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


Question

I need a python routine that can open and import TIFF images into numpy arrays, so I can analyze and modify the contained data and afterwards save them as TIFFs again. (They are basically light intensity maps in greyscale, representing the respective values per pixel)

I tried to find something, but there is no documentation on PIL methods concerning TIFF. I tried to figure it out, but only got bad mode/ file type not supported errors.

What do I need to use here?

1
61
5/29/2014 7:02:41 AM

Accepted Answer

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>
80
9/23/2014 5:46:45 PM

I use matplotlib for reading TIFF files:

import matplotlib.pyplot as plt
I = plt.imread(tiff_file)

and I will be of type ndarray.

According to the documentation though it is actually PIL that works behind the scenes when handling TIFFs as matplotlib only reads PNGs natively, but this has been working fine for me.

There's also a plt.imsave function for saving.


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