Mailman 3 December 2021 - SciPy-User

How to display a RGB image (MFISH)?
by jp 03 Apr '23

03 Apr '23

Hi, I have written a script to try to combine five images into a three channels RGB images<http://dip4fish.blogspot.com/2011/05/trying-to-combine-mfish-images-into-rg…> . The resulting RGB image looks like a grey scale image instead of a color one. I have three np.array Rnorm, Gnorm, Bnorm which are copied into a rgb array: *rgb = np.zeros((shape[0],shape[1],3),dtype=float) mxr=np.max(R) mxg=np.max(G) mxb=np.max(B) Rnorm=np.uint8((255*(R/mxr)))Gnorm=np.uint8((255*(R/mxg)))Bnorm=np.uint8((255*(R/mxb)))#copy each RGB component in an RGB array rgb[:,:,0]=Rnorm rgb[:,:,1]=Gnorm rgb[:,:,2]=Bnorm* *pylab.subplot(224, aspect='equal',frameon=False, xticks=[], yticks=[]) pylab.imshow(rgb) pylab.show()* Any advice? Thank you Jean-Patrick

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Invitation to connect on LinkedIn
by Jelle Feringa via LinkedIn 28 Jul '22

28 Jul '22

LinkedIn ------------ Jelle Feringa requested to add you as a connection on LinkedIn: ------------------------------------------ Jose, I'd like to add you to my professional network on LinkedIn. - Jelle Accept invitation from Jelle Feringa http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/Q6WKH0LACopGJkAw_6fSqajo6R7VM… View invitation from Jelle Feringa http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/Q6WKH0LACopGJkAw_6fSqajo6R7VM… ------------------------------------------ DID YOU KNOW your LinkedIn profile helps you control your public image when people search for you? Setting your profile as public means your LinkedIn profile will come up when people enter your name in leading search engines. Take control of your image! http://www.linkedin.com/e/-3wy1w2-gpkzwpgn-5n/ewp/inv-22/ -- (c) 2011, LinkedIn Corporation

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Help required regding Eigenvectors
by Sudheer Phani 14 Mar '22

14 Mar '22

Hello All, I have been encountering some strange problems with the calculation of eigen vectors using python. The problem is with the sign of the eigen vectors calculated. On Very few occasions the eigen vectors calculated using python have an opposite sign than the actual eigenvectors, though the magnitude is correct. Can any one of you plz help me in this regard and suggest me some solution if you have encoutered similar problems . Any help in this regd is appreciated Thanks in Advace regds Sudheer

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ANN: SfePy 2021.4
by Robert Cimrman 29 Dec '21

29 Dec '21

I am pleased to announce the release of SfePy 2021.4. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by finite element methods. It is distributed under the new BSD license. Home page: https://sfepy.org Mailing list: https://mail.python.org/mm3/mailman3/lists/sfepy.python.org/ Git (source) repository, issue tracker: https://github.com/sfepy/sfepy Highlights of this release -------------------------- - improved pyvista-based visualization script resview.py - gallery images generated using resview.py - homogenization tools: new parallel recovery of multiple microstructures - new "dry water" flow example For full release notes see [1]. Cheers, Robert Cimrman [1] http://docs.sfepy.org/doc/release_notes.html#id1 --- Contributors to this release in alphabetical order: Robert Cimrman Yves Delley Florian Le Bourdais Vladimir Lukes Brylie Christopher Oxley Tomáš Zítka

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NumPy 1.21.5 released
by Charles R Harris 20 Dec '21

20 Dec '21

Hi All, On behalf of the NumPy team I am pleased to announce the release of NumPy 1.21.5. NumPy 1.21.5 is a maintenance release that fixes a few bugs discovered after the 1.21.4 release and does some maintenance to extend the 1.21.x lifetime. The Python versions supported in this release are 3.7-3.10. If you want to compile your own version using gcc-11, you will need to use gcc-11.2+ to avoid problems. The Python versions supported in this release are 3.7-3.10. If you want to compile your own version using gcc-11 you will need to use gcc-11.2+ to avoid problems. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.21.5/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.21.5>. Linux users will need pip >= 0.19.3 in order to install manylinux2010 and manylinux2014 wheels. A recent version of pip is needed to install the universal2 macos wheels. *Contributors* A total of 7 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - Bas van Beek - Charles Harris - Matti Picus - Rohit Goswami - Ross Barnowski - Sayed Adel - Sebastian Berg *Pull requests merged* A total of 11 pull requests were merged for this release. - #20357: MAINT: Do not forward `__(deep)copy__` calls of `_GenericAlias`\... - #20462: BUG: Fix float16 einsum fastpaths using wrong tempvar - #20463: BUG, DIST: Print os error message when the executable not exist - #20464: BLD: Verify the ability to compile C++ sources before initiating\... - #20465: BUG: Force `npymath` to respect `npy_longdouble` - #20466: BUG: Fix failure to create aligned, empty structured dtype - #20467: ENH: provide a convenience function to replace `npy_load_module` - #20495: MAINT: update wheel to version that supports python3.10 - #20497: BUG: Clear errors correctly in F2PY conversions - #20613: DEV: add a warningfilter to fix pytest workflow. - #20618: MAINT: Help boost::python libraries at least not crash Cheers, Charles Harris

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NumPy 1.22.0rc3 released
by Charles R Harris 18 Dec '21

18 Dec '21

Hi All, On behalf of the NumPy team, I'm pleased to announce the release of NumPy 1.22.0rc3. NumPy 1.22.0rc3 is a big release featuring the work of 152 contributors spread over 602 pull requests. There have been many improvements, highlights are: - Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release. - A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across applications such as CuPy and JAX. - NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data. - New methods for `quantile`, `percentile`, and related functions. Thenew methods provide a complete set of the methods commonly found in the literature. - A new configurable allocator for use by downstream projects. These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation. The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.22.0rc3/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.22.0rc3>. Linux users will need pip >= 0.19.3 in order to install the manylinux2014 wheels. A recent version of pip is needed to install the universal2 macos wheels. *Contributors* A total of 151 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - @DWesl - @Illviljan - @h-vetinari - @yan-wyb + - Aaron Meurer - Abel Aoun + - Adrian Gao + - Ahmet Can Solak + - Ajay DS + - Alban Colley + - Alberto Rubiales + - Alessia Marcolini + - Amit Kumar + - Andrei Batomunkuev + - Andrew Watson + - Anirudh Dagar + - Ankit Dwivedi + - Antony Lee - Arfy Slowy + - Arryan Singh + - Arun Palaniappen + - Arushi Sharma + - Bas van Beek - Brent Brewington + - Carl Johnsen + - Carl Michal + - Charles Harris - Chiara Marmo - Chris Fu (傅立业) + - Christoph Buchner + - Christoph Reiter + - Chunlin Fang - Clément Robert + - Constanza Fierro - Damien Caliste - Daniel Ching - David Badnar + - David Cortes + - David Okpare + - Derek Huang + - Developer-Ecosystem-Engineering + - Dima Pasechnik - Dimitri Papadopoulos + - Dmitriy Fishman + - Eero Vaher + - Elias Koromilas + - Eliaz Bobadilla + - Elisha Hollander + - Eric Wieser - Eskild Eriksen + - Evan Miller + - Fayas Noushad + - Gagandeep Singh + - Ganesh Kathiresan - Ghiles Meddour + - Greg Lucas - Gregory R. Lee - Guo Shuai + - Gwyn Ciesla + - Hameer Abbasi - Hector Martin + - Henry Schreiner + - Himanshu + - Hood Chatham + - Hugo Defois + - Hugo van Kemenade - I-Shen Leong + - Imen Rajhi + - Irina Maria Mocan + - Irit Katriel + - Isuru Fernando - Jakob Jakobson - Jerry Morrison + - Jessi J Zhao + - Joe Marshall + - Johan von Forstner + - Jonas I. Liechti + - Jonathan Reichelt Gjertsen + - Joshua Himmens + - Jérome Eertmans - Jérôme Kieffer + - KIU Shueng Chuan + - Kazuki Sakamoto + - Kenichi Maehashi - Kenny Huynh + - Kent R. Spillner + - Kevin Granados + - Kevin Modzelewski + - Kevin Sheppard - Lalit Musmade + - Malik Idrees Hasan Khan + - Marco Aurelio da Costa + - Margret Pax + - Mars Lee + - Marten van Kerkwijk - Matthew Barber + - Matthew Brett - Matthias Bussonnier - Matthieu Dartiailh - Matti Picus - Melissa Weber Mendonça - Michael McCann + - Mike Jarvis + - Mike McCann + - Mike Toews - Mukulika Pahari - Nick Pope + - Nick Wogan + - Niels Dunnewind + - Niko Savola + - Nikola Forró - Niyas Sait + - Pamphile ROY - Paul Ganssle + - Pauli Virtanen - Pearu Peterson - Peter Hawkins + - Peter Tillema + - Prathmesh Shirsat + - Raghuveer Devulapalli - Ralf Gommers - Robert Kern - Rohit Goswami + - Ronan Lamy - Ross Barnowski - Roy Jacobson + - Samyak S Sarnayak + - Sayantika Banik + - Sayed Adel - Sebastian Berg - Sebastian Schleehauf + - Serge Guelton - Shriraj Hegde + - Shubham Gupta + - Sista Seetaram + - Stefan van der Walt - Stephannie Jimenez Gacha + - Tania Allard - Theodoros Nikolaou + - Thomas J. Fan - Thomas Li + - Tim Hoffmann - Tom Tan + - Tyler Reddy - Vijay Arora + - Vinith Kishore + - Warren Weckesser - Yang Hau - Yashasvi Misra - Yuval Ofek + - Zac Hatfield-Dodds - Zhang Na + Cheers, Charles Harris

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NumPy 1.22. 0rc2 Release
by Charles R Harris 11 Dec '21

11 Dec '21

Hi All, On behalf of the NumPy team, I'm pleased to announce the release of NumPy 1.22.0rc1. NumPy 1.22.0rc1 is a big release featuring the work of 151 contributers spread over 589 pull requests. There have been many improvements, highlights are: - Annotations of the main namespace are essentially complete. Upstream is a moving target, so there will likely be further improvements, but the major work is done. This is probably the most user visible enhancement in this release. - A preliminary version of the proposed Array-API is provided. This is a step in creating a standard collection of functions that can be used across applications such as CuPy and JAX. - NumPy now has a DLPack backend. DLPack provides a common interchange format for array (tensor) data. - New methods for `quantile`, `percentile`, and related functions. Thenew methods provide a complete set of the methods commonly found in the literature. - A new configurable allocator for use by downstream projects. These are in addition to the ongoing work to provide SIMD support for commonly used functions, improvements to F2PY, and better documentation. The Python versions supported in this release are 3.8-3.10, Python 3.7 has been dropped. Note that 32 bit wheels are only provided for Python 3.8 and 3.9 on Windows, all other wheels are 64 bits on account of Ubuntu, Fedora, and other Linux distributions dropping 32 bit support. All 64 bit wheels are also linked with 64 bit integer OpenBLAS, which should fix the occasional problems encountered by folks using truly huge arrays. Wheels can be downloaded from PyPI <https://pypi.org/project/numpy/1.22.0rc2/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.22.0rc2>. Linux users will need pip >= 0.19.3 in order to install the manylinux2014 wheels. A recent version of pip is needed to install the universal2 macos wheels. *Contributors* A total of 151 people contributed to this release. People with a "+" by their names contributed a patch for the first time. - @DWesl - @Illviljan - @h-vetinari - @yan-wyb + - Aaron Meurer - Abel Aoun + - Adrian Gao + - Ahmet Can Solak + - Ajay DS + - Alban Colley + - Alberto Rubiales + - Alessia Marcolini + - Amit Kumar + - Andrei Batomunkuev + - Andrew Watson + - Anirudh Dagar + - Ankit Dwivedi + - Antony Lee - Arfy Slowy + - Arryan Singh + - Arun Palaniappen + - Arushi Sharma + - Bas van Beek - Brent Brewington + - Carl Johnsen + - Carl Michal + - Charles Harris - Chiara Marmo - Chris Fu (傅立业) + - Christoph Buchner + - Christoph Reiter + - Chunlin Fang - Clément Robert + - Constanza Fierro - Damien Caliste - Daniel Ching - David Badnar + - David Cortes + - David Okpare + - Derek Huang + - Developer-Ecosystem-Engineering + - Dima Pasechnik - Dimitri Papadopoulos + - Dmitriy Fishman + - Eero Vaher + - Elias Koromilas + - Eliaz Bobadilla + - Elisha Hollander + - Eric Wieser - Eskild Eriksen + - Evan Miller + - Fayas Noushad + - Gagandeep Singh + - Ganesh Kathiresan - Ghiles Meddour + - Greg Lucas - Gregory R. Lee - Guo Shuai + - Gwyn Ciesla + - Hameer Abbasi - Hector Martin + - Henry Schreiner + - Himanshu + - Hood Chatham + - Hugo Defois + - Hugo van Kemenade - I-Shen Leong + - Imen Rajhi + - Irina Maria Mocan + - Irit Katriel + - Isuru Fernando - Jakob Jakobson - Jerry Morrison + - Jessi J Zhao + - Joe Marshall + - Johan von Forstner + - Jonas I. Liechti + - Jonathan Reichelt Gjertsen + - Joshua Himmens + - Jérome Eertmans - Jérôme Kieffer + - KIU Shueng Chuan + - Kenichi Maehashi - Kenny Huynh + - Kent R. Spillner + - Kevin Granados + - Kevin Modzelewski + - Kevin Sheppard - Lalit Musmade + - Malik Idrees Hasan Khan + - Marco Aurelio da Costa + - Margret Pax + - Mars Lee + - Marten van Kerkwijk - Matthew Barber + - Matthew Brett - Matthias Bussonnier - Matthieu Dartiailh - Matti Picus - Melissa Weber Mendonça - Michael McCann + - Mike Jarvis + - Mike McCann + - Mike Toews - Mukulika Pahari - Nick Pope + - Nick Wogan + - Niels Dunnewind + - Niko Savola + - Nikola Forró - Niyas Sait + - Pamphile ROY - Paul Ganssle + - Pauli Virtanen - Pearu Peterson - Peter Hawkins + - Peter Tillema + - Prathmesh Shirsat + - Raghuveer Devulapalli - Ralf Gommers - Robert Kern - Rohit Goswami + - Ronan Lamy - Ross Barnowski - Roy Jacobson + - Samyak S Sarnayak + - Sayantika Banik + - Sayed Adel - Sebastian Berg - Sebastian Schleehauf + - Serge Guelton - Shriraj Hegde + - Shubham Gupta + - Sista Seetaram + - Stefan van der Walt - Stephannie Jimenez Gacha + - Tania Allard - Theodoros Nikolaou + - Thomas J. Fan - Thomas Li + - Tim Hoffmann - Tom Tan + - Tyler Reddy - Vijay Arora + - Vinith Kishore + - Warren Weckesser - Yang Hau - Yashasvi Misra - Yuval Ofek + - Zac Hatfield-Dodds - Zhang Na + Cheers, Charles Harris

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ANN: scikit-image 0.19.0
by Gregory Lee 04 Dec '21

04 Dec '21

*We’re happy to announce scikit-image v0.19.0!* scikit-image is an image processing toolbox for SciPy that includes algorithms for segmentation, geometric transformations, color space manipulation, analysis, filtering, morphology, feature detection, and more. For more information, examples, and documentation, please visit our website: https://scikit-image.org A highlight of this release is the addition of the popular scale-invariant feature transform (SIFT) feature detector and descriptor. This release also introduces a perceptual blur metric, new pixel graph algorithms, and most functions now operate in single-precision when single-precision inputs are provided. Many other bug fixes, enhancements and performance improvements are detailed below. A significant change in this release is in the treatment of multichannel images. The existing multichannel argument to functions has been deprecated in favor of a new channel_axis argument. channel_axis can be used to specify which axis of an array contains channel information (with channel_axis=None indicating a grayscale image). scikit-image now uses “lazy loading”, which enables users to access the functions from all skimage submodules without the overhead of eagerly importing all submodules. As a concrete example, after calling “import skimage” a user can directly call a function such as skimage.transform.warp whereas previously it would have been required to first “import skimage.transform”. An exciting change on the development side is the introduction of support for Pythran as an alternative to Cython for generating compiled code. We plan to keep Cython support as well going forward, so developers are free to use either one as appropriate. For those curious about Pythran, a good overview was given in the SciPy 2021 presentation, “Building SciPy Kernels with Pythran” (Building SciPy Kernels with Pythran | SciPy 2021 - YouTube <https://www.youtube.com/watch?v=6a9D9WL6ZjQ>). This release supports Python 3.7-3.10. Apple M1 architecture (arm64) support is new to this release. MacOS 12 wheels are provided for Python 3.8-3.10. For a full list of new features, bug fixes and deprecations see the full release notes at: https://scikit-image.org/docs/stable/release_notes.html

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