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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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  • pyplot: really slow creating heatmaps

    - by cvondrick
    I have a loop that executes the body about 200 times. In each loop iteration, it does a sophisticated calculation, and then as debugging, I wish to produce a heatmap of a NxM matrix. But, generating this heatmap is unbearably slow and significantly slow downs an already slow algorithm. My code is along the lines: import numpy import matplotlib.pyplot as plt for i in range(200): matrix = complex_calculation() plt.set_cmap("gray") plt.imshow(matrix) plt.savefig("frame{0}.png".format(i)) The matrix, from numpy, is not huge --- 300 x 600 of doubles. Even if I do not save the figure and instead update an on-screen plot, it's even slower. Surely I must be abusing pyplot. (Matlab can do this, no problem.) How do I speed this up?

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  • matplotlib.pyplot, preserve aspect ratio of the plot

    - by Headcrab
    Assuming we have a polygon coordinates as polygon = [(x1, y1), (x2, y2), ...], the following code displays the polygon: import matplotlib.pyplot as plt plt.fill(*zip(*polygon)) plt.show() By default it is trying to adjust the aspect ratio so that the polygon (or whatever other diagram) fits inside the window, and automatically changing it so that it fits even after resizing. Which is great in many cases, except when you are trying to estimate visually if the image is distorted. How to fix the aspect ratio to be strictly 1:1? (Not sure if "aspect ratio" is the right term here, so in case it is not - I need both X and Y axes to have 1:1 scale, so that (0, 1) on both X and Y takes an exact same amount of screen space. And I need to keep it 1:1 no matter how I resize the window.)

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  • matplotlib.pyplot/pylab not updating figure while isinteractive(), using ipython -pylab

    - by NumberOverZero
    There are a lot of questions about matplotlib, pylab, pyplot, ipython, so I'm sorry if you're sick of seeing this asked. I'll try to be as specific as I can, because I've been looking through people's questions and looking at documentation for pyplot and pylab, and I still am not sure what I'm doing wrong. On with the code: Goal: plot a figure every .5 seconds, and update the figure as soon as the plot command is called. My attempt at coding this follows (running on ipython -pylab): import time ion() x=linspace(-1,1,51) plot(sin(x)) for i in range(10): plot([sin(i+j) for j in x]) #see ** print i time.sleep(1) print 'Done' It correctly plots each line, but not until it has exited the for loop. I have tried forcing a redraw by putting draw() where ** is, but that doesn't seem to work either. Ideally, I'd like to have it simply add each line, instead of doing a full redraw. If redrawing is required however, that's fine. Additional attempts at solving: just after ion(), tried adding hold(True) to no avail. for kicks tried show() for ** The closest answer I've found to what I'm trying to do was at http://stackoverflow.com/questions/2310851/plotting-lines-without-blocking-execution, but show() isn't doing anything. I apologize if this is a straightforward request, and I'm looking past something so obvious. For what it's worth, this came up while I was trying to convert matlab code from class to some python for my own use. The original matlab (initializations removed) which I have been trying to convert follows: for i=1:time plot(u) hold on pause(.01) for j=2:n-1 v(j)=u(j)-2*u(j-1) end v(1)= pi u=v end Any help, even if it's just "look up this_method" would be excellent, so I can at least narrow my efforts to figuring out how to use that method. If there's any more information that would be useful, let me know.

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  • Pyplot connect to timer event?

    - by Baron Yugovich
    The same way I now have plt.connect('button_press_event', self.on_click) I would like to have something like plt.connect('each_five_seconds_event', self.on_timer) How can I achieve this in a way that's most similar to what I've shown above? EDIT: I tried fig = plt.subplot2grid((num_cols, num_rows), (col, row), rowspan=rowspan, colspan=colspan) timer = fig.canvas.new_timer(interval=100, callbacks=[(self.on_click)]) timer.start() And got AttributeError: 'AxesSubplot' object has no attribute 'canvas'

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  • pyplot.scatter changes the data limits of the axis

    - by Erotemic
    I have some code which plots some points. I substituted ax.scatter for ax.plot so I could control the color of each point individually. However when I make this change the axis x and y ranges seem to increase. I can't pinpoint why this is happening. The only thing I've changed is plot to scatter. This code makes an axis that is too big ax.scatter(x, y, c=color_list, s=pts_size, marker='o', edgecolor='none') #ax.plot(x, y, linestyle='None', marker='o', markerfacecolor=pts_color, markersize=pts_size, markeredgewidth=0) This code does the right thing (but I can't control the color) #ax.scatter(x, y, c=color_list, s=pts_size, marker='o', edgecolor='none') ax.plot(x, y, linestyle='None', marker='o', markerfacecolor=pts_color, markersize=pts_size, markeredgewidth=0) Is there a way I can call scatter such that it doesn't mess with my current axis limits?

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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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  • 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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  • python networkx

    - by krisdigitx
    hi, i am trying to use networkx with python, when i run this program, it get this error, is there anything missing? #!/usr/bin/env python import networkx as nx import matplotlib import matplotlib.pyplot import matplotlib.pyplot as plt G=nx.Graph() G.add_node(1) G.add_nodes_from([2,3,4,5,6,7,8,9,10]) #nx.draw_graphviz(G) #nx_write_dot(G, 'node.png') nx.draw(G) plt.savefig("/var/www/node.png") Traceback (most recent call last): File "graph.py", line 13, in <module> nx.draw(G) File "/usr/lib/pymodules/python2.5/networkx/drawing/nx_pylab.py", line 124, in draw cf=pylab.gcf() File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 276, in gcf return figure() File "/usr/lib/pymodules/python2.5/matplotlib/pyplot.py", line 254, in figure **kwargs) File "/usr/lib/pymodules/python2.5/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager window = Tk.Tk() File "/usr/lib/python2.5/lib-tk/Tkinter.py", line 1650, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: no display name and no $DISPLAY environment variable

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  • Problem running python/matplotlib in background after ending ssh session.

    - by Jamie
    Hi there, I have to VPN and then ssh from home to my work server and want to run a python script in the background, then log out of the ssh session. My script makes several histogram plots using matplotlib, and as long as I keep the connection open everything is fine, but if I log out I keep getting an error message in the log file I created for the script. File "/Home/eud/jmcohen/.local/lib/python2.5/site-packages/matplotlib/pyplot.py", line 2058, in loglog ax = gca() File "/Home/eud/jmcohen/.local/lib/python2.5/site-packages/matplotlib/pyplot.py", line 582, in gca ax = gcf().gca(**kwargs) File "/Home/eud/jmcohen/.local/lib/python2.5/site-packages/matplotlib/pyplot.py", line 276, in gcf return figure() File "/Home/eud/jmcohen/.local/lib/python2.5/site-packages/matplotlib/pyplot.py", line 254, in figure **kwargs) File "/Home/eud/jmcohen/.local/lib/python2.5/site-packages/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager window = Tk.Tk() File "/Home/eud/jmcohen/.local/lib/python2.5/lib-tk/Tkinter.py", line 1647, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: couldn't connect to display "localhost:10.0" I'm assuming that it doesn't know where to create the figures I want since I close my X11 ssh session. If I'm logged in while the script is running I don't see any figures popping up (although that's because I don't have the show() command in my script), and I thought that python uses tkinter to display figures. The way that I'm creating the figures is, loglog() hist(list,x) ylabel('y') xlabel('x') savefig('%s_hist.ps' %source.name) close() The script requires some initial input, so the way I'm running it in the background is python scriptToRun.py << start>& logfile.log& Is there a way around this, or do I just have to stay ssh'd into my machine? Thanks.

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  • Graphing a line and scatter points using Matplotlib?

    - by Patrick O'Doherty
    Hi guys I'm using matplotlib at the moment to try and visualise some data I am working on. I'm trying to plot around 6500 points and the line y = x on the same graph but am having some trouble in doing so. I can only seem to get the points to render and not the line itself. I know matplotlib doesn't plot equations as such rather just a set of points so I'm trying to use and identical set of points for x and y co-ordinates to produce the line. The following is my code from matplotlib import pyplot import numpy from pymongo import * class Store(object): """docstring for Store""" def __init__(self): super(Store, self).__init__() c = Connection() ucd = c.ucd self.tweets = ucd.tweets def fetch(self): x = [] y = [] for t in self.tweets.find(): x.append(t['positive']) y.append(t['negative']) return [x,y] if __name__ == '__main__': c = Store() array = c.fetch() t = numpy.arange(0., 0.03, 1) pyplot.plot(array[0], array[1], 'ro', t, t, 'b--') pyplot.show() Any suggestions would be appreciated, Patrick

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  • I am getting this error on using matplotlib

    - by Arun Abraham
    I get this error on typing this in python command prompt: import matplotlib.pyplot as plt Traceback (most recent call last): File "<pyshell#1>", line 1, in <module> import matplotlib.pyplot as plt File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/pyplot.py", line 97, in <module> _backend_mod, new_figure_manager, draw_if_interactive, _show = pylab_setup() File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/__init__.py", line 25, in pylab_setup globals(),locals(),[backend_name]) File "/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/backend_macosx.py", line 21, in <module> from matplotlib.backends import _macosx ImportError: dlopen(/Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/_macosx.so, 2): Library not loaded: /System/Library/Frameworks/CoreText.framework/Versions/A/CoreText Referenced from: /Library/Python/2.7/site-packages/matplotlib-1.3.x-py2.7-macosx-10.8-intel.egg/matplotlib/backends/_macosx.so Reason: image not found Can someone suggest me, how i can fix this ? I had installed all the packages with this shell script https://github.com/fonnesbeck/ScipySuperpack Is there anything that i am missing ? Any additional configuration ?

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  • pymatplotlib without xserver

    - by vigilant
    Is it possible to use networkx or pymatplotlib without an xserver running? I keep getting the following error with their first example (of networkx): Traceback (most recent call last): File "test.py", line 17, in <module> nx.draw(G,pos,node_color='#A0CBE2',edge_color=colors,width=4,edge_cmap=plt.cm.Blues,with_labels=False) File "/usr/local/lib/python2.6/dist-packages/networkx-1.3-py2.6.egg/networkx/drawing/nx_pylab.py", line 124, in draw cf=pylab.gcf() File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 276, in gcf return figure() File "/usr/lib/pymodules/python2.6/matplotlib/pyplot.py", line 254, in figure **kwargs) File "/usr/lib/pymodules/python2.6/matplotlib/backends/backend_tkagg.py", line 90, in new_figure_manager window = Tk.Tk() File "/usr/lib/python2.6/lib-tk/Tkinter.py", line 1646, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, wantobjects, useTk, sync, use) _tkinter.TclError: couldn't connect to display ""

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  • creating a color coded time chart using colorbar and colormaps in python

    - by Rusty
    I'm trying to make a time tracking chart based on a daily time tracking file that I used. I wrote code that crawls through my files and generates a few lists. endTimes is a list of times that a particular activity ends in minutes going from 0 at midnight the first day of the month to however many minutes are in a month. labels is a list of labels for the times listed in endTimes. It is one shorter than endtimes since the trackers don't have any data about before 0 minute. Most labels are repeats. categories contains every unique value of labels in order of how well I regard that time. I want to create a colorbar or a stack of colorbars (1 for eachday) that will depict how I spend my time for a month and put a color associated with each label. Each value in categories will have a color associated. More blue for more good. More red for more bad. It is already in order for the jet colormap to be right, but I need to get desecrate color values evenly spaced out for each value in categories. Then I figure the next step would be to convert that to a listed colormap to use for the colorbar based on how the labels associated with the categories. I think this is the right way to do it, but I am not sure. I am not sure how to associate the labels with color values. Here is the last part of my code so far. I found one function to make a discrete colormaps. It does, but it isn't what I am looking for and I am not sure what is happening. Thanks for the help! # now I need to develop the graph import numpy as np from matplotlib import pyplot,mpl import matplotlib from scipy import interpolate from scipy import * def contains(thelist,name): # checks if the current list of categories contains the one just read for val in thelist: if val == name: return True return False def getCategories(lastFile): ''' must determine the colors to use I would like to make a gradient so that the better the task, the closer to blue bad labels will recieve colors closer to blue read the last file given for the information on how I feel the order should be then just keep them in the order of how good they are in the tracker use a color range and develop discrete values for each category by evenly spacing them out any time not found should assume to be sleep sleep should be white ''' tracker = open(lastFile+'.txt') # open the last file # find all the categories categories = [] for line in tracker: pos = line.find(':') # does it have a : or a ? if pos==-1: pos=line.find('?') if pos != -1: # ignore if no : or ? name = line[0:pos].strip() # split at the : or ? if contains(categories,name)==False: # if the category is new categories.append(name) # make a new one return categories # find good values in order of last day newlabels=[] for val in getCategories(lastDay): if contains(labels,val): newlabels.append(val) categories=newlabels # convert discrete colormap to listed colormap python for ii,val in enumerate(labels): if contains(categories,val)==False: labels[ii]='sleep' # create a figure fig = pyplot.figure() axes = [] for x in range(endTimes[-1]%(24*60)): ax = fig.add_axes([0.05, 0.65, 0.9, 0.15]) axes.append(ax) # figure out the colors to use # stole this function to make a discrete colormap # http://www.scipy.org/Cookbook/Matplotlib/ColormapTransformations def cmap_discretize(cmap, N): """Return a discrete colormap from the continuous colormap cmap. cmap: colormap instance, eg. cm.jet. N: Number of colors. Example x = resize(arange(100), (5,100)) djet = cmap_discretize(cm.jet, 5) imshow(x, cmap=djet) """ cdict = cmap._segmentdata.copy() # N colors colors_i = np.linspace(0,1.,N) # N+1 indices indices = np.linspace(0,1.,N+1) for key in ('red','green','blue'): # Find the N colors D = np.array(cdict[key]) I = interpolate.interp1d(D[:,0], D[:,1]) colors = I(colors_i) # Place these colors at the correct indices. A = zeros((N+1,3), float) A[:,0] = indices A[1:,1] = colors A[:-1,2] = colors # Create a tuple for the dictionary. L = [] for l in A: L.append(tuple(l)) cdict[key] = tuple(L) # Return colormap object. return matplotlib.colors.LinearSegmentedColormap('colormap',cdict,1024) # jet colormap goes from blue to red (good to bad) cmap = cmap_discretize(mpl.cm.jet, len(categories)) cmap.set_over('0.25') cmap.set_under('0.75') #norm = mpl.colors.Normalize(endTimes,cmap.N) print endTimes print labels # make a color list by matching labels to a picture #norm = mpl.colors.ListedColormap(colorList) cb1 = mpl.colorbar.ColorbarBase(axes[0],cmap=cmap ,orientation='horizontal' ,boundaries=endTimes ,ticks=endTimes ,spacing='proportional') pyplot.show()

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  • How can I show figures separately in matplotlib?

    - by Federico Ramponi
    Say that I have two figures in matplotlib, with one plot per figure: import matplotlib.pyplot as plt f1 = plt.figure() plt.plot(range(0,10)) f2 = plt.figure() plt.plot(range(10,20)) Then I show both in one shot plt.show() Is there a way to show them separately, i.e. to show just f1? Or better: how can I manage the figures separately like in the following 'wishful' code (that doesn't work): f1 = plt.figure() f1.plot(range(0,10)) f1.show()

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  • Creating a Colormap Legend in Matplotlib

    - by Vince
    Hi fellow Stackers! I am using imshow() in matplotlib like so: import numpy as np import matplotlib.pyplot as plt mat = '''SOME MATRIX''' plt.imshow(mat, origin="lower", cmap='gray', interpolation='nearest') plt.show() How do I add a legend showing the numeric value for the different shades of gray. Sadly, my googling has not uncovered an answer :( Thank you in advance for the help. Vince

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  • AttributeError while adding colorbar in matplotlib

    - by bgbg
    The following code fails to run on Python 2.5.4: from matplotlib import pylab as pl import numpy as np data = np.random.rand(6,6) fig = pl.figure(1) fig.clf() ax = fig.add_subplot(1,1,1) ax.imshow(data, interpolation='nearest', vmin=0.5, vmax=0.99) pl.colorbar() pl.show() The error message is C:\temp>python z.py Traceback (most recent call last): File "z.py", line 10, in <module> pl.colorbar() File "C:\Python25\lib\site-packages\matplotlib\pyplot.py", line 1369, in colorbar ret = gcf().colorbar(mappable, cax = cax, ax=ax, **kw) File "C:\Python25\lib\site-packages\matplotlib\figure.py", line 1046, in colorbar cb = cbar.Colorbar(cax, mappable, **kw) File "C:\Python25\lib\site-packages\matplotlib\colorbar.py", line 622, in __init__ mappable.autoscale_None() # Ensure mappable.norm.vmin, vmax AttributeError: 'NoneType' object has no attribute 'autoscale_None' How can I add colorbar to this code? Following is the interpreter information: Python 2.5.4 (r254:67916, Dec 23 2008, 15:10:54) [MSC v.1310 32 bit (Intel)] on win32 Type "help", "copyright", "credits" or "license" for more information. >>>

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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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  • Sans-serif math with latex in matplotlib

    - by Morgoth
    The following script: import matplotlib matplotlib.use('Agg') import matplotlib.pyplot as mpl mpl.rc('font', family='sans-serif') mpl.rc('text', usetex=True) fig = mpl.figure() ax = fig.add_subplot(1,1,1) ax.text(0.2,0.5,r"Math font: $451^\circ$") ax.text(0.2,0.7,r"Normal font (except for degree symbol): 451$^\circ$") fig.savefig('test.png') is an attempt to use a sans-serif font in matplotlib with LaTeX. The issue is that the math font is still a serif font (as indicated by the axis numbers, and as demonstrated by the labels in the center). Is there a way to set the math font to also be sans-serif?

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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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  • How can I plot NaN values as a special color with imshow in matplotlib?

    - by Adam Fraser
    example: import numpy as np import matplotlib.pyplot as plt f = plt.figure() ax = f.add_subplot(111) a = np.arange(25).reshape((5,5)).astype(float) a[3,:] = np.nan ax.imshow(a, interpolation='nearest') f.canvas.draw() The resultant image is unexpectedly all blue (the lowest color in the jet colormap). However, if I do the plotting like this: ax.imshow(a, interpolation='nearest', vmin=0, vmax=24) --then I get something better, but the NaN values are drawn the same color as vmin... Is there a graceful way that I can set NaNs to be drawn with a special color (eg: gray or transparent)?

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  • Confusion Matrix with number of classified/misclassified instances on it (Python/Matplotlib)

    - by Pinkie
    I am plotting a confusion matrix with matplotlib with the following code: from numpy import * import matplotlib.pyplot as plt from pylab import * conf_arr = [[33,2,0,0,0,0,0,0,0,1,3], [3,31,0,0,0,0,0,0,0,0,0], [0,4,41,0,0,0,0,0,0,0,1], [0,1,0,30,0,6,0,0,0,0,1], [0,0,0,0,38,10,0,0,0,0,0], [0,0,0,3,1,39,0,0,0,0,4], [0,2,2,0,4,1,31,0,0,0,2], [0,1,0,0,0,0,0,36,0,2,0], [0,0,0,0,0,0,1,5,37,5,1], [3,0,0,0,0,0,0,0,0,39,0], [0,0,0,0,0,0,0,0,0,0,38] ] norm_conf = [] for i in conf_arr: a = 0 tmp_arr = [] a = sum(i,0) for j in i: tmp_arr.append(float(j)/float(a)) norm_conf.append(tmp_arr) plt.clf() fig = plt.figure() ax = fig.add_subplot(111) res = ax.imshow(array(norm_conf), cmap=cm.jet, interpolation='nearest') cb = fig.colorbar(res) savefig("confmat.png", format="png") But I want to the confusion matrix to show the numbers on it like this graphic (the right one): http://i48.tinypic.com/2e30kup.jpg How can I plot the conf_arr on the graphic?

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