.roh file format: PHP parsing library

Avantes USB spectrometers are supplied with a Windows binary which generates one ROH and one RCM file when the user clicks "Save experiment". In the version of 6.0, the ROH file contains a header of 22 four-byte floats, then the spectrum as a float array and a footer of 3 floats. The first and last pixel numbers are specified in the header and determine the (length+1) of the spectral data. In the tested files, the length is (2032-211-1)=1820 pixels, but Kaitai determines this automatically anyway.

The wavelength calibration is stored as a polynomial with coefficients of 'wlintercept', 'wlx1', ... 'wlx4', the argument of which is the (pixel number + 1), as found out by comparing with the original Avantes converted data files. There is no intensity calibration saved, but it is recommended to do it in your program - the CCD in the spectrometer is so uneven that one should prepare exact pixel-to-pixel calibration curves to get reasonable spectral results.

The rest of the header floats is not known to the author. Note that the newer version of Avantes software has a different format, see also https://kr.mathworks.com/examples/matlab/community/20341-reading-spectra-from-avantes-binary-files-demonstration

The RCM file contains the user-specified comment, so it may be useful for automatic conversion of data.

Written and tested by Filip Dominec, 2017

File extension

roh

KS implementation details

License: CC0-1.0

This page hosts a formal specification of .roh file format using Kaitai Struct. This specification can be automatically translated into a variety of programming languages to get a parsing library.

PHP source code to parse .roh file format

AvantesRoh60.php

<?php
// This is a generated file! Please edit source .ksy file and use kaitai-struct-compiler to rebuild

/**
 * Avantes USB spectrometers are supplied with a Windows binary which 
 * generates one ROH and one RCM file when the user clicks "Save
 * experiment". In the version of 6.0, the ROH file contains a header 
 * of 22 four-byte floats, then the spectrum as a float array and a 
 * footer of 3 floats. The first and last pixel numbers are specified in the 
 * header and determine the (length+1) of the spectral data. In the tested 
 * files, the length is (2032-211-1)=1820 pixels, but Kaitai determines this 
 * automatically anyway.
 * 
 * The wavelength calibration is stored as a polynomial with coefficients
 * of 'wlintercept', 'wlx1', ... 'wlx4', the argument of which is the
 * (pixel number + 1), as found out by comparing with the original 
 * Avantes converted data files. There is no intensity calibration saved,
 * but it is recommended to do it in your program - the CCD in the spectrometer 
 * is so uneven that one should prepare exact pixel-to-pixel calibration curves 
 * to get reasonable spectral results.
 * 
 * The rest of the header floats is not known to the author. Note that the 
 * newer version of Avantes software has a different format, see also
 * https://kr.mathworks.com/examples/matlab/community/20341-reading-spectra-from-avantes-binary-files-demonstration
 * 
 * The RCM file contains the user-specified comment, so it may be useful
 * for automatic conversion of data.
 * 
 * Written and tested by Filip Dominec, 2017
 */

class AvantesRoh60 extends \Kaitai\Struct\Struct {
    public function __construct(\Kaitai\Struct\Stream $_io, \Kaitai\Struct\Struct $_parent = null, \AvantesRoh60 $_root = null) {
        parent::__construct($_io, $_parent, $_root);
        $this->_read();
    }

    private function _read() {
        $this->_m_unknown1 = $this->_io->readF4le();
        $this->_m_wlintercept = $this->_io->readF4le();
        $this->_m_wlx1 = $this->_io->readF4le();
        $this->_m_wlx2 = $this->_io->readF4le();
        $this->_m_wlx3 = $this->_io->readF4le();
        $this->_m_wlx4 = $this->_io->readF4le();
        $this->_m_unknown2 = [];
        $n = 9;
        for ($i = 0; $i < $n; $i++) {
            $this->_m_unknown2[] = $this->_io->readF4le();
        }
        $this->_m_ipixfirst = $this->_io->readF4le();
        $this->_m_ipixlast = $this->_io->readF4le();
        $this->_m_unknown3 = [];
        $n = 4;
        for ($i = 0; $i < $n; $i++) {
            $this->_m_unknown3[] = $this->_io->readF4le();
        }
        $this->_m_spectrum = [];
        $n = ((intval($this->ipixlast()) - intval($this->ipixfirst())) - 1);
        for ($i = 0; $i < $n; $i++) {
            $this->_m_spectrum[] = $this->_io->readF4le();
        }
        $this->_m_unknown4 = [];
        $n = 3;
        for ($i = 0; $i < $n; $i++) {
            $this->_m_unknown4[] = $this->_io->readF4le();
        }
    }
    protected $_m_unknown1;
    protected $_m_wlintercept;
    protected $_m_wlx1;
    protected $_m_wlx2;
    protected $_m_wlx3;
    protected $_m_wlx4;
    protected $_m_unknown2;
    protected $_m_ipixfirst;
    protected $_m_ipixlast;
    protected $_m_unknown3;
    protected $_m_spectrum;
    protected $_m_unknown4;
    public function unknown1() { return $this->_m_unknown1; }
    public function wlintercept() { return $this->_m_wlintercept; }
    public function wlx1() { return $this->_m_wlx1; }
    public function wlx2() { return $this->_m_wlx2; }
    public function wlx3() { return $this->_m_wlx3; }
    public function wlx4() { return $this->_m_wlx4; }
    public function unknown2() { return $this->_m_unknown2; }
    public function ipixfirst() { return $this->_m_ipixfirst; }
    public function ipixlast() { return $this->_m_ipixlast; }
    public function unknown3() { return $this->_m_unknown3; }
    public function spectrum() { return $this->_m_spectrum; }
    public function unknown4() { return $this->_m_unknown4; }
}