Skip to content

Latest commit

 

History

History
75 lines (64 loc) · 2.15 KB

README.md

File metadata and controls

75 lines (64 loc) · 2.15 KB
Raw

Usage:

  1. In your python project

    git clone https://github.com/aaalgo/ljpeg.git

    Or if you are using git already:

    git submodule add https://github.com/aaalgo/ljpeg.git

  2. Produce the jpeg binary.

    cd jpegdir; make

  3. In your python code:

    from ljpeg import ljpeg

x = ljpeg.read(path)

    The loaded is a matrix of type uint16. Typically you want to convert that to float for subsequent processing.

    x = ljpeg.read(path).astype('float')

    The LJPEG format sometimes has wrong values for width and height (transposed). One has to read the correct values of width and height from the associating .ics file. Below is a sample snippet for this purpose:

        W = None
    H = None
    # find the shape of image
    for l in open(ics, 'r'):
	l = l.strip().split(' ')
	if len(l) < 7:
	    continue
	if l[0] == name:
	    W = int(l[4])
	    H = int(l[2])
	    bps = int(l[6])
	    if bps != 12:
		logging.warn('BPS != 12: %s' % path)
	    break

    assert W != None
    assert H != None

    if W != image.shape[1]:
	logging.warn('reshape: %s' % path)
	image = image.reshape((H, W))

  4. Using ljpeg.py standalone:

    • Convert to TIFF (requires the .ics file in the same directory as LJPEG)
    ./ljpeg.py cases/benigns/benign_01/case0029/C_0029_1.LEFT_CC.LJPEG output.tiff
    • Convert to TIFF and verify that no information has been lost
    ./ljpeg.py cases/benigns/benign_01/case0029/C_0029_1.LEFT_CC.LJPEG output.tiff --verify
    • Convert to jpeg for visualization with down-sizing scale=0.3 (16-bit TIFF is not good for direct visualization)
    ./ljpeg.py cases/benigns/benign_01/case0029/C_0029_1.LEFT_CC.LJPEG output.jpg --visual --scale 0.3

    Note that output file can be any format that's supported by OpenCV (which includes all common types). Most file formats only support 8-bit images, so directly saving into such file formats will cause problems. Add "--visual" to normalize color into 8-bit before saving to such file formats.

The Stanford ljpeg code is in public domain and is therefore OK to be included here. I did minor modification to make the code compile under modern Linux.