Re: [Matplotlib-users] plot a data stream with matplotlib
I see that you first build your array and then display it at the end... is it possible in matplotlib to update the plot while the class is evolving? like: f.evolve(6) f.display() f.evolve(.27) f.display() f.evolve(10) f.display() f.evolve(2) f.display() best regards, simone 2009/1/19 C Lewis chle...@nature.berkeley.edu: #Skeleton example of a taking snapshots of an evolving class import pylab as p from math import log class foo: def __init__(self): self.red = 0 self.green = 1 self.age = 0 self.history = ([self.age],[self.red],[self.green]) def snapshot(self): self.history[0].append(self.age) self.history[1].append(self.red) self.history[2].append(self.green) def evolve(self, time): self.red = self.red + time/2 self.green = self.green * log(time) self.age = self.age + time self.snapshot() def display(self): p.plot(self.history[0],self.history[1],self.history[0],self.history[2]) p.show() if __name__ == '__main__': f = foo() f.snapshot() f.evolve(6); f.evolve(.27);f.evolve(10);f.evolve(2) print f.history f.display() On Jan 18, 2009, at 3:18 PM, Simone Gabbriellini wrote: thanks, it is exactly what I need... I have undestood the logic, I build a plot, put my traits values into an array and then I call the add_current_state_to_plot function to update the plot with the new values... I am an absolute beginner of matplotlib, can you give me a little example of add_current_state_to_plot function? Because I don't know the right way to update: do I have to pass all the array, or just the new values? best regards, simone 2009/1/18 C Lewis chle...@nature.berkeley.edu: Guessing about what you want: Does the class change with time? that is, perhaps you have a class foo, and foo evolves, and you would like to plot a history of some traits of foo, but at any given moment foo only contains its current state? If so, I think you need to have a function in foo, or even a separate class, that takes `snapshots' of foo's traits on one schedule, and stores them, and can also plot them on some schedule. Choosing how to do that is more a python problem than a matplotlib problem; personally, I have something set up so class 'profile' has functions to 'setup_plot' and 'add_current_state_to_plot', and I just have to choose when to call the latter. Or you can just store the values and plot at the end; once you have one list of the times, and a separate list of each trait's history at those times, you're set up for matplotlib plotting, e.g. from pylab import * plot(times, traitA, times, traitB, times, traitC) show() although, while looking for a simple example, I found this: http://matplotlib.sourceforge.net/examples/pylab_examples/plotfile_demo.html which is not totally simple but looks great. C On Jan 18, 2009, at 9:36 AM, Simone Gabbriellini wrote: Dear List, I have some variables I want to plot... the values of those variable change in time... I would like to plot the result with a traditional line plot those variables are traits of a class (don't know if this can make a difference...) is there any example of this with matplotlib? best regards, simone gabbriellini -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users Chloe Lewis Graduate student, Amundson Lab Division of Ecosystem Sciences, ESPM University of California, Berkeley 137 Mulford Hall - #3114 Berkeley, CA 94720-3114 chle...@nature.berkeley.edu -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] Building matplotlib from source - compile error - defined in discarded section - _backend_agg.so
Hi, I have been trying to build matplotlib on SLED 10: + python setup.py build BUILDING MATPLOTLIB matplotlib: 0.98.5.2 python: 2.5.2 (r252:60911, Aug 21 2008, 18:45:08) [GCC 3.3.6] platform: linux2 REQUIRED DEPENDENCIES numpy: 1.2.1 freetype2: found, but unknown version (no pkg-config) OPTIONAL BACKEND DEPENDENCIES libpng: found, but unknown version (no pkg-config) Tkinter: Tkinter: 50704, Tk: 8.4, Tcl: 8.4 * Guessing the library and include directories for * Tcl and Tk because the tclConfig.sh and * tkConfig.sh could not be found and/or parsed. wxPython: no * wxPython not found Gtk+: no * Building for Gtk+ requires pygtk; you must be able * to import gtk in your build/install environment Mac OS X native: no Qt: no Qt4: no Cairo: no OPTIONAL DATE/TIMEZONE DEPENDENCIES datetime: present, version unknown dateutil: matplotlib will provide pytz: matplotlib will provide adding pytz OPTIONAL USETEX DEPENDENCIES dvipng: no ghostscript: 7.05 latex: no pdftops: 3.01 [Edit setup.cfg to suppress the above messages] but have encountered some problems: g++ -pthread -shared -L/app/gcc/3.3.6/lib -L/app/zlib/1.2.x/lib -L/app/tk/8.4.x/lib -L/app/tcl/8.4.x/lib -L/app/readline/5.0/lib -L/app/openssl/0.9.x/lib -L/app/ncurses/5.5/lib -L/app/gdbm/1.8.3/lib -L/app/expect/5.x/lib -L/app/expat/2.0.x/lib -L/app/db/4.3.x/lib -L/usr/X11R6/lib -Wl,--rpath=/app/Python/2.5.x/lib:/app/gcc/3.3.6/lib:/app/zlib/1.2.x/lib:/app/tk/8.4.x/lib:/app/tcl/8.4.x/lib:/app/readline/5.0/lib:/app/openssl/0.9.x/lib:/app/ncurses/5.5/lib:/app/gdbm/1.8.3/lib:/app/expect/5.x/lib:/app/expat/2.0.x/lib:/app/db/4.3.x/lib:/usr/X11R6/lib -L /app/Python/2.5.x/lib -L/app/gcc/3.3.6/lib -L/app/zlib/1.2.x/lib -L/app/tk/8.4.x/lib -L/app/tcl/8.4.x/lib -L/app/libpng/1.2.x/lib -L/app/freetype/2.1.x/lib -L/usr/X11R6/lib -Wl,--rpath=/app/Python/modules/2.5/matplotlib/0.98.5.2/lib:/app/gcc/3.3.6/lib:/app/zlib/1.2.x/lib:/app/tk/8.4.x/lib:/app/tcl/8.4.x/lib:/app/libpng/1.2.x/lib:/app/freetype/2.1.x/lib:/usr/X11R6/lib -O2 -g -march=i386 -mcpu=i686 -fno-strict-aliasing build/temp.linux-i686-2.5/agg24/src/agg_trans_affine.o build/temp.linux-i686-2.5/agg24/src/agg_bezier_arc.o build/temp.linux-i686-2.5/agg24/src/agg_curves.o build/temp.linux-i686-2.5/agg24/src/agg_vcgen_dash.o build/temp.linux-i686-2.5/agg24/src/agg_vcgen_stroke.o build/temp.linux-i686-2.5/agg24/src/agg_image_filters.o build/temp.linux-i686-2.5/src/_image.o build/temp.linux-i686-2.5/src/ft2font.o build/temp.linux-i686-2.5/src/mplutils.o build/temp.linux-i686-2.5/CXX/cxx_extensions.o build/temp.linux-i686-2.5/CXX/cxxsupport.o build/temp.linux-i686-2.5/CXX/IndirectPythonInterface.o build/temp.linux-i686-2.5/CXX/cxxextensions.o build/temp.linux-i686-2.5/src/backend_agg.o -L/app/libpng/1.2.x/lib -L/app/freetype/2.1.x/lib -L/app/tcl/8.4.x/lib -L/app/tk/8.4.x/lib -L/app/libpng/1.2.x/lib -L/app/freetype/2.1.x/lib -L/app/tcl/8.4.x/lib -L/app/tk/8.4.x/lib -L/app/Python/2.5.x/lib -lstdc++ -lm -lfreetype -lz -lstdc++ -lm -lpython2.5 -o build/lib.linux-i686-2.5/matplotlib/backends/_backend_agg.so `.L53185' referenced in section `.rodata' of build/temp.linux-i686-2.5/src/backend_agg.o: defined in discarded section `.gnu.linkonce.t._ZN3agg18rasterizer_sl_clipINS_12ras_conv_intEE7line_toINS_19rasterizer_cells_aaINS_7cell_aaEvRT_ii' of build/temp.linux-i686-2.5/src/backend_agg.o `.L53186' referenced in section `.rodata' of build/temp.linux-i686-2.5/src/backend_agg.o: defined in discarded section `.gnu.linkonce.t._ZN3agg18rasterizer_sl_clipINS_12ras_conv_intEE7line_toINS_19rasterizer_cells_aaINS_7cell_aaEvRT_ii' of build/temp.linux-i686-2.5/src/backend_agg.o `.L53196' referenced in section `.rodata' of build/temp.linux-i686-2.5/src/backend_agg.o: defined in discarded section `.gnu.linkonce.t._ZN3agg18rasterizer_sl_clipINS_12ras_conv_intEE7line_toINS_19rasterizer_cells_aaINS_7cell_aaEvRT_ii' of build/temp.linux-i686-2.5/src/backend_agg.o `.L53206' referenced in section `.rodata' of build/temp.linux-i686-2.5/src/backend_agg.o: defined in discarded section `.gnu.linkonce.t._ZN3agg18rasterizer_sl_clipINS_12ras_conv_intEE7line_toINS_19rasterizer_cells_aaINS_7cell_aaEvRT_ii' of build/temp.linux-i686-2.5/src/backend_agg.o `.L53207' referenced in section `.rodata' of build/temp.linux-i686-2.5/src/backend_agg.o: defined in discarded section
[Matplotlib-users] bug in NavigationToolbar2QT ?
I have noticed that in the NavigationToolbar2QT there is a small display of
x,y coordinates at the rightmost corner of the toolbar.
However, when using Axes.set_ticklabels, for example, to normalize through
the labels and not through the data itself or to make a reciprocal scale -
set locations and labels, the display of coordinates is lost.
I have attached the example embedding in qt4 with minimal additions to
show this.
Notice how the x coordinate is still alive in the bottom toolbar, while the
y coordinate isn't.
I haven't found any way in the documentation to tell the navigation toolbar
anything related to this change.
This isn't crucial in any way, just a pity that it is not working properly.
Miki
My operating system is Windows XP.
matplotlib version 0.98.5.2 on python 2.5 installed by the standard binary
installer.
#!/usr/bin/env python
# embedding_in_qt4.py --- Simple Qt4 application embedding matplotlib canvases
#
# Copyright (C) 2005 Florent Rougon
# 2006 Darren Dale
#
# This file is an example program for matplotlib. It may be used and
# modified with no restriction; raw copies as well as modified versions
# may be distributed without limitation.
import sys, os, random
from PyQt4 import QtGui, QtCore
from numpy import arange, sin, pi
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
from matplotlib.backends.backend_qt4 import NavigationToolbar2QT as
NavigationToolbar
progname = os.path.basename(sys.argv[0])
progversion = 0.1
class MyMplCanvas(FigureCanvas):
Ultimately, this is a QWidget (as well as a FigureCanvasAgg, etc.).
def __init__(self, parent=None, width=5, height=4, dpi=100):
fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
#
FigureCanvas.__init__(self, fig)
self.setParent(parent)
FigureCanvas.setSizePolicy(self,
QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def compute_initial_figure(self):
pass
class MyStaticMplCanvas(MyMplCanvas):
Simple canvas with a sine plot.
def compute_initial_figure(self):
t = arange(0.0, 3.0, 0.01)
s = sin(2*pi*t)
self.axes.plot(t, s)
class MyDynamicMplCanvas(MyMplCanvas):
A canvas that updates itself every second with a new plot.
def __init__(self, *args, **kwargs):
MyMplCanvas.__init__(self, *args, **kwargs)
timer = QtCore.QTimer(self)
QtCore.QObject.connect(timer, QtCore.SIGNAL(timeout()),
self.update_figure)
timer.start(1000)
def compute_initial_figure(self):
self.axes.plot([0, 1, 2, 3], [1, 2, 0, 4], 'r')
def update_figure(self):
# Build a list of 4 random integers between 0 and 10 (both inclusive)
l = [ random.randint(0, 10) for i in xrange(4) ]
self.axes.plot([0, 1, 2, 3], l, 'r')
self.axes.yaxis.set_ticklabels([1, 2, 3])
self.draw()
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
self.setWindowTitle(application main window)
self.file_menu = QtGui.QMenu('File', self)
self.file_menu.addAction('Quit', self.fileQuit,
QtCore.Qt.CTRL + QtCore.Qt.Key_Q)
self.menuBar().addMenu(self.file_menu)
self.help_menu = QtGui.QMenu('Help', self)
self.menuBar().addSeparator()
self.menuBar().addMenu(self.help_menu)
self.help_menu.addAction('About', self.about)
self.main_widget = QtGui.QWidget(self)
l = QtGui.QVBoxLayout(self.main_widget)
sc = MyStaticMplCanvas(self.main_widget, width=5, height=4, dpi=100)
dc = MyDynamicMplCanvas(self.main_widget, width=5, height=4, dpi=100)
toolbar = NavigationToolbar(dc, dc)
l.addWidget(sc)
l.addWidget(dc)
l.addWidget(toolbar)
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.statusBar().showMessage(All hail matplotlib!, 2000)
def fileQuit(self):
self.close()
def closeEvent(self, ce):
self.fileQuit()
def about(self):
QtGui.QMessageBox.about(self, About %s % progname,
u%(prog)s version %(version)s
Copyright \N{COPYRIGHT SIGN} 2005 Florent Rougon, 2006 Darren Dale
This program is a simple example of a Qt4 application embedding matplotlib
canvases.
It may be used and modified with no restriction; raw copies as well as
modified versions may be distributed without limitation.
% {prog: progname, version: progversion})
qApp = QtGui.QApplication(sys.argv)
aw = ApplicationWindow()
[Matplotlib-users] Extending a plot outside of axes
Hi all.
is it not possible to extend plot outside of a plot area? To
illustrate what I want
to do take for example the wind barbs example from the matplotlib
gallery.
(see below)
I only changed line 23 from ax.barbs(X, Y, U, V) to ax.barbs(X, Y, -
U, -V)
But now we don't see the tail of the barbs in the first subplot.
So Is it possible to let matplotlib plot the tail, without extending
the axes?
Best Regards
Einar M. Einarsson
'''
Demonstration of wind barb plots
'''
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(-5, 5, 5)
X,Y = np.meshgrid(x, x)
U, V = 12*X, 12*Y
data = [(-1.5, .5, -6, -6),
(1, -1, -46, 46),
(-3, -1, 11, -11),
(1, 1.5, 80, 80),
(0.5, 0.25, 25, 15),
(-1.5, -0.5, -5, 40)]
data = np.array(data, dtype=[('x', np.float32), ('y', np.float32),
('u', np.float32), ('v', np.float32)])
#Default parameters, uniform grid
ax = plt.subplot(2,2,1)
ax.barbs(X, Y, -U, -V)
#Arbitrary set of vectors, make them longer and change the pivot point
#(point around which they're rotated) to be the middle
ax = plt.subplot(2,2,2)
ax.barbs(data['x'], data['y'], data['u'], data['v'], length=8,
pivot='middle')
#Showing colormapping with uniform grid. Fill the circle for an
empty barb,
#don't round the values, and change some of the size parameters
ax = plt.subplot(2,2,3)
ax.barbs(X, Y, U, V, np.sqrt(U*U + V*V), fill_empty=True,
rounding=False,
sizes=dict(emptybarb=0.25, spacing=0.2, height=0.3))
#Change colors as well as the increments for parts of the barbs
ax = plt.subplot(2,2,4)
ax.barbs(data['x'], data['y'], data['u'], data['v'], flagcolor='r',
barbcolor=['b','g'], barb_increments=dict(half=10, full=20,
flag=100),
flip_barb=True)
plt.show()
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Re: [Matplotlib-users] Extending a plot outside of axes
Einar M. Einarsson wrote:
Hi all.
is it not possible to extend plot outside of a plot area? To
illustrate what I want
to do take for example the wind barbs example from the matplotlib
gallery.
(see below)
I only changed line 23 from ax.barbs(X, Y, U, V) to ax.barbs(X, Y, -
U, -V)
But now we don't see the tail of the barbs in the first subplot.
So Is it possible to let matplotlib plot the tail, without extending
the axes?
Einar: You can use the set_clip_box method of the barbs instance to
turn clipping off:
bb = ax.barbs(X, Y, -U, -V)
bb.set_clip_box(None)
-Jeff
Best Regards
Einar M. Einarsson
'''
Demonstration of wind barb plots
'''
import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(-5, 5, 5)
X,Y = np.meshgrid(x, x)
U, V = 12*X, 12*Y
data = [(-1.5, .5, -6, -6),
(1, -1, -46, 46),
(-3, -1, 11, -11),
(1, 1.5, 80, 80),
(0.5, 0.25, 25, 15),
(-1.5, -0.5, -5, 40)]
data = np.array(data, dtype=[('x', np.float32), ('y', np.float32),
('u', np.float32), ('v', np.float32)])
#Default parameters, uniform grid
ax = plt.subplot(2,2,1)
ax.barbs(X, Y, -U, -V)
#Arbitrary set of vectors, make them longer and change the pivot point
#(point around which they're rotated) to be the middle
ax = plt.subplot(2,2,2)
ax.barbs(data['x'], data['y'], data['u'], data['v'], length=8,
pivot='middle')
#Showing colormapping with uniform grid. Fill the circle for an
empty barb,
#don't round the values, and change some of the size parameters
ax = plt.subplot(2,2,3)
ax.barbs(X, Y, U, V, np.sqrt(U*U + V*V), fill_empty=True,
rounding=False,
sizes=dict(emptybarb=0.25, spacing=0.2, height=0.3))
#Change colors as well as the increments for parts of the barbs
ax = plt.subplot(2,2,4)
ax.barbs(data['x'], data['y'], data['u'], data['v'], flagcolor='r',
barbcolor=['b','g'], barb_increments=dict(half=10, full=20,
flag=100),
flip_barb=True)
plt.show()
--
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[Matplotlib-users] HTML area for a matplotlib picture
Hello, This code worked with matplotlib 0.87: fig = Figure() ax = fig.add_subplot(121) width = 0.5 # the width of the bars self.dpi = 70 yoff = array([0.0] * len(self.__labels)) # the bottom values for stacked bar chart self.__bars = () for row in xrange(rows): self.__bars += (ax.bar(ind, self.__data[row], width, bottom=yoff, color=colours),) yoff = yoff + self.__data[row] #... fig.set_size_inches(self.size[0], self.size[1]) imdata=StringIO() fig.savefig(imdata,format='png', dpi=self.dpi) self.__image = imdata.getvalue() self.height = fig.get_figheight()* self.dpi #... coords = [] for bar in self.__bars: x1 = [] y1 = [] x2 = [] y2 = [] # For each bars, we get values of rectangles for b in bar: x1 += [b.get_x(),] y1 += [b.get_y(),] if matplotlib.compare_versions(matplotlib.__version__, '0.97'): x2 += [b.get_x() + b.get_width(),] y2 += [b.get_y() + b.get_height(),] else: x2 += [b.get_x() + b.width,] y2 += [b.get_y() + b.height,] if matplotlib.compare_versions(matplotlib.__version__, '0.97'): xys1 = zip(x1, y1) xys2 = zip(x2, y2) # We get the top left points for each bars... xys1 = bar[0].get_transform().transform(xys1) # ...and the bottom right points for each bars. xys2 = bar[0].get_transform().transform(xys2) else: xys1 = zip(bar[0].get_transform().seq_x_y(x1, y1)) xys2 = zip(bar[0].get_transform().seq_x_y(x2, y2)) # Now for each bars, we can make a (x,y,w,h) data coords for HTML map area. for (sx1, sy1), (sx2, sy2) in zip(xys1, xys2): coords.append(sx1, self.height - sy2, sx2, self.height)) #...then coords is used to build the html area tags Where it works with matplotlib 0.87, the behavior isn't correct with matplotlib 0.98. There are some version tests to run correctly compatible code. Blocks are equivalents, but as the v0.87 code works, the v0.98 code doesn't produce the same behavior. For example, if xys1 and xys2 are: xys1 = [(0.0, 0.0), (0.5, 0.0), (1.0, 0.0), (1.5, 0.0), (2.0, 0.0), (2.5, 0.0), (3.0, 0.0), (3.5, 0.0), (4.0, 0.0), (4.5, 0.0)] xys2 = [(0.5, 992.0), (1.0, 1025.0), (1.5, 972.0), (2.0, 1004.0), (2.5, 1007.0), (3.0, 1004.0), (3.5, 974.0), (4.0, 995.0), (4.5, 981.0), (5.0, 964.0)] The arrays produced by the transform() methods will be: xys1 = [[ 50.20. ] [ 65.5 20. ] [ 81.20. ] [ 96.5 20. ] [ 112.20. ] [ 127.5 20. ] [ 143.20. ] [ 158.5 20. ] [ 174.20. ] [ 189.5 20. ]] xys2 = [[ 6.5500e+01 1.31228533e+05] [ 8.1000e+01 1.3559e+05] [ 9.6500e+01 1.28583200e+05] [ 1.1200e+02 1.32815733e+05] [ 1.2750e+02 1.33212533e+05] [ 1.4300e+02 1.32815733e+05] [ 1.5850e+02 1.28847733e+05] [ 1.7400e+02 1.31625333e+05] [ 1.8950e+02 1.29773600e+05] [ 2.0500e+02 1.27525067e+05]] Firstly, the horizontal axe is separated with 15.5 points, but on picture, 28 are needed. Then, vertical values are around 1.0e+05, but self.height=175! Is there any matplotlib behavior changed in new versions? Thanks, regards -- Romain Bignon -- http://romain.peerfuse.org http://peerfuse.org pgp5uo6Mn4iCs.pgp Description: PGP signature -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
[Matplotlib-users] PS backend
Hello,
I am having some problems with the PS backend. I used the following
script to create a PostScript file
#!/usr/bin/env python
import matplotlib
matplotlib.use('PS')
import matplotlib.pyplot as plt
import numpy
x1 = numpy.arange(0,5)
y1 = x1
plt.plot(x1, y1)
plt.savefig('ps_backend.ps')
plt.show()
When I tried to open the PostScript file in GSview, there is the
following warning, and the file does not render properly. I have
attached the PostScript file and a screenshot of the incorrect rendering.
DSC Error
At line 233:
%%Page: 1 1
This %%Page: line occurred in the trailer, which is not legal.
EPS files should be encapsulated in %%BeginDocument / %%EndDocument.
If is possible that an EPS file was incorrectly encapsulated,
and that we have been confused by the %%Trailer in an EPS file.
The error can be eliminated by removing the line with %%EOF at line 230,
but I don't know anything about PostScript or if that change would have
any other effects. I only found this solution after comparing with the
output from the Cairo backend. The same change to PostScript output can
be achieved with the following diff (from svn diff), but again, I don't
know if it is appropriate.
Index: ttconv/pprdrv_tt.cpp
===
--- ttconv/pprdrv_tt.cpp(revision 6810)
+++ ttconv/pprdrv_tt.cpp(working copy)
@@ -1070,7 +1070,6 @@
} /* end of if Type 42 not understood. */
stream.putline(FontName currentdict end definefont pop);
-stream.putline(%%EOF);
} /* end of ttfont_trailer() */
/*--
Paul Novak
ps_backend.ps
Description: PostScript document
inline: incorrect_rendering.png--
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[Matplotlib-users] Two bugs in quiver?
I think there may be two bugs in quiver.
1. Quiver doesn't seem to accept 1D arrays X and Y if they are
different sizes -- they need to be turned into 2d arrays with meshgrid
for the program to work. With line 13 uncommented I get the following
error message:
File quivtest.py, line 13, in module
ax.quiver(XT,YT,uu,vv) #fails
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axes.py,
line 5533, in quiver
q = mquiver.Quiver(self, *args, **kw)
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/quiver.py,
line 343, in __init__
self.XY = np.hstack((X[:,np.newaxis], Y[:,np.newaxis]))
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/shape_base.py,
line 488, in hstack
return _nx.concatenate(map(atleast_1d,tup),1)
ValueError: array dimensions must agree except for d_0
2. Masking is not working properly with quiver, while it works fine
with contour -- see the attached quivtest.png
quiver.py:
import numpy as np
import numpy.ma as ma
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
XT = np.arange(10.)
YT = np.arange(20.)
uu = np.zeros([20,10])+7.
vv = np.zeros([20,10])+3.
fig = plt.figure()
ax = fig.add_subplot(121)
# ax.quiver(XT,YT,uu,vv) #fails
XX,YY = np.meshgrid(XT,YT)
ax.quiver(XX,YY,uu,vv) #Ok
ax = fig.add_subplot(122)
msk = XX**2+YY**2 50
uumsk = ma.masked_array(uu,mask=msk)
vvmsk = ma.masked_array(vv,mask=msk)
ax.contour(XT,YT,uumsk*XX) # works
ax.quiver(XX,YY,uumsk,vvmsk) # gives strange shapes
plt.show()
fig.savefig('quivtest.png',dpi=100)
George Nurser.
attachment: quivtest.png--
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[Matplotlib-users] Strange problem with savefig?
I am finding a very strange error. I have a program that integrates a partial differential equation using fortran code in an f2py module. Data in arrays held in the f2py module is updated in the fortran code. The module arrays are exposed to python (but not changed by python code). After each increment of timestep the array is plotted using matplotlib, and a figure saved with savefig, so as to create an animation. What I am finding is that the fortran module array is becoming corrupted with NaNs. If, however, I simply comment out the call to savefig in my python code, there is no corruption of the module arrays. WxAgg backend, Intel Mac OS 10.5.6, python 2.5.2, matplotlib svn revision 6739, numpy 1.3.0.dev6297 I have the same problem with GtkAgg python 2.5.1 + matplotlib svn 6757.+ numpy 1.3.0.dev6297 on suse linux 10.1, amd_64. George Nurser. . -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Two bugs in quiver?
George Nurser wrote:
I think there may be two bugs in quiver.
Thanks for the report. I can reproduce both problems, and I will try to
solve them.
Eric
1. Quiver doesn't seem to accept 1D arrays X and Y if they are
different sizes -- they need to be turned into 2d arrays with meshgrid
for the program to work. With line 13 uncommented I get the following
error message:
File quivtest.py, line 13, in module
ax.quiver(XT,YT,uu,vv) #fails
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/axes.py,
line 5533, in quiver
q = mquiver.Quiver(self, *args, **kw)
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/matplotlib/quiver.py,
line 343, in __init__
self.XY = np.hstack((X[:,np.newaxis], Y[:,np.newaxis]))
File
/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site-packages/numpy/lib/shape_base.py,
line 488, in hstack
return _nx.concatenate(map(atleast_1d,tup),1)
ValueError: array dimensions must agree except for d_0
2. Masking is not working properly with quiver, while it works fine
with contour -- see the attached quivtest.png
quiver.py:
import numpy as np
import numpy.ma as ma
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
XT = np.arange(10.)
YT = np.arange(20.)
uu = np.zeros([20,10])+7.
vv = np.zeros([20,10])+3.
fig = plt.figure()
ax = fig.add_subplot(121)
# ax.quiver(XT,YT,uu,vv) #fails
XX,YY = np.meshgrid(XT,YT)
ax.quiver(XX,YY,uu,vv) #Ok
ax = fig.add_subplot(122)
msk = XX**2+YY**2 50
uumsk = ma.masked_array(uu,mask=msk)
vvmsk = ma.masked_array(vv,mask=msk)
ax.contour(XT,YT,uumsk*XX) # works
ax.quiver(XX,YY,uumsk,vvmsk) # gives strange shapes
plt.show()
fig.savefig('quivtest.png',dpi=100)
George Nurser.
--
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Re: [Matplotlib-users] NOAA .bull file parsing
Hi Pierre, Thanks for the quick and thorough response! What I ended up doing is writing a custom function that does all the stuff that I needed without using numpy or mlab. Anton Pierre GM-2 wrote: Anton, You may wanna check on the numpy list as well. I recently reimplemented a function to read text file as a combination of numpy.loadtxt and mlab.csv2rec, that handles missing data nicely. You can get it here for the moment: https://code.launchpad.net/~pierregm/numpy/numpy_addons The function you would need is mafromtxt, in fromascii. Alternatively, you can try using the scikits.timeseries package (http://pytseries.sourceforge.net/ ): recent SVN versions introduced tsfromtxt, that read a text file and return a timeseries. However, none of these possibilities will work out-of-the-box, because of the presence of the footer. What you could do is write a first function that gets rid of this footer (example of MO: open the file, read all the lines in a list, get rid of the first 7 rows (header) and last 8 ones, store the result in a file). Once you have only the data, use mafromtxt (for example) using space as a delimiter, and specify the columns you want to use with usecols (that way, you can get rid of the column with the '*'). The missing data should be taken into account properly. Let me know how it goes. P. On Jan 17, 2009, at 2:16 AM, antonv wrote: Dear all, I know this is not related to matplotlib but this seems to be the only place where I found people that have knowledge of both NOAA data and python so please bear with me. The .bull file that NOAA gives for upload is an ascii file formatted for human readability but it creates a lot of issues when I am trying to parse it. Here is a link to one of these files: ftp://ftpprd.ncep.noaa.gov/pub/data/nccf/com/wave/prod/wave.20090117/bulls.t00z/akw.46001.bull Do you have any idea on how to extract the data there in columns for plotting with matplotlib? If you look at the file you'll notice that there is both a header and a footer for the file that needs to be eliminated and the main columns have sub columns also. Another issue is that in a column there is missing data that should keep it's relationship with the time column. And the last issue, some of the values there are preceded by a * sign that should just be removed too. Any ideas are greatly appreciated! Anton -- View this message in context: http://www.nabble.com/NOAA-.bull-file-parsing-tp21513800p21513800.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users -- View this message in context: http://www.nabble.com/NOAA-.bull-file-parsing-tp21513800p21554671.html Sent from the matplotlib - users mailing list archive at Nabble.com. -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] Two bugs in quiver?
George Nurser wrote: I think there may be two bugs in quiver. Actually just 1... 1. Quiver doesn't seem to accept 1D arrays X and Y if they are different sizes -- they need to be turned into 2d arrays with meshgrid for the program to work. With line 13 uncommented I get the following error message: This is a bug. It is fixed now in svn trunk and 98.5 maintenance branch. 2. Masking is not working properly with quiver, while it works fine with contour -- see the attached quivtest.png This is a numpy.ma bug that has been fixed in numpy. I don't know exactly when it was fixed, but after I tracked it down to numpy.ma, I updated my copy of numpy from svn, and the problem went away. Somehow, when a multiplication was done with broadcasting, the mask was getting handled and propagated incorrectly. I suspect this bug was present only for a moderate interval of time, because quiver with masked points worked for a long time before you ran into the bug. Eric -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
Re: [Matplotlib-users] plot a data stream with matplotlib
Simone Gabbriellini wrote: I see that you first build your array and then display it at the end... is it possible in matplotlib to update the plot while the class is evolving? like: f.evolve(6) f.display() f.evolve(.27) f.display() f.evolve(10) f.display() f.evolve(2) f.display() You'd want to look at the animation examples in examples/animation. The exact details will depend upon what backend you want to use, but strip_chart_demo.py, simple_anim_gtk.py, and gtk_timeout.py are good places to start. HTH, Ryan -- Ryan May Graduate Research Assistant School of Meteorology University of Oklahoma -- This SF.net email is sponsored by: SourcForge Community SourceForge wants to tell your story. http://p.sf.net/sfu/sf-spreadtheword ___ Matplotlib-users mailing list Matplotlib-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/matplotlib-users
