I am trying to build a machine learning algorithm where I need to convert pictures to their binaries. I am using Pillow library to get the data from images. Since the performance of the algorithm is not great, I need extra parameters to thoroughly train the network and one of the extra parameters might be hue.
So is there a method in Python that gives me hue value of an image?
I am not sure what you are really trying to do, as Christoph says in the comments, but you can find the mean hue of all the pixels in an image with PIL like this:
from PIL import Image, ImageStat
# Load image, convert to HSV and split the channels, retain H, discard S and V
H, _, _ = Image.open('image.png').convert('RGB').convert('HSV').split()
# Print the mean Hue across all pixels
print(ImageStat.Stat(H).mean)
Note that I converted to RGB first to avoid problems that may arise if you try this with palette images, CMYK images, images with transparency and greyscale images. See here.
I have applied Laplacian filter to the image for detecting the edges in the image.
import matplotlib.pyplot as plt
from skimage import filters
output= filters.laplace(image)
plt.imshow(output, cmap = 'gray')
plt.title('Laplace', size=20)
plt.show()
I need to reconstruct the original image using the output obtained from the code above.
I'm not sure if 'filters.inverse' works or if there is any other method available.
What you are looking for is called deconvolution. If you search for "scikit-image deconvolution", you will probably land at the documentation for the Richardson-Lucy deconvolution function, or at this example usage. Note: it is not always theoretically possible to reconstruct the original signal (it's a little bit like unmixing paint), but you can get reasonable approximations, especially if your convolution is exactly known.
You can look at the source code for the Laplace filter, where you see that the image is convolved with a laplacian kernel. That is the kernel we need to deconvolve the image. (Note that you can always regenerate the kernel by convolving an image containing just a 1 in the center and 0s everywhere else. That's why the kernel in deconvolution is referred to as the point-spread function.)
So, to restore your image:
from skimage.restoration.uft import laplacian
from skimage.restoration import richardson_lucy
kernel_size = 3 # default for filters.laplace, increase if needed
kernel = laplacian(output.ndim, (kernel_size,) * output.ndim)
restored = richardson_lucy(output, kernel)
I am fairly new to coding, but I have been doing a lot of research. I have been trying to make my own haar cascade using python and open cv. I have all of my negative samples and a few pictures for my positive ones. I was hoping to run a create_samples command with cv2 but can't find anything for how to do it on windows (only linux, which I tried but my digital oceans server wasn't working). If you have any experience or know of any resources please send them my way.
Basically what I need to do is impose my positive images onto my negatives ones with a tilt angle to create a lot of samples.
You Don't Need OpenCV for image Creation. This is how you can create an image from a 2D array.
import numpy as np
from PIL import Image
#gradient between 0 and 1 for 256*256 1d arrray
array = np.linspace(0,1,256*256)
#reshape to 2d
mat = np.reshape(array,(256,256))
#creates PIL image
img = Image.fromarray(np.uint8(mat*255) , 'L')
img.show()
this code will give you your deserved custom image.
Thank You
I am microbiology student new to computer vision, so any help will be extremely appreciated.
This question involves microscope images that I am trying to analyze. The goal I am trying to accomplish is to count bacteria in an image but I need to pre-process the image first to enhance any bacteria that are not fluorescing very brightly. I have thought about using several different techniques like enhancing the contrast or sharpening the image but it isn't exactly what I need.
I want to reduce the noise(black spaces) to 0's on the RBG scale and enhance the green spaces. I originally was writing a for loop in OpenCV with threshold limits to change each pixel but I know that there is a better way.
Here is an example that I did in photo shop of the original image vs what I want.
Original Image and enhanced Image.
I need to learn to do this in a python environment so that I can automate this process. As I said I am new but I am familiar with python's OpenCV, mahotas, numpy etc. so I am not exactly attached to a particular package. I am also very new to these techniques so I am open to even if you just point me in the right direction.
Thanks!
You can have a look at histogram equalization. This would emphasize the green and reduce the black range. There is an OpenCV tutorial here. Afterwards you can experiment with different thresholding mechanisms that best yields the bacteria.
Use TensorFlow:
create your own dataset with images of bacteria and their positions stored in accompanying text files (the bigger the dataset the better).
Create a positive and negative set of images
update default TensorFlow example with your images
make sure you have a bunch of convolution layers.
train and test.
TensorFlow is perfect for such tasks and you don't need to worry about different intensity levels.
I initially tried histogram equalization but did not get the desired results. So I used adaptive threshold using the mean filter:
th = cv2.adaptiveThreshold(img, 255, cv2.ADAPTIVE_THRESH_MEAN_C, cv2.THRESH_BINARY_INV, 3, 2)
Then I applied the median filter:
median = cv2.medianBlur(th, 5)
Finally I applied morphological closing with the ellipse kernel:
k1 = cv2.getStructuringElement(cv2.MORPH_ELLIPSE,(5,5))
dilate = cv2.morphologyEx(median, cv2.MORPH_CLOSE, k1, 3)
THIS PAGE will help you modify this result however you want.
For example, I have 100 pictures whose resolution is the same, and I want to merge them into one picture. For the final picture, the RGB value of each pixel is the average of the 100 pictures' at that position. I know the getdata function can work in this situation, but is there a simpler and faster way to do this in PIL(Python Image Library)?
Let's assume that your images are all .png files and they are all stored in the current working directory. The python code below will do what you want. As Ignacio suggests, using numpy along with PIL is the key here. You just need to be a little bit careful about switching between integer and float arrays when building your average pixel intensities.
import os, numpy, PIL
from PIL import Image
# Access all PNG files in directory
allfiles=os.listdir(os.getcwd())
imlist=[filename for filename in allfiles if filename[-4:] in [".png",".PNG"]]
# Assuming all images are the same size, get dimensions of first image
w,h=Image.open(imlist[0]).size
N=len(imlist)
# Create a numpy array of floats to store the average (assume RGB images)
arr=numpy.zeros((h,w,3),numpy.float)
# Build up average pixel intensities, casting each image as an array of floats
for im in imlist:
imarr=numpy.array(Image.open(im),dtype=numpy.float)
arr=arr+imarr/N
# Round values in array and cast as 8-bit integer
arr=numpy.array(numpy.round(arr),dtype=numpy.uint8)
# Generate, save and preview final image
out=Image.fromarray(arr,mode="RGB")
out.save("Average.png")
out.show()
The image below was generated from a sequence of HD video frames using the code above.
I find it difficult to imagine a situation where memory is an issue here, but in the (unlikely) event that you absolutely cannot afford to create the array of floats required for my original answer, you could use PIL's blend function, as suggested by #mHurley as follows:
# Alternative method using PIL blend function
avg=Image.open(imlist[0])
for i in xrange(1,N):
img=Image.open(imlist[i])
avg=Image.blend(avg,img,1.0/float(i+1))
avg.save("Blend.png")
avg.show()
You could derive the correct sequence of alpha values, starting with the definition from PIL's blend function:
out = image1 * (1.0 - alpha) + image2 * alpha
Think about applying that function recursively to a vector of numbers (rather than images) to get the mean of the vector. For a vector of length N, you would need N-1 blending operations, with N-1 different values of alpha.
However, it's probably easier to think intuitively about the operations. At each step you want the avg image to contain equal proportions of the source images from earlier steps. When blending the first and second source images, alpha should be 1/2 to ensure equal proportions. When blending the third with the the average of the first two, you would like the new image to be made up of 1/3 of the third image, with the remainder made up of the average of the previous images (current value of avg), and so on.
In principle this new answer, based on blending, should be fine. However I don't know exactly how the blend function works. This makes me worry about how the pixel values are rounded after each iteration.
The image below was generated from 288 source images using the code from my original answer:
On the other hand, this image was generated by repeatedly applying PIL's blend function to the same 288 images:
I hope you can see that the outputs from the two algorithms are noticeably different. I expect this is because of accumulation of small rounding errors during repeated application of Image.blend
I strongly recommend my original answer over this alternative.
One can also use numpy mean function for averaging. The code looks better and works faster.
Here the comparison of timing and results for 700 noisy grayscale images of faces:
def average_img_1(imlist):
# Assuming all images are the same size, get dimensions of first image
w,h=Image.open(imlist[0]).size
N=len(imlist)
# Create a numpy array of floats to store the average (assume RGB images)
arr=np.zeros((h,w),np.float)
# Build up average pixel intensities, casting each image as an array of floats
for im in imlist:
imarr=np.array(Image.open(im),dtype=np.float)
arr=arr+imarr/N
out = Image.fromarray(arr)
return out
def average_img_2(imlist):
# Alternative method using PIL blend function
N = len(imlist)
avg=Image.open(imlist[0])
for i in xrange(1,N):
img=Image.open(imlist[i])
avg=Image.blend(avg,img,1.0/float(i+1))
return avg
def average_img_3(imlist):
# Alternative method using numpy mean function
images = np.array([np.array(Image.open(fname)) for fname in imlist])
arr = np.array(np.mean(images, axis=(0)), dtype=np.uint8)
out = Image.fromarray(arr)
return out
average_img_1()
100 loops, best of 3: 362 ms per loop
average_img_2()
100 loops, best of 3: 340 ms per loop
average_img_3()
100 loops, best of 3: 311 ms per loop
BTW, the results of averaging are quite different. I think the first method lose information during averaging. And the second one has some artifacts.
average_img_1
average_img_2
average_img_3
in case anybody is interested in a blueprint numpy solution (I was actually looking for it), here's the code:
mean_frame = np.mean(([frame for frame in frames]), axis=0)
I would consider creating an array of x by y integers all starting at (0, 0, 0) and then for each pixel in each file add the RGB value in, divide all the values by the number of images and then create the image from that - you will probably find that numpy can help.
I ran into MemoryErrors when trying the method in the accepted answer. I found a way to optimize that seems to produce the same result. Basically, you blend one image at a time, instead of adding them all up and dividing.
N=len(images_to_blend)
avg = Image.open(images_to_blend[0])
for im in images_to_blend: #assuming your list is filenames, not images
img = Image.open(im)
avg = Image.blend(avg, img, 1/N)
avg.save(blah)
This does two things, you don't have to have two very dense copies of the image while you're turning the image into an array, and you don't have to use 64-bit floats at all. You get similarly high precision, with smaller numbers. The results APPEAR to be the same, though I'd appreciate if someone checked my math.