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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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  • python logparse search specific text

    - by krisdigitx
    hi, I am using this function in my code to return the strings i want from reading the log file, I want to grep the "exim" process and return the results, but running the code gives no error, but the output is limited to three lines, how can i just get the output only related to exim process.. #output: {'date': '13', 'process': 'syslogd', 'time': '06:27:33', 'month': 'May'} {'date': '13', 'process': 'exim[23168]:', 'time': '06:27:33', 'month': 'May'} {'May': ['syslogd']} #function: def generate_log_report(logfile): report_dict = {} for line in logfile: line_dict = dictify_logline(line) print line_dict try: month = line_dict['month'] date = line_dict['date'] time = line_dict['time'] #process = line_dict['process'] if "exim" in line_dict['process']: process = line_dict['process'] break else: process = line_dict['process'] except ValueError: continue report_dict.setdefault(month, []).append(process) return report_dict

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  • Python decorator question

    - by nsharish
    decorator 1: def dec(f): def wrap(obj, *args, **kwargs): f(obj, *args,**kwargs) return wrap decorator 2: class dec: def __init__(self, f): self.f = f def __call__(self, obj, *args, **kwargs): self.f(obj, *args, **kwargs) A sample class, class Test: @dec def disp(self, *args, **kwargs): print(*args,**kwargs) The follwing code works with decorator 1 but not with decorator 2. a = Test() a.disp("Message") I dont understand why decorator 2 is not working here. Can someone help me with this?

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  • Find last match with python regular expression

    - by SDD
    I wanto to match the last occurence of a simple pattern in a string, e.g. list = re.findall(r"\w+ AAAA \w+", "foo bar AAAA foo2 AAAA bar2) print "last match: ", list[len(list)-1] however, if the string is very long, a huge list of matches is generated. Is there a more direct way to match the second occurence of "AAAA" or should I use this workaround?

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  • Generating Mouse-Keyboard combination events in python

    - by freakazo
    I want to be able to do a combination of keypresses and mouseclicks simultaneously, as in for example Control+LeftClick At the moment I am able to do Control and then a left click with the following code: import win32com, win32api, win32con def CopyBox( x, y): time.sleep(.2) wsh = win32com.client.Dispatch("WScript.Shell") wsh.SendKeys("^") win32api.SetCursorPos((x,y)) win32api.mouse_event(win32con.MOUSEEVENTF_LEFTDOWN, x, y, 0, 0) win32api.mouse_event(win32con.MOUSEEVENTF_LEFTUP, x, y, 0, 0) What this does is press control on the keyboard, then it clicks. I need it to keep the controll pressed longer and return while it's still pressed to continue running the code. Is there a maybe lower level way of saying press the key and then later in the code tell it to lift up the key such as like what the mouse is doing?

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  • Python:Comparing Two Dictionaries

    - by saun jean
    The first Dict is fixed.This Dict will remain as it is List of Countries with there Short Names. firstDict={'ERITREA': 'ER', 'LAOS': 'LA', 'PORTUGAL': 'PT', "D'IVOIRE": 'CI', 'MONTENEGRO': 'ME', 'NEW CALEDONIA': 'NC', 'SVALBARD AND JAN MAYEN': 'SJ', 'BAHAMAS': 'BS', 'TOGO': 'TG', 'CROATIA': 'HR', 'LUXEMBOURG': 'LU', 'GHANA': 'GH'} However This Tuple result has multiple Dict inside it.This is the format in which MySQLdb returns result: result =({'count': 1L, 'country': 'Eritrea'}, {'count': 1L, 'country': 'Togo'}, {'count': 1L, 'country': 'Sierra Leone'}, {'count': 3L, 'country': 'Bahamas'}, {'count': 1L, 'country': 'Ghana'}) Now i want to compare these both results With COUNTRY Names and If 'Country' in Result is present in firstDict then put the value.else put the 0 The result desired is: mainRes={'ER':1,'TG':1,'BS':3,'GH':0,'LU':0}

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  • python / sets / dictionary / initialization

    - by Mario D
    Can someone explain help me understand how the this bit of code works? Particularly how the myHeap assignment works. I know the freq variable is assigned as a dictionary. But what about my myHeap? is it a Set? exe_Data = { 'e' : 0.124167, 't' : 0.0969225, 'a' : 0.0820011, 'i' : 0.0768052, } freq = exe_Data) myHeap = [[pct, [symbol, ""]] for symbol, pct in freq.items()]

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  • Can't iterate over a list class in Python

    - by Vicky
    I'm trying to write a simple GUI front end for Plurk using pyplurk. I have successfully got it to create the API connection, log in, and retrieve and display a list of friends. Now I'm trying to retrieve and display a list of Plurks. pyplurk provides a GetNewPlurks function as follows: def GetNewPlurks(self, since): '''Get new plurks since the specified time. Args: since: [datetime.datetime] the timestamp criterion. Returns: A PlurkPostList object or None. ''' offset = jsonizer.conv_datetime(since) status_code, result = self._CallAPI('/Polling/getPlurks', offset=offset) return None if status_code != 200 else \ PlurkPostList(result['plurks'], result['plurk_users'].values()) As you can see this returns a PlurkPostList, which in turn is defined as follows: class PlurkPostList: '''A list of plurks and the set of users that posted them.''' def __init__(self, plurk_json_list, user_json_list=[]): self._plurks = [PlurkPost(p) for p in plurk_json_list] self._users = [PlurkUser(u) for u in user_json_list] def __iter__(self): return self._plurks def GetUsers(self): return self._users def __eq__(self, other): if other.__class__ != PlurkPostList: return False if self._plurks != other._plurks: return False if self._users != other._users: return False return True Now I expected to be able to do something like this: api = plurk_api_urllib2.PlurkAPI(open('api.key').read().strip(), debug_level=1) plurkproxy = PlurkProxy(api, json.loads) user = plurkproxy.Login('my_user', 'my_pass') ps = plurkproxy.GetNewPlurks(datetime.datetime(2009, 12, 12, 0, 0, 0)) print ps for p in ps: print str(p) When I run this, what I actually get is: <plurk.PlurkPostList instance at 0x01E8D738> from the "print ps", then: for p in ps: TypeError: __iter__ returned non-iterator of type 'list' I don't understand - surely a list is iterable? Where am I going wrong - how do I access the Plurks in the PlurkPostList?

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  • Python ctypes argument errors

    - by Patrick Moriarty
    Hello. I wrote a test dll in C++ to make sure things work before I start using a more important dll that I need. Basically it takes two doubles and adds them, then returns the result. I've been playing around and with other test functions I've gotten returns to work, I just can't pass an argument due to errors. My code is: import ctypes import string nDLL = ctypes.WinDLL('test.dll') func = nDLL['haloshg_add'] func.restype = ctypes.c_double func.argtypes = (ctypes.c_double,ctypes.c_double) print(func(5.0,5.0)) It returns the error for the line that called "func": ValueError: Procedure probably called with too many arguments (8 bytes in excess) What am I doing wrong? Thanks.

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  • use/run python's 2to3 as or like a unittest

    - by Vincent
    I have used the 2to3 utility to convert code from the command line. What I would like to do is run it basically as a unittest. Even if it tests the file rather than parts(funtions, methods...) as would be normal for a unittest. It does not need to be a unittest and I don't what to automatically convert the files I just want to monitor the py3 compliance of files in a unittest like manor. I can't seem to find any documentation or examples for this. An example and/or documentation would be great. Thanks

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  • Python Eggs on Google App Engine

    - by ott
    Usually I would use virtualenv and pip for deployment of web applications. With Google App Engine this doesn't work, because all import statement are relative to directory of the application. The most common approach I saw was to simply copy the packages from site-packages to the directory of the application. This involves manual work and is error-prone. Another approach was to changes install_lib and install_scripts in ~/.pydisutils.cfg, but this doesn't allow me to use pip in my home directory simultaneously. Do you have any suggestions for this?

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  • Python meta programming question

    - by orokusaki
    I have a meta class MyClass which adds an attribute to a class based on some of the properties of the class's methods. When I subclass MyClass I want it to still have that attribute, and append to the attribute's value based on the sub-class's methods (ie, sub-classing extends the same attribute that the base's meta creates.). Can this be done via the bases argument passed to __new__(cls, name, bases, dct)?

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  • How does this If conditional work in Python?

    - by Sergio Boombastic
    from google.appengine.api import users from google.appengine.ext import webapp from google.appengine.ext.webapp.util import run_wsgi_app class MainPage(webapp.RequestHandler): def get(self): user = users.get_current_user() if user: self.response.headers['Content-Type'] = 'text/plain' self.response.out.write('Hello, ' + user.nickname()) else: self.redirect(users.create_login_url(self.request.uri)) application = webapp.WSGIApplication( [('/', MainPage)], debug=True) def main(): run_wsgi_app(application) if __name__ == "__main__": main() I don't understand how this line works: if user: self.response.headers['Content-Type'] = 'text/plain' self.response.out.write('Hello, ' + user.nickname()) else: self.redirect(users.create_login_url(self.request.uri)) I'm guessing the users.get_current_user() return a boolean? Then, if that is the case how can it get a .nickname() method? Thanks for the guidance.

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  • Python: For loop problem

    - by James
    I have a PSP page with html embedded. I need to place another for loop so i can insert another %s next to background-color: which will instert a appropriate colour to colour in the html table. For example i need to insert for z in colours so it can loop over the colours list and insert the correct colour. Where ever i try to insert the for loop it doesnt seem to work it most commonly colours each cell in the table 60 times then moves onto the next cell and repeats itself and crashes my web browser. The colours are held in a table called colours. code below: <table> <% s = ''.join(aa[i] for i in table if i in aa) for i in range(0, len(s), 60): req.write('<tr><td><TT>%04d</td>' % (i+1)); for k in s[i:i+60]: req.write('<TT><td><TT><font style="background-color:">%s<font></td>' % (k)); req.write('</TT></tr>') #end %> </table>

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  • Python: Repeat elements in a list comprehension?

    - by User
    I have the following list comprehension which returns a list of coordinate objects for each location. coordinate_list = [Coordinates(location.latitude, location.longitude) for location in locations] This works. Now suppose the location object has a number_of_times member. I want a list comprehension to generate n Coordinate objects where n is the number_of_times for the particular location. So if a location has number_of_times = 5 then the coordinates for that location will be repeated 5 times in the list. (Maybe this is a case for a for-loop but I'm curious if it can be done via list comprehensions)

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  • Python - calendar.timegm() vs. time.mktime()

    - by ibz
    I seem to have a hard time getting my head around this. What's the difference between calendar.timegm() and time.mktime()? Say I have a datetime.datetime with no tzinfo attached, shouldn't the two give the same output? Don't they both give the number of seconds between epoch and the date passed as a parameter? And since the date passed has no tzinfo, isn't that number of seconds the same? >>> import calendar >>> import time >>> import datetime >>> d = datetime.datetime(2010, 10, 10) >>> calendar.timegm(d.timetuple()) 1286668800 >>> time.mktime(d.timetuple()) 1286640000.0 >>>

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  • Assign to a slice of a Python list from a lambda

    - by Bushman
    I know that there are certain "special" methods of various objects that represent operations that would normally be performed with operators (i.e. int.__add__ for +, object.__eq__ for ==, etc.), and that one of them is list.__setitem, which can assign a value to a list element. However, I need a function that can assign a list into a slice of another list. Basically, I'm looking for the expression equivalent of some_list[2:4] = [2, 3].

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  • Sending http headers with python

    - by Niklas R
    I've set up a little script that should feed a client with html. import socket sock = socket.socket() sock.bind(('', 8080)) sock.listen(5) client, adress = sock.accept() print "Incoming:", adress print client.recv(1024) print client.send("Content-Type: text/html\n\n") client.send('<html><body></body></html>') print "Answering ..." print "Finished." import os os.system("pause") But it is shown as plain text in the browser. Can you please tell what I need to do ? I just can't find something in google that helps me.. Thanks.

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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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  • Python: Count lines and differentiate between them

    - by Mister X
    I'm using an application that gives a timed output based on how many times something is done in a minute, and I wish to manually take the output (copy paste) and have my program, and I wish to count how many times each minute it is done. An example output is this: 13:48 An event happened. 13:48 Another event happened. 13:49 A new event happened. 13:49 A random event happened. 13:49 An event happened. So, the program would need to understand that 2 things happened at 13:48, and 3 at 13:49. I'm not sure how the information would be stored, but I need to average them after, to determine an average of how often it happens. Sorry for being so complicated!

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  • Python: Created nested dictionary from list of paths

    - by sberry2A
    I have a list of tuples the looks similar to this (simplified here, there are over 14,000 of these tuples with more complicated paths than Obj.part) [ (Obj1.part1, {<SPEC>}), (Obj1.partN, {<SPEC>}), (ObjK.partN, {<SPEC>}) ] Where Obj goes from 1 - 1000, part from 0 - 2000. These "keys" all have a dictionary of specs associated with them which act as a lookup reference for inspecting another binary file. The specs dict contains information such as the bit offset, bit size, and C type of the data pointed to by the path ObjK.partN. For example: Obj4.part500 might have this spec, {'size':32, 'offset':128, 'type':'int'} which would let me know that to access Obj4.part500 in the binary file I must unpack 32 bits from offset 128. So, now I want to take my list of strings and create a nested dictionary which in the simplified case will look like this data = { 'Obj1' : {'part1':{spec}, 'partN':{spec} }, 'ObjK' : {'part1':{spec}, 'partN':{spec} } } To do this I am currently doing two things, 1. I am using a dotdict class to be able to use dot notation for dictionary get / set. That class looks like this: class dotdict(dict): def __getattr__(self, attr): return self.get(attr, None) __setattr__ = dict.__setitem__ __delattr__ = dict.__delitem__ The method for creating the nested "dotdict"s looks like this: def addPath(self, spec, parts, base): if len(parts) > 1: item = base.setdefault(parts[0], dotdict()) self.addPath(spec, parts[1:], item) else: item = base.setdefault(parts[0], spec) return base Then I just do something like: for path, spec in paths: self.lookup = dotdict() self.addPath(spec, path.split("."), self.lookup) So, in the end self.lookup.Obj4.part500 points to the spec. Is there a better (more pythonic) way to do this?

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