Ratio Plus

Author: Paulo Magalh�es (pamaga_A_T_bio_DOT_unipd_DOT_it)
University of Padua, Italy
History: 2003/12/04: first version
2003/12/10: added constant background subtraction; implemented "zero divided by zero equals one" feature (any other value divided by zero yields infinity)
Source: Ratio_Plus.java
Installation: Download Ratio_Plus.class to the plugins folder, or subfolder, and restart ImageJ.
This plugin calculates the ratio between two images (single frames or stacks),
as used in Fura-2 experiments, for example. The code -- heavily annotated to help
beginners like myself explore the world of ImageJ -- is largely based on Image
Calculator Plus. Paulo Magalh�es, 10dec03.

The plugin requires two images of the same width and height,
and of the same type (8-, 16-, or 32-bit); the images must be:
    i) two single images;
   ii) two stacks with the same number of frames; or
  iii) a stack as a first image and a single frame as a second - in this case,
       the single frame will be applied throughtout the complete stack.

The resulting image (in 32-bit) is calculated as follows:

    intR = (intA - bkgA) / (int B - bkgB) * MF

where intA, intB and intR are the intensities of the first, second and ratio images,
respectively; bkgA and bkgB are constant background values (entered by the user)
for the first and second images, respectively; MF is an arbitrary multiplication factor.

If a pixel value becomes negative after background subtraction, it is set to zero
before ratio calculation.

In addition, the plugin can accept clipping values for either of the images:
if the pixel intensity (after background subtraction) is lower than the clipping value
for that image, it is set to zero before ratio calculation; the clipping values for either
image are set by the user.

NB: if two corresponding pixels in the first and second images are zero, their ratio
is set to 1 (one); i.e., "zero by zero" division equals one.

Future plans:
    background correction using a ROI (in one or both images).

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