A team at my school has an existing Image Analysis Pipeline built in Python for identifying regions of interest automatically, among other functions. I wanted to adapt the linearlization tools from mica to Python, so I’d like to know where the source code for the linearization models is. I found the .ijm macro script in the GitHub repository, but after having scanned that I couldn’t find the raw equations for each linearization model or how the program was converting the pixel value data to a linear model.
Would someone mind pointing me to the correct file to pore over to find the math underlying this operation?
First you create a linearisation function using the tool for that. This saves the model in “plugins/micaToolbox/Linearisation models”. The equations are then handled by the scripts which open up mspec images. These read the type of equation (generally a customised equation works best) and its parameters from the .mspec file itself. The pixel transforms are all then done by the “Linearisation_Function.java” script (in the “mica_toolbox.jar” file container).