nag::SpecImageFactory< FPType > Class Template Reference

This class contains a function which reads in a configuration file and creates a new nag::SIMSpecImage of nag::MALDISpecImage object accordingly. More...

#include <SpecImageFactory.hpp>

Static Public Member Functions
static SpecImage< FPType > *	NewSpecImage (const std::string &config)
	Static factory function to return an object of the type decided by the contents of a configuration file. More...

Detailed Description

template<class FPType>
class nag::SpecImageFactory< FPType >

This class contains a function which reads in a configuration file and creates a new nag::SIMSpecImage of nag::MALDISpecImage object accordingly.

Member Function Documentation

template<class FPType >

static SpecImage<FPType>* nag::SpecImageFactory< FPType >::NewSpecImage ( const std::string &  config )

static

Static factory function to return an object of the type decided by the contents of a configuration file.

Returns either a nag::SIMSpecImage or a nag::MALDISpecImage object, depending on the contents of the input configuration file named by the string config.

The config file has the following syntax for nag::SIMSpecImage types. Items in brackets are optional:

       tofs = <path to time-of-flight data file>
       [coords = <path to coordinates data file>]
       [scans = <path to scans data file>]
       [props = <path to properties text file>]
       [limits = <path to limits text file>]
       [mem = <integer number of bytes to use as memory limit. Default = 0 (i.e. no memory limit).>]
       [xbin = <integer bin size in x dimension>]
       [ybin = <integer bin size in y dimension>]
       [zbin = <integer bin size in z dimension>]
       [tofbin = <integer bin size for channels (ToF values)>]
       [K0 = <integer K0 calibration constant>]
       [SF = <integer SF calibration constant>]
       [NPP = <integer total number of primary pulses over whole image>]

Note that values given in the properties file take precedence over those defined directly in the config file.

The config file has the following syntax for nag::MALDISpecImage types:

       imzml = <path to ImzML input file>
       [limits = <path to limits text file>]
       [mem = <integer number of bytes to use as memory limit. Default = 0 (i.e. no memory limit).>]
       [xbin = <integer bin size in x dimension>]
       [ybin = <integer bin size in y dimension>]
       [zbin = <integer bin size in z dimension>]
       [mzbin = <real bin size for channels (m/z values)>]

Any line in the configuration file starting with # is commented. File paths may be delimited within single quotes.

Limits files have the following format: the first line is ignored (treated as a header), the following lines are read as 2-column space-separated intervals such that, on line n, the first value is the lower limit, and the second value is the upper limit of the (n-1)th peak selection interval. If the values contain a decimal point they are taken to be limits expressed as m/z values; if they do not they are taken to be expressed as ToF values (the latter is valid only for SIMS input).

Below is an example of a ToF limits file defining 4 peaks:

        lower limit  upper limit
        121520       121572
        126413       126439
        126441       126484
        131160       131206

Below is an example of a m/z limits file defining 4 peaks:

        lower limit  upper limit
        3.219190     3.221899
        3.479011     3.480419
        3.480527     3.482856
        3.740715     3.743297

A more detailed discussion of these options can be found in the respective class constructors, and a discussion of the limited memory option (mem) can be found in the class introductions.

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The documentation for this class was generated from the following file:

• SpecImageFactory.hpp