Skip to content

Instantly share code, notes, and snippets.

@jimrybarski

jimrybarski/cheeseburger.py

Last active August 29, 2015 14:12
Show Gist options
  • Save jimrybarski/34d50de70a4b51128eab to your computer and use it in GitHub Desktop.
Save jimrybarski/34d50de70a4b51128eab to your computer and use it in GitHub Desktop.
Download ZIP

Revisions

  1. jimrybarski revised this gist Jan 7, 2015. 1 changed file with 6 additions and 3 deletions.
    9 changes: 6 additions & 3 deletions cheeseburger.py
    View file
    Original file line number Diff line number Diff line change
    @@ -1,4 +1,7 @@
    import os, skimage.io, skimage.exposure, numpy
    files = ["/".join([dir_name, image_name]) for dir_name, dir_names, filenames in os.walk("/home/jim/Desktop/experiments/141111/kymograph") for image_name in filenames]
    enhanced_images = [skimage.exposure.rescale_intensity(original_image, in_range=tuple(numpy.percentile(original_image, (2, 98)))) for original_image in map(skimage.io.imread, files)]
    map(lambda (filename, enhanced_image): skimage.io.imsave(filename, enhanced_image), zip(map(lambda x: x.split(".")[0] + "_enhanced.png", files), enhanced_images))
    for dir_name, dir_names, filenames in os.walk("/home/jim/Desktop/experiments/141111/kymograph"):
    for image_name in filenames:
    filename = "/".join([dir_name, image_name])
    original_image = skimage.io.imread(filename)
    enhanced_image = skimage.exposure.rescale_intensity(original_image, in_range=tuple(numpy.percentile(original_image, (2, 98))))
    skimage.io.imsave(filename.split(".")[0] + "_enhanced.png", enhanced_image)
  2. jimrybarski revised this gist Jan 7, 2015. 1 changed file with 2 additions and 1 deletion.
    3 changes: 2 additions & 1 deletion cheeseburger.py
    View file
    Original file line number Diff line number Diff line change
    @@ -1,3 +1,4 @@
    import os, skimage.io, skimage.exposure, numpy
    files = ["/".join([dir_name, image_name]) for dir_name, dir_names, filenames in os.walk("/home/jim/Desktop/experiments/141111/kymograph") for image_name in filenames]
    map(lambda (filename, enhanced_image): skimage.io.imsave(filename, enhanced_image), zip(map(lambda x: x.split(".")[0] + "_enhanced.png", files), [skimage.exposure.rescale_intensity(original_image, in_range=tuple(numpy.percentile(original_image, (2, 98)))) for original_image in map(skimage.io.imread, files)]))
    enhanced_images = [skimage.exposure.rescale_intensity(original_image, in_range=tuple(numpy.percentile(original_image, (2, 98)))) for original_image in map(skimage.io.imread, files)]
    map(lambda (filename, enhanced_image): skimage.io.imsave(filename, enhanced_image), zip(map(lambda x: x.split(".")[0] + "_enhanced.png", files), enhanced_images))
  3. jimrybarski created this gist Jan 7, 2015.
    3 changes: 3 additions & 0 deletions cheeseburger.py
    View file
    Original file line number Diff line number Diff line change
    @@ -0,0 +1,3 @@
    import os, skimage.io, skimage.exposure, numpy
    files = ["/".join([dir_name, image_name]) for dir_name, dir_names, filenames in os.walk("/home/jim/Desktop/experiments/141111/kymograph") for image_name in filenames]
    map(lambda (filename, enhanced_image): skimage.io.imsave(filename, enhanced_image), zip(map(lambda x: x.split(".")[0] + "_enhanced.png", files), [skimage.exposure.rescale_intensity(original_image, in_range=tuple(numpy.percentile(original_image, (2, 98)))) for original_image in map(skimage.io.imread, files)]))