> > > I would like to start to contribute to scikit-learn, I never = > contributed to<br class=3D""> > > open-source code before, and I'm not sure if that's a problem.<br = > class=3D""> > <br class=3D""> > > I'm reeealy sorry if that the wrong address to contact you for = > contributions<br class=3D""> > > btw.<br class=3D""> > <br class=3D""> > > Best regards, Heitor Boschirolli c:<br class=3D""> > <br class=3D""> > > _______________________________________________<br class=3D""> > > scikit-image mailing list -- <a = > href=3D"mailto:scikit-image@python.org" target=3D"_blank" = > class=3D"">scikit-image(a)python.org</a><br class=3D""> > > To unsubscribe send an email to <a = > href=3D"mailto:scikit-image-leave@python.org" target=3D"_blank" = > class=3D"">scikit-image-leave(a)python.org</a><br class=3D""> > _______________________________________________<br class=3D""> > scikit-image mailing list -- <a href=3D"mailto:scikit-image@python.org" = > target=3D"_blank" class=3D"">scikit-image(a)python.org</a><br class=3D""> > To unsubscribe send an email to <a = > href=3D"mailto:scikit-image-leave@python.org" target=3D"_blank" = > class=3D"">scikit-image-leave(a)python.org</a><br class=3D""> > </blockquote></div> > </blockquote></div> > _______________________________________________<br class=3D"">scikit-image= > mailing list -- <a href=3D"mailto:scikit-image@python.org" = > class=3D"">scikit-image(a)python.org</a><br class=3D"">To unsubscribe send = > an email to <a href=3D"mailto:scikit-image-leave@python.org" = > class=3D"">scikit-image-leave(a)python.org</a><br = > class=3D""></div></blockquote></div><br class=3D""></div></body></html>= > > --Apple-Mail=_E545562F-EEA5-47A4-AB1A-E38BE531237D-- > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > scikit-image mailing list -- scikit-image(a)python.org > To unsubscribe send an email to scikit-image-leave(a)python.org > > > ------------------------------ > > End of scikit-image Digest, Vol 31, Issue 1 > ******************************************* >

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Starting to contribute
by Heitor Boschirolli 07 Apr '19

07 Apr '19

Hello! I would like to start to contribute to scikit-learn, I never contributed to open-source code before, and I'm not sure if that's a problem. I'm reeealy sorry if that the wrong address to contact you for contributions btw. Best regards, Heitor Boschirolli c:

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