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  • Unable to plot graph using matplotlib

    - by Aman Deep Gautam
    I have the following code which searches all the directory in the current directory and then takes data from those files to plot the graph. The data is read correctly as verified by printing but there are no points plotted on graph. import argparse import os import matplotlib.pyplot as plt #find the present working directory pwd=os.path.dirname(os.path.abspath(__file__)) #find all the folders in the present working directory. dirs = [f for f in os.listdir('.') if os.path.isdir(f)] plt.figure() plt.xlim(0, 20000) plt.ylim(0, 1) for directory in dirs: os.chdir(os.path.join(pwd, directory)); chd_dir = os.path.dirname(os.path.abspath(__file__)) files = [ fl for fl in os.listdir('.') if os.path.isfile(fl) ] print files for f in files: f_obj = open(os.path.join(chd_dir, f), 'r') list_x = [] list_y = [] for i in xrange(0,4): f_obj.next() for line in f_obj: temp_list = line.split() print temp_list list_y.append(temp_list[0]) list_x.append(temp_list[1]) print 'final_lsit' print list_x print list_y plt.plot(list_x, list_y, 'r.') f_obj.close() os.chdir(pwd) plt.savefig("test.jpg") The input files look like the following: 5 865 14709 15573 14709 1.32667e-06 664 0.815601 14719 1.55333e-06 674 0.813277 14729 1.82667e-06 684 0.810185 14739 1.4e-06 694 0.808459 Can anybody help me with why this is happening? Being new I would like to know some tutorial where I can get help with kind of plotting as the tutorial I was following made me end up here. Any help appreciated.

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  • Finding a list of indices from master array using secondary array with non-unique entries

    - by fideli
    I have a master array of length n of id numbers that apply to other analogous arrays with corresponding data for elements in my simulation that belong to those id numbers (e.g. data[id]). Were I to generate a list of id numbers of length m separately and need the information in the data array for those ids, what is the best method of getting a list of indices idx of the original array of ids in order to extract data[idx]? That is, given: a=numpy.array([1,3,4,5,6]) # master array b=numpy.array([3,4,3,6,4,1,5]) # secondary array I would like to generate idx=numpy.array([1,2,1,4,2,0,3]) The array a is typically in sequential order but it's not a requirement. Also, array b will most definitely have repeats and will not be in any order. My current method of doing this is: idx=numpy.array([numpy.where(a==bi)[0][0] for bi in b]) I timed it using the following test: a=(numpy.random.uniform(100,size=100)).astype('int') b=numpy.repeat(a,100) timeit method1(a,b) 10 loops, best of 3: 53.1 ms per loop Is there a better way of doing this?

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  • App Engine Django Form Uniqueness Validation?

    - by GeekTantra
    Is there a simpler way to use uniqueness validation with Django Forms in AppEngine? I understand that performance would be problem if we keep an uniqueness constraint but since the amount of data being added is very small performance is not a big concern, rather development time is a concern here. Any help is appreciated.

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  • django url matching

    - by ben
    can anyone see why this wouldn't be working. Fairly new to django so any help would be much appreciated actual url: http://127.0.0.1:8000/2010/may/12/my-second-blog-post/ urls.py: (r'(?P<year>d{4})/(?P<month>[a-z]{3})/(?P<day>w{1,2})/(?P<slug>[-w]+)/$', 'object_detail', dict(info_dict, slug_field='slug',template_name='blog/detail.html')),

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  • Where is the help.py for Android's monkeyrunner

    - by Keyboardsurfer
    Hi, I just can't find the help.py file in order to create the API reference for the monkeyrunner. The command described at the Android references monkeyrunner <format> help.py <outfile> does not work when i call monkeyrunner html help.py /path/to/place/the/doc.html. It's quite obvious that the help.py file is not found and the monkeyrunner also tells me "Can't open specified script file". But a locate on my system doesn't bring me a help.py file that has anything to do with monkeyrunner or Android. So my question is: Where did they hide the help.py file for creating the API reference?

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  • django admin site - filtering available objects for user

    - by JPG
    I have models that belong to some 'group' (Company class). I want to add users, who will also belong to a one group and should be able to edit/manage/add objects with membership in associated group. something like: class Company() class Something() company = ForeignKey(Company) user Microsoft_admin company = ForeignKey(Company) and this user should only see and edit objects belonging to associated Company in the Admin Interface. How to acomplish that?

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  • Problem opening Solr *.jsp pages with urllib2.urlopen.

    - by nestling
    I'm trying to open a page at http://localhost:8983/solr/admin/stats.jsp but urllib2.urlopen returns a blank string. It works fine for solr/ and solr/admin, but for all the pages above /solr/admin/ I get nothing but a blank string. 76]: t = urllib2.urlopen('http://localhost:8983/solr/admin/stats.jsp') 77]: s = t.read() 78]: s 78]: 79]: type(s) 79]: <type 'str'> 80]: urllib2.urlopen('http://localhost:8983/solr/admin/registry.jsp').read() 80]: In [84]: urllib2.urlopen('http://localhost:8983/solr/admin/schema.jsp').read() Out[84]: I know this isn't a problem with urllib2, but beyond that I am at a loss. I wish solr (or jetty) had an easy to get to log file, so that perhaps it could tell me its side of the story.

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  • Paramiko ssh output stops at --more--

    - by Anesh
    The output stops printing at --more-- any idea how to get the end of the output >>> import paramiko >>> ssh = paramiko.SSHClient() >>> ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy()) >>> conn=ssh.connect("ipaddress",username="user", password="pass") >>> channel = ssh.invoke_shell() >>> channel.send("en\n") 3 >>> channel.send("password\n") 9 >>> channel.send("show security local-user-list\n") 30 >>> results = '' >>> channel.send("\n") 1 >>> results += channel.recv(5000) >>> print results bluecoat>en Password: bluecoat#show security local-user-list Default List: local_user_database Append users loaded from file to default list: false local_user_database Lockout parameters: Max failed attempts: 60 Lockout duration: 3600 Reset interval: 7200 Users: Groups: admin_local Lockout parameters: Max failed attempts: 60 Lockout duration: 3600 Reset interval: 7200 Users: <username> Hashed Password: Enabled: true Groups: <username> Hashed Password: Enabled: true **--More--** As you can see above the output stops printing at --more-- any idea how to get the output to print till the end.

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  • strange Django problem

    - by Pounds
    Sorrt to bother you everyone, but I really suffer a strange problem. I am working on a Django project for a company. This project worked very well before today. Today I found a page can not show images (and their corrsponding links). I checked source code of THAT PAGE, I found there are images and links, I just can not find them on the page. I checked the auth of the server and I am sure I can write things to the database. In fact, I think it is not database mistake because I can find what I want in the page source code, I just can not find them on the page. Oh my Gosh, I am going to be crazy... Has anyone suffered similar problem? What kind of problem could it be? Please help me! Thank you very much! PS: I can not provide any source code of the project because some business limit...I am really sorry...

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  • A RAM error of big array

    - by flint
    I have a big file, more than 400M. In that file, there are 13496*13496 number, means 13496 rows and 13496 cols. I want to read them to a array. This is my code: _L1 = [[0 for col in range(13496)] for row in range(13496)] _L1file = open('distanceCMD.function.txt') while (i<13496): print "i="+str(i) _strlf = _L1file.readline() _strlf = _strlf.split('\t') _strlf = _strlf[:-1] _L1[i] = _strlf i += 1 _L1file.close() And this is my error massage: MemoryError: File "D:\research\space-function\ART3.py", line 30, in <module> _strlf = _strlf.split('\t')

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  • Capturing stdout from an imported module in wxpython and sending it to a textctrl, without blocking the GUI

    - by splafe
    There are alot of very similar questions to this but I can't find one that applies specifically to what I'm trying to do. I have a simulation (written in SimPy) that I'm writing a GUI for, the main output of the simulation is text - to the console from 'print' statements. Now, I thought the simplest way would be to create a seperate module GUI.py, and import my simulation program into it: import osi_model I want all the print statements to be captured by the GUI and appear inside a Textctrl, which there's countless examples of on here, along these lines: class MyFrame(wx.Frame): def __init__(self, *args, **kwds): <general frame initialisation stuff..> redir=RedirectText(self.txtCtrl_1) sys.stdout=redir class RedirectText: def __init__(self,aWxTextCtrl): self.out=aWxTextCtrl def write(self,string): self.out.WriteText(string) I am also starting my simulation from a 'Go' button: def go_btn_click(self, event): print 'GO' self.RT = threading.Thread(target=osi_model.RunThis()) self.RT.start() This all works fine, and the output from the simulation module is captured by the TextCtrl, except the GUI locks up and becomes unresponsive - I still need it to be accessible (at the very minimum to have a 'Stop' button). I'm not sure if this is a botched attempt at creating a new thread that I've done here, but I assume a new thread will be needed at some stage in this process. People suggest using wx.CallAfter, but I'm not sure how to go about this considering the imported module doesn't know about wx, and also I can't realistically go through the entire simulation architecture and change all the print statements to wx.CallAfter, and any attempt to capture the shell from inside the imported simulation program leads to the program crashing. Does anybody have any ideas about how I can best achieve this? So all I really need is for all console text to be captured by a TextCtrl while the GUI remains responsive, and all text is solely coming from an imported module. (Also, secondary question regarding a Stop button - is it bad form to just kill the simulation thread?). Thanks, Duncan

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  • Can this django query be improved?

    - by Hobhouse
    Given a model structure like this: class Book(models.Model): user = models.ForeignKey(User) class Readingdate(models.Model): book = models.ForeignKey(Book) date = models.DateField() One book may have several readingdates. How do I list books having at least one readingdate within a specific year? I can do this: from_date = datetime.date(2010,1,1) to_date = datetime.date(2010,12,31) book_ids = Readingdate.objects\ .filter(date__range=(from_date,to_date))\ .values_list('book_id', flat=True) books_read_2010 = Book.objects.filter(id__in=book_ids) Is it possible to do this with one queryset, or is this the best way?

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  • Django extending user model and displaying form

    - by MichalKlich
    Hello, I am writing website and i`d like to implement profile managment. Basic thing would be to edit some of user details by themself, like first and last name etc. Now, i had to extend User model to add my own stuff, and email address. I am having troubles with displaying form. Example will describe better what i would like achieve. This is mine extended user model. class UserExtended(models.Model): user = models.ForeignKey(User, unique=True) kod_pocztowy = models.CharField(max_length=6,blank=True) email = models.EmailField() This is how my form looks like. class UserCreationFormExtended(UserCreationForm): def __init__(self, *args, **kwargs): super(UserCreationFormExtended, self).__init__(*args, **kwargs) self.fields['email'].required = True self.fields['first_name'].required = False self.fields['last_name'].required = False class Meta: model = User fields = ('username', 'first_name', 'last_name', 'email') It works fine when registering, as i need allow users to put username and email but when it goes to editing profile it displays too many fields. I would not like them to be able to edit username and email. How could i disable fields in form? Thanks for help.

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  • problem installing mysqldb for python2.6

    - by apoorva
    Hi.. My mysql database is located on a remote machine... So i dont have any local copy of mysql on my local machine.. i get the registry key error... (file not found)... serverKey = _winreg.OpenKey(_winreg.HKEY_LOCAL_MACHINE, options['registry_key']) WindowsError: [Error 2] The system cannot find the file specified I think it requires to have a local copy of mysql... How do i install the mysqldb for database residing on another machine???

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  • Django admin page dropdowns

    - by zen
    I am building a high school team application using Django. Here is my working models file: class Directory(models.Model): school = models.CharField(max_length=60) website = models.URLField() district = models.SmallIntegerField() conference = models.ForeignKey(Conference) class Conference(models.Model): conference_name = models.CharField(max_length=50) url = models.URLField() class Meta: ordering = ['conference_name'] When I open my admin pages and go to edit a school's conference the drop down looks like this: <select> <option value="1">Conference Object</option> <option value="2">Conference Object</option> <select> How do I replace "Conference Object" with the conference_name?

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  • Get local network interface addresses using only proc?

    - by Matt Joiner
    How can I obtain the (IPv4) addresses for all network interfaces using only proc? After some extensive investigation I've discovered the following: ifconfig makes use of SIOCGIFADDR, which requires open sockets and advance knowledge of all the interface names. It also isn't documented in any manual pages on Linux. proc contains /proc/net/dev, but this is a list of interface statistics. proc contains /proc/net/if_inet6, which is exactly what I need but for IPv6. Generally interfaces are easy to find in proc, but actual addresses are very rarely used except where explicitly part of some connection. There's a system call called getifaddrs, which is very much a "magical" function you'd expect to see in Windows. It's also implemented on BSD. However it's not very text-oriented, which makes it difficult to use from non-C languages.

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  • Access to field in extended flatpage in django

    - by Stanislav Feldman
    How to access field in extended flatpage in django? I wrote this: class ExtendedFlatPage(FlatPage): teaser = CharField(max_length=150) class ExtendedFlatPageForm(FlatpageForm): teaser = CharField(max_length=150) class Meta: model = ExtendedFlatPage class ExtendedFlatPageAdmin(FlatPageAdmin): form = ExtendedFlatPageForm fieldsets = ( (None, {'fields': ('url', 'title', 'teaser', 'content', 'sites',)}), ) admin.site.unregister(FlatPage) admin.site.register(ExtendedFlatPage, ExtendedFlatPageAdmin) And creation in admin is ok. But then in flatpages/default.html I tried this: <html> <body> <h1>{{ flatpage.title }}</h1> <strong>{{ flatpage.teaser }}</strong> <p>{{ flatpage.content }}</p> </body> </html> And there was no flatpage.teaser! What is wrong?

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  • how to let the parser print help message rather than error and exit

    - by fluter
    Hi, I am using argparse to handle cmd args, I wanna if there is no args specified, then print the help message, but now the parse will output a error, and then exit. my code is: def main(): print "in abing/start/main" parser = argparse.ArgumentParser(prog="abing")#, usage="%(prog)s <command> [args] [--help]") parser.add_argument("-v", "--verbose", action="store_true", default=False, help="show verbose output") subparsers = parser.add_subparsers(title="commands") bkr_subparser = subparsers.add_parser("beaker", help="beaker inspection") bkr_subparser.set_defaults(command=beaker_command) bkr_subparser.add_argument("-m", "--max", action="store", default=3, type=int, help="max resubmit count") bkr_subparser.add_argument("-g", "--grain", action="store", default="J", choices=["J", "RS", "R", "T", "job", "recipeset", "recipe", "task"], type=str, help="resubmit selection granularity") bkr_subparser.add_argument("job_ids", nargs=1, action="store", help="list of job id to be monitored") et_subparser = subparsers.add_parser("errata", help="errata inspection") et_subparser.set_defaults(command=errata_command) et_subparser.add_argument("-w", "--workflows", action="store_true", help="generate workflows for the erratum") et_subparser.add_argument("-r", "--run", action="store_true", help="generate workflows, and run for the erratum") et_subparser.add_argument("-s", "--start-monitor", action="store_true", help="start monitor the errata system") et_subparser.add_argument("-d", "--daemon", action="store_true", help="run monitor into daemon mode") et_subparser.add_argument("erratum", action="store", nargs=1, metavar="ERRATUM", help="erratum id") if len(sys.argv) == 1: parser.print_help() return args = parser.parse_args() args.command(args) return how can I do that? thanks.

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  • failure on creating a Scikits.TimeSeries object

    - by user311906
    Hi All I am trying to create a scikit.timeseries object starting from 2 datetime objects. If I understood correctly it should be possible to create a scikits.timeseries starting from datetime objects. I try the following code but it says that Insufficient parameters. The 2 datetime differs for few microseconds. In this case what should be the value for freq parameter? Is what I am trying allowed? In theory, since timeseries can be based on datetime objects it should be possible to hanlde up to microsecond , is this correct? I think that this is not really clear to me. Regards Eo import datetime import sckilits.timeseries as ts tm1 = datetime.datetime( 2010,1,1, 10,10,2, 123456 ) tm2 = datetime.datetime( 2010,1,1, 10,10,2, 345678 ) d = [ tm1, tm2 ] tseries = ts.time_series( dates=d ) tseries = ts.time_series( d )

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  • re.sub emptying list

    - by jmau5
    def process_dialect_translation_rules(): # Read in lines from the text file specified in sys.argv[1], stripping away # excess whitespace and discarding comments (lines that start with '##'). f_lines = [line.strip() for line in open(sys.argv[1], 'r').readlines()] f_lines = filter(lambda line: not re.match(r'##', line), f_lines) # Remove any occurances of the pattern '\s*<=>\s*'. This leaves us with a # list of lists. Each 2nd level list has two elements: the value to be # translated from and the value to be translated to. Use the sub function # from the re module to get rid of those pesky asterisks. f_lines = [re.split(r'\s*<=>\s*', line) for line in f_lines] f_lines = [re.sub(r'"', '', elem) for elem in line for line in f_lines] This function should take the lines from a file and perform some operations on the lines, such as removing any lines that begin with ##. Another operation that I wish to perform is to remove the quotation marks around the words in the line. However, when the final line of this script runs, f_lines becomes an empty lines. What happened? Requested lines of original file: ## English-Geek Reversible Translation File #1 ## (Moderate Geek) ## Created by Todd WAreham, October 2009 "TV show" <=> "STAR TREK" "food" <=> "pizza" "drink" <=> "Red Bull" "computer" <=> "TRS 80" "girlfriend" <=> "significant other"

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  • Parse large XML file w/ script or use BioPython API ?

    - by jeremy04
    Hey guys this is my first question on here. I'm trying to make a local copy of the UniprotKB in SQL. The UniprotKB is 2.1GB, and it comes in XML and a special text format used by SwissProt Here are my options: 1) Use a SAX parser (XML) - I chose Ruby, and Nokogiri. I started writing the parser, but my initial reaction: how would I map the XML schema to the SAX parser? 2) BioPython - I already have BioSQL/Biopython installed, which literally created my SQL schema for me, and I was able to successfully insert one SwissProt/Uniprot txt file into the database. I'm running it right now (crosses fingers) on the entire 2.1gb. Here is the code I'm running: from Bio import SeqIO from BioSQL import BioSeqDatabase from Bio import SwissProt server = BioSeqDatabase.open_database(driver = "MySQLdb", user = "root", passwd = "", host="localhost", db = "bioseqdb") db = server["uniprot"] iterator = SeqIO.parse(open("/path/to/uniprot_sprot.dat", "r"), "swiss") db.load(iterator) server.commit() Edit: it's now crashing because the transactions are getting locked (since the tables are Innodb) Error Number: 1205 Lock wait timeout exceeded; try restarting transaction. I'm using MySQL version: 5.1.43 Should I switch my database to Postgrelsql ?

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  • Which class should store the lookup table?

    - by max
    The world contains agents at different locations, with only a single agent at any location. Each agent knows where he's at, but I also need to quickly check if there's an agent at a given location. Hence, I also maintain a map from locations to agents. I have a problem deciding where this map belongs to: class World, class Agent (as a class attribute) or elsewhere. In the following I put the lookup table, agent_locations, in class World. But now agents have to call world.update_agent_location every time they move. This is very annoying; what if I decide later to track other things about the agents, apart from their locations - would I need to add calls back to the world object all across the Agent code? class World: def __init__(self, n_agents): # ... self.agents = {} self.agent_locations = {} for id in range(n_agents): x, y = self.find_location() agent = Agent(self,x,y) self.agents.append(agent) self.agent_locations[x,y] = agent def update_agent_location(self, agent, x, y): del self.agent_locations[agent.x, agent.y] self.agent_locations[x, y] = agent def update(self): # next step in the simulation for agent in self.agents: agent.update() # next step for this agent # ... class Agent: def __init__(self, world, x, y): self.world = world self.x, self.y = x, y def move(self, x1, y1): self.world.update_agent_location(self, x1, y1) self.x, self.y = x1, y1 def update(): # find a good location that is not occupied and move there for x, y in self.valid_locations(): if not self.location_is_good(x, y): continue if self.world.agent_locations[x, y]: # location occupied continue self.move(x, y) I can instead put agent_locations in class Agent as a class attribute. But that only works when I have a single World object. If I later decide to instantiate multiple World objects, the lookup tables would need to be world-specific. I am sure there's a better solution... EDIT: I added a few lines to the code to show how agent_locations is used. Note that it's only used from inside Agent objects, but I don't know if that would remain the case forever.

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  • Add string to another string

    - by daemonfire300
    Hi there, I currently encountered a problem: I want to handle adding strings to other strings very efficiently, so I looked up many methods and techniques, and I figured the "fastest" method. But I quite can not understand how it actually works: def method6(): return ''.join([`num` for num in xrange(loop_count)]) From source (Method 6) Especially the ([numfor num in xrange(loop_count)]) confused me totally.

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  • Appengine filter inequality and ordering fails

    - by davezor
    I think I'm overlooking something simple here, I can't imagine this is impossible to do. I want to filter by a datetime attribute and then order the result by a ranking integer attribute. When I try to do this: query.filter("submitted >=" thisweek).order("ranking") I get the following: BadArgumentError: First ordering property must be the same as inequality filter property, if specified for this query; received ranking, expected submitted Huh? What am I missing? Thanks.

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