GSTools

A set of matlab functions to read, write and deal with .spc spectra and spectral descriptions

Description

GSTools v0.4.3

This toolbox is an implementation to open and save SPC-spectra in matlab.

Additional routines are supplied as well: e.g.:
- GSImportspec: loads all SPC-files in a map
- GSDendrogram: this is to be used as a supplement to the matlab's toolbox function Dendrogram. GSDendrogram allows the user to put coloured labels with the samples names under the dendrogram. properly are added.
- BTree class: a binary tree implementation, which offers the user to easily inspect the different items in a list, as well as the positions of these different items. This combined approach makes it easy to work with numeric arrays and stringlists, such as spectral descriptions.

A PDF with detailed information on the usage (including some sample code) is supplied in the zip-archive.

GSTools is also included in the Biodata toolbox (doi: 10.1016/j.chemolab.2008.08.003).

• Required Products: Statistics Toolbox
• MATLAB release: MATLAB 6.5 (R13)
• Other requirements: Statistics toolbox is only required in order to make dendrograms.

[Rachel Rohde]

I have only used this for reading in an .spc file. It worked great. It even plots the spectra so you know it was loaded properly.

[Rich Williams]

Haven't used it for .spc files, but it includes an easy to use BTree class. Note that the @BTree\private\DoCompare.m method will fail upon unsigned types unless you replace the line

     tmp = item - value;

with

     tmp = (item > value) - (item < value);

[Dominique Bertrand]

I needed to import SPC files and it works immediately.

[Gerbe van Dreumel]

Use it for importing multi-dimensional spectra: and it works perfect!

[Pall Thordarson]

Just downloaded it to convert SPC Raman data and it works perfectly! Noted a small error in the manual on page 2: plot (SData.xaxis, data);
doesn't work, just change to:
plot (SData.xaxis, Sdata.data); and it works fine.

[matt o'brien]

fantastic bit of code, works better than the old GRAMS converter ive been using until now!

[Cameron Bowles]

fixed-point signed fractions,

I ran into one last problem, the exponent values in the headers/subheaders are in char form, meaning that if they are between 129 - 255, then they are actually between -127 to -1, or at least they are in the files I am reading in.

this causes the Y-axis to be incorrectly scaled, the fix I put in for this is in GSSpcRead; line 689, I inserted the following check loop at 689;

if YScalingExp > 128
      YScalingExp = YScalingExp-256;
end
 then the file should continue
CurrSpec = ........

I assume the process would be the same for the 16 bit input integers, in which case you would have to also put that check into line 675.

[Cameron Bowles]

I found an error for opening multifiles using GSSpcRead.m.

line 437 is;
data = zeros (l,Specdata.spectra(1).data);

and it should be;
data = zeros (l,length(Specdata.spectra(1).data));

Other then that I have had no problems, a great piece of code, good work Kris

[Joseph]

This is exactly what I was looking for! Unfortunately, when I try to import multiple files, I get the following error:

EDU>> GSImportspec()
Warning: Multifile flag is set. But SPC-file does not contain multiple spectra.
> In GSSpcRead at 236
  In GSImportspec at 245
??? Subscripted assignment between dissimilar structures.

Error in ==> GSImportspec at 245
            spectra(i) = GSSpcRead (spcfiles(i).name, -1, 0);

[Joseph]

Oops, I'm sorry. I was inputting the wrong compatibility. Never mind.

[Larry Weber]

I found an error in GSSpcWrite.m . It outputs the xtype, ytype, and ztype to the header as a string instead of the correct single byte binary format. This is especially bad if the string has more than one byte since the rest of the header will get messed up.

The fix is to change lines 578 through 592 to the following code which simply converts the string to a single binary byte.

Thanks to Kris for making this very helpful set of routines available to us.

if isfield (spectra, 'xtype')
    ThisSpcHdr.fxtype = uint8(str2double(LocateItem (spectra.xtype, Types.X, 2))); %%std%%%BYTE: Type of X units
else
    ThisSpcHdr.fxtype = 13; %%std%%%BYTE: Type of X units
end
if isfield (spectra, 'ytype')
    ThisSpcHdr.fytype = uint8(str2double(LocateItem (spectra.ytype, Types.Y, 2))); %%std%%%BYTE: Type of Y units
else
    ThisSpcHdr.fytype = 0; %%std%%%BYTE: Type of Y units
end
if isfield (spectra, 'ztype')
    ThisSpcHdr.fztype = uint8(str2double(LocateItem (spectra.ztype, Types.X, 2))); %%std%%%BYTE: Type of z units
else
    ThisSpcHdr.fztype = 0; %%std%%%BYTE: Type of Z units
end