The following
Matlab commands are available with installed APE Toolkit:
APE
Overview of all APE components
APEaddDose
% [ EC ] = APEaddDose(datasetname, doseIn)
%
% allows to add a new variable containing X-ray dose received by
% the sample. most usefull for kinetic data.
%
% INPUT datasetname : .mat file to process
% [doseIn] : avoid GUI and enter dose directly for
% single spectrum [optional]
%
% OUTPUT EC : Error Code (0 = OK, 1 = Error)
% (c) F. Dworkowski, 2012
% Version 1.0, 2012-03-19
APEanimateAVI
%[ EC ] = APEanimateAVI( anidatax, anidatay, framerate, outname )
%
% Script to animate kinetic datasets to an AVI video file
%
% INPUT anidatax : X data for animation
% anidatay : Y data for animation
% outname : filename for AVI
% frmrate : frames per second of AVI ([30])
% qulity : Quality in percent ([75])
% includeaxis : 0 = only plot area
% [1]= include Axis etc.
%
% OUTPUT EC : error code (0 = success, 1 = error)
%
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-09-26
APEbatchALS
% [ EC ] = APEbatchALS(lambda, p, itter)
%
% Script to batch-convert all .sif files in one folder to APE-.mat format
% as well as to CSV or Excel
%
% INPUT lambda : Lambda paramter of ALS routine (def= 10000)
% (opt.) p : p paramter of ALS routine (def= 0.01)
% itter : Itterations (def= 10)
%
% OUTPUT EC : error code (0 = success, 1 = error)
%
% (c) F. Dworkowski, 2011
% Version 1.1, 2011-08-02
APEbatchgenerateoverview
% generates overviews for all files in chosen folder using
% APEgenerateoverview
APEbatchloadsif
% [ EC ] = APEbatchloadsif( savetype )
%
% Script to batch-convert all .sif files in one folder to APE-.mat format
% as well as to CSV or Excel
%
% INPUT savetype : 0 = only .mat
% 1 = .mat & CSV
% 2 = .mat & Excel (.xls)
%
% OUTPUT EC : error code (0 = success, 1 = error)
%
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-07-20
APEbatchramanshift
% [ EC ] = APEbatchramanshift( exwavelength )
%
% Converts the raw datax in datasetname from assumed wavelength in nm to
% Raman shift in cm^-^1 using the Laser Excitation Wavelength
% exwavelength in nm.
% The result will be saved in the same file as ramandatax.
%
% INPUT exwavelength : Laser excitation wavelength in nm
%
% OUTPUT EC : Error Code. (0=success, 1=error)
% DEPENDENCIES - ramanshift.m
% (c) F. Dworkowski, 2012
% Version 1.1, 2012-03-20
APEcombinedatasets
% [ EC ] = APEcombinedatasets( )
%
% Allows for semi-interactive combination of APE datasets into a single
% file.
% ATTENTION:
% Not robust! User has to make sure beforehand that all datafiles
% intended to be combined have the same X- and Y-content and -scale !!
%
% OUTPUT EC : Error Code (0 = OK, 1 = Error)
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-07-27
APEconvert
%[ Energy_Joule, Energy_eV, Wavelength, Wavenumber, Frequency ] = ...
% APEconvert( inputvalue, inputtype )
%
% APEconvert converts between Energy (in eV), Wavelength (in nm),
% Wavenumber (in cm^-1) and Frequency (in Hz).
%
% INPUT inputvalue : Value to convert (see above)
% inputtype : Identity of inputvalue
% 'en' = Energy (in eV)
% 'ej' = Energy (in Joule)
% 'wl' = Wavelength (in nm)
% 'wn' = Wavenumber (in cm^-1)
% 'fq' = Frequency (in Hz)
%
% OUTPUT Energy_Joule : in Joule
% Energy_eV : in eV
% Wavelength : in nm
% Wavenumber : in 1/cm
% Frequency : in Hz
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-07-29
APEextractspectrum
%[ EC ] = APEextractspectrum( datasetname, framenumber )
%
% Extracts a single Spectrum from a Kinetic time series and saves it to a
% new .mat file, conserving all additional information present.
%
% INPUT datasetname : File name of source
% framenumber : Index of the spectrum to extract
%
% OUTPUT EC : Error Code. (0=success, 1=error)
% DEPENDENCIES -
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-08-05
APEfullshebang
%[ EC ] = APEfullshebang(exwave, batchfullfolder, outtype, slicewave)
%
% Process a SIF file completly and produces a PDF report in a
% subdirectory of the data folder
%
% INPUT exwave : wavelenght of Raman laser. Use 0 for
% non-raman data.
% batchfullfolder : [0] = process single file
% 1 = process all files in folder
% outtype : sets the type of file to convert to.
% 1 or 'csv' = comma seperated value (*.csv)
% [2] or 'tsv' = TAB seperated value (*.asc)
% 3 or 'ssv' = SPACE seperated value (*.asc)
% 4 or 'xls' = Excel file (*.xls)
% slicewave : wavelenght at which to slice kinetic data.
% Use 0 for non-kinetic data. Multiple
% wavelength can be entered [300 420 500].
%
% OUTPUT EC : error code (0 = success, 1 = error)
%
% EXAMPLE: process all files in one folder with a determined Laser
% wavelength (=> see RaCaTo) of 404.8nm and CSV output:
% [!! All files in folder must be of Raman type!!]
%
% > APEfullshebang(404.8, 1, 0, 1)
APEgenerateoverview
%[ EC ] = APEgenerateoverview( datasetname )
%
% Generate overview and savees as PDF
% Contain following plots and informations:
% 1) Filename
% 2) RAW data
% 3) Ramanshifted Data
% 4) ALS corrected Data
% 5) Footer conversion parameters
%
% INPUT datasetname : filename of APE-MAT file to process
%
% OUTPUT EC : error code (0 = success, 1 = error)
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-09-26
APEmat2asc
%[ EC, tictoctime ] = APEmat2asc( filename, outtype)
%
% APEmat2asc converts APE MAT files to comma seperated value (CSV), tab
% seperated value (TSV), space seperated value (SSV) or even Excel type
% (xls) files.
% Converted files will be saved in the same folder as the source.
%
% !!!! ATTENTION: if files are already present they will be overwriten
% without warning !!!!
%
% INPUT filename : name of file to convert with full path. MUST be
% in APE MAT format (i.e. produced with the
% SLS APE toolkit).
% outtype : sets the type of file to convert to.
% 1 or 'csv' = comma seperated value (*.csv)
% 2 or 'tsv' = TAB seperated value (*.asc)
% 3 or 'ssv' = SPACE seperated value (*.asc)
% 4 or 'xls' = Excel file (*.xls)
% --> DEFAULT is 'csv'
%
% OUTPUT EC : Error Code.(0 = success, 1 = error)
% tictoctime : time in second to perform conversion
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-07-25
APEpeakdet
% [maxtab, mintab]=APEpeakdet(datax, datay, delta, minmax)
%
% Detects peaks (minima) in datay and plots datax vs datay with annotated
% peaks (minima). Also puts out Vectors for peaks (minima).
%
% INPUT datax : dependend data or Index
% datay : Signal
% delta : detection threashold
% minmax : sets detection;
% [1] = peaks (maxima only)
% 2 = minima only
% 3 = both
%
% OUTPUT maxtab : [i-by-2] vector containing index and value of maxima
% mintab : [i-by-2] vector containing index and value of minima
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-10-05
APEraman2lambda
%[ convresult ] = APEraman2lambda( val2conv, valtype, laserWL )
%
% Convert Raman shift to wavelenght or vise versa
%
% INPUT val2conv : Value to convert
% valtype : Type of val2conv:
% 'r' = Raman shift (-> conv. to wavelength (nm))
% 'w' = Wavelength (-> conv. to Raman shift (cm^-1))
% laserWL : Wavelength of ex. Laser (in nm)
%
% OUPUT convresult : Result of the performed conversion.
% (c) F. Dworkowski, 2011
% Version 1.0
APEramanshift
% [ EC ] = APEramanshift( datasetname, exwavelength )
%
% Converts the raw datax in datasetname from assumed wavelength in nm to
% Raman shift in cm^-^1 using the Laser Excitation Wavelength
% exwavelength in nm.
% The result will be saved in the same file as ramandatax.
%
% INPUT datasetname : file name to process
% exwavelength : Laser excitation wavelength in nm
%
% OUTPUT EC : Error Code. (0=success, 1=error)
% DEPENDENCIES - ramanshift.m
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-07-28
APEreducedata
[ EC ] = APEreducedata( datasetname, framenumber, inputtype , alongaxis)
Extracts a single Spectrum from a Kinetic time series and saves it to a
new .mat file, conserving all additional information present.
INPUT datasetname : File name of source
frames : [start:end]
inputtype : Start and End frames are given as data
values instead of frame index
'raman' = Ramanshift
'wave' = Wavelength
'counts'= Y signal
'ALS' = ALS corrected Y signal
alongaxis : 'x' = reduce Data along X (datax),
otherwise along Y (datay)
OUTPUT EC : Error Code. (0=success, 1=error)
APEsingleALS
% [ EC ] = APEsingleALS(lambda, p, itter)
%
% Script to convert single .sif file into APE-.mat format as well as to
% CSV or Excel
%
% INPUT lambda : Lambda paramter of ALS routine (def= 10000)
% (opt.) p : p paramter of ALS routine (def= 0.01)
% itter : Itterations (def= 10)
%
% OUTPUT EC : error code (0 = success, 1 = error)
%
% (c) F. Dworkowski, 2011
% Version 1.0, 2011-08-03