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Python Image Processing Cookbook

Loading Image File

matplotlib has matplotlib.image.imread, and PIL also has similar file input methods. The former is limited to png files and the latter is limited to 8-bit images. For this reason, we focus on openCV and TiffFile modules.

openCV

Tiff file to numpy.ndarray

>>> import cv
>>> img = cv.imread('/Users/miura/img/blobs.tif')
>>> type(img)
>>> <type 'numpy.ndarray'>

  • cv.imread reads only the first frame in tiff stack.
  • 8bit image becomes RGB-like format, triplet of 8 bits per pixel.

Tiff file to Iplimage

In [40]: img = cv.LoadImage('/Users/miura/img/blobs.tif')
In [41]: img
Out[41]: <iplimage(nChannels=3 width=256 height=254 widthStep=768 )>

Tiff file to cvMat

Tifffile.py

Tiff to numpy.ndarray, Single Image

In [44]: import tifffile as tff
In [50]: tiffimg = tff.TIFFfile('/Users/miura/img/blobs.tif')
In [51]: type(tiffimg)
Out[51]: <class 'tifffile.TIFFfile'>
In [52]: img = tiffimg.asarray()
In [53]: type(img)
Out[53]: <type 'numpy.ndarray'>

Tiff to numpy.ndarray, Stack Image

In [54]: tiffimg = tff.TIFFfile('/Users/miura/img/flybrainG.tif')
In [55]: img = tiffimg.asarray()
In [57]: tiffimg
Out[57]: <tifffile.TIFFfile object at 0x1299ac910>
In [65]: type(img)
Out[65]: <type 'numpy.ndarray'>
In [61]: img10 = tiffimg[10].asarray()
In [62]: type(img10)
Out[62]: <type 'numpy.ndarray'>

  • if the image file is a single frame image, not so different from the others
  • Stack tiff file is loaded peroperly. Single frame is extractable by indexing. In above case, 11th frame is extracted.

Conversion between types

OpenCV Mat object to numpy.ndarray object

  • tested with python2.6, openCV 2.2, numpy 1.6.1, OSX10.6.8

>>> import cv
>>> import numpy as np
>>> mat = cv.CreateMat( 3 , 5 , cv.CV_32FC1 )
>>> cv.Set( mat , 7 )
>>> a = np.asarray( mat[:,:] )
>>> a
array([[ 7.,  7.,  7.,  7.,  7.],
       [ 7.,  7.,  7.,  7.,  7.],
       [ 7.,  7.,  7.,  7.,  7.]], dtype=float32)

<link>

OpenCV Image object to numpy.ndarray object

  • tested with python2.6, openCV 2.2, numpy 1.6.1, OSX10.6.8

>>> im = cv.CreateImage( ( 5 , 5 ) , 8 , 1 )
>>> cv.Set( im , 100 )
>>> im_array = np.asarray( im )
>>> im_array
array(<iplimage(nChannels=1 width=5 height=5 widthStep=8 )>, dtype=object)
>>> im_array = np.asarray( im[:,:] )
>>> im_array
array([[100, 100, 100, 100, 100],
       [100, 100, 100, 100, 100],
       [100, 100, 100, 100, 100],
       [100, 100, 100, 100, 100],
       [100, 100, 100, 100, 100]], dtype=uint8)

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documents/110816pyip_cooking.1313537967.txt.gz · Last modified: 2016/05/24 12:46 (external edit)

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