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  • pylab.savefig() and pylab.show() image difference

    - by Jack1990
    I'm making an script to automatically create plots from .xvg files, but there's a problem when I'm trying to use pylab's savefig() method. Using pylab.show() and saving from there, everything's fine. Using pylab.show() Using pylab.savefig() def producePlot(timestep, energy_values,type_line = 'r', jump = 1,finish = 100): fc = sp.interp1d(timestep[::jump], energy_values[::jump],kind='cubic') xnew = numpy.linspace(0, finish, finish*2) pylab.plot(xnew, fc(xnew),type_line) pylab.xlabel('Time in ps ') pylab.ylabel('kJ/mol') pylab.xlim(xmin=0, xmax=finish) def produceSimplePlot(timestep, energy_values,type_line = 'r', jump = 1,finish = 100): pylab.plot(timestep, energy_values,type_line) pylab.xlabel('Time in ps ') pylab.ylabel('kJ/mol') pylab.xlim(xmin=0, xmax=finish) def linearRegression(timestep, energy_values, type_line = 'g'): #, jump = 1,finish = 100): from scipy import stats import numpy #print 'fuck' timestep = numpy.asarray(timestep) slope, intercept, r_value, p_value, std_err = stats.linregress(timestep,energy_values) line = slope*timestep+intercept pylab.plot(timestep, line, type_line) def plottingTime(Title,file_name, timestep, energy_values ,loc, jump , finish): pylab.title(Title) producePlot(timestep,energy_values, 'b',jump, finish) linearRegression(timestep,energy_values) import numpy Average = numpy.average(energy_values) #print Average pylab.legend(("Average = %.2f" %(Average),'Linear Reg'),loc) #pylab.show() pylab.savefig('%s.jpg' %file_name[:-4], bbox_inches= None, pad_inches=0) #if __name__ == '__main__': #plottingTime(Title,timestep1, energy_values, jump =10, finish = 4800) def specialCase(Title,file_name, timestep, energy_values,loc, jump, finish): #print 'Working here ...?' pylab.title(Title) producePlot(timestep,energy_values, 'b',jump, finish) import numpy from pylab import * Average = numpy.average(energy_values) #print Average pylab.legend(("Average = %.2g" %(Average), Title),loc) locs,labels = yticks() yticks(locs, map(lambda x: "%.3g" % x, locs)) #pylab.show() pylab.savefig('%s.jpg' %file_name[:-4] , bbox_inches= None, pad_inches=0) Thanks in advance, John

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  • Best way to get back to using the power of lxml after having to use a regex to find something in an

    - by PyNEwbie
    I am trying to rip some text out of a large number of html documents (numbers in the hundreds of thousands). The documents are really forms but they are prepared by a very large group of different organizations so there is significant variation in how they create the document. For example, the documents are divided into chapters. I might want to extract the contents of Chapter 5 from every document so I can analyze the content of the chapter. Initially I thought this would be easy but it turns out that the authors might use a set of non-nested tables throughout the document to hold the content so that Chapter n could be displayed using td tags inside a table. Or they might use other elements such as p tags H tags, div tags or any other block level element. After trying repeatedly to use lxml to help me identify the beginning and end of each chapter I have determined that it is a lot cleaner to use a regular expression because in every case, no matter what the enclosing html element is the chapter label is always in the form of >Chapter # It is a little more complicated in that there might be some white space or non-breaking space represented in different ways (  or   or just spaces). Nonetheless it was trivial to write a regular expression to identify the beginning of each section. (The beginning of one section is the end of the previous section.) But now I want to use lxml to get the text out. My thought is that I have really no choice but to walk along my string to find the close tag for the element that encloses the text I am using to find the relevant section. That is here is one example where the element holding the Chapter name is a div <div style="DISPLAY: block; MARGIN-LEFT: 0pt; TEXT-INDENT: 0pt; MARGIN-RIGHT: 0pt" align="left"><font style="DISPLAY: inline; FONT-WEIGHT: bold; FONT-SIZE: 10pt; FONT-FAMILY: Times New Roman">Chapter 1.&#160;&#160;&#160;Our Beginnings.</font></div> So I am imagining that I would begin at the location where I found the match for chapter 1 and set up a regular expressions to find the next </div|</td|</p|</h1 . . . So at this point I have identified the type of element holding my chapter heading I can use the same logic to find all of the text that is within that element that is set up a regular expression to help me mark from >Chapter 1.&#160;&#160;&#160;Our Beginnings.< So I have identified where my Chapter 1 begins I can do the same for chapter 2 (which is where Chapter 1 ends) Now I am imagining that I am going to snip the document beginning at the opening of the element that I identified as the element the indicates where chapter 1 begins and ending just before the opening of the element that I identified as the element that indicates where Chapter 2 begins. The string that I have identified will then be fed to lxml to use its power to get the content. I am going to all of this trouble because I have read over and over - never use a regular expression to extract content from html documents and I have not hit on a way to be as accurate with lxml to identify the starting and ending locations for the text I want to extract. For example, I can never be certain that the subtitle of Chapter 1 is Our Beginnings it could be Our Red Canary. Let me say that I spent two solid days trying with lxml to be confident that I had the beginning and ending elements and I could only be accurate <60% of the time but a very short regular expression has given me better than 95% success. I have a tendency to make things more complicated than necessary so I am wondering if anyone has seen or solved a similar problems and if they had an approach (not the details mind you) that they would like to offer.

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  • Shaders with pygtkglext

    - by qba
    Do someone know how to get glsl shaders work in gtk-opengl window? With glut all glCreateProgram etc. functions works, but when I tried to put the same gl code into pygtkglext window, its complaining about NullReference: OpenGL.error.NullFunctionError: Attempt to call an undefined function glCreateProgram, check for bool(glCreateProgram) before calling So then I from OpenGL.GL.ARB.shader_objects import *, but the result is similar: OpenGL.error.NullFunctionError: Attempt to call an undefined function glCreateProgramObjectARB, check for bool(glCreateProgramObjectARB) before calling Any idea will be useful.

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  • Sending data from one Protocol to another Protocol in Twisted?

    - by veb
    Hi! One of my protocols is connected to a server, and with the output of that I'd like to send it to the other protocol. I need to access the 'msg' method in ClassA from ClassB but I keep getting: exceptions.AttributeError: 'NoneType' object has no attribute 'write' Actual code: http://pastebin.com/MQPhduSY Any ideas please? :-)

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  • gae error : Error: Server Error, how to debut it .

    - by zjm1126
    when i upload my project to google-app-engine , it show this : Error: Server Error The server encountered an error and could not complete your request. If the problem persists, please report your problem and mention this error message and the query that caused it. why ? how can i debug this error ? thanks

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  • Convert a sequence of sequences to a dictionary and vice-versa

    - by louis
    One way to manually persist a dictionary to a database is to flatten it into a sequence of sequences and pass the sequence as an argument to cursor.executemany(). The opposite is also useful, i.e. reading rows from a database and turning them into dictionaries for later use. What's the best way to go from myseq to mydict and from mydict to myseq? >>> myseq = ((0,1,2,3), (4,5,6,7), (8,9,10,11)) >>> mydict = {0: (1, 2, 3), 8: (9, 10, 11), 4: (5, 6, 7)}

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  • Inexpensive ways to add seek to a filetype object

    - by becomingGuru
    PdfFileReader reads the content from a pdf file to create an object. I am querying the pdf from a cdn via urllib.urlopen(), this provides me a file like object, which has no seek. PdfFileReader, however uses seek. What is the simple way to create a PdfFileReader object from a pdf downloaded via url. Now, what can I do to avoid writing to disk and reading it again via file(). Thanks in advance.

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  • Regex for Matching First Alphanumeric Character skipping (The |An? )

    - by TheLizardKing
    I have a list of artists, albums and tracks that I want to sort using the first letter of their respective name. The issue arrives when I want to ignore "The ", "A ", "An " and other various non-alphanumeric characters (Talking to you "Weird Al" Yankovic and [dialog]). Django has a nice start '^(An?|The) +' but I want to ignore those and a few others of my choice. I am doing this in Django, using a MySQL db with utf8_bin collation.

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  • Geocoding non-addresses: Geopy

    - by Phil Donovan
    Using geopy to geocode alcohol outlets in NZ. The problem I have is that some places do not have street addresses but are places in Google Maps. For example, plugging: Furneaux Lodge, Endeavour Inlet, Queen Charlotte Sound, Marlborough 7250 into Google Maps via the browser GUI gives me However, using that in Geopy I get a GQueryError saying this geographic location does not exist. Here is the code for geocoding: def GeoCode(address): g=geocoders.Google(domain="maps.google.co.nz") geoloc = g.geocode(address, exactly_one=False) place, (lat, lng) = geoloc[0] GeoOut = [] GeoOut.extend([place, lat, lng]) return GeoOut GeoCode("Furneaux Lodge, Endeavour Inlet, Queen Charlotte Sound, Marlboroguh 7250") Meanwhile, I notice that "Eiffel Tower" works fine. Is there away to solve this and can someone explain the difference between The Eiffel Tower and Furneaux Lodge within Google 'locations'?

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  • Sort a list of tuples without case sensitivity

    - by dound
    How can I efficiently and easily sort a list of tuples without being sensitive to case? For example this: [('a', 'c'), ('A', 'b'), ('a', 'a'), ('a', 5)] Should look like this once sorted: [('a', 5), ('a', 'a'), ('A', 'b'), ('a', 'c')] The regular lexicographic sort will put 'A' before 'a' and yield this: [('A', 'b'), ('a', 5), ('a', 'a'), ('a', 'c')]

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  • Why do I get rows of zeros in my 2D fft?

    - by Nicholas Pringle
    I am trying to replicate the results from a paper. "Two-dimensional Fourier Transform (2D-FT) in space and time along sections of constant latitude (east-west) and longitude (north-south) were used to characterize the spectrum of the simulated flux variability south of 40degS." - Lenton et al(2006) The figures published show "the log of the variance of the 2D-FT". I have tried to create an array consisting of the seasonal cycle of similar data as well as the noise. I have defined the noise as the original array minus the signal array. Here is the code that I used to plot the 2D-FT of the signal array averaged in latitude: import numpy as np from numpy import ma from matplotlib import pyplot as plt from Scientific.IO.NetCDF import NetCDFFile ### input directory indir = '/home/nicholas/data/' ### get the flux data which is in ### [time(5day ave for 10 years),latitude,longitude] nc = NetCDFFile(indir + 'CFLX_2000_2009.nc','r') cflux_southern_ocean = nc.variables['Cflx'][:,10:50,:] cflux_southern_ocean = ma.masked_values(cflux_southern_ocean,1e+20) # mask land nc.close() cflux = cflux_southern_ocean*1e08 # change units of data from mmol/m^2/s ### create an array that consists of the seasonal signal fro each pixel year_stack = np.split(cflux, 10, axis=0) year_stack = np.array(year_stack) signal_array = np.tile(np.mean(year_stack, axis=0), (10, 1, 1)) signal_array = ma.masked_where(signal_array > 1e20, signal_array) # need to mask ### average the array over latitude(or longitude) signal_time_lon = ma.mean(signal_array, axis=1) ### do a 2D Fourier Transform of the time/space image ft = np.fft.fft2(signal_time_lon) mgft = np.abs(ft) ps = mgft**2 log_ps = np.log(mgft) log_mgft= np.log(mgft) Every second row of the ft consists completely of zeros. Why is this? Would it be acceptable to add a randomly small number to the signal to avoid this. signal_time_lon = signal_time_lon + np.random.randint(0,9,size=(730, 182))*1e-05 EDIT: Adding images and clarify meaning The output of rfft2 still appears to be a complex array. Using fftshift shifts the edges of the image to the centre; I still have a power spectrum regardless. I expect that the reason that I get rows of zeros is that I have re-created the timeseries for each pixel. The ft[0, 0] pixel contains the mean of the signal. So the ft[1, 0] corresponds to a sinusoid with one cycle over the entire signal in the rows of the starting image. Here are is the starting image using following code: plt.pcolormesh(signal_time_lon); plt.colorbar(); plt.axis('tight') Here is result using following code: ft = np.fft.rfft2(signal_time_lon) mgft = np.abs(ft) ps = mgft**2 log_ps = np.log1p(mgft) plt.pcolormesh(log_ps); plt.colorbar(); plt.axis('tight') It may not be clear in the image but it is only every second row that contains completely zeros. Every tenth pixel (log_ps[10, 0]) is a high value. The other pixels (log_ps[2, 0], log_ps[4, 0] etc) have very low values.

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  • how to format date when i load data from google-app-engine..

    - by zjm1126
    i use remote_api to load data from google-app-engine. appcfg.py download_data --config_file=helloworld/GreetingLoad.py --filename=a.csv --kind=Greeting helloworld the setting is: class AlbumExporter(bulkloader.Exporter): def __init__(self): bulkloader.Exporter.__init__(self, 'Greeting', [('author', str, None), ('content', str, None), ('date', str, None), ]) exporters = [AlbumExporter] and i download a.csv is : the date is not readable , and the date in appspot.com admin is : so how to get the full date ?? thanks i change this : class AlbumExporter(bulkloader.Exporter): def __init__(self): bulkloader.Exporter.__init__(self, 'Greeting', [('author', str, None), ('content', str, None), ('date', lambda x: datetime.datetime.strptime(x, '%m/%d/%Y').date(), None), ]) exporters = [AlbumExporter] but the error is :

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  • How to draw the "trail" in a maze solving application

    - by snow-spur
    Hello i have designed a maze and i want to draw a path between the cells as the 'person' moves from one cell to the next. So each time i move the cell a line is drawn Also i am using the graphics module The graphics module is an object oriented library Im importing from graphics import* from maze import* my circle which is my cell center = Point(15, 15) c = Circle(center, 12) c.setFill('blue') c.setOutline('yellow') c.draw(win) p1 = Point(c.getCenter().getX(), c.getCenter().getY()) this is my loop if mazez.blockedCount(cloc)> 2: mazez.addDecoration(cloc, "grey") mazez[cloc].deadend = True c.move(-25, 0) p2 = Point(getX(), getY()) line = graphics.Line(p1, p2) cloc.col = cloc.col - 1 Now it says getX not defined every time i press a key is this because of p2???

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  • What's an appropriate HTTP status code to return by a REST API service for a validation failure?

    - by michaeljoseph
    I'm currently returning 401 Unauthorized whenever I encounter a validation failure in my Django/Piston based REST API application. Having had a look at the HTTP Status Code Registry I'm not convinced that this is an appropriate code for a validation failure, what do y'all recommend? 400 Bad Request 401 Unauthorized 403 Forbidden 405 Method Not Allowed 406 Not Acceptable 412 Precondition Failed 417 Expectation Failed 422 Unprocessable Entity 424 Failed Dependency Update: "Validation failure" above means an application level data validation failure ie. incorrectly specified datetime, bogus email address etc.

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  • wxPython: Change a buttons text in a wx.FileDialog

    - by Sascha
    Hello I have a wx.FileDialog (with the wx.FD_OPEN flag) & I would like to know if I can (& how) I could change the button in the bottom right of the FileDialog from "Open" to "Create" or "Delete", etc. What I am doing is I have a button with the text "Delete Portfolio", when pressed it opens a FileDialog & allows the user to select a portfolio file(.db) to delete. So instead of the File Dialog's bottom right confirm button displaying "Open" I would like to be able to change the text to "Confirm" or "Delete" or whatever. Is this possible, its a rather superficial thing to do, but if the button says open when the user wants to select a file to delete, it can be a little confusing even if the title of the dialog says "please select a file to delete"

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  • Matplotlib: plotting discrete values

    - by Arkapravo
    I am trying to plot the following ! from numpy import * from pylab import * import random for x in range(1,500): y = random.randint(1,25000) print(x,y) plot(x,y) show() However, I keep getting a blank graph (?). Just to make sure that the program logic is correct I added the code print(x,y), just the confirm that (x,y) pairs are being generated. (x,y) pairs are being generated, but there is no plot, I keep getting a blank graph. Any help ?

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  • 'NoneType' object has no attribute 'data'

    - by Bill Jordan
    Hello guys, I am sending a SOAP request to my server and getting the response back. sample of the response string is shown below: <?xml version = '1.0' ?> <env:Envelope xmlns:env=http:////www.w3.org/2003/05/soap-envelop . .. .. <env:Body> <epas:get-all-config-resp xmlns:epas="urn:organization:epas:soap"> ^M ... ... <epas:property name="Tom">12</epas:property> > > <epas:property name="Alice">34</epas:property> > > <epas:property name="John">56</epas:property> > > <epas:property name="Danial">78</epas:property> > > <epas:property name="George">90</epas:property> > > <epas:property name="Luise">11</epas:property> ... ^M </env:Body? </env:Envelop> What I noticed in the response is that there is an extra character shown in the body which is "^M". Not sure if this could be the issue. Note the ^M shown! when I tried parsing the string returned from the server to get the names and values using the code sample: elements = minidom.parseString(xmldoc).getElementsByTagName("property") myDict = {} for element in elements: myDict[element.getAttribute('name')] = element.firstChild.data But, I am getting this error: 'NoneType' object has no attribute 'data'. May be its something to do with the "^M" shown on the xml response back! Any ideas/comments would be appreciated, Cheers

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  • Dynamic Spacer in ReportLab

    - by ptikobj
    I'm automatically generating a PDF-file with Platypus that has dynamic content. This means that it might happen that the length of the text content (which is directly at the bottom of the pdf-file) may vary. However, it might happen that a page break is done in cases where the content is too long. This is because i use a "static" spacer: s = Spacer(width=0, height=23.5*cm) as i always want to have only one page, I somehow need to dynamically set the height of the Spacer, so that it takes the "rest" of the space that is on the page as its height. Now, how do i get the "rest" of height that is left on my page?

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  • How to turn a list of tuples into a string?

    - by matt
    I have a list of tuples that I'm trying to incorporate into a SQL query but I can't figure out how to join them together without adding slashes. My like this: list = [('val', 'val'), ('val', 'val'), ('val', 'val')] If I turn each tuple into a string and try to join them with a a comma I'll get something like ' (\'val\, \'val\'), ... ' What's the right way to do this, so I can get the list (without brackets) as a string?

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  • How do I find the "concrete class" of a django model baseclass

    - by Mr Shark
    I'm trying to find the actual class of a django-model object, when using model-inheritance. Some code to describe the problem: class Base(models.model): def basemethod(self): ... class Child_1(Base): pass class Child_2(Base): pass If I create various objects of the two Child classes and the create a queryset containing them all: Child_1().save() Child_2().save() (o1, o2) = Base.objects.all() I want to determine if the object is of type Child_1 or Child_2 in basemethod, I can get to the child object via o1.child_1 and o2.child_2 but that reconquers knowledge about the childclasses in the baseclass. I have come up with the following code: def concrete_instance(self): instance = None for subclass in self._meta.get_all_related_objects(): acc_name = subclass.get_accessor_name() try: instance = self.__getattribute__(acc_name) return instance except Exception, e: pass But it feels brittle and I'm not sure of what happens when if I inherit in more levels.

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  • How to manually create a DBRef using pymongo?

    - by Soviut
    I want to create a DBRef manually so that I can add an additional field to it. However, when I try to pass the following: {'$ref': 'projects', '$id': '1029412409721', 'project_name': 'My Project'} Pymongo raises an error: pymongo.errors.InvalidName: key '$id' must not start with '$' It would seem that pymongo reserve the $ for the special key, leading me to wonder if it is even possible to do what I'm trying to do?

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