Introduction

SAENO's provides an easy way to perform unconstrained 3-D force reconstruction in semi-affine materials. As input the algorithm either takes stacks of confocal reflection data from which it measures the local displacements on its own, or it takes an already measured displacement field as input. SAENO can also solve boundary value problems imposed to semi-affine materials. Checkout the modes page for more information about the possibilities that SAENO provides.

Specifying Parameters

For all purposes SAENO is run from the command line in the following way:

SAENO CONFIG somedir/config.txt PARAM1 value1 PARAM2 value2 ...

For all its parameters SAENO first loads the default values, which are defined in the source code. Next it opens the config-file stated in the command prompt (in the example that is somedir/config.txt) and load the stated parameters (overwriting the defaults). Then it reads the parameter-value pairs that were further set in the command prompt (as PARAM1 value1 PARAM2 value2 ...) and again overwrites the previously set values with the ones stated in the command prompt. Taken together there are three sources of values for the parameters. The default values with lowest priority, then the config-file and finally the command prompt with highest priority.

Modules

The work flow of SAENO is organized into modules. The particular sequence of modules that SAENO runs is controlled through the MODE parameter (see modes page). Every module has its own set of parameters. For example the loadStacks module has parameters that specify the filenames of the two confocal reflection stacks that are loaded in this module.

That said, how to make SAENO do what I want?

1. Chose a mode and write the needed parameters into a config-file
2. Go through all modules that your chosen mode runs and specify their parameters in the same config-file.
3. Run SAENO with your config-file