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• problem with hierarchical clustering in Python

  - by user248237

  I am doing a hierarchical clustering a 2 dimensional matrix by correlation distance metric (i.e. 1 - Pearson correlation). My code is the following (the data is in a variable called "data"): from hcluster import * Y = pdist(data, 'correlation') cluster_type = 'average' Z = linkage(Y, cluster_type) dendrogram(Z) The error I get is: ValueError: Linkage 'Z' contains negative distances. What causes this error? The matrix "data" that I use is simply: [[ 156.651968 2345.168618] [ 158.089968 2032.840106] [ 207.996413 2786.779081] [ 151.885804 2286.70533 ] [ 154.33665 1967.74431 ] [ 150.060182 1931.991169] [ 133.800787 1978.539644] [ 112.743217 1478.903191] [ 125.388905 1422.3247 ]] I don't see how pdist could ever produce negative numbers when taking 1 - pearson correlation. Any ideas on this? thank you.

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• float change from python 3.0.1 to 3.1.2

  - by Jeremy

  Im trying to learn python. I am using 3.1.2 and the o'reilly book is using 3.0.1 here is my code import urllib.request price = (99.99) while price 4.74: page = urllib.request.urlopen ("http://www.beans-r-us.biz/prices-loyalty.html") text = page.read().decode("utf8") where = text.find('>$') start_of_price = where + 2 end_of_price = start_of_price + 6 price = float(text[start_of_price:end_of_price]) print ("Buy!") - here is my error Traceback (most recent call last): File "/Users/odin/Desktop/Coffe.py", line 14, in price = float(text[start_of_price:end_of_price]) ValueError: invalid literal for float(): 4.59 what is wrong? please help!!

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• python list directory , subdirectory and files

  - by thomytheyon

  Hi Alls, I'm trying to make a script to list all directory, subdirectory, and files in a given directory. I tried this : import sys,os root="/home/patate/directory/" path=os.path.join(root,"targetdirectory") for r,d,f in os.walk(path): for file in f: print os.path.join(root,file) Unfortunatly it doesn't work properly, i get all the files, but not them complete path. like : if the dir struct would be : /home/patate/directory/targetdirectory/123/456/789/file.txt It would print: /home/patate/directory/targetdirectory/file.txt What i need is the first result, any help would be greatly appreciated ! Thanks

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• python: multiline regular expression

  - by facha

  Hi, everyone I have a piece of text and I've got to parse usernames and hashes out of it. Right now I'm doing it with two regular expressions. Could I do it with just one multiline regular expression? #!/usr/bin/env python import re test_str = """ Hello, UserName. Please read this looooooooooooooooong text. hash Now, write down this hash: fdaf9399jef9qw0j. Then keep reading this loooooooooong text. Hello, UserName2. Please read this looooooooooooooooong text. hash Now, write down this hash: gtwnhton340gjr2g. Then keep reading this loooooooooong text. """ logins = re.findall('Hello, (?P<login>.+).',test_str) hashes = re.findall('hash: (?P<hash>.+).',test_str)

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• Logical python question - handeling directories and files in them

  - by Konstantin

  Hello! I'm using this function to extract files from .zip archive and store it on the server: def unzip_file_into_dir(file, dir): import sys, zipfile, os, os.path os.makedirs(dir, 0777) zfobj = zipfile.ZipFile(file) for name in zfobj.namelist(): if name.endswith('/'): os.mkdir(os.path.join(dir, name)) else: outfile = open(os.path.join(dir, name), 'wb') outfile.write(zfobj.read(name)) outfile.close() And the usage: unzip_file_into_dir('/var/zips/somearchive.zip', '/var/www/extracted_zip') somearchive.zip have this structure: somearchive.zip 1.jpeg 2.jpeg another.jpeg or, somethimes, this one: somearchive.zip somedir/ 1.jpeg 2.jpeg another.jpeg Question is: how do I modify my function, so that my extracted_zip catalog would always contain just images, not images in another subdirectory, even if images are stored in somedir inside an archive.

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• J2EE: Default values for custom tag attributes

  - by Nick

  So according to Sun's J2EE documentation (http://docs.sun.com/app/docs/doc/819-3669/bnani?l=en&a=view), "If a tag attribute is not required, a tag handler should provide a default value." My question is how in the hell do I define a default value as per the documentation's description. Here's the code: <%@ attribute name="visible" required="false" type="java.lang.Boolean" %> <c:if test="${visible}"> My Tag Contents Here </c:if> Obviously, this tag won't compile because it's lacking the tag directive and the core library import. My point is that I want the "visible" property to default to TRUE. The "tag attribute is not required," so the "tag handler should provide a default value." I want to provide a default value, so what am I missing? Any help is greatly appreciated.

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• stting environment variables in powershell by calling python script that prints $env:myVar=myvalue

  - by leeg

  I have some legacy python scripts that manage my shell environment for all the programs and plugins I am running on Linux (bash) and windows (cmd.exe). I want to port this to powershell. How do I set environment variables in powershell by calling python script that prints $env:myVar=myvalue and causes my environment variable to persist in the powershell. In Bash I can use a bash function to call my python script which prints export var=value to stdout and the function will set the environment variables in my shell. This will also work in windows cmd shell by calling a .bat file. I cannot figure out how to do this in powershell. I think it should be something like this: setvar.ps1: function SETVAR {c:\python26\python.exe varconfig.py } varconfig.py: import sys print >> sys.stdout, '$env:myVar=foo'

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• Self-signed ceritificates for many users/browsers/sites

  - by Demiurg

  Here is my problem - I have a lot of users using different browsers accessing many internal web sites using https. I can create my own Certificate Authority, than create a certificate for each server and after that have all the users import it. Obviously, it cannot work in reality - there are too many users and too many sites, and some sites will be added in the future. I'm looking for a way to automate this. Is there a way to create a certificate so that all major browsers (IE, FF, Opera, Chrome and Safari) would trust it for all servers ? If so, what is the best way to install it automatically in all major browsers ?

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• How to write two-dimensional array to xml in Scala 2.8.0

  - by Shadowlands

  The following code (copied from a question from about a year ago) works fine under Scala 2.7.7, but does not behave correctly under Scala 2.8.0 (Beta 1, RC8). import scala.xml class Person(name : String, age : Int) { def toXml(): xml.Elem = <person><name>{ name }</name><age>{ age }</age></person> } def peopleToXml(people: Array[Person]): xml.Elem = { <people>{ for {person <- people} yield person.toXml }</people> } val data = Array(new Person("joe",40), new Person("mary", 35)) println(peopleToXml(data)) The output (according to 2.7.7) should be: <people><person><name>joe</name><age>40</age></person><person><name>mary</name><age>35</age></person></people> but instead comes out as: <people>\[Lscala.xml.Elem;@17821782</people> How do I get this to behave as it did in 2.7.x?

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• Windows environment variables change when opening command line?

  - by Jakobud

  Sometimes when I change my environment variables in Windows, and then use software the depends on those variables, they are not properly updated. And good example is to change a variable, then open up Windows Command Line and echo the variable and see that it hasn't been changed, even though you properly changed it in the Environment Variables window. Another example I'm dealing with right now: I've been using Python 2.4.x for a while for a project, which uses the env var PYTHONPATH who's value has been: C:\Python24;C:\Python24\lib Today I installed Python 2.5.x for the project. I changed my PYTHONPATH to be: C:\Python25;C:\Python25\lib When I use Python 2.5 to run a script and do this: import sys print sys.path It prints: 'C:\\PYTHON24', 'C:\\PYTHON24\\lib' (and some other Python 2.5 related default installation paths) So clearly, the old PYTHONPATH environment variable changes aren't really sticking.... Does anyone know why this happens and how to fix it?

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• Python: how to run several scripts (or functions) at the same time under windows 7 multicore processor 64bit

  - by Gianni

  sorry for this question because there are several examples in Stackoverflow. I am writing in order to clarify some of my doubts because I am quite new in Python language. i wrote a function: def clipmyfile(inFile,poly,outFile): ... # doing something with inFile and poly and return outFile Normally I do this: clipmyfile(inFile="File1.txt",poly="poly1.shp",outFile="res1.txt") clipmyfile(inFile="File2.txt",poly="poly2.shp",outFile="res2.txt") clipmyfile(inFile="File3.txt",poly="poly3.shp",outFile="res3.txt") ...... clipmyfile(inFile="File21.txt",poly="poly21.shp",outFile="res21.txt") I had read in this example Run several python programs at the same time and i can use (but probably i wrong) from multiprocessing import Pool p = Pool(21) # like in your example, running 21 separate processes to run the function in the same time and speed my analysis I am really honest to say that I didn't understand the next step. Thanks in advance for help and suggestion Gianni

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• Python 2.6, 3 abstract base class misunderstanding

  - by Aaron

  I'm not seeing what I expect when I use ABCMeta and abstractmethod. This works fine in python3: from abc import ABCMeta, abstractmethod class Super(metaclass=ABCMeta): @abstractmethod def method(self): pass a = Super() TypeError: Can't instantiate abstract class Super ... And in 2.6: class Super(): __metaclass__ = ABCMeta @abstractmethod def method(self): pass a = Super() TypeError: Can't instantiate abstract class Super ... They both also work fine (I get the expected exception) if I derive Super from object, in addition to ABCMeta. They both "fail" (no exception raised) if I derive Super from list. I want an abstract base class to be a list but abstract, and concrete in sub classes. Am I doing it wrong, or should I not want this in python?

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• How to create a HTML world map with GeoDjango ?

  - by pierre-guillaume-degans

  The GeoDjango tutorial explains how to insert world borders into a spatial database. I would like to create a world Map in HTML with these data, with both map and area tags. Something like that. I just don't know how to retrieve the coordinates for each country (required for the area's coords attribute). from world.models import WorldBorders for country in WorldBorders.objects.all(): print u'<area shape="poly" title="%s" alt="%s" coords="%s" />' % (v.name, v.name, "???") Thanks !

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• Is there a strategy to back-port C# code?

  - by ianmayo

  Hi all, I intend using the Argotic framework in support of a .Net Atom server. Unfortunately my target server (over which I have no control) only has .Net 1.1 - any the Argotic library is only in .Net 2 and 3.5. So, I now need to back-port the code to 1.1. Can anybody provide any strategic tips for this undertaking? I'm aware of the merits of using Unit Tests to verify the ported code (here). should I be looking for automated tools? should I just import the code into VS2003 .Net 1.1 project and work through the compiler warnings? Any tips appreciated. cheers, Ian

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• Weak reference and Strong reference

  - by theband

  package uk.co.bigroom.utils { import flash.utils.Dictionary; /** * Class to create a weak reference to an object. A weak reference * is a reference that does not prevent the object from being * garbage collected. If the object has been garbage collected * then the get method will return null. */ public class WeakRef { private var dic:Dictionary; /** * The constructor - creates a weak reference. * * @param obj the object to create a weak reference to */ public function WeakRef( obj:* ) { dic = new Dictionary( true ); dic[obj] = 1; } /** * To get a strong reference to the object. * * @return a strong reference to the object or null if the * object has been garbage collected */ public function get():* { for ( var item:* in dic ) { return item; } return null; } } } In this Class, how they denote one as Weak Reference and one as Strong reference.

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• The conceptual process of populating related tables in a database (MySql) from a CSV file

  - by user322772

  I'm new to relational databases and all the material I've read covered primary and foreign keys, normal forms, and joins but left out to populate the database once it's created. How do you import a CSV file so the fields match their related table? Say you were tying to build a beer database and had a CSV file with each line as a record. Header: brewer, beer_name, country, city, state, beer_category, beer_type, alcohol_content Record 1: Anheuser-Busch, Budweiser, United States, St. Louis, Mo, Pale lager, Regular, 5.0% Record 2: Anheuser-Busch, Bud Light, United States, St. Louis, Mo, Pale lager Light, 4.2% Record 3: Miller Brewing Company, Miller Lite, United States, Milwaukee, WI, Pale lager, Light, 4.2% You can create a "Brewer" table and a "Beer" table. When importing how does you connect the primary keys between the tables?

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• Find&Replace using Python - Binary file

  - by Aaron Hoffman

  Hello, I'm attempting to do a "find and replace" in a file on a Mac OS X computer. Although it appears to work correctly. It seems that the file is somehow altered. The text editor that I use (Text Wrangler) is unable to even open the file once this is completed. Here is the code as I have it: import fileinput for line in fileinput.FileInput("testfile.txt",inplace=1): line = line.replace("newhost",host) print line, When I view the file from the terminal, it does say "testfile" may be a binary file. See it anyway? Is there a chance that this replace is corrupting the file? Do I have another option for this to work? I really appreciate the help. Thank you, Aaron UPDATE: the actual file is NOT a .txt file it is a .plist file which is preference file in Mac OS X if that makes any difference

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• Can this loop be sped up in pure Python?

  - by Noctis Skytower

  I was trying out an experiment with Python, trying to find out how many times it could add one to an integer in one minute's time. Assuming two computers are the same except for the speed of the CPUs, this should give an estimate of how fast some CPU operations may take for the computer in question. The code below is an example of a test designed to fulfill the requirements given above. This version is about 20% faster than the first attempt and 150% faster than the third attempt. Can anyone make any suggestions as to how to get the most additions in a minute's time span? Higher numbers are desireable. EDIT: This experiment is being written in Python 3.1 and is 15% faster than the fourth speed-up attempt. def start(seconds): import time, _thread def stop(seconds, signal): time.sleep(seconds) signal.pop() total, signal = 0, [None] _thread.start_new_thread(stop, (seconds, signal)) while signal: total += 1 return total if __name__ == '__main__': print('Testing the CPU speed ...') print('Relative speed:', start(60))

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• Python+Windows+GStreamer = Impossible (for me)?

  - by james

  Hi :) essentially, my problem is, ater a long time searching, finding only this other question, i decided i was just going to ask my own... i am on windows 7 with python 2.6 and ossbuild GStreamer, but i am trying to get the python binding for it, and struggling. i have got gst-python from http://gstreamer.freedesktop.org/src/gst-python/ but as my eyes and research tell me, it does not work in the setup.py way, and the other question has a link to a site that he says has a binary avaiable, which no longer does, http://www.gstreamer-winbuild.ylatuya.es/doku.php?id=download and even the sdk is gone, and ossbuild dont seem to have anything useful either. so essentially, my question is, can anyone tell me a method, however convoluted, of getting my setup so if i write a script for (py)gst, with an import gst it will work? not the best of explanations... im tired k? xxx :)

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• Running Python code from Java program, shoudl i be doing this?

  - by Space Rocker

  i have a scenario where i draw a network and set all it's paraments on swing based gui, after that i have to translate this network into a python based script which another framework reads and realize this network in the form of virtual machines. As an example have look here: from mininet.topo import Topo, Node class MyTopo( Topo ): def *__init__*( self, enable_all = True ): super( MyTopo, self ).__init__() Host = 1 Switch = 2 self.add_node( Switch, Node( is_switch=True ) ) self.add_node( Host, Node( is_switch=False ) ) self.add_edge( Host, Switch ) self.enable_all() topos = { 'mytopo': ( lambda: MyTopo() ) } It simply connects a host to a switch and realize this topology on mininet framework. Now for now in order to realize the drawn network on java GUI here is what i am doing: I simply take the information from GUI and creates a new python file like the one above using java code and then run this file in mininet, which works fine somehow. I want to know, is this the correct and robust way how i am doing this or should i be looking further into java-python bridge like scenarios to be more effective or so as to say more professional.

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• Images to video - converting to IplImage makes video blue

  - by user891908

  I want to create a video from images using opencv. The strange problem is that if i will write image (bmp) to disk and then load (cv.LoadImage) it it renders fine, but when i try to load image from StringIO and convert it to IplImage, it turns video to blue. Heres the code: import StringIO output = StringIO.StringIO() FOREGROUND = (0, 0, 0) TEXT = 'MY TEXT' font_path = 'arial.ttf' font = ImageFont.truetype(font_path, 18, encoding='unic') text = TEXT.decode('utf-8') (width, height) = font.getsize(text) # Create with background with place for text w,h=(600,600) contentimage=Image.open('0.jpg') background=Image.open('background.bmp') x, y = contentimage.size # put content onto background background.paste(contentimage,(((w-x)/2),0)) draw = ImageDraw.Draw(background) draw.text((0,0), text, font=font, fill=FOREGROUND) pi = background pi.save(output, "bmp") #pi.show() #shows image in full color output.seek(0) pi= Image.open(output) print pi, pi.format, "%dx%d" % pi.size, pi.mode cv_im = cv.CreateImageHeader(pi.size, cv.IPL_DEPTH_8U, 3) cv.SetData(cv_im, pi.tostring()) print pi.size, cv.GetSize(cv_im) w = cv.CreateVideoWriter("2.avi", cv.CV_FOURCC('M','J','P','G'), 1,(cv.GetSize(cv_im)[0],cv.GetSize(cv_im)[1]), is_color=1) for i in range(1,5): cv.WriteFrame(w, cv_im) del w

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• Creating a unique key based on file content in python

  - by Cawas

  I got many, many files to be uploaded to the server, and I just want a way to avoid duplicates. Thus, generating a unique and small key value from a big string seemed something that a checksum was intended to do, and hashing seemed like the evolution of that. So I was going to use hash md5 to do this. But then I read somewhere that "MD5 are not meant to be unique keys" and I thought that's really weird. What's the right way of doing this? edit: by the way, I took two sources to get to the following, which is how I'm currently doing it and it's working just fine, with Python 2.5: import hashlib def md5_from_file (fileName, block_size=2**14): md5 = hashlib.md5() f = open(fileName) while True: data = f.read(block_size) if not data: break md5.update(data) f.close() return md5.hexdigest()

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• what is wrong: "value Parsers is not a member of package scala.util.parsing.combinator"?

  - by Nick Fortescue

  I've got the above odd error message that I don't understand "value Parsers is not a member of package scala.util.parsing.combinator". I'm trying to learn Parser combinators by writing a C parser step by step. I started at token, so I have the classes: import util.parsing.combinator.JavaTokenParsers object CeeParser extends JavaTokenParsers { def token: Parser[CeeExpr] = ident } abstract class CeeExpr case class Token(name: String) extends CeeExpr This is as simple as I could make it. The code below works fine, but if I uncomment the commented line I get the error message given above: object Play { def main(args: Array[String]) { //val parser: _root_.scala.util.parsing.combinator.Parsers.Parser[CeeExpr] CeeParser.token val x = CeeParser.token print(x) } } In case it is a problem with my setup, I'm using scala 2.7.6 via the scala-plugin for intellij. Can anyone shed any light on this? The message is wrong, Parsers is a member of scala.util.parsing.combinator.

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• Python problem with resize animate GIF

  - by gigimon

  Hello! I'm want to resize animated GIF with save animate. I'm try use PIL and PythonMagickWand (ImageMagick) and with some GIF's get bad frame. When I'm use PIL, it mar frame in read frame. For test, I'm use this code: from PIL import Image im = Image.open('d:/box_opens_closes.gif') im.seek(im.tell()+1) im.seek(im.tell()+1) im.seek(im.tell()+1) im.show() When I'm use MagickWand with this code: wand = NewMagickWand() MagickReadImage(wand, 'd:/Box_opens_closes.gif') MagickSetLastIterator(wand) length = MagickGetIteratorIndex(wand) MagickSetFirstIterator(wand) for i in range(0, length+1): MagickSetIteratorIndex(wand,i) MagickScaleImage(wand, 87, 58) MagickWriteImages(wand, 'path', 1) My GIF where I'm get bad frame this: test gif In GIF editor software, all freme is ok. Where problem? Thx

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• Magento images not showing on front end

  - by Robin Williams

  I'm using Magento 1.4. I have two website set up. If I upload images to Website A, they appear fine on both front and back end. If I upload or import images to Website B, they do not appear on the front end, only the backend. I'm completely stuck. I'm happy to provide any additional details that may be helpful, but am so frustrated I'm not sure what is necessary info to fix the problem. Thanks!

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