I need to read 64x64 pgm plain format image files and put the resulting values in a numpy matrix. I can do it only if I use Opencv and PIL functions to open the image, but the final numpy matrix yielded has 3-channel and the values returned are 0 and 255, instead of 0 and 1 (the image is binary). I also tried to use genfromtxt but it can't put the values in a numpy matrix.
I only want a 1 channel numpy matrix with 0 and 1's from the pgm image. How can I do that with python?
If PIL opens your image files as RGB but you want them in binary, I think your only choice is to convert after opening.
im = Image.open('imagefile').convert('1')
Related
I am trying to write(save) a int16 numpy array as an image using openCV. Find the numpy file of an image in the link below: https://drive.google.com/file/d/1nEq_CeNmSgacARa2ADr_f_qVaSfJSZZX/view?usp=sharing
The image I saved in bmp or png or tiff format is look like this:
Uint16
I converted the numpy array to uint8 and the image become very dark and the maximum value of the image is just 34 as shown below:
uint8
Please let me know how to properly save and visualize this int16 format image.
Note: plt.imshow of int16 numpy array showing proper visual. matplotlib_imshow
I have saved the image properly using the following syntax
from skimage.util import img_as_ubyte
img=np.load('brain.npy')
img1=img/img.max()
img2=img_as_ubyte(img1)
cv2.imwrite('brain_u8.png', img2)
correct_output
I am reading an image from S3 bucket, then resize the image and get the numpy array of the resized image, called "a". I also save the resized image and reopen it and get the numpy array of that called "b". My question is why a and b are different?
resp = s3.get_object(Bucket=event['bucket'], Key=event['image_keys'][0])
data = resp['Body']
image_as_bytes = io.BytesIO(data.read())
image = Image.open(image_as_bytes).convert('RGB').resize((299, 299),Image.NEAREST)
a = np.asarray(image)
image.save('IMAGE_58990004_110132026B_13d64039_resized_lambda.jpg')
b = np.asarray(Image.open('IMAGE_58990004_110132026B_13d64039_resized_lambda.jpg'))
Does ".save" changes the numpy array?
Assuming that image.save(...) uses the filename ending (.jpg) to pick a file format (I don't know if it does. but it seems reasonable), then you are saving as a JPEG file, and the JPEG compression algorithm is lossy, i.e, it discards some information to make the file smaller.
Try using a file format with lossless compression, such as PNG.
I am trying to read this tiff image with python. I have tried PIL to and save this image. The process goes smoothly, but the output image seems to be plain dark. Here is the code I used.
from PIL import Image
im = Image.open('file.tif')
imarray = np.array(im)
data = Image.fromarray(imarray)
data.save('x.tif')
Please let me know if I have done anything wrong, or if there is any other working way to read and save tif images. I mainly need it as NumPy array for processing purposes.
The problem is simply that the image is dark. If you open it with PIL, and convert to a Numpy array, you can see the maximum brightness is 2455, which on a 16-bit image with possible range 0..65535, means it is only 2455/65535, or 3.7% bright.
from PIL import Image
# Open image
im = Image.open('5 atm_gain 80_C001H001S0001000025.tif')
# Make into Numpy array
na = np.array(im)
print(na.max()) # prints 2455
So, you need to normalise your image or scale up the brightnesses. A VERY CRUDE method is to multiply by 50, for example:
Image.fromarray(na*50).show()
But really, you should use a proper normalisation, like PIL.ImageOps.autocontrast() or OpenCV normalize().
I'm trying to save a 16-bit numpy array as a 16-bit PNG but what I obtain is only a black picture. I put here a minimum example of what I'm talking aboout.
im = np.random.randint(low=1, high=6536, size=65536).reshape(256,256) #sample numpy array to save as image
plt.imshow(im, cmap=plt.cm.gray)
Given the above numpy array this is the image I see with matplotlib, but when then I save the image as 16-bit png I obtain the picture below:
import imageio
imageio.imwrite('result.png', im)
Image saved:
where some light grey spots are visible but the image is substantially black. Anyway when I read back the image and visualize it again with matplotlib I see the same starting image. I also tried other libraries instead of imageio (like PIL or PyPNG) but with the same result.
I know that 16-bit image values range from 0 to 65535 and in the array numpy array here there only values from 1 to 6536, but I need to save numpy arrays images similar to this, i.e. where the maximum value represented in the image isn't the maximum representable value. I think that some sort of nornalization is involved in the saving process. I need to save the array exactly as I see them in matplotlib at their maximum resolution and without compression or shrinkage in their values (so division by 255 or conversion to 8-bit array are not suitable).
It looks like imageio.imwrite will do the right thing if you convert the data type of the array to numpy.uint16 before writing the PNG file:
imageio.imwrite('result.png', im.astype(np.uint16))
When I do that, result.png is a 16 bit gray-scale PNG file.
If you want the image to have the full grayscale range from black to white, you'll have to scale the values to the range [0, 65535]. E.g. something like:
im2 = (65535*(im - im.min())/im.ptp()).astype(np.uint16)
Then you can save that array with
imageio.imwrite('result2.png', im2)
For writing a NumPy array to a PNG file, an alternative is numpngw (a package that I created). For example,
from numpngw import write_png
im2 = (65535*(im - im.min())/im.ptp()).astype(np.uint16)
write_png('result2.png', im2)
If you are already using imageio, there is probably no signficant advantage to using numpngw. It is, however, a much lighter dependency than imageio--it depends only on NumPy (no dependence on PIL/Pillow and no dependence on libpng).
I want to save floating-point numbers as pixels in an image file. I am currently working in OpenCV-python, but I had also tried it with Pillow (PIL). Both packages convert float pixel data to integer before writing them to the file.
I want to save pixel values such as:
(245.7865, 123.18788, 98.9866)
But when I read back the image file I get:
(246, 123, 99)
Somehow my floating-point numbers get rounded off and converted to integers.
How to stop PIL or OpenCV from converting them to integer?
Raster images are normally stored as integer values only. Instead save the numpy array directly like so
x = numpy.array([1, 2, 3])
with open('x.npy', 'wb') as f:
numpy.save(f, x)
Then load the variable back like so
x = numpy.load('x.npy')
Other alternatives include
Save one or more GRAY16 png images, with your floats multiplied and truncated.
Use the Netpbm format supporting floats.
Save a pickle.
The behavior you observe depends on the file format in which you save the image. Few image formats have a specification for floating-point pixel values. Though some do, first and foremost TIFF.
To demonstrate the desired behavior with a TIFF image writer, consider the following script. It uses the versatile image input/output library ImageIO, which relies on PILlow as one of its back-ends:
# Use Stack Overflow logo as sample image.
import imageio
logo = 'https://cdn.sstatic.net/Sites/stackoverflow/img/logo.png'
image = imageio.imread(logo)
# Normalize to 1. Pixel values are now floating-point.
image = image / image.max()
# Save as image file and read back in.
format = 'tiff'
imageio.imwrite(f'image.{format}', image)
print(f'wrote: {image.dtype}')
image = imageio.imread(f'image.{format}')
print(f'read: {image.dtype}')
The output of that script is:
wrote: float64
read: float64
If, on the other hand, you change the format to PNG (format = 'png' in the code), the output is:
Lossy conversion from float64 to uint8. Range [0, 1].
Convert image to uint8 prior to saving to suppress this warning.
wrote: float64
read: uint8