Develop Reference

How to merge two RGBA images

I'm trying to merge two RGBA images (with a shape of (h,w,4)), taking into account their alpha channels.
Example :
What I've tried
I tried to do this using opencv for that, but I getting some strange pixels on the output image.
Images Used:
and
import cv2
import numpy as np
import matplotlib.pyplot as plt
image1 = cv2.imread("image1.png", cv2.IMREAD_UNCHANGED)
image2 = cv2.imread("image2.png", cv2.IMREAD_UNCHANGED)
mask1 = image1[:,:,3]
mask2 = image2[:,:,3]
mask2_inv = cv2.bitwise_not(mask2)
mask2_bgra = cv2.cvtColor(mask2, cv2.COLOR_GRAY2BGRA)
mask2_inv_bgra = cv2.cvtColor(mask2_inv, cv2.COLOR_GRAY2BGRA)
# output = image2*mask2_bgra + image1
output = cv2.bitwise_or(cv2.bitwise_and(image2, mask2_bgra), cv2.bitwise_and(image1, mask2_inv_bgra))
output[:,:,3] = cv2.bitwise_or(mask1, mask2)
plt.figure(figsize=(12,12))
plt.imshow(cv2.cvtColor(output, cv2.COLOR_BGRA2RGBA))
plt.axis('off')
Output :
So what I figured out is that I'm getting those weird pixels because I used cv2.bitwise_and function (Which btw works perfectly with binary alpha channels).
I tried using different approaches
Question
Is there an approach to do this (While keeping the output image as an 8bit image).

I was able to obtain the expected result in 2 stages.
# Read both images preserving the alpha channel
hh1 = cv2.imread(r'C:\Users\524316\Desktop\Stack\house.png', cv2.IMREAD_UNCHANGED)
hh2 = cv2.imread(r'C:\Users\524316\Desktop\Stack\memo.png', cv2.IMREAD_UNCHANGED)
# store the alpha channels only
m1 = hh1[:,:,3]
m2 = hh2[:,:,3]
# invert the alpha channel and obtain 3-channel mask of float data type
m1i = cv2.bitwise_not(m1)
alpha1i = cv2.cvtColor(m1i, cv2.COLOR_GRAY2BGRA)/255.0
m2i = cv2.bitwise_not(m2)
alpha2i = cv2.cvtColor(m2i, cv2.COLOR_GRAY2BGRA)/255.0
# Perform blending and limit pixel values to 0-255 (convert to 8-bit)
b1i = cv2.convertScaleAbs(hh2*(1-alpha2i) + hh1*alpha2i)
Note: In the b=above the we are using only the inverse alpha channel of the memo image
But I guess this is not the expected result. So moving on ....
# Finding common ground between both the inverted alpha channels
mul = cv2.multiply(alpha1i,alpha2i)
# converting to 8-bit
mulint = cv2.normalize(mul, dst=None, alpha=0, beta=255,norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8U)
# again create 3-channel mask of float data type
alpha = cv2.cvtColor(mulint[:,:,2], cv2.COLOR_GRAY2BGRA)/255.0
# perform blending using previous output and multiplied result
final = cv2.convertScaleAbs(b1i*(1-alpha) + mulint*alpha)
Sorry for the weird variable names. I would request you to analyze the result in each line. I hope this is the expected output.

You could use PIL library to achieve this
from PIL import Image
def merge_images(im1, im2):
bg = Image.open(im1).convert("RGBA")
fg = Image.open(im2).convert("RGBA")
x, y = ((bg.width - fg.width) // 2 , (bg.height - fg.height) // 2)
bg.paste(fg, (x, y), fg)
# convert to 8 bits (pallete mode)
return bg.convert("P")
we can test it using the provided images:
result_image = merge_images("image1.png", "image2.png")
result_image.save("image3.png")
Here's the result:

OpenCV Python Frequency Domain Filtering Result Is Not As Expected

hope you are all doing well.
Right now I am doing a homework which requires me to create High Pass Filters in the frequency domain. I created all of my filters. After I apply my filters (of course after converting the input image to the frequency domain and then applying Inverse Fourier to get to spatial domain), the output images are in purple tones, whereas the input image is gray level. Here is the output from my Ideal High Pass Filter:
Here is the input image:
Here is my High Pass filter function:
import numpy as np
# The function takes two dimension inputs for the filter image;
# the third filter is D0, which defines the circle area of the High Pass Filter.
def idealHighPass(M, N, D0):
# Initializing the filter with ones; since the filter is a complex function,
# it has two channels, representing the real and imaginary parts:
filter = np.ones((M, N, 2), dtype=np.uint8)
# Scanning through each pixel and calculating the distance of each pixel
# to the image center. If the pixel is within D0, it is changed to 0:
for i in range(M):
for j in range(N):
filter[i][j] = 0
return filter
Here is my main code:
import cv2
import numpy as np
from matplotlib import pyplot as plt
from idealHighPass import idealHighPass
from highButterworth import highButterworth
from highGaussian import highGaussian
#img = cv2.imread("airfield-05small-auto.tif")
img = cv2.imread("input.png")
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
m, n = img.shape
ft = cv2.dft(np.float32(img), flags=cv2.DFT_COMPLEX_OUTPUT)
ft_shifted = dft_shift = np.fft.fftshift(ft)
# - IDEAL HIGH-PASS FILTER EXECUTION START -
filter = idealHighPass(m, n, 80)
filter = filter.astype((np.float32))
applied = ft_shifted * filter
fshift_mask_mag = 20 * np.log(cv2.magnitude(applied[:, :, 0], applied[:, :, 1]))
f_ishift = np.fft.ifftshift(applied)
img_back = cv2.idft(f_ishift)
img_back = cv2.magnitude(img_back[:, :, 0], img_back[:, :, 1])
cv2.imwrite("high_passed.png", img_back)
print(img_back.shape)
imgplot = plt.imshow(img_back)
plt.show()
# - IDEAL HIGH-PASS FILTER EXECUTION END -

Detecting the volume/overlap region in image registration for OCT data

I am working on image registration of OCT data. I would like to locate the regions/area in my targeted registered image, where image registration has actually occurred from the source images. I am working in Python. Can anyone please tell me what are the available techniques?
Any suggestions on how to proceed with the problem are also welcomed. I have done some trial image registration on two images initially. The goal is to do registration of a large dataset.
My code is given below:
#importing libraries
import cv2
import numpy as np
# from skimage.measure import structural_similarity as ssim
# from skimage.measure import compare_ssim
import skimage
from skimage import measure
import matplotlib.pyplot as plt
def imageRegistration():
# open the image files
path = 'D:/Fraunhofer Thesis/LatestPythonImplementations/Import_OCT_Vision/sliceImages(_x_)/'
image1 = cv2.imread(str(path) + '104.png')
image2 = cv2.imread(str(path) + '0.png')
# converting to greyscale
img1 = cv2.cvtColor(image1, cv2.COLOR_BGR2GRAY)
img2 = cv2.cvtColor(image2, cv2.COLOR_BGR2GRAY)
height, width = img2.shape
# Create ORB detector with 5000 features.
orb_detector = cv2.ORB_create(5000)
# Find keypoints and descriptors.
# The first arg is the image, second arg is the mask
# (which is not reqiured in this case).
kp1, d1 = orb_detector.detectAndCompute(img1, None)
kp2, d2 = orb_detector.detectAndCompute(img2, None)
# Match features between the two images.
# We create a Brute Force matcher with
# Hamming distance as measurement mode.
matcher = cv2.BFMatcher(cv2.NORM_HAMMING, crossCheck=True)
# Match the two sets of descriptors.
matches = matcher.match(d1, d2)
# Sort matches on the basis of their Hamming distance.
matches.sort(key=lambda x: x.distance)
# Take the top 90 % matches forward.
matches = matches[:int(len(matches) * 90)]
no_of_matches = len(matches)
# Define empty matrices of shape no_of_matches * 2.
p1 = np.zeros((no_of_matches, 2))
p2 = np.zeros((no_of_matches, 2))
for i in range(len(matches)):
p1[i, :] = kp1[matches[i].queryIdx].pt
p2[i, :] = kp2[matches[i].trainIdx].pt
# Find the homography matrix.
homography, mask = cv2.findHomography(p1, p2, cv2.RANSAC)
# Use this matrix to transform the
# colored image wrt the reference image.
transformed_img = cv2.warpPerspective(image1,
homography, (width, height))
# Save the output.
cv2.imwrite('output.jpg', transformed_img)
#following is the code figuring out difference in the source image, target image and the registered image
# 0 mse means perfect similarity , no difference
# mse >1 means there is difference and as the value increases , the difference increases
def findingDifferenceMSE():
path = 'D:/Fraunhofer Thesis/LatestPythonImplementations/Import_OCT_Vision/sliceImages(_x_)/'
image1 = cv2.imread(str(path) + '104.png')
image2 = cv2.imread(str(path) + '0.png')
image3 = cv2.imread('D:/Fraunhofer Thesis/LatestPythonImplementations/Import_OCT_Vision/output.jpg')
err = np.sum((image1.astype("float") - image3.astype("float")) ** 2)
err /= float(image1.shape[0] * image3.shape[1])
print("MSE:")
print('Image 104 and output image: ', + err)
err1 = np.sum((image2.astype("float") - image3.astype("float")) ** 2)
err1 /= float(image2.shape[0] * image3.shape[1])
print('Image 0 and output image: ', + err1)
def findingDifferenceSSIM():
path = 'D:/Fraunhofer Thesis/LatestPythonImplementations/Import_OCT_Vision/sliceImages(_x_)/'
image1 = cv2.imread(str(path) + '104.png')
image2 = cv2.imread(str(path) + '0.png')
image3 = cv2.imread('D:/Fraunhofer Thesis/LatestPythonImplementations/Import_OCT_Vision/output.jpg')
result1=measure.compare_ssim(image1,image3)
print(result1)
#calling the fucntion
imageRegistration()
findingDifferenceMSE()
#findingDifferenceSSIM()
This is the registered image:
This image is the first reference image:
This is the second reference image:

Image differentiation technique can be used to identify the registered area in the images by comparing it with base images. In this way, the different areas will be recognized.

convert IR image to RGB with python

The code below is intended to take an infrared image (B&W) and convert it to RGB. It does so successfully, but with significant noise. I have included a few lines for noise reduction but they don't seem to help. I've included the starting/resulting photos below. Any advice/corrections are welcome and thank you in advance!
from skimage import io
import numpy as np
import glob, os
from tkinter import Tk
from tkinter.filedialog import askdirectory
import cv2
path = askdirectory(title='Select PNG Folder') # shows dialog box and return the path
outpath = askdirectory(title='Select SAVE Folder')
# wavelength in microns
MWIR = 4.5
R = .642
G = .532
B = .44
vector = [R, G, B]
vectorsum = np.sum(vector)
vector = vector / vectorsum #normalize
vector = vector*255 / MWIR #changing this value changes the outcome significantly so I
#have been messing with it in the hopes of fixing it but no luck so far.
vector = np.power(vector, 4)
for file in os.listdir(path):
if file.endswith(".png"):
imIn = io.imread(os.path.join(path, file))
imOut = imIn * vector
ret,thresh = cv2.threshold(imOut,64,255,cv2.THRESH_BINARY)
kernel = np.ones((5, 5), np.uint8)
erode = cv2.erode(thresh, kernel, iterations = 1)
result = cv2.bitwise_or(imOut, erode)
io.imsave(os.path.join(outpath, file) + '_RGB.png',imOut.astype(np.uint8))

Your noise looks like completely random values, so I suspect you have an error in your conversion from float to uint8. But instead of rolling everything for yourself, why don't you just use:
imOut = cv2.cvtColor(imIn,cv2.COLOR_GRAY2BGR)

Here is one way to do that in Python/OpenCV.
Your issue is likely that your channel values are exceeding the 8-bit range.
Sorry, I do not understand the relationship between your R,G,B weights and your MWIR. Dividing by MWIR will do nothing if your weights are properly normalized.
Input:
import cv2
import numpy as np
# read image
img = cv2.imread('car.jpg')
# convert to gray
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
# make color channels
red = gray.copy()
green = gray.copy()
blue = gray.copy()
# set weights
R = .642
G = .532
B = .44
MWIR = 4.5
# get sum of weights and normalize them by the sum
R = R**4
G = G**4
B = B**4
sum = R + G + B
R = R/sum
G = G/sum
B = B/sum
print(R,G,B)
# combine channels with weights
red = (R*red)
green = (G*green)
blue = (B*blue)
result = cv2.merge([red,green,blue])
# scale by ratio of 255/max to increase to fully dynamic range
max=np.amax(result)
result = ((255/max)*result).clip(0,255).astype(np.uint8)
# write result to disk
cv2.imwrite("car_colored.png", result)
# display it
cv2.imshow("RESULT", result)
cv2.waitKey(0)
Result

If the noise is coming from the sensor itself, like a grainy noise, you'll need to look into denoising algorithms. scikit-image and opencv provide some denoising algorithms you can try. Maybe take a look at this and this.

I recently learned about matplotlib.cm, which handles colormaps. I've been using those to artificially color IR images, and made a brief example using the same black & white car image used above. Basically, I create a colormap .csv file locally, then refer to it for RGB weights. You may have to pick and choose which colormap you prefer, but that's up to personal preference.
Input image:
Python:
import os
import numpy as np
import cv2
from matplotlib import cm
# Multiple colormap options are available- I've hardcoded viridis for this example.
colormaps = ["viridis", "plasma", "inferno", "magma", "cividis"]
def CreateColormap():
if not os.path.exists("viridis_colormap.csv"):
# Get 256 entries from "viridis" or any other Matplotlib colormap
colormap = cm.get_cmap("viridis", 256)
# Make a Numpy array of the 256 RGB values
# Each line corresponds to an RGB colour for a greyscale level
np.savetxt("viridis_colormap.csv", (colormap.colors[...,0:3]*255).astype(np.uint8), fmt='%d', delimiter=',')
def RecolorInfraredImageToRGB(ir_image):
# Load RGB lookup table from CSV file
lookup_table = np.loadtxt("viridis_colormap.csv", dtype=np.uint8, delimiter=",")
# Make output image, same height and width as IR image, but 3-channel RGB
result = np.zeros((*ir_image.shape, 3), dtype=np.uint8)
# Take entries from RGB LUT according to greyscale values in image
np.take(lookup_table, ir_image, axis=0, out=result)
return result
if __name__ == "__main__":
CreateColormap()
img = cv2.imread("bwcar.jpg")
gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
recolored = RecolorInfraredImageToRGB(gray)
cv2.imwrite("car_recolored.png", recolored)
cv2.imshow("Viridis recolor", recolored)
cv2.waitKey(0)
Output:

Intensity normalization of image using Python+PIL - Speed issues

I'm working on a little problem in my sparetime involving analysis of some images obtained through a microscope. It is a wafer with some stuff here and there, and ultimately I want to make a program to detect when certain materials show up.
Anyways, first step is to normalize the intensity across the image, since the lens does not give uniform lightning. Currently I use an image, with no stuff on, only the substrate, as a background, or reference, image. I find the maximum of the three (intensity) values for RGB.
from PIL import Image
from PIL import ImageDraw
rmax = 0;gmax = 0;bmax = 0;rmin = 300;gmin = 300;bmin = 300
im_old = Image.open("test_image.png")
im_back = Image.open("background.png")
maxx = im_old.size[0] #Import the size of the image
maxy = im_old.size[1]
im_new = Image.new("RGB", (maxx,maxy))
pixback = im_back.load()
for x in range(maxx):
for y in range(maxy):
if pixback[x,y][0] > rmax:
rmax = pixback[x,y][0]
if pixback[x,y][1] > gmax:
gmax = pixback[x,y][1]
if pixback[x,y][2] > bmax:
bmax = pixback[x,y][2]
pixnew = im_new.load()
pixold = im_old.load()
for x in range(maxx):
for y in range(maxy):
r = float(pixold[x,y][0]) / ( float(pixback[x,y][0])*rmax )
g = float(pixold[x,y][1]) / ( float(pixback[x,y][1])*gmax )
b = float(pixold[x,y][2]) / ( float(pixback[x,y][2])*bmax )
pixnew[x,y] = (r,g,b)
The first part of the code determines the maximum intensity of the RED, GREEN and BLUE channels, pixel by pixel, of the background image, but needs only be done once.
The second part takes the "real" image (with stuff on it), and normalizes the RED, GREEN and BLUE channels, pixel by pixel, according to the background. This takes some time, 5-10 seconds for an 1280x960 image, which is way too slow if I need to do this to several images.
What can I do to improve the speed? I thought of moving all the images to numpy arrays, but I can't seem to find a fast way to do that for RGB images.
I'd rather not move away from python, since my C++ is quite low-level, and getting a working FORTRAN code would probably take longer than I could ever save in terms of speed :P

import numpy as np
from PIL import Image
def normalize(arr):
"""
Linear normalization
http://en.wikipedia.org/wiki/Normalization_%28image_processing%29
"""
arr = arr.astype('float')
# Do not touch the alpha channel
for i in range(3):
minval = arr[...,i].min()
maxval = arr[...,i].max()
if minval != maxval:
arr[...,i] -= minval
arr[...,i] *= (255.0/(maxval-minval))
return arr
def demo_normalize():
img = Image.open(FILENAME).convert('RGBA')
arr = np.array(img)
new_img = Image.fromarray(normalize(arr).astype('uint8'),'RGBA')
new_img.save('/tmp/normalized.png')

See http://docs.scipy.org/doc/scipy/reference/generated/scipy.misc.fromimage.html#scipy.misc.fromimage
You can say
databack = scipy.misc.fromimage(pixback)
rmax = numpy.max(databack[:,:,0])
gmax = numpy.max(databack[:,:,1])
bmax = numpy.max(databack[:,:,2])
which should be much faster than looping over all (r,g,b) triplets of your image.
Then you can do
dataold = scip.misc.fromimage(pixold)
r = dataold[:,:,0] / (pixback[:,:,0] * rmax )
g = dataold[:,:,1] / (pixback[:,:,1] * gmax )
b = dataold[:,:,2] / (pixback[:,:,2] * bmax )
datanew = numpy.array((r,g,b))
imnew = scipy.misc.toimage(datanew)
The code is not tested, but should work somehow with minor modifications.

This is partially from FolksTalk webpage:
from PIL import Image
import numpy as np
# Read image file
in_file = "my_image.png"
# convert('RGB') for PNG file type
image = Image.open(in_file).convert('RGB')
pixels = np.asarray(image)
# Convert from integers to floats
pixels = pixels.astype('float32')
# Normalize to the range 0-1
pixels /= 255.0