Mailman 3 March 2017 - scikit-image

Re: [scikit-image] Request to try a GitHub integration for automatic code style review | "PEP8Speaks"
by Stefan van der Walt 20 Mar '17

20 Mar '17

This also came across my radar today: https://landscape.io/ Stéfan On Mon, Mar 20, 2017, at 14:33, Stefan van der Walt wrote: > Hi Himanshu > > On Mon, Mar 20, 2017, at 12:24, Himanshu Mishra wrote: >> I am not sure if this is the right place to talk about it, but a lot >> of times I have witnessed reviewers leave a little comment after >> reviewing the whole PR, and it is more or less about "some style >> issues. :)". It should be better for the reviewer to focus more on >> the implementation of the PR and leave the style issues to a bot. >> Thinking this in mind, a while ago, I created a Github Integration >> called PEP8 Speaks which automatically reviews the code style and >> comments on the Pull Request. It is written in Python and is open >> source. Github - https://github.com/orkohunter/pep8speaks > > I've been wanting to put something like this in place for a while; so, > if you're willing to help out, we'd be grateful. > > We've also looked at Code Climate before; do you know how your > proposed solution compares? > > Thanks! > Stéfan >

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Re: [scikit-image] Request to try a GitHub integration for automatic code style review | "PEP8Speaks"
by Stefan van der Walt 20 Mar '17

20 Mar '17

Hi Himanshu On Mon, Mar 20, 2017, at 12:24, Himanshu Mishra wrote: > I am not sure if this is the right place to talk about it, but a lot > of times I have witnessed reviewers leave a little comment after > reviewing the whole PR, and it is more or less about "some style > issues. :)". It should be better for the reviewer to focus more on the > implementation of the PR and leave the style issues to a bot. Thinking > this in mind, a while ago, I created a Github Integration called PEP8 > Speaks which automatically reviews the code style and comments on the > Pull Request. It is written in Python and is open source. Github - > https://github.com/orkohunter/pep8speaks I've been wanting to put something like this in place for a while; so, if you're willing to help out, we'd be grateful. We've also looked at Code Climate before; do you know how your proposed solution compares? Thanks! Stéfan

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Request to try a GitHub integration for automatic code style review | "PEP8Speaks"
by Himanshu Mishra 20 Mar '17

20 Mar '17

Hello everyone, I had made small contributions to scikit-image during January 2016 during my initial days of learning Image Processing. It was really fun and I am thankful to the community. I am not sure if this is the right place to talk about it, but a lot of times I have witnessed reviewers leave a little comment after reviewing the whole PR, and it is more or less about "some style issues. :)". It should be better for the reviewer to focus more on the implementation of the PR and leave the style issues to a bot. Thinking this in mind, a while ago, I created a Github Integration called PEP8 Speaks which automatically reviews the code style and comments on the Pull Request. It is written in Python and is open source. Github - https://github.com/orkohunter/pep8speaks Few pointers about it: 1. The bot puts all its efforts in not being annoying. It makes a single comment (within seconds), and keeps updating it as the user updates the PR. 2. It supports all of the configurations of pycodestyle (formerly known as pep8)[1]. So, line length, specific error ignores, etc. are all possible and can be customized. 3. The bot upon asking, can suggest a diff of changes and/or create a PR against that branch with the fixes. Few users of the integration include SunPy and scikit-learn-contrib. I would appreciate any feedback from the scikit-image community about the idea or the integration. Keenly looking forward to the discussion. [1]. https://github.com/PyCQA/pycodestyle Thank you. -- Himanshu Mishra Third Year Undergraduate Mathematics and Computing IIT Kharagpur https://orkohunter.net

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Warning from view_as_blocks
by Carlton Banks 15 Mar '17

15 Mar '17

I am currently using view_as_blocks to extract sub matrices from a bigger matrices, these submatrices has to non-overlapping. but i am getting this error: /usr/local/lib/python2.7/dist-packages/skimage/util/shape.py:94: RuntimeWarning: Cannot provide views on a non-contiguous input array without copying. warn(RuntimeWarning("Cannot provide views on a non-contiguous input " Something i should be worried about?

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Re: [scikit-image] Regarding RGSoC'17
by Juan Nunez-Iglesias 10 Mar '17

10 Mar '17

Hi Soha, Sorry for the delay in responding. Are you asking about what you can do as a project, or a small task to make a contribution to include in your application? For the project task, please look at our two papers, which include some ideas for a roadmap. For a small task, you can look at our github issues list, as well as image analysis questions on stack overflow for Python. Many of them contain great ideas for documentation improvements! Juan. On 8 Mar 2017, 1:11 AM +1100, Soha Midha <sohamidha(a)gmail.com>, wrote: > Hi, > > Good Evening! > My team applying for the RGSoC'17. We are interested in the project scikit-image. We understand and can write code in Python and have been learning Python past one month. Also we have already worked with Image Processing Toolbox of MATLAB in one of our project (implemented a code for Finger Vein Recognition Based on a Personalized Best Bit Map) and are familiar with the various terminologies used in image analysis with 2-D images. There are various resources to learn as mentioned in the project page of RGSoC ,so, it won't be difficult t pick up this project .But there are so many tasks, it's kind of difficult to choose a focused goal that could be completed in three months. > Can anyone please guide me what tasks and features are best suited for us? > > Thanks, > Soha Midha > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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IPTA
by Marianne Corvellec 09 Mar '17

09 Mar '17

Hello, Only lurking on this list and in the world of image processing... By any chance, do some scikit-image folks participate in http://www.ipta-conference.com/ipta17/ ? Thank you, Marianne

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Regarding RGSoC'17
by Soha Midha 07 Mar '17

07 Mar '17

Hi, Good Evening! My team applying for the RGSoC'17. We are interested in the project scikit-image. We understand and can write code in Python and have been learning Python past one month. Also we have already worked with Image Processing Toolbox of MATLAB in one of our project (implemented a code for Finger Vein Recognition Based on a Personalized Best Bit Map) and are familiar with the various terminologies used in image analysis with 2-D images. There are various resources to learn as mentioned in the project page of RGSoC ,so, it won't be difficult t pick up this project .But there are so many tasks, it's kind of difficult to choose a focused goal that could be completed in three months. Can anyone please guide me what tasks and features are best suited for us? Thanks, Soha Midha

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Docathon starting tomorrow
by Stefan van der Walt 05 Mar '17

05 Mar '17

Hi, everyone A reminder that the Docathon starts tomorrow, 6 March. Please join us by improving the documentation for your favorite function, adding an example to the gallery, or helping with the docs tooling for scikit-image. https://bids.github.io/docathon/pages/projects/scikit-image.html Please prefix all documentation commits with "DOC:" so that we can get ahead in the leaderboard :) Best regards Stéfan

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Re: [scikit-image] Converting RGB values from pandas dataframe to LAB
by Juan Nunez-Iglesias 05 Mar '17

05 Mar '17

Hi Michael, You can use the `.values` property to get a NumPy array out of a pandas DataFrame. After that it’s just a matter of slight reshaping to make skimage think that it’s a long, thin image. =) ======================================== In [1]: x = np.array([[0, 0, 255], [55, 0, 25], [4, 0, 5]]).astype(np.uint8) In [2]: from skimage import img_as_float, color In [12]: x = img_as_float(x) In [15]: df = pd.DataFrame(dict(RGB_r=x[:, 0], RGB_g=x[:, 1], RGB_b=x[:, 2])) In [16]: df[['RGB_r', 'RGB_g', 'RGB_b']].values Out[16]: array([[ 0. , 0. , 1. ], [ 0.21568627, 0. , 0.09803922], [ 0.01568627, 0. , 0.01960784]]) In [17]: lab = color.rgb2lab(df[['RGB_r', 'RGB_g’, 'RGB_b']].values[np.newaxis])[0] In [18]: lab Out[18]: array([[ 32.29567257, 79.18559091, -107.85730021], [ 7.97293614, 28.7263062 , -0.51735934], [ 0.33216914, 1.74121634, -1.52356365]]) In [19]: df['Lab_l'], df['Lab_a'], df['Lab_b'] = lab.T In [20]: df Out[20]: RGB_b RGB_g RGB_r Lab_l Lab_a Lab_b 0 1.000000 0.0 0.000000 32.295673 79.185591 -107.857300 1 0.098039 0.0 0.215686 7.972936 28.726306 -0.517359 2 0.019608 0.0 0.015686 0.332169 1.741216 -1.523564 ======================================== Just make sure your RGB values are in the right data type and range for scikit-image: http://scikit-image.org/docs/dev/user_guide/data_types.html Typically that means uint8s in [0, 255] or floats in [0, 1]. Hope this helps! Juan. On 4 Mar 2017, 1:44 AM +1100, Michael O'Brien <mob.irl(a)gmail.com>, wrote: > Hi all, > > I was hoping the community may be able to help me. I want to convert rgb values to their L*A*B* value but I'm not sure of the best way to do so so the setup will scale when the dataframe size increases. > > I saw on stackoverflow that skimage's conversion method http://scikit-image.org/docs/dev/api/skimage.color.html?highlight=rgb2lab#s… was suggested to be faster than alternatives but I'm having trouble understanding how to use my dataframe as the input instead of an image and if the conversion is successful how I can store the LAB values back into the dataframe. At the moment my dataframe has a shape > > (827, 8) where Rgb_r, Rgb_g, Rgb_b are the column names I'm interested in, you could think of the dataframe of 827 individual pixels with associated metadata. > > Is it possible to pass a pandas dataframe to scikit-image color.rgb2.lab or should I do row by row calculates for the situation where the number of rows increases to possibly 200,000 or more > > Hope you can help me > > Michael > _______________________________________________ > scikit-image mailing list > scikit-image(a)python.org > https://mail.python.org/mailman/listinfo/scikit-image

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Converting RGB values from pandas dataframe to LAB
by Michael O'Brien 03 Mar '17

03 Mar '17

Hi all, I was hoping the community may be able to help me. I want to convert rgb values to their L*A*B* value but I'm not sure of the best way to do so so the setup will scale when the dataframe size increases. I saw on stackoverflow that skimage's conversion method http://scikit-image.org/docs/dev/api/skimage.color.html?highlight=rgb2lab#s… was suggested to be faster than alternatives but I'm having trouble understanding how to use my dataframe as the input instead of an image and if the conversion is successful how I can store the LAB values back into the dataframe. At the moment my dataframe has a shape (827, 8) where Rgb_r, Rgb_g, Rgb_b are the column names I'm interested in, you could think of the dataframe of 827 individual pixels with associated metadata. Is it possible to pass a pandas dataframe to scikit-image color.rgb2.lab or should I do row by row calculates for the situation where the number of rows increases to possibly 200,000 or more Hope you can help me Michael

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