CODEWITHSUNDEEP
pythonpython-imaging-librarytiffpygame16-bit
Ain Britain
Ain Britain

Reputation: 380

Python: Manipulating a 16-bit .tiff image in PIL &/or pygame: convert to 8-bit somehow?

enter image description hereHello all,

I am working on a program which determines the average colony size of yeast from a photograph, and it is working fine with the .bmp images I tested it on. The program uses pygame, and might use PIL later.

However, the camera/software combo we use in my lab will only save 16-bit grayscale tiff's, and pygame does not seem to be able to recognize 16-bit tiff's, only 8-bit. I have been reading up for the last few hours on easy ways around this, but even the Python Imaging Library does not seem to be able to work with 16-bit .tiff's, I've tried and I get "IOError: cannot identify image file".

import Image

img = Image.open("01 WT mm.tif")

My ultimate goal is to have this program be user-friendly and easy to install, so I'm trying to avoid adding additional modules or requiring people to install ImageMagick or something.

Does anyone know a simple workaround to this problem using freeware or pure python? I don't know too much about images: bit-depth manipulation is out of my scope. But I am fairly sure that I don't need all 16 bits, and that probably only around 8 actually have real data anyway. In fact, I once used ImageMagick to try to convert them, and this resulted in an all-white image: I've since read that I should use the command "-auto-levels" because the data does not actually encompass the 16-bit range.

I greatly appreciate your help, and apologize for my lack of knowledge.

P.S.: Does anyone have any tips on how to make my Python program easy for non-programmers to install? Is there a way, for example, to somehow bundle it with Python and pygame so it's only one install? Can this be done for both Windows and Mac? Thank you.

EDIT: I tried to open it in GIMP, and got 3 errors:

1) Incorrect count for field "DateTime" (27, expecting 20); tag trimmed 2) Sorry, can not handle images with 12-bit samples 3) Unsupported layout, no RGBA loader

What does this mean and how do I fit it?

Upvotes: 4

Views: 7398

Answers (3)

WombatPM
WombatPM

Reputation: 2619

py2exe is the way to go for packaging up your application if you are on a windows system.

Regarding the 16bit tiff issue:

This example http://ubuntuforums.org/showthread.php?t=1483265 shows how to convert for display using PIL.

Now for the unasked portion question: When doing image analysis, you want to maintain the highest dynamic range possible for as long as possible in your image manipulations - you lose less information that way. As you may or may not be aware, PIL provides you with many filters/transforms that would allow you enhance the contrast of an image, even out light levels, or perform edge detection. A future direction you might want to consider is displaying the original image (scaled to 8 bit of course) along side a scaled image that has been processed for edge detection.

Check out http://code.google.com/p/pyimp/wiki/screenshots for some more examples and sample code.

Upvotes: 2

whatnick
whatnick

Reputation: 5470

This is actually a 2 part question:

1) 16 bit image data mangling for Python - I usually use GDAL + Numpy. This might be a bit too much for your requirements, you can use PIL + Numpy instead.

2) Release engineering Python apps can get messy. Depending on how complex your app is you can get away with py2deb, py2app and py2exe. Learning distutils will help too.

Upvotes: 1

user227667
user227667

Reputation:

I would look at pylibtiff, which has a pure python tiff reader.

For bundling, your best bet is probably py2exe and py2app.

Upvotes: 2

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