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Thanks, I read some of your previous posts dealing with the pcolor and tried this route but didn't succeed yet... I really agree with you on the interest of having an option to pass an array rather than value for the alpha keyword ! ________________________________ De : Benjamin Root <ben...@ou...> À : Auré Gourrier <aur...@ya...> Cc : mat...@li... Envoyé le : Jeu 10 mars 2011, 18h 43min 31s Objet : Re: [Matplotlib-users] alternative to imshow with polar axes ? On Thu, Mar 10, 2011 at 8:40 AM, Auré Gourrier <aur...@ya...> wrote: Dear all, > >Once again, I turn for help. >I'm trying to plot a polar image using colormap values for the theta values and >increasing alpha values along the radius. >I do this using imshow passing the rgba tuple at each pixel position which works >very nicely with rectangular axes, but fails to display using polar axes (see >code below). > >As usual, I've done a fair bit of digging to find where the problem is and >whether I could make out an alternate solution but haven't managed to come >through. I've tried using pcolormesh but I don't see how to pass the rgba tuple >Can anyone point me in the right direction. >I'm using matplotlib 1.0.1 and Python 2.4 > >Cheers, > >Auré > > It appears that imshow() (and matshow()) do not support non-rectilinear axes. I don't know if this is a bug or if there is no way to make it support polar projections. Hopefully, someone else more knowledgable could chime in on this. I am also not exactly sure how to accomplish what you want using pcolor. A really slow, painful way would be to pcolor each row with the rest masked out, setting the alpha value for that row. I have long wondered if the alpha kwarg in various functions could be improved by allowing array values and take advantage of numpy broadcasting. Ben Root
Hi, When I do an errorbar plot (a.errorbar(), a = axis) with negative values and then try to change the yscale to log (a.set_yscale('log')) matplotlib crashes with: Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 14636, in <lambda> lambda event: event.callable(*event.args, **event.kw) ) File "/home/specuser/new_workspace/TestDriven/src/RAWPlot.py", line 371, in plotSASM line, ec, el = a.errorbar(sasm.q[q_min:q_max], sasm.i[q_min:q_max], sasm.err[q_min:q_max], picker = 3, label = legend_label, **kwargs) File "/usr/lib64/python2.6/site-packages/matplotlib/axes.py", line 4872, in errorbar barcols.append( self.vlines(x, lower, upper, **lines_kw) ) File "/usr/lib64/python2.6/site-packages/matplotlib/axes.py", line 3302, in vlines self.autoscale_view() File "/usr/lib64/python2.6/site-packages/matplotlib/axes.py", line 1627, in autoscale_view YL = self.yaxis.get_major_locator().view_limits(y0, y1) File "/usr/lib64/python2.6/site-packages/matplotlib/ticker.py", line 1119, in view_limits if not is_decade(vmin,self._base): vmin = decade_down(vmin,self._base) File "/usr/lib64/python2.6/site-packages/matplotlib/ticker.py", line 1030, in is_decade return lx==int(lx) OverflowError: cannot convert float infinity to integer Traceback (most recent call last): File "/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 14636, in <lambda> lambda event: event.callable(*event.args, **event.kw) ) File "/home/specuser/new_workspace/TestDriven/src/RAW.py", line 1953, in addItem newItem = ManipItemPanel(self.underpanel, sasm, font_colour = item_colour) File "/home/specuser/new_workspace/TestDriven/src/RAW.py", line 2353, in __init__ color = conv.to_rgb(self.sasm.line.get_mfc()) AttributeError: 'NoneType' object has no attribute 'get_mfc' I don't think this should be the expected outcome.. rather it should not plot values that are illegal/negative (i.e. ignore them). Is there a way I can get around this without having to search through my data and remove points that are negative or NaN or INF when the yscale needs to be log? That would also show an incorrect curve since a line would be drawn across the points that were removed.. It should rather be gaps in the line. Thanks, Soren
Yung-Yu, We are advertised on this blog http://pycon.blogspot.com/2011/03/pycon-2011-outside-talks-poster-session.html I will be in the conference venue by tomorrow morning. There are many interesting talks and posters that I look forward seeing plus meeting those presenters. See you in Atlanta. On 3/9/11, Yung-Yu Chen <yy...@so...> wrote: > I will be there tomorrow, and giving a talk about solving PDEs on Saturday > morning (plus a poster). Looking forward to meet you guys and to learn more > about contribution to the community. > > with regards, > Yung-Yu Chen > > -- > Yung-Yu Chen > PhD candidate of Mechanical Engineering > The Ohio State University, Columbus, Ohio > +1 (614) 859 2436 > http://solvcon.net/yyc/ > -- Gökhan
I'm a frequent user of matplotlib on my Windows XP machine. I recently attempted to install a program that modified my Tcl installation, and I now get an error message when I attempt to plot anything in matplotlib. Here is the error message: --- Traceback (most recent call last): File "<stdin>", line 1, in <module> File "C:\Python25\lib\lib-tk\Tkinter.py", line 3758, in _test root = Tk() File "C:\Python25\lib\lib-tk\Tkinter.py", line 1647, in __init__ self.tk = _tkinter.create(screenName, baseName, className, interactive, want objects, useTk, sync, use) _tkinter.TclError: Can't find a usable init.tcl in the following directories: {C:\Program Files\Tcl\lib\tcl8.3} {C:\Program Files\Tcl\lib \tcl8.3} {C:/Prog ram Files/Tcl/lib/tcl8.4} C:/Python25/lib/tcl8.4 C:/lib/tcl8.4 C:/ library This probably means that Tcl wasn't installed properly. --- I attempted a complete reinstall of python (hoping it would reinstall Tcl with correct file paths), but I get the same error. Any suggestions would be appreciated. Thanks! Steve Skripnik, P.E. Project Engineer LimnoTech 1705 DeSales St NW Suite 600 Washington, DC 20036 ssk...@li...<mailto:ssk...@li...> http://www.limno.com<http://www.limno.com/> Phone: (202) 833-9140 Fax: (202) 833-9094 Water | Environment | Scientists | Engineers
On Thu, Mar 10, 2011 at 8:40 AM, Auré Gourrier <aur...@ya...>wrote: > Dear all, > > Once again, I turn for help. > I'm trying to plot a polar image using colormap values for the theta values > and increasing alpha values along the radius. > I do this using imshow passing the rgba tuple at each pixel position which > works very nicely with rectangular axes, but fails to display using polar > axes (see code below). > As usual, I've done a fair bit of digging to find where the problem is and > whether I could make out an alternate solution but haven't managed to come > through. I've tried using pcolormesh but I don't see how to pass the rgba > tuple > Can anyone point me in the right direction. > I'm using matplotlib 1.0.1 and Python 2.4 > > Cheers, > > Auré > > It appears that imshow() (and matshow()) do not support non-rectilinear axes. I don't know if this is a bug or if there is no way to make it support polar projections. Hopefully, someone else more knowledgable could chime in on this. I am also not exactly sure how to accomplish what you want using pcolor. A really slow, painful way would be to pcolor each row with the rest masked out, setting the alpha value for that row. I have long wondered if the alpha kwarg in various functions could be improved by allowing array values and take advantage of numpy broadcasting. Ben Root
Hi Ben, thanks a lot, this really helpes in the simple example, I'll try to find out how to use it in the complex script. It seems 1.0.0 is recent enough for this! Thanks again, Daniel 2011年3月10日 Benjamin Root <ben...@ou...>: > > > On Thu, Mar 10, 2011 at 4:54 AM, Daniel Mader > <dan...@go...> wrote: >> >> Hi, >> >> is it possible to change the default y-axis scaling so that the >> ticks/label are not with respect to the large offset? >> >> For example: >> >> import scipy >> import pylab >> >> x = scipy.arange(100) >> y = scipy.rand(100) + 1000006 >> >> pylab.figure() >> pylab.plot(x,y) >> pylab.grid() >> >> pylab.show() >> >> This gives the y-limits as (0,1) with respect to 1000006. This makes >> it very hard to read. I'd like to be able to configure this manually. >> >> Thanks in advance, >> Daniel >> > > I tried to fix matplotlib to be smarter about choosing the offset value a > while back, but I couldn't come up with something that worked well in the > general case. You can manually turn it off completely, and have the full > value displayed (or even manually set the offset value). If you have a very > recent matplotlib: > > import matplotlib.pyplot as plt > import numpy as np > > x = np.arange(100) > y = np.random.rand(100) + 1000006 > > plt.figure() > plt.plot(x, y) > plt.grid() > plt.ticklabel_format(useOffset=1000000, axis='y') > > plt.show() > > Or you can turn it off by setting useOffset to False. > > If you don't have a recent enough matplotlib, you can turn it off completely > by doing something like this: > > import matplotlib.pyplot as plt > import numpy as np > from matplotlib.ticker import ScalarFormatter > > x = np.arange(100) > y = np.random.rand(100) + 1000006 > > fig = plt.figure() > ax = fig.gca() > ax.plot(x, y) > ax.grid() > ax.yaxis.set_major_formatter(ScalarFormatter(useOffset=False)) > > plt.show() > > > I hope this helps! > Ben Root > >
On Thu, Mar 10, 2011 at 4:54 AM, Daniel Mader < dan...@go...> wrote: > Hi, > > is it possible to change the default y-axis scaling so that the > ticks/label are not with respect to the large offset? > > For example: > > import scipy > import pylab > > x = scipy.arange(100) > y = scipy.rand(100) + 1000006 > > pylab.figure() > pylab.plot(x,y) > pylab.grid() > > pylab.show() > > This gives the y-limits as (0,1) with respect to 1000006. This makes > it very hard to read. I'd like to be able to configure this manually. > > Thanks in advance, > Daniel > > I tried to fix matplotlib to be smarter about choosing the offset value a while back, but I couldn't come up with something that worked well in the general case. You can manually turn it off completely, and have the full value displayed (or even manually set the offset value). If you have a very recent matplotlib: import matplotlib.pyplot as plt import numpy as np x = np.arange(100) y = np.random.rand(100) + 1000006 plt.figure() plt.plot(x, y) plt.grid() plt.ticklabel_format(useOffset=1000000, axis='y') plt.show() Or you can turn it off by setting useOffset to False. If you don't have a recent enough matplotlib, you can turn it off completely by doing something like this: import matplotlib.pyplot as plt import numpy as np from matplotlib.ticker import ScalarFormatter x = np.arange(100) y = np.random.rand(100) + 1000006 fig = plt.figure() ax = fig.gca() ax.plot(x, y) ax.grid() ax.yaxis.set_major_formatter(ScalarFormatter(useOffset=False)) plt.show() I hope this helps! Ben Root
The hist function expects a list of values that it bins up and counts to form the histogram (see numpy.hist). That's why it is plotting one "count" for each of the values you gave it. You already have your counts, you just want to make a step plot out of them. Look at the "drawstyle" keyword of the "plot" function: drawstyle: [ 'default' | 'steps' | 'steps-pre' | 'steps-mid' | 'steps-post' ] Hope that puts you on the right track. -Roban On Thu, Mar 10, 2011 at 4:18 PM, Andrea Crotti <and...@gm...> wrote: > I'm having some troubles understanding basic concepts. > Suppose I want to do something like this, given a dictionary > > values = { (0,10) : 0.5, > (10, 20) : 0.3 } > and so on, where the key is a time slot interval and the value is the > value I want to plot. > > What should be the correct way to get what I want? > > In theory the data that I want to plot is [0.5, 0.3] > but if I do > > plt.hist(values.values()) > > I don't get that, but I get 2 bars of length 1 located in that x > coordinate. So how should I proceed then? > > Thanks, > Andrea > > ------------------------------------------------------------------------------ > Colocation vs. Managed Hosting > A question and answer guide to determining the best fit > for your organization - today and in the future. > http://p.sf.net/sfu/internap-sfd2d > _______________________________________________ > Matplotlib-users mailing list > Mat...@li... > https://lists.sourceforge.net/lists/listinfo/matplotlib-users >
I'm having some troubles understanding basic concepts. Suppose I want to do something like this, given a dictionary values = { (0,10) : 0.5, (10, 20) : 0.3 } and so on, where the key is a time slot interval and the value is the value I want to plot. What should be the correct way to get what I want? In theory the data that I want to plot is [0.5, 0.3] but if I do plt.hist(values.values()) I don't get that, but I get 2 bars of length 1 located in that x coordinate. So how should I proceed then? Thanks, Andrea
I'm having some troubles understanding basic concepts. Suppose I want to do something like this, given a dictionary values = { (0,10) : 0.5, (10, 20) : 0.3 } and so on, where the key is a time slot interval and the value is the value I want to plot. What should be the correct way to get what I want? In theory the data that I want to plot is [0.5, 0.3] but if I do plt.hist(values.values()) I don't get that, but I get 2 bars of length 1 located in that x coordinate. So how should I proceed then? Thanks, Andrea
Andrea Crotti <and...@gm...> writes: > values = { (0,10) : 0.5, > (10, 20) : 0.3 } > and so on, where the key is a time slot interval and the value is the > value I want to plot. > > What should be the correct way to get what I want? Something like this perhaps: left, width = zip(*[(a, b-a) for (a,b) in values.keys()]) bar(left, values.values(), width) That is, turn the sequence of intervals into a sequence of coordinates where the bars should start (left) and another sequence of bar widths. Then use bar to plot the values. > In theory the data that I want to plot is [0.5, 0.3] > but if I do > > plt.hist(values.values()) The hist function not only plots the histogram bars but computes them from the data. Use bar when you already have the coordinates you want to plot. -- Jouni K. Seppänen http://www.iki.fi/jks
Dear all, Once again, I turn for help. I'm trying to plot a polar image using colormap values for the theta values and increasing alpha values along the radius. I do this using imshow passing the rgba tuple at each pixel position which works very nicely with rectangular axes, but fails to display using polar axes (see code below). As usual, I've done a fair bit of digging to find where the problem is and whether I could make out an alternate solution but haven't managed to come through. I've tried using pcolormesh but I don't see how to pass the rgba tuple Can anyone point me in the right direction. I'm using matplotlib 1.0.1 and Python 2.4 Cheers, Auré ------ import matplotlib as mpl from matplotlib import pylab import numpy as np #build custom colormap cm_sym =customfunc() #define mesh grid theta = np.arange(0.,2.*math.pi+2.*math.pi/9,2.*math.pi/9) r = np.arange(0,1.1,0.1) X,Y = np.meshgrid(r,theta) #define rgba array polarcolorseq = mpl.cm.ScalarMappable(cmap=cm_hsvsym).to_rgba(Y) #set an increasing alpha value along the radius polarcolorseq[:,:,-1] = [list(np.arange(0,1.1,.1))]*10 pylab.figure(figsize=(10,5),dpi=100,facecolor='white') #display using rectangular axis ax = pylab.subplot((121),axisbg='k') ax.imshow(np.flipud(np.swapaxes(polarcolorseq,0,1))) #display using polar axis ax2 = pylab.subplot((122),axisbg='k',projection='polar') #also tried with polar=True ax2.imshow(np.flipud(np.swapaxes(polarcolorseq,0,1))) pylab.draw()
I'm having some troubles understanding basic concepts. Suppose I want to do something like this, given a dictionary values = { (0,10) : 0.5, (10, 20) : 0.3 } and so on, where the key is a time slot interval and the value is the value I want to plot. What should be the correct way to get what I want? In theory the data that I want to plot is [0.5, 0.3] but if I do plt.hist(values.values()) I don't get that, but I get 2 bars of length 1 located in that x coordinate. So how should I proceed then? Thanks, Andrea
Maybe I should mention that there are actually two reasons why I don't like this behavior: 1) it's sometimes very hard to read what's going on, 2) there also seems to be a bug when the limits are changed later, see attached results: the upper subplot is default, the lower subplot uses the padding. ##-------------------------- def update_ax2(ax1): ''' Automatically update ylim of ax2 when ylim of ax1 changes. ''' y1, y2 = ax1.get_ylim() ## modify the limits ax2.set_ylim((Tc(y1), Tc(y2))) ax2.figure.canvas.draw() Both plots are actually identical but use a different x-axis. In ordert to create a nicely padded plot, I use the following function, which breaks the scaling information AND the calculation of the second axis limits: ##-------------------------- def axispaddingAX(ax): ''' Saubere bzw. schoene Achsenskalierung für MPL-Skripten. ''' lines = ax.get_lines() xtemp = [] ytemp = [] for line in lines: xtemp.append(min(line.get_xdata())) xtemp.append(max(line.get_xdata())) ytemp.append(min(line.get_ydata())) ytemp.append(max(line.get_ydata())) xmin,xmax = min(xtemp),max(xtemp) ymin,ymax = min(ytemp),max(ytemp) span = 0.05 rangex = (xmin-span*(xmax-xmin), xmax+span*(xmax-xmin)) rangey = (ymin-span*(ymax-ymin), ymax+span*(ymax-ymin)) ax.set_xlim(rangex) ax.set_ylim(rangey) Thanks a lot in advance for any hint or comment on this, Daniel 2011年3月10日 Daniel Mader <dan...@go...>: > Hi, > > is it possible to change the default y-axis scaling so that the > ticks/label are not with respect to the large offset? > > For example: > > import scipy > import pylab > > x = scipy.arange(100) > y = scipy.rand(100) + 1000006 > > pylab.figure() > pylab.plot(x,y) > pylab.grid() > > pylab.show() > > This gives the y-limits as (0,1) with respect to 1000006. This makes > it very hard to read. I'd like to be able to configure this manually. > > Thanks in advance, > Daniel >
Hi, is it possible to change the default y-axis scaling so that the ticks/label are not with respect to the large offset? For example: import scipy import pylab x = scipy.arange(100) y = scipy.rand(100) + 1000006 pylab.figure() pylab.plot(x,y) pylab.grid() pylab.show() This gives the y-limits as (0,1) with respect to 1000006. This makes it very hard to read. I'd like to be able to configure this manually. Thanks in advance, Daniel
Hi all, I am stuck on matplotlib generating a segfault when invoking 'plot'. I've ben trying to solve this problem for a while now but no luck. I've seen many duplicates of this problem on the web, some with solutions, some without. The solution must be something more generic that I'm missing. Here are some of these pointers to the same problem that I have (the backtrace, that I pasted further below, has the same properties) http://old.nabble.com/101-Point-Segmentation-Fault-td27552745.html http://old.nabble.com/weird-error-with-gcc-4.4,-gomp,-cython,-and-matplotlib-td27351399.html http://bugs.gentoo.org/show_bug.cgi?id=338513 So here's my specific setup and backtrace. I hope I can find some help! I'm using the 'agg' backend that's it, and the build and install dir were cleaned up. Thanks so much! === Solaris10, 64bits, Python 2.7, numpy 1.5.1, gcc 4.4.1 #all compiled from source backtrace: gdb python (gdb) run -c 'import pylab;pylab.clf(); pylab.plot([4])' Starting program: python -c 'import pylab;pylab.clf(); pylab.plot([4])' [Thread debugging using libthread_db enabled] [New Thread 1 (LWP 1)] terminate called after throwing an instance of 'std::exception' terminate called recursively Program received signal SIGABRT, Aborted. [Switching to Thread 1 (LWP 1)] 0xfffffd7fff0ae88a in _lwp_kill () from /lib/64/libc.so.1 #0 0xfffffd7fff0ae88a in _lwp_kill () from /lib/64/libc.so.1 #1 0xfffffd7fff0a98b3 in thr_kill () from /lib/64/libc.so.1 #2 0xfffffd7fff0577e9 in raise () from /lib/64/libc.so.1 #3 0xfffffd7fff03a7d0 in abort () from /lib/64/libc.so.1 #4 0xfffffd7ff46d1a56 in __gnu_cxx::__verbose_terminate_handler () at ../../../../../libstdc++-v3/libsupc++/vterminate.cc:48 #5 0xfffffd7ff46cef6a in __cxxabiv1::__terminate (handler=0x1) at ../../../../../libstdc++-v3/libsupc++/eh_terminate.cc:38 #6 0xfffffd7ff46cefb3 in std::terminate () at ../../../../../libstdc++-v3/libsupc++/eh_terminate.cc:48 #7 0xfffffd7ff46cf03e in __cxxabiv1::__cxa_rethrow () at ../../../../../libstdc++-v3/libsupc++/eh_throw.cc:116 #8 0xfffffd7ff46d1af6 in __gnu_cxx::__verbose_terminate_handler () at ../../../../../libstdc++-v3/libsupc++/vterminate.cc:78 #9 0xfffffd7ff46cef6a in __cxxabiv1::__terminate (handler=0x1) at ../../../../../libstdc++-v3/libsupc++/eh_terminate.cc:38 #10 0xfffffd7ff46cefb3 in std::terminate () at ../../../../../libstdc++-v3/libsupc++/eh_terminate.cc:48 #11 0xfffffd7ff46cf0b6 in __cxxabiv1::__cxa_throw (obj=<value optimized out>, tinfo=<value optimized out>, dest=<value optimized out>) at ../../../../../libstdc++-v3/libsupc++/eh_throw.cc:83 #12 0xfffffd7ff4a22fd8 in py_to_agg_transformation_matrix (obj=0x774380, errors=<value optimized out>) at src/agg_py_transforms.cpp:22 #13 0xfffffd7ff4a32e7c in _path_module::update_path_extents (this=<value optimized out>, args=...) at src/path.cpp:380 #14 0xfffffd7ff4a34d90 in Py::ExtensionModule<_path_module>::invoke_method_varargs (this=<value optimized out>, method_def=<value optimized out>, args=...) at ./CXX/Python2/ExtensionModule.hxx:184 #15 0xfffffd7ff4a209b7 in Py::method_varargs_call_handler (_self_and_name_tuple=<value optimized out>, _args=<value optimized out>) at CXX/Python2/cxx_extensions.cxx:1714 #16 0x00000000004a6071 in call_function (f=0x2024770, throwflag=<value optimized out>) at /usr/local/src/lang/Python-2.7.1/Python/ceval.c:4012 #17 PyEval_EvalFrameEx (f=0x2024770, throwflag=<value optimized out>) at /usr/local/src/lang/Python-2.7.1/Python/ceval.c:2665 #18 0x00000000004a79c1 in PyEval_EvalCodeEx (co=0x124e230, globals=<value optimized out>, locals=<value optimized out>, args=0x2024910, argcount=<value optimized out>, kws=0x3, kwcount=2, defs=0x155c888, defcount=3, closure=0x0)
On Wed, Mar 9, 2011 at 8:25 PM, Andrew Chapkowski <ach...@es...>wrote: > Can someone please explain how to coordinates need to be passed to > contour for 3D graphs? I see all the examples use sample data, but I can't > find any information on how the input points need to be formatted. > Currently I have three array, one for the X, one for Y, and another for a Z > value, and I was to plot each set on a 3D contour graph. What do I need to > do to format these points correctly? > > > Thank you > > Andrew > > Andrew, The data input for contourf3d is pretty much the same as it is for regular 2-D contourf. Essentially, X and Y are the grid coordinates, while Z represents the value at those grid points. Z should be a NxM array. X and Y should be NxM, or X is length N, with Y being length M. I hope that clears it up. Ben Root
Can someone please explain how to coordinates need to be passed to contour for 3D graphs? I see all the examples use sample data, but I can't find any information on how the input points need to be formatted. Currently I have three array, one for the X, one for Y, and another for a Z value, and I was to plot each set on a 3D contour graph. What do I need to do to format these points correctly? Thank you Andrew