473,544 Members | 1,967 Online
Bytes | Software Development & Data Engineering Community
+ Post

Home Posts Topics Members FAQ

why scipy cause my program slow?

Why the exec time of test(readdata() ) and test(randomdata ()) of
following program is different?
my test file 150Hz10dB.wav has 2586024 samples, so I set randomdata
function
to return a list with 2586024 samples.
the exec result is:
2586024
<type 'list'>
10.8603842736
2586024
<type 'list'>
2.16525233979
test(randomdata ()) is 5x faster than test(readdata() )
if I remove "from scipy import *" then I get the following result:
2586024
<type 'list'>
2.21851601473
2586024
<type 'list'>
2.13885042216

So, what the problem with scipy?
Python 2.4.2, scipy ver. 0.5.1
import wave
from scipy import *
from time import *
import random
from array import array

def readdata():
f = wave.open("150H z10dB.wav", "rb")
t = f.getparams()
SampleRate = t[2]
data = array("h", f.readframes(t[3]))
f.close()
left = data[0::2]
mean = sum(left)/float(len(left) )
left = [abs(x-mean) for x in left]
return left

def randomdata():
return [random.random() *32768.0 for i in xrange(2586024)]

def test(data):
print len(data)
print type(data)
envelop = []
e = 0.0
ga, gr = 0.977579425259, 0.999773268338
ga1, gr1 = 1.0 - ga, 1.0 - gr
start = clock()
for x in data:
if e < x:
e *= ga
e += ga1*x
else:
e *= gr
e += gr1*x
envelop.append( e)
print clock() - start
return envelop

test(readdata() )
test(randomdata ())

Jan 16 '07 #1
4 2806
HYRY wrote:
Why the exec time of test(readdata() ) and test(randomdata ()) of
following program is different?
my test file 150Hz10dB.wav has 2586024 samples, so I set randomdata
function
to return a list with 2586024 samples.
the exec result is:
2586024
<type 'list'>
10.8603842736
2586024
<type 'list'>
2.16525233979
test(randomdata ()) is 5x faster than test(readdata() )
if I remove "from scipy import *" then I get the following result:
2586024
<type 'list'>
2.21851601473
2586024
<type 'list'>
2.13885042216

So, what the problem with scipy?
You're importing (through scipy) numpy's sum() function. The result type of that
function is a numpy scalar type. The set of scalar types was introduced for a
number of reasons, mostly having to do with being able to represent the full
range of numerical datatypes that Python does not have builtin types for.
Unfortunately, the code paths that get executed when arithmetic is performed
sith such scalars are still suboptimal; I believe they are still going through
the full ufunc machinery.

--
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

Jan 16 '07 #2
Thanks, by your hint, I change type(data) to type(data[0]), and I get
<type 'float'>
<type 'numpy.float64' >
So, calculate with float is about 5x faster numpy.float64.

Robert Kern wrote:
HYRY wrote:
Why the exec time of test(readdata() ) and test(randomdata ()) of
following program is different?
my test file 150Hz10dB.wav has 2586024 samples, so I set randomdata
function
to return a list with 2586024 samples.
the exec result is:
2586024
<type 'list'>
10.8603842736
2586024
<type 'list'>
2.16525233979
test(randomdata ()) is 5x faster than test(readdata() )
if I remove "from scipy import *" then I get the following result:
2586024
<type 'list'>
2.21851601473
2586024
<type 'list'>
2.13885042216

So, what the problem with scipy?

You're importing (through scipy) numpy's sum() function. The result type of that
function is a numpy scalar type. The set of scalar types was introduced for a
number of reasons, mostly having to do with being able to represent the full
range of numerical datatypes that Python does not have builtin types for.
Unfortunately, the code paths that get executed when arithmetic is performed
sith such scalars are still suboptimal; I believe they are still going through
the full ufunc machinery.

--
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
Jan 16 '07 #3
HYRY wrote:
Thanks, by your hint, I change type(data) to type(data[0]), and I get
<type 'float'>
<type 'numpy.float64' >
So, calculate with float is about 5x faster numpy.float64.
approx..
numpy funcs all upcast int to int32 and float to float32 and
int32/float to float32 etc. This is probably ill behavior.
float32 arrays should only arise if numpy.array(l,d type=numpy.floa t32)

In your example you'll best go to numpy/scipy types very early
(not mixing with the python array type in addition) and do the
array computations with scipy

left = [abs(x-mean) for x in left]

->

data = scipy.array(f.r eadframes(t[3]),"h")
...
left = abs(left-mean)

code the test(data) similar - see also scipy.signal.lf ilter etc.

and cast types down to Python types late like float(mynumfloa t) ...
The type magic and speed loss will and pickle problems will
probably only disapear, when float & int are handled as extra
(more conservative) types in numpy - with numpy scalar types only
on request. Currently numpy uses Python.
Robert
Jan 16 '07 #4
Robert Kern wrote:
HYRY wrote:
>>Why the exec time of test(readdata() ) and test(randomdata ()) of
following program is different?
my test file 150Hz10dB.wav has 2586024 samples, so I set randomdata
function
to return a list with 2586024 samples.
the exec result is:
2586024
<type 'list'>
10.86038427 36
2586024
<type 'list'>
2.165252339 79
test(randomda ta()) is 5x faster than test(readdata() )
if I remove "from scipy import *" then I get the following result:
2586024
<type 'list'>
2.218516014 73
2586024
<type 'list'>
2.138850422 16

So, what the problem with scipy?


You're importing (through scipy) numpy's sum() function. The result type of that
function is a numpy scalar type. The set of scalar types was introduced for a
number of reasons, mostly having to do with being able to represent the full
range of numerical datatypes that Python does not have builtin types for.
Unfortunately, the code paths that get executed when arithmetic is performed
sith such scalars are still suboptimal; I believe they are still going through
the full ufunc machinery.
This should not be true in the 1.0 release of NumPy. The numpy scalars
do their own math which has less overhead than ufunc-based math. But,
there is still more overhead than with simple floats because mixed-type
arithmetic is handled more generically (the same algorithm covers all
the cases).

The speed could be improved but hasn't been because it is so easy to get
a Python float if you are concerned about speed.

-Travis

Jan 17 '07 #5

This thread has been closed and replies have been disabled. Please start a new discussion.

Similar topics

3
2622
by: hawkesed | last post by:
Hi All, has anyone out there recently set up scipy on Windows? Cause I am trying to do so know and I am not having much luck. I have ActiveState and Plone. When I try to import scipy in ActiveState it says >>> import scipy Traceback (most recent call last): File "<interactive input>", line 1, in ? ImportError: No module named scipy >>>...
1
8048
by: tkpmep | last post by:
I installed SciPy and NumPy (0.9.5, because 0.9.6 does not work with the current version of SciPy), and had some teething troubles. I looked around for help and observed that the tutorial is dated October 2004, and is not as thorough as Python's documentation. Is there an alternative source of information that lists all the functions and...
0
1491
by: Julien Fiore | last post by:
Hi, I have problems trying to install the scipy.weave package. I run Python 2.4 on windows XP and my C compiler is MinGW. Below is the output of scipy.weave.test(). I read that the tests should last several minutes, but in my case it only lasts a few seconds. Thanks in advance for any help. Julien Fiore
5
1902
by: robert | last post by:
Simple Python code obviously cannot use the dual core by Python threads. Yet, a program drawing CPU mainly for matrix computations - preferably with Numeric/SciPy - will this profit from a dual core when using 2 (or more) Python threads? robert
2
3922
by: robert | last post by:
I'm using latest numpy & scipy. What is this problem ? : RuntimeError: module compiled against version 1000002 of C-API but this version of numpy is 1000009 Traceback (most recent call last): File "<interactive input>", line 1, in ? File "C:\PYTHON23\Lib\site-packages\scipy\stats\__init__.py", line 7, in ? from stats import * File...
18
22373
by: robert | last post by:
Is there a ready made function in numpy/scipy to compute the correlation y=mx+o of an X and Y fast: m, m-err, o, o-err, r-coef,r-coef-err ? Or a formula to to compute the 3 error ranges? -robert PS: numpy.corrcoef computes only the bare coeff:
1
1709
by: filipefilipe | last post by:
Dear All, I'm trying extensively to install scipy in my Fedora 6.0. In fact after hard work I 'think' I got it. If I run a test inside python, it works well. My problem is when I try to run a program that wasn't written by me. In doing this (runnign the program), the following error message appears to me: File "/root/marder/optimize.py",...
6
3803
by: redcic | last post by:
Hi all, I've just downloaded scipy v 0.5.2 and I would like to be able to draw plots. I've tried: import scipy.gplt import scipy.plt import scipy.xplt and none of them work. Are these modules still included in scipy ? If not, where can I find them ?
5
5198
by: Stef Mientki | last post by:
hello, The import statement "import sqlite3" gives the error given below. In simple programs, the import statement (sometimes) succeed, and I can indeed access the database. So I guess there is some conflict with another part of my program, but as the program is rather large (and dynamic) it's not easy to isolate the problem. Does anyone...
0
7362
by: Hystou | last post by:
Most computers default to English, but sometimes we require a different language, especially when relocating. Forgot to request a specific language before your computer shipped? No problem! You can effortlessly switch the default language on Windows 10 without reinstalling. I'll walk you through it. First, let's disable language...
0
7602
Oralloy
by: Oralloy | last post by:
Hello folks, I am unable to find appropriate documentation on the type promotion of bit-fields when using the generalised comparison operator "<=>". The problem is that using the GNU compilers, it seems that the internal comparison operator "<=>" tries to promote arguments from unsigned to signed. This is as boiled down as I can make it. ...
1
7368
by: Hystou | last post by:
Overview: Windows 11 and 10 have less user interface control over operating system update behaviour than previous versions of Windows. In Windows 11 and 10, there is no way to turn off the Windows Update option using the Control Panel or Settings app; it automatically checks for updates and installs any it finds, whether you like it or not. For...
0
7704
tracyyun
by: tracyyun | last post by:
Dear forum friends, With the development of smart home technology, a variety of wireless communication protocols have appeared on the market, such as Zigbee, Z-Wave, Wi-Fi, Bluetooth, etc. Each protocol has its own unique characteristics and advantages, but as a user who is planning to build a smart home system, I am a bit confused by the...
1
5291
isladogs
by: isladogs | last post by:
The next Access Europe User Group meeting will be on Wednesday 1 May 2024 starting at 18:00 UK time (6PM UTC+1) and finishing by 19:30 (7.30PM). In this session, we are pleased to welcome a new presenter, Adolph Dupré who will be discussing some powerful techniques for using class modules. He will explain when you may want to use classes...
0
4911
by: conductexam | last post by:
I have .net C# application in which I am extracting data from word file and save it in database particularly. To store word all data as it is I am converting the whole word file firstly in HTML and then checking html paragraph one by one. At the time of converting from word file to html my equations which are in the word document file was convert...
0
3407
by: TSSRALBI | last post by:
Hello I'm a network technician in training and I need your help. I am currently learning how to create and manage the different types of VPNs and I have a question about LAN-to-LAN VPNs. The last exercise I practiced was to create a LAN-to-LAN VPN between two Pfsense firewalls, by using IPSEC protocols. I succeeded, with both firewalls in...
1
1837
by: 6302768590 | last post by:
Hai team i want code for transfer the data from one system to another through IP address by using C# our system has to for every 5mins then we have to update the data what the data is updated we have to send another system
0
657
bsmnconsultancy
by: bsmnconsultancy | last post by:
In today's digital era, a well-designed website is crucial for businesses looking to succeed. Whether you're a small business owner or a large corporation in Toronto, having a strong online presence can significantly impact your brand's success. BSMN Consultancy, a leader in Website Development in Toronto offers valuable insights into creating...

By using Bytes.com and it's services, you agree to our Privacy Policy and Terms of Use.

To disable or enable advertisements and analytics tracking please visit the manage ads & tracking page.