Develop Reference

Combining 3 channel numpy array to form an rgb image

I was trying to combine 3 gray scale images into a single overlapping image with three different colors for each.
For that, I added each into a 3 channel numpy array.
But when plotting with im.show I don't get a colourful image. Till adding 2nd channel it works, but when I add the third channel, it doesn't work. The final image has only red and blue colour.
It is supposed to be red, green and blue for corresponding to the overlapping images.
Why would it be?
image1 = Image.open("E:/imaging/04102022_Bronze/Copper_4_2/10.tif") #openingimage1
image1_norm =(np.array(image1)-np.array(image1).min() ) / (np.array(image1).max() -
np.array(image1).min()) #normalisingimage1
image2 = Image.open("E:/imaging/04102022_Bronze/Oxygen_1_2/10.tif")#openingimage2
image2_norm = (np.array(image2)-np.array(image2).min()) / (np.array(image2).max() -
np.array(image2).min())#normalisingimage2
image3 = Image.open("E:/imaging/04102022_Bronze/Oxygen_1_2/10.tif")#openingimage3
image3_norm = (np.array(image3)-np.array(image3).min()) / (np.array(image3).max() -
np.array(image3).min())#normalisingimage3
im=np.array(image2)
new_image = np.zeros(im.shape + (3,)) #creating an empty 3 channel numpy array .shape of this
array is (255, 1024, 3)
new_image[:,:,0] = image1_norm #adding the three images into three channels
new_image[:,:,1] = image2_norm
new_image[:,:,2] = image3_norm
new_image1=new_image*255.999
new_image2= new_image1.astype(np.uint8)
final_image=final_image=Image.fromarray(new_image2, mode='RGB')

A few possible issues...
When you open an image in PIL, if you want to be sure it is single-channel greyscale, and not accidentally 3-channel RGB, or a palette image, force it to greyscale:
im = Image.open('image.png').convert('L')
Try not to repeat complicated calculations or expressions several times - it just makes for a maintenance nightmare. Maybe use a function instead:
def normalize(im):
# Normalise image to range 0..1
min, max = im.min(), im.max()
return (im.astype(float)-min)/(max-min)
You can use Numpy's dstack() to merge channels - it means "depth"-stack, as opposed to np.vstack() which stacks images vertically above/below each other and np.hstack() which stacks images side-by-side horizontally. It is a lot simpler than creating an image of the right size and individually pushing each channel into it.
result = np.dstack((im1, im2, im3))
That would make the overall code more like this:
#!/usr/bin/env python3
from PIL import Image
import numpy as np
def normalize(im):
# Normalise image to range 0..1
min, max = im.min(), im.max()
return (im.astype(float)-min)/(max-min)
# Load images as single channel Numpy arrays
im1 = np.array(Image.open('ch1.png').convert('L'))
im2 = np.array(Image.open('ch2.png').convert('L'))
im3 = np.array(Image.open('ch3.png').convert('L'))
# Normalize and scale
n1 = normalize(im1) * 255.999
n2 = normalize(im2) * 255.999
n3 = normalize(im3) * 255.999
# Merge channels to RGB
result = np.dstack((n1,n2,n3))
result = Image.fromarray(result.astype(np.uint8))
result.save('result.png')
That makes these three input images:
into this merged image:

Using python to fill an image with one color in steps from 0% to 100%

I have a black image that I need to fill with a new color.
I want to generate new images starting from 1% to 100% (generating an
image for every 1% filled).
Examples for 4 fill-ratios
Heart image filled with 1%, 5%, 10% and 15%
Research I did
I did a lot of research on the internet and the closest I came was this link:
Fill an image with color but keep the alpha (Color overlay in PIL)
However, as I don't have much experience with Python for image editing, I couldn't move forward or modify the code as needed.
Edit:
I was trying with this code from the link
from PIL import Image
import numpy as np
# Open image
im = Image.open('2746646.png')
# Make into Numpy array
n = np.array(im)
# Set first three channels to red
n[..., 0:3] = [ 255, 0, 0 ]
# Convert back to PIL Image and save
Image.fromarray(n).save('result.png')
But it only generates a single image (as if it were 100%, I need 100 images with 1% filled in each one).

Updated Answer
Now you have shared your actual starting image, it seems you don't really want to replace black pixels, but actually opaque pixels. If you split your image into its constituent RGBA channels and lay them out left-to-right R,G,B then A, you can see you want to fill where the alpha (rightmost) channel is white, rather than where the RGB channels are black:
That changes the code to this:
#!/usr/bin/env python3
from PIL import Image
import numpy as np
# Load image, ensure not palettised, and make into Numpy array
im = Image.open('muscle.png').convert('RGBA')
# Make Numpy array
RGBA = np.array(im)
# Get RGB part
RGB = RGBA[..., :3]
# Get greyscale version of image as Numpy array
alpha = RGBA[..., 3]
# Find X,Y coordinates of all black pixels in image
blkY, blkX = np.where(alpha==255)
# Just take one entry per row, even if multiple black pixels in it
uniqueRows = np.unique(blkY)
# How many rows are there with black pixels in?
nUniqueRows = len(uniqueRows)
for percent in range(2,101):
# Work out filename based on percentage
filename = f'result-{percent:03d}.png'
# How many rows do we need to fill?
nRows = int(nUniqueRows * percent/100.0)
# Which rows are they? Negative index because filling bottom-up.
rows = uniqueRows[-nRows:]
print(f'DEBUG: filename: {filename}, percent: {percent}, nRows: {nRows}, rows: {rows}')
# What are the indices onto blkY, blkX ?
indices = np.argwhere(np.isin(blkY, rows))
# Make those pixels black
RGB[blkY[indices.ravel()], blkX[indices.ravel()], :3] = [0,255,0]
res = Image.fromarray(RGBA).save(filename)
Original Answer
That was fun! This seems to work - though it's not that efficient. It is not a true "floodfill", see note at end.
#!/usr/bin/env python3
from PIL import Image
import numpy as np
# Load image, ensure not palettised, and make into Numpy array
im = Image.open('heart.png').convert('RGB')
# Make Numpy array
na = np.array(im)
# Get greyscale version of image as Numpy array
grey = np.array(im.convert('L'))
# Find X,Y coordinates of all black pixels in image
blkY, blkX = np.where(grey==0)
# Just take one entry per row, even if multiple black pixels in it
uniqueRows = np.unique(blkY)
# How many rows are there with black pixels in?
nUniqueRows = len(uniqueRows)
for percent in range(1,101):
# Work out filename based on percentage
filename = f'result-{percent:03d}.png'
# How many rows do we need to fill?
nRows = int(nUniqueRows * percent/100.0)
# Which rows are they? Negative index because filling bottom-up.
rows = uniqueRows[-nRows:]
# print(f'DEBUG: filename: {filename}, percent: {percent}, nRows: {nRows}, rows: {rows}')
# What are the indices onto blkY, blkX ?
indices = np.argwhere(np.isin(blkY, rows))
# Make those pixels green
na[blkY[indices.ravel()], blkX[indices.ravel()], :] = [0,255,0]
res = Image.fromarray(na).save(filename)
Note that this isn't actually a true "flood fill" - it is more naïve than that - because it doesn't seem necessary for your image. If you add another shape, it will fill that too:

How to change the colour of pixels in an image depending on their initial luminosity?

The aim is to take a coloured image, and change any pixels within a certain luminosity range to black. For example, if luminosity is the average of a pixel's RGB values, any pixel with a value under 50 is changed to black.
I’ve attempted to begin using PIL and converting to grayscale, but having trouble trying to find a solution that can identify luminosity value and use that info to manipulate a pixel map.

There are many ways to do this, but the simplest and probably fastest is with Numpy, which you should get accustomed to using with image processing in Python:
from PIL import Image
import numpy as np
# Load image and ensure RGB, not palette image
im = Image.open('start.png').convert('RGB')
# Make into Numpy array
na = np.array(im)
# Make all pixels of "na" where the mean of the R,G,B channels is less than 50 into black (0)
na[np.mean(na, axis=-1)<50] = 0
# Convert back to PIL Image to save or display
result = Image.fromarray(na)
result.show()
That turns this:
Into this:
Another slightly different way would be to convert the image to a more conventional greyscale, rather than averaging for the luminosity:
# Load image and ensure RGB
im = Image.open('start.png').convert('RGB')
# Calculate greyscale version
grey = im.convert('L')
# Point process over pixels to make mask of darker ones
mask = grey.point(lambda p: 255 if p<50 else 0)
# Paste black (i.e. 0) into image where mask indicates it is dark
im.paste(0, mask=mask)
Notice that the blue channel is given considerably less significance in the ITU-R 601-2 luma transform that PIL uses (see the lower 114 weighting for Blue versus 299 for Red and 587 for Green) in the formula:
L = R * 299/1000 + G * 587/1000 + B * 114/1000
so the blue shades are considered darker and become black.
Another way would be to make a greyscale and a mask as above. but then choose the darker pixel at each location when comparing the original and the mask:
from PIL import Image, ImageChops
im = Image.open('start.png').convert('RGB')
grey = im.convert('L')
mask = grey.point(lambda p: 0 if p<50 else 255)
res = ImageChops.darker(im, mask.convert('RGB'))
That gives the same result as above.
Another way, pure PIL and probably closest to what you actually asked, would be to derive a luminosity value by averaging the channels:
# Load image and ensure RGB
im = Image.open('start.png').convert('RGB')
# Calculate greyscale version by averaging R,G and B
grey = im.convert('L', matrix=(0.333, 0.333, 0.333, 0))
# Point process over pixels to make mask of darker ones
mask = grey.point(lambda p: 255 if p<50 else 0)
# Paste black (i.e. 0) into image where mask indicates it is dark
im.paste(0, mask=mask)
Another approach could be to split the image into its constituent RGB channels, evaluate a mathematical function over the channels and mask with the result:
from PIL import Image, ImageMath
# Load image and ensure RGB
im = Image.open('start.png').convert('RGB')
# Split into RGB channels
(R, G, B) = im.split()
# Evaluate mathematical function over channels
dark = ImageMath.eval('(((R+G+B)/3) <= 50) * 255', R=R, G=G, B=B)
# Paste black (i.e. 0) into image where mask indicates it is dark
im.paste(0, mask=dark)

I created a function that returns a list with True if the pixel has a luminosity of less than a parameter, and False if it doesn't. It includes an RGB or RGBA option (True or False)
def get_avg_lum(pic,avg=50,RGBA=False):
num=3
numd=4
if RGBA==False:
num=2
numd=3
li=[[[0]for y in range(0,pic.size[1])] for x in range(0,pic.size[0])]
for x in range(0,pic.size[0]):
for y in range(0,pic.size[1]):
if sum(pic.getpixel((x,y))[:num])/numd<avg:
li[x][y]=True
else:
li[x][y]=False
return(li)
a=get_avg_lum(im)
The pixels match in the list, so (0,10) on the image is [0][10] in the list.
Hopefully this helps. My module is for standard PIL objects.

Python 3: I am trying to find find all green pixels in an image by traversing all pixels using an np.array, but can't get around index error

My code currently consists of loading the image, which is successful and I don't believe has any connection to the problem.
Then I go on to transform the color image into a np.array named rgb
# convert image into array
rgb = np.array(img)
red = rgb[:,:,0]
green = rgb[:,:,1]
blue = rgb[:,:,2]
To double check my understanding of this array, in case that may be the root of the issue, it is an array such that rgb[x-coordinate, y-coordinate, color band] which holds the value between 0-255 of either red, green or blue.
Then, my idea was to make a nested for loop to traverse all pixels of my image (620px,400px) and sort them based on the ratio of green to blue and red in an attempt to single out the greener pixels and set all others to black or 0.
for i in range(xsize):
for j in range(ysize):
color = rgb[i,j] <-- Index error occurs here
if(color[0] > 128):
if(color[1] < 128):
if(color[2] > 128):
rgb[i,j] = [0,0,0]
The error I am receiving when trying to run this is as follows:
IndexError: index 400 is out of bounds for axis 0 with size 400
I thought it may have something to do with the bounds I was giving i and j so I tried only sorting through a small inner portion of the image but still got the same error. At this point I am lost as to what is even the root of the error let alone even the solution.

In direct answer to your question, the y axis is given first in numpy arrays, followed by the x axis, so interchange your indices.
Less directly, you will find that for loops are very slow in Python and you are generally better off using numpy vectorised operations instead. Also, you will often find it easier to find shades of green in HSV colourspace.
Let's start with an HSL colour wheel:
and assume you want to make all the greens into black. So, from that Wikipedia page, the Hue corresponding to Green is 120 degrees, which means you could do this:
#!/usr/local/bin/python3
import numpy as np
from PIL import Image
# Open image and make RGB and HSV versions
RGBim = Image.open("image.png").convert('RGB')
HSVim = RGBim.convert('HSV')
# Make numpy versions
RGBna = np.array(RGBim)
HSVna = np.array(HSVim)
# Extract Hue
H = HSVna[:,:,0]
# Find all green pixels, i.e. where 100 < Hue < 140
lo,hi = 100,140
# Rescale to 0-255, rather than 0-360 because we are using uint8
lo = int((lo * 255) / 360)
hi = int((hi * 255) / 360)
green = np.where((H>lo) & (H<hi))
# Make all green pixels black in original image
RGBna[green] = [0,0,0]
count = green[0].size
print("Pixels matched: {}".format(count))
Image.fromarray(RGBna).save('result.png')
Which gives:
Here is a slightly improved version that retains the alpha/transparency, and matches red pixels for extra fun:
#!/usr/local/bin/python3
import numpy as np
from PIL import Image
# Open image and make RGB and HSV versions
im = Image.open("image.png")
# Save Alpha if present, then remove
if 'A' in im.getbands():
savedAlpha = im.getchannel('A')
im = im.convert('RGB')
# Make HSV version
HSVim = im.convert('HSV')
# Make numpy versions
RGBna = np.array(im)
HSVna = np.array(HSVim)
# Extract Hue
H = HSVna[:,:,0]
# Find all red pixels, i.e. where 340 < Hue < 20
lo,hi = 340,20
# Rescale to 0-255, rather than 0-360 because we are using uint8
lo = int((lo * 255) / 360)
hi = int((hi * 255) / 360)
red = np.where((H>lo) | (H<hi))
# Make all red pixels black in original image
RGBna[red] = [0,0,0]
count = red[0].size
print("Pixels matched: {}".format(count))
result=Image.fromarray(RGBna)
# Replace Alpha if originally present
if savedAlpha is not None:
result.putalpha(savedAlpha)
result.save('result.png')
Keywords: Image processing, PIL, Pillow, Hue Saturation Value, HSV, HSL, color ranges, colour ranges, range, prime.

Create a steganographically hidden image with Pillow

I'm trying to learn how to create a set of images like this: this. The idea is that there are two seemingly random images, but when you XOR them, you find a secret message. I want to use Python Pillow, probably along with a simple image editor like paint.net. So my question consists of a few parts:
How do I generate an image full of random black or white pixels in Pillow.
How can I ensure certain areas of my images aren't actually random, but instead identical, ensuring an XOR compare will reveal them.

The process of creating those images is really simple. Here is an example how you could do it (not the most efficient):
Create two output images of same size
Create a template of same size, where 1 (white) means foreground (the hidden message) and 0 (black) means background (purely random).
Iterate over both images and the template in one loop:
If the template at current position says 0, draw two random numbers (zero or one) and assign them to the current pixel of each output image
If the template says 1, draw only one random number and assign it to both pixels
I will not go into detail on how you read your template image, create binary output images and iterate over them using Pillow, as I never tried Pillow. Drawing random numbers however is very simple:
x = random.randint(0,1) (see https://docs.python.org/2/library/random.html#random.randint)

To get you started, here's a way to make random binary images:
from PIL import Image
import numpy as np
# Make lots of ones and zeros.
data = np.random.randint(2, size=(100,100))
# Cast as 8-bit ints, 0 and 255.
data = data.astype(np.uint8) * 255
# Cast as an image. Pillow guesses mode.
img = Image.fromarray(data)
Result (magnified to 300 × 300 pixels):

For future posterity, here's what I did:
First I made a mask image. It was a white background with a red box and black text in the box. Looks like this:
Here's the script I wrote to make the two fuzzy images:
from PIL import Image
import random
WHITE = (255, 255, 255, 255)
RED = (255, 0, 0, 255)
BLACK = (0, 0, 0, 255)
wb = [WHITE,BLACK]
rng = random.SystemRandom()
orig = Image.open('mask.png')
origData = list(orig.getdata())
n1 = Image.new(orig.mode, orig.size)
n2 = Image.new(orig.mode, orig.size)
n1data = []
n2data = []
for x in origData:
if x == WHITE:
n1data.append(rng.choice(wb))
n2data.append(rng.choice(wb))
elif x == RED:
y = bool(rng.getrandbits(1))
if y:
n1data.append(WHITE)
n2data.append(BLACK)
else:
n1data.append(BLACK)
n2data.append(WHITE)
elif x == BLACK:
y = bool(rng.getrandbits(1))
if y:
n1data.append(WHITE)
n2data.append(WHITE)
else:
n1data.append(BLACK)
n2data.append(BLACK)
n1.putdata(n1data)
n2.putdata(n2data)
n1.save('n1.png')
n2.save('n2.png')
orig.close()
n1.close()
n2.close()
Resulted in these:
XOR them together and you get this: