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Re: [SciPy-user] Update to my SciPy document

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Subject: Re: [SciPy-user] Update to my SciPy document
Date: Dijous 22 Juny 2006 20:53
From: Francesc Altet  I've made a few minor updates to my SciPy document.  And, with the
> help of Nicky Van Foreest, I've also added an example to the
> section on stats.  You can find it here:
>
>     http://www.rexx.com/~dkuhlman/scipy_course_01.html
>
> Comments and suggestions are welcome.

Good stuff indeed.  Regarding PyTables section:

- From PyTables 1.3 on, NumPy (and hence SciPy) arrays are supported right
 out of the box in Array objects (the ones you are using). So, if you write a
 NumPy array, you will get a NumPy array (the same goes for Numeric and
 numarray). In other objects (EArray, VLArray or Table) you can make use of
 the 'flavor' parameter in constructors to tell PyTables: 'Hey, every time
 that I read from this object, please, return me an (rec)array with the
 appropriate flavor'. Of course, PyTables will try hard to avoid doing data
 copies in conversions (i.e. the array protocol is used whenever possible).

- The procedure for installation can be simplified somewhat:

$ tar xvzf orig/pytables-1.3.2.tar.gz
$ cd pytables-1.3.2
$ python setup.py build
$ sudo python setup.py install

- Perhaps a nice feature of PyTables that you could document is its
 capability to read slices of arrays directly from disk. You can do this by
 providing the start, stop and step parameters to node.read() method, but it
 would be more appropriate (specially when dealing with multidimensional
 data) using the __getitem__ method that expose all the data nodes. Examples:
node[1]   # Get the first element of potentially multidimensional node
node[1:4:3]  # Get an slice
node[1:4:3, 2:10:2, ..., 3]  # The complete syntax for slices is supported.

Cheers!

--

>0,0<	Francesc Altet     http://www.carabos.com/

V   V	Cárabos Coop. V.   Enjoy Data
 "-"

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Re: [SciPy-user] Update to my SciPy document

On 6/22/06, Dave Kuhlman  I've made a few minor updates to my SciPy document.  And, with the
> help of Nicky Van Foreest, I've also added an example to the
> section on stats.  You can find it here:
>
>     http://www.rexx.com/~dkuhlman/scipy_course_01.html

Great!	You should add a little blurb about it on the wiki:

http://scipy.org/Topical_Software

If that page stays up to date, it will be a good resource to point
newcomers to for finding docs, tools, etc.

And thanks for the effort!

Cheers,

f

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Re: [SciPy-user] Update to my SciPy document

>  You can find it here:
>
>     http://www.rexx.com/~dkuhlman/scipy_course_01.html

Wow .. haven't looked at it yet, but just want to thank you for  
putting that together!

> Comments and suggestions are welcome.

  I'll try to check it out over the next couple of days.

Thanks again,
-steve

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Re: [SciPy-user] Update to my SciPy document

Dave Kuhlman wrote:

>I've made a few minor updates to my SciPy document.  And, with the
>help of Nicky Van Foreest, I've also added an example to the
>section on stats.  You can find it here:
>
>    http://www.rexx.com/~dkuhlman/scipy_course_01.html
>
>Comments and suggestions are welcome.
>
>Dave
>
>  
>
Looking good!	 fyi:  the links to PyTables seem to be broken.
-gary

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[SciPy-user] Update to my SciPy document

I've made a few minor updates to my SciPy
document.  And, with the
help of Nicky Van Foreest, I've also added an example to the
section on stats.  You can find it here:

    http://www.rexx.com/~dkuhlman/scipy_course_01.html

Comments and suggestions are welcome.

Dave

-- 
Dave Kuhlman
http://www.rexx.com/~dkuhlman

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Re: [SciPy-user] shape mismatch: objects cannot be broadcast to a single shape

On Thu, 22 Jun 2006 12:21:15 -0500
  Robert Kern  Nils Wagner wrote:
>> Please can you run the script
> 
> No, I won't run your script. You show me the output you 
>get and describe to me 
> the output you were expecting and why. *Then* I might 
>run the script if there 
> might be problem that will differ between 
>machines/installed versions or if I 
> want to explore a problem that's displayed. But I'm not 
>going to read your mind.
> 
> -- 
OK I didn't expect nan

>>> special.jn(2,0.1)
0.0012489586587999691
>>> special.jn(2,0.01)
1.2499895833805591e-05
>>> special.jn(2,0.0001)
1.2500001157853685e-09
>>> special.jn(2,0.0000001)
1.3897845548005439e-15
>>> special.jn(2,0.0000000001)
0.0
>>> special.jn(2,0.000000000)
nan


>>> scipy.__version__
'0.5.0.1988'



Nils


> Robert Kern
> 
> "I have come to believe that the whole world is an 
>enigma, a harmless enigma
>  that is made terrible by our own mad attempt to 
>interpret it as though it had
>  an underlying truth."
>   -- Umberto Eco
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user@...
> http://www.scipy.net/mailman/listinfo/scipy-user

  

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Re: [SciPy-user] Creating a 2D matrix with a gausian hump?

Fantastic, Thanks Favre-Nicolin and
Gerald!

I generalized this just a bit to:

def makeGaussian(size, fwhm = 3):
    """ Make a square gaussian kernel.

    size is the length of a side of the square
    fwhm is full-width-half-maximum, which
    can be thought of as an effective radius.
    """

    x = arange(0, size, 1, Float32)
    y = x[:,NewAxis]
    x0 = y0 = size // 2
    return exp(-4*log(2) * ((x-x0)**2 + (y-y0)**2) / fwhm**2)
#

which suits my newbie need to spell out what fwhm is..


On 6/22/06, Favre-Nicolin Vincent  > What's a good way to create a 2d gaussian kernel with numpy?
> >
> > I'm trying to create a 9x9 matrix with 1.0 in the center, and 0.0 in
> > the corners, and a gaussian distribution from the center out.
>
> from scipy import *
> x=arange(0,9,1,Float)
> x=arange(0,9,1,Float)
> y=x[:,NewAxis]
> x0,y0=4,4
> fwhm=3
> g=exp(-4*log(2)*((x-x0)**2+(y-y0)**2)/fwhm**2)
> print g
>
>    If you want exactly 0 in the corners, just use g-g[0,0].
>
> --
> Vincent Favre-Nicolin
> Université Joseph Fourier
> http://v.favrenicolin.free.fr
> ObjCryst & Fox : http://objcryst.sourceforge.net
>
>

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Re: [SciPy-user] shape mismatch: objects cannot be broadcast to a single shape

Nils Wagner wrote:
> Please can you run the script

No, I won't run your script. You show me the output you get and describe to me 
the output you were expecting and why. *Then* I might run the script if there 
might be problem that will differ between machines/installed versions or if I 
want to explore a problem that's displayed. But I'm not going to read your mind.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco

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Re: [SciPy-user] shape mismatch: objects cannot be broadcast to a single shape

On Thu, 22 Jun 2006 11:37:55 -0500
  Robert Kern  Nils Wagner wrote:
>> Hi all,
>> 
>>>>> k = arange(0,4)
>>>>> r = linspace(0,3,10)
>>>>> special.jn(k,r)
>> Traceback (most recent call last):
>>   File "", line 1, in ?
>> ValueError: shape mismatch: objects cannot be broadcast 
>>to a single shape
>> 
>> It would be nice if special.jn(k,r) returns a 
>>two-dimensional array
>> corresponding to the length of k and r.
>> 
>> How can I resolve this problem ?
> 
> Pass in the right arguments. Make k a column vector.
> 
> -- 
> Robert Kern
> 
> "I have come to believe that the whole world is an 
>enigma, a harmless enigma
>  that is made terrible by our own mad attempt to 
>interpret it as though it had
>  an underlying truth."
>   -- Umberto Eco
> 
> _______________________________________________
> SciPy-user mailing list
> SciPy-user@...
> http://www.scipy.net/mailman/listinfo/scipy-user

Thank you.
Please can you run the script

from scipy import *
k = arange(1,10)
r = reshape(linspace(0,3,10),(len(linspace(0,3,10)),1))
H = special.jn(k,r)
print H[0,:]



Am I missing something ?

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Re: [SciPy-user] shape mismatch: objects cannot be broadcast to a single shape

Nils Wagner wrote:
> Hi all,
> 
>>>> k = arange(0,4)
>>>> r = linspace(0,3,10)
>>>> special.jn(k,r)
> Traceback (most recent call last):
>   File "", line 1, in ?
> ValueError: shape mismatch: objects cannot be broadcast to a single shape
> 
> It would be nice if special.jn(k,r) returns a two-dimensional array
> corresponding to the length of k and r.
> 
> How can I resolve this problem ?

Pass in the right arguments. Make k a column vector.

-- 
Robert Kern

"I have come to believe that the whole world is an enigma, a harmless enigma
  that is made terrible by our own mad attempt to interpret it as though it had
  an underlying truth."
   -- Umberto Eco

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