.roh file format: Java 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. You may wish to divide the spectra by the integration time before comparing them.

Written and tested by Filip Dominec, 2017-2018

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.

Usage

Parse a local file and get structure in memory:

AvantesRoh60 data = AvantesRoh60.fromFile("path/to/local/file.roh");

Or parse structure from a byte array:

byte[] someArray = new byte[] { ... };
AvantesRoh60 data = new AvantesRoh60(new KaitaiStream(someArray));

After that, one can get various attributes from the structure by invoking getter methods like:

data.unknown1() // => get unknown1

Java source code to parse .roh file format

AvantesRoh60.java

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

import io.kaitai.struct.ByteBufferKaitaiStream;
import io.kaitai.struct.KaitaiStruct;
import io.kaitai.struct.KaitaiStream;
import java.io.IOException;
import java.util.ArrayList;


/**
 * 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. You may wish to divide the spectra by 
 * the integration time before comparing them.
 * 
 * Written and tested by Filip Dominec, 2017-2018
 */
public class AvantesRoh60 extends KaitaiStruct {
    public static AvantesRoh60 fromFile(String fileName) throws IOException {
        return new AvantesRoh60(new ByteBufferKaitaiStream(fileName));
    }

    public AvantesRoh60(KaitaiStream _io) {
        this(_io, null, null);
    }

    public AvantesRoh60(KaitaiStream _io, KaitaiStruct _parent) {
        this(_io, _parent, null);
    }

    public AvantesRoh60(KaitaiStream _io, KaitaiStruct _parent, AvantesRoh60 _root) {
        super(_io);
        this._parent = _parent;
        this._root = _root == null ? this : _root;
        _read();
    }
    private void _read() {
        this.unknown1 = this._io.readF4le();
        this.wlintercept = this._io.readF4le();
        this.wlx1 = this._io.readF4le();
        this.wlx2 = this._io.readF4le();
        this.wlx3 = this._io.readF4le();
        this.wlx4 = this._io.readF4le();
        unknown2 = new ArrayList<Float>((int) (9));
        for (int i = 0; i < 9; i++) {
            this.unknown2.add(this._io.readF4le());
        }
        this.ipixfirst = this._io.readF4le();
        this.ipixlast = this._io.readF4le();
        unknown3 = new ArrayList<Float>((int) (4));
        for (int i = 0; i < 4; i++) {
            this.unknown3.add(this._io.readF4le());
        }
        spectrum = new ArrayList<Float>((int) ((((int) (ipixlast() + 0) - (int) (ipixfirst() + 0)) - 1)));
        for (int i = 0; i < (((int) (ipixlast() + 0) - (int) (ipixfirst() + 0)) - 1); i++) {
            this.spectrum.add(this._io.readF4le());
        }
        this.integrationMs = this._io.readF4le();
        this.averaging = this._io.readF4le();
        this.pixelSmoothing = this._io.readF4le();
    }
    private float unknown1;
    private float wlintercept;
    private float wlx1;
    private float wlx2;
    private float wlx3;
    private float wlx4;
    private ArrayList<Float> unknown2;
    private float ipixfirst;
    private float ipixlast;
    private ArrayList<Float> unknown3;
    private ArrayList<Float> spectrum;
    private float integrationMs;
    private float averaging;
    private float pixelSmoothing;
    private AvantesRoh60 _root;
    private KaitaiStruct _parent;
    public float unknown1() { return unknown1; }
    public float wlintercept() { return wlintercept; }
    public float wlx1() { return wlx1; }
    public float wlx2() { return wlx2; }
    public float wlx3() { return wlx3; }
    public float wlx4() { return wlx4; }
    public ArrayList<Float> unknown2() { return unknown2; }
    public float ipixfirst() { return ipixfirst; }
    public float ipixlast() { return ipixlast; }
    public ArrayList<Float> unknown3() { return unknown3; }
    public ArrayList<Float> spectrum() { return spectrum; }
    public float integrationMs() { return integrationMs; }
    public float averaging() { return averaging; }
    public float pixelSmoothing() { return pixelSmoothing; }
    public AvantesRoh60 _root() { return _root; }
    public KaitaiStruct _parent() { return _parent; }
}