Dear Matt,
We have upgraded to scipy 0.14.0 and this is what I get now when I run the script:
Read ASCII File:
['array_labels', 'attrs', 'column_labels', 'data', 'energy', 'filename', 'header', 'i0', 'mu']
After pre-edge:
['array_labels', 'attrs', 'column_labels', 'data', 'dmude', 'e0', 'edge_step', 'energy', 'filename', 'flat', 'header', 'i0', 'mu', 'nnorm', 'norm', 'norm1', 'norm2', 'norm_c0', 'norm_c1', 'norm_c2', 'norm_c3', 'nvict', 'post_edge', 'pre1', 'pre2', 'pre_edge', 'pre_offset', 'pre_slope']
After autobk:
['array_labels', 'attrs', 'autobk_details', 'bkg', 'chi', 'chie', 'column_labels', 'data', 'dmude', 'e0', 'edge_step', 'energy', 'filename', 'flat', 'header', 'i0', 'k', 'mu', 'nnorm', 'norm', 'norm1', 'norm2', 'norm_c0', 'norm_c1', 'norm_c2', 'norm_c3', 'nvict', 'post_edge', 'pre1', 'pre2', 'pre_edge', 'pre_offset', 'pre_slope']
[ 5.22014125e-01 4.68863165e-01 4.23387732e-01 3.84601353e-01
3.51517555e-01 3.23149862e-01 2.98511802e-01 2.76616899e-01
2.56478680e-01 2.37110672e-01 2.17526399e-01 1.96774248e-01
1.74202338e-01 1.49312809e-01 1.21645288e-01 9.07843838e-02
5.63993015e-02 1.85571728e-02 -2.03243717e-02 -5.75444687e-02
-9.14850299e-02 -1.18154030e-01 -1.36108084e-01 -1.45468821e-01
-1.47073697e-01 -1.50934997e-01 -1.54219769e-01 -1.56582731e-01
-1.55007074e-01 -1.50082523e-01 -1.35737843e-01 -1.13771275e-01
-8.25087559e-02 -4.62194044e-02 9.36626084e-04 4.42260206e-02
8.89877045e-02 1.27496716e-01 1.50717679e-01 1.52846156e-01
1.34118361e-01 1.02181582e-01 6.49568133e-02 3.22399885e-02
6.46113335e-03 -6.98123272e-03 -4.09343210e-03 1.83744265e-02
5.17624756e-02 8.65303295e-02 9.62396887e-02 7.69122752e-02
4.26727610e-02 7.49257701e-03 -1.81363351e-02 -3.96258643e-02
-6.15635768e-02 -7.97519898e-02 -8.77310666e-02 -8.66687826e-02
-8.15835644e-02 -7.32081259e-02 -6.02706951e-02 -4.24399368e-02
-2.10497270e-02 5.08304985e-04 2.06241750e-02 3.91292189e-02
5.77145097e-02 7.15135419e-02 7.45516578e-02 6.38238728e-02
4.35580179e-02 2.02712305e-02 -4.46692821e-03 -2.41242981e-02
-3.66799760e-02 -4.33587597e-02 -4.46705006e-02 -4.05827015e-02
-3.30819589e-02 -2.70683602e-02 -2.59245042e-02 -2.90609922e-02
-2.95609304e-02 -2.38858773e-02 -1.50880484e-02 -9.19969595e-03
-8.33417313e-03 -7.93651142e-03 -3.05461694e-03 7.13301998e-03
1.82026094e-02 2.66824286e-02 3.30622138e-02 4.00340894e-02
4.90608443e-02 6.02648286e-02 7.00942393e-02 7.31115967e-02
6.75011510e-02 5.35389324e-02 3.48700770e-02 1.69745209e-02
1.72454146e-03 -1.20611024e-02 -2.27968218e-02 -2.76882865e-02
-3.34147477e-02 -4.57197498e-02 -6.05078349e-02 -7.24893051e-02
-7.70420692e-02 -7.26272010e-02 -6.11005811e-02 -4.55265529e-02
-3.00707518e-02 -1.68398434e-02 -7.56863503e-03 -3.68954861e-03
-3.43061853e-03 -3.06004774e-03 2.55862832e-03 1.71655046e-02
4.20159830e-02 6.75693679e-02 8.23617564e-02 8.56835153e-02
8.13427954e-02 7.37373718e-02 6.28271473e-02 4.67098172e-02
2.60081154e-02 2.82900268e-03 -2.26376028e-02 -4.78755329e-02
-6.99617777e-02 -8.35343661e-02 -8.44844001e-02 -7.18198681e-02
-5.08207746e-02 -2.73111366e-02 -8.63745041e-03 2.79708853e-03
8.16043004e-03 7.92863690e-03 5.11229300e-03 3.49449875e-03
3.87115590e-03 2.85022886e-03 -1.51356430e-04 -2.71617609e-03
7.99093220e-04 1.28770189e-02 2.97511624e-02 4.23481503e-02
4.61655216e-02 4.49878002e-02 4.16959342e-02 3.51358326e-02
2.30338982e-02 7.71870254e-03 -6.49914172e-03 -1.95979278e-02
-2.91442689e-02 -3.34105565e-02 -3.22190201e-02 -2.83765449e-02
-2.52463396e-02 -2.32145504e-02 -2.10720714e-02 -1.84390441e-02
-1.47681365e-02 -1.01599056e-02 -4.95494275e-03 -3.16814647e-04
4.11336090e-03 7.87342088e-03 1.02960668e-02 1.29127543e-02
1.55124154e-02 1.78762099e-02 1.96778316e-02 2.12245457e-02
1.92318426e-02 1.52708347e-02 1.00532965e-02 3.93556366e-03
-2.00861226e-04 -3.92225374e-03 -5.30239979e-03 -4.82306995e-03
-4.47717083e-03 -6.19650760e-03 -1.00134814e-02 -1.42494639e-02
-1.54978616e-02 -1.35397676e-02 -1.13623819e-02 -9.41262041e-03
-7.58206760e-03 -5.06296458e-03 -2.48585060e-03 -4.00416183e-04
1.87050218e-03 3.62541073e-03 6.07766518e-03 7.21786016e-03
8.77502787e-03 9.95603332e-03 1.03558434e-02 9.73912155e-03
7.63280475e-03 5.35276100e-03 2.20653640e-03 -9.84994816e-05
-1.37884146e-03 -1.12248811e-03 -8.47538380e-04 -6.26076861e-04
-5.87386385e-04 -8.97700051e-04 -2.24337187e-03 -3.92268068e-03
-4.69266928e-03 -4.80954070e-03 -4.76843389e-03 -5.05903965e-03
-4.98518712e-03 -4.01197097e-03 -3.00891314e-03 -1.46903844e-03
3.53683094e-05 1.59446778e-03 3.12390382e-03 4.76890345e-03
5.59846498e-03 5.63295324e-03 5.09371953e-03 3.49773838e-03
1.79393075e-03 4.66522098e-04 -1.52569918e-04 -7.15600312e-04
-9.34996770e-04 -1.13022725e-03 -8.06959189e-04 -8.41610248e-04
-1.14800547e-03 -1.28965094e-03 -1.24884820e-03 -1.44400047e-03
-2.04579669e-03 -2.17836113e-03 -2.08363191e-03 -1.81376431e-03
-1.41088949e-03 -8.75421280e-04 -4.54586404e-04 8.29150513e-05
6.78654789e-04 1.04647304e-03 1.59651631e-03 1.75850262e-03
1.71743579e-03 1.72121567e-03 1.67674127e-03 1.26223831e-03
1.09938217e-03 6.79160864e-04 2.74810773e-04 2.51510300e-04
-1.81502999e-05 -2.49024384e-04 -6.74164538e-04 -7.71579948e-04
-8.51008782e-04 -7.46019036e-04 -7.91883682e-04 -1.02615516e-03
-1.27411149e-03 -1.14412599e-03 -1.10888173e-03 -1.24436555e-03
-5.70511174e-04 -2.67727213e-04 -5.10544602e-05 -7.44585105e-05
3.32434599e-04 6.16025534e-04 4.60911522e-04 4.52806510e-04
5.17149268e-04 8.86203824e-04 8.06249536e-04 7.62364216e-04
6.89168671e-04 6.48290053e-04 5.50507466e-04 5.00420100e-04
4.91031520e-04 1.90660816e-04 1.42033309e-04 7.11215401e-05
-4.54097265e-05 -3.46351385e-05 -3.10631849e-05 -9.24403309e-05
-1.47993095e-04 -2.10994331e-04 -2.82751339e-04 -2.75720314e-04
-2.00919076e-04 -1.47717375e-04 -6.51029766e-05 -3.22735306e-05
-1.15212367e-04 -1.80394605e-04 -1.91644236e-04 -2.09229079e-04
-2.87571537e-04 -2.91770309e-04 -3.03029185e-04 -3.65472126e-04
-2.40079196e-04 -2.57480565e-04 -2.13293922e-04 -2.23895882e-04
-2.05898811e-04 -2.51361361e-04 -2.15835935e-04 -3.26122661e-04
-3.60578368e-04 -3.48674339e-04 -2.51265522e-04 -9.42783246e-05
1.05407722e-05 1.35324496e-04 1.32768084e-04 2.38054795e-04
2.37051097e-04 2.60387811e-04 3.17263146e-04 4.05326800e-04
5.37145496e-04 6.98105861e-04 8.02577998e-04 8.44690107e-04
8.42747086e-04 9.18552333e-04]
It seems to work! For certainty, is this consistent with what you obtain?
Many thanks for your help,
Matthias
________________________________________
Van: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] namens Matt Newville [newville@cars.uchicago.edu]
Verzonden: woensdag 5 november 2014 14:23
Aan: XAFS Analysis using Ifeffit
Onderwerp: Re: [Ifeffit] Larch-0.9.24 with Python2
Hi Matthias,
OK, having scipy 0.9.0 is almost certainly the problem. I'm not
entirely sure how far back in scipy versions would be supported, but I
believe that version 0.12 will work, and am certain that 0.13 will
work. In fact, I'm pretty sure that version 0.13 is made several
changes to the minimization package. I believe I may be relying on
some of those changes for being able to use minimization method other
than the default Levenberg-Marquardt least-squares algorithm (not
that this is recommended for autobk() or feffit(), but it can
sometimes be useful in other fitting problems).
The version of numpy you have should be not be a problem.
I'll set the required versions of scipy to 0.13 and numpy to 1.5.
On Wed, Nov 5, 2014 at 1:39 AM, Matthias Filez wrote:
Dear Matt, Bruce,
I verified the scipy version: 0.9.0.
The installed numpy version is 1.6.1.
What versions are required?
Thanks a lot!
Matthias
________________________________________
Van: ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces@millenia.cars.aps.anl.gov] namens Matt Newville [newville@cars.uchicago.edu]
Verzonden: dinsdag 4 november 2014 18:59
Aan: XAFS Analysis using Ifeffit
Onderwerp: Re: [Ifeffit] Larch-0.9.24 with Python2
Hi Matthias,
Hmm, looking at this more closely, my guess is that you're using an
older version scipy than I am. Can you verify what scipy version you
have?
That is, I do see that the return value for this call did change
sometime in the past 2 years, though I'm not sure exactly which
version. I'll try to commit a patch to allow this older version to
github today. But, I suspect that older scipy versions might cause
other problems.
I should probably put in a more exact check for required scipy version.
--Matt
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_______________________________________________
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
--Matt
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Ifeffit mailing list
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