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  • Converting python objects for rpy2

    - by bgbg
    The following code is supposed to created a heatmap in rpy2 import numpy as np from rpy2.robjects import r data = np.random.random((10,10)) r.heatmap(data) However, it results in the following error Traceback (most recent call last): File "z.py", line 8, in <module> labRow=rowNames, labCol=colNames) File "C:\Python25\lib\site-packages\rpy2\robjects\__init__.py", line 418, in __call__ new_args = [conversion.py2ri(a) for a in args] File "C:\Python25\lib\site-packages\rpy2\robjects\__init__.py", line 93, in default_py2ri raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o)))) ValueError: Nothing can be done for the type <type 'numpy.ndarray'> at the moment. From the documentation I learn that r.heatmap expects "a numeric matrix". How do I convert np.array to the required data type?

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  • How can I plot NaN values as a special color with imshow in matplotlib?

    - by Adam Fraser
    example: import numpy as np import matplotlib.pyplot as plt f = plt.figure() ax = f.add_subplot(111) a = np.arange(25).reshape((5,5)).astype(float) a[3,:] = np.nan ax.imshow(a, interpolation='nearest') f.canvas.draw() The resultant image is unexpectedly all blue (the lowest color in the jet colormap). However, if I do the plotting like this: ax.imshow(a, interpolation='nearest', vmin=0, vmax=24) --then I get something better, but the NaN values are drawn the same color as vmin... Is there a graceful way that I can set NaNs to be drawn with a special color (eg: gray or transparent)?

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  • Plot smooth line with PyPlot

    - by Paul
    I've got the following simple script that plots a graph: import matplotlib.pyplot as plt import numpy as np T = np.array([6, 7, 8, 9, 10, 11, 12]) power = np.array([1.53E+03, 5.92E+02, 2.04E+02, 7.24E+01, 2.72E+01, 1.10E+01, 4.70E+00]) plt.plot(T,power) plt.show() As it is now, the line goes straight from point to point which looks ok, but could be better in my opinion. What I want is to smooth the line between the points. In Gnuplot I would have plotted with smooth cplines. Is there an easy way to do this in PyPlot? I've found some tutorials, but they all seem rather complex.

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  • Python Imaging: YCbCr problems

    - by daver
    Hi, I'm doing some image processing in Python using PIL, I need to extract the luminance layer from a series of images, and do some processing on that using numpy, then put the edited luminance layer back into the image and save it. The problem is, I can't seem to get any meaningful representation of my Image in a YCbCr format, or at least I don't understand what PIL is giving me in YCbCr. PIL documentation claims YCbCr format gives three channels, but when I grab the data out of the image using np.asarray, I get 4 channels. Ok, so I figure one must be alpha. Here is some code I'm using to test this process: import Image as im import numpy as np pengIm = im.open("Data\\Test\\Penguins.bmp") yIm = pengIm.convert("YCbCr") testIm = np.asarray(yIm) grey = testIm[:,:,0] grey = grey.astype('uint8') greyIm = im.fromarray(grey, "L") greyIm.save("Data\\Test\\grey.bmp") I'm expecting a greyscale version of my image, but what I get is this jumbled up mess: http://i.imgur.com/zlhIh.png Can anybody explain to me where I'm going wrong? The same code in matlab works exactly as I expect.

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  • How to make scipy.interpolate give a an extrapolated result beyond the input range?

    - by Salim Fadhley
    I'm trying to port a program which uses a hand-rolled interpolator (developed by a mathematitian colleage) over to use the interpolators provided by scipy. I'd like to use or wrap the scipy interpolator so that it has as close as possible behavior to the old interpolator. A key difference between the two functions is that in our original interpolator - if the input value is above or below the input range, our original interpolator will extrapolate the result. If you try this with the scipy interpolator it raises a ValueError. Consider this program as an example: import numpy as np from scipy import interpolate x = np.arange(0,10) y = np.exp(-x/3.0) f = interpolate.interp1d(x, y) print f(9) print f(11) # Causes ValueError, because it's greater than max(x) Is there a sensible way to make it so that instead of crashing, the final line will simply do a linear extrapolate, continuing the gradients defined by the first and last two pouints to infinity. Note, that in the real software I'm not actually using the exp function - that's here for illustration only!

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  • TypeError: 'NoneType' object does not support item assignment

    - by R S John
    I am trying to do some mathematical calculation according to the values at particular index of a NumPy array with the following code X = np.arange(9).reshape(3,3) temp = X.copy().fill(5.446361E-01) ind = np.where(X < 4.0) temp[ind] = 0.5*X[ind]**2 - 1.0 ind = np.where(X >= 4.0 and X < 9.0) temp[ind] = (5.699327E-1*(X[ind]-1)**4)/(X[ind]**4) print temp But I am getting the following error Traceback (most recent call last): File "test.py", line 7, in <module> temp[ind] = 0.5*X[ind]**2 - 1.0 TypeError: 'NoneType' object does not support item assignment Would you please help me in solving this? Thanks

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  • Confusion between numpy, scipy, matplotlib and pylab

    - by goFrendiAsgard
    Numpy, scipy, matplotlib, and pylab are common terms among they who use python for scientific computation. I just learn a bit about pylab, and I got a lot of confusion. Whenever I want to import numpy, I can always do: import numpy as np I just consider, that once I do from pylab import * The numpy will be imported as well (with np alias). So basically the second one do more things compared to the first one. There are few things I want to ask. Is it right that pylab is just a wrapper for numpy, scipy and matplotlib? As np is the numpy alias, what is the scipy and matplotlib alias? (as far as I know, plt is alias of matplotlib.pyplot, but I don't know the alias for the matplotlib itself) Thanks in advance.

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  • Multiplying Block Matrices in Numpy

    - by Ada Xu
    Hi Everyone I am python newbie I have to implement lasso L1 regression for a class assignment. This involves solving a quadratic equation involving block matrices. minimize x^t * H * x + f^t * x where x 0 Where H is a 2 X 2 block matrix with each element being a k dimensional matrix and x and f being a 2 X 1 vectors each element being a k dimension vector. I was thinking of using nd arrays. such that np.shape(H) = (2, 2, k, k) np.shape(x) = (2, k) But I figured out that np.dot(X, H) doesn't work here. Is there an easy way to solve this problem? Thanks in advance.

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  • Construct Numpy index given list of starting and ending positions

    - by Abiel
    I have two identically-sized numpy.array objects (both one-dimensional), one of which contains a list of starting index positions, and the other of which contains a list of ending index positions (alternatively you could say I have a list of starting positions and window lengths). In case it matters, the slices formed by the starting and ending positions are guaranteed to be non-overlapping. I am trying to figure out how to use these starting and ending positions to form an index for another array object, without having to use a loop. For example: import numpy as np start = np.array([1,7,20]) end = np.array([3,10,25]) Want to reference somearray[1,2,7,8,9,20,21,22,23,24])

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  • C# TextBox Autocomplete (Winforms) key events and customization?

    - by m0s
    Hi, I was wondering if it is possible to catch key events for auto-complete list. For example instead of Enter key press for auto-complete use lets say Tab key. Also is it possible to change the colors and add background image for the auto-complete pop-up list? Currently I have my own implementation which is a separate window(form) with a list-box, which works OK, but Id really like to use .net's auto-complete if it can do what I need. Thanks for attention.

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  • How to remove the boundary effects arising due to zero padding in scipy/numpy fft?

    - by Omkar
    I have made a python code to smoothen a given signal using the Weierstrass transform, which is basically the convolution of a normalised gaussian with a signal. The code is as follows: #Importing relevant libraries from __future__ import division from scipy.signal import fftconvolve import numpy as np def smooth_func(sig, x, t= 0.002): N = len(x) x1 = x[-1] x0 = x[0] # defining a new array y which is symmetric around zero, to make the gaussian symmetric. y = np.linspace(-(x1-x0)/2, (x1-x0)/2, N) #gaussian centered around zero. gaus = np.exp(-y**(2)/t) #using fftconvolve to speed up the convolution; gaus.sum() is the normalization constant. return fftconvolve(sig, gaus/gaus.sum(), mode='same') If I run this code for say a step function, it smoothens the corner, but at the boundary it interprets another corner and smoothens that too, as a result giving unnecessary behaviour at the boundary. I explain this with a figure shown in the link below. Boundary effects This problem does not arise if we directly integrate to find convolution. Hence the problem is not in Weierstrass transform, and hence the problem is in the fftconvolve function of scipy. To understand why this problem arises we first need to understand the working of fftconvolve in scipy. The fftconvolve function basically uses the convolution theorem to speed up the computation. In short it says: convolution(int1,int2)=ifft(fft(int1)*fft(int2)) If we directly apply this theorem we dont get the desired result. To get the desired result we need to take the fft on a array double the size of max(int1,int2). But this leads to the undesired boundary effects. This is because in the fft code, if size(int) is greater than the size(over which to take fft) it zero pads the input and then takes the fft. This zero padding is exactly what is responsible for the undesired boundary effects. Can you suggest a way to remove this boundary effects? I have tried to remove it by a simple trick. After smoothening the function I am compairing the value of the smoothened signal with the original signal near the boundaries and if they dont match I replace the value of the smoothened func with the input signal at that point. It is as follows: i = 0 eps=1e-3 while abs(smooth[i]-sig[i])> eps: #compairing the signals on the left boundary smooth[i] = sig[i] i = i + 1 j = -1 while abs(smooth[j]-sig[j])> eps: # compairing on the right boundary. smooth[j] = sig[j] j = j - 1 There is a problem with this method, because of using an epsilon there are small jumps in the smoothened function, as shown below: jumps in the smooth func Can there be any changes made in the above method to solve this boundary problem?

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  • change password.......

    - by shimaTun
    I've created a code to change a password. Now it seem contain an error. When I fill in the form to change password, and click save the error message: You forgot enter your userid! Please try again. I really don’t know what the error message means. Please guys. Help me fix it. Here's is the code: <?php # change password.php //set the page title and include the html header. $page_title = 'Change Your Password'; //include('templates/header.inc'); if(isset($_POST['submit'])){//handle the form require_once('connectioncomplaint.php');//connect to the db. //include "connectioncomplaint.php"; //create a function for escaping the data. function escape_data($data){ global $dbc;//need the connection. if(ini_get('magic_quotes_gpc')){ $data=stripslashes($data); } return mysql_real_escape_string($data); }//end function $message=NULL;//create the empty new variable. //check for a username if(empty($_POST['userid'])){ $u=FALSE; $message .='<p> You forgot enter your userid!</p>'; }else{ $u=escape_data($_POST['userid']); } //check for existing password if(empty($_POST['password'])){ $p=FALSE; $message .='<p>You forgot to enter your existing password!</p>'; }else{ $p=escape_data($_POST['password']); } //check for a password and match againts the comfirmed password. if(empty($_POST['password1'])) { $np=FALSE; $message .='<p> you forgot to enter your new password!</p>'; }else{ if($_POST['password1'] == $_POST['password2']){ $np=escape_data($_POST['password1']); }else{ $np=FALSE; $message .='<p> your new password did not match the confirmed new password!</p>'; } } if($u && $p && $np){//if everything's ok. $query="SELECT userid FROM access WHERE (userid='$u' AND password=PASSWORD('$p'))"; $result=@mysql_query($query); $num=mysql_num_rows($result); if($num == 1){ $row=mysql_fetch_array($result, MYSQL_NUM); //make the query $query="UPDATE access SET password=PASSWORD('$np') WHERE userid=$row[0]"; $result=@mysql_query($query);//run the query. if(mysql_affected_rows() == 1) {//if it run ok. //send an email,if desired. echo '<p><b>your password has been changed.</b></p>'; //include('templates/footer.inc');//include the HTML footer. exit();//quit the script. }else{//if it did not run OK. $message= '<p>Your password could not be change due to a system error.We apolpgize for any inconvenience.</p><p>' .mysql_error() .'</p>'; } }else{ $message= '<p> Your username and password do not match our records.</p>'; } mysql_close();//close the database connection. }else{ $message .='<p>Please try again.</p>'; } }//end of the submit conditional. //print the error message if there is one. if(isset($message)){ echo'<font color="red">' , $message, '</font>'; } ?> <form action="<?php echo $_SERVER['PHP_SELF']; ?>" method="post">

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  • working with arrays

    - by user295189
    I currently do a query which goes through the records and forms an array. the print_r on query gives me this print_r($query) yields the following: Array ( [0] = ( [field1] = COMPLETE [field2] = UNKNOWN [field3] = Test comment ) [1] = ( [field1] = COMPLETE [field2] = UNKNOWN [field3] = comment here ) [2] = ( [field1] = COMPLETE [field2] = UNKNOWN [field3] = checking ) [3] = ( [field1] = COMPLETE [field2] = UNKNOWN [field3] = testing ) [4] = ( [field1] = COMPLETE [field2] = UNKNOWN [field3] = working ) ) somehow I want to take this array and convert it back to php. So for example some thing like this $myArray = array( ...) then $myArray should yield the samething as the print_r($query) yeilds. Thanks

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  • Algorithm to aggregate values from child tree nodes

    - by user222164
    I have objects in a tree structure, I would like to aggregate status information from children nodes and update parent node with aggregated status. Lets say node A has children B1, B2, and B1 has C1, C2, C3 as children. Each of the nodes have a status attribute. Now if C1, C2, C3 are all complete then I would like to mark B1 as completed. And if C4, C5,C6,C7 are complete make B2 as complete. When B1 and B2 are both complete mark A as complete. I can go through these nodes in brute force method and make updates, could someone suggest an efficient algorithm to do it. A { B1 { C1, C2, C3}, B2 { C4, C5, C6, C7} }

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  • CentOS: make python 2.6 see django

    - by NP
    In a harrowing attempt to get mod_wsgi to run on CentOS 5.4, I've added python 2.6 as an optional library following the instructions here. The configuration seems fine except that when trying to ping the server the Apache log prints this error: mod_wsgi (pid=20033, process='otalo', application='127.0.0.1|'): Loading WSGI script '...django.wsgi'. [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] mod_wsgi (pid=20033): Target WSGI script '...django.wsgi' cannot be loaded as Python module. [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] mod_wsgi (pid=20033): Exception occurred processing WSGI script '...django.wsgi'. [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] Traceback (most recent call last): [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] File "...django.wsgi", line 8, in [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] import django.core.handlers.wsgi [Sat Mar 27 16:11:45 2010] [error] [client 171.66.52.218] ImportError: No module named django.core.handlers.wsgi when I go to my python2.6 install's command line and try 'import django', the module is not found (ImportError). However, my default python 2.4 installation (still working fine) is able to import successfully. How do I point python 2.6 to django? Thanks in advance.

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  • Lua SQL: peeking at cursors

    - by NP
    I am using LuaSQL, and query for a result set using con:execute(sql_stmt), which returns a cursor. How do I see if there is at least one row in that resultset, without doing a cursor:fetch to pop that first row?

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  • Creating flash slideshlow c#

    - by np
    Hi We have a few flash files f1.swf, f2.swf .... fn.swf. We would like to be able to display a slide show of these different files in c# using winforms. Each flash file is a slideshow by itself. At the end of slideshow for f1 we need to display a message and ask the user to repeat it or continue. Just wondering if anyone has any suggestions how to achieve this. Thanks N

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  • CentOS: revert python version back to original

    - by NP
    Hi all, I installed python 2.6 using the instructions here on CentOS 5.4. However I realized it was a bad move and I need to revert back to 2.4, which was there originally. Can anyone guide me on how to undo what I did here? In particular, I am not sure how to undo this: Configure ld to find your shared libs: $ cat /etc/ld.so.conf.d/opt-python2.5.conf /opt/python2.5/lib (hit enter) (hit ctrl-d to return to shell) $ ldconfig I tried removing the alias and the symlink and even re-aliasing python to /usr/bin/python, but when I try to install an RPM i get this error: error: Failed dependencies: libpython2.4.so.1.0 is needed by ... Thanks in advance.

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  • Django Admin: Many-to-Many listbox doesn't show up with a through parameter

    - by NP
    Hi All, I have the following models: class Message(models.Model): date = models.DateTimeField() user = models.ForeignKey(User) thread = models.ForeignKey('self', blank=True, null=True) ... class Forum(models.Model): name = models.CharField(max_length=24) messages = models.ManyToManyField(Message, through="Message_forum", blank=True, null=True) ... class Message_forum(models.Model): message = models.ForeignKey(Message) forum = models.ForeignKey(Forum) status = models.IntegerField() position = models.IntegerField(blank=True, null=True) tags = models.ManyToManyField(Tag, blank=True, null=True) In the admin site, when I go to add/change a forum, I don't see the messages listbox as you'd expect. However, it shows up if I remove the 'through' parameter in the ManyToManyField declaration. What's up with that? I've registered all three models (plus Tag) to the admin site in admin.py. TIA

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  • The operation has timed out

    - by np
    We shave this code which result in timeout when downlaoding the file programatically: System.Net.WebClient Client = new System.Net.WebClient(); if (!File.Exists(fileName)) { Client.DownloadFile(downloadLink, fileName); HtFilesSuccessfullyDownloaded[fileName] = fileName; string SuccessfullyDownloadedFiles = Path.Combine(dirName, "SuccessfullyDownloadedFiles.txt"); File.AppendAllText(SuccessfullyDownloadedFiles, Environment.NewLine + fileName); } It looks like when the files are large we are getting the timeout error when DownloadFile method is called. We have added the followign in web.config but it does not look like it helps: <httpRuntime maxRequestLength="1048576" executionTimeout="3600" /> Please let me know if you have any suggestions.

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  • Django admin: how do I add an unrelated model field to a model change/add page?

    - by NP
    I have the following models: class Foo(models.Model): field1 = models.IntegerField() ... class Bar(models.Model): field1 = models.IntegerField() ... class Foo_bar(models.Model): foo = models.ForeignKey(Foo) bar = models.ForeignKey(Bar) ... In the admin, I want it so that in the Foo change/add page, you can specify a Bar object, and on save I want to create a Foo_bar object to represent the relationship. How can I do this through customizing the Admin site/ModelAdmins? Thanks.

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  • MySQL 5 left join unknown column

    - by NP
    I had the below query working in mysql 4.1, but does not in 5.0: SELECT * FROM email e, event_email ee LEFT JOIN member m on m.email=e.email WHERE ee.email_id = e.email_id The error: 1054 (Unknown column 'e.email' in 'on clause')

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  • Dataset size limit as an xml file.

    - by np
    Hi We are currently using DataSet for loading and saving our data to an xml file using Dataset and there is a good possibility that the size of the xml file could get very huge. Either way we are wondering if there is any limit on the size for an xml file so the Dataset would not run into any issues in the future due to the size of it. Please advise. Thanks N

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