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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 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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  • what does "from MODULE import _" do in python?

    - by Paul
    Hi all, In the Getting things gnome code base I stumbled upon this import statement from GTG import _ and have no idea what it means, never seen this in the documentation and a quick so / google search didn't turn anything up. Thank you all in advance Paul

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  • Python: How do sets work

    - by Guy
    I have a list of objects which I want to turn into a set. My objects contain a few fields that some of which are o.id and o.area. I want two objects to be equal if these two fields are the same. ie: o1==o2 if and only if o1.area==o2.area and o1.id==o2.id. I tried over-writing __eq__ and __cmp__ but I get the error: TypeError: unhashable instance. What should I over-write?

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  • Python 3.1 - Memory Error during sampling of a large list

    - by jimy
    The input list can be more than 1 million numbers. When I run the following code with smaller 'repeats', its fine; def sample(x): length = 1000000 new_array = random.sample((list(x)),length) return (new_array) def repeat_sample(x): i = 0 repeats = 100 list_of_samples = [] for i in range(repeats): list_of_samples.append(sample(x)) return(list_of_samples) repeat_sample(large_array) However, using high repeats such as the 100 above, results in MemoryError. Traceback is as follows; Traceback (most recent call last): File "C:\Python31\rnd.py", line 221, in <module> STORED_REPEAT_SAMPLE = repeat_sample(STORED_ARRAY) File "C:\Python31\rnd.py", line 129, in repeat_sample list_of_samples.append(sample(x)) File "C:\Python31\rnd.py", line 121, in sample new_array = random.sample((list(x)),length) File "C:\Python31\lib\random.py", line 309, in sample result = [None] * k MemoryError I am assuming I'm running out of memory. I do not know how to get around this problem. Thank you for your time!

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  • filtering elements from list of lists in Python?

    - by user248237
    I want to filter elements from a list of lists, and iterate over the elements of each element using a lambda. For example, given the list: a = [[1,2,3],[4,5,6]] suppose that I want to keep only elements where the sum of the list is greater than N. I tried writing: filter(lambda x, y, z: x + y + z >= N, a) but I get the error: <lambda>() takes exactly 3 arguments (1 given) How can I iterate while assigning values of each element to x, y, and z? Something like zip, but for arbitrarily long lists. thanks, p.s. I know I can write this using: filter(lambda x: sum(x)..., a) but that's not the point, imagine that these were not numbers but arbitrary elements and I wanted to assign their values to variable names.

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  • Exposing classes inside modules within a Python package directly in the package's namespace

    - by Richard Waite
    I have a wxPython application with the various GUI classes in their own modules in a package called gui. With this setup, importing the main window would be done as follows: from gui.mainwindow import MainWindow This looked messy to me so I changed the __init__.py file for the gui package to import the class directly into the package namespace: from mainwindow import MainWindow This allows me to import the main window like this: from gui import MainWindow This looks better to me aesthetically and I think it also more closely represents what I'm doing (importing the MainWindow class from the gui "namespace"). The reason I made the gui package was to keep all the GUI stuff together. I could have just as easily made a single gui module and stuffed all the GUI classes in it, but I think that would have been unmanageable. The package now appears to work like a module, but allows me to separate the classes into their own modules (along with helper functions, etc.). This whole thing strikes me as somewhat petty, I just thought I'd throw it out there to see what others think about the idea.

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  • Python/Django Concatenate a string depending on whether that string exists

    - by Douglas Meehan
    I'm creating a property on a Django model called "address". I want address to consist of the concatenation of a number of fields I have on my model. The problem is that not all instances of this model will have values for all of these fields. So, I want to concatenate only those fields that have values. What is the best/most Pythonic way to do this? Here are the relevant fields from the model: house = models.IntegerField('House Number', null=True, blank=True) suf = models.CharField('House Number Suffix', max_length=1, null=True, blank=True) unit = models.CharField('Address Unit', max_length=7, null=True, blank=True) stex = models.IntegerField('Address Extention', null=True, blank=True) stdir = models.CharField('Street Direction', max_length=254, null=True, blank=True) stnam = models.CharField('Street Name', max_length=30, null=True, blank=True) stdes = models.CharField('Street Designation', max_length=3, null=True, blank=True) stdessuf = models.CharField('Street Designation Suffix',max_length=1, null=True, blank=True) I could just do something like this: def _get_address(self): return "%s %s %s %s %s %s %s %s" % (self.house, self.suf, self.unit, self.stex, self.stdir, self.stname, self.stdes, self.stdessuf) but then there would be extra blank spaces in the result. I could do a series of if statements and concatenate within each, but that seems ugly. What's the best way to handle this situation? Thanks.

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  • I have an Errno 13 Permission denied with subprocess in python

    - by wDroter
    The line with the issue is ret=subprocess.call(shlex.split(cmd)) cmd = /usr/share/java -cp pig-hadoop-conf-Simpsons:lib/pig-0.8.1-cdh3u1-core.jar:lib/hadoop-core-0.20.2-cdh3u1.jar org.apache.pig.Main -param func=cat -param from =foo.txt -x mapreduce fsFunc.pig The error is. File "./run_pig.py", line 157, in process ret=subprocess.call(shlex.split(cmd)) File "/usr/lib/python2.7/subprocess.py", line 493, in call return Popen(*popenargs, **kwargs).wait() File "/usr/lib/python2.7/subprocess.py", line 679, in __init__ errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1249, in _execute_child raise child_exception OSError: [Errno 13] Permission denied Let me know if any more info is needed. Any help is appreciated. Thanks.

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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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  • Search for a pattern in a list of strings - Python

    - by Holtz
    I have a list of strings containing filenames such as, file_names = ['filei.txt','filej.txt','filek.txt','file2i.txt','file2j.txt','file2k.txt','file3i.txt','file3j.txt','file3k.txt'] I then remove the .txt extension using: extension = os.path.commonprefix([n[::-1] for n in file_names])[::-1] file_names_strip = [n[:-len(extension)] for n in file_names] And then return the last character of each string in the list file_names_strip: h = [n[-1:] for n in file_names_strip] Which gives h = ['i', 'j', 'k', 'i', 'j', 'k', 'i', 'j', 'k'] How can i test for a pattern of strings in h? So if i,j,k occur sequentially it would return True and False if not. I need to know this because not all file names are formatted like they are in file_names. So: test_ijk_pattern(h) = True no_pattern = ['1','2','3','1','2','3','1','2','3'] test_ijk_pattern(no_pattern) = False

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  • Caching result of setUp() using Python unittest

    - by dbr
    I currently have a unittest.TestCase that looks like.. class test_appletrailer(unittest.TestCase): def setup(self): self.all_trailers = Trailers(res = "720", verbose = True) def test_has_trailers(self): self.failUnless(len(self.all_trailers) > 1) # ..more tests.. This works fine, but the Trailers() call takes about 2 seconds to run.. Given that setUp() is called before each test is run, the tests now take almost 10 seconds to run (with only 3 test functions) What is the correct way of caching the self.all_trailers variable between tests? Removing the setUp function, and doing.. class test_appletrailer(unittest.TestCase): all_trailers = Trailers(res = "720", verbose = True) ..works, but then it claims "Ran 3 tests in 0.000s" which is incorrect.. The only other way I could think of is to have a cache_trailers global variable (which works correctly, but is rather horrible): cache_trailers = None class test_appletrailer(unittest.TestCase): def setUp(self): global cache_trailers if cache_trailers is None: cache_trailers = self.all_trailers = all_trailers = Trailers(res = "720", verbose = True) else: self.all_trailers = cache_trailers

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  • Python combinations no repeat by constraint

    - by user2758113
    I have a tuple of tuples (Name, val 1, val 2, Class) tuple = (("Jackson",10,12,"A"), ("Ryan",10,20,"A"), ("Michael",10,12,"B"), ("Andrew",10,20,"B"), ("McKensie",10,12,"C"), ("Alex",10,20,"D")) I need to return all combinations using itertools combinations that do not repeat classes. How can I return combinations that dont repeat classes. For example, the first returned statement would be: tuple0, tuple2, tuple4, tuple5 and so on.

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  • Python 2.6 + PIL + Google App Engine issue

    - by mswallace
    I am using OS X 1.6 snow leopard and I successfully got PIL installed. I am able to open terminal and type import Image without any errors. However, When using app engine I get Image error still saying that PIL is not installed. I am wondering if any of you have an thoughts as to how I can resolve this issue. -Matthew

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  • Exporting dates properly formatted on Google Appengine in Python

    - by Chris M
    I think this is right but google appengine seems to get to a certain point and cop-out; Firstly is this code actually right; and secondly is there away to skip the record if it cant output (like an ignore errors and continue)? class TrackerExporter(bulkloader.Exporter): def __init__(self): bulkloader.Exporter.__init__(self, 'SearchRec', [('__key__', lambda key:key.name(), None), ('WebSite', str, None), ('DateStamp', lambda x: datetime.datetime.strptime(x, '%d-%m-%Y').date(), None), ('IP', str, None), ('UserAgent', str, None)]) Thanks

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  • Python ZSI : error while serializing an object ?

    - by KaluSingh Gabbar
    this is the code, I get error that it can not serialize reference (sumReq) sumReqClass = GED("http://www.some-service.com/sample", "getSumRequest").pyclass sumReq = sumReqClass() rq = GetSumSoapIn() sum._sumReqObj = sumReq rs=proxy.GetSum(rq, soapheaders=[credentials]) I get error : TypeError: bad usage, failed to serialize element reference (http://www.some-service.com/sample, getSumRequest), in: /SOAP-ENV:Body

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  • Python: Embed Chaco in PyQt4 Mystery

    - by random guy
    How do i go about adding Chaco to an existing PyQt4 application? Hours of searches yielded little (search for yourself). So far i've figured i need the following lines: import os os.environ['ETS_TOOLKIT']='qt4' i could not find PyQt4-Chaco code anywhere on the internets i would be very grateful to anyone filling in the blanks to show me the simplest line plot possible (with 2 points) from PyQt4 import QtCore, QtGui import sys import os os.environ['ETS_TOOLKIT']='qt4' from enthought <blanks> : : app = QtGui.QApplication(sys.argv) main_window = QtGui.QMainWindow() main_window.setCentralWidget(<blanks>) main_window.show() app.exec_() print('bye') what Chaco/Enthought class inherits from QWidget ?

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  • Copying 2D lists in python

    - by SuperString
    Hi I want to copy a 2D list, so that if I modify 1 list, the other is not modified. For 1 D list, I just do this: a = [1,2] b = a[:] And now if I modify b, a is not modified. But this doesn't work for 2D list: a = [[1,2],[3,4]] b = a[:] If I modify b, a gets modified as well. How do I fix this?

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  • python decorator to add function to list in current scope

    - by AlexH
    Goal: Make a decorator which can modify the scope that it is used in. If it worked: class Blah(): # or perhaps class Blah(ParentClassWhichMakesThisPossible) def one(self): pass @decorated def two(self): pass Blah.decorated ["two"] Why? I essentially want to write classes which can maintain specific dictionaries of methods, so that I can retrieve lists of available methods of different types on a per class basis. errr..... I want to do this: class RuleClass(ParentClass): @rule def blah(self): pass @rule def kapow(self): pass def shazam(self): class OtherRuleClass(ParentClass): @rule def foo(self): pass def bar(self): pass RuleClass.rules.keys() ["blah", "kapow"] OtherRuleClass.rules.keys() ["foo"]

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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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  • Python Tkinter after loop not working fast enough

    - by user2658538
    I am making a simple metronome where it plays a tick sound every few milliseconds depending on the bpm and plays the sound using the winsound module. I use tkinter because there will be a gui component later but for now the metronome code is working, it plays the sound at a constant rate, but even though I set the after loop to play the sound every few milliseconds, it waits longer and the beat is slower than it should be. Is it a problem with the code or a problem with the way I calculate the time? Thanks. Here is my code. from Tkinter import * import winsound,time,threading root=Tk() c=Canvas(root) c.pack() class metronome(): def __init__(self,root,canvas,tempo=100): self.root=root self.root.bind("<1>",self.stop) self.c=canvas self.thread=threading.Thread(target=self.play) self.thread.daemon=True self.pause=False self.tempo=tempo/60.0 self.tempo=1.0/self.tempo self.tempo*=1000 def play(self): winsound.PlaySound("tick.wav",winsound.SND_FILENAME) self.sound=self.c.after(int(self.tempo),self.play) def stop(self,e): self.c.after_cancel(self.sound) beat=metronome(root,c,120) beat.thread.start() root.mainloop()

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