Drawing and Bitwise Operations
OverviewTeaching: 45 min
Exercises: 45 minQuestions
How can we draw on skimage images and use bitwise operations and masks to select certain parts of an image?Objectives
Create a blank, black skimage image.
Draw rectangles and other shapes on skimage images.
Explain how a white shape on a black background can be used as a mask to select specific parts of an image.
Use bitwise operations to apply a mask to an image.
The next series of episodes covers a basic toolkit of skimage operators. With these tools, we will be able to create programs to perform simple analyses of images based on changes in colour or shape.
Drawing on images
Often we wish to select only a portion of an image to analyze, and ignore the rest. Creating a rectangular sub-image with slicing, as we did in the Image Representation in skimage episode is one option for simple cases. Another option is to create another special image, of the same size as the original, with white pixels indicating the region to save and black pixels everywhere else. Such an image is called a mask. In preparing a mask, we sometimes need to be able to draw a shape - a circle or a rectangle, say - on a black image. skimage provides tools to do that.
Consider this image of maize seedlings:
Now, suppose we want to analyze only the area of the image containing the roots themselves; we do not care to look at the kernels, or anything else about the plants. Further, we wish to exclude the frame of the container holding the seedlings as well. Hovering over the image with our mouse, could tell us that the upper-left coordinate of the sub-area we are interested in is (44, 357), while the lower-right coordinate is (720, 740). These coordinates are shown in (x, y) order.
A Python program to create a mask to select only that area of the image would start with a now-familiar section of code to open and display the original image:
import imageio.v3 as iio import skimage.draw import numpy as np import matplotlib.pyplot as plt %matplotlib widget # Load and display the original image image = iio.imread(uri="data/maize-seedlings.tif") fig, ax = plt.subplots() plt.imshow(image)
As before, we first import the
v3 submodule of
We also import the NumPy library, which we need to create the initial mask
Then, we import the
draw submodule of
We load and display the initial image in the same way we have done before.
NumPy allows indexing of images/arrays with “boolean” arrays of the same size.
Indexing with a boolean array is also called mask indexing.
The “pixels” in such a mask array can only take two values:
When indexing an image with such a mask,
only pixel values at positions where the mask is
True are accessed.
But first, we need to generate a mask array of the same size as the image.
Luckily, the NumPy library provides a function to create just such an array.
The next section of code shows how:
# Create the basic mask mask = np.ones(shape=image.shape[0:2], dtype="bool")
The first argument to the
ones() function is the shape of the original image,
so that our mask will be exactly the same size as the original.
Notice, that we have only used the first two indices of our shape.
We omitted the channel dimension.
Indexing with such a mask will change all channel values simultaneously.
The second argument,
dtype = "bool",
indicates that the elements in the array should be booleans -
i.e., values are either
Thus, even though we use
np.ones() to create the mask,
its pixel values are in fact not
You could check this, e.g., by
Next, we draw a filled, rectangle on the mask:
# Draw filled rectangle on the mask image rr, cc = skimage.draw.rectangle(start=(357, 44), end=(740, 720)) mask[rr, cc] = False # Display mask image fig, ax = plt.subplots() plt.imshow(mask, cmap="gray")
Here is what our constructed mask looks like:
The parameters of the
(357, 44) and
are the coordinates of the upper-left (
start) and lower-right (
of a rectangle in (ry, cx) order.
The function returns the rectangle as row (
rr) and column (
cc) coordinate arrays.
Check the documentation!
When using an skimage function for the first time - or the fifth time - it is wise to check how the function is used, via the skimage documentation or other usage examples on programming-related sites such as Stack Overflow. Basic information about skimage functions can be found interactively in Python, via commands like
help(skimage.draw.rectangle). Take notes in your lab notebook. And, it is always wise to run some test code to verify that the functions your program uses are behaving in the manner you intend.
Variable naming conventions!
You may have wondered why we called the return values of the rectangle function
cc?! You may have guessed that
ris short for
cis short for
column. However, the rectangle function returns mutiple rows and columns; thus we used a convention of doubling the letter
cc) to indicate that those are multiple values. In fact it may have even been clearer to name those variables
columns; however this would have been also much longer. Whatever you decide to do, try to stick to some already existing conventions, such that it is easier for other people to understand your code.
Other drawing operations (15 min)
There are other functions for drawing on images, in addition to the
skimage.draw.rectangle()function. We can draw circles, lines, text, and other shapes as well. These drawing functions may be useful later on, to help annotate images that our programs produce. Practice some of these functions here.
Circles can be drawn with the
skimage.draw.disk()function, which takes two parameters: the (ry, cx) point of the centre of the circle, and the radius of the circle. There is an optional
shapeparameter that can be supplied to this function. It will limit the output coordinates for cases where the circle dimensions exceed the ones of the image.
Lines can be drawn with the
skimage.draw.line()function, which takes four parameters: the (ry, cx) coordinate of one end of the line, and the (ry, cx) coordinate of the other end of the line.
Other drawing functions supported by skimage can be found in the skimage reference pages.
First let’s make an empty, black image with a size of 800x600 pixels:
# create the black canvas image = np.zeros(shape=(600, 800, 3), dtype="uint8")
Now your task is to draw some other coloured shapes and lines on the image, perhaps something like this:
Drawing a circle:
# Draw a blue circle with centre (200, 300) in (ry, cx) coordinates, and radius 100 rr, cc = skimage.draw.disk(center=(200, 300), radius=100, shape=image.shape[0:2]) image[rr, cc] = (0, 0, 255)
Drawing a line:
# Draw a green line from (400, 200) to (500, 700) in (ry, cx) coordinates rr, cc = skimage.draw.line(r0=400, c0=200, r1=500, c1=700) image[rr, cc] = (0, 255, 0)
# Display the image fig, ax = plt.subplots() plt.imshow(image)
We could expand this solution, if we wanted, to draw rectangles, circles and lines at random positions within our black canvas. To do this, we could use the
randompython module, and the function
random.randrange, which can produce random numbers within a certain range.
Let’s draw 15 randomly placed circles:
import random # create the black canvas image = np.zeros(shape=(600, 800, 3), dtype="uint8") # draw a blue circle at a random location 15 times for i in range(15): rr, cc = skimage.draw.disk(center=( random.randrange(600), random.randrange(800)), radius=50, shape=image.shape[0:2], ) image[rr, cc] = (0, 0, 255) # display the results fig, ax = plt.subplots() plt.imshow(image)
We could expand this even further to also randomly choose whether to plot a rectangle, a circle, or a square. Again, we do this with the
randommodule, now using the function
random.randomthat returns a random number between 0.0 and 1.0.
import random # Draw 15 random shapes (rectangle, circle or line) at random positions for i in range(15): # generate a random number between 0.0 and 1.0 and use this to decide if we # want a circle, a line or a sphere x = random.random() if x < 0.33: # draw a blue circle at a random location rr, cc = skimage.draw.disk(center=( random.randrange(600), random.randrange(800)), radius=50, shape=image.shape[0:2], ) color = (0, 0, 255) elif x < 0.66: # draw a green line at a random location rr, cc = skimage.draw.line( r0=random.randrange(600), c0=random.randrange(800), r1=random.randrange(600), c1=random.randrange(800), ) color = (0, 255, 0) else: # draw a red rectangle at a random location rr, cc = skimage.draw.rectangle( start=(random.randrange(600), random.randrange(800)), extent=(50, 50), shape=image.shape[0:2], ) color = (255, 0, 0) image[rr, cc] = color # display the results fig, ax = plt.subplots() plt.imshow(image)
All that remains is the task of modifying the image using our mask in such a
way that the areas with
True pixels in the mask are not shown in the image
How does a mask work? (optional, not included in timing)
Now, consider the mask image we created above. The values of the mask that corresponds to the portion of the image we are interested in are all
False, while the values of the mask that corresponds to the portion of the image we want to remove are all
How do we change the original image using the mask?
When indexing the image using the mask, we access only those pixels at positions where the mask is
True. So, when indexing with the mask, one can set those values to 0, and effectively remove them from the image.
Now we can write a Python program to use a mask to retain only the portions of our maize roots image that actually contains the seedling roots. We load the original image and create the mask in the same way as before:
# Load the original image image = iio.imread(uri="data/maize-seedlings.tif") # Create the basic mask mask = np.ones(shape=image.shape[0:2], dtype="bool") # Draw a filled rectangle on the mask image rr, cc = skimage.draw.rectangle(start=(357, 44), end=(740, 720)) mask[rr, cc] = False
Then, we use numpy indexing to remove the portions of the image,
where the mask is
# Apply the mask image[mask] = 0
Then, we display the masked image.
fig, ax = plt.subplots() plt.imshow(image)
The resulting masked image should look like this:
Masking an image of your own (optional, not included in timing)
Now, it is your turn to practice. Using your mobile phone, tablet, webcam, or digital camera, take an image of an object with a simple overall geometric shape (think rectangular or circular). Copy that image to your computer, write some code to make a mask, and apply it to select the part of the image containing your object. For example, here is an image of a remote control:
And, here is the end result of a program masking out everything but the remote:
Here is a Python program to produce the cropped remote control image shown above. Of course, your program should be tailored to your image.
# Load the image image = iio.imread(uri="data/remote-control.jpg") # Create the basic mask mask = np.ones(shape=image.shape[0:2], dtype="bool") # Draw a filled rectangle on the mask image rr, cc = skimage.draw.rectangle(start=(93, 1107), end=(1821, 1668)) mask[rr, cc] = False # Apply the mask image[mask] = 0 # Display the result fig, ax = plt.subplots() plt.imshow(image)
Masking a 96-well plate image (30 min)
Consider this image of a 96-well plate that has been scanned on a flatbed scanner.
# Load the image image = iio.imread(uri="data/wellplate-01.jpg") # Display the image fig, ax = plt.subplots() plt.imshow(image)
Suppose that we are interested in the colours of the solutions in each of the wells. We do not care about the colour of the rest of the image, i.e., the plastic that makes up the well plate itself.
Your task is to write some code that will produce a mask that will mask out everything except for the wells. To help with this, you should use the text file
data/centers.txtthat contains the (cx, ry) coordinates of the centre of each of the 96 wells in this image. You may assume that each of the wells has a radius of 16 pixels.
Your program should produce output that looks like this:
# read in original image image = iio.imread(uri="data/wellplate-01.jpg") # create the mask image mask = np.ones(shape=image.shape[0:2], dtype="bool") # open and iterate through the centers file... with open("data/centers.txt", "r") as center_file: for line in center_file: # ... getting the coordinates of each well... coordinates = line.split() cx = int(coordinates) ry = int(coordinates) # ... and drawing a circle on the mask rr, cc = skimage.draw.disk(center=(ry, cx), radius=16, shape=image.shape[0:2]) mask[rr, cc] = False # apply the mask image[mask] = 0 # display the result fig, ax = plt.subplots() plt.imshow(image)
Masking a 96-well plate image, take two (optional, not included in timing)
If you spent some time looking at the contents of the
data/centers.txtfile from the previous challenge, you may have noticed that the centres of each well in the image are very regular. Assuming that the images are scanned in such a way that the wells are always in the same place, and that the image is perfectly oriented (i.e., it does not slant one way or another), we could produce our well plate mask without having to read in the coordinates of the centres of each well. Assume that the centre of the upper left well in the image is at location cx = 91 and ry = 108, and that there are 70 pixels between each centre in the cx dimension and 72 pixels between each centre in the ry dimension. Each well still has a radius of 16 pixels. Write a Python program that produces the same output image as in the previous challenge, but without having to read in the
centers.txtfile. Hint: use nested for loops.
Here is a Python program that is able to create the masked image without having to read in the
# read in original image image = iio.imread(uri="data/wellplate-01.jpg") # create the mask image mask = np.ones(shape=image.shape[0:2], dtype="bool") # upper left well coordinates cx0 = 91 ry0 = 108 # spaces between wells deltaCX = 70 deltaRY = 72 cx = cx0 ry = ry0 # iterate each row and column for row in range(12): # reset cx to leftmost well in the row cx = cx0 for col in range(8): # ... and drawing a circle on the mask rr, cc = skimage.draw.disk(center=(ry, cx), radius=16, shape=image.shape[0:2]) mask[rr, cc] = False cx += deltaCX # after one complete row, move to next row ry += deltaRY # apply the mask image[mask] = 0 # display the result fig, ax = plt.subplots() plt.imshow(image)
We can use the NumPy
zeros()function to create a blank, black image.
We can draw on skimage images with functions such as
skimage.draw.line(), and more.
The drawing functions return indices to pixels that can be set directly.