From mael.primet at gmail.com Wed Oct 27 16:43:42 2010 From: mael.primet at gmail.com (mael) Date: Wed, 27 Oct 2010 13:43:42 -0700 (PDT) Subject: denoising algorithms / working with Github In-Reply-To: References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> Message-ID: <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Hello, I had lots of things to do lately, haven't had much time to work on the library, but I'll do it quickly, here are the new things: http://github.com/maelp/scikits.image (some new filters, and some nice zooms) here are other projects that I work on in parallel, and I'd be happy to have some contribution: - image viewer: this should become the image viewer of scikits.image in our opinion (although it is not yet complete). Basically, it is a modulable efficient viewer, that handles zoom properly, displays level lines, etc and should be easily extensible. This is only a stub yet, and I'd be happy to merge it with your viewer, in particular have the threaded computations to have faster computations, and add the histrograms, normalization, etc. It can show grey and color int / float images, and should be pretty fast even for large images since it only computes the strictly required part that is needed to be viewed, and has a cache to speed-up the next recomputations (if you move the view a little, most of the rendered image does not change, and it only recomputes what needs be ) - tutorial: http://github.com/maelp/tutorial This should become a standard way to describe scikits.image algorithms in a dynamic way (this is basically the Qt Webkit that has been extended to include scikits.image algorithm) This could be a good advantage of the library: it is often difficult to find interactive use-case for algorithms, etc, and many times, old algorithms aren't properly documented, or we don't know in which case they do and don't apply. If we have a standard "documentation" in interactive format (where people can try our algorithms, have a mathematical presentation, upload their images etc) this will help keep up with a large image library. I made it such that it is visually attractive because I'm pretty sure this is extremely important (have beautiful documentation ) I will add new filters to the library soon, please give some inputs on the new projects and feel free to extend and/or modify anything I haven't had time to properly document everything yet, I'll do that soon From mael.primet at gmail.com Wed Oct 27 16:44:30 2010 From: mael.primet at gmail.com (mael) Date: Wed, 27 Oct 2010 13:44:30 -0700 (PDT) Subject: denoising algorithms / working with Github In-Reply-To: <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: <237cdc4a-be45-4a30-a591-f9b3948f8c87@d8g2000yqf.googlegroups.com> Of course the viewer is stored here http://github.com/maelp/viewer On Oct 27, 10:43?pm, mael wrote: > Hello, > > I had lots of things to do lately, haven't had much time to work on > the library, but > I'll do it quickly, > > here are the new things:http://github.com/maelp/scikits.image > (some new filters, and some nice zooms) > > here are other projects that I work on in parallel, and I'd be happy > to have some contribution: > - image viewer: this should become the image viewer of scikits.image > in our ?opinion (although it is not yet complete). Basically, it is a > modulable efficient viewer, that handles zoom properly, displays level > lines, etc and should be easily extensible. This is only ?a stub yet, > and I'd be happy to merge it with your viewer, in particular have the > threaded computations to have faster computations, and add the > histrograms, normalization, etc. > It can show grey and color ? int / float images, and should be pretty > fast even for large images since it only computes the strictly > required part that is needed to be viewed, and has a cache to speed-up > the next recomputations (if you move the view a little, most of the > rendered image does not change, and it only recomputes what ?needs > be ? ?) > > - tutorial:http://github.com/maelp/tutorial > This should become a standard way to describe scikits.image algorithms > in a dynamic way (this is basically the Qt Webkit that has been > extended to include scikits.image algorithm) > This could be a good advantage of the library: it is often difficult > to find interactive use-case for algorithms, etc, and many times, old > algorithms aren't properly documented, or we don't know in which case > they do and don't apply. If we have a standard "documentation" in > interactive format (where people can try our algorithms, have a > mathematical presentation, upload their images etc) this will help > keep ?up ?with a large image library. > I made it such that it is visually attractive because I'm pretty sure > this is extremely important (have beautiful documentation ) > > I will add new filters to the library soon, please give ?some inputs > on the ?new projects and feel free to extend and/or modify anything > > I haven't had time to properly document everything yet, I'll do that > soon From sccolbert at gmail.com Wed Oct 27 17:11:52 2010 From: sccolbert at gmail.com (Chris Colbert) Date: Wed, 27 Oct 2010 17:11:52 -0400 Subject: denoising algorithms / working with Github In-Reply-To: <237cdc4a-be45-4a30-a591-f9b3948f8c87@d8g2000yqf.googlegroups.com> References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> <237cdc4a-be45-4a30-a591-f9b3948f8c87@d8g2000yqf.googlegroups.com> Message-ID: these look really promising at first glance. I wrote Scivi in a weekend then basically never touched it again. I've been wanting to make it proper. So I will definitely take a look at your view and incorporate some of Scivi's threaded utilities. Cheers, Chris On Wed, Oct 27, 2010 at 4:44 PM, mael wrote: > Of course the viewer is stored here http://github.com/maelp/viewer > > On Oct 27, 10:43 pm, mael wrote: > > Hello, > > > > I had lots of things to do lately, haven't had much time to work on > > the library, but > > I'll do it quickly, > > > > here are the new things:http://github.com/maelp/scikits.image > > (some new filters, and some nice zooms) > > > > here are other projects that I work on in parallel, and I'd be happy > > to have some contribution: > > - image viewer: this should become the image viewer of scikits.image > > in our opinion (although it is not yet complete). Basically, it is a > > modulable efficient viewer, that handles zoom properly, displays level > > lines, etc and should be easily extensible. This is only a stub yet, > > and I'd be happy to merge it with your viewer, in particular have the > > threaded computations to have faster computations, and add the > > histrograms, normalization, etc. > > It can show grey and color int / float images, and should be pretty > > fast even for large images since it only computes the strictly > > required part that is needed to be viewed, and has a cache to speed-up > > the next recomputations (if you move the view a little, most of the > > rendered image does not change, and it only recomputes what needs > > be ) > > > > - tutorial:http://github.com/maelp/tutorial > > This should become a standard way to describe scikits.image algorithms > > in a dynamic way (this is basically the Qt Webkit that has been > > extended to include scikits.image algorithm) > > This could be a good advantage of the library: it is often difficult > > to find interactive use-case for algorithms, etc, and many times, old > > algorithms aren't properly documented, or we don't know in which case > > they do and don't apply. If we have a standard "documentation" in > > interactive format (where people can try our algorithms, have a > > mathematical presentation, upload their images etc) this will help > > keep up with a large image library. > > I made it such that it is visually attractive because I'm pretty sure > > this is extremely important (have beautiful documentation ) > > > > I will add new filters to the library soon, please give some inputs > > on the new projects and feel free to extend and/or modify anything > > > > I haven't had time to properly document everything yet, I'll do that > > soon > -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Wed Oct 27 18:02:37 2010 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Thu, 28 Oct 2010 00:02:37 +0200 Subject: denoising algorithms / working with Github In-Reply-To: <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: Hi Mael On Wed, Oct 27, 2010 at 10:43 PM, mael wrote: > here are the new things: http://github.com/maelp/scikits.image > (some new filters, and some nice zooms) That looks really interesting. How does the zooming algorithm differ from, for example, transform.homography? That one is based on scipy.ndimage's map_coordinates. > - tutorial: http://github.com/maelp/tutorial I love this idea! I couldn't get this to work on my system, but maybe I'll check it out again when you've got a README of some sorts. > I made it such that it is visually attractive because I'm pretty sure > this is extremely important (have beautiful documentation ) Definitely. Cheers St?fan From mael.primet at gmail.com Thu Oct 28 04:57:00 2010 From: mael.primet at gmail.com (=?UTF-8?B?TWHDq2wgUHJpbWV0?=) Date: Thu, 28 Oct 2010 10:57:00 +0200 Subject: denoising algorithms / working with Github In-Reply-To: References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: Interesting, I didn't know about those functions. From what I see from the description, I'd say that my zoom has more interpolation choices (constant, bilinear, bicubic and spline 3-11) and should be more efficient, which might be critical for visualization purposes (we don't have to create the intermediate coordinates array) Could you tell me the problem with the tutorial? Have you tried running ipaper? (And you should probably install mathjax too) Is the viewer working properly? > Hi Mael > > On Wed, Oct 27, 2010 at 10:43 PM, mael wrote: >> here are the new things: http://github.com/maelp/scikits.image >> (some new filters, and some nice zooms) > > That looks really interesting. How does the zooming algorithm differ > from, for example, transform.homography? That one is based on > scipy.ndimage's map_coordinates. > >> - tutorial: http://github.com/maelp/tutorial > > I love this idea! I couldn't get this to work on my system, but maybe > I'll check it out again when you've got a README of some sorts. > >> I made it such that it is visually attractive because I'm pretty sure >> this is extremely important (have beautiful documentation ) > > Definitely. > > Cheers > St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Thu Oct 28 06:45:04 2010 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Thu, 28 Oct 2010 12:45:04 +0200 Subject: denoising algorithms / working with Github In-Reply-To: References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: Hi Ma?l On Thu, Oct 28, 2010 at 10:57 AM, Ma?l Primet wrote: > Interesting, I didn't know about those functions. From what I see from the > description, I'd say that my zoom has more interpolation choices (constant, > bilinear, bicubic and spline 3-11) and should be more efficient, which might > be critical for visualization purposes (we don't have to create the > intermediate coordinates array) It may be worth benchmarking the two. Ndimage has order 0, 1, 2 and 3 interpolation. Maintaining accurate spline interpolation routines is a sensitive task, so if we go that route we need to document everything carefully and add the necessary references. Ndimage has a big maintenance problem with spline interp. > Could you tell me the problem with the tutorial? Have you tried running > ipaper? (And you should probably install mathjax too) I did, but it required some other packages I didn't have. What is the exact procedure for generating and viewing the paper? Cheers St?fan From mael.primet at gmail.com Thu Oct 28 07:47:43 2010 From: mael.primet at gmail.com (=?UTF-8?B?TWHDq2wgUHJpbWV0?=) Date: Thu, 28 Oct 2010 13:47:43 +0200 Subject: denoising algorithms / working with Github In-Reply-To: References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: I'll try it, but adding more interpolation algorithms also means complexifying the ndimage api and that making changes to the interpolation algorithms will require changing ndimage (this might be problematic, because users will have to keep up to date with both librairies) > Hi Ma?l > > On Thu, Oct 28, 2010 at 10:57 AM, Ma?l Primet wrote: >> Interesting, I didn't know about those functions. From what I see from the >> description, I'd say that my zoom has more interpolation choices (constant, >> bilinear, bicubic and spline 3-11) and should be more efficient, which might >> be critical for visualization purposes (we don't have to create the >> intermediate coordinates array) > > It may be worth benchmarking the two. Ndimage has order 0, 1, 2 and 3 > interpolation. Maintaining accurate spline interpolation routines is > a sensitive task, so if we go that route we need to document > everything carefully and add the necessary references. Ndimage has a > big maintenance problem with spline interp. > >> Could you tell me the problem with the tutorial? Have you tried running >> ipaper? (And you should probably install mathjax too) > > I did, but it required some other packages I didn't have. What is the > exact procedure for generating and viewing the paper? > > Cheers > St?fan -------------- next part -------------- An HTML attachment was scrubbed... URL: From stefan at sun.ac.za Thu Oct 28 17:40:10 2010 From: stefan at sun.ac.za (=?ISO-8859-1?Q?St=E9fan_van_der_Walt?=) Date: Thu, 28 Oct 2010 23:40:10 +0200 Subject: denoising algorithms / working with Github In-Reply-To: References: <20100909214336.GB23543@phare.normalesup.org> <20100910125611.GA31060@phare.normalesup.org> <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: On Thu, Oct 28, 2010 at 1:47 PM, Ma?l Primet wrote: > I'll try it, but adding more interpolation algorithms also means > complexifying the ndimage api and that making changes to the interpolation > algorithms will require changing ndimage (this might be problematic, because > users will have to keep up to date with both librairies) I thought order 0, 1, 2 and 3 in ndimage corresponded to your routines? I could be mistaken! Regards St?fan From emmanuelle.gouillart at normalesup.org Sat Oct 30 17:56:39 2010 From: emmanuelle.gouillart at normalesup.org (Emmanuelle Gouillart) Date: Sat, 30 Oct 2010 23:56:39 +0200 Subject: denoising algorithms In-Reply-To: <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> References: <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> Message-ID: <20101030215639.GA30142@phare.normalesup.org> Hi Mael, thanks for all these contributions! I had a look at the new filters. I added some documentation to the existing docstrings (http://github.com/emmanuelle/scikits.image/commits/denoise), could you please check that I didn't write anything wrong? I'm planning to add tests for these denoising functions in the next few days. After the code is fully tested, I think it will be time to start to start a new branch, cherry-pick the commits corresponding to the denoising algorithms only, rebase... and ask for a merge. It's important to make sure that your work can be re-used into the main branch. As you seem to have plenty of new stuff (the viewer for example) to keep you busy, I can take care of this refactoring if you like. Concerning the tutorial, I couldn't make the demos run. I understood that Mathjax had to be installed, but the installation instructions of Mathjax did not appear very clear to me, so I did not really know where I should put it. So I guess I will also wait for some documentation from your side. The idea of an interactive tutorial that explains the algorithms and let the user execute some demo is really cool, however! Do you plan to have the tutorial on a single web server, or that users run it on their own computer? In the first case, you may use any kind of top-notch not-so-standard software such as Mathjax, but if every user has to install it, it will be more of a problem... In any case, I'm eager to know more about this tutorial project! Finally, for the viewer, I had to make a small addition to the setup.py to install the package (see my comment on github, I needed to specify the location of numpy headers). I was glad to see that you were able to code some of the features that Lionel and you really need, such as being able to flip between two images, or representing the level lines of an image. However, I know almost nothing about visualization, so I'm afraid I don't have very constructive comments about the viewer. Maybe just one remark: as a lot of scientists work interactively within the Python shell, e.g. Ipython, it is important that calls to the viewer are not blocking, i.e., that the user gets the prompt back. Cheers, Emmanuelle On Wed, Oct 27, 2010 at 01:43:42PM -0700, mael wrote: > Hello, > I had lots of things to do lately, haven't had much time to work on > the library, but > I'll do it quickly, > here are the new things: http://github.com/maelp/scikits.image > (some new filters, and some nice zooms) > here are other projects that I work on in parallel, and I'd be happy > to have some contribution: > - image viewer: this should become the image viewer of scikits.image > in our opinion (although it is not yet complete). Basically, it is a > modulable efficient viewer, that handles zoom properly, displays level > lines, etc and should be easily extensible. This is only a stub yet, > and I'd be happy to merge it with your viewer, in particular have the > threaded computations to have faster computations, and add the > histrograms, normalization, etc. > It can show grey and color int / float images, and should be pretty > fast even for large images since it only computes the strictly > required part that is needed to be viewed, and has a cache to speed-up > the next recomputations (if you move the view a little, most of the > rendered image does not change, and it only recomputes what needs > be ) > - tutorial: http://github.com/maelp/tutorial > This should become a standard way to describe scikits.image algorithms > in a dynamic way (this is basically the Qt Webkit that has been > extended to include scikits.image algorithm) > This could be a good advantage of the library: it is often difficult > to find interactive use-case for algorithms, etc, and many times, old > algorithms aren't properly documented, or we don't know in which case > they do and don't apply. If we have a standard "documentation" in > interactive format (where people can try our algorithms, have a > mathematical presentation, upload their images etc) this will help > keep up with a large image library. > I made it such that it is visually attractive because I'm pretty sure > this is extremely important (have beautiful documentation ) > I will add new filters to the library soon, please give some inputs > on the new projects and feel free to extend and/or modify anything > I haven't had time to properly document everything yet, I'll do that > soon From sccolbert at gmail.com Sun Oct 31 13:34:26 2010 From: sccolbert at gmail.com (Chris Colbert) Date: Sun, 31 Oct 2010 13:34:26 -0400 Subject: denoising algorithms In-Reply-To: References: <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> <20101030215639.GA30142@phare.normalesup.org> Message-ID: It would be nice if you made the viewer I plugin for the io framework. Plugins are *really* simple to create. Just checkout how I did the qt plugin for io.imshow(). If you follow the plugin architecture, the viewer will by default be compatible from an interactive prompt. Cheers, Chris On Sun, Oct 31, 2010 at 10:46 AM, Ma?l Primet wrote: > Hello Emmanuelle, > > thanks for your input > > I had a look at the new filters. I added some documentation to >> the existing docstrings >> (http://github.com/emmanuelle/scikits.image/commits/denoise), could you >> please check that I didn't write anything wrong? I'm planning to add >> tests for these denoising functions in the next few days. After the code >> is fully tested, I think it will be time to start to start a new branch, >> cherry-pick the commits corresponding to the denoising algorithms only, >> rebase... and ask for a merge. It's important to make sure that your work >> can be re-used into the main branch. As you seem to have plenty of new >> stuff (the viewer for example) to keep you busy, I can take care of this >> refactoring if you like. >> > Thanks this looks very good > > >> Concerning the tutorial, I couldn't make the demos run. I >> understood that Mathjax had to be installed, but the installation >> instructions of Mathjax did not appear very clear to me, so I did not >> really know where I should put it. So I guess I will also wait for some >> documentation from your side. The idea of an interactive tutorial that >> explains the algorithms and let the user execute some demo is really >> cool, however! Do you plan to have the tutorial on a single web server, >> or that users run it on their own computer? In the first case, you may >> use any kind of top-notch not-so-standard software such as Mathjax, but >> if every user has to install it, it will be more of a problem... In any >> case, I'm eager to know more about this tutorial project! >> >> Yes, sorry for the lack of documentation, I wanted it to go this way: > we distribute the webbrowser with required fonts and JS libraries that > might be used by most of > the tutorials, and they might be loaded at run-time by the browser, so > distributing new tutorials won't require also distributing (heavy!) > libraries > now, you don't need MathJax to see how the thing work, but if you want to > use it, simply uncompress it as image_denoising_tutorial/js/MathJax > to compile, you need to run the Makefile in lib/, then call ipaper.py with > the directory "image_denoising_tutorial" as argument, ie. ./ipaper.py > /path/to/image_denoising_tutorial/ > > > >> Finally, for the viewer, I had to make a small addition to the >> setup.py to install the package (see my comment on github, I needed to >> specify the location of numpy headers). I was glad to see that you were >> able to code some of the features that Lionel and you really need, such >> as being able to flip between two images, or representing the level lines >> of an image. However, I know almost nothing about visualization, so I'm >> afraid I don't have very constructive comments about the viewer. Maybe >> just one remark: as a lot of scientists work interactively within the >> Python shell, e.g. Ipython, it is important that calls to the viewer are >> not blocking, i.e., that the user gets the prompt back. >> > I included it, > > for the comments regarding this viewer: I think my zooming functions are > slightly more suited here: there are more zooms, it's faster and IMO more > convenient to use, > and most of all, the zooming code is MUCH easier to access (both in term of > understandability and ease of modification if we need to update it) than > that of ndimage, > so I'd recommend using it for the viewer. > > I'd like to add some GUI rather than having only keyboard shortcuts for the > viewer, but I created it in a modular way, such that we could build a > very simple viewer with only keyboard accelerators, that would be nice when > debugging an algorithm, or quickly looking at the result of an algorithm, > and > also embedd it in a more full-fledged application if we need a real image > viewer. > > I guess it shouldn't be too hard to return the input to the user > -------------- next part -------------- An HTML attachment was scrubbed... URL: From sccolbert at gmail.com Sun Oct 31 15:22:10 2010 From: sccolbert at gmail.com (Chris Colbert) Date: Sun, 31 Oct 2010 15:22:10 -0400 Subject: denoising algorithms In-Reply-To: References: <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> <20101030215639.GA30142@phare.normalesup.org> Message-ID: The same way you are. i.e. just recompile everything. If you are building in place, I *think* you can get away with just running the setup.py script in the directory that has changed files. But don't quote me on that. On Sun, Oct 31, 2010 at 2:54 PM, Ma?l Primet wrote: > Sure, this was the idea, however since it was easier > for me to develop the viewer as a side program, I haven't done it yet > > btw I find it hard to develop directly inside scikits.image, because each > time I compile the library, it recompiles everything, rather than the things > that changed. How do you > handle developpment of new modules.? > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mael.primet at gmail.com Sun Oct 31 10:46:02 2010 From: mael.primet at gmail.com (=?UTF-8?B?TWHDq2wgUHJpbWV0?=) Date: Sun, 31 Oct 2010 15:46:02 +0100 Subject: denoising algorithms In-Reply-To: <20101030215639.GA30142@phare.normalesup.org> References: <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> <20101030215639.GA30142@phare.normalesup.org> Message-ID: Hello Emmanuelle, thanks for your input I had a look at the new filters. I added some documentation to > the existing docstrings > (http://github.com/emmanuelle/scikits.image/commits/denoise), could you > please check that I didn't write anything wrong? I'm planning to add > tests for these denoising functions in the next few days. After the code > is fully tested, I think it will be time to start to start a new branch, > cherry-pick the commits corresponding to the denoising algorithms only, > rebase... and ask for a merge. It's important to make sure that your work > can be re-used into the main branch. As you seem to have plenty of new > stuff (the viewer for example) to keep you busy, I can take care of this > refactoring if you like. > Thanks this looks very good > Concerning the tutorial, I couldn't make the demos run. I > understood that Mathjax had to be installed, but the installation > instructions of Mathjax did not appear very clear to me, so I did not > really know where I should put it. So I guess I will also wait for some > documentation from your side. The idea of an interactive tutorial that > explains the algorithms and let the user execute some demo is really > cool, however! Do you plan to have the tutorial on a single web server, > or that users run it on their own computer? In the first case, you may > use any kind of top-notch not-so-standard software such as Mathjax, but > if every user has to install it, it will be more of a problem... In any > case, I'm eager to know more about this tutorial project! > > Yes, sorry for the lack of documentation, I wanted it to go this way: we distribute the webbrowser with required fonts and JS libraries that might be used by most of the tutorials, and they might be loaded at run-time by the browser, so distributing new tutorials won't require also distributing (heavy!) libraries now, you don't need MathJax to see how the thing work, but if you want to use it, simply uncompress it as image_denoising_tutorial/js/MathJax to compile, you need to run the Makefile in lib/, then call ipaper.py with the directory "image_denoising_tutorial" as argument, ie. ./ipaper.py /path/to/image_denoising_tutorial/ > Finally, for the viewer, I had to make a small addition to the > setup.py to install the package (see my comment on github, I needed to > specify the location of numpy headers). I was glad to see that you were > able to code some of the features that Lionel and you really need, such > as being able to flip between two images, or representing the level lines > of an image. However, I know almost nothing about visualization, so I'm > afraid I don't have very constructive comments about the viewer. Maybe > just one remark: as a lot of scientists work interactively within the > Python shell, e.g. Ipython, it is important that calls to the viewer are > not blocking, i.e., that the user gets the prompt back. > I included it, for the comments regarding this viewer: I think my zooming functions are slightly more suited here: there are more zooms, it's faster and IMO more convenient to use, and most of all, the zooming code is MUCH easier to access (both in term of understandability and ease of modification if we need to update it) than that of ndimage, so I'd recommend using it for the viewer. I'd like to add some GUI rather than having only keyboard shortcuts for the viewer, but I created it in a modular way, such that we could build a very simple viewer with only keyboard accelerators, that would be nice when debugging an algorithm, or quickly looking at the result of an algorithm, and also embedd it in a more full-fledged application if we need a real image viewer. I guess it shouldn't be too hard to return the input to the user -------------- next part -------------- An HTML attachment was scrubbed... URL: From mael.primet at gmail.com Sun Oct 31 14:54:26 2010 From: mael.primet at gmail.com (=?UTF-8?B?TWHDq2wgUHJpbWV0?=) Date: Sun, 31 Oct 2010 19:54:26 +0100 Subject: denoising algorithms In-Reply-To: References: <20100921160523.GB31763@phare.normalesup.org> <20100921193017.GE31763@phare.normalesup.org> <20100922172444.GA10153@phare.normalesup.org> <0ac62f51-486c-43d6-a360-237faca3871b@h7g2000yqn.googlegroups.com> <20101030215639.GA30142@phare.normalesup.org> Message-ID: Sure, this was the idea, however since it was easier for me to develop the viewer as a side program, I haven't done it yet btw I find it hard to develop directly inside scikits.image, because each time I compile the library, it recompiles everything, rather than the things that changed. How do you handle developpment of new modules.? -------------- next part -------------- An HTML attachment was scrubbed... URL: