1 Python Lesson 5

1.1 Lesson outline

  1. Input and Output: dealing with files in Python and with NumPy
  2. More on NumPy
  3. More on Graphics
  4. Exercises

1.2 Writing and Reading data from files

We first explain the basics of file reading and writing in native Python and then move into the more specialized NumPy functions, better for dealing with data arrays.

1.2.1 File access in native Python

Using the native Python function open (with an absolute or a relative trajectory with respect to the notebook active directory) and the method close allows to set a filehandle. By default files are opened in the r mode (readonly).

path = "~/.bashrc"
fileh = open(path) # fileh is the filehandle

You can treat the filehandle as an iterator and build a loop. In this case the number of characters in each line is printed

for line in fileh:
    print(len(line))

It is important to close the filehandle once finished with it to return resources to the processor.

fileh.close

The usual form to open files makes unnecessary the last step, and once the file is dealt with it is automatically closed

with open(path) as fileh:
    bashrc_lines = [line.rstrip() for line in fileh]

We are reading each line, removing the trailing spaces and carriage return into a list using a list comprehension.

The complete syntax for open would be open(path, mode) and the major modes are:

mode r
Default mode. Read only.
mode w
Write only. Beware, it deletes an existing file and overwrites it.
mode x
Write only. It exits if the file exists.
mode a
Write only. Append to the file if it exists.
mode r+
Read and Write.
mode b
add to the mode for binary files. E.g. “rb”, “ab”…

The write and writelines methods allow to write into a filehandle. If, for example, we want to read a file and save it stripping the first and last lines we can run

with open("test_write.txt", "w") as tw_handle:
    tw_handle.writelines([line for line in open(path)][1:-2])

The most commonly used native Python file methods are

read([size])
Read data from file, with optional argument of the number of bytes to read. The method returns the specified number of bytes from the file. Default is -1 which means the whole file.
readlines([size])
Return list of lines from file, with optional argument of the number of bytes to read.
write(str)
Write string to file.
writelines(strings)
Write list of lines to file.
close()
Close the filehandle.
flush()
Flush the internal buffered I/O to the disk.
seek(pos)
Move to position pos in the file.
tell()
Tell the current position in the file.
closed
True if the filehandle is closed.
Exercise 5.1 Code a function that reads a given ASCII filename and encrypts or decrypts its content using the Caesar’s algorithm from Exercise 4.2. A keyword parameter should indicate whether the file is going to be encrypted or decrypted, and the result should be saved in a new file and shown in the standard output if the user wishes so.

1.2.2 File access with NumPy

We have already used the NumPy function loadtxt that, together with savetxt, allows to load and save data to text files. For example

array_a = np.random.randn(3,3)
np.savetxt("array_a_saved.txt", array_a, delimiter=":")
!cat array_a_saved.txt
array_b = np.loadtxt("array_a_saved.txt", delimiter=":")
np.array_equal(array_a, array_b)

These functions are specially handy for reading csv and tsv data files

But using the load and save functions you can also save an array in binary format -saving cpu, time, and precision at the cost of not being able to open/edit the file- with standard suffix npy.

array_a = np.random.randn(5,5)
np.save("array_a_saved", array_a)
!ls -l array_a_saved.*
array_b = np.load("array_a_saved.npy")
np.array_equal(array_a, array_b)

With the function savez you can also save multiple arrays in an npz file that is not a compressed file. If you want to compress the data use the function savez_compressed

np.savez("savez_example", a=array_a, b=array_b, c=array_a)
np.savez_compressed("savez_example_compressed", a=array_a, b=array_b, c=array_a)
!ls -l savez*

Once you read them they are loaded into a hash-like NumPy object with the array argument names as keys

arr_hash = np.load("savez_example_compressed.npz")
print(type(arr_hash))
print(arr_hash["a"])

To improve portability, and especially when you read several files in your code, and probably in different code sections, it is considered a good practice to define variables for your home and data folders and then use the variables to define the path when needed. This improves the readability of your code and helps its maintenance. A possible example, using the dataset provided at the beginning of the course is the following:

home_dir = "/home/curro/"
data_dir = "files/TData/"
##
##
metdata_orig = np.loadtxt(fname=home_dir + data_dir + 'T_Alicante_EM.csv', delimiter=',', skiprows=1) 

1.2.3 Saving Python objects with pickle

Pickling is used to save Python objects into a filesystem; lists, dictionaries, class objects, and more can be saved as a pickle file. Strictly speaking, pickling is the serializing and de-serializing of python objects to a byte stream. The opposite is unpickling.

This methodology is called serialization, marshalling, or flattening in other programming languages. Pickling is most useful when performing routine tasks on massive datasets or when you want to store, after sometimes massive calculations, a given Python object.

Once you import the pickle library, to save and load objects one makes use of the pickle.dump and pickle.load combined with the right filehandles. You can make this with the following two functions

import pickle

def save_obj(obj, name ):
    with open('./'+ name + '.pkl', 'wb') as f:
        pickle.dump(obj, f, pickle.HIGHEST_PROTOCOL)

def load_obj(name ):
    with open('./' + name + '.pkl', 'rb') as f:
        return pickle.load(f)

We can try saving a hash

test_hash = {0:"a", 1:"E",2:"I", 3: "J", 4: "H"}
save_obj(test_hash, "arr_hash_saving_test")
test_read = load_obj( "arr_hash_saving_test")

1.3 More on NumPy

The vectorization provided by NumPy is a great advantage when dealing with large datasets and the computing times required are at least an order of magnitude less than the equivalent times for interpreted code alternatives.

We illustrate this with a simple example, plotting the 3D function f(x,y) = np.exp(-xs ** 2 - ys ** 2)*xs**2*ys as a heatmap

points = np.linspace(-2, 2, 200)
xs, ys = np.meshgrid(points, points) # Build a grid of x and a grid of y values
z = np.exp(-xs ** 2 - ys ** 2)*xs**2*ys

We plot the figure as a heatmap in the XY plane

plt.title("Image plot of $ x^2 y e^{-x^2 - y^2}$ for a grid of values")
plt.imshow(z, cmap=plt.cm.autumn); plt.colorbar()

1.3.1 Random number generation

NumPy is very efficient in pseudorandom number generation as it also applies vectorization techniques. In the course, we have already run into the function np.random.randn, np.random.normal, and np.random.randint. The first two generate arrays of random numbers from a normal distribution (zero mean and unity standard deviation in the first case, and given mean and standard deviation in the second case) and the third one provide random integer values uniformly distributed in a given range. However, the preferred approach to pseudorandom number generation is the use of default_rng to get a new instance of a Generator, and then call the generator methods to obtain different distribution samples. You can find an quick reference to random numbers in NumPy in this link. For normally distributed standardized random data

rng = np.random.default_rng() 
normal_arr = rng.standard_normal((6,6))
normal_arr

These numbers are called pseudorandom as they are not true random numbers and are derived through a deterministic algorithm that makes use of a seed value. To check or replicate your results you can fix the seed value as an argument in the call to default_rng as in the next example. Using the rng generator you can select from a set of different statistical distributions from which you can sample the data

rng = np.random.default_rng(12345) 
gauss_arr = rng.normal(loc = 1, scale = 2, size=(6,6))
beta_arr = rng.beta(1.0, 0.4, size=(6,6))
integer_arr = rng.integers(0, high = 6, size=(6,6))
print(gauss_arr)
print(beta_arr)
print(integer_arr)

This is a global random seed value, you can also create different pseudorandom number generators isolated from each other

rng1 = np.random.default_rng(12345) 
rng2 = np.random.default_rng(123456789) 

We can check how efficient NumPy is in pseudorandom number generation. We compare the NumPy results with the normalvariate function in the random library. We can benchmark them

from random import normalvariate
N = 1000000
# non-vectorized
%timeit gaussian_samples = [normalvariate(0,2) for _ in range(N)]
# vectorized
%timeit gaussian_samples_vec = rng.normal(scale = 2, size = (N))

Notice that, depending on the system, the gain can be as large as one order of magnitude due to the lack of vectorization in the normalvariate case. This approach is far slower for large datasets. Notice also that in the list comprehension we have used the conventional name for the loop variable in case the variable is not used in the loop body: _.

Other available functions provided in np.random are

permutation
Return a random permutation of a sequence, or return a permuted range
shuffle
Randomly permute a sequence in-place
rand
Draw samples from a uniform distribution
randint
Draw random integers from a given low-to-high range
randn
Draw samples from a normal distribution with mean 0 and standard deviation 1 (MATLAB-like interface)
binomial
Draw samples from a binomial distribution
normal
Draw samples from a normal (Gaussian) distribution
beta
Draw samples from a beta distribution
chisquare
Draw samples from a chi-square distribution
gamma
Draw samples from a gamma distribution
uniform
Draw samples from a uniform [0, 1) distribution
Exercise 5.2 Define and test a function that estimates the value of the special constant pi by generating N pairs of random numbers in the interval -1 and 1 and checking how many of the generated number fall into a circumference of radius 1 centered in the origin. Improve the function showing in a graphical output the square, the circumference, and the points inside and outside the circumference with different colors.

1.3.2 Boolean indexing and np.where

Another powerful NumPy feature, already presented in Lesson 2, is the possibility of Boolean indexing. This is specially adequate when combined with the NumPy function np.where, presented in Lesson 3, a vectorized version of the standard Python ternary expression. In a previous example we replaced positive and negative values of a random array by one and minus one, respectively. This can be very conveniently done using np.where

arr_rand = rng.standard_normal((6,6))
print(arr_rand)
np.where(arr_rand>0,1,-1)

You could also just replace negative values by -1

arr_rand = rng.standard_normal((6,6))
print(arr_rand)
np.where(arr_rand>0,arr_rand,-1)

Avoiding the use of scalars, if we have two arrays and, depending on the sign of a third array, we would like to choose elements from one or the other.

arr_rand_A = rng.standard_normal((4,4))
arr_rand_B = rng.standard_normal((4,4))
arr_rand_C = rng.standard_normal((4,4))
print(arr_rand_A)
print(arr_rand_B)
print(arr_rand_C > 0)
np.where(arr_rand_C>0,arr_rand_A,arr_rand_B)

1.3.3 Useful NumPy functions

There are a set of statistical and mathematical functions available in NumPy, we quickly outline the main ones, applying them to a GOE matrix (Gaussian Orthogonal Ensamble, real and symmetric random matrices). We first define the matrix as a matrix of random normally distributed numbers with zero mean and unity variance, and then add it to its transpose, to get a symmetric matrix

GOE_arr =  rng.standard_normal((20,20))
GOE_arr += GOE_arr.T

We can now compute the mean and standard deviation of the full array or just the values for the main diagonal

GOE_arr.mean()
GOE_arr.std()
#
# Extract the diagonal of the array
np.diag(GOE_arr).mean()
np.diag(GOE_arr).std()

We already know that the option axis allows for limiting the calculation to rows or columns (or a given index in a multi index array)

print(GOE_arr.mean(axis=0))
print(GOE_arr.std(axis=0))
print(GOE_arr.mean(axis=1))
print(GOE_arr.std(axis=1))

Other useful functions are cumsum and cumprod for cumulative addition and product

print(GOE_arr.cumsum())
print(GOE_arr.cumprod())

Finally another useful NumPy methods are min (argmin) and max (argmax)

# min and argmin
print(GOE_arr.min())
print(GOE_arr.argmin())
# max and argmax
print(GOE_arr.max())
print(GOE_arr.argmax())

The indices are provided for a flattened array, if you need the row and column index values this can be obtained using the np.unravel_index function

print(np.unravel_index(GOE_arr.argmax(), GOE_arr.shape))
print(np.unravel_index(GOE_arr.argmin(), GOE_arr.shape))

You can sort values using the np.sort function or the sort method. There is a basic difference between these two. The function provides a sorted copy of the original array, while the method performs an in-place sort, without data copying.

# Sliced array copy 
GOE_arr_copy = GOE_arr[:4,:4].copy()

# Notice that array is sorted by row (axis = 1) by default
sorted_array = np.sort(GOE_arr_copy)
print(sorted_array)

# True if there are at least one non-zero element
print(np.any(sorted_array-GOE_arr_copy))

# In-place sorting
GOE_arr_copy.sort()
print(np.any(sorted_array-GOE_arr_copy))

Numpy also provides basic linear algebra functions, e.g. you can compute the trace of a matrix

print(np.trace(GOE_arr))

You can also calculate the product of two matrices with the dot or matmul method or function. Both provide the same result in the case of 2D array multiplication

dot_result = np.dot(GOE_arr,GOE_arr)
matmul_result=np.matmul(GOE_arr,GOE_arr)
#
np.all(np.equal(dot_result,matmul_result))

There are two main differences between these two functions. On the first hand multiplication by scalars is not allowed with matmul (use * instead). On the second hand, when the array dimension is larger than two, in the matmul case the operation is broadcasted together as if the matrices were elements residing in the last two indexes, respecting the signature (n,k),(k,m)->(n,m). In the dot case it is a sum product over the last axis of first matrix and the second-to-last of the second matrix

a = rng.standard_normal((2,3,4))
b = rng.standard_normal((2,4,2))
c = np.matmul(a,b)
print(c)
print(c.shape)
d = np.dot(a,b)
print(d)
print(d.shape)

In the case of two vectors, matmul provides the inner product (without taking complex conjugate)

print(np.matmul(GOE_arr[0,:], GOE_arr[0,:]))

In Python 3.5 the @ symbol works as an infix operator for matrix multiplication

print(np.any(np.matmul(GOE_arr, GOE_arr)-GOE_arr @ GOE_arr))

In np.linalg several functions of linear algebra are found.

det
Matrix determinant
eigvals
Eigenvalues of a square matrix
eig
Eigenvalues and eigenstates of a square matrix
eigvalsh
Eigenvalues of a symmetric or Hermitian square matrix
eigh
Eigenvalues and eigenstates of a symmetric or Hermitian matrix
inv
Inverse of a square matrix
pinv
Compute the Moore-Penrose pseudo-inverse of a matrix.
qr
Compute the QR decomposition.
svd
Compute the singular value decomposition (SVD).
solve
Solve the linear system Ax = b for x, where A is a square matrix.
lstsq
Compute the least-squares solution to Ax = b.

For example

print(np.linalg.trace(GOE_arr))
print(np.linalg.det(GOE_arr))
print(np.linalg.eigvalsh(GOE_arr))
Exercise 5.3 The NIST Digital Library of Mathematical Functions (DLMF) is a very useful site, where you can find an updated and expanded version of the well-known reference Handbook of Mathematical Functions compiled by Abramowitz and Stegun. Define a function to compute the Bessel function of the first kind of integer index from the series 10.2.2 in the DLMF, add a docscript and plot the functions of order 0, 1, and 2 in the interval of x between 0 and 10.

1.4 More on Graphics

We are going to elaborate on a seemingly neverending topic. You can find the complete Matplotlib documentation in https://matplotlib.org/stable/index.html We will cover some basic aspects with examples. Now, let’s load the library and create some data to display and learn some useful techniques

import numpy as np
import matplotlib.pyplot as plt
#
x_data = np.linspace(0,4*np.pi,500)
y_data = np.cos(x_data**2)*np.cosh(x_data)

Let’s first create a plot with a single panel. The recommended way is using subplot without arguments, as follows

import numpy as np
import matplotlib.pyplot as plt
#
x_data = np.linspace(0,4*np.pi,500)
y_data = np.cos(x_data**2)/np.cosh(x_data/5)

fig, ax = plt.subplots()
ax.plot(x_data, y_data, label="Some data")
ax.set_title('Single plot', fontsize = 20) # Set plot title and fontsize
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("F(w) (a.u.)", fontsize = 16) # idem for y axis
ax.legend() # Display labels

We have customized the x and y axis labels, the plot title and included a legend. There are several ways of plotting various curves in the same panel. The easiest one is to run one plot instance for each curve, as in the example that follows

x_data = np.linspace(0,4*np.pi,500)
y1_data = np.cos(x_data**2)/np.cosh(x_data/5)
y2_data = np.cos(x_data**3-5*x_data**2)/np.cosh(x_data/2)

fig, ax = plt.subplots()
ax.plot(x_data, y1_data, label="Data 1")
ax.plot(x_data, y2_data, label="Data 2")
ax.set_title('Single plot, several curves', fontsize = 20) # Set plot title and fontsize
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("F(w) (a.u.)", fontsize = 16) # idem for y axis
ax.legend()

We will later see other ways of plotting several curves. We can customize the style of the line and include symbols in the points in the plot command using one of the set of Line 2D properties. For example

c or ~color~=/color/
Control line color. Possible color abbreviations: {'b', 'g', 'r', 'c', 'm', 'y', 'k', 'w'}. You can also use colors from the xkcd color name survey with the prefix xkcd: or an RGB or RGBA (red, green, blue, alpha) tuple of float values or hex string.
~alpha~=/float/
Set the alpha value used for blending. This is not supported on all backends.
ls or linestyle
Control line style. Possible options: {'-', '--', '-.', ':', '', (offset, on-off-seq), ...}.
lw or linewidth float
Control linewidth.
marker markerstyle
Control marker style. For possible options check Matplotlib Markers.
markersize or ms float
Control marker size in points.
markevery None or int or (int, int) or slice or List[int] or float or (float, float)
Control markers display

In this example we use some of these parameters

x_data = np.linspace(0,4*np.pi,500)
y1_data = np.cos(x_data**2)/np.cosh(x_data/5)
y2_data = np.cos(x_data**3-5*x_data**2)/np.cosh(x_data/2)

fig, ax = plt.subplots()
ax.plot(x_data, y1_data, label="Data 1", c="b", ls="-.", alpha = 0.6, marker="o", markersize=4)
ax.plot(x_data, y2_data, label="Data 2", linestyle="-", color="xkcd:olive", lw=2.0, marker = "+", markevery=3)
ax.set_title('Single plot, several curves', fontsize = 20) # Set plot title and fontsize
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("F(w) (a.u.)", fontsize = 16) # idem for y axis
ax.legend()

As already mentioned in the exercises of Lesson 2, you can also depict data using the pyplot.scatter function and another useful tool is the pyplot.bar. Let’s try these two. We can try scatter with the previous function

x_data = np.linspace(0,4*np.pi,500)
y1_data = np.cos(x_data**2)/np.cosh(x_data/5)

fig, ax = plt.subplots()
ax.scatter(x_data, y1_data, s=10, label="Data 1", c="b", alpha = 0.6)
ax.set_title('Single scatter plot', fontsize = 20) # Set plot title and fontsize
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("$F(\theta)$ (a.u.)", fontsize = 16) # idem for y axis
ax.legend() 

And we can plot the squared components of two GOE arrays eigenvectors as a bar plot. In this case we fix the figure width and height using the figsize option in subplots (default units are inches, you can change to cm using a conversion factor cm = 1/2.54).

x = np.diag(GOE_arr)  # Using the diagonal GOE_arr values as an index
width = 0.11  # bars width

fig, ax = plt.subplots(figsize=(9,5))
rects1 = ax.bar(x - width/2, avec_GOE[:,0]**2, width, label="G.S.")
rects2 = ax.bar(x + width/2, avec_GOE[:,6]**2, width, label='6th exc. state')

# Add text for labels, title etc.
ax.set_ylabel('Squared Eigenvector Components')
ax.set_xlabel('GOE diagonal value')
ax.set_title('Diagonal value of the basis state in the GOE matrix')
ax.legend()

You can also include insets into the plot. A simple way is declaring a new axis in the figure, you can provide in unitless percentages of the figure size the position of the new axis -(0,0 is bottom left)- and the width and height of the inset.

x_data = np.linspace(0,3*np.pi,700)
y_data = ((np.sin(6*x_data**2-x_data**0.5)+2)*np.exp(-x_data/2))**2

fig, ax = plt.subplots(figsize=(9,9))
ax.plot(x_data, y_data, label="$[sin{(6\\theta^2-\sqrt{\\theta})}+2]^2e^{-\\theta}$")
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 20) # Set x axis label and fontsize
ax.set_ylabel("$F(\\theta)$ (a.u.)", fontsize = 20)   # idem for y axis
ax.tick_params(axis='x', labelsize=16) # size of x axis tick labels
ax.tick_params(axis='y', labelsize=16) # idem for y axis
# 
left, bottom, width, height = [0.55, 0.35, 0.25, 0.3]
ax_new = fig.add_axes([left, bottom, width, height])

ax_new.plot(x_data[:200], (np.sin(6*x_data[:200]**2-x_data[:200]**0.5)+2)**2 , color='green')
ax_new.tick_params(axis='x', labelsize=14) # size of x axis ticks
ax_new.tick_params(axis='y', labelsize=14) # idem for y axis

ax.legend(fontsize = 22, loc="upper right")

You can get a finer control using the inset_axes function

from mpl_toolkits.axes_grid1.inset_locator import inset_axes
#
x_data = np.linspace(0,3*np.pi,700)
y_data = ((np.sin(6*x_data**2-x_data**0.5)+2)*np.exp(-x_data/2))**2

fig, ax = plt.subplots(figsize=(9,9))
ax.plot(x_data, y_data, label="$[sin{(6\\theta^2-\sqrt{\\theta})}+2]^2e^{-\\theta}$")
#ax.set_title('Single plot, several curves', fontsize = 20) # Set plot title and fontsize
ax.set_xlabel("Angle $\\theta$ (rad)", fontsize = 20) # Set x axis label and fontsize
ax.set_ylabel("$F(\\theta)$ (a.u.)", fontsize = 20)   # idem for y axis
ax.tick_params(axis='x', labelsize=16) # size of x axis ticks
ax.tick_params(axis='y', labelsize=16) # idem for y axis
axins = inset_axes(ax, width="30%", height="40%", loc=1, borderpad = 2)
axins.plot(x_data, np.log(y_data))
axins.set_xlim(0,3)  # Setting the x coordinate range in the inset
axins.set_ylim(-3,2) # Setting the y coordinate range in the inset
axins.set_ylabel("$\\log(F(\\theta))$ (a.u.)",fontsize = 12)
axins.tick_params(axis='x', labelsize=14) # size of x axis ticks
axins.tick_params(axis='y', labelsize=14) # idem for y axis
ax.legend(fontsize = 22, bbox_to_anchor=(0.3,0.43)) # another way of locating the legend

1.4.1 Subplots

If we need to add several subplots we can do it as we did in Lesson 2, but we can also make use of loops to automatize the task. Imagine that we need to plot the previous function np.cos(x_data**A)/np.cosh(x_data/B) for (A,B) = {(1,2),(1,5),(2,2),(2,5),(3,2),(3,5)}. We can use subplots as follows

x_data = np.linspace(0,2*np.pi,500)
#
A_parameter = [1,2,3]
A_index = list(range(0,3))
#
B_parameter = [2,5]
B_index = list(range(0,2))
#
fig, ax = plt.subplots(3,2,figsize=(9,7))
fig.suptitle("Title centered above subplots", fontsize=18)
#
for (A_value, A_i) in zip(A_parameter,A_index):
    for (B_value, B_j) in zip(B_parameter, B_index):
        #
        y_data = np.cos(x_data**A_value)/np.cosh(x_data/B_value)
        ax[A_i,B_j].plot(x_data, y_data, label="A = {0}, B = {1}".format(A_value, B_value))
        ax[A_i,B_j].set_xlabel("Angle $\\theta$ (rad)", fontsize = 14) # Set x axis label and fontsize
        ax[A_i,B_j].set_ylabel("F(w) (a.u.)", fontsize = 14) # idem for y axis
        ax[A_i,B_j].legend()
#
fig.tight_layout(pad=3.0) # Control the extra padding around the figure border and between subplots. The pads are specified in fraction of fontsize.

You can also plot several lines in each subplot

x_data = np.linspace(0,2*np.pi,500)
#
A_parameter = [1,2,3]
A_index = list(range(0,3))
#
B_parameter = [2,5]
B_index = list(range(0,2))
#
fig, ax = plt.subplots(3,2,figsize=(9,7))
#
for (A_value, A_i) in zip(A_parameter,A_index):
    for (B_value, B_j) in zip(B_parameter, B_index):
        y_data = np.cos(x_data**A_value)/np.cosh(x_data/B_value)
        y_data = np.vstack((y_data,np.sin(x_data**A_value)*np.tanh(x_data/B_value)))
        ax[A_i,B_j].plot(x_data, y_data.T, label="A = {0}, B = {1}".format(A_value, B_value))
        ax[A_i,B_j].set_xlabel("Angle $\\theta$ (rad)", fontsize = 14) # Set x axis label and fontsize
        ax[A_i,B_j].set_ylabel("F(w) (a.u.)", fontsize = 14) # idem for y axis
        ax[A_i,B_j].legend()
#
fig.tight_layout(pad=3.0)
fig.suptitle("Title centered above subplots", fontsize=18)

As all the panels share the same axis scaling you can only add ticks to the outer panels

x_data = np.linspace(0,2*np.pi,500)
#
A_parameter = [1,2,3]
A_index = list(range(0,3))
#
B_parameter = [1,2]
B_index = list(range(0,2))
#
fig, ax = plt.subplots(3,2,figsize=(9,7),sharex=True, sharey=True)
#
for (A_value, A_i) in zip(A_parameter,A_index):
    for (B_value, B_j) in zip(B_parameter, B_index):
        y_data = np.cos(x_data**A_value)/np.cosh(x_data/B_value)
        ax[A_i,B_j].plot(x_data, y_data, label="A = {0}, B = {1}".format(A_value, B_value))
        if A_i == 2:
            ax[A_i,B_j].set_xlabel("Angle $\\theta$ (rad)", fontsize = 14) # Set x axis label and fontsize
        if B_j == 0:
            ax[A_i,B_j].set_ylabel("F(w) (a.u.)", fontsize = 14) # idem for y axis
        ax[A_i,B_j].legend()
#
fig.tight_layout(pad=1)
fig.suptitle("Title centered above subplots", fontsize=18, y=1.020)

1.4.2 Histograms

To generate 1D histograms a data vector is needed. We create one with the eigenvalues of a GOE array. We can create the array using a randn, a convenience function for users porting Matlab code

np.random.seed(123454321)
GOE_dim  = 2000
GOE_arr_old = np.random.randn(GOE_dim, GOE_dim)
GOE_arr_old += GOE_arr.T
aval_GOE_old = np.linalg.eigvalsh(GOE_arr)
from numpy.random import default_rng
rng = default_rng()
GOE_arr = rng.standard_normal((GOE_dim, GOE_dim))
GOE_arr += GOE_arr.T
aval_GOE = np.linalg.eigvalsh(GOE_arr)

We can then plot the histogram, taking into account that the hist method returns as an output the number associated to each bin, the bins, and a set of patches that allows to operate on the histogram. In the left panel we display the absolute histogram while in the right one we normalize by the total number of counts and display a percentage.

n_bins = 51
fig, ax = plt.subplots(tight_layout=True)
bins_result_old = ax.hist(aval_GOE_old, bins=n_bins)
bins_result = ax.hist(aval_GOE, bins=n_bins)

You can combine a histogram with a plot. Let’s plot the value of the theoretical GOE level density (a semicircle). Let’s first compute it

sigma_nd = 2     # variance of non-diagonal GOE matrix elements
A_value = 1/(4*sigma_nd)
sqrd_a_value = GOE_dim/A_value

We now make use of the information about the bins in the output of hist.

n_bins = 71
fig, ax = plt.subplots(tight_layout=True)
bins_result = ax.hist(aval_GOE, bins=n_bins, density=True)
#
GOE_density = np.sqrt(sqrd_a_value-bins_result[1][1:]**2)/(np.pi*sqrd_a_value/2)
#
ax.plot(bins_result[1][1:], GOE_density)

To plot a 2D histogram, one only needs two data vectors of the same length, corresponding to each axis of the histogram.

x = np.random.normal(3, 1, 200)
y = np.random.normal(4, 0.1, 200)

It is not mandatory, but one can also define the plot bins

### Bin Edges
xedges = [0, 1, 3, 5, 7, 9, 11]
yedges = [0, 2, 3, 4, 6, 8]

The histogram is computed as

H, xedges, yedges = np.histogram2d(x, y, bins=(xedges, yedges))
# Histogram does not follow Cartesian convention (see Matplotlib Notes),
H = H.T

And it can be depicted using imshow or meshgrid

fig = plt.figure(figsize=(7, 3))
ax = fig.add_subplot(121, title='imshow: square bins')
plt.imshow(H, interpolation='nearest', origin='lower',
        extent=[xedges[0], xedges[-1], yedges[0], yedges[-1]])
##
ax = fig.add_subplot(122, title='pcolormesh: actual edges',
        aspect='equal')
X, Y = np.meshgrid(xedges, yedges)
ax.pcolormesh(X, Y, H)

plt.show()

1.4.3 Saving your figures

You should save a script to easily recreate any of your figures, but you can also save them in a graphic format. The available formats depend on your Python distribution. To know them run

fig = plt.gcf()
fig.canvas.get_supported_filetypes()

To save a figure you can issue the command

plt.savefig("figure_name.extension")

If you want to further modify the figure in a program as inkscape or xfig you can save the figure as svg file -vector graphics- but in this case, when you import the matplotlib library, you should run the following statement

from matplotlib import rcParams 
rcParams['svg.fonttype'] = 'none'

And now you can save the figure of your interest

rcParams['svg.fonttype'] = 'none'
#
x_data = np.linspace(0,2*np.pi,500)
#
A_parameter = [1,2,3]
A_index = list(range(0,3))
#
B_parameter = [1,2]
B_index = list(range(0,2))
#
fig, ax = plt.subplots(3,2,figsize=(10,7),sharex=True, sharey=True, linewidth=3.0)
#
for (A_value, A_i) in zip(A_parameter,A_index):
    for (B_value, B_j) in zip(B_parameter, B_index):
        y_data = np.cos(x_data**A_value)/np.cosh(x_data/B_value)
        ax[A_i,B_j].plot(x_data, y_data, label="A = {0}, B = {1}".format(A_value, B_value))
        if A_i == 2:
            ax[A_i,B_j].set_xlabel("Angle $\\theta$ (rad)", fontsize = 14) # Set x axis label and fontsize
        if B_j == 0:
            ax[A_i,B_j].set_ylabel("F(w) (a.u.)", fontsize = 14) # idem for y axis
        ax[A_i,B_j].legend()
#
fig.tight_layout()
fig.suptitle("Title centered above subplots", fontsize=18, y=1.020)
plt.savefig("test.svg")
plt.savefig("test.pdf",facecolor="r",edgecolor="g",bbox_inches="tight")

The savefig command accepts some options that are quite useful:

dpi
Figure resolution in dots-per-inch. Default value is 100.
facecolor
Color of the background. Default value w, white.
edgecolor
Color of the figure edge line. Default value w, white. Notice that in this case the figure linewidth option needs to be set to a value different from the null default one.
bboxinches
Portion of the figure saved. The value trim attempts to trim empty white space around the figure.

Some of these options are used in the second savefig command in the previous example.

Exercise 5.4 The aim of this exercise is to generate a set of two-dimensional random walks, plot their trajectories and look and the end point distribution. The random walks considered always begin at the origin and take Nstep random steps of unit or zero size in both directions in the x and y axis. For a total number of Nw walks:
  1. Compute the trajectories and save the final point of all of them.
  2. Plot a sample of these random walks in the plane.
  3. Plot all the final points together.
  4. Compute the average distance of the final points from the origin.
  5. Plot a histogram with the values of the distance to the origin.
Exercise 5.5 The Julia set is an important concept in fractal theory. Given a complex number a, a point z in the complex plane is said to be in the filled-in Julia set of a function f(z) = z² + a if the iteration of the function over the point does not finish with the point going to infinity. It can be proved that, if at some iterate of a point under f(z) the result has a module larger than 2 and larger than the module of a, this point will finish going to infinity. Build and plot the filled-in Julia sets for f(z) with a = (-0.5,0),(0.25,-0.52), (-1,0), (-0.2, 0.66) in the interval of -1 < Re(z), Im(z) < 1 and consider that the point belongs to the set once the previous condition has not been accomplished after Niter = 100. Hint: You can make use of the NumPy meshgrid and the PyPlot pplot functions for displaying the filled-in Julia sets.

1.5 Optimizing and function fitting with SciPy.

The ScyPy library provides many user-friendly and efficient numerical routines, such as routines for numerical integration, interpolation, optimization, linear algebra, and statistics. In this course we will only very briefly explain how to use it to perform linear and non-ĺinear data fittings. You can find more information about this useful library in its documentation.

In a linear fit case you should import the Scipy module stats.

from scipy import stats

We consider that we have a data set that we suspect it follows the functional law f(N) = a*N**b. Let’s first prepare our dataset and add to it a normal error.

# Prepare Data assumint a power law f(N) = a*N**b
a_theor = 5.05
b_theor = -1.25
N_values = np.array(range(500,10600,500))
f_values = a_theor*N_values**b_theor
f_errors = np.array(list(map(lambda x:np.random.normal(x,np.abs(x)/20), f_values)))

The dependence is not linear but we can transform it into a linear dependence taking logarithm of both abscyssa and ordinate values

x_data = np.log10(N_values)
y_data = np.log10(f_errors)
result = stats.linregress(x_data, y=y_data)
result

The obtained result provides the straight line slope and intercept values, the correlation coefficient (rvalue), the p-value of the fit, and the coefficient errors. We can depict the data plus errors and the best fit line

fig, ax = plt.subplots()
ax.plot(x_data, y_data, label="Reference values", linestyle="-", color="xkcd:olive", lw=1.0, marker = "o", markevery=1, markersize=2)
ax.plot(x_data, result.slope*x_data + result.intercept, label="log-log linear fit", linestyle="-.", color="xkcd:red", lw=1.0, alpha = 0.76)
ax.set_xlabel("$log(N)$", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("$log[f(N)]$", fontsize = 16) # idem for y axis
ax.legend()

In case you cannot linearize your function dependence, as in the next example, you import the optimize module.

from scipy import optimize

We now prepare our dataset and add again a random normal error.

# Prepare Data assumint a function g(x) = a + b*x + c/x**d
a_theor = 1.05
b_theor = 1.25
c_theor = -2.5
d_theor = 2
x_values = np.arange(0.5,12,0.25)
f_values = a_theor+ b_theor * x_values + c_theor/(x_values**d_theor)
f_errors = np.array(list(map(lambda x:np.random.normal(x,np.abs(x)/20), f_values)))

You now define the function that will be used to perform the nonlinear fit

def f_fit(x, a, b, c, d):
    '''    
    a + b*x + c*x**-d 
    '''
    return a + b*x + c/x**d

And the fit can be performed now as follows

params, pcov = optimize.curve_fit(f_fit,x_values,f_errors, p0=(0.5,0.7,-0.9,3)) #, method='trf')
parerr = np.sqrt(np.diag(pcov))
params, parerr

The array pcov is the covariance matrix and therefore the parerr vector is the vector that contains the error of the obtained parameters. We can plot the original values and the resulting optimized function.

fig, ax = plt.subplots()
ax.plot(x_values, f_errors, label="Reference values", linestyle="-", color="xkcd:olive", lw=1.0, marker = "o", markevery=1, markersize=2)
ax.plot(x_values, f_fit(x_values, *params) , label="nonlinear fit", linestyle="-.", color="xkcd:red", lw=1.0, alpha = 0.76)
ax.set_xlabel("$x$", fontsize = 16) # Set x axis label and fontsize
ax.set_ylabel("$f(x)$", fontsize = 16) # idem for y axis
ax.legend()

1.6 Exercises

Exercise 5.1
Code a function that reads a given ASCII filename and encrypts or decrypts its content using the Caesar’s algorithm from Exercise 4.2. A keyword parameter should indicate whether the file is going to be encrypted or decrypted, and the result should be saved in a new file and shown in the standard output if the user wishes so.
Exercise 5.2
Define and test a function that estimates the value of the special constant pi by generating N pairs of random numbers in the interval -1 and 1 and checking how many of the generated number fall into a circumference of radius 1 centered in the origin. Improve the function showing in a graphical output the square, the circumference, and the points inside and outside the circumference with different colors.
Exercise 5.3
The NIST Digital Library of Mathematical Functions (DLMF) is a very useful site, where you can find an updated and expanded version of the well-known reference Handbook of Mathematical Functions compiled by Abramowitz and Stegun. Define a function to compute the Bessel function of the first kind of integer index from the series 10.2.2 in the DLMF, add a docscript and plot the functions of order 0, 1, and 2 in the interval of x between 0 and 10.
Exercise 5.4
The aim of this exercise is to generate a set of two-dimensional random walks, plot their trajectories and look and the end point distribution. The random walks considered always begin at the origin and take Nstep random steps of unit or zero size in both directions in the x and y axes. For a total number of Nw walks:
  1. Compute the trajectories and save the final point of all of them.
  2. Plot a sample of these random walks in the plane.
  3. Plot all the final points together.
  4. Compute the average distance of the final points from the origin.
  5. Plot a histogram with the values of the distance to the origin.
Exercise 5.5
The Julia set is an important concept in fractal theory. Given a complex number a, a point z in the complex plane is said to be in the filled-in Julia set of a function f(z) = z² + a if the iteration of the function over the point does not finish with the point going to infinity. It can be proved that, if at some iterate of a point under f(z) the result has a module larger than 2 and larger than the module of a, this point will finish going to infinity. Build and plot the filled-in Julia sets for f(z) with a = (-0.5,0),(0.25,-0.52), (-1,0), (-0.2, 0.66) in the interval of -1 < Re(z), Im(z) < 1 and consider that the point belongs to the set once the previous condition has not been accomplished after Niter = 100. Hint: You can make use of the NumPy meshgrid and the PyPlot pplot functions for displaying the filled-in Julia sets.

Author: Curro Pérez Bernal

Created: 2022-08-28 Sun 23:16

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