CoCalc -- 0912387498757918.ipynb

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ubuntu2004

Kernel: Python 3 (system-wide)

In [2]:

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.image as mpimg # import the image module

A = mpimg.imread("bw.png") # read the image into an array A
A = np.mean(A, axis=2)

print(np.round(A, 2)) # print x, rounding to 2 d.p.

Out[2]:

[[0.27 0.35 0.27 0.37 0.31 0.25 0.29 0.29]
 [0.37 0.46 0.51 0.53 0.45 0.31 0.3  0.28]
 [0.45 0.6  0.75 0.8  0.57 0.43 0.34 0.31]
 [0.46 0.76 0.9  0.89 0.82 0.45 0.32 0.34]
 [0.51 0.79 0.9  0.92 0.75 0.49 0.43 0.29]
 [0.44 0.56 0.75 0.76 0.59 0.56 0.62 0.42]
 [0.36 0.48 0.49 0.47 0.45 0.61 1.   0.56]
 [0.28 0.34 0.31 0.26 0.31 0.4  0.49 0.37]]

In [3]:

print(A.shape)

Out[3]:

(8, 8)

In [11]:

import scipy.ndimage as sn # import the scipy.ndimage package

# Label the connected components (blobs) of binary image A_threshold
A_labels, n = sn.label(A_threshold) 
print("number of blobs:", n)

# Count the number of pixels in each blob and return as array "sizes"
sizes = sn.sum(A_threshold, A_labels, range(1, n+1))
print("sizes:", sizes)

# Get the index of the largest value in sizes (corresponding to the largest blob)
idx = np.argmax(sizes) 
print("index:", idx)

# Determine the co-ordinates of the largest blob (returned as row, column indices)
y_pos, x_pos = sn.center_of_mass(A_threshold, A_labels, idx + 1) 
print("co-ordinates of largest blob:", x_pos, y_pos)

Out[11]:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/tmp/ipykernel_846/1674472634.py in <module>
      2 
      3 # Label the connected components (blobs) of binary image A_threshold
----> 4 A_labels, n = sn.label(A_threshold)
      5 print("number of blobs:", n)
      6 
NameError: name 'A_threshold' is not defined

In [12]:

plt.imshow(A) # show the original image
plt.scatter(x_pos, y_pos, color="black", marker="x", s=200)

Out[12]:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/tmp/ipykernel_846/3753039670.py in <module>
----> 1 plt.imshow(A) # show the original image
      2 plt.scatter(x_pos, y_pos, color="black", marker="x", s=200)
NameError: name 'plt' is not defined

In [0]:

def largest_blob_coords(image, thresh):
    # Threshold the image
    bw = (image > thresh).astype(int)
    # Label the blobs
    labels, n = sn.label(bw)
    
    # Remaining code ...
    
    return x_pos, y_pos

In [13]:

num_frames = 20

# Create arrays for storing blob coordinates
x_pos_array = np.zeros(num_frames)
y_pos_array = np.zeros(num_frames)

for i in range(num_frames):
    
    f = data[i, y_min:y_max, x_min:x_max]
    
    # Add code to obtain the x and y coordinates of the largest particle in the current frame here
    # ...
    
    # Store the current coordinates in the corresponding position 
    x_pos_array[i] = x_pos
    y_pos_array[i] = y_pos

Out[13]:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/tmp/ipykernel_846/2136523447.py in <module>
      2 
      3 # Create arrays for storing blob coordinates
----> 4 x_pos_array = np.zeros(num_frames)
      5 y_pos_array = np.zeros(num_frames)
      6 
NameError: name 'np' is not defined

In [14]:

plt.figure(figsize=(5,5))
ax = plt.gca()
 
plt.plot(x_pos_array, y_pos_array)
plt.xlim(0, x_max-x_min)
plt.ylim(0, y_max-y_min)

ax.invert_yaxis()
ax.set_aspect('equal')

Out[14]:

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
/tmp/ipykernel_846/4140317672.py in <module>
----> 1 plt.figure(figsize=(5,5))
      2 ax = plt.gca()
      3 
      4 plt.plot(x_pos_array, y_pos_array)
      5 plt.xlim(0, x_max-x_min)
NameError: name 'plt' is not defined

In [0]:

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