Working with TIFFs import export in Python using numpy

Question

I need a python method to open and import TIFF images into numpy arrays so I can analyze and modify the pixel data and then save them as TIFFs again   They are basically light intensity maps in greyscale  representing the respective values per pixel   I couldn t find any documentation on PIL methods concerning TIFF  I tried to figure it out  but only got  bad mode  or  file type not supported  errors   What do I need to use here

User · Answer

You can also use pytiff of which I m the author        import pytiff      with pytiff Tiff  filename tif   as handle          part   handle 100 200  200 400         multipage tif     with pytiff Tiff  multipage tif   as handle          for page in handle              part   page 100 200  200 400    It s a fairly small module and may not have as many features as other modules  but it supports tiled tiffs and bigtiff  so you can read parts of large images

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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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First  I downloaded a test TIFF image from this page called a image tif  Then I opened with PIL like this    gt  gt  gt  from PIL import Image  gt  gt  gt  im   Image open  a image tif    gt  gt  gt  im show     This showed the rainbow image  To convert to a numpy array  it s as simple as    gt  gt  gt  import numpy  gt  gt  gt  imarray   numpy array im    We can see that the size of the image and the shape of the array match up    gt  gt  gt  imarray shape  44  330   gt  gt  gt  im size  330  44    And the array contains uint8 values    gt  gt  gt  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    gt  gt  gt  Image fromarray imarray   lt Image Image image mode L size 330x44 at 0x2786518 gt

User · Answer

Using cv2 import cv2 image   cv2 imread tiff file tif  cv2 imshow  tif image  image

User · Answer

You could also use GDAL to do this   I realize that it is a geospatial toolkit  but nothing requires you to have a cartographic product   Link to precompiled GDAL binaries for windows  assuming windows here  http   www gisinternals com sdk   To access the array   from osgeo import gdal  dataset   gdal Open  path to dataset tiff   gdal GA ReadOnly  for x in range 1  dataset RasterCount   1       band   dataset GetRasterBand x      array   band ReadAsArray

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In case of image stacks  I find it easier to use scikit-image to read  and matplotlib to show or save  I have handled 16-bit TIFF image stacks with the following code   from skimage import io import matplotlib pyplot as plt    read the image stack img   io imread  a image tif     show the image plt imshow mol cmap  gray   plt axis  off     save the image plt savefig  output tif   transparent True  dpi 300  bbox inches  tight   pad inches 0 0

User · Answer

PyLibTiff worked better for me than PIL  which as of December 2020 still doesn t support color images with more than 8 bits per color  from libtiff import TIFF  tif   TIFF open  filename tif     open tiff file in read mode   read an image in the currect TIFF directory as a numpy array image   tif read image      read all images in a TIFF file  for image in tif iter images         pass  tif   TIFF open  filename tif   mode  w   tif write image image   You can install PyLibTiff with pip3 install numpy libtiff  The readme of PyLibTiff also mentions the tifffile library but I haven t tried it

User · Answer

I recommend using the python bindings to OpenImageIO  it s the standard for dealing with various image formats in the vfx world  I ve ovten found it more reliable in reading various compression types compared to PIL   import OpenImageIO as oiio input   oiio ImageInput open    path to image tif

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

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