CODEWITHSUNDEEP
python
Rui Li
Rui Li

Reputation: 41

How to read gzip compressed CZI image?

I'm reading CZI images with the first code block, successfully. I want to read xx.czi.gz with the second code block, but failed. How can I read 'czi.gz' in to an array?

Thanks a lot!

from czifile import CziFile
import gzip

fname='xxx.czi'
with CziFile(fname) as czi:
  image_arrays = czi.asarray()

fname2='xxx.czi.gz'
with gzip.open(fname2, 'rb') as f:
  with CziFile(f) as czi:
    image_arrays = czi.asarray()

Upvotes: 0

Views: 290

Answers (2)

Nick ODell
Nick ODell

Reputation: 25299

I think @Nico238 is correct - you need to unzip the file first. However, you don't need to do that manually. You can do it with your Python program. That would look like this:

import shutils
import gzip
from czifile import CziFile
fname='xxx.czi'
fname2='xxx.czi.gz'

# decompress fname2 and put it in fname
with gzip.open(fname2, 'rb') as f_in:
  with open(fname, 'wb') as f_out:
    shutil.copyfileobj(f_in, f_out)

with CziFile(fname) as czi:
  image_arrays = czi.asarray()

(Source.)

Upvotes: 0

user1531591
user1531591

Reputation:

I think the problem is that CziFile expect a file path. In case 2, you give it a file descriptor. I didn't see a method to initialize from a stream/fd. You might have to unzip then save the gz before reading the czi

Upvotes: 1

Related Questions