Mailman 3 October 2021 - SciPy-User

How to display a RGB image (MFISH)?
by jp April 2, 2023

April 2, 2023

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 July 28, 2022

July 28, 2022

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Help required regding Eigenvectors
by Sudheer Phani March 14, 2022

March 14, 2022

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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Using ndimage.gaussian_filter for 3d array
by ashwin .D Oct. 26, 2021

Oct. 26, 2021

Hello, I am wanting to use ndimage.gaussian_filter for a 3d array in order to smooth the data . When I do this - abc[:,:,:] = ndimage.gaussian_filter(abc[:,:,:]*1e2,sigma=2,order=0) I get unreal values. However the function call when done within a loop like this for k in range(0,N): abc[k,:,:] = ndimage.gaussian_filter(abc[k,:,:]*1e2,sigma=2,order=0) gives reasonable smoothed values. From the docs - https://docs.scipy.org/doc/scipy/reference/generated/scipy.ndimage.gaussian… the input array does not seem to have any restriction on the dimensionality . So where am I going wrong ? Best regards, Ashwin.

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make_lsq_spline and conversion to float
by Thomas Hilger Oct. 26, 2021

Oct. 26, 2021

Hello, When using make_lsq_spline(x,y,t) with x being int64, I am running into the issue that the x-array is internally converted to float. While on an int64-level the input x-values are ordered, after the internal conversion to float, an exception is raised, because as a result some of these values are identical to each other. I was wondering about the reason for that internal conversion to float (it seems to reside only in handling complex dtypes or is there some other mechanism in Cox-de-Bor algorithm or Cholesky?). It is not obvious to me. Right now I can solve this problem by shifting the x-values, such that the numbers are smaller and the conversion does not harm this way. However, this makes things really slow or very unhandy codewise. Maybe it is feasible to modify _get_dtype a little? Thanks and cheers, Thomas.

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NumPy 1.21.3 released
by Charles R Harris Oct. 20, 2021

Oct. 20, 2021

Hi All, On behalf of the NumPy team I am pleased to announce the release of NumPy 1.21.3. NumPy 1.21.3 is a maintenance release that fixes a few bugs discovered after the 1.21.2 release. It also provides 64 bit Python 3.10.0 wheels. Note a few oddities about the Python 3.10 wheels: - There are no 32 bit wheels for Windows, Mac, or Linux. - The Mac Intel builds are only available in universal2 wheels. 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/1.21.3/>; source archives, release notes, and wheel hashes are available on Github <https://github.com/numpy/numpy/releases/tag/v1.21.3>. 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. - Aaron Meurer - Bas van Beek - Charles Harris - Developer-Ecosystem-Engineering + - Kevin Sheppard - Sebastian Berg - Warren Weckesser *Pull requests merged* A total of 8 pull requests were merged for this release. - #19745: ENH: Add dtype-support to 3 ```generic``/``ndarray`` methods - #19955: BUG: Resolve Divide by Zero on Apple silicon + test failures... - #19958: MAINT: Mark type-check-only ufunc subclasses as ufunc aliases... - #19994: BUG: np.tan(np.inf) test failure - #20080: BUG: Correct incorrect advance in PCG with emulated int128 - #20081: BUG: Fix NaT handling in the PyArray_CompareFunc for datetime... - #20082: DOC: Ensure that we add documentation also as to the dict for... - #20106: BUG: core: result_type(0, np.timedelta64(4)) would seg. fault. Cheers, Charles Harris

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Sympy IRC?
by Schuldei, Andreas Oct. 13, 2021

Oct. 13, 2021

Hi, Is there an IRC channel for SymPy? I found one on Libra.Chat, #sympy, which was archived until a few months ago, but is dead now. Are there other, active ones?

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[installation] troubles installing scipy on M1 Mac with python 3.10
by lorenzo.barsotti＠hotmail.com Oct. 13, 2021

Oct. 13, 2021

hi, I am using a Mac book air M1, Where is installed Python 3.10. I am not able to install SciPy with the command python3 -m pip install scipy That give me this error: Collecting scipy Using cached scipy-1.6.1.tar.gz (27.3 MB) Installing build dependencies ... done Getting requirements to build wheel ... done Preparing wheel metadata (pyproject.toml) ... error ERROR: Command errored out with exit status 1: command: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/tmpycf4rz1z cwd: /private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-install-16fimo5m/scipy_a848fbf1084441eb9c80507d478e1152 Complete output (104 lines): setup.py:461: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-modern-metadata-c3fs2ro3'), proceeding with generating Cython sources and expanding templates warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " Running from SciPy source directory. lapack_opt_info: lapack_mkl_info: customize UnixCCompiler libraries mkl_rt not found in ['/Library/Frameworks/Python.framework/Versions/3.10/lib', '/usr/lib'] NOT AVAILABLE openblas_lapack_info: libraries openblas not found in ['/Library/Frameworks/Python.framework/Versions/3.10/lib', '/usr/lib'] NOT AVAILABLE openblas_clapack_info: libraries openblas,lapack not found in ['/Library/Frameworks/Python.framework/Versions/3.10/lib', '/usr/lib'] NOT AVAILABLE flame_info: libraries flame not found in ['/Library/Frameworks/Python.framework/Versions/3.10/lib', '/usr/lib'] NOT AVAILABLE accelerate_info: NOT AVAILABLE atlas_3_10_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries tatlas,tatlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries lapack_atlas not found in /usr/lib libraries tatlas,tatlas not found in /usr/lib <class 'numpy.distutils.system_info.atlas_3_10_threads_info'> NOT AVAILABLE atlas_3_10_info: libraries lapack_atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries satlas,satlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries lapack_atlas not found in /usr/lib libraries satlas,satlas not found in /usr/lib <class 'numpy.distutils.system_info.atlas_3_10_info'> NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries lapack_atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries ptf77blas,ptcblas,atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries lapack_atlas not found in /usr/lib libraries ptf77blas,ptcblas,atlas not found in /usr/lib <class 'numpy.distutils.system_info.atlas_threads_info'> NOT AVAILABLE atlas_info: libraries lapack_atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries f77blas,cblas,atlas not found in /Library/Frameworks/Python.framework/Versions/3.10/lib libraries lapack_atlas not found in /usr/lib libraries f77blas,cblas,atlas not found in /usr/lib <class 'numpy.distutils.system_info.atlas_info'> NOT AVAILABLE lapack_info: libraries lapack not found in ['/Library/Frameworks/Python.framework/Versions/3.10/lib', '/usr/lib'] NOT AVAILABLE /private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/numpy/distutils/system_info.py:1858: UserWarning: Lapack (http://www.netlib.org/lapack/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [lapack]) or by setting the LAPACK environment variable. return getattr(self, '_calc_info_{}'.format(name))() lapack_src_info: NOT AVAILABLE /private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/numpy/distutils/system_info.py:1858: UserWarning: Lapack (http://www.netlib.org/lapack/) sources not found. Directories to search for the sources can be specified in the numpy/distutils/site.cfg file (section [lapack_src]) or by setting the LAPACK_SRC environment variable. return getattr(self, '_calc_info_{}'.format(name))() NOT AVAILABLE Traceback (most recent call last): File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 349, in <module> main() File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 331, in main json_out['return_val'] = hook(**hook_input['kwargs']) File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 151, in prepare_metadata_for_build_wheel return hook(metadata_directory, config_settings) File "/private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 161, in prepare_metadata_for_build_wheel self.run_setup() File "/private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 253, in run_setup super(_BuildMetaLegacyBackend, File "/private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 145, in run_setup exec(compile(code, __file__, 'exec'), locals()) File "setup.py", line 588, in <module> setup_package() File "setup.py", line 584, in setup_package setup(**metadata) File "/private/var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/pip-build-env-pk9zlbp7/overlay/lib/python3.10/site-packages/numpy/distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 499, in configuration raise NotFoundError(msg) numpy.distutils.system_info.NotFoundError: No BLAS/LAPACK libraries found. Note: Accelerate is no longer supported. To build Scipy from sources, BLAS & LAPACK libraries need to be installed. See site.cfg.example in the Scipy source directory and https://docs.scipy.org/doc/scipy/reference/building/index.html for details. ---------------------------------------- WARNING: Discarding https://files.pythonhosted.org/packages/26/68/84dbe18583e79e56e4cee8d00232a… (from https://pypi.org/simple/scipy/) (requires-python:>=3.7). Command errored out with exit status 1: /Library/Frameworks/Python.framework/Versions/3.10/bin/python3 /Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py prepare_metadata_for_build_wheel /var/folders/n0/r8n34lk526q8h3g5zp2t0mvh0000gn/T/tmpycf4rz1z Check the logs for full command output. Using cached scipy-1.6.0.tar.gz (27.3 MB) Installing build dependencies ... -^Z I also tried to install scipy from source, with the commands: git clone https://github.com/scipy/scipy.git cd scipy python3 setup.py build but also here it give me an error. How can I achieve the installation of scipy? Thanks

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[JOBS] Solar & Storage Energy Analyst
by Dr. Mark Alexander Mikofski PhD Oct. 7, 2021

Oct. 7, 2021

Dear Pythonistas, If you're an experienced solar energy analyst looking to accelerate the energy transition & make a bigger impact on the climate crisis by using your Python analytical skills to help deploy more solar power & energy storage cheaper, better, & faster, then please come join my team at DNV. I'm not looking for superstars. I just need a few friendly folks who value diversity & are open to using the best tools to save our planet. Please follow the links below or email me for more info: US: https://careers-dnv.icims.com/jobs/16829/job Canada: https://careers-dnv.icims.com/jobs/16831/job Thanks, Mark -- Mark Mikofski, PhD (2005) *Fiat Lux*

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spectrogram: Is 'nfft' used only to increase frequency resolution?
by broccolee90210＠gmail.com Oct. 4, 2021

Oct. 4, 2021

Hi, Just needed a little clarifications for the spectrogram usage. What use would there be in defining 'nfft' when 'window' is defined? Assuming the windowing function of choice zeroed out the side values already. Is it only to increase frequency resolution? Thanks.

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