We Keep Coding

adding an overlay on a DICOM image using open CV

I am trying to create a layer on a DICOM image, below code works fine for jpg/png images but not for DICOM.
import cv2
import numpy as np
import pydicom as dicom
ds=dicom.dcmread('D0009.dcm')
img=ds.pixel_array
blank = np.zeros(shape=(img.shape[0],img.shape[1],3), dtype=np.uint8)
font = cv2.FONT_HERSHEY_SIMPLEX
cv2.putText(blank,
text='Logo',
org=(img.shape[1]//8, img.shape[0]//2),
fontFace=font,
fontScale= 2,color=(163,163,163),
thickness=11,
lineType=cv2.LINE_4)
blend=cv2.addWeighted(img,0.7,blank,1, 0, dtype = cv2.CV_32F)
cv2.imshow('sample image dicom',blend)
cv2.waitKey()
any help would be apreciated

I was able to get this working by normalizing the value range of the DICOM image and converting the DICOM image from greyscale to RGB image. Replace your line
img=ds.pixel_array
with these lines:
img = np.array(ds.pixel_array, dtype='float32')
img /= np.max(img)
img = cv2.cvtColor(img, cv2.COLOR_GRAY2RGB)

skimage convert to grayscale resulting to a black image

I am scraping image and trying to convert them into grayscale. But if i view the image. It is plain black. Can someone tell me what is wrong with this? Thanks
Here is my snippet
import cv2
from skimage import io
from skimage import data
from skimage.color import rgb2gray
#...some codes
for i in elements:
try:
i.click()
except ElementClickInterceptedException:
driver.execute_script("window.scrollTo(0, document.body.scrollHeight);")
i.click()
url = driver.find_element_by_xpath('//*[#class="slider-list"]/div/img').get_attribute('src').replace('height=600','height=1200').replace('quality=70','quality=100')
print (url)
name = driver.find_element_by_xpath('//*[#class="slider-list"]/div/img').get_attribute('alt') + '.jpg'
print (name)
img = io.imread(url)
new = rgb2gray(img)
cv2.imwrite(os.path.join(fldrnm, name), new)

Import cv2
Img = cv2.inread(filepath)
Img = cv2.cvtColor(Img, cv2.COLOR_RGB2GRAY)
cv2.imwrite(path,img)

The original cause of the problem is that skimage.color.rgb2gray will rescale an image to floating point values in [0, 1], even if the original image contains uint8 values in [0, 255]. This is done to preserve precision during long sequences of operations. Using skimage.io.imsave instead of cv2.imwrite in the original question would work, as well as using skimage.util.img_as_ubyte before saving.
See this page for more details:
https://scikit-image.org/docs/dev/user_guide/data_types.html

How to reshape png image read by skimage.imread

Then I read some jpg file, this way
image = imread('aa.jpg')
As result I get dataframe with numbers from 1 to 255
I can resize it this way:
from cv2 import resize
image = resize(image, (256, 256)
But then I doing same think with png, result not desired.
image = imread('aa2.png') # array with number within 0-1 range
resize(image, (256,256)) # returns 1 channel image
resize(image, (256,256, 3)) # returns 3 channel image
Weird image
But imshow(image)

cv2.imread reads the image in 3 channel by default instead of 4. Pass the parameter cv.IMREAD_UNCHANGED to read your PNG file and then try to resize it as shown in the code below.
import numpy as np
import cv2 as cv
import matplotlib.pyplot as plt
img = cv.imread('Snip20190412_12.png', cv.IMREAD_UNCHANGED)
print(img.shape) #(215, 215, 4)
height, width = img.shape[:2]
res = cv.resize(img,(2*width, 2*height))
print(res.shape)#(430, 430, 4)
plt.imshow(res)

I guess is some problem with your image or code.
Here a free image to try: https://pixabay.com/vectors/copyright-free-creative-commons-98566/
Maybe you have problem with libpng, check this answers: libpng warning: iCCP: known incorrect sRGB profile
Check this simple code that works on PNG images.
import cv2 as cv
image = cv.imread("foto.png")
if __name__ == "__main__":
while True:
image = cv.resize(image,(200,200))
cv.imshow("prueba",image)
key = cv.waitKey(10)
if key == 27:
cv.destroyAllWindows()
break
cv.destroyAllWindows()

Want to append colored images to a list and convert that list to grayscale using OpenCV

So basically I'm trying to convert a set of RGB images to grayscale using cv2.cvtColor and python is throwing the following error:
Traceback (most recent call last):
File "MCG.py", line 53, in
gray = cv2.cvtColor(data, cv2.COLOR_BGR2GRAY)
TypeError: src is not a numpy array, neither a scalar.
This here is the code:
import numpy as np
import cv2
import dlib
import sys
import skimage
from PIL import Image
import os
import glob
folderpath = sys.argv[1]
cascPath = sys.argv[2]
imageformat = ".tif"
path = folderpath
imfilelist = [os.path.join(path,f) for f in os.listdir(path) if f.endswith(imageformat)]
data = []
for IMG in imfilelist:
print IMG
image = cv2.imread(IMG)
data.append(image)
cv2.imshow('Image', image)
cv2.waitKey(0)
faceCascade = cv2.CascadeClassifier(cascPath)
predictor = dlib.shape_predictor(PREDICTOR_PATH)
gray = cv2.cvtColor(data, cv2.COLOR_BGR2GRAY)
faces = faceCascade.detectMultiScale(
gray,
scaleFactor=1.05,
minNeighbors=5,
minSize=(100,100)
)
As you can see, I'm trying to append all these images to a list, which will then be converted using the cv2.cvtColor function. However, that error is thrown. What am I doing wrong? Thank you.
P.S if anyone is wondering why I imported modules that don't seem to be used in this code, this code is just a segment of the whole thing and all of those modules have are being utilized in one way or the other.

If you read the cv2.cvtColor documentation, you can see that the first parameter is the Src 8-bit single channel image. However, in your case you are giving an entire list of images.
So change the code as
gray = []
for j in range(0,len(data)):
gray.append(cv2.cvtColor(np.array(data[j]), cv2.COLOR_BGR2GRAY))
I guess this should work.

You are collecting the images into a list with
data = []
for IMG in imfilelist:
...
data.append(image)
....
and then trying to convert the list with
gray = cv2.cvtColor(data, cv2.COLOR_BGR2GRAY)
This is why you are getting the error - the error is telling you that data is not an image (numpy array) but is a list. You need to convert one image at a time with cv2.cvtColor().
You could try
gray = []
for img in data:
gray.append(cv2.cvtColor(img, cv2.COLOR_BGR2GRAY))
This would give you a list of greyscaled images, which is what I think you want to do.

How can i read input only a part of the image without creating another image?

import cv2
fname = '1.png'
img=cv2.imread(fname, 0)
print (img)//the outcome is an array of values from 0 to 255 (grayscale)
ret, thresh = cv2.threshold(img, 254, 255, cv2.THRESH_BINARY)
thresh = cv2.bitwise_not(thresh)
nums, labels = cv2.connectedComponents(thresh, None, 4, cv2.CV_32S)
dst = cv2.convertScaleAbs(255.0*labels/nums)
cv2.imwrite(dest_dir+"output.png", dst)
that code works just fine, so i moved on to adjusting my code so it can take a portion of the image not the entire image:
from PIL import Image
img = Image.open(fname)
img2 = img.crop((int(xmin), int(yMin),int(xMax), int(yMax))
xmin ymin xmax ymax simply being the top left bottom right coordinates of the box.
then i did img = cv2.imread(img2) to continue as the previous code but got an error, i printed img2 and got <PIL.Image.Image image mode=RGB size=54x10 at 0x7F4D283AFB70> how can i adjust it to be able to input that crop or image portion instead of fname in my code above, and kindly note i don't want to save img2 as an image and carry on from there because i need to work on the main image.

try cv2.imshow() instead of printing it. In order to see an image you cropped, you need to use cv2 function. here is a sample code:
import numpy as np
import cv2
# Load an color image in grayscale
img = cv2.imread('messi5.jpg',0)
cv2.imshow('image',img)
cv2.waitKey(0)
cv2.destroyAllWindows()

The simple answer is NO you cannot.
Open up your terminal /IDE and type in help(cv2.imread).
It clearly states that The function imread loads an image from the specified file and returns it. So in order to use cv2.imread() you must pass it in as a file not an image.
Your best bet would be to save your cropped image as a file and then read it.