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• Easiest way to plot values as symbols in scatter plot?

  - by AllenH

  In an answer to an earlier question of mine regarding fixing the colorspace for scatter images of 4D data, Tom10 suggested plotting values as symbols in order to double-check my data. An excellent idea. I've run some similar demos in the past, but I can't for the life of me find the demo I remember being quite simple. So, what's the easiest way to plot numerical values as the symbol in a scatter plot instead of 'o' for example? Tom10 suggested plt.txt(x,y,value)- and that is the implementation used in a number of examples. I however wonder if there's an easy way to evaluate "value" from my array of numbers? Can one simply say: str(valuearray) ? Do you need a loop to evaluate the values for plotting as suggested in the matplotlib demo section for 3D text scatter plots? Their example produces: However, they're doing something fairly complex in evaluating the locations as well as changing text direction based on data. So, is there a cute way to plot x,y,C data (where C is a value often taken as the color in the plot data- but instead I wish to make the symbol)? Again, I think we have a fair answer to this- I just wonder if there's an easier way?

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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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• how to set a fixed color bar for pcolor in python matplotlib?

  - by user248237

  I am using pcolor with a custom color map to plot a matrix of values. I set my color map so that low values are white and high values are red, as shown below. All of my matrices have values between 0 and 20 (inclusive) and I'd like 20 to always be pure red and 0 to always be pure white, even if the matrix has values that don't span the entire range. For example, if my matrix only has values between 2 and 7, I don't want it to plot 2 as white and 7 as red, but rather color it as if the range is still 0 to 20. How can I do this? I tried using the "ticks=" option of colorbar but it did not work. Here is my current code (assume "my_matrix" contains the values to be plotted): cdict = {'red': ((0.0, 1.0, 1.0), (0.5, 1.0, 1.0), (1.0, 1.0, 1.0)), 'green': ((0.0, 1.0, 1.0), (0.5, 1.0, 1.0), (1.0, 0.0, 0.0)), 'blue': ((0.0, 1.0, 1.0), (0.5, 1.0, 1.0), (1.0, 0.0, 0.0))} my_cmap = matplotlib.colors.LinearSegmentedColormap('my_colormap', cdict, 256) colored_matrix = plt.pcolor(my_matrix, cmap=my_cmap) plt.colorbar(colored_matrix, ticks=[0, 5, 10, 15, 20]) any idea how I can fix this to get the right result? thanks very much.

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• Doing arithmetic with up to two decimal places in Python?

  - by user248237

  I have two floats in Python that I'd like to subtract, i.e. v1 = float(value1) v2 = float(value2) diff = v1 - v2 I want "diff" to be computed up to two decimal places, that is compute it using %.2f of v1 and %.2f of v2. How can I do this? I know how to print v1 and v2 up to two decimals, but not how to do arithmetic like that. The particular issue I am trying to avoid is this. Suppose that: v1 = 0.982769777778 v2 = 0.985980444444 diff = v1 - v2 and then I print to file the following: myfile.write("%.2f\t%.2f\t%.2f\n" %(v1, v2, diff)) then I will get the output: 0.98 0.99 0.00, suggesting that there's no difference between v1 and v2, even though the printed result suggests there's a 0.01 difference. How can I get around this? thanks.

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• displaying a colored 2d array in matplotlib in Python

  - by user248237

  I'd like to plot a 2-d matrix from numpy as a colored matrix in Matplotlib. I have the following 9-by-9 array: my_array = diag(ones(9)) # plot the array pcolor(my_array) I'd like to set the first three elements of the diagonal to be a certain color, the next three to be a different color, and the last three a different color. I'd like to specify the color by a hex code string, like "#FF8C00". How can I do this? Also, how can I set the color of 0-valued elements for pcolor?

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• Better way to compare neighboring cells in matrix

  - by HyperCube

  Suppose I have a matrix of size 100x100 and I would like to compare each pixel to its direct neighbor (left, upper, right, lower) and then do some operations on the current matrix or a new one of the same size. A sample code in Python/Numpy could look like the following: (the comparison 0.5 has no meaning, I just want to give a working example for some operation while comparing the neighbors) import numpy as np my_matrix = np.random.rand(100,100) new_matrix = np.array((100,100)) my_range = np.arange(1,99) for i in my_range: for j in my_range: if my_matrix[i,j+1] > 0.5: new_matrix[i,j+1] = 1 if my_matrix[i,j-1] > 0.5: new_matrix[i,j-1] = 1 if my_matrix[i+1,j] > 0.5: new_matrix[i+1,j] = 1 if my_matrix[i-1,j] > 0.5: new_matrix[i-1,j] = 1 if my_matrix[i+1,j+1] > 0.5: new_matrix[i+1,j+1] = 1 if my_matrix[i+1,j-1] > 0.5: new_matrix[i+1,j-1] = 1 if my_matrix[i-1,j+1] > 0.5: new_matrix[i-1,j+1] = 1 This can get really nasty if I want to step into one neighboring cell and start from it to do a similar task... Do you have some suggestions how this can be done in a more efficient manner? Is this even possible?

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• doing arithmetic upto two significant figures in Python?

  - by user248237

  I have two floats in Python that I'd like to subtract, i.e. v1 = float(value1) v2 = float(value2) diff = v1 - v2 I want "diff" to be computed upto two significant figures, that is compute it using %.2f of v1 and %.2f of v2. How can I do this? I know how to print v1 and v2 up to two decimals, but not how to do arithmetic like that. thanks.

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• converting python list of strings to their type

  - by user248237

  given a list of python strings, how can I automatically convert them to their correct type? Meaning, if I have: ["hello", "3", "3.64", "-1"] I'd like this to be converted to the list ["hello", 3, 3.64, -1] where the first element is a stirng, the second an int, the third a float and the fourth an int. how can I do this? thanks.

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• how do I remove rows/columns from this matrix using python

  - by banditKing

  My matrix looks like this. ['Hotel', ' "excellent"', ' "very good"', ' "average"', ' "poor"', ' "terrible"', ' "cheapest"', ' "rank"', ' "total reviews"'] ['westin', ' 390', ' 291', ' 70', ' 43', ' 19', ' 215', ' 27', ' 813'] ['ramada', ' 136', ' 67', ' 53', ' 30', ' 24', ' 149', ' 49', ' 310 '] ['sutton place', '489', ' 293', ' 106', ' 39', ' 20', ' 299', ' 24', ' 947'] ['loden', ' 681', ' 134', ' 17', ' 5', ' 0', ' 199', ' 4', ' 837'] ['hampton inn downtown', ' 241', ' 166', ' 26', ' 5', ' 1', ' 159', ' 21', ' 439'] ['shangri la', ' 332', ' 45', ' 20', ' 8', ' 2', ' 325', ' 8', ' 407'] ['residence inn marriott', ' 22', ' 15', ' 5', ' 0', ' 0', ' 179', ' 35', ' 42'] ['pan pacific', ' 475', ' 262', ' 86', ' 29', ' 16', ' 249', ' 15', ' 868'] ['sheraton wall center', ' 277', ' 346', ' 150', ' 80', ' 26', ' 249', ' 45', ' 879'] ['westin bayshore', ' 390', ' 291', ' 70', ' 43', ' 19', ' 199', ' 813'] I want to remove the top row and the 0th column from this and create a new matrix. How do I do this? Normally in java or so Id use the following code: for (int y; y< matrix[x].length; y++) for(int x; x < matrix[Y].length; x++) { if(x == 0 || y == 0) { continue } else { new_matrix[x][y] = matrix[x][y]; } } Is there a way such as this in python to iterate and selectively copy elements? Thanks EDIT Im also trying to convert each matrix element from a string to a float as I iterate over the matrix. This my updated modified code based on the answer below. A = [] f = open("csv_test.csv",'rt') try: reader = csv.reader(f) for row in reader: A.append(row) finally: f.close() new_list = [row[1:] for row in A[1:]] l = np.array(new_list) l.astype(np.float32) print l However Im getting an error --> l.astype(np.float32) print l ValueError: setting an array element with a sequence.

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• averaging matrix efficiently

  - by user248237

  in Python, given an n x p matrix, e.g. 4 x 4, how can I return a matrix that's 4 x 2 that simply averages the first two columns and the last two columns for all 4 rows of the matrix? e.g. given: a = array([[1, 2, 3, 4], [5, 6, 7, 8], [9, 10, 11, 12], [13, 14, 15, 16]]) return a matrix that has the average of a[:, 0] and a[:, 1] and the average of a[:, 2] and a[:, 3]. I want this to work for an arbitrary matrix of n x p assuming that the number of columns I am averaging of n is obviously evenly divisible by n. let me clarify: for each row, I want to take the average of the first two columns, then the average of the last two columns. So it would be: 1 + 2 / 2, 3 + 4 / 2 <- row 1 of new matrix 5 + 6 / 2, 7 + 8 / 2 <- row 2 of new matrix, etc. which should yield a 4 by 2 matrix rather than 4 x 4. thanks.

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• making errorbars not clipped in matplotlib with Python

  - by user248237

  I am using matplotlib in Python to plot a line with errorbars as follows: plt.errorbar(xvalues, up_densities, yerr=ctl_sds, fmt='-^', lw=1.2, markersize=markersize, markeredgecolor=up_color, color=up_color, label="My label", clip_on=False) plt.xticks(xvalues) I set the ticks on the x-axis using "xticks". However, the error bars of the last point in xvalues (i.e. xvalues[-1]) are clipped on the right -- meaning only half an error bar appears. This is true even with the clip_on=False option. How can I fix this, so that the error bars appear in full, even though their right side is technically outside xvalues[-1]? thanks.

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• merging indexed array in Python

  - by leon

  Suppose that I have two numpy arrays of the form x = [[1,2] [2,4] [3,6] [4,NaN] [5,10]] y = [[0,-5] [1,0] [2,5] [5,20] [6,25]] is there an efficient way to merge them such that I have xmy = [[0, NaN, -5 ] [1, 2, 0 ] [2, 4, 5 ] [3, 6, NaN] [4, NaN, NaN] [5, 10, 20 ] [6, NaN, 25 ] I can implement a simple function using search to find the index but this is not elegant and potentially inefficient for a lot of arrays and large dimensions. Any pointer is appreciated.

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• getting smallest of coordinates that differ by N or more in Python

  - by user248237

  suppose I have a list of coordinates: data = [[(10, 20), (100, 120), (0, 5), (50, 60)], [(13, 20), (300, 400), (100, 120), (51, 62)]] and I want to take all tuples that either appear in each list in data, or any tuple that differs from all tuples in lists other than its own by 3 or less. How can I do this efficiently in Python? For the above example, the results should be: [[(100, 120), # since it occurs in both lists (10, 20), (13, 20), # since they differ by only 3 (50, 60), (51, 60)]] (0, 5) and (300, 400) would not be included, since they don't appear in both lists and are not different from elements in lists other than their own by 3 or less. how can this be computed? thanks.

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• Choosing randomly all the elements in the the list just once

  - by Dalek

  How is it possible to randomly choose a number from a list with n elements, n time without picking the same element of the list twice. I wrote a code to choose the sequence number of the elements in the list but it is slow: >>>redshift=np.array([0.92,0.17,0.51,1.33,....,0.41,0.82]) >>>redshift.shape (1225,) exclude=[] k=0 ng=1225 while (k < ng): flag1=0 sq=random.randint(0, ng) while (flag1<1): if sq in exclude: flag1=1 sq=random.randint(0, ng) else: print sq exclude.append(sq) flag1=0 z=redshift[sq] k+=1 It doesn't choose all the sequence number of elements in the list.

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• speeding up parsing of files

  - by user248237

  the following function parses a CSV file into a list of dictionaries, where each element in the list is a dictionary where the values are indexed by the header of the file (assumed to be the first line.) this function is very very slow, taking ~6 seconds for a file that's relatively small (less than 30,000 lines.) how can I speed it up? def csv2dictlist_raw(filename, delimiter='\t'): f = open(filename) header_line = f.readline().strip() header_fields = header_line.split(delimiter) dictlist = [] # convert data to list of dictionaries for line in f: values = map(tryEval, line.strip().split(delimiter)) dictline = dict(zip(header_fields, values)) dictlist.append(dictline) return (dictlist, header_fields) thanks.

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• Does Python/Scipy have a firls( ) replacement (i.e. a weighted, least squares, FIR filter design)?

  - by delicasso

  I am porting code from Matlab to Python and am having trouble finding a replacement for the firls( ) routine. It is used for, least-squares linear-phase Finite Impulse Response (FIR) filter design. I looked at scipy.signal and nothing there looked like it would do the trick. Of course I was able to replace my remez and freqz algorithsm, so that's good. On one blog I found an algorithm that implemented this filter without weighting, but I need one with weights. Thanks, David

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• compiling numpy with sunperf atlas libraries

  - by user288558

  I would like to use the sunperf libraries when compiling scipy and numpy. I tried using setupscons.py which seems to check from SUNPERF libraries, but it didnt recognize where mine are: here is a listing of /pkg/linux/SS12/sunstudio12.1 (thats where the sunperf library lives): wkerzend@mosura:/home/wkerzend>ls /pkg/linux/SS12/sunstudio12.1/lib/ CCios/ libdbx_agent.so@ libsunperf.so.3@ amd64/ libfcollector.so@ libtha.so@ collector.jar@ libfsu.so@ libtha.so.1@ dbxrc@ libfsu.so.1@ locale/ debugging.so@ libfui.so@ make.rules@ er.rc@ libfui.so.1@ rw7/ libblacs_openmpi.so@ librtc.so@ sse2/ libblacs_openmpi.so.1@ libscalapack.so@ stlport4/ libcollectorAPI.so@ libscalapack.so.1@ svr4.make.rules@ libcollectorAPI.so.1@ libsunperf.so@ tools_svc_mgr@ I tried to specify this directory in sites.cfg, but I still get the following errors: Checking if g77 needs dummy main - MAIN__. Checking g77 name mangling - '_', '', lower-case. Checking g77 C compatibility runtime ...-L/usr/lib/gcc/x86_64-redhat-linux/3.4.6 - L/usr/lib/gcc/x86_64-redhat-linux/3.4.6 -L/usr/lib/gcc/x86_64-redhat- linux/3.4.6/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../.. -L/lib/../lib64 -L/usr/lib/../lib64 -lfrtbegin -lg2c -lm Checking MKL ... Failed (could not check header(s) : check config.log in build/scons/scipy/integrate for more details) Checking ATLAS ... Failed (could not check header(s) : check config.log in build/scons/scipy/integrate for more details) Checking SUNPERF ... Failed (could not check symbol cblas_sgemm : check config.log in build/scons/scipy/integrate for more details)) Checking Generic BLAS ... yes Checking for BLAS (Generic BLAS) ... Failed: BLAS (Generic BLAS) test could not be linked and run Exception: Could not find F77 BLAS, needed for integrate package: File "/priv/manana1/wkerzend/install_dir/scipy-0.7.1/scipy/integrate/SConstruct", line 2: GetInitEnvironment(ARGUMENTS).DistutilsSConscript('SConscript') File "/home/wkerzend/python_coala/numscons-0.10.1-py2.6.egg/numscons/core/numpyenv.py", line 108: build_dir = '$build_dir', src_dir = '$src_dir') File "/priv/manana1/wkerzend/python_coala/numscons-0.10.1-py2.6.egg/numscons/scons-local/scons-local-1.2.0/SCons/Script/SConscript.py", line 549: return apply(_SConscript, [self.fs,] + files, subst_kw) File "/priv/manana1/wkerzend/python_coala/numscons-0.10.1-py2.6.egg/numscons/scons-local/scons-local-1.2.0/SCons/Script/SConscript.py", line 259: exec _file_ in call_stack[-1].globals File "/priv/manana1/wkerzend/install_dir/scipy-0.7.1/build/scons/scipy/integrate/SConscript", line 15: raise Exception("Could not find F77 BLAS, needed for integrate package") error: Error while executing scons command. See above for more information. If you think it is a problem in numscons, you can also try executing the scons command with --log-level option for more detailed output of what numscons is doing, for example --log-level=0; the lowest the level is, the more detailed the output it.----- any help is appreciated Wolfgang

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• Binomial test in Python

  - by Morlock

  I need to do a binomial test in Python that allows calculation for 'n' numbers of the order of 10000. I have implemented a quick binomial_test function using scipy.misc.comb, however, it is pretty much limited around n = 1000, I guess because it reaches the biggest representable number while computing factorials or the combinatorial itself. Here is my function: from scipy.misc import comb def binomial_test(n, k): """Calculate binomial probability """ p = comb(n, k) * 0.5**k * 0.5**(n-k) return p How could I use a native python (or numpy, scipy...) function in order to calculate that binomial probability? If possible, I need scipy 0.7.2 compatible code. Many thanks!

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• Binomial test in Python for very large numbers

  - by Morlock

  I need to do a binomial test in Python that allows calculation for 'n' numbers of the order of 10000. I have implemented a quick binomial_test function using scipy.misc.comb, however, it is pretty much limited around n = 1000, I guess because it reaches the biggest representable number while computing factorials or the combinatorial itself. Here is my function: from scipy.misc import comb def binomial_test(n, k): """Calculate binomial probability """ p = comb(n, k) * 0.5**k * 0.5**(n-k) return p How could I use a native python (or numpy, scipy...) function in order to calculate that binomial probability? If possible, I need scipy 0.7.2 compatible code. Many thanks!

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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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• How to incorporate existing open source software from a licensing perspective?

  - by Matt

  I'm working on software that uses the following libraries: Biopython SciPy NumPy All of the above have licenses similar to MIT or BSD. Three scenarios: First, if I don't redistribute those dependencies, and only my code, then all I need is my own copyright and license (planing on using the MIT License) for my code. Correct? What if I use py2exe or py2app to create a binary executable to distribute so as to make it easy for people to run the application without needing to install python and all the dependencies. Of course this also means that my binary file(s) contains python itself (along with any other packages I might have performed a pip install xyz). What if I bundle Biopython, SciPy, and NumPy binaries in my package? In the latter two cases, what do I need to do to comply with copyright laws.

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• Which python mpi library to use?

  - by Dana the Sane

  I'm starting work on some simulations using MPI and want to do the programming in Python/scipy. The scipy site lists a number of mpi libraries, but I was hoping to get feedback on quality, ease of use, etc from anyone who has used one.

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• How to install matplotlib on OS X?

  - by Paperflyer

  I want to install matplotlib on OS X. If possible, using homebrew. I installed Python 2.7.1 using brew install python, I modified my path to use it I installed pip using brew install pip I installed numpy 1.5.1 using pip install numpy I installed scipy 0.8.0 using pip install scipy This is where it gets hairy. pip install matplotlib will fetch the wrong version of matplotlib, which is incompatible with the recent version of numpy. The solution is to fetch the correct version of matplotlib manually: pip install -f http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.0.1/matplotlib-1.0.1.tar.gz matplotlib But, that version fails to compile since it can't find the freetype headers: In file included from src/ft2font.cpp:1: src/ft2font.h:14:22: error: ft2build.h: No such file or directory These headers are actually installed in /usr/X11/include as part of the X11 developer tools. So, how can I make matplotlib use these headers?

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• Installing a python wrapper for a c++ library

  - by Eugene Kogan

  Hi all, I am trying to install the python wrapper for the ANN (approx near neighbors) c++ library: link is http://www.scipy.org/scipy/scikits/wiki/AnnWrapper . I am on Windows 7 32-bit. Unfortunately the documentation is a bit terse and I am a newbie to programming in general, so I cannot decipher the instructions found within. I have not built a C++ library before and am not even sure how to get that far. Can anyone please guide? Thanks! gene

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• Finding matching submatrics inside a matrix

  - by DaveO

  I have a 100x200 2D array expressed as a numpy array consisting of black (0) and white (255) cells. It is a bitmap file. I then have 2D shapes (it's easiest to think of them as letters) that are also 2D black and white cells. I know I can naively iterate through the matrix but this is going to be a 'hot' portion of my code so speed is an concern. Is there a fast way to perform this in numpy/scipy? I looked briefly at Scipy's correlate function. I am not interested in 'fuzzy matches', only exact matches. I also looked at some academic papers but they are above my head.

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