We Keep Coding

Cannot plot my function : return array(a, dtype, copy=False, order=order) TypeError: float() argument must be a string or a number

I'm trying to plot a function that gives the arctan of the angle of several scatterplots (it's a physics experiment):
Here is my code:
import numpy as np
import matplotlib.pyplot as plt
filename='rawPhaseDataf2f_17h_15m.dat'
datatype=np.dtype( [('Shotnumber',np.dtype('>f8')),('A1',np.dtype('>f8')), ('A2',np.dtype('>f8')), ('f2f',np.dtype('>f8')), ('intensity',np.dtype('>f8'))])
data=np.fromfile(filename,dtype=datatype)
#time=data['Shotnumber']/9900 # reprate is 9900 Hz -> time in seconds
A1=data['A1']
A2=data['A2']
#np.sort()
i=range(1,209773)
def x(i) :
return arctan((A1.item(i)/A2.item(i))*(i/209772))
def y(i) :
return i*2*pi/209772
plot(x,y)
plt.figure('Scatterplot')
plt.plot(A1,A2,',') #Scatterplot
plt.xlabel('A1')
plt.ylabel('A2')
plt.figure('2D Histogram')
plt.hist2d(A1,A2,100) # 2D Histogram
plt.xlabel('A1')
plt.ylabel('A2')
plt.show()
My error is:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python2.7/dist-packages/spyderlib/widgets/externalshell /sitecustomize.py", line 540, in runfile
execfile(filename, namespace)
File "/home/nelly/Bureau/ Téléchargements/Kr4 Experiment/read_rawPhaseData.py", line 21, in <module>
plot(x,y)
File "/usr/lib/pymodules/python2.7/matplotlib/pyplot.py", line 2987, in plot
ret = ax.plot(*args, **kwargs)
File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 4138, in plot
self.add_line(line)
File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 1497, in add_line
self._update_line_limits(line)
File "/usr/lib/pymodules/python2.7/matplotlib/axes.py", line 1508, in _update_line_limits
path = line.get_path()
File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 743, in get_path
self.recache()
File "/usr/lib/pymodules/python2.7/matplotlib/lines.py", line 420, in recache
x = np.asarray(xconv, np.float_)
File "/usr/lib/python2.7/dist-packages/numpy/core/numeric.py", line 460, in asarray
return array(a, dtype, copy=False, order=order)
TypeError: float() argument must be a string or a number
I know that the problem is from the plot(x,y). I think that my error comes from the definition of x and y. A1 and A2 are matrix, N the number of points and Ak is the index of the matrix. I want to have arctan(A1k/A2k)*(k/N).

There are lots of problems with your code, and your understanding of python and array operations. I'm just going to handle the first part of the code (and the error you get), and hopefully you can continue to fix it from there.
This should fix the error you're getting and generate a plot:
# size = 209772
size = A1.size # I'm assuming that the size of the array is 209772
z = np.arange(1, size+1)/(size+1) # construct an array from [1/209773, 1.0]
# Calculate the x and y arrays
x = np.arctan((A1/A2)*z)
y = z*2*pi
# Plot x and y
plt.plot(x, y)
Discussion:
There are lots of issues with this chunk of code:
i=range(1,209773)
def x(i) :
return arctan((A1.item(i)/A2.item(i))*(i/209772))
def y(i) :
return i*2*pi/209772
plot(x, y)
You're defining two functions called x and y, and then you are passing those functions to the plotting method. The plotting method accepts numbers (in lists or arrays), not functions. That is the reason for the error that you are getting. So you instead need to construct a list/array of numbers and pass that to the function.
You're defining a variable i which is a list of numbers. But when you define the functions x and y, you are creating new variables named i which have nothing to do with the list you created earlier. This is because of how "scope" works in python.
The functions arctan and plot are not defined "globally", instead they are only defined in the packages numpy and matplotlib. So you need to call them from those packages.

ValueError: Maximum allowed size exceeded

So I'm trying to get some data from a set of equations in the code below. The equations are correct and I've checked them. I'm trying to loop the data over the array set as x in the hopes of scanning or looping across it later, but when I try to run the code I get the ValueError: Maximum allowed size exceeded. The problem appeared when I tried to loop the array of x in reverse. The non-working code is below:
from numpy import *
r=1.0 #radius
d=0.01 #separation of lines
L=1.0 #Length
i=0.01
n=1/d #number of lines
b=-r #position of each line with respect to the radial component
xs=[]
ys=[]
zs=[]
while b<=r:
x=arange(0,L,i) #sets up the x-coordinate system needed for each data point
for i in x:
y=0*x+b
z1=sqrt((r**2)-(y**2)) #plotting the straight lines
xs.append(x)
ys.append(y)
zs.append(z1)
for i in reversed(x):
u=d*x+b
z2=sqrt((r**2)-(u**2)) #plotting the diagonal lines
xs.append(x)
ys.append(u)
zs.append(z2)
b=b+d
print(xs,ys,zs)
And the error I get is:Traceback (most recent call last):
File "", line 1, in
runfile('/Users/Alex/Desktop/fibre_data.py', wdir='/Users/Alex/Desktop')
File "/anaconda/lib/python3.6/site-packages/spyder/utils/site/sitecustomize.py", line 880, in runfile
execfile(filename, namespace)
File "/anaconda/lib/python3.6/site-packages/spyder/utils/site/sitecustomize.py", line 102, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File "/Users/Alex/Desktop/fibre_data.py", line 22, in
x=arange(0,L,i) #sets up the x-coordinate system needed for each data point
ValueError: Maximum allowed size exceeded

Export graph to graphml with node positions using NetworkX

I'm using NetworkX 1.9.1.
I have a graph that I need to organize with positions and I then export to graphml format.
I've tried code in this question. It does not work, here is my example
import networkx as nx
import matplotlib.pyplot as plt
G = nx.read_graphml("colored.graphml")
pos=nx.spring_layout(G) # an example of quick positioning
nx.set_node_attributes(G, 'pos', pos)
nx.write_graphml(G, "g.graphml")
nx.draw_networkx(G, pos)
plt.savefig("g.pdf")
Here are the errors I get, the problem is how positions are saved (graphml does not accept arrays).
C:\Anaconda\python.exe C:/Users/sturaroa/Documents/PycharmProjects/node_labeling_test.py
Traceback (most recent call last):
File "C:/Users/sturaroa/Documents/PycharmProjects/node_labeling_test.py", line 11, in <module>
nx.write_graphml(G, "g.graphml")
File "<string>", line 2, in write_graphml
File "C:\Anaconda\lib\site-packages\networkx\utils\decorators.py", line 220, in _open_file
result = func(*new_args, **kwargs)
File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 82, in write_graphml
writer.add_graph_element(G)
File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 350, in add_graph_element
self.add_nodes(G,graph_element)
File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 307, in add_nodes
self.add_attributes("node", node_element, data, default)
File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 300, in add_attributes
scope=scope, default=default_value)
File "C:\Anaconda\lib\site-packages\networkx\readwrite\graphml.py", line 288, in add_data
'%s as data values.'%element_type)
networkx.exception.NetworkXError: GraphML writer does not support <type 'numpy.ndarray'> as data values.
I'm under the impression that I would be better off defining positions as 2 separate node attributes, x and y, and save them separately, defining a key for each of them in the graphml format, like this.
However, I'm not that familiar with Python, and would like your opinion before I make a mess iterating back and forth.
Thanks.

You are right, GraphML want's simpler attributes (no numpy arrays or lists).
You can set the x and y positions of the nodes as attributes like this
G = nx.path_graph(4)
pos = nx.spring_layout(G)
for node,(x,y) in pos.items():
G.node[node]['x'] = float(x)
G.node[node]['y'] = float(y)
nx.write_graphml(G, "g.graphml")

matplotlib text (and figtext) error

I'm trying to plot text values instead of symbols (for an MDS solution), and matplotlib.pyplot is giving me errors I don't understand. I've updated ipython and matplotlib to make sure it's not an old problem (or a problem with old versions), and I haven't been able to find any answers or reports of similar problems here (or elsewhere via google).
So, for example, after invoking ipython --pylab, if I type:
x = random.rand(4)
y = random.rand(4)
s = [str(i) for i in arange(4)+1]
text(x,y,s)
I get this error:
Traceback (most recent call last):
File "//anaconda/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in
draw_wrapper draw(artist, renderer, *args, **kwargs)
File "//anaconda/lib/python2.7/site-packages/matplotlib/figure.py", line 1034, in draw
func(*args)
File "//anaconda/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in
draw_wrapper draw(artist, renderer, *args, **kwargs)
File "//anaconda/lib/python2.7/site-packages/matplotlib/axes.py", line 2086, in draw
a.draw(renderer)
File "//anaconda/lib/python2.7/site-packages/matplotlib/artist.py", line 55, in
draw_wrapper draw(artist, renderer, *args, **kwargs)
File "//anaconda/lib/python2.7/site-packages/matplotlib/text.py", line 547, in draw
bbox, info, descent = self._get_layout(renderer)
File "//anaconda/lib/python2.7/site-packages/matplotlib/text.py", line 287, in
_get_layout key = self.get_prop_tup()
File "//anaconda/lib/python2.7/site-packages/matplotlib/text.py", line 696, in
get_prop_tup x, y = self.get_position()
File "//anaconda/lib/python2.7/site-packages/matplotlib/text.py", line 684, in
get_position x = float(self.convert_xunits(self._x))
TypeError: only length-1 arrays can be converted to Python scalars
I get the same error if I try calling text with scalars rather than vectors/lists (e.g., text(x[0],y[0],s[0]), or any number of variants of the arguments to the text function). The same thing happens:
with figtext,
if I manually import matplotlib.pyplot as plt and call plt.text, and
if I explicitly make figure and subplot objects and/or call scatter(x,y) first.
Also, for what it's worth, once this problem occurs, the error message appears again if I manually resize the figure. Possibly related is the fact that changes to figures don't update automatically, but only after I plot in another subplot or manually resize the figure. But I digress.
I've got an updated installation of Anaconda on a Mac (with Mavericks), and, as mentioned above, I'm using iPython.

plt.text expects a single x, y, and string values, not sequences. (See: http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.text )
Just use a loop.
For example:
import numpy as np
import matplotlib.pyplot as plt
x, y = np.random.rand(2,4)
s = [str(i) for i in np.arange(1, 5)]
fig, ax = plt.subplots()
text = [ax.text(*item) for item in zip(x, y, s)]
plt.show()

ZeroDivisionError when using scipy.interpolate.griddata

I'm getting a ZeroDivisionError from the following code:
#stacking the array into a complex array allows np.unique to choose
#truely unique points. We also keep a handle on the unique indices
#to allow us to index `self` in the same order.
unique_points,index = np.unique(xdata[mask]+1j*ydata[mask],
return_index=True)
#Now we break it into the data structure we need.
points = np.column_stack((unique_points.real,unique_points.imag))
xx1,xx2 = self.meta['rcm_xx1'],self.meta['rcm_xx2']
yy1 = self.meta['rcm_yy2']
gx = np.arange(xx1,xx2+dx,dx)
gy = np.arange(-yy1,yy1+dy,dy)
GX,GY = np.meshgrid(gx,gy)
xi = np.column_stack((GX.ravel(),GY.ravel()))
gdata = griddata(points,self[mask][index],xi,method='linear',
fill_value=np.nan)
Here, xdata,ydata and self are all 2D numpy.ndarrays (or subclasses thereof) with the same shape and dtype=np.float32. mask is a 2d ndarray with the same shape and dtype=bool. Here's a link for those wanting to peruse the scipy.interpolate.griddata documentation.
Originally, xdata and ydata are derived from a non-uniform cylindrical grid that has a 4 point stencil -- I thought that the error might be coming from the fact that the same point was defined multiple times, so I made the set of input points unique as suggested in this question. Unfortunately, that hasn't seemed to help. The full traceback is:
Traceback (most recent call last):
File "/xxxxxxx/rcm.py", line 428, in <module>
x[...,1].to_pz0()
File "/xxxxxxx/rcm.py", line 285, in to_pz0
fill_value=fill_value)
File "/usr/local/lib/python2.7/site-packages/scipy/interpolate/ndgriddata.py", line 183, in griddata
ip = LinearNDInterpolator(points, values, fill_value=fill_value)
File "interpnd.pyx", line 192, in scipy.interpolate.interpnd.LinearNDInterpolator.__init__ (scipy/interpolate/interpnd.c:2935)
File "qhull.pyx", line 996, in scipy.spatial.qhull.Delaunay.__init__ (scipy/spatial/qhull.c:6607)
File "qhull.pyx", line 183, in scipy.spatial.qhull._construct_delaunay (scipy/spatial/qhull.c:1919)
ZeroDivisionError: float division
For what it's worth, the code "works" (No exception) if I use the "nearest" method.