Finnee: The User's Manual

"The real problem in speech is not precise language. The problem is clear language", Richard Feynman

Forewords

This wiki is because there is no point of making a good software without clear explanations. Sadly, clear and correct writing does not come easily to all of us; if you detect errors, imprecisions or incoherencies let me know. You can also rectify the wiki and "push" the corrections for me to accept them.

What Finnee2016 is

A general toolbox. Finnee was initially though for the clusters plot when using separation techniques hyphenated high-resolution mass spectrometry. Nevertheless, while Finnee2016 will provide the same functionalities, it is aimed to be a general Matlab toolbox dedicate to the postprocessing of hyphenated separation techniques.
A collaborative work. Or it ought to be… GitHub greatly facilitates collaborative work, do not hesitate to comment, “fork” and ”push”. If you are not a programmer, we are looking for sets of experiments (especially in “profile spectrum“ format) that can be used to validate or compare algorithms. We are also open to new approaches and can help in concretising them.
An Open project. This also means that detail explanations and tutorials are needed. I will try to give precise information in this wiki as well as in the Matlab. Video tutorials can also be made if required.

What Finnee2016 is not

A software. Finnee2016 is a Matlab toolbox and cannot be used without a working version of Matlab. It has been programmed with Matlab 2016a, but it may be compatible with older versions. Trial versions of Matlab can be requested from MathWorks. Standalone applications made be done in the future (GUI) if there is a demand for it.
A finished product. Every classes or function are likely to change.
Made by computer geniuses. I am a self-taught Matlab programmer, I am aware that the code may not be the most efficient, and I know nothing about “do's and don'ts” of coding but I am always open to constructive criticisms.

What Finnee do

Extract and visualise the information contained in a dataset. Finnee is organised using multiple objects, those allow to filter the data, for example, extracted ions profiles (EIP), but also include algorithms to further analyse those data. Objects can be included in a routine or saved as independent objects.
Clean datasets from baseline drift and background noise. Finnee aims to filter the original data to remove the baseline drift and background noise. This not only allows reducing the size by more 95% but also facilitate and improve mining for unknown features-
Record every transformation. Finnee is designed in such a way that every transformation can be recorded. This allows checking for the data integrity at every step.