Here’s how to plot x or y errorbars (or both) and how to customize the resulting plot.
Continue reading ‘Errorbars in matplotlib’
Archive for the 'Python' Category
Page 3 of 6
Here’s how to create a movie out of a collection of images, along with a more detailed example on creating multiple images with nested folders of images. Continue reading ‘Convert images into a movie with mencoder’
The matplotlibrc file contains many useful parameters for tweaking your setup to your liking, and it’s worth at least skimming through to get an idea of what it contains. Editing the file makes more permanent changes, while using the pylab rcParams dictionary or rc() and rcdefaults() functions lets you make and revert changes on the fly.
View the rc parameters by using
import pylab as p
print p.rcParamsExamples ensue.
Continue reading ‘Adjust settings for matplotlib using rc and matplotlibrc’
Set the rc parameters using the rc function.
import pylab as p
p.rc(('xtick.major','xtick.minor','ytick.major','ytick.minor'), pad=10)
p.plot([1,2,3])
If you only want to change one of the tick labels, say, the x major ticks, use
p.rc(‘xtick.major), pad=10)
When you’re done and want to reset the rc settings, use
p.rcdefaults()See matplotlibrc for more settings you can change via the rc command.
Here is some code from the matplotlib mailing list, sent by Rob Hetland, for selecting points from a plot.
from matplotlib.pyplot import *
class ginput(object):
"""docstring for on_click"""
def __init__(self):
self.x = []
self.y = []
connect('button_press_event', self)
def __call__(self, event):
xd, yd = event.xdata, event.ydata
if event.button==1:
if event.inaxes is not None:
# print 'data coords', event.xdata, event.ydata
self.x.append(xd)
self.y.append(yd)
plot((xd,), (yd,), 'r+', ms=5)
map_points = ginput()
#!/usr/bin/env python
# encoding: utf-8
"""Polygon geometry.
Copyright (C) 2006, Robert Hetland
Copyright (C) 2006, Stefan van der Walt
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the
distribution.
3. The name of the author may not be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS OR
IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
"""
import numpy as np
import sys
try:
import scipy.weave as weave
def npnpoly(verts,points):
verts = verts.astype(np.float64)
points = points.astype(np.float64)
xp = np.ascontiguousarray(verts[:,0])
yp = np.ascontiguousarray(verts[:,1])
x = np.ascontiguousarray(points[:,0])
y = np.ascontiguousarray(points[:,1])
out = np.empty(len(points),dtype=np.uint8)
code = """
/* Code from:
http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html
Copyright (c) 1970-2003, Wm. Randolph Franklin
Permission is hereby granted, free of charge, to any person
obtaining a copy of this software and associated documentation
files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy,
modify, merge, publish, distribute, sublicense, and/or sell copies
of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
1. Redistributions of source code must retain the above
copyright notice, this list of conditions and the following
disclaimers.
2. Redistributions in binary form must reproduce the above
copyright notice in the documentation and/or other materials
provided with the distribution.
3. The name of W. Randolph Franklin may not be used to endorse
or promote products derived from this Software without
specific prior written permission.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE. */
int i,j,n;
unsigned int c;
int nr_verts = Nxp[0];
for (n = 0; n < Nx[0]; n++) {
c = 0;
for (i = 0, j = nr_verts-1; i < nr_verts; j = i++) {
if ((((yp(i)<=y(n)) && (y(n)= 3, 'Need 3 vertices to create polygon.'
# close polygon, if needed
if not np.all(verts[0]==verts[-1]):
verts = np.vstack((verts,verts[0]))
self.verts = verts
return verts.view(Polygeom).copy()
def inside(self,points):
points = np.atleast_2d(points)
assert points.shape[1] == 2, \
"Points should be of shape Nx2, is %s" % str(points.shape)
return npnpoly(self.verts,points).astype(bool)
def get_area(self):
"""
Return the area of the polygon.
From Paul Bourke's webpage:
http://astronomy.swin.edu.au/~pbourke/geometry
"""
v = self.verts
v_first = v[:-1][:,[1,0]]
v_second = v[1:]
return np.diff(v_first*v_second).sum()/2.0
def get_centroid(self):
"Return the centroid of the polygon"
v = self.verts
a = np.diff(v[:-1][:,[1,0]]*v[1:])
area = a.sum()/2.0
return ((v[:-1,:] + v[1:,:])*a).sum(axis=0) / (6.0*area)
area = property(get_area)
centroid = property(get_centroid)
if __name__ == '__main__':
import pylab as pl
grid = np.mgrid[0:1:10j,0:1:10j].reshape(2,-1).swapaxes(0,1)
# simple area test
verts = np.array([[0.15,0.15],
[0.85,0.15],
[0.85,0.85],
[0.15,0.85]])
pa = Polygeom(verts)
print pa.area
print (0.85-0.15)**2
print pa
print pa.centroid
# concave enclosure test-case for inside.
verts = np.array([[0.15,0.15],
[0.25,0.15],
[0.45,0.15],
[0.45,0.25],
[0.25,0.25],
[0.25,0.55],
[0.65,0.55],
[0.65,0.15],
[0.85,0.15],
[0.85,0.85],
[0.15,0.85]])
pb = Polygeom(verts)
inside = pb.inside(grid)
pl.plot(grid[:,0][inside], grid[:,1][inside], 'g.')
pl.plot(grid[:,0][~inside], grid[:,1][~inside],'r.')
pl.plot(pb.verts[:,0],pb.verts[:,1], '-k')
print pb.centroid
xc, yc = pb.centroid
print xc, yc
pl.plot([xc], [yc], 'co')
pl.show()
pl.figure()
# many points in a semicircle, to test speed.
grid = np.mgrid[0:1:1000j,0:1:1000j].reshape(2,-1).swapaxes(0,1)
xp = np.sin(np.arange(0,np.pi,0.01))
yp = np.cos(np.arange(0,np.pi,0.01))
pc = Polygeom(np.hstack([xp[:,np.newaxis],yp[:,np.newaxis]]))
print "%d points inside %d vertex poly..." % (grid.size/2,len(verts)),
sys.stdout.flush()
inside = pc.inside(grid)
print "done."
pl.plot(grid[:,0][inside], grid[:,1][inside], 'g+')
pl.plot(grid[:,0][~inside], grid[:,1][~inside], 'r.')
pl.plot(pc.verts[:,0], pc.verts[:,1], '-k')
xc, yc = pc.centroid
print xc, yc
pl.plot([xc], [yc], 'co')
pl.show()
- I had a Python datetime object, T.
- I knew it was in Eastern time and wanted to convert to UTC.
- I also wanted it to keep track of daylight savings time, for when I have dates later in the year.
- Python datetime objects have “support” for timezone info, but you have to implement it yourself. Read: more coding overhead that I’m trying to avoid.
Here’s how to do it the easy way. Continue reading ‘Timezones in Python’
There are no built-in functions (that I know of) for returning a list of codons from a sequence, but making your own is quite simple. This function is from Solution A.5 from the Python Course in Bioinformatics
def codons(s, frame=0):
"""Return a list of codons from a string, s, giving an optional frameshift."""
codons=[]
end=len(s[frame:]) - (len(s[frame:]) % 3) - 1
for i in range(frame,end,3):
codons.append(s[i:i+3])
return codons
If you have some different options in your program and you want to turn them on or off, or feed your functions different arguments, then you can specify all of this from the command line.
You can read about the details of the optparser module here, but here are the basics: Continue reading ‘Sending command line options to Python scripts’
I had heard of unittest and how I really needed to use it to make sure my code is doing what I expect . . . but it just seemed so clunky. Plus, a program would have to reach a certain threshold of complexity before I would make the effort to test with unittest.
Then I ran across doctest. And it is so astoundingly easy to use that I might start writing tests even for one-line scripts. Continue reading ‘Test your code: so easy there’s no excuse!’
Sometimes it’s nice to be able to have a codon table handy. Rather than typing out one by hand, theTranslate module contains the codon table of your choice in dictionary form: Continue reading ‘A quick codon table’