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a simple program to rapidly analyze color TIFF files for energy values.
Legal Stuff
© 2002 by Randal Cox 1 and Richard Benya 2 ,All Rights Reserved
1 Bioinformatics Group, Department of Genetics, University of Illinois at Chicago
2 Department of Medicine, University of Illinois at Chicago
This software is provided ``AS IS'' and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose, are disclaimed. In no event shall the authors or the University of Illinois be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.
Contacting the author
You can contact the author (Randal Cox) for updates or platform-specific compilations by email at randal@uic.edu
Getting the program
For Mac OSX, you can download a simple droplet. If this link brings up a page of gibberish, you may need option-click (on a mac) or control-click (on windows) to download the file to your hard disk. This download comes as a dmg archive. Double click the archive and a virtual disk called "tiffalyzer.osx" will mount on your desktop. Inside is a README file and the actual droplet, "tiffalyzer.osx". Drag the droplet to wherever you need it (e.g., your Applications folder).
For Mac OS9, a prototype is currently in testing.
For *nix machines , we provide a tgz archive of the source code, suitable for compilation. Extract the document, cd into the directory, and type make. The application "tiffalyzer" can be placed wherever is convenient (e.g., /usr/local/bin). Typing "./tiffalyzer -?" gives help on the application and there is a README that discusses this as well.
For Windows, a java client is in testing.
For other platforms, the source code in the tgz archive is sufficient for anyone skilled with a compiler to port it to their platform.
Using the program
Tiffalyzer is provided either as a droplet for Mac OSX or as a command line program for *nix operating systems. Simply drop an image onto the droplet or execute the command with a file name as an argument.
Tiffalyzer only accepts certain files for analysis. The input file MUST be
- in TIFF format
- 8 bits R, 8 bits G, 8 bits B (24 bits total)
- uncompressed
If the file fails in any of these regards, the output file will contain an error message to that effect.
If the file is an acceptable format, tiffalyzer will analyze each pixel, ignoring those that are pure white or pure black . This feature of disregarding white or black pixels allows you to mark relevant areas in your image by deleting the background. For example, this is done readily in Adobe Photoshop with the magic wantd tool.
The output file will contain some summary image information plus information about the image energy. Below is an example of the output file.
| Image Information ----------------- File : /Users/thel/Desktop/tiffalyzer/tests/test.tiff : -> /Users/thel/Desktop/tiffalyzer/tests/test.tiff.out Size : 40 wide by 40 tall Pixels : 1600 total : 1600 (100.0%) used Energy ------ color energy [ avg +/- std] [min..max] ----- ------ ----- +/- ----- ---..--- red 118.5 [118.0 +/- 11.4] [102..135] green 118.5 [118.0 +/- 11.4] [102..135] blue 118.5 [118.0 +/- 11.4] [102..135] ----- ------ ----- +/- ----- ---..--- sum 355.6 [354.0 +/- 34.1] [306..405] Elapsed time ------------ load file = 0.0 seconds analyze = 0.0 seconds total = 0.0 seconds |
Most of this is self-explanatory. For the rest, more detail appears below.
Under pixels, the second line shows how many were actually used. The unused pixels are either pure white or pure black. This feature allows one to select all the background of an image in, for example, Photoshop or Gimp or some other image editing program, and replace it with white. Then, tiffalyzer will only consider the non-background pixels.
Under Energy, seperate lines appear for each color seperately. In addition, there is a line for overall energy (i.e., the sum of the R+G+B channels). Energy is the root-mean-square of all the non-white and non-black points. The average and standard deviations as well as total ranges are provided as an additional service.
The time information describes what is taking the most time in this analysis. If you need faster analysis, the load time can be reduced by faster hard drives (e.g., SCSI arrays, fast Firewire, etc) while the analyze time can be reduced with faster CPUs. 21MB files can be finished in just seconds on a 600 MHz G3 laptop.
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