Re: [discuss] R - setwd("~/Desktop") in Windows
Raniere,
Yes, I've had lots of issues similar to this one, where "~/Desktop" is
actually some other directory (not the Desktop that users "see" when they
log in). I don't know a good solution other than to ask them to keep this
folder open in a file manager. It's good to be prepared to deal with this
issue at each workshop.
Thanks,
Ashwin
On Thu, Sep 13, 2018 at 9:31 AM, Raniere Silva wrote:
> Hi all,
>
> I was teaching R yesterday and when running
>
> setwd(("~/Desktop"))
>
> the users of Windows went to "C:\Users\Foo\Documents\Desktop" instead of
> "C:\Users\Foo\Desktop".
>
> Did you see similar behaviour before?
>
> Cheers,
> Raniere
> *The Carpentries * / discuss /
> see discussions +
> participants +
> delivery
> options
> Permalink
>
>
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Re: [discuss] Slide of Joel Grus' JupyterCon Talk "I Don't Like Notebooks"
I'm very interested to see these examples? We use and advocate the use of conda environments and I'm happy to be convinced otherwise. Thanks, Ashwin On Tue, Aug 28, 2018 at 2:17 PM, Maxime Boissonneault wrote: > Regarding performance, we have example of code using Anaconda-provided > packages that run 10 times slower than the same code using locally built > packages, optimized for the cluster architectures. That's not *a bit* > slower, that's a lot slower. > > Regarding "cheating on your partner", that analogy is not by me, but the > point he is trying to carry is that Anaconda basically replaces any cluster > provided versions, which HPC center people are working hard to optimize. > Recent versions of Anaconda are even worse, by packaging things like > compilers and linkers, creating conflicts with cluster-provided system > libraries and tools, and creating a lot of debugging problems for users and > support people alike. > > Regards, > > Maxime > > > On 2018-08-28 12:48 PM, Rémi Rampin wrote: > > 2018-08-28 12:27 EDT, Maxime Boissonneault > : >> >> As a side-discussion, I think we should also be wary of using Anaconda, >> and tell users not to use it in a cluster environment. For reasons, see >> here : >> https://twitter.com/mboisso/status/1034476890353020928 > > > Hi Maxime, > > All I see in this thread is that "it's like cheating on your partner" (!!!) > and it's "generically optimized software" that might be a bit slower than > locally-built libs (interesting concern when using Python, an interpreted > scripting language (and on the slow side too)). > > Could you elaborate on those reasons? > > Best > -- > Rémi > > > The Carpentries / discuss / see discussions + participants + delivery > options Permalink -- The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/T1505f74d7f6e32f8-Mad4fadc6a6da6de2b5f2aeb9 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
Re: [discuss] Image processing with Python
Hello Carlos, My lesson on packaging/testing/documenting/performance has graduated to the following website: https://python-102.readthedocs.io/en/latest/ I will be very glad if you could update your URL to reflect the same. Any feedback on these materials is welcome and appreciated! Ashwin On Mon, Aug 20, 2018 at 11:02 AM, Carlos Martinez Ortiz wrote: > Hi all, > > > I've written it into more of a blog post format: > > > https://medium.com/@c.martinez/software-carpentry-and-image-processing-5727d2347de2 > > > Would everybody be ok for me to posting this on the eScience center blog > (https://blog.esciencecenter.nl/)? And maybe cross posting on the > carpentries blog ? > > > Cheers, > > Carlos > > > From: Tim McNamara > Sent: 16 August 2018 01:39:57 > To: discuss > Subject: Re: [discuss] Image processing with Python > > Feel free to harvest the source of this file if anyone would like to publish > something in a more visible location: > > https://git.nzoss.org.nz/tim-mcnamara/notebook/blob/master/image-processing-tutorials.md > > Tim McNamara > https://tim.mcnamara.nz | @timClicks > > > On 16 August 2018 at 11:04, Steven Haddock wrote: > > Maybe someone could collate this info into a blog post to preserve? > > -Steve > > >> On Aug 15, 2018, at 12:16 , Pablo Hernandez via discuss >> wrote: >> >> Hello all, such a good collection of resources! >> >> I would like to add the effort of the image analysis library Insight >> ToolKit (ITK) to quickly create 3D visualizations in the web and/or with >> jupyter notebooks. >> >> They are not in a lesson format, but it is promising! >> >> Here is a mybinder with all the dependencies installed: >> >> >> https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples%2F3DImage.ipynb >> >> >> https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SpecifyAColormap.ipynb >> >> >> https://mybinder.org/v2/gh/InsightSoftwareConsortium/itk-jupyter-widgets/master?filepath=examples/SelectRegionOfInterest.ipynb >> >> Based on this repo: >> https://github.com/InsightSoftwareConsortium/itk-jupyter-widgets >> >> There is also a course of Biomedical Image Analysis and Visualization: >> https://github.com/KitwareMedical/2018-05-30-KRSCourseInBiomedicalImageAnalysisAndVisualization >> >> If the user is running the notebooks locally, instead of in mybinder, we >> just need: >> `pip install --user itkwidgets` >> >> Best regards, >> Pablo >> >> >> On Wed, Aug 15, 2018 at 12:59 PM, mbgoodman via discuss >> wrote: >> Hello all, >> I am sorry I missed this thread in May. As Amy Hodge noted, we have been >> developing image processing lessons at Stanford. The first iteration was >> held in 2017 and was built by a team of Stanford grad students mentored by >> Greg Wilson. We are in the midst of updating four lessons for the next >> iteration, to be held in 2018. I need to check in with the current TA team >> about updates, but initial github repo is here: >> https://github.com/DataLucence/images >> >> I am digesting all of the other resources noted in this thread over the >> next 6 weeks. >> >> -Miriam Goodman >> >> The Carpentries / discuss / see discussions + participants + delivery >> options Permalink > > -- > The Carpentries: discuss > Permalink: > https://carpentries.topicbox.com/groups/discuss/T4240adcd25206bde-Me7b8397d57155e8c76fbf60b > Delivery options: > https://carpentries.topicbox.com/groups/discuss/subscription > > > The Carpentries / discuss / see discussions + participants + delivery > options Permalink -- The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/T4240adcd25206bde-M9d9f73eaa7bd8034dbed5593 Delivery options: https://carpentries.topicbox.com/groups/discuss/subscription
Re: [discuss] Image processing with Python
Carlos, Here's a Python tutorial focused on packaging, testing, and performance using very simple image analysis: https://github.com/clemsonciti/scientific-python I'm not sure if it's appropriate for complete novices, but I'm leaving it here in case you can salvage anything from it. Let me know if you have any questions! Thanks, Ashwin On Fri, May 25, 2018 at 7:34 AM, Carlos Martinez Ortiz wrote: > Hello! > > > Does anybody have material for an image processing lesson? I am preparing a > workshop for a group of people who will mostly be working with image > analysis and thought it might be good if I can tune the content a little bit > to make it more interesting to them. > > > Any would be most welcome. > > > Best, > > Carlos > > > | dr. Carlos Martinez-Ortiz | eScience Research Engineer | > | Netherlands eScience Center | www.esciencecenter.nl | > | Calls for Contributions IEEE eScience | > | We are proud to host | 14th IEEE International Conference on eScience 2018 > | | 29 Oct – 1 Nov 2018 | Amsterdam, the Netherlands | www.eScience2018.com > > The Carpentries / discuss / Permalink Delivery options -- The Carpentries: discuss Permalink: https://carpentries.topicbox.com/groups/discuss/discussions/T4240adcd25206bde-M1614bc7a7978daae4e299d24 Delivery options: https://carpentries.topicbox.com/groups
