Open and read unique spectrum file .spc
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I have some old wave spectra data I need to process, but I'm having trouble getting MatLab to read the files.
%% I - Load files of wave data
SpecFiles = dir("RawData\*.spc");
numfiles = length(SpecFiles);
SpecData = cell(1,numfiles);
for k = 1:numfiles
SpecData{k} = readtable(SpecFiles(k).name);
%SpecData{k} = dlmread(SpecFiles(k).name,' ',5,0);
%SpecData{k} = readSPC(SpecFiles(k));
%SpecData{k} = tgspcread(SpecFiles(k));
end
%data = fileDatastore("RawData\",@tgspcread,@fcn);
%test = tgspcread(SJCSPC195401010000.spc)
Below is an example of the file format. The first 4 rows are unimportant to me, the 5th row begins the data that I need out of them with the fith row being the time stamp and other information and the 6th through the 28th row being the spectral info.
23 35
122 762 100.0
2177571.00 408574.12 255.0 1
0.0390 0.0429 0.0472 0.0520 0.0572 0.0630 0.0693 0.0763 0.0840 0.0924 0.1017 0.1120 0.1233 0.1357 0.1493 0.1643 0.1809 0.1991 0.2191 0.2412 0.2655 0.2922 0.3216
1954010100 82 52 -0.08 1.00 0.0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0.001 0.004 0.010 0.022 0.043 0.076 0.111 0.133 0.144 0.141 0.124 0.097 0.065 0.038 0.021 0.014 0.009 0.004 0.001 0 0 0 0 0
0 0.001 0.002 0.003 0.005 0.008 0.014 0.020 0.023 0.025 0.030 0.033 0.035 0.037 0.040 0.050 0.073 0.105 0.140 0.183 0.225 0.246 0.227 0.176 0.116 0.070 0.048 0.029 0.013 0.005 0.001 0 0 0 0
0 0.001 0.003 0.003 0.005 0.007 0.013 0.018 0.021 0.024 0.027 0.031 0.034 0.038 0.046 0.061 0.087 0.120 0.154 0.200 0.256 0.309 0.342 0.339 0.296 0.240 0.196 0.142 0.085 0.044 0.016 0.003 0 0 0
0 0.001 0.002 0.003 0.004 0.005 0.009 0.012 0.013 0.011 0.008 0.005 0.004 0.007 0.015 0.029 0.059 0.103 0.160 0.246 0.357 0.460 0.523 0.538 0.507 0.454 0.403 0.325 0.227 0.136 0.058 0.012 0.001 0 0
0 0 0 0 0 0 0 0 0 0.001 0.003 0.008 0.014 0.020 0.027 0.042 0.081 0.144 0.218 0.314 0.425 0.533 0.621 0.679 0.701 0.687 0.652 0.578 0.459 0.315 0.160 0.046 0.007 0 0
0 0 0 0 0 0.001 0.002 0.003 0.006 0.010 0.014 0.018 0.020 0.023 0.029 0.039 0.059 0.091 0.131 0.191 0.273 0.363 0.453 0.541 0.619 0.673 0.695 0.690 0.635 0.511 0.319 0.124 0.026 0.001 0
0 0 0 0 0 0.000 0.001 0.003 0.006 0.010 0.017 0.023 0.030 0.039 0.050 0.065 0.093 0.134 0.178 0.224 0.270 0.318 0.374 0.438 0.504 0.559 0.594 0.616 0.611 0.555 0.420 0.221 0.070 0.006 0
0 0 0 0 0 0 0 0 0 0 0.002 0.007 0.014 0.028 0.051 0.077 0.103 0.129 0.154 0.179 0.204 0.231 0.264 0.304 0.345 0.383 0.412 0.436 0.446 0.436 0.387 0.268 0.123 0.021 0
0 0 0 0 0 0 0 0 0 0 0.004 0.013 0.023 0.041 0.068 0.096 0.117 0.132 0.146 0.157 0.166 0.175 0.191 0.213 0.235 0.255 0.271 0.286 0.298 0.305 0.302 0.265 0.173 0.052 0
0 0 0 0 0 0 0 0.004 0.011 0.020 0.026 0.031 0.036 0.046 0.063 0.080 0.091 0.095 0.100 0.108 0.120 0.132 0.145 0.157 0.169 0.180 0.191 0.201 0.209 0.211 0.213 0.206 0.179 0.095 0
0 0 0 0 0 0 0 0.002 0.006 0.009 0.017 0.028 0.040 0.048 0.052 0.056 0.062 0.069 0.077 0.085 0.092 0.100 0.108 0.115 0.122 0.128 0.135 0.141 0.144 0.143 0.141 0.138 0.133 0.105 0
0 0 0 0 0.005 0.015 0.025 0.030 0.031 0.031 0.033 0.036 0.040 0.041 0.042 0.042 0.044 0.047 0.050 0.056 0.063 0.070 0.077 0.084 0.090 0.094 0.096 0.100 0.100 0.100 0.099 0.097 0.092 0.085 0
0 0.001 0.002 0.004 0.007 0.012 0.016 0.019 0.021 0.023 0.025 0.028 0.031 0.033 0.033 0.033 0.035 0.038 0.042 0.045 0.049 0.052 0.056 0.058 0.061 0.062 0.063 0.064 0.064 0.063 0.062 0.061 0.060 0.059 0
1954010100 82 56 -0.08 1.00 0.0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 Comments
Stephen23
on 30 Aug 2024
Please upload a sample data file by clicking the paperclip button.
Peter Bohn
on 31 Aug 2024
Moved: Voss
on 31 Aug 2024
You need to use special parameters to read the data correctly.
format long g
T = readmatrix('TestFile.txt', 'headerlines', 4, 'Delimiter', ' ');
disp(T(1:50,1:6))
"it will not be feasible to change each extiension to a .txt."
Do not change the file extension when importing using READTABLE or READMATRIX.
Instead specify the FileType:
dpb
on 31 Aug 2024
"it will not be feasible to change each extiension to a .txt."
Of course it is a trivial exercise to do that with either an OS command or in Matlab with movefile, but I didn't suggest to change the working file names, only that the Answers forum won't accept anything excepting one of a very small set of file extensions.
Peter Bohn
on 2 Sep 2024
dpb
on 2 Sep 2024
If you use one of the fancy new(ish) i/o functions like readmatrix or readcell, etc., they also have a very short list of builtin file extensions they recognize as text files automagically, so it is a problem unless you tell them explicitly as @Walter Roberson noted, I believe. I figure it would have been better to lmit the list to auto the various Excel and similar formats and then try anything else as text first rather than just failing to accept the file name--but, they didn't ask my opinion. :)
Accepted Answer
L=[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0];
numel(L)
:The first 4 rows are unimportant to me, ..."
Well, you may think it unimportant, but that first row
% 23 35
% 122 762 100.0
% 2177571.00 408574.12 255.0 1
% 0.0390 0.0429 0.0472 0.0520 0.0572 0.0630 0.0693 0.0763 0.0840 0.0924 0.1017 0.1120 0.1233 0.1357 0.1493 0.1643 0.1809 0.1991 0.2191 0.2412 0.2655 0.2922 0.3216
% 1954010100 82 52 -0.08 1.00 0.0
is vital because it tells you how may row and columns of data are there to be read...
I pasted your text above into a file and the following seems to work although I haven't vetted it throroughly.
@Stephen23 has noted often in the past that replica and/or sample files don't count, and that may be true here, too, so as he suggests, attaching a copy of a real file would be most useful.
NOTA BENE: You'll have to change the extension to .txt, .dat or something else that the Answers forum 'bot will accept to upload it....
fid=fopen('spectrum.txt','r');
r=fscanf(fid,'%d',1)
c=fscanf(fid,'%d',1)
for i=1:4, l=fgetl(fid); end
fmt=[repmat('%f ',1,6)];
tdata=fscanf(fid,fmt,6);
fprintf(fmt,tdata), fprintf('%s',newline)
fmt1=[repmat('%f ',1,c) newline];
fmt2=repmat(fmt1,1,r);
s=fscanf(fid,fmt2,r*c);
whos s
plot(s)
Repeat until run out of data...
2 Comments
Peter Bohn
on 31 Aug 2024
dpb
on 31 Aug 2024
As noted, "rinse and repeat"...
fid=fopen('spectrum.txt','r');
r=fscanf(fid,'%d',1)
c=fscanf(fid,'%d',1)
fmt=[repmat('%f ',1,6)];
fmt1=[repmat('%f ',1,c) newline];
fmt2=repmat(fmt1,1,r);
for i=1:4, l=fgetl(fid); end
tdata=fscanf(fid,fmt,6);
s=fscanf(fid,fmt2,r*c);
while ~feof(fid)
tdata=[tdata;fscanf(fid,fmt,6)];
s=[s;fscanf(fid,fmt2,r*c)];
end
fid=fclose(fid);
More Answers (1)
Image Analyst
on 2 Sep 2024
If youi're dealing with Spectroscopy, you really need to get GSTools library. It has functions to read SPC file(s), and other useful spectroscopy functions.
GSTools version 0.4.2
A set of matlab functions to read, write and deal with .spc spectra
using MATLAB ...®
By Kris De Gussem
Research assistant of the Research Foundation Flanders
Ghent University
Department of analytical chemistry
Proeftuinstraat 86
B-9000 Ghent
web: http://www.AnalChem.UGent.be/Raman/
e-mail: Kris.DeGussem @ gmail.com
%function GSimportspec
%
%GSimportspec imports all spc-files in a folder. All files are collected in
%a single structure array containing all spectra with all spectral information.
%
%Syntax:
% [spectra, path] = GSimportspec (path, compatibility);
% [spectra, path] = GSimportspec (path);
This is the package I used to read files that our spectroscopists gave me (they recommended it to me). Then you don't have to do all the quirky MATLAB gymnastics to read a file format MATLAB is not familiar with natively.
See my attached SPC file plotter.
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