Merge pull request #774 from schorschinho/develop

Update to version 2.7.0

GUI/Osprey.m

@@ -15,6 +15,9 @@
 %
 %   HISTORY:
 %       2019-07-11: First version of the code.
+%% Get version
+VersionStruct  = getCurrentVersion;
+
 %% Check for available add-ons
   [~,~] = osp_Toolbox_Check ('OspreyGUI',0);
 %% Set up Layout
@@ -30,7 +33,7 @@
 logoFcn = @()imread('osprey.png', 'BackgroundColor', gui.colormap.Background);
 logoBanner = uiw.utility.loadIcon(logoFcn);
 % Here the intro banner is created
-gui.d = uiw.dialog.About('Name', 'Osprey','Version','2.6.0','Date', 'July 15, 2024',...
+gui.d = uiw.dialog.About('Name', 'Osprey','Version',VersionStruct.Version,'Date', VersionStruct.Date,...
 'Timeout', 3,'CustomText', 'Osprey is provided by Johns Hopkins University.',...
 'ContactInfo', '[email protected]','LogoCData', logoBanner);
 

GUI/osp_Toolbox_Check.m

@@ -31,8 +31,8 @@
 %   HISTORY:
 %       2020-05-15: First version of the code.
 %% % 1. SAVE OSPREY VERSION%%%
-%%% 1. SAVE OSPREY VERSION%%%
-OspreyVersion = 'Osprey 2.6.0';
+VersionStruct  = getCurrentVersion;
+OspreyVersion = ['Osprey ' VersionStruct.Version];
 fprintf(['Timestamp %s ' OspreyVersion '  ' Module '\n'], datestr(now,'mmmm dd, yyyy HH:MM:SS'));
 hasSPM = 1; % For the compiled GUI
 %% % 2. GET SPMPATH AND TOOLBOXES%%%

docs_source/05-tutorial_cmd.Rmd

@@ -14,7 +14,7 @@ MRSCont = OspreyJob('Path/To/Job/File');
 MRSCont will now contain the options and file locations for your data, as specified in the job file. Next, the data can be loaded:
 
 ```octave
-MRSCont = OspreyLoad(MRScont);
+MRSCont = OspreyLoad(MRSCont);
 ```
 
 The substructure, MRSCont.raw, now contains the raw MRS data, as extracted from their native format. We may now preprocess these data:
@@ -56,4 +56,4 @@ At any point during a command-line analysis, it is possible to visualize the dat
 
 ```octave
 OspreyGUI(MRSCont);
-```
+```

job/OspreyJob.m

@@ -44,6 +44,7 @@
 
 %%% 1. INITIALISE DATA CONTAINER WITH DEFAULT SETTINGS
 [MRSCont] = OspreySettings;
+VersionStruct  = getCurrentVersion;
 
 %%% 2. CHECK JOB INPUT FILE FORMAT %%%
 [~,~,ext] = fileparts(jobFile);
@@ -210,6 +211,16 @@
         fprintf('Adding macromolecule and lipid basis functions to the fit (default). Please indicate otherwise in the csv-file or the GUI \n');
         MRSCont.opts.fit.fitMM = 1;
     end
+    if isfield(jobStruct,'RelaxationAtlas')
+        MRSCont.opts.quantify.RelaxationAtlas = jobStruct(1).RelaxationAtlas;
+    else
+        MRSCont.opts.quantify.RelaxationAtlas = 0;
+    end
+    if isfield(jobStruct,'RelaxationAtlasAge')
+        MRSCont.opts.quantify.RelaxationAtlasAge = jobStruct(1).RelaxationAtlasAge;
+    else
+        MRSCont.opts.quantify.RelaxationAtlasAge = 0;
+    end
     if isfield(jobStruct,'deface')
         MRSCont.opts.img.deface = jobStruct.deface;
     else
@@ -397,6 +408,16 @@
     else
         MRSCont.opts.fit.fitMM = 1;
     end
+    if isfield(jobStruct,'RelaxationAtlas')
+        MRSCont.opts.quantify.RelaxationAtlas = jobStruct.RelaxationAtlas;
+    else
+        MRSCont.opts.quantify.RelaxationAtlas = 0;
+    end
+    if isfield(jobStruct,'RelaxationAtlasAge')
+        MRSCont.opts.quantify.RelaxationAtlasAge = jobStruct.RelaxationAtlasAge;
+    else
+        MRSCont.opts.quantify.RelaxationAtlasAge = 0;
+    end
     if isfield(jobStruct,'basisSet')
         if isfolder(jobStruct.basisSet)
             opts.fit.basissetFolder = jobStruct.basisSet;
@@ -781,7 +802,7 @@
 %%% 7. SET FLAGS AND VERSION %%%
 MRSCont.flags.didJob        = 1;
 MRSCont.loadedJob           = jobFile;
-MRSCont.ver.Osp             = 'Osprey 2.6.0';
+MRSCont.ver.Osp             = ['Osprey ' VersionStruct.Version];
 
 
 %%% 8. CHECK IF OUTPUT STRUCTURE ALREADY EXISTS IN OUTPUT FOLDER %%%

libraries/FID-A/inputOutput/io_loadspec_dicom.m

@@ -3,35 +3,97 @@
 %Georg Oeltzschner, Johns Hopkins University 2019.
 %
 % USAGE:
-% out=io_loadspec_dicom(folder);
-% 
+% out=io_loadspec_dicom(source);
+%
 % DESCRIPTION:
 % Loads a DICOM (.dcm, .ima) file into matlab structure format.
-% 
+%
 % INPUTS:
-% filename       = Name of a folder with DICOM (.dcm, .ima) data to load.
+% source     = Name of a folder (or file) with DICOM (.dcm, .ima) data to load.
 %
 % OUTPUTS:
 % out        = Input dataset in FID-A structure format.
 
-function out=io_loadspec_dicom(folder);
+function out=io_loadspec_dicom(source);
 
-% If path to a .dcm is provided, then extract the folder location:
-if ~isfolder(folder) && isfile(folder)
-    folder =fileparts(folder);
+% ARC170724 : Source may be a folder, or an individual file. We later determine
+% how this should be interpreted.
+if ~isfolder(source) && isfile(source)
+    [folder,filename,ext] =fileparts(source);
+    requested_file=[filename ext];
+else
+    folder=source;
+    requested_file=[];
 end
 
 % Create list of complete filenames (incl. path) in the folder
 dirFolder = dir(folder);
 filesInFolder = dirFolder(~[dirFolder.isdir]);
 hidden = logical(ones(1,length(filesInFolder)));
-for jj = 1:length(filesInFolder) 
+for jj = 1:length(filesInFolder)
     if strcmp(filesInFolder(jj).name(1),'.')
         hidden(jj) = 0;
     end
 end
-filesInFolder = filesInFolder(hidden);%delete hidden files 
-filesInFolder = fullfile(folder, {filesInFolder.name});        
+filesInFolder = filesInFolder(hidden);%delete hidden files
+
+if length(filesInFolder)==0
+    % No files survived. This will not end well.
+    error([ 'io_loadspec_dicom did not find any files in ' folder ])
+end
+
+requested_file_ix=find(strcmp(requested_file,{filesInFolder.name})); % NB, may be empty
+
+if isfolder(folder)
+    filesInFolder = fullfile(folder, {filesInFolder.name});
+else
+    % this can happen if the function is called with a wildcard, eg /path/to/abc*dcm
+    filesInFolder = fullfile(dirname(folder), {filesInFolder.name});
+end
+
+% ARC170724 : If a single file is specified (rather than a directory), check
+% whether this file should be considered in isolation (pre-averaged data) or
+% if it should be combined with other items in the folder. We do this by
+% inspecting the Series Number header.
+
+if ~isempty(requested_file_ix)
+    % check header of the first, last and requested items; if Series Number
+    % does not match, don't try to combine
+    check_header_ix = unique([1, requested_file_ix, length(filesInFolder) ]);
+    encountered_series_numbers = [];
+    encountered_problems = [];
+
+    for ix = check_header_ix
+        try
+            dh = dicominfo(filesInFolder{ix});
+            encountered_series_numbers(end+1) = dh.SeriesNumber;
+        catch
+            encountered_problems(end+1) = ix;
+        end
+    end
+
+    encountered_series_numbers=unique(encountered_series_numbers);
+
+    if any(encountered_problems == requested_file_ix)
+
+        warning([ 'io_loadspec_dicom could not determine SeriesNumber of the requested file: ' source ]);
+        % in this case, fall back on default behaviour
+
+    elseif length(encountered_series_numbers)>1 || length(encountered_problems)>0
+
+        % if we found more than one series, OR we found some unreadable files
+        % (probably non-DICOM), then just retain that one specific file the
+        % caller originally asked for
+
+        if length(encountered_problems)>0
+            warning([ 'io_loadspec_dicom encountered some non-DICOM data in ' source ]);
+        end
+
+        filesInFolder={source};
+    end
+
+    % in any other scenario, full back on the default behaviour
+end
 
 % Get the header of the first file to make some decisions.
 DicomHeader = read_dcm_header(filesInFolder{1});
@@ -41,7 +103,7 @@
     seqorig = DicomHeader.seqorig;
 else
 % deal with missing seqorig field for dicom data load on Siemens Minnesota
-% sequences (Auerbach and Deelchand versions, VB17A & VE11C)    
+% sequences (Auerbach and Deelchand versions, VB17A & VE11C)
     if contains(DicomHeader.sequenceFileName, 'slaser_dkd') %Deelchand/Oz
         seqorig = 'CMRR';
     elseif contains(DicomHeader.sequenceFileName, 'eja_svs') %Auerbach/Marjanska
@@ -80,7 +142,7 @@
 end
 % Collect all FIDs and sort them into fids array
 for kk = 1:length(filesInFolder)
-    
+
     % First, attempt to retrieve the FID from the DICOM header:
     infoDicom = dicominfo(filesInFolder{kk});
     if isfield(infoDicom, 'SpectroscopyData')
@@ -95,7 +157,7 @@
         fids(:,kk) = dicom_get_spectrum_siemens(fd);
         fclose(fd);
     end
-    
+
 end
 
 
@@ -115,16 +177,16 @@
     else
         out.flags.averaged = 0;
     end
-    
+
     % Currently, the DICOM recon of the universal sequence is flawed.
     % Kick out empty lines here and see if data can be reconstructed.
     if strcmp(seqorig, 'Universal') && out.flags.averaged == 0
         fids(:,size(fids,2)/2+1:end) = [];
     end
-        
+
     % Rearrange into subspecs
     fids = reshape(fids,[size(fids,1) size(fids,2)/2 2]);
-    
+
 elseif strcmp(seqtype,'PRESS') || strcmp(seqtype,'STEAM') || strcmp(seqtype,'sLASER')
     % If the number of stored FIDs does not match the number of averages
     % stored in the DICOM header, the data are averaged.
@@ -137,9 +199,9 @@
 
 elseif strcmp(seqtype,'HERMES')
 
-    out.flags.averaged = 0; 
+    out.flags.averaged = 0;
     % Currently, the DICOM recon of the universal sequence is flawed.
-    % Kick out empty lines here and see if data can be reconstructed.    
+    % Kick out empty lines here and see if data can be reconstructed.
     if strcmp(seqorig, 'Universal') && out.flags.averaged == 0
         fids(:,size(fids,2)/2+1:end) = [];
     end
@@ -222,7 +284,7 @@
 
 %Find the number of averages.  'averages' will specify the current number
 %of averages in the dataset as it is processed, which may be subject to
-%change.  'rawAverages' will specify the original number of acquired 
+%change.  'rawAverages' will specify the original number of acquired
 %averages in the dataset, which is unchangeable.
 if dims.subSpecs ~=0
     if dims.averages~=0
@@ -244,7 +306,7 @@
 
 %Find the number of subspecs.  'subspecs' will specify the current number
 %of subspectra in the dataset as it is processed, which may be subject to
-%change.  'rawSubspecs' will specify the original number of acquired 
+%change.  'rawSubspecs' will specify the original number of acquired
 %subspectra in the dataset, which is unchangeable.
 if dims.subSpecs ~=0
     subspecs=sz(dims.subSpecs);
@@ -288,8 +350,8 @@
 out.fids=fids;
 out.specs=specs;
 out.sz=sz;
-out.ppm=ppm;  
-out.t=t;    
+out.ppm=ppm;
+out.t=t;
 out.spectralwidth=spectralwidth;
 out.dwelltime=dwelltime;
 out.txfrq=txfrq;

libraries/FID-A/inputOutput/io_loadspec_twix.m

@@ -77,7 +77,8 @@
 isjnseq=~isempty(strfind(sequence,'jn_')); %Is this another one of Jamie Near's sequences?
 isWIP529=~isempty(strfind(sequence,'edit_529'));%Is this WIP 529 (MEGA-PRESS)?
 ismodWIP=((~isempty(strfind(sequence,'\svs_edit'))||...
-        ~isempty(strfind(sequence,'\wip_svs_edit'))) && isempty(strfind(sequence,'edit_859'))); %Modified WIP
+        ~isempty(strfind(sequence,'\wip_svs_edit'))) && ...
+        (isempty(strfind(sequence,'edit_859')) && isempty(strfind(sequence,'univ')))); %Modified WIP
 isWIP859=~isempty(strfind(sequence,'edit_859'))||...;%Is this WIP 859 (MEGA-PRESS)?
         ~isempty(strfind(sequence,'WIP_859'));%Is this WIP 859 (MEGA-PRESS)? Other naming
 isTLFrei=~isempty(strfind(sequence,'md_svs_edit')) ||... %Is Thomas Lange's MEGA-PRESS sequence
@@ -353,9 +354,8 @@
     else
         % GO 6/2024: Encountered a VD13 Siemens product sequence that had
         % transients in Set, not in Ave... 
-        if strcmp(sqzDims,'Ave')
-            dims.averages=find(strcmp(sqzDims,'Ave'));
-        else
+        dims.averages=find(strcmp(sqzDims,'Ave'));
+        if isempty(dims.averages)
             dims.averages=find(strcmp(sqzDims,'Set'));
         end
     end

process/OspreyProcess.m

@@ -745,18 +745,18 @@
                 end
             end
             if MRSCont.flags.hasRef
-                MRSCont.QM.SNR.ref(ref_ll,kk)    = op_getSNR(MRSCont.processed.ref{kk});
-                MRSCont.QM.FWHM.ref(ref_ll,kk)   = op_getLW(MRSCont.processed.ref{kk},4.2,5.2);
+                MRSCont.QM.SNR.ref(ref_ll,kk)    = op_getSNR(MRSCont.processed.ref{kk},3.7,5.7);
+                MRSCont.QM.FWHM.ref(ref_ll,kk)   = op_getLW(MRSCont.processed.ref{kk},3.7,5.7);
                 MRSCont.processed.ref{kk}.QC_names = {'water'};
             end
             if MRSCont.flags.hasWater
-                MRSCont.QM.SNR.w(w_ll,kk)    = op_getSNR(MRSCont.processed.w{kk});
-                MRSCont.QM.FWHM.w(w_ll,kk)   = op_getLW(MRSCont.processed.w{kk},4.2,5.2);
+                MRSCont.QM.SNR.w(w_ll,kk)    = op_getSNR(MRSCont.processed.w{kk},3.7,5.7);
+                MRSCont.QM.FWHM.w(w_ll,kk)   = op_getLW(MRSCont.processed.w{kk},3.7,5.7);
                 MRSCont.processed.w{kk}.QC_names = {'water'};
             end
             if MRSCont.flags.hasMMRef
-                MRSCont.QM.SNR.mm_ref(mm_ref_ll,kk)    = op_getSNR(MRSCont.processed.mm_ref{kk});
-                MRSCont.QM.FWHM.mm_ref(mm_ref_ll,kk)   = op_getLW(MRSCont.processed.mm_ref{kk},4.2,5.2);
+                MRSCont.QM.SNR.mm_ref(mm_ref_ll,kk)    = op_getSNR(MRSCont.processed.mm_ref{kk},3.7,5.7);
+                MRSCont.QM.FWHM.mm_ref(mm_ref_ll,kk)   = op_getLW(MRSCont.processed.mm_ref{kk},3.7,5.7);
                 MRSCont.processed.mm_ref{kk}.QC_names = {'water'};
             end
         end