Working with Tiffs (Import, Export) in Python Using Numpy

Working with TIFFs (import, export) in Python using numpy

First, I downloaded a test TIFF image from this page called a_image.tif. Then I opened with PIL like this:

>>> from PIL import Image
>>> im = Image.open('a_image.tif')
>>> im.show()

This showed the rainbow image. To convert to a numpy array, it's as simple as:

>>> import numpy
>>> imarray = numpy.array(im)

We can see that the size of the image and the shape of the array match up:

>>> imarray.shape
(44, 330)
>>> im.size
(330, 44)

And the array contains uint8 values:

>>> imarray
array([[  0,   1,   2, ..., 244, 245, 246],
       [  0,   1,   2, ..., 244, 245, 246],
       [  0,   1,   2, ..., 244, 245, 246],
       ..., 
       [  0,   1,   2, ..., 244, 245, 246],
       [  0,   1,   2, ..., 244, 245, 246],
       [  0,   1,   2, ..., 244, 245, 246]], dtype=uint8)

Once you're done modifying the array, you can turn it back into a PIL image like this:

>>> Image.fromarray(imarray)
<Image.Image image mode=L size=330x44 at 0x2786518>

Python: How do I read the data in this multipage TIFF file to produce the desired image?

"produce a numpy array representing the new image that looks as it is meant to.": The PNG image looks like a thumbnail image, a somewhat arbitrary preview of the data in the TIFF file obtained by binning and scaling:

import tifffile
im = tifffile.imread('20180309_Vn_ribosome_0001.tif', maxworkers=6)
binsize = 25
height = im.shape[1] // binsize
width = im.shape[2] // binsize
im = im[:, :height * binsize, : width * binsize]
im = im.reshape(im.shape[0], height, binsize, width, binsize)
im = im.sum((0, 2, 4), dtype='uint32')

from matplotlib import pyplot
pyplot.imshow(im, cmap='gray')
pyplot.show()

Python PIL For Loop to work with Multi-image TIFF

You can use the "seek" method of a PIL image to have access to the different pages of a tif (or frames of an animated gif).

from PIL import Image

img = Image.open('multipage.tif')

for i in range(4):
    try:
        img.seek(i)
        print img.getpixel( (0, 0))
    except EOFError:
        # Not enough frames in img
        break

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