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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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• 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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• Variable alpha blending in pylab

  - by Hooked

  How does one control the transparency over a 2D image in pylab? I'd like to give two sets of values (X,Y,Z,T) where X,Y are arrays of positions, Z is the color value, and T is the transparency to a function like imshow but it seems that the function only takes alpha as a scalar. As a concrete example, consider the code below that attempts to display two Gaussians. The closer the value is to zero, the more transparent I'd like the plot to be. from pylab import * side = linspace(-1,1,100) X,Y = meshgrid(side,side) extent = (-1,1,-1,1) Z1 = exp(-((X+.5)**2+Y**2)) Z2 = exp(-((X-.5)**2+(Y+.2)**2)) imshow(Z1, cmap=cm.hsv, alpha=.6, extent=extent) imshow(Z2, cmap=cm.hsv, alpha=.6, extent=extent) show() Note: I am not looking for a plot of Z1+Z2 (that would be trivial) but for a general way to specify the alpha blending across an image.

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• PyLab - changing text color and background fill color of text box

  - by Mark

  Hey all, I'm using PyLab to make some graphs in Python. I want to make a text box that is colored magenta with black text, but cannot get the text to be black. text(x, y, 'Summary', backgroundcolor = 'm', color = 'k') This gives me a magenta background and then text that is almost just as pink. Any ideas what I'm doing wrong? Many thanks!

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• Matplotlib and pylab doesn't work in python cgi

  - by Nimmy

  Hi all, Matplotlib and pylab doesn't work in python cgi. but it's working properly in python shell.. Any one can help me....... Plz....... Thanks in advance......

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• Changing font size of legend title in Python pylab rose/polar plot

  - by LaurieW

  I'm trying to change the font size of the title of an existing legend on a rose, or 'polar', plot. Most of the code was written by somebody else, who is away. I've added:- ax.legend(title=legend_title) setp(l.get_title(), fontsize=8) to add the title 'legend_title', which is a variable that the user enters a string for in a a different function that uses this code. The second line of this doesn't return an error but doesn't appear to do anything either. The complete code is below. 'Rose' and 'RoseAxes' are modules/functions written by somebody. Does anyone know of a way to change the legend title font size? I've found some examples for normal plots but can't find any for rose/polar plots. from Rose.RoseAxes import RoseAxes from pylab import figure, title, setp, close, clf from PlotGeneration import color_map_xml fig = figure(1) rect = [0.02, 0.1, 0.8, 0.8] ax = RoseAxes(fig, rect, axisbg='w') fig.add_axes(ax) if cmap == None: (XMLcmap,colors) = color_map_xml.get_cmap('D:/HRW/VET/HrwPyLibs/ColorMapLibrary/paired.xml',255) else: XMLcmap = cmap bqs = kwargs.pop('CTfigname', None) ax.box(Dir, U, bins = rose_binX, units = unit, nsector = nsector, cmap = XMLcmap, lw = 0, **kwargs ) l = ax.legend() ax.legend(title=legend_title) setp(l.get_texts(), fontsize=8) setp(l.get_title(), fontsize=8) Thanks for any help

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• Using PyLab to create a 2D graph from two separate lists

  - by user324333

  Hey Guys, This seems like a basic problem with an easy answer but I simply cannot figure it out no matter how much I try. I am trying to create a line graph based on two lists. For my x-axis, I want my list to be a set of strings. x_axis_list = ["Jan-06","Jul-06","Jan-07","Jul-07","Jan-08"] y_axis_list = [5,7,6,8,9] Any suggestions on how to best graph these items?

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• Python, Matplotlib, subplot: How to set the axis range?

  - by someone

  How can I set the y axis range of the second subplot to e.g. [0,1000] ? The FFT plot of my data (a column in a text file) results in a (inf.?) spike so that the actual data is not visible. pylab.ylim([0,1000]) has no effect, unfortunately. This is the whole script: # based on http://www.swharden.com/blog/2009-01-21-signal-filtering-with-python/ import numpy, scipy, pylab, random xs = [] rawsignal = [] with open("test.dat", 'r') as f: for line in f: if line[0] != '#' and len(line) > 0: xs.append( int( line.split()[0] ) ) rawsignal.append( int( line.split()[1] ) ) h, w = 3, 1 pylab.figure(figsize=(12,9)) pylab.subplots_adjust(hspace=.7) pylab.subplot(h,w,1) pylab.title("Signal") pylab.plot(xs,rawsignal) pylab.subplot(h,w,2) pylab.title("FFT") fft = scipy.fft(rawsignal) #~ pylab.axis([None,None,0,1000]) pylab.ylim([0,1000]) pylab.plot(abs(fft)) pylab.savefig("SIG.png",dpi=200) pylab.show() Other improvements are also appreciated!

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• Confusion between numpy, scipy, matplotlib and pylab

  - by goFrendiAsgard

  Numpy, scipy, matplotlib, and pylab are common terms among they who use python for scientific computation. I just learn a bit about pylab, and I got a lot of confusion. Whenever I want to import numpy, I can always do: import numpy as np I just consider, that once I do from pylab import * The numpy will be imported as well (with np alias). So basically the second one do more things compared to the first one. There are few things I want to ask. Is it right that pylab is just a wrapper for numpy, scipy and matplotlib? As np is the numpy alias, what is the scipy and matplotlib alias? (as far as I know, plt is alias of matplotlib.pyplot, but I don't know the alias for the matplotlib itself) Thanks in advance.

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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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• Matplotlib subplots_adjust hspace so titles and xlabels don't overlap ?

  - by Denis

  With say 3 rows of subplots in matplotlib, xlabels of one row can overlap the title of the next; one has to fiddle with pl.subplots_adjust( hspace ), annoying. Is there a recipe for hspace that prevents overlaps and works for any nrow ? """ matplotlib xlabels overlap titles ? """ import sys import numpy as np import pylab as pl nrow = 3 hspace = .4 # of plot height, titles and xlabels both fall within this ?? exec "\n".join( sys.argv[1:] ) # nrow= ... y = np.arange(10) pl.subplots_adjust( hspace=hspace ) for jrow in range( 1, nrow+1 ): pl.subplot( nrow, 1, jrow ) pl.plot( y**jrow ) pl.title( 5 * ("title %d " % jrow) ) pl.xlabel( 5 * ("xlabel %d " % jrow) ) pl.show() My versions: matplotlib 0.99.1.1, python 2.6.4, Mac osx 10.4.11, backend: Qt4Agg (TkAgg = Exception in Tkinter callback) (For many extra points, can anyone outline how matplotlib's packer / spacer works, along the lines of chapter 17 "the packer" in the Tcl/Tk book ?)

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• slicing a 2d numpy array

  - by MedicalMath

  The following code: import numpy as p myarr=[[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6],[0,1],[0,6]] copy=p.array(myarr) p.mean(copy)[:,1] Is generating the following error message: Traceback (most recent call last): File "<pyshell#3>", line 1, in <module> p.mean(copy)[:,1] IndexError: 0-d arrays can only use a single () or a list of newaxes (and a single ...) as an index I looked up the syntax at this link and I seem to be using the correct syntax to slice. However, when I type copy[:,1] into the Python shell, it gives me the following output, which is clearly wrong, and is probably what is throwing the error: array([1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6, 1, 6]) Can anyone show me how to fix my code so that I can extract the second column and then take the mean of the second column as intended in the original code above? EDIT: Thank you for your solutions. However, my posting was an oversimplification of my real problem. I used your solutions in my real code, and got a new error. Here is my real code with one of your solutions that I tried: filteredSignalArray=p.array(filteredSignalArray) logical=p.logical_and(EndTime-10.0<=matchingTimeArray,matchingTimeArray<=EndTime) finalStageTime=matchingTimeArray.compress(logical) finalStageFiltered=filteredSignalArray.compress(logical) for j in range(len(finalStageTime)): if j == 0: outputArray=[[finalStageTime[j],finalStageFiltered[j]]] else: outputArray+=[[finalStageTime[j],finalStageFiltered[j]]] print 'outputArray[:,1].mean() is: ',outputArray[:,1].mean() And here is the error message that is now being generated by the new code: File "mypath\myscript.py", line 1545, in WriteToOutput10SecondsBeforeTimeMarker print 'outputArray[:,1].mean() is: ',outputArray[:,1].mean() TypeError: list indices must be integers, not tuple Second EDIT: This is solved now that I added: outputArray=p.array(outputArray) above my code. I have been at this too many hours and need to take a break for a while if I am making these kinds of mistakes.

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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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• 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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• slicing 2d numpy array

  - by MedicalMath

  I have a 2d numpy array called FilteredOutput that has 2 columns and 10001 rows, though the number of rows is a variable. I am trying to take the 2nd column of FilteredOutput and use it to populate a new 1d numpy array called timeSeriesArray using the following line of code: timeSeriesArray=p.array(FilteredOutput[:,0]) I got this syntax from the following link. But the problem is that I am getting the following error message: TypeError: list indices must be integers, not tuple Can anyone show me the proper syntax for populating the 1d array timeSeriesArray with the contents of the second column of the 2d array FilteredOutput?

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• Putting newline in matplotlib label with TeX in Python?

  - by user248237

  How can I add a newline to a plot's label (e.g. xlabel or ylabel) in Matplotlib? For example, plt.bar([1, 2], [4, 5]) plt.xlabel("My x label") plt.ylabel(r"My long label with $\Sigma_{C}$ math \n continues here") Ideally i'd like the y-labeled to be centered too. Is there a way to do this? It's important that the label have both tex (enclosed in '$') and the newline. thanks.

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• Trouble using latex in Matplotlib / Scipy etc.

  - by ajhall

  I'm having some issues with my first attempts at using matplotlib and scipy to make some scatter plots of my data (too many variables, trying to see many things at once). Here's some code of mine that is working fairly well... import numpy from scipy import * import pylab from matplotlib import * import h5py FileID = h5py.File('3DiPVDplot1.mat','r') # (to view the contents of: list(FileID) ) group = FileID['/'] CurrentsArray = group['Currents'].value IvIIIarray = group['IvIII'].value PFarray = group['PF'].value growthTarray = group['growthT'].value fig = pylab.figure() ax = fig.add_subplot(111) cax = ax.scatter(IvIIIarray, growthTarray, PFarray, CurrentsArray, alpha=0.75) cbar = fig.colorbar(cax) ax.set_xlabel('Cu / III') ax.set_ylabel('Growth T') ax.grid(True) pylab.show() I tried to change the code to include latex fonts and interpreting, none of it seems to work for me, however. Here's an example attempt that didn't work: import numpy from scipy import * import pylab from matplotlib import * import h5py rc('text', usetex=True) rc('font', family='serif') FileID = h5py.File('3DiPVDplot1.mat','r') # (to view the contents of: list(FileID) ) group = FileID['/'] CurrentsArray = group['Currents'].value IvIIIarray = group['IvIII'].value PFarray = group['PF'].value growthTarray = group['growthT'].value fig = pylab.figure() ax = fig.add_subplot(111) cax = ax.scatter(IvIIIarray, growthTarray, PFarray, CurrentsArray, alpha=0.75) cbar = fig.colorbar(cax) ax.set_xlabel(r'Cu / III') ax.set_ylabel(r'Growth T') ax.grid(True) pylab.show() I'm using fink installed python26 with corresponding packages for scipy matplotlib etc. I've been using iPython and manual work instead of scripts in python. Since I'm completely new to python and scipy, I'm sure I'm making some stupid simple mistakes. Please enlighten me! I greatly appreciate the help!

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• Matplotlib PDF export uses wrong font

  - by Konrad Rudolph

  I want to generate high-quality diagrams for a presentation. I’m using Python’s matplotlib to generate the graphics. Unfortunately, the PDF export seems to ignore my font settings. I tried setting the font both by passing a FontProperties object to the text drawing functions and by setting the option globally. For the record, here is a MWE to reproduce the problem: import scipy import matplotlib matplotlib.use('cairo') import matplotlib.pylab as pylab import matplotlib.font_manager as fm data = scipy.arange(5) for font in ['Helvetica', 'Gill Sans']: fig = pylab.figure() ax = fig.add_subplot(111) ax.bar(data, data) ax.set_xticks(data) ax.set_xticklabels(data, fontproperties = fm.FontProperties(family = font)) pylab.savefig('foo-%s.pdf' % font) In both cases, the produced output is identical and uses Helvetica (and yes, I do have both fonts installed). Just to be sure, the following doesn’t help either: matplotlib.rc('font', family = 'Gill Sans') Finally, if I replace the backend, instead using the native viewer: matplotlib.use('MacOSX') I do get the correct font displayed – but only in the viewer GUI. The PDF output is once again wrong. To be sure – I can set other fonts – but only other classes of font families: I can set serif fonts or fantasy or monospace. But all sans-serif fonts seem to default to Helvetica.

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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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• Multiple data series in real time plot

  - by Gr3n

  Hi, I'm kind of new to Python and trying to create a plotting app for values read via RS232 from a sensor. I've managed (after some reading and copying examples online) to get a plot working that updates on a timer which is great. My only trouble is that I can't manage to get multiple data series into the same plot. Does anyone have a solution to this? This is the code that I've worked out this far: import os import pprint import random import sys import wx # The recommended way to use wx with mpl is with the WXAgg backend import matplotlib matplotlib.use('WXAgg') from matplotlib.figure import Figure from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigCanvas, NavigationToolbar2WxAgg as NavigationToolbar import numpy as np import pylab DATA_LENGTH = 100 REDRAW_TIMER_MS = 20 def getData(): return int(random.uniform(1000, 1020)) class GraphFrame(wx.Frame): # the main frame of the application def __init__(self): wx.Frame.__init__(self, None, -1, "Usart plotter", size=(800,600)) self.Centre() self.data = [] self.paused = False self.create_menu() self.create_status_bar() self.create_main_panel() self.redraw_timer = wx.Timer(self) self.Bind(wx.EVT_TIMER, self.on_redraw_timer, self.redraw_timer) self.redraw_timer.Start(REDRAW_TIMER_MS) def create_menu(self): self.menubar = wx.MenuBar() menu_file = wx.Menu() m_expt = menu_file.Append(-1, "&Save plot\tCtrl-S", "Save plot to file") self.Bind(wx.EVT_MENU, self.on_save_plot, m_expt) menu_file.AppendSeparator() m_exit = menu_file.Append(-1, "E&xit\tCtrl-X", "Exit") self.Bind(wx.EVT_MENU, self.on_exit, m_exit) self.menubar.Append(menu_file, "&File") self.SetMenuBar(self.menubar) def create_main_panel(self): self.panel = wx.Panel(self) self.init_plot() self.canvas = FigCanvas(self.panel, -1, self.fig) # pause button self.pause_button = wx.Button(self.panel, -1, "Pause") self.Bind(wx.EVT_BUTTON, self.on_pause_button, self.pause_button) self.Bind(wx.EVT_UPDATE_UI, self.on_update_pause_button, self.pause_button) self.hbox1 = wx.BoxSizer(wx.HORIZONTAL) self.hbox1.Add(self.pause_button, border=5, flag=wx.ALL | wx.ALIGN_CENTER_VERTICAL) self.vbox = wx.BoxSizer(wx.VERTICAL) self.vbox.Add(self.canvas, 1, flag=wx.LEFT | wx.TOP | wx.GROW) self.vbox.Add(self.hbox1, 0, flag=wx.ALIGN_LEFT | wx.TOP) self.panel.SetSizer(self.vbox) #self.vbox.Fit(self) def create_status_bar(self): self.statusbar = self.CreateStatusBar() def init_plot(self): self.dpi = 100 self.fig = Figure((3.0, 3.0), dpi=self.dpi) self.axes = self.fig.add_subplot(111) self.axes.set_axis_bgcolor('white') self.axes.set_title('Usart data', size=12) pylab.setp(self.axes.get_xticklabels(), fontsize=8) pylab.setp(self.axes.get_yticklabels(), fontsize=8) # plot the data as a line series, and save the reference # to the plotted line series # self.plot_data = self.axes.plot( self.data, linewidth=1, color="blue", )[0] def draw_plot(self): # redraws the plot xmax = len(self.data) if len(self.data) > DATA_LENGTH else DATA_LENGTH xmin = xmax - DATA_LENGTH ymin = 0 ymax = 4096 self.axes.set_xbound(lower=xmin, upper=xmax) self.axes.set_ybound(lower=ymin, upper=ymax) # enable grid #self.axes.grid(True, color='gray') # Using setp here is convenient, because get_xticklabels # returns a list over which one needs to explicitly # iterate, and setp already handles this. # pylab.setp(self.axes.get_xticklabels(), visible=True) self.plot_data.set_xdata(np.arange(len(self.data))) self.plot_data.set_ydata(np.array(self.data)) self.canvas.draw() def on_pause_button(self, event): self.paused = not self.paused def on_update_pause_button(self, event): label = "Resume" if self.paused else "Pause" self.pause_button.SetLabel(label) def on_save_plot(self, event): file_choices = "PNG (*.png)|*.png" dlg = wx.FileDialog( self, message="Save plot as...", defaultDir=os.getcwd(), defaultFile="plot.png", wildcard=file_choices, style=wx.SAVE) if dlg.ShowModal() == wx.ID_OK: path = dlg.GetPath() self.canvas.print_figure(path, dpi=self.dpi) self.flash_status_message("Saved to %s" % path) def on_redraw_timer(self, event): if not self.paused: newData = getData() self.data.append(newData) self.draw_plot() def on_exit(self, event): self.Destroy() def flash_status_message(self, msg, flash_len_ms=1500): self.statusbar.SetStatusText(msg) self.timeroff = wx.Timer(self) self.Bind( wx.EVT_TIMER, self.on_flash_status_off, self.timeroff) self.timeroff.Start(flash_len_ms, oneShot=True) def on_flash_status_off(self, event): self.statusbar.SetStatusText('') if __name__ == '__main__': app = wx.PySimpleApp() app.frame = GraphFrame() app.frame.Show() app.MainLoop()

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• Polynomial fitting with log log plot

  - by viral parekh

  I have a simple problem to fit a straight line on log-log scale. My code is, data=loadtxt(filename) xdata=data[:,0] ydata=data[:,1] polycoeffs = scipy.polyfit(xdata, ydata, 1) yfit = scipy.polyval(polycoeffs, xdata) pylab.plot(xdata, ydata, 'k.') pylab.plot(xdata, yfit, 'r-') Now I need to plot fit line on log scale so I just change x and y axis, ax.set_yscale('log') ax.set_xscale('log') then its not plotting correct fit line. So how can I change fit function (in log scale) so that it can plot fit line on log-log scale? Thanks -Viral

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• Matplotlib, plotting discreet 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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• fit a ellipse in Python given a set of points xi=(xi,yi)

  - by Gianni

  I am computing a series of index from a 2D points (x,y). One index is the ratio between minor and major axis. To fit the ellipse i am using the following post when i run these function the final results looks strange because the center and the axis length are not in scale with the 2D points center = [ 560415.53298363+0.j 6368878.84576771+0.j] angle of rotation = (-0.0528033467597-5.55111512313e-17j) axes = [0.00000000-557.21553487j 6817.76933256 +0.j] thanks in advance for help import numpy as np from numpy.linalg import eig, inv def fitEllipse(x,y): x = x[:,np.newaxis] y = y[:,np.newaxis] D = np.hstack((x*x, x*y, y*y, x, y, np.ones_like(x))) S = np.dot(D.T,D) C = np.zeros([6,6]) C[0,2] = C[2,0] = 2; C[1,1] = -1 E, V = eig(np.dot(inv(S), C)) n = np.argmax(np.abs(E)) a = V[:,n] return a def ellipse_center(a): b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0] num = b*b-a*c x0=(c*d-b*f)/num y0=(a*f-b*d)/num return np.array([x0,y0]) def ellipse_angle_of_rotation( a ): b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0] return 0.5*np.arctan(2*b/(a-c)) def ellipse_axis_length( a ): b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0] up = 2*(a*f*f+c*d*d+g*b*b-2*b*d*f-a*c*g) down1=(b*b-a*c)*( (c-a)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a)) down2=(b*b-a*c)*( (a-c)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a)) res1=np.sqrt(up/down1) res2=np.sqrt(up/down2) return np.array([res1, res2]) if __name__ == '__main__': points = [(560036.4495758876, 6362071.890493258), (560036.4495758876, 6362070.890493258), (560036.9495758876, 6362070.890493258), (560036.9495758876, 6362070.390493258), (560037.4495758876, 6362070.390493258), (560037.4495758876, 6362064.890493258), (560036.4495758876, 6362064.890493258), (560036.4495758876, 6362063.390493258), (560035.4495758876, 6362063.390493258), (560035.4495758876, 6362062.390493258), (560034.9495758876, 6362062.390493258), (560034.9495758876, 6362061.390493258), (560032.9495758876, 6362061.390493258), (560032.9495758876, 6362061.890493258), (560030.4495758876, 6362061.890493258), (560030.4495758876, 6362061.390493258), (560029.9495758876, 6362061.390493258), (560029.9495758876, 6362060.390493258), (560029.4495758876, 6362060.390493258), (560029.4495758876, 6362059.890493258), (560028.9495758876, 6362059.890493258), (560028.9495758876, 6362059.390493258), (560028.4495758876, 6362059.390493258), (560028.4495758876, 6362058.890493258), (560027.4495758876, 6362058.890493258), (560027.4495758876, 6362058.390493258), (560026.9495758876, 6362058.390493258), (560026.9495758876, 6362057.890493258), (560025.4495758876, 6362057.890493258), (560025.4495758876, 6362057.390493258), (560023.4495758876, 6362057.390493258), (560023.4495758876, 6362060.390493258), (560023.9495758876, 6362060.390493258), (560023.9495758876, 6362061.890493258), (560024.4495758876, 6362061.890493258), (560024.4495758876, 6362063.390493258), (560024.9495758876, 6362063.390493258), (560024.9495758876, 6362064.390493258), (560025.4495758876, 6362064.390493258), (560025.4495758876, 6362065.390493258), (560025.9495758876, 6362065.390493258), (560025.9495758876, 6362065.890493258), (560026.4495758876, 6362065.890493258), (560026.4495758876, 6362066.890493258), (560026.9495758876, 6362066.890493258), (560026.9495758876, 6362068.390493258), (560027.4495758876, 6362068.390493258), (560027.4495758876, 6362068.890493258), (560027.9495758876, 6362068.890493258), (560027.9495758876, 6362069.390493258), (560028.4495758876, 6362069.390493258), (560028.4495758876, 6362069.890493258), (560033.4495758876, 6362069.890493258), (560033.4495758876, 6362070.390493258), (560033.9495758876, 6362070.390493258), (560033.9495758876, 6362070.890493258), (560034.4495758876, 6362070.890493258), (560034.4495758876, 6362071.390493258), (560034.9495758876, 6362071.390493258), (560034.9495758876, 6362071.890493258), (560036.4495758876, 6362071.890493258)] a_points = np.array(points) x = a_points[:, 0] y = a_points[:, 1] from pylab import * plot(x,y) show() a = fitEllipse(x,y) center = ellipse_center(a) phi = ellipse_angle_of_rotation(a) axes = ellipse_axis_length(a) print "center = ", center print "angle of rotation = ", phi print "axes = ", axes from pylab import * plot(x,y) plot(center[0:1],center[1:], color = 'red') show() each vertex is a xi,y,i point plot of 2D point and center of fit ellipse

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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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