Mailman 3 April 2012 - SciPy-User

How to display a RGB image (MFISH)?
by jp April 3, 2023

April 3, 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

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 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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Linear interpolation in 3D
by Hardock, Andreas June 13, 2013

June 13, 2013

Hi, I'm trying to interpolate a 3D data (from the pic attached) with the interp2d command. What I have, are three vectors f, z, A (x, y, z respectively, A is the percentage data given on the isolines). I first put the f and z in a meshgrid and afterwards in the griddata to get a 3D-grid then started the interpolateion. I plotted the the data after gridding, and I observed that almost all nodes are ignored. Do you have any idea how to prepare data to the interp2d command? Don't hesitate to suggest any other solution. my code so far is: import numpy as np from mpl_toolkits.mplot3d import axes3d from scipy.interpolate import interp2d import matplotlib.pyplot as plt from matplotlib import mlab plt.clf() fig = plt.figure(1) ax = axes3d.Axes3D(fig) #read data (ff,ZZ,A,a) = np.loadtxt("accuracy-map.txt", unpack=True) f=np.log10(ff) z=np.log10(ZZ) ##grid everything fgrid, zgrid=np.meshgrid(f,z) #define grid ef=np.linspace(min(f), max(f), len(f)) ez=np.linspace(min(z), max(z), len(f)) Agrid=mlab.griddata(f,z,A, ef,ez) int2d=interp2d(fgrid, zgrid, Agrid, kind='linear') ax.plot(f, z, A, 'ok', markerfacecolor='w') ax.plot_surface(fgrid, zgrid, Agrid) ax.set_xlim3d((min(f), max(f))) ax.set_ylim3d(min(z), max(z)) ax.set_zlim3d(0,100) plt.show()

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pupynere/scipy.io.netcdf
by Ryan May March 6, 2013

March 6, 2013

Hi, Anyone know if pupynere (a version of which is in scipy.io.netcdf) supports writing files with 64-bit offsets? This allows writing files larger than 2GB. Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma

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Reading TDM/TDMS Files with scipy
by Nils Wagner Feb. 20, 2013

Feb. 20, 2013

Hi all, Is it possible to read TDM/TDMS files with scipy ? I found a tool for Matlab http://zone.ni.com/devzone/cda/epd/p/id/5957 Nils

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Request for usage examples on scipy.stats.rv_continuous and scipy.ndimage.grey_dilate(structure)
by Christoph Deil Dec. 5, 2012

Dec. 5, 2012

Hi, I am having some trouble figuring out how to use the following two aspects of scipy: 1) How can I create a random distribution given by some python formula, e.g. pdf(x) = x**2 in the range x = 1 to 2. The example given in the rv_continuous docstring doesn't work for me: In [1]: import matplotlib.pyplot as plt In [2]: numargs = generic.numargs AttributeError: type object 'numpy.generic' has no attribute 'numargs' Is it also possible to use rv_continuous for multidimensional distributions, say pdf(x,y)=x*y in the range x = 1 to 2 and y = 0 to 3? Or for pdfs that are just given numerically on a grid (say as the result of a gaussian_kde() ), not by a python function? It would be nice if someone could add a few examples that show rv_continuous usage to the docstring or tutorial. 2) How to use the 'structure' argument of scipy.ndimage.grey_dilate() correctly? There are some explanations at http://docs.scipy.org/doc/scipy/reference/tutorial/ndimage.html but I think they are inconsistent with the implementation: -------------------------------------------------------------- In [98]: a = zeros((7,7)); a[3,3]=1; a Out[98]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 1., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) In [100]: s = generate_binary_structure(2,2); s Out[100]: array([[ True, True, True], [ True, True, True], [ True, True, True]], dtype=bool) In [101]: grey_dilation(a,size=(3,3)) Out[101]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) In [102]: grey_dilation(a,size=(3,3),structure=s) Out[102]: array([[ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 2., 2., 2., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.], [ 1., 1., 1., 1., 1., 1., 1.]]) In [103]: grey_dilation(a,structure=s) --------------------------------------------------------------------------- TypeError Traceback (most recent call last) /Users/deil/<ipython console> in <module>() /opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/scipy/ndimage/morphology.pyc in grey_dilation(input, size, footprint, structure, output, mode, cval, origin) 354 sz = footprint.shape[ii] 355 else: --> 356 sz = size[ii] 357 if not sz & 1: 358 origin[ii] -= 1 TypeError: 'NoneType' object is unsubscriptable In [104]: grey_dilation(a,footprint=s) Out[104]: array([[ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 1., 1., 1., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.], [ 0., 0., 0., 0., 0., 0., 0.]]) -------------------------------------------------------------- Why doesn't grey_dilation(a,structure=s) work? Why doesn't grey_dilation(a,size=(3,3),structure=s) give the same result as grey_dilation(a,size=(3,3),footprint=s)? I am running on numpy version 1.4.0 and scipy version 0.7.1 Thanks! --Christoph

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Problem with Installation of Scipy on Macbook
by manisha pujari Nov. 22, 2012

Nov. 22, 2012

Hello everyone, This is the first time I am using scipy and I am having much trouble to just install it on my macbook. I am using Python 2.6 and numpy 1.6.0. I downloaded scipy0.9.0 tar.gz file from the web link http://sourceforge.net/projects/scipy/files/scipy/ and tried to install it from the source. But on giving the command scipy-0.9.0$ python setup.py build it is always giving the following problem : Warning: No configuration returned, assuming unavailable.blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers'] non-existing path in 'scipy/io': 'docs' lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] umfpack_info: libraries umfpack not found in /System/Library/Frameworks/Python.framework/Versions/2.6/lib libraries umfpack not found in /usr/local/lib libraries umfpack not found in /usr/lib /Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/system_info.py:463: UserWarning: UMFPACK sparse solver (http://www.cise.ufl.edu/research/sparse/umfpack/) not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [umfpack]) or by setting the UMFPACK environment variable. warnings.warn(self.notfounderror.__doc__) NOT AVAILABLE Traceback (most recent call last): File "setup.py", line 181, in <module> setup_package() File "setup.py", line 173, in setup_package configuration=configuration ) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/core.py", line 152, in setup config = configuration() File "setup.py", line 122, in configuration config.add_subpackage('scipy') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/setup.py", line 20, in configuration config.add_subpackage('special') File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 972, in add_subpackage caller_level = 2) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 941, in get_subpackage caller_level = caller_level + 1) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 878, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "scipy/special/setup.py", line 54, in configuration extra_info=get_info("npymath") File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2184, in get_info pkg_info = get_pkg_info(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/misc_util.py", line 2136, in get_pkg_info return read_config(pkgname, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 390, in read_config v = _read_config_imp(pkg_to_filename(pkgname), dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 326, in _read_config_imp meta, vars, sections, reqs = _read_config(filenames) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 309, in _read_config meta, vars, sections, reqs = parse_config(f, dirs) File "/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/distutils/npy_pkg_config.py", line 281, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Python/2.6/site-packages/numpy-1.6.0-py2.6-macosx-10.6-universal.egg/numpy/core/lib/npy-pkg-config/npymath.ini'] I am unable to understand where and what exactly the problem is. Can anyone please help me? I will be really thankful for a response. -- Regards, Manisha

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Installing issue with python 2.7, numpy 1.5.0b1 in my Mac
by Markus Hubig Sept. 5, 2012

Sept. 5, 2012

Hi @all, maybe this is a known issue but I didn't find any useful information out there. When I try to install scipy-0.8.0 with pip I get this strange error about missing files ... File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/distutils/npy_pkg_config.py", line 276, in parse_config raise PkgNotFound("Could not find file(s) %s" % str(filenames)) numpy.distutils.npy_pkg_config.PkgNotFound: Could not find file(s) ['/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/core/lib/npy-pkg-config/npymath.ini'] The complete error can be found here: http://gist.github.com/527697 Is there a known solution for this? Any help would be nice ... - Markus -- Can't read my mail? Just don't hold it that way!

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[SciPy-user] adaptive simulated annealing (ASA)
by Dieter Werthmüller July 14, 2012

July 14, 2012

Hi there, The message 'adaptive simulated annealing (ASA)' is over four years old now, asking for a python implementation of ASA (http://www.ingber.com/#ASA). I was wondering if such an implementation is around today? Kind regards, Dieter -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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