Added function for loading in Bruker 1i and 1r MRS files (io_loadspec…

…_irBruk.m). Also modified the manual to reflect this change.

inputOutput/io_loadspec_irBruk.m

@@ -0,0 +1,153 @@
+%io_loadspec_irBruk.m
+%Jamie Near, McGill University 2014.
+%
+% USAGE:
+% out=io_loadspec_irBruk(filename);
+% 
+% DESCRIPTION:
+% Reads in Bruker MRS data (1i and 1r files).  Generally with this data,
+% the averages and coil channels have already been combined.
+%
+% op_loadspec_brukIR outputs the data in structure format, with fields corresponding to time
+% scale, fids, frequency scale, spectra, and header fields containing
+% information about the acquisition.  The resulting matlab structure can be
+% operated on by the other functions in this MRS toolbox.
+% 
+% INPUTS:
+% inDir   = Path to the scan directory that contains the 'pdata' folder.
+
+function out=io_loadspec_irBruk(inDir)
+
+real_fileID=fopen([inDir '/pdata/1/1r']);
+imag_fileID=fopen([inDir '/pdata/1/1i']);
+
+real=fread(real_fileID,'int');
+imag=fread(imag_fileID,'int');
+
+specs=real-1i*imag;
+
+%convert back to time domain
+%if the length of Fids is odd, then you have to do a circshift of one to
+%make sure that you don't introduce a small frequency shift into the fids
+%vector.
+if mod(length(specs),2)==0
+    %disp('Length of vector is even.  Doing normal conversion');
+    fids=fft(fftshift(specs,1),[],1);
+else
+    %disp('Length of vector is odd.  Doing circshift by 1');
+    fids=fft(circshift(fftshift(specs,1),1),[],1);
+end
+
+
+%calculate the size;
+sz=size(fids);
+
+%Now get some of the relevent spectral parameters
+
+%First get the spectral width
+method_fid=fopen([inDir '/method']);
+line=fgets(method_fid);
+index=findstr(line,'$PVM_DigSw=');
+while isempty(index)
+    line=fgets(method_fid);
+    index=findstr(line,'$PVM_DigSw=');
+end
+equals_index=findstr(line,'=');
+spectralwidth=line(equals_index+1:end);
+spectralwidth=str2double(spectralwidth);
+fclose(method_fid);
+
+%Now get the transmitter frequency
+acqp_fid=fopen([inDir '/acqp']);
+line=fgets(acqp_fid);
+index=findstr(line,'$BF1=');
+while isempty(index)
+    line=fgets(acqp_fid);
+    index=findstr(line,'$BF1=');
+end
+equals_index=findstr(line,'=');
+txfrq=line(equals_index+1:end);
+txfrq=str2double(txfrq);
+txfrq=txfrq*1e6;
+fclose(acqp_fid);
+
+%B0
+Bo=txfrq/42577000;
+
+%Spectral width in PPM
+spectralwidthppm=spectralwidth/(txfrq/1e6);
+
+%Now get the original number of averages
+averages=1; %Because Bruker does the averaging online.
+method_fid=fopen([inDir '/method']);
+line=fgets(method_fid);
+index=findstr(line,'$PVM_NAverages=');
+while isempty(index)
+    line=fgets(method_fid);
+    index=findstr(line,'$PVM_NAverages=');
+end
+equals_index=findstr(line,'=');
+rawAverages=line(equals_index+1:end);
+rawAverages=str2double(rawAverages);
+fclose(method_fid);
+
+%Specify the number of subspecs.  For now, this will always be zero.
+subspecs=0;
+rawSubspecs=0;
+
+
+%calculate the ppm scale
+ppm=[4.65+(spectralwidthppm/2):-spectralwidthppm/(length(specs)-1):4.65-(spectralwidthppm/2)];
+
+%calculate the dwelltime:
+dwelltime=1/spectralwidth;
+
+%calculate the time scale
+t=[0:dwelltime:(sz(1)-1)*dwelltime];
+
+%specify the dims
+dims.t=1;
+dims.coils=0;
+dims.averages=0;
+dims.subSpecs=0;
+dims.extra=0;
+
+%FILLING IN DATA STRUCTURE
+out.fids=fids;
+out.specs=specs;
+out.sz=sz;
+out.ppm=ppm;  
+out.t=t;    
+out.spectralwidth=spectralwidth;
+out.dwelltime=dwelltime;
+out.txfrq=txfrq;
+out.date=date;
+out.dims=dims;
+out.Bo=Bo;
+out.averages=averages;
+out.rawAverages=rawAverages;
+out.subspecs=subspecs;
+out.rawSubspecs=rawSubspecs;
+out.pointsToLeftshift=0;
+
+
+%FILLING IN THE FLAGS
+out.flags.writtentostruct=1;
+out.flags.gotparams=1;
+out.flags.leftshifted=0;
+out.flags.filtered=0;
+out.flags.zeropadded=0;
+out.flags.freqcorrected=0;
+out.flags.phasecorrected=0;
+out.flags.averaged=1;
+out.flags.addedrcvrs=1;
+out.flags.subtracted=0;
+out.flags.writtentotext=0;
+out.flags.downsampled=0;
+out.flags.avgNormalized=0;
+if out.dims.subSpecs==0
+    out.flags.isISIS=0;
+else
+    out.flags.isISIS=(out.sz(out.dims.subSpecs)==4);
+end
+