OpenCV imshow shows very grainy image. How to fix this? - python

I have a CT image that look like this when I plot it using dicom:
But when I try to use opencv, it appears like this:
Array is dtype=uint16. My code to visualize in OpenCV:
img = np.array(ct_img * 255, dtype = np.uint16)
cv2.imshow('Annotated',img)
cv2.waitKey(0)
Please help fix the image. Image quality gets worse when I convert to np.uint32 or np.unint8

exposure.equalize_adapthist() solved the issue.

Related

Image.open() gives a plain white image

I am trying to edit this image:
However, when I run
im = Image.open(filename)
im.show()
it outputs a completely plain white image of the same size. Why is Image.open() not working? How can I fix this? Is there another library I can use to get non-255 pixel values (the correct pixel array)?
Thanks,
Vinny
Image.open actually seems to work fine, as does getpixel, putpixel and save, so you can still load, edit and save the image.
The problem seems to be that the temp file the image is saved in for show is just plain white, so the image viewer shows just a white image. Your original image is 16 bit grayscale, but the temp image is saved as an 8 bit grayscale.
My current theory is that there might actually be a bug in show where a 16 bit grayscale image is just "converted" to 8 bit grayscale by capping all pixel values to 255, resulting in an all-white temp image since all the pixels values in the original are above 30,000.
If you set a pixel to a value below 255 before calling show, that pixel shows correctly. Thus, assuming you want to enhance the contrast in the picture, you can open the picture, map the values to a range from 0 to 255 (e.g. using numpy), and then use show.
from PIL import Image
import numpy as np
arr = np.array(Image.open("Rt5Ov.png"))
arr = (arr - arr.min()) * 255 // (arr.max() - arr.min())
img = Image.fromarray(arr.astype("uint8"))
img.show()
But as said before, since save seems to work as it should, you could also keep the 16 bit grayscale depth and just save the edited image instead of using show.
you can use openCV library for loading images.
import cv2
img = cv2.imread('image file')
plt.show(img)

PIL image to array and back

EDIT: Sorry, the first version of the code was bullshit, I tried to remove useless information and made a mistake. Problem stays the same, but now it's the code I actually used
I think my problem is probably very basic but I cant find a solution. I basically just wanted to play around with PIL and convert an image to an array and backward, then save the image. It should look the same, right? In my case the new image is just gibberish, it seems to have some structure but it is not a picture of a plane like it should be:
def array_image_save(array, image_path ='plane_2.bmp'):
image = Image.fromarray(array, 'RGB')
image.save(image_path)
print("Saved image: {}".format(image_path))
im = Image.open('plane.bmp').convert('L')
w,h = im.size
array_image_save(np.array(list(im.getdata())).reshape((w,h)))
Not entirely sure what you are trying to achieve but if you just want to transform the image to a numpy array and back, the following works:
from PIL import Image
import numpy as np
def array_image_save(array, image_path ='plane_2.bmp'):
image = Image.fromarray(array)
image.save(image_path)
print("Saved image: {}".format(image_path))
im = Image.open('plane.bmp')
array_image_save(np.array(im))
You can just pass a PIL image to np.array and it takes care of the proper shaping. The reason you get distorted data is because you convert the pil image to greyscale (.convert('L')) but then try to save it as RGB.

OpenCV cv2.rectangle output binary image

I have been trying to draw rectangle on a black image, uscv2.rectangle.Here is my code : (It is just a sample, in actual code there is a loop i.e values x2,y2,w2,h2 changes in a loop)
heir = np.zeros((np.shape(image1)[0],np.shape(image1)[1]),np.uint8);
cv2.rectangle(heir,(x2,y2),(x2+w2,y2+h2),(255,255,0),5)
cv2.imshow("img",heir);
cv2.waitKey()
It is giving the following output:
Why the image is like that? Why the boundaries are not just a line a width 5.
I have tried, but I am not able to figure it out.
Can't post this in a comment, but it's a negative answer: the same operations work for me on Windows/python 2.7.8/opencv3.1
import numpy as np
import cv2
heir = np.zeros((100,200),np.uint8);
x2=10
y2=20
w2=30
h2=40
cv2.rectangle(heir,(x2,y2),(x2+w2,y2+h2),(255,255,0),5)
cv2.imshow("img",heir);
cv2.waitKey()
Because you are loading the image to be tagged (draw rectangles) in grayscale, thats why when you are adding rectangles/bounding boxes the colors are being converted to grayscale.
To fix the issue, open image in "color" format. Since, you didn't included that part of code, here is the proposed solution:
tag_img = cv2.imread(MYIMAGE,1)
Pay attention to the second parameter here, which is "1" and means load image as color. Read more about reading images here: https://docs.opencv.org/3.0-beta/doc/py_tutorials/py_gui/py_image_display/py_image_display.html

Python opencv drawContours does not show anything

I followed the tutorial at this page but nothing seems to happen when the line cv2.drawContours(im,contours,-1,(0,255,0),3) is executed. I was expecting to see star.jpg with a green outline, as shown in the tutorial. Here is my code:
import numpy as np
import cv2
im = cv2.imread('C:\Temp\ip\star.jpg')
print im.shape #check if the image is loaded correctly
imgray = cv2.cvtColor(im,cv2.COLOR_BGR2GRAY)
ret,thresh = cv2.threshold(imgray,127,255,0)
contours, hierarchy = cv2.findContours(thresh,cv2.RETR_TREE,cv2.CHAIN_APPROX_SIMPLE)
cv2.drawContours(im,contours,-1,(0,255,0),3)
pass
There are no error messages. star.jpg is the star from the above mentioned webpage.
I am using opencv version 2.4.8 and Python 2.7.
Is drawContours supposed to show an image on my screen? If so, what did I do wrong? If not, how do I show the image?
Thanks
Edit:
Adding the following lines will show the image:
cv2.imshow("window title", im)
cv2.waitKey()
waitKey() is needed otherwise the window will just show a gray background. According to this post, that's because waitKey() tells it to start handling the WM_PAINT event.
I had the same issue. I believe the issue is that the underlying image is 1-channel rather than 3-channel. Therefore, you need to set the color so it's nonzero in the first element (e.g. (255,0,0)).
i too had the same problem. The thing is it shows, but too dark for our eyes to see.
Solution:
change the colour from (0,255,0) (for some weird reason, i too had give exactly the same color!) to (128,255,0) (or some better brighter colour)
You have to do something to the effect of:
cv2.drawContours(im,contours,-1,(255,255,0),3)
cv2.imshow("Keypoints", im)
cv2.waitKey(0)
I guess your original image is in gray bit plane. Since your bit plane is Gray instead of BGR and so the contour is not showing up. Because it's slightly black and grey which you cannot distinguish. Here's the simple solution [By converting the bit plane]:
im=cv2.cvtColor(im,cv2.COLOR_GRAY2BGR)
cv2.drawContours(im,contours,-1,(0,255,0),3)

Python PIL: Convert RGBA->P - ValueError: image has wrong mode [duplicate]

I would like to convert a PNG32 image (with transparency) to PNG8 with Python Image Library.
So far I have succeeded converting to PNG8 with a solid background.
Below is what I am doing:
from PIL import Image
im = Image.open("logo_256.png")
im = im.convert('RGB').convert('P', palette=Image.ADAPTIVE, colors=255)
im.save("logo_py.png", colors=255)
After much searching on the net, here is the code to accomplish what I asked for:
from PIL import Image
im = Image.open("logo_256.png")
# PIL complains if you don't load explicitly
im.load()
# Get the alpha band
alpha = im.split()[-1]
im = im.convert('RGB').convert('P', palette=Image.ADAPTIVE, colors=255)
# Set all pixel values below 128 to 255,
# and the rest to 0
mask = Image.eval(alpha, lambda a: 255 if a <=128 else 0)
# Paste the color of index 255 and use alpha as a mask
im.paste(255, mask)
# The transparency index is 255
im.save("logo_py.png", transparency=255)
Source: http://nadiana.com/pil-tips-converting-png-gif
Although the code there does not call im.load(), and thus crashes on my version of os/python/pil. (It looks like that is the bug in PIL).
As mentioned by Mark Ransom, your paletized image will only have one transparency level.
When saving your paletized image, you'll have to specify which color index you want to be the transparent color like this :
im.save("logo_py.png", transparency=0)
to save the image as a paletized colors and using the first color as a transparent color.
This is an old question so perhaps older answers are tuned to older version of PIL?
But for anyone coming to this with Pillow>=6.0.0 then the following answer is many magnitudes faster and simpler.
im = Image.open('png32_or_png64_with_alpha.png')
im = im.quantize()
im.save('png8_with_alpha_channel_preserved.png')
Don't use PIL to generate the palette, as it can't handle RGBA properly and has quite limited quantization algorithm.
Use pngquant instead.

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