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• Purge complete Python installation on OS X

  - by Konrad Rudolph

  I’m working on a recently-upgraded OS X Snow Leopard and MacPorts and I’m running into problems at every corner. The first problem is the sheer number of installed Python versions: altogether, there are four: 2.5, 2.6 and 3.0 in /Library/Frameworks/Python.framework 2.6 in /opt/local/Library/Frameworks/Python.framework/ (MacPorts installation) So there are at least two useless/redundant versions: 2.5 and the redundant 2.6. Additionally, the pre-installed Python is giving me severe problems because some of the pre-installed libraries (in particular, scipy, numpy and matplotlib) don’t work properly. I am sorely tempted to purge the complete /Library/Frameworks/Python.framework path, as well as the MacPorts Python installation. After that, I’ll start from a clean slate by installing a properly configured Python, e.g. that from Enthought. Am I running headlong into trouble? Or is this a sane undertaking? (In particular, I need a working Python in the next few days and if I end up with a non-working Python this would be a catastrophe of medium proportions. On the other hand, some features I need from matplotlib aren’t working now.)

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• How can I share my python scripts with my less python-savvy business person partner?

  - by Alex

  I'm taking financial mathematics as an elective, and I'm working with real life finance industry worker type people. It's actually kind of fun. When I pulled out a macbook at one of our meetings, I had four lifelong windows users look at me like I had three heads. Anyway, I'm helping with design and simulation of our trading strategy, and I wrote a little thing using matplotlib to visualize historical stock data. However, these guys don't know how to use git, or install python, or deal with path-related package management things. I need to be able to send my scripts to them to use, and I need to do it with absolutely minimal effort on their part. I was thinking something on the lines of py2exe, but I'd like to hear some advice before I go ahead.

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• How to use OO for data analysis? [closed]

  - by Konsta

  In which ways could object-orientation (OO) make my data analysis more efficient and let me reuse more of my code? The data analysis can be broken up into get data (from db or csv or similar) transform data (filter, group/pivot, ...) display/plot (graph timeseries, create tables, etc.) I mostly use Python and its Pandas and Matplotlib packages for this besides some DB connectivity (SQL). Almost all of my code is a functional/procedural mix. While I have started to create a data object for a certain collection of time series, I wonder if there are OO design patterns/approaches for other parts of the process that might increase efficiency?

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• C++ vs Matlab vs Python as a main language for Computer Vision Postgraduate

  - by Hough

  Hi all, Firstly, sorry for a somewhat long question but I think that many people are in the same situation as me and hopefully they can also gain some benefit from this. I'll be starting my PhD very soon which involve the fields of computer vision, pattern recognition and machine learning. Currently, I'm using opencv (2.1) C++ interface and I especially like its powerful Mat class and the overloaded operations available for matrix and image seamless operations and transformations. I've also tried (and implemented many small vision projects) using opencv python interface (new bindings; opencv 2.1) and I really enjoy python's ability to integrate opencv, numpy, scipy and matplotlib. But recently, I went back to opencv C++ interface because I felt that the official python new bindings were not stable enough and no overloaded operations are available for matrices and images, not to mention the lack of machine learning modules and slow speeds in certain operations. I've also used Matlab extensively in the past and although I've used mex files and other means to speed up the program, I just felt that Matlab's performance was inadequate for real-time vision tasks, be it for fast prototyping or not. When the project becomes larger and larger, many tasks have to be re-written in C and compiled into Mex files increasingly and Matlab becomes nothing more than a glue language. Here comes the sub-questions: For postgrad studies in these fields (machine learning, vision, pattern recognition), what is your main or ideal programming language for rapid prototyping of ideas and testing algorithms contained in papers? For postgrad studies, can you list down the pros and cons of using the following languages? C++ (with opencv + gsl + svmlib + other libraries) vs Matlab (with all its toolboxes) vs python (with the imcomplete opencv bindings + numpy + scipy + matplotlib). Are there computer vision PhD/postgrad students here who are using only C++ (with all its availabe libraries including opencv) without even needing to resort to Matlab or python? In other words, given the current existing computer vision or machine learning libraries, is C++ alone sufficient for fast prototyping of ideas? If you're currently using Java or C# for your postgrad work, can you list down the reasons why they should be used and how they compare to other languages in terms of available libraries? What is the de facto vision/machine learning programming language and its associated libraries used in your university research group? Thanks in advance.

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• Why does not the Python MSI installers come with Tcl/Tk header files?

  - by srid

  The MSI installers downloadable from python.org does not include Tcl/Tk header (not source) files (that are required to compile some packages like matplotlib). Does anyone know of the rationale behind not including them?

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• C++ vs Matlab vs Python as a main language for Computer Vision Research

  - by Hough

  Hi all, Firstly, sorry for a somewhat long question but I think that many people are in the same situation as me and hopefully they can also gain some benefit from this. I'll be starting my PhD very soon which involves the fields of computer vision, pattern recognition and machine learning. Currently, I'm using opencv (2.1) C++ interface and I especially like its powerful Mat class and the overloaded operations available for matrix and image operations and seamless transformations. I've also tried (and implemented many small vision projects) using opencv python interface (new bindings; opencv 2.1) and I really enjoy python's ability to integrate opencv, numpy, scipy and matplotlib. But recently, I went back to opencv C++ interface because I felt that the official python new bindings were not stable enough and no overloaded operations are available for matrices and images, not to mention the lack of machine learning modules and slow speeds in certain operations. I've also used Matlab extensively in the past and although I've used mex files and other means to speed up the program, I just felt that Matlab's performance was inadequate for real-time vision tasks, be it for fast prototyping or not. When the project becomes larger and larger, many tasks have to be re-written in C and compiled into Mex files increasingly and Matlab becomes nothing more than a glue language. Here comes the sub-questions: For carrying out research in these fields (machine learning, vision, pattern recognition), what is your main or ideal programming language for rapid prototyping of ideas and testing algorithms contained in papers? For computer vision research work, can you list down the pros and cons of using the following languages? C++ (with opencv + gsl + svmlib + other libraries) vs Matlab (with all its toolboxes) vs python (with the imcomplete opencv bindings + numpy + scipy + matplotlib). Are there computer vision PhD/postgrad students here who are using only C++ (with all its availabe libraries including opencv) without even needing to resort to Matlab or python? In other words, given the current existing computer vision or machine learning libraries, is C++ alone sufficient for fast prototyping of ideas? If you're currently using Java or C# for your research, can you list down the reasons why they should be used and how they compare to other languages in terms of available libraries? What is the de facto vision/machine learning programming language and its associated libraries used in your research group? Thanks in advance. Edit: As suggested, I've opened the question to both academic and non-academic computer vision/machine learning/pattern recognition researchers and groups.

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• ggplot2 heatmap : how to preserve the label order ?

  - by Tg

  I'm trying to plot heatmap in ggplot2 using csv data following casbon's solution in http://biostar.stackexchange.com/questions/921/how-to-draw-a-csv-data-file-as-a-heatmap-using-numpy-and-matplotlib the problem is x-label try to re-sort itself. For example, if I swap label COG0002 and COG0001 in that example data, the x-label still come out in sort order (cog0001, cog0002, cog0003.... cog0008). Is there anyway to prevent this ? I want to it to be ordered as in csv file thanks pp

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• Compiler options wrong with python setup.py

  - by John Smith

  I'm trying to install matplotlib on my mac setup. I find that setup.py has inaccurate flags, in particular the isysroot points to an earlier SDK. Where does setup.py get its info and how can i fix it?

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• Enthought Python, Sage, or others (in Unix clusters)

  - by vailen

  I am currently get access to a cluster of Unix machines, but they don't have the software I need (numpy, scipy, matplotlib, etc), and I have to install them by myself (I don't have the root permission, either, so commands like apt-get or yast doesn't work). In the worst case, I have to compile them all from source. Is there any better way to do so? I hear something about Enthought Python and Sage, but not sure what is the best way to do so. Any suggestion?

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• Generate terminal graphics

  - by Werner

  Hi, which open source software options exist for generating terminal graphics? I mean, there is for instance the nice matplotlib, which can generate beautiful plots from data, in PNG or similar formats. But there are similar alternatives for generating just kind of ascii graphics? Thanks

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• Estimating the boundary of arbitrarily distributed data

  - by Dave

  I have two dimensional discrete spatial data. I would like to make an approximation of the spatial boundaries of this data so that I can produce a plot with another dataset on top of it. Ideally, this would be an ordered set of (x,y) points that matplotlib can plot with the plt.Polygon() patch. My initial attempt is very inelegant: I place a fine grid over the data, and where data is found in a cell, a square matplotlib patch is created of that cell. The resolution of the boundary thus depends on the sampling frequency of the grid. Here is an example, where the grey region are the cells containing data, black where no data exists. OK, problem solved - why am I still here? Well.... I'd like a more "elegant" solution, or at least one that is faster (ie. I don't want to get on with "real" work, I'd like to have some fun with this!). The best way I can think of is a ray-tracing approach - eg: from xmin to xmax, at y=ymin, check if data boundary crossed in intervals dx y=ymin+dy, do 1 do 1-2, but now sample in y An alternative is defining a centre, and sampling in r-theta space - ie radial spokes in dtheta increments. Both would produce a set of (x,y) points, but then how do I order/link neighbouring points them to create the boundary? A nearest neighbour approach is not appropriate as, for example (to borrow from Geography), an isthmus (think of Panama connecting N&S America) could then close off and isolate regions. This also might not deal very well with the holes seen in the data, which I would like to represent as a different plt.Polygon. The solution perhaps comes from solving an area maximisation problem. For a set of points defining the data limits, what is the maximum contiguous area contained within those points To form the enclosed area, what are the neighbouring points for the nth point? How will the holes be treated in this scheme - is this erring into topology now? Apologies, much of this is me thinking out loud. I'd be grateful for some hints, suggestions or solutions. I suspect this is an oft-studied problem with many solution techniques, but I'm looking for something simple to code and quick to run... I guess everyone is, really! Cheers, David

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• Running iPython from the OSX terminal.

  - by Az

  So I'm going through the matplotlib documentation and prepared to use the iPython interactive Python shell with ipython -pylab. However I get this: Az's MBP:~ Az$ ipython -pylab -bash: ipython: command not found Did I fail to install iPython? I used easy_install as advised. Any ideas?

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• Help getting iPython to run from the OSX terminal.

  - by Azfar

  Hi there, Got a heads up from stackoverflow.com to ask the question here. I'm going through the matplotlib documentation and prepared to use the iPython interactive Python shell with ipython -pylab. However I get this: MBP:~ Me$ ipython -pylab -bash: ipython: command not found Did I fail to install iPython? I used easy_install as advised. Any ideas? Update Thought I'd just say that I found the iPython "executable" in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin after doing a Spotlight search. Still a little confused as to what to do.

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• How do you know where macports installs python packages to?

  - by xmaslist

  I am running macports to install scipy and such on OS X leopard with python 2.7. The install runs successfully, but running python and trying to import the packages I've installed, they're not found. What I'm running is: sudo python_select python27 sudo port install py27-wxpython py27-numpy py27-matplotlib sudo port install py27-scipy py27-ipython Opening up python in interactive mode (it is the correct version of python), I type 'import scipy' and get a module not found error. What gives? How can I find out where it is installing the packages to instead?

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• Creating dynamic plots

  - by geoff92

  I'm completely new to web programming but I do have a programming background. I'd like to create a site that allows users to visit, enter some specifications into a form, submit the form, and then receive a graph. I have a few questions about this, only because I'm pretty ignorant: Is there a good framework I should start in? I know a lot of java, I'm okay with python, and I learned Ruby in the past. I figure I might use ruby on rails only because I hear of it so often and I think I've also heard it's easy. If anyone has some other recommendation, please suggest. The user will be entering data into a form. I'm guessing the request they'll be making should be one of a GET request, right? Because I don't intend for any of the data they're entering to modify my server (in fact, I don't intend on having a database). The data the user inputs will be used to perform calculations involving lots of matrices. I've written this functionality in python. If I use ruby on rails, should it be instead written in Ruby? Somewhere I've heard that you can either place the load of the work on your server or on the client's computer. Since the code performs heavy math, which option is preferable? How do I alter the setup to either make the client do the work or my server? Should I be using a "cgi-bin"? In the code that I have now, I use matplotlib, a python library, and then "show" the plot in order to see the graph. I specify the x and y limits, but I am able to "drag" the graph in order to see more data within the plot window. Ultimately, I want a graph to be shown on my site with the drag functionality. Is this possible? What if the client drags the graph so far, more computations must be made? Thanks!

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• Reordering matrix elements to reflect column and row clustering in naiive python

  - by bgbg

  Hello, I'm looking for a way to perform clustering separately on matrix rows and than on its columns, reorder the data in the matrix to reflect the clustering and putting it all together. The clustering problem is easily solvable, so is the dendrogram creation (for example in this blog or in "Programming collective intelligence"). However, how to reorder the data remains unclear for me. Eventually, I'm looking for a way of creating graphs similar to the one below using naive Python (with any "standard" library such as numpy, matplotlib etc, but without using R or other external tools).

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• STFT and ISTFT in Python

  - by endolith

  Is there any form of short-time Fourier transform with corresponding inverse transform built into SciPy or NumPy or whatever? There's the pyplot specgram function in matplotlib, which calls ax.specgram(), which calls mlab.specgram(), which calls _spectral_helper(): #The checks for if y is x are so that we can use the same function to #implement the core of psd(), csd(), and spectrogram() without doing #extra calculations. We return the unaveraged Pxy, freqs, and t. I'm not sure if this can be used to do an STFT and ISTFT, though. Is there anything else, or should I translate something like this?

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• confused about python decorators

  - by nbv4

  I have a class that has an output() method which returns a matplotlib Figure instance. I have a decorator I wrote that takes that fig instance and turns it into a Django response object. My decorator looks like this: class plot_svg(object): def __init__(self, view): self.view = view def __call__(self, *args, **kwargs): print args, kwargs fig = self.view(*args, **kwargs) canvas=FigureCanvas(fig) response=HttpResponse(content_type='image/svg+xml') canvas.print_svg(response) return response and this is how it was being used: def as_avg(self): return plot_svg(self.output)() The only reason I has it that way instead of using the "@" syntax is because when I do it with the "@": @plot_svg def as_svg(self): return self.output() I get this error: as_svg() takes exactly 1 argument (0 given) I'm trying to 'fix' this by putting it in the "@" syntax but I can't figure out how to get it working. I'm thinking it has something to do with self not getting passed where it's supposed to...

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• Python Least-Squares Natural Splines

  - by Eldila

  I am trying to find a numerical package which will fit a natural which minimizes weighted least squares. There is a package in scipy which does what I want for unnatural splines. import numpy as np import matplotlib.pyplot as plt from scipy import interpolate import random x = np.arange(0,5,1.0/2) xs = np.arange(0,5,1.0/500) y = np.sin(x+1) for i in range(len(y)): y[i] += .2*random.random() - .1 knots = np.array([1,2,3,4]) tck = interpolate.splrep(x,y,s=1,k=3,t=knots,task=-1) ynew = interpolate.splev(xs,tck,der=0) plt.figure() plt.plot(xs,ynew,x,y,'x')

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• Plot smooth line with PyPlot

  - by Paul

  I've got the following simple script that plots a graph: import matplotlib.pyplot as plt import numpy as np T = np.array([6, 7, 8, 9, 10, 11, 12]) power = np.array([1.53E+03, 5.92E+02, 2.04E+02, 7.24E+01, 2.72E+01, 1.10E+01, 4.70E+00]) plt.plot(T,power) plt.show() As it is now, the line goes straight from point to point which looks ok, but could be better in my opinion. What I want is to smooth the line between the points. In Gnuplot I would have plotted with smooth cplines. Is there an easy way to do this in PyPlot? I've found some tutorials, but they all seem rather complex.

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• Converting excel files to python to frequency

  - by Jacob

  Essentially I've got an excel files with voltage in the first column, and time in the second. I want to find the period of the voltages, as it returns a graph of voltage in y axis and time in x axis with a periodicity, looking similar to a sine function. To find the frequency I have uploaded my excel file to python as I think this will make it easier- there may be something I've missed that will simplify this. So far in python I have: import xlrd import numpy as N import numpy.fft as F import matplotlib.pyplot as P wb = xlrd.open_workbook('temp7.xls') #LOADING EXCEL FILE wb.sheet_names() sh = wb.sheet_by_index(0) first_column = sh.col_values(1) #VALUES FROM EXCEL second_column = sh.col_values(2) #VALUES FROM EXCEL Now how do I find the frequency from this? Huge thanks to anyone who can help! Jacob

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• How to update the contents of a FigureCanvasTkAgg

  - by Copo

  I'm plotting some data in a Tkinter FigureCanvasTkagg using matplotlib. I need to clear the figure where i plot data and draw new data when a button is pressed. here is the plotting part of the code (there's an App class defined before..) self.fig = figure() self.ax = self.fig.add_subplot(111) self.ax.set_ylim( min(y), max(y) ) self.line, = self.ax.semilogx(x,y,'.-') #tuple of a single element self.canvas = FigureCanvasTkAgg(self.fig,master=master) self.ax.semilogx(x,y,'o-') self.canvas.show() self.canvas.get_tk_widget().pack(side='top', fill='both', expand=1) self.frame.pack() how do i update the contents of such a canvas? regards, Jacopo

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• How to generate graphs and statistics from SQLAlchemy tables [Python]?

  - by Az

  Hi all, After running a bunch of simulations I'm going to be outputting the results into a table created using SQLAlchemy. I plan to use this data to generatw statistics - mean and variance being key. These, in turn, will be used to generate some graphs - histograms/line graphs, pie-charts and box-and-whisker plots specifically. I'm aware of the Python graphing libraries like matplotlib. The thing is, I'm not sure how to have this integrate with the information contained within the database tables. Any suggestions on how to make these two play with each other? The main problem is that I'm not sure how to supply the information as "data sets" to the graphing library. Thanks in advance.

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• Get information about a function in python, looking at source code

  - by Werner

  Hi, the following code comes from the matplotlib gallery: #!/usr/bin/env python from pylab import * x = array([10, 8, 13, 9, 11, 14, 6, 4, 12, 7, 5]) y = array([8.04, 6.95, 7.58, 8.81, 8.33, 9.96, 7.24, 4.26, 10.84, 4.82, 5.68]) I am new to python, and would like to change the content of x and y from an input file. I have two short questions: I could guess what array means, but once I see it on the code, how can I know to which library it belongs and more information about it? Should I use some kind of python debug commands? How do I insert the content of my input file into x? Thanks

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• python how to put data on y-axis when plotting histogram

  - by user3041107

  I don't quite understand how to control y - axis when using plt.hist plot in python. I read my .txt data file - it contains 10 columns with various data. If I want to plot distribution of strain on x axis I take column n.5. But what kind of value appears on y axis ??? Don't understand that. here is the code: import numpy import matplotlib.pyplot as plt from pylab import * from scipy.stats import norm import sys strain = [] infile = sys.argv[1] for line in infile: ret = numpy.loadtxt(infile) strain += list(ret[:,5]) fig = plt.figure() plt.hist(strain, bins = 20) plt.show() Thanks for help!

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