There is a folder with 65 images. When i import(read in spyder) one by one(by first below code) images, the size of each image is (168, 192) which is according to data sheet. But when i import all these images together as a list with 65 members(by second below code) the size of each image(each member of list which it's name is image_list) changes to (192,168). Can anyone explain the reason of this change?
from PIL import Image
def read_img():
im = Image.open("E:\\Face Recognition Projet\\CroppedYale\\yaleB01\\yaleB01_P00A-060E-20.pgm")
im.show() # Show pictures
print(im.size) # Output image size
if __name__ == "__main__":
read_img() # Call read_img()
import numpy as np
from PIL import Image
import glob
image_list = []
for filename in glob.glob('E:\\Face Recognition Projet\\CroppedYale\\yaleB02\\*.pgm'): #assuming gif
im=Image.open(filename)
image_list.append(im)
The data sheet you have, whatever it is, may be listing sizes as height x width; PIL sizes are width x height.
Related
I am trying to convert this .tif file to a .png, here is the image (I attached a link because it is 250mb): https://drive.google.com/file/d/1nEvG8O5NM1bsKM-fSo66QJF7mZyR_fh-/view?usp=sharing
Here is my current code, it returns an grayscale image with multiple copies of the original .tif in one .png, it is suppose to return an RGB image:
import rasterio
import numpy as np
from PIL import Image
dataset = rasterio.open("world.tif")
window = rasterio.windows.Window(0, 0, 21600, 10800)
out = dataset.read(window=window)
out = out.reshape(10800, 21600, 3).astype(np.uint8)
img = Image.fromarray(out, "RGB")
img.save("out.png")
I'm not sure why you are mixing up PIL/Pillow and raster like that. You can just do the following with PIL:
from PIL import Image
# Allow monster large images
Image.MAX_IMAGE_PIXELS = None
# Load image
im = Image.open('world.tif')
# Reduce to manageable size and save as PNG
small = im.resize((2160,1080))
small.save('result.png')
I created an model in blender. From here I took 2d slices through the y-plane of that model leading to the following.
600 png files each corresponding to a ylocation i.e y=0, y=0.1 etc
Each png file has a resolution of 500 x 600.
I am now trying to merge the 600 pngs into a h5 file using python before loading the .h5 into some software. I find that each individual png file is read fine and looks great. However when I look at the final 3d image there is some stretching of the image, and im not sure how this is being created.
The images are resized (from 600x600 to 500x600, but I have checked and this is not the cause of the stretching). I would like to know why I am introducing such stretching in other planes (not y-plane).
Here is my code, please note that there is some work in progress here, hence why I append the dataset to a list (this is to be used for later code)
from PIL import Image
import sys
import os
import h5py
import numpy as np
import cv2
from datetime import datetime
dir_path = os.path.dirname(os.path.realpath(__file__))
sys.path.append(dir_path + '//..//..')
Xlen=500
Ylen=600
Zlen=600
directory=dir_path+"/LowPolyA21/"
for filename in os.listdir(directory):
if fnmatch.fnmatch(filename, '*.png'):
image = Image.open(directory+filename)
new_image = image.resize((Zlen, Xlen))
new_image.save(directory+filename)
dataset = np.zeros((Xlen, Zlen, Ylen), np.float)
# traverse all the pictures under the specified address
cnt_num = 0
img_list = sorted(os.listdir(directory))
os.chdir(directory)
for img in (img_list):
if img.endswith(".png"):
gray_img = cv2.imread(img, 0)
dataset[:, :, cnt_num] = gray_img
cnt_num += 1
dataset[dataset == 0] = -1
dataset=dataset.swapaxes(1,2)
datasetlist=[]
datasetlist.append(dataset)
dz_dy_dz = (float(0.001),float(0.001),float(0.001))
for j in range(Xlen):
for k in range(Ylen):
for l in range(Zlen):
if datasetlist[i][j,k,l]>1:
datasetlist[i][j,k,l]=1
now = datetime.now()
timestamp = now.strftime("%d%m%Y_%H%M%S%f")
out_h5_path='voxelA_'+timestamp+'_flipped'
out_h5_path2='voxelA_'+timestamp+'_flipped.h5'
with h5py.File(out_h5_path2, 'w') as f:
f.attrs['dx_dy_dz'] = dz_dy_dz
f['data'] = datasetlist[i] # Write data to the file's primary key data below
Example of image without stretching (in y-plane)
Example of image with stretching (in x-plane)
I have a folder with 230400 images, each representing one pixel in a 480 x 480 image.
How can I use Python to make a single image out of each image?
I tried to creat a npy-array but I believe it resulted in a 3d array instead of a 2d array:
import cv2
import glob
import numpy as np
data = []
files = glob.glob("./data/*.PNG")
for myFile in files:
print(myFile)
image = cv2.imread(myFile)
data.append(image)
print('shape:', np.array(data).shape)
np.save('data',data)
Output: shape: (230400, 100, 100, 3)
How do I create a 2d array of images? And how do I convert it to an image?
Start by creating an empty numpy image with the size of your output image. For each pixel load the image in.
import numpy as np
import cv2
import glob
image_x = 480
image_y =480
files = glob.glob("./data/*.PNG")
output = np.zeros((image_x, image_y, 3))
for i in range(image_x):
for j in range(image_y):
pixel = cv2.imread(files[image_x*i+j])
output[i,j] = pixel[0,0]
Note: This is neither fast nor nice, but explicit.
For saving, use cv2.imwrite on the resulting array as in:
cv2.imwrite('output.png', output)
I am trying to use a dicom image and manipulate it using OpenCV in a Python environment. So far I have used the pydicom library to read the dicom(.dcm) image data and using the pixel array attribute to display the picture using OpenCV imshow method. But the output is just a blank window. Here is the snippet of code I am using at this moment.
import numpy as np
import cv2
import pydicom as dicom
ds=dicom.dcmread('sample.dcm')
cv2.imshow('sample image dicom',ds.pixel_array)
cv2.waitkey()
If i print out the array which is used here, the output is different from what i would get with a normal numpy array. I have tried using matplotlib imshow method as well and it was able to display the image with some colour distortions. Is there a way to convert the array into a legible format for OpenCV?
Faced a similar issue. Used exposure.equalize_adapthist() (source). The resulting image isn't a hundred percent to that you would see using a DICOM Viewer but it's the best I was able to get.
import numpy as np
import cv2
import pydicom as dicom
from skimage import exposure
ds=dicom.dcmread('sample.dcm')
dcm_sample=ds.pixel_array
dcm_sample=exposure.equalize_adapthist(dcm_sample)
cv2.imshow('sample image dicom',dcm_sample)
cv2.waitkey()
I have figured out a way to get the image to show. As Dan mentioned in the comments, the value of the matrix was scaled down and due to the imshow function, the output was too dark for the human eye to differentiate. So, in the end the only thing i needed to do was multiply the entire mat data with 128. The image is showing perfectly now. multiplying the matrix by 255 over exposes the picture and causes certain features to blow. Here is the revised code.
import numpy as np
import cv2
import pydicom as dicom
ds=dicom.dcmread('sample.dcm')
dcm_sample=ds.pixel_array*128
cv2.imshow('sample image dicom',dcm_sample)
cv2.waitkey()
I don't think that is a correct answer. It works for that particular image because most of your pixel values are in the lower range. Check this OpenCV: How to visualize a depth image. It is for c++ but easily adapted to Python.
This is the best way(in my opinion) to open image in opencv as a numpy array while perserving the image quality:
import numpy as np
import pydicom, os, cv2
def dicom_to_numpy(ds):
DCM_Img = ds
rows = DCM_Img.get(0x00280010).value #Get number of rows from tag (0028, 0010)
cols = DCM_Img.get(0x00280011).value #Get number of cols from tag (0028, 0011)
Instance_Number = int(DCM_Img.get(0x00200013).value) #Get actual slice instance number from tag (0020, 0013)
Window_Center = int(DCM_Img.get(0x00281050).value) #Get window center from tag (0028, 1050)
Window_Width = int(DCM_Img.get(0x00281051).value) #Get window width from tag (0028, 1051)
Window_Max = int(Window_Center + Window_Width / 2)
Window_Min = int(Window_Center - Window_Width / 2)
if (DCM_Img.get(0x00281052) is None):
Rescale_Intercept = 0
else:
Rescale_Intercept = int(DCM_Img.get(0x00281052).value)
if (DCM_Img.get(0x00281053) is None):
Rescale_Slope = 1
else:
Rescale_Slope = int(DCM_Img.get(0x00281053).value)
New_Img = np.zeros((rows, cols), np.uint8)
Pixels = DCM_Img.pixel_array
for i in range(0, rows):
for j in range(0, cols):
Pix_Val = Pixels[i][j]
Rescale_Pix_Val = Pix_Val * Rescale_Slope + Rescale_Intercept
if (Rescale_Pix_Val > Window_Max): #if intensity is greater than max window
New_Img[i][j] = 255
elif (Rescale_Pix_Val < Window_Min): #if intensity is less than min window
New_Img[i][j] = 0
else:
New_Img[i][j] = int(((Rescale_Pix_Val - Window_Min) / (Window_Max - Window_Min)) * 255) #Normalize the intensities
return New_Img
file_path = "C:/example.dcm"
image = pydicom.read_file(file_path)
image = dicom_to_numpy(image)
#show image
cv2.imshow('sample image dicom',image)
cv2.waitKey(0)
cv2.destroyAllWindows()
I'm using PIL and numpy to combine two images while one is a .jpg and the other image is represented by a numpy array, which defines a mask that I want to put on top of the original image (basically just a matrix with one and zero entries and the same size as the .jpg). PIL’s composite function works just fine for that but for some reason, after saving the composite image, the file size shrinks to approximately 1/3 of the original image size. Can someone explain this behavior to me?
Here's a code snippet:
import numpy as np
import PIL
from PIL import Image
from PIL import ImageColor
rgb = ImageColor.getrgb('black')
# Read image and write into numpy array
image = Image.open('test_image.jpg')
(im_width, im_height) = image.size
# Create empty mask
mask = np.zeros((im_width, im_height))
# Composite image and mask
solid_color = np.expand_dims(np.ones_like(mask), axis=2) *
np.reshape(list(rgb), [1, 1, 3])
pil_solid_color =
Image.fromarray(np.uint8(solid_color)).convert('RGBA')
pil_mask = Image.fromarray(np.uint8(255.*mask)).convert('L')
image = Image.composite(pil_solid_color, image, pil_mask)
# save image
image.save('test_image_with_mask.jpg')
Code was inspired by tnesorflow's object detection api. Thanks in advance.