AtomProbeLab Files

AtomProbeLab v0.2.3

README
Welcome to AtomProbeLab, MATLAB based tools for atom probe 
microscopy data analysis.

REQUIRE
'MATLAB' > 2016a with the following toolboxes:
'Statistics and Machine Learning Toolbox'
'Curve Fitting Toolbox'

INSTALL
To install AtomProbeLab, unzip the files and copy them to your 
MATLAB directory (usually “YourName/Documents/MATLAB/” on 
windows). 

USAGE
Most of the m-files (the main contents of AtomProbeLab) are 
contained in the /src folder. Example data and demo scripts are
in the root directory. Add addpath('src\'); to your script so that
MATLAB can access the files within.
Read through the demoScripts for example code on useful functions.
The per-ion deconvolution tool is contained by the localDecomp_atom 
function. To see how to use this function please see the example 
script “demoScript_localDecomp.m”.
demoScript_bulkDecomp.m demonstrates how to perform composition 
analysis on a single dataset or pos-file. This script also shows 
how to make use of the output of the bulk overlap solver to 
investigate the goodness of fit and retrieve composition values 
with confidence intervals. 
demoScript_bulkDecompParts.m similar to above, but takes an
index list which allows a single data file to split into sub-volumes.

More details are given at: 
https://sourceforge.net/p/atomprobelab/wiki/Home/

AUTHORS
All of this software was written by Andrew J. London, with the exception 
of (licence details within each file):
- parfor_progressbar.m function which was written by Daniel Terry
- fminsearchbnd.m Copyright (c) 2006, John D'Errico
- test rrng files from the http://threedepict.sourceforge.net project (gplv3+)

COPYING / LICENSE
See LICENSE.txt for full details.
AtomProbeLab  Copyright (C) 2019  Andrew J. London
  
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
  
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
  
You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.




Isotopic abundance data has the following copyright notice:
MX Cheminformatics Tools for Java

Copyright (c) 2007, 2008 Metamolecular, LLC
http://metamolecular.com

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.

This system of atomic masses is quoted from:

de Laeter, J.R.; Boehlke, J.K.; de Bievre, P.; Hidaka, H.; Peiser, H.S.; Rosman, K.J.R.;
Taylor, P.D.P. Atomic Weights of the Elements: Review 2000 (IUPAC Technical Report)
Pure Appl. Chem. 2003, 75, 683-800.

http://www.iupac.org/publications/pac/2003/7506/7506x0683.html