We Keep Coding

Plotting a line between a pair of y coordinates

I am trying to plot the following code where data1, data2, data3 are vectors.
data1 = np.array(means1)
print('data1=',data1)
data2 = np.array(ci_l)
print('data2',data2)
data3 = np.array(ci_h)
print('data3',data3)
x = data1
y = np.concatenate([data2[:,None],data3[:,None]], axis=1)
print('x=', x,'y=',y)
plt.plot(x, [i for (i,j) in y], 'rs', markersize = 4)
plt.plot(x, [j for (i,j) in y], 'bo', markersize = 4)
plt.show()
For each x points as you see in the code I have two y points. When I run the code I obtain the following output:
data1= [[22.8]
[31.6]
[27.4]
[30.4]
[30.6]]
data2 [[21.80474319]
[30.60474319]
[26.40474319]
[29.40474319]
[29.60474319]]
data3 [[23.79525681]
[32.59525681]
[28.39525681]
[31.39525681]
[31.59525681]]
x= [[22.8]
[31.6]
[27.4]
[30.4]
[30.6]] y= [[[21.80474319]
[23.79525681]]
[[30.60474319]
[32.59525681]]
[[26.40474319]
[28.39525681]]
[[29.40474319]
[31.39525681]]
[[29.60474319]
[31.59525681]]]
and this figure:
My question is how to plot a line that connect each y pair? My problem is similar to this:
< Matplotlib how to draw vertical line between two Y points >
I try to add the following line as suggested to the code:
plt.plot((x,x),([i for (i,j) in y], [j for (i,j) in y]),c='black')
but I obtain the following error:
Traceback (most recent call last):
File "/Users/oltiana/Desktop/datamining/chapter4.py", line 151, in <module>
plt.plot((x,x),([i for (i,j) in y], [j for (i,j) in y]),c='black')
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/pyplot.py", line 3019, in plot
return gca().plot(
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/axes/_axes.py", line 1605, in plot
lines = [*self._get_lines(*args, data=data, **kwargs)]
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 315, in __call__
yield from self._plot_args(this, kwargs)
File "/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 504, in _plot_args
raise ValueError(f"x and y can be no greater than 2D, but have "
ValueError: x and y can be no greater than 2D, but have shapes (2, 5, 1) and (2, 5, 1)
I try to solve the problem using shape and reshape bout still does not work. Any suggestion would be helpful for me. Thank you!

I notice that your arrays of data all look like two-dimensional lists - each number is the only element in a list of its own! ([[22.8], [31.6], ...] instead of [22.8, 31.6, ...])
That's why you're getting the shape error. There are a few ways to fix this, but one easy way is to call .flatten() on each array. This reduces it to be one-dimensional, and your code will work fine with data like that.
data1 = np.array(means1).flatten()
data2 = np.array(ci_l).flatten()
data3 = np.array(ci_h).flatten()
...

try writing
for x1,y1y2 in zip(x,y):
plt.plot([x1,x1],y1y2,'k-') #'k-' to prevent automatic coloring
BEFORE
plt.plot(x, [i for (i,j) in y], 'ro', markersize = 4)
plt.plot(x, [j for (i,j) in y], 'bs', markersize = 4)
This will make a two-point plot for each pair of points.
This will work visually, but may mess up automatic legends

Using Polyfit to create 3rd degree polynomial with dynamic CSV's

What the data look like although I may end up with more than just three columns:
TotalArea,Pressure,Intensity
12054.2,-0.067,39.579
11980.2,-0.061,41.011
11948,-0.055,42.08
11889.5,-0.04,45.732
11863.6,-0.03,50.573
My goal: I would like to take this CSV file and create A polynomial that will fit the column labeled Intensity and TotalArea.
My code (omitting anything I believe to be purely decorative):
Graph = pd.read_csv("C:Data.csv")
Pl = Graph.dropna()
Bottom = Pl["TotalArea"]
Right = Pl["Intensity"]
arr = Pl.values
x = Bottom
y2 = Right
fig = plt.figure()
ax1 = fig.add_subplot(1, 1, 1)
xx = arr[:, [0]]
b = xx.ravel()
print(b)
yy = arr[:, [2]]
c = xx.ravel()
y3 = np.polyfit(b, c, 3)
ax2 = ax1.twinx()
ax2.plot(x, y2, color = "r", label='Intensity /Area')
plt.show()
My error: (has to do with polyfit values)
Traceback (most recent call last):
File "/mnt/WinPartition/Users/tomchi/Documents/Programming/Eclipse/PythonDevFiles/so_test.py", line 47, in <module>
ax2.plot(x, y3)
File "/usr/local/lib/python3.5/dist-packages/matplotlib/__init__.py", line 1855, in inner
return func(ax, *args, **kwargs)
File "/usr/local/lib/python3.5/dist-packages/matplotlib/axes/_axes.py", line 1527, in plot
for line in self._get_lines(*args, **kwargs):
File "/usr/local/lib/python3.5/dist-packages/matplotlib/axes/_base.py", line 406, in _grab_next_args
for seg in self._plot_args(this, kwargs):
File "/usr/local/lib/python3.5/dist-packages/matplotlib/axes/_base.py", line 383, in _plot_args
x, y = self._xy_from_xy(x, y)
File "/usr/local/lib/python3.5/dist-packages/matplotlib/axes/_base.py", line 242, in _xy_from_xy
"have shapes {} and {}".format(x.shape, y.shape))
ValueError: x and y must have same first dimension, but have shapes (310,) and (2,)
So, my question is: What exactly does this mean? Is it due to pandas dataframe? Can I solve this in a quick manner? Can I be of any more assistance?
I realise now that polyfit just gives me the coefficients to my polynomial
[ -2.27230868e-23 2.74362531e-19 1.00000000e+00 -1.90568829e-12]

matplotlib.scatter color argument not accepting numpy array

I have written the following python plotting script using matplotlib:
import pynbody as pyn
import numpy as np
import matplotlib.pyplot as plt
import glob
s = pyn.load('./ballsV2.00001')
sl = s.g[np.where((s.g['z'] < 0.005) & (s.g['z']>-0.005))]
sx = s.s['x'][0]
sy = s.s['y'][0]
sz = s.s['z'][0]
r2 = ((s.g['x']-sx)**2+(s.g['y']-sy)**2+(s.g['z']-sz)**2)
Flux = np.array(1./(4*np.pi*r2)*np.exp(-1*7.00114988051*np.sqrt(r2)))
print(type(np.log10(sl['radFlux'])))
print(type(np.log10(Flux)))
plt.figure(figsize = (15,12))
#plt.scatter(sl['x'],sl['y'],c=np.log10(sl['radFlux']),s=75,edgecolors='none', marker = '.',vmin=-6,vmax=1)
plt.scatter(sl['x'],sl['y'],c=np.log10(Flux),s=75,edgecolors='none', marker = '.',vmin=-8,vmax=4)
plt.xlim([-0.5,0.5])
plt.ylim([-0.5,0.5])
plt.xlabel("x")
plt.ylabel("y")
plt.colorbar(label="log(Code Flux)")
plt.savefig('./ballsV2_0.1.pdf')
plt.savefig('./ballsV2_0.1.png')
plt.show()
plt.close()
When I run the script I get the following error:
foo#bar ~/Data/RadTransfer/Scaling_Tests/ballsV2 $ py
balls.py
balls.py:15: RuntimeWarning: divide by zero encountered in log10
print(type(np.log10(sl['radFlux'])))
<class 'numpy.ndarray'>
<class 'numpy.ndarray'>
Traceback (most recent call last):
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/colors.py", line 141, in to_rgba
rgba = _colors_full_map.cache[c, alpha]
KeyError: (-4.1574455411341349, None)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/colors.py", line 192, in _to_rgba_no_colorcycle
c = tuple(map(float, c))
TypeError: 'numpy.float64' object is not iterable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "balls.py", line 17, in <module>
plt.scatter(sl['x'],sl['y'],c=np.log10(Flux),s=75,edgecolors='none', marker = '.',vmin=-8,vmax=4)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/pyplot.py", line 3435, in scatter
edgecolors=edgecolors, data=data, **kwargs)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/__init__.py", line 1892, in inner
return func(ax, *args, **kwargs)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py", line 4028, in scatter
alpha=alpha
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/collections.py", line 890, in __init__
Collection.__init__(self, **kwargs)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/collections.py", line 139, in __init__
self.set_facecolor(facecolors)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/collections.py", line 674, in set_facecolor
self._set_facecolor(c)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/collections.py", line 659, in _set_facecolor
self._facecolors = mcolors.to_rgba_array(c, self._alpha)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/colors.py", line 237, in to_rgba_array
result[i] = to_rgba(cc, alpha)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/colors.py", line 143, in to_rgba
rgba = _to_rgba_no_colorcycle(c, alpha)
File "/home/grondjj/anaconda3/lib/python3.6/site-packages/matplotlib/colors.py", line 194, in _to_rgba_no_colorcycle
raise ValueError("Invalid RGBA argument: {!r}".format(orig_c))
ValueError: Invalid RGBA argument: -4.1574455411341349
Ignore the divide by zero stuff,the issue is the scatter plot function isn't taking my array of values to map colour to. What is strange is that the commented out scatter plot command above it runs fine. The only difference is the array of values I am passing it. I made sure to cast them to the same type (they are both <class 'numpy.ndarray'>). Also, the values themselves are more sane ranging between ~4000 and 1E-7 in the Flux array, it is only the np.log10(sl['radFlux'] that has the divide by zero errors and that one works. Any suggestions?

Flux and np.log10(sl['radFlux']) ended up being different lengths. sl (a slice of s) was not used to compute r2, so Flux ended up being to big. It would be nice if matplotlib checked that the color array was the same length as the scatter x and y arrays and had an error message like it does when the x and y arrays are different lengths.

Python Plot sees Reals but Bar sees Strings

In short, when I use the plot command, my data is recognized as real double precision numbers, but asking for a bar graph for some reason returns the complaint that the data are strings, not reals. Here is my simple code:
#!/usr/bin/env python
import numpy as np
import matplotlib.pyplot as plt
#for counter in range(102,401):
for counter in range(400,401):
temp1=str(counter)
temp="column_1_file_"+temp1
temp2="column_2_file_"+temp1
xdata=np.loadtxt(temp,delimiter=" ",dtype=str)
ydata=np.loadtxt(temp2,delimiter=" ",dtype=str)
plt.plot(xdata,ydata,'or')
# width=1.0
# plt.bar(xdata,ydata,width,color="blue")
plt.xlabel(r' Particle Radius ($\mu$m)')
plt.ylabel("Frequency")
plt.title("Histogram of Particle Radius")
plt.xlim(-1,40)
plt.ylim(0,1.1)
# plt.show()
var1=str(counter)+".png"
plt.savefig(var1,format='png')
counter=counter+1
When executed, the program above works fine, producing the desired line plot just fine. When I comment out "plt.plot(xdata,ydata,'or')" and un-comment the plt.bar and width lines, I get the below error:
On the command line, the commands and responses given are:
python Histogram_Evolution.py
Traceback (most recent call last):
File "Histogram_Evolution.py", line 13, in <module>
plt.bar(xdata,ydata,width,color="blue")
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib- 1.3.1-py2.7-linux-x86_64.egg/matplotlib/pyplot.py", line 2515, in bar
ret = ax.bar(left, height, width=width, bottom=bottom, **kwargs)
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 5053, in bar
self.add_patch(r)
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 1562, in add_patch
self._update_patch_limits(p)
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/axes.py", line 1580, in _update_patch_limits
xys = patch.get_patch_transform().transform(vertices)
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/patches.py", line 576, in get_patch_transform
self._update_patch_transform()
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/patches.py", line 569, in _update_patch_transform
bbox = transforms.Bbox.from_bounds(x, y, width, height)
File "/N/soft/rhel6/python/2.7.3/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/transforms.py", line 821, in from_bounds
return Bbox.from_extents(x0, y0, x0 + width, y0 + height)
TypeError: cannot concatenate 'str' and 'float' objects
Here is an example of the xdata file that is read, followed by an example of the ydata file that is read:
0.3454E-03
0.3801E-03
0.4095E-03
0.4245E-03
0.4456E-03
0.4661E-03
0.4861E-03
0.5049E-03
0.5292E-03
0.5435E-03
0.5588E-03
0.5732E-03
0.5840E-03
0.5925E-03
0.6037E-03
0.6158E-03
0.6852E-03
0.9102E-03
0.1083E-02
0.1197E-02
0.1306E-02
0.1477E-02
0.1986E-02
0.2352E-02
0.2577E-02
0.2810E-02
0.3253E-02
0.4226E-02
0.5017E-02
0.5535E-02
0.6018E-02
0.6973E-02
0.9046E-02
0.1079E-01
0.1192E-01
0.1294E-01
0.1502E-01
0.1948E-01
0.2325E-01
0.2568E-01
0.2789E-01
0.3235E-01
0.4198E-01
0.5012E-01
0.5532E-01
0.6012E-01
0.781791E-01
0.782330E-01
0.105108E-02
0.108144E-02
0.180879E-04
0.544883E-03
0.545426E-03
0.544242E-04
0.298458E-06
0.287814E-06
0.329474E-06
0.473319E-07
0.829702E-07
0.123443E-08
0.411156E-07
0.421080E-07
0.218848E+00
0.279559E+00
0.234184E+00
0.291552E+00
0.240008E+00
0.449513E+00
0.485745E+00
0.434142E+00
0.473585E+00
0.457689E+00
0.576471E+00
0.551371E+00
0.493782E+00
0.456229E+00
0.409499E+00
0.497298E+00
0.529838E+00
0.529549E+00
0.533233E+00
0.531061E+00
0.635727E+00
0.654071E+00
0.653801E+00
0.655098E+00
0.653899E+00
0.712113E+00
0.721604E+00
0.721187E+00
0.721345E+00
0.726954E+00
0.793069E+00
0.806902E+00
0.805833E+00

Matplotlib's plot has a convenience function integrated that automatically converts strings to numbers. bar does not have this functionality. So in order to plot a bar plot, you need to use numerical data.
This shouldn't be a problem, just don't specify str as dtype when reading in the data
np.loadtxt(temp,delimiter=" ")

matplotlib.pyplot.pcolor message of mismatch error: an L is missing

I often use pcolor method of matplotlib but it sometimes gives me something like a dimension mismatch error that I don't understand. Here a sample code
import numpy as np
import matplotlib.pyplot as plt
idx1 = 180
idx2 = 220
Range1 = range(idx1, idx2, 1)
Range2 = range(512)
z = np.random.randn( len( Range1 ), 512)
x, y = np.meshgrid( Range1 , Range2)
plt.figure()
plt.pcolor(x, y, z)
plt.show()
As you can try by yourself the mismatch error is
Traceback (most recent call last):
File "<ipython-input-1-7d51fd1b710e>", line 13, in <module>
plt.pcolor(x, y, z)
File "C:\Users\fedel\Anaconda2c\lib\site-packages\matplotlib\pyplot.py", line 3083, in pcolor
ret = ax.pcolor(*args, **kwargs)
File "C:\Users\fedel\Anaconda2c\lib\site-packages\matplotlib\__init__.py", line 1818, in inner
return func(ax, *args, **kwargs)
File "C:\Users\fedel\Anaconda2c\lib\site-packages\matplotlib\axes\_axes.py", line 5168, in pcolor
X, Y, C = self._pcolorargs('pcolor', *args, allmatch=False)
File "C:\Users\fedel\Anaconda2c\lib\site-packages\matplotlib\axes\_axes.py", line 4996, in _pcolorargs
C.shape, Nx, Ny, funcname))
TypeError: Dimensions of C (40L, 512L) are incompatible with X (40) and/or Y (512); see help(pcolor)
What is the difference between a "40L" dimension and a "40" without L dimension? And what do you suggest me to do in order to avoid this error and plot the data?

The L is not the issue. That's an artifact of using an old Python version (Python 2 has two integer types).
It looks like your z (C to the pcolor method) has a transposed shape, 40 × 512 instead of 512 × 40:
for a in [x, y, z]:
print(a.shape)
# (512, 40)
# (512, 40)
# (40, 512)
Transposing z makes it work: plt.pcolor(x, y, z.T)