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black pixels when save MRI dicom after applying lut

I'm trying to apply LUT to MR images using following codes. the original dicom pixel intensities ranges from 0 to 4334 and the pixel intensities after applying LUT function ranges from 0 to 254. I need to preserve the metadata info for the resulted image. When I plot the resulted image, it displays correct but when I save the image, it is all black pixels. I know I need to change some meta data tags but I'm new to dicom image processing and couldn't figure out what is causing the problem.
def make_lut(dcm_data, width, center, p_i):
"""
LUT: look-up tables
VOI: volume of interest
"""
slope= 1.0
intercept= 0.0
min_px= int(np.amin(dcm_data))
max_px= int(np.amax(dcm_data))
lut= [0] * (max_px + 1)
invert= False
if p_i == "MONOCHROME1":
invert= True
else:
center = (max_px - min_px) - center
for px_value in range(min_px, max_px):
lut_value = px_value * slope + intercept
voi_value= (((lut_value - center) / width + 0.5) * 255.0)
clamped_value= min(max(voi_value, 0), 255)
if invert:
lut[px_value] = round(255 - clamped_value)
else:
lut[px_value] = round(clamped_value)
return lut
def apply_lut(pixels_in, lut):
pixels= pixels_in.flatten()
pixels_out= [0] * len(pixels)
for i in range (0, len(pixels)):
pixel= pixels[i]
if pixel > 0:
pixels_out[i] = int(lut[pixel])
return np.reshape(pixels_out, (pixels_in.shape[0], pixels_in.shape[1]))
# apply the function
idx= 30
ds= pydicom.dcmread(dcm_files[idx])
raw_pixels= dcm_data.pixel_array
if dcm_data.WindowWidth != '' and dcm_data.WindowCenter != '':
window_width = dcm_data.WindowWidth
window_center = dcm_data.WindowCenter
lut = make_lut(raw_pixels, window_width, window_center, dcm_data.PhotometricInterpretation)
dcm_default_windowing = apply_lut(raw_pixels, lut)
# save the result
ds.PixelData = dcm_default_windowing.tobytes()
ds.save_as("test_luted.dcm")

Image stitching problem using Python and OpenCV

I got output like below after stitching result of 24 stitched images to next 25th image. Before that stitching was good.
Is anyone aware of why/when output of stitching comes like this? What are the possibilities of output coming like that? What may be the reason of that?
Stitching code is following standard stitching steps like finding keypoints, descriptors then matching points, calculating homography and then warping of images. But I am not understanding why that output is coming.
Core part of stitching is like below:
detector = cv2.SIFT_create(400)
# find the keypoints and descriptors with SIFT
gray1 = cv2.cvtColor(image1,cv2.COLOR_BGR2GRAY)
ret1, mask1 = cv2.threshold(gray1,1,255,cv2.THRESH_BINARY)
kp1, descriptors1 = detector.detectAndCompute(gray1,mask1)
gray2 = cv2.cvtColor(image2,cv2.COLOR_BGR2GRAY)
ret2, mask2 = cv2.threshold(gray2,1,255,cv2.THRESH_BINARY)
kp2, descriptors2 = detector.detectAndCompute(gray2,mask2)
keypoints1Im = cv2.drawKeypoints(image1, kp1, outImage = cv2.DRAW_MATCHES_FLAGS_DEFAULT, color=(0,0,255))
keypoints2Im = cv2.drawKeypoints(image2, kp2, outImage = cv2.DRAW_MATCHES_FLAGS_DEFAULT, color=(0,0,255))
# BFMatcher with default params
matcher = cv2.BFMatcher()
matches = matcher.knnMatch(descriptors2,descriptors1, k=2)
# Apply ratio test
good = []
for m, n in matches:
if m.distance < 0.75 * n.distance:
good.append(m)
print (str(len(good)) + " Matches were Found")
if len(good) <= 10:
return image1
matches = copy.copy(good)
matchDrawing = util.drawMatches(gray2,kp2,gray1,kp1,matches)
#Aligning the images
src_pts = np.float32([ kp2[m.queryIdx].pt for m in matches ]).reshape(-1,1,2)
dst_pts = np.float32([ kp1[m.trainIdx].pt for m in matches ]).reshape(-1,1,2)
H = cv2.findHomography(src_pts, dst_pts, cv2.RANSAC,5.0)[0]
h1,w1 = image1.shape[:2]
h2,w2 = image2.shape[:2]
pts1 = np.float32([[0,0],[0,h1],[w1,h1],[w1,0]]).reshape(-1,1,2)
pts2 = np.float32([[0,0],[0,h2],[w2,h2],[w2,0]]).reshape(-1,1,2)
pts2_ = cv2.perspectiveTransform(pts2, H)
pts = np.concatenate((pts1, pts2_), axis=0)
# print("pts:", pts)
[xmin, ymin] = np.int32(pts.min(axis=0).ravel() - 0.5)
[xmax, ymax] = np.int32(pts.max(axis=0).ravel() + 0.5)
t = [-xmin,-ymin]
Ht = np.array([[1,0,t[0]],[0,1,t[1]],[0,0,1]]) # translate
result = cv2.warpPerspective(image2, Ht.dot(H), (xmax-xmin, ymax-ymin))
resizedB = np.zeros((result.shape[0], result.shape[1], 3), np.uint8)
resizedB[t[1]:t[1]+h1,t[0]:w1+t[0]] = image1
# Now create a mask of logo and create its inverse mask also
img2gray = cv2.cvtColor(result,cv2.COLOR_BGR2GRAY)
ret, mask = cv2.threshold(img2gray, 0, 255, cv2.THRESH_BINARY)
kernel = np.ones((5,5),np.uint8)
k1 = (kernel == 1).astype('uint8')
mask = cv2.erode(mask, k1, borderType=cv2.BORDER_CONSTANT)
mask_inv = cv2.bitwise_not(mask)
difference = cv2.bitwise_or(resizedB, resizedB, mask=mask_inv)
result2 = cv2.bitwise_and(result, result, mask=mask)
result = cv2.add(result2, difference)
Edit:
This image shows match drawing while stitching 25 to result until 24 images:
And before that match drawing:
I have total 97 images to stitch. If I stitch 24 and 25 image separately they stitches properly. If I start stitching from 23rd image onwards then also stitching is good but it gives me problem when I stitches starting from 1st image. I am not able to understand the problem.
Result after stitching 23rd image:
Result after stitching 24th image:
Result after stitching 25th image is as above which went wrong.
Strange Observation: If I stitch 23,24,25 images seperately with same code it gets stitches. If I stitch images after 23 till 97 , it gets stitches. But somehow if I stitch images from 1st, it breaks while stitching 25th image. I am not understanding why this happens.
I have tried different combination like different keypoint detection, extraction methods, matching methods, different homography calculations, different warping code but those combinations didn't work. Something is missing or wrong in the steps combination code. I am not able to figure it out.
Sorry for this long question. As I am completely new to this I am not able to explain and get the things properly. Thanks for your help and guidance.
Stitched result of 23,24,25 images separately with SAME code:
With different code (gives black lines in between stitching), if I stitched 97 images then 25th goes up in stitching and stitches as shown below (right corner point):

Firstly, I was not able to recreate your problem and solve it as the images were too big for my system to process. However, I had faced the same problem in my Panorama Stitching project, so I am sharing the reason behind it and my approach to solving my problem. Hope this helps you too.
Here's what my problem looked like when I stitched 4 images together just like you did.
As you can see, the 4th image was getting distorted a lot which must not happen. The same thing happened with you but on a greater level.
Now, here's the output when I stitched 8 images after some image pre-processing.
After some pre-processing on the input images, I was able to stitch 8 images together perfectly without any distortion.
To understand the exact reason behind this kind of distortion, watch this video by Joseph Redmon between 50:26 - 1:07:23.
As suggested in the video, we'll first have to project the images onto a cylinder and then unroll them and then stitch these unrolled images together.
Below is the initial input image(left) and the image after projection and unrolling onto a cylinder(right).
For your problem, as you are using satellite images, I guess projection onto a sphere would work better than the cylinder however you'll have to give it a try.
Sharing below my code for projecting the image onto a cylinder and unrolling it for reference. The mathematics used behind it is the same as given in the video.
def Convert_xy(x, y):
global center, f
xt = ( f * np.tan( (x - center[0]) / f ) ) + center[0]
yt = ( (y - center[1]) / np.cos( (x - center[0]) / f ) ) + center[1]
return xt, yt
def ProjectOntoCylinder(InitialImage):
global w, h, center, f
h, w = InitialImage.shape[:2]
center = [w // 2, h // 2]
f = 1100 # 1100 field; 1000 Sun; 1500 Rainier; 1050 Helens
# Creating a blank transformed image
TransformedImage = np.zeros(InitialImage.shape, dtype=np.uint8)
# Storing all coordinates of the transformed image in 2 arrays (x and y coordinates)
AllCoordinates_of_ti = np.array([np.array([i, j]) for i in range(w) for j in range(h)])
ti_x = AllCoordinates_of_ti[:, 0]
ti_y = AllCoordinates_of_ti[:, 1]
# Finding corresponding coordinates of the transformed image in the initial image
ii_x, ii_y = Convert_xy(ti_x, ti_y)
# Rounding off the coordinate values to get exact pixel values (top-left corner)
ii_tl_x = ii_x.astype(int)
ii_tl_y = ii_y.astype(int)
# Finding transformed image points whose corresponding
# initial image points lies inside the initial image
GoodIndices = (ii_tl_x >= 0) * (ii_tl_x <= (w-2)) * \
(ii_tl_y >= 0) * (ii_tl_y <= (h-2))
# Removing all the outside points from everywhere
ti_x = ti_x[GoodIndices]
ti_y = ti_y[GoodIndices]
ii_x = ii_x[GoodIndices]
ii_y = ii_y[GoodIndices]
ii_tl_x = ii_tl_x[GoodIndices]
ii_tl_y = ii_tl_y[GoodIndices]
# Bilinear interpolation
dx = ii_x - ii_tl_x
dy = ii_y - ii_tl_y
weight_tl = (1.0 - dx) * (1.0 - dy)
weight_tr = (dx) * (1.0 - dy)
weight_bl = (1.0 - dx) * (dy)
weight_br = (dx) * (dy)
TransformedImage[ti_y, ti_x, :] = ( weight_tl[:, None] * InitialImage[ii_tl_y, ii_tl_x, :] ) + \
( weight_tr[:, None] * InitialImage[ii_tl_y, ii_tl_x + 1, :] ) + \
( weight_bl[:, None] * InitialImage[ii_tl_y + 1, ii_tl_x, :] ) + \
( weight_br[:, None] * InitialImage[ii_tl_y + 1, ii_tl_x + 1, :] )
# Getting x coorinate to remove black region from right and left in the transformed image
min_x = min(ti_x)
# Cropping out the black region from both sides (using symmetricity)
TransformedImage = TransformedImage[:, min_x : -min_x, :]
return TransformedImage, ti_x-min_x, ti_y
You just have to call the function ProjectOntoCylinder and pass it an image to get the resultant image and the coordinates of white pixels in the mask image. Use the code below to call this function and get the mask image.
# Applying Cylindrical projection on Image
Image_Cyl, mask_x, mask_y = ProjectOntoCylinder(Image)
# Getting Image Mask
Image_Mask = np.zeros(Image_Cyl.shape, dtype=np.uint8)
Image_Mask[mask_y, mask_x, :] = 255
Here are links to my project and its detailed documentation for reference:
Part 1:
Source Code,
Documentation
Part 2:
Source Code,
Documentation

Make objects of an image the closest to each other

I don't have much experience with PIL and I've got these images edited from a stack of microscopy image cells, each one is in a mask of an image size 30x30. I've been struggling to put these cells in a black background as closest as possible to each other without overlapping.
My code is the following:
def spread_circles(circles, rad, iterations,step):
radsqr = rad**2
for i in range(iterations):
for ix,c in enumerate(circles):
vecs = c-circles
dists = np.sum((vecs)**2,axis=1)
if len(dists)>0:
push = (vecs[dists<radsqr,:].T*dists[dists<radsqr]).T
push = np.sum(push,axis=0)
pushmag = np.sum(push*push)**0.5
if pushmag>0:
push = push/pushmag*step
circles[ix]+=push
return circles
def gen_image(sample,n_iter, height=850, width = 850, max_shape=30, num_circles=150):
circles = np.random.uniform(low=max_shape,high=height-max_shape,size=(num_circles,2))
circles = spread_circles(circles, max_shape, n_iter, 1).astype(int)
img = Image.new(mode='F',size=(height,width),color=0).convert('RGBA')
final1 = Image.new("RGBA", size=(height,width))
final1.paste(img, (0,0), img)
for n,c in enumerate(circles):
foreground = sample[n]
final1.paste(foreground, (c[0],c[1]), foreground)
return final1
But it's hard to avoid overlapping if I do few iterations, and if I Increase they'd be too much sparsed, like this:
What I want it's something similar like inside the red circles that I drew :
I need them closer as they can get, almost like tiles. How can I do that?

I have started thinking about this and have got a couple of strategies implemented. Anyone else fancying some fun is more than welcome to borrow, steal, appropriate or hack any chunks of my code that they can use! I'll probably play some more tomorrow.
#!/usr/bin/env python3
from PIL import Image, ImageOps
import numpy as np
from glob import glob
import math
def checkCoverage(im):
"""Determines percentage of image that is cells rather than background"""
N = np.count_nonzero(im)
return N * 100 / im.size
def loadImages():
"""Load all cell images in current directory into list of trimmed Numpy arrays"""
images = []
for filename in glob('*.png'):
# Open and convert to greyscale
im = Image.open(filename).convert('L')
# Trim to bounding box
im = im.crop(im.getbbox())
images.append(np.array(im))
return images
def Strategy1():
"""Get largest image and pad all images to that size - at least it will tesselate perfectly"""
images = loadImages()
N = len(images)
# Find height of tallest image and width of widest image
maxh = max(im.shape[0] for im in images)
maxw = max(im.shape[1] for im in images)
# Determine how many images we will pack across and down the output image - could be improved
Nx = int(math.sqrt(N))+1
Ny = int(N/Nx)+1
print(f'Padding {N} images each to height:{maxh} x width:{maxw}')
# Create output image
res = Image.new('L', (Nx*maxw,Ny*maxh), color=0)
# Pack all images from list onto regular grid
x, y = 0, 0
for im in images:
this = Image.fromarray(im)
h, w = im.shape
# Pack this image into top-left of its grid-cell, unless
# a) in first row, in which case pack to bottom
# b) in first col, in which case pack to right
thisx = x*maxw
thisy = y*maxh
if y==0:
thisy += maxh - h
if x==0:
thisx += maxw - w
res.paste(this, (thisx,thisy))
x += 1
if x==Nx:
x = 0
y += 1
# Trim extraneous black edges
res = res.crop(res.getbbox())
# Save as JPEG so we don't find it as a PNG in next strategy
res.save('strategy1.jpg')
cov = checkCoverage(np.array(res))
print(f'Strategy1 coverage: {cov}')
def Strategy2():
"""Rotate all images to portrait (tall rather than wide) and order by height so we tend to stack equal height images side-by-side"""
tmp = loadImages()
# Recreate list with all images in portrait format, i.e. tall
portrait = []
for im in tmp:
if im.shape[0] >= im.shape[1]:
# Already portrait, add as-is
portrait.append(im)
else:
# Landscape, so rotate
portrait.append(np.rot90(im))
images = sorted(portrait, key=lambda x: x.shape[0], reverse=True)
N = len(images)
maxh, maxw = 31, 31
# Determine how many images we will pack across and down the output image
Nx = int(math.sqrt(N))+1
Ny = int(N/Nx)+1
print(f'Packing images by height')
# Create output image
resw, resh = Nx*maxw, Ny*maxh
res = Image.new('L', (resw,resh), color=0)
# Pack all from list
xpos, ypos = 0, 0
# Pack first row L->R, second row R->L and alternate
packToRight = True
for im in images:
thisw, thish = im.shape
this = Image.fromarray(im)
if packToRight:
if xpos+thisw < resw:
# If it fits to the right, pack it there
res.paste(this,(xpos,ypos))
xpos += thisw
else:
# Else start a new row, pack at right end and continue packing to left
packToRight = False
res.paste(this,(resw-thisw,ypos))
ypos = res.getbbox()[3]
else:
if xpos>thisw:
# If it fits to the left, pack it there
res.paste(this,(xpos-thisw,ypos))
xpos -= thisw
else:
# Else start a new row, pack at left end and continue packing to right
ypos = res.getbbox()[3]
packToRight = True
res.paste(this,(0,ypos))
# Trim any black edges
res = res.crop(res.getbbox())
# Save as JPEG so we don't find it as a PNG in next strategy
res.save('strategy2.jpg')
cov = checkCoverage(np.array(res))
print(f'Strategy2 coverage: {cov}')
Strategy1()
Strategy2()
Strategy1 gives this at 42% coverage:
Strategy2 gives this at 64% coverage:

Opencv, how to overcrop an image?

I have a set of arbitrary images. Half the images are pictures, half are masks defining ROIS.
In the current version of my program I use the ROI to crop the image (i.e I extract the rectangle in the image matching the bounding box of the ROI mask). The problem is, the ROI mask isn't perfect and it's better to over predict than under predict in my case.
So I want to copy more than the ROI rectangle, but if I do this, I may be trying to crop out of the image.
i.e:
x, y, w, h = cv2.boundingRect(mask_contour)
img = img[int(y-h*0.05):int(y + h * 1.05), int(x-w*0.05):int(x + w * 1.05)]
can fail because it tries to access out of bounds pixels. I could just clamp the values, but I wanted to know if there is a better approach

You can add a boarder using OpenCV
import cv2 as cv
import random
src = cv.imread('/home/stephen/lenna.png')
borderType = cv.BORDER_REPLICATE
boarderSize = .5
top = int(boarderSize * src.shape[0]) # shape[0] = rows
bottom = top
left = int(boarderSize * src.shape[1]) # shape[1] = cols
right = left
value = [random.randint(0,255), random.randint(0,255), random.randint(0,255)]
dst = cv.copyMakeBorder(src, top, bottom, left, right, borderType, None, value)
cv.imshow('img', dst)
c = cv.waitKey(0)

Maybe you could try to limit the coordinates beforehand. Please see the code below:
[ymin, ymax] = [max(0,int(y-h*0.05)), min(h, int(y+h*1.05))]
[xmin, xmax] = [max(0,int(x-w*1.05)), min(w, int(x+w*1.05))]
img = img[ymin:ymax, xmin:xmax]

Crop image with settable center and scale in Python PIL

I would like to crop an image using PIL, although it could be some other module. I need the method to crop with a scale factor, ie 1.5 meaning that the output would be 1.5x zoomed in. Additionally, I would need to set the center where it zooms. This means setting x/2,y/2 as the center would zoom straight to the center, but other x,y values would zoom into those pixels.
If anyone knows how to do this I would really appreciate any help.
Right now I have some cropping working with ims = im.crop((int((x-x/i)/2), int((y-y/i)/2), int((x+(x/i))/2), int((y+(y/i))/2)))
but that only zooms into the center, and "i" doesn't give a nice scale factor.
Again, that you for your help.

It is just a matter of getting the center and the sizes right.
Determine the center of the spot where you want to crop
Determine the new size using the scale factor
Determine the bounding box of the cropped image
The following script should do the trick.
import os.path
from PIL import Image
def get_img_dir():
src_dir = os.path.dirname(__file__)
img_dir = os.path.join(src_dir, '..', 'img')
return img_dir
def open_img():
img_dir = get_img_dir()
img_name = 'amsterdam.jpg'
full_img_path = os.path.join(img_dir, img_name)
img = Image.open(full_img_path)
return img
def crop_image(img, xy, scale_factor):
'''Crop the image around the tuple xy
Inputs:
-------
img: Image opened with PIL.Image
xy: tuple with relative (x,y) position of the center of the cropped image
x and y shall be between 0 and 1
scale_factor: the ratio between the original image's size and the cropped image's size
'''
center = (img.size[0] * xy[0], img.size[1] * xy[1])
new_size = (img.size[0] / scale_factor, img.size[1] / scale_factor)
left = max (0, (int) (center[0] - new_size[0] / 2))
right = min (img.size[0], (int) (center[0] + new_size[0] / 2))
upper = max (0, (int) (center[1] - new_size[1] / 2))
lower = min (img.size[1], (int) (center[1] + new_size[1] / 2))
cropped_img = img.crop((left, upper, right, lower))
return cropped_img
def save_img(img, img_name):
img_dir = get_img_dir()
full_img_path = os.path.join(img_dir, img_name)
img.save(full_img_path)
if __name__ == '__main__':
ams = open_img()
crop_ams = crop_image(ams, (0.50, 0.50), 0.95)
save_img(crop_ams, 'crop_amsterdam_01.jpg')
crop_ams = crop_image(ams, (0.25, 0.25), 2.5)
save_img(crop_ams, 'crop_amsterdam_02.jpg')
crop_ams = crop_image(ams, (0.75, 0.45), 3.5)
save_img(crop_ams, 'crop_amsterdam_03.jpg')
Original image:
crop_amsterdam_01.jpg:
crop_amsterdam_02.jpg:
crop_amsterdam_03.jpg: