Merge branch 'master' into docker-github-action

CHANGELOG.md

@@ -10,13 +10,15 @@ Most recent version numbers *should* follow the [Semantic Versioning](https://se
 - set default WM percent value in hmri_defaults.
 - spatial processing: add explicit mask creation and fix implicit mask (0 to NaN in float images)
 - update FIL seste seq parameters in get_metadata_val_classic
+- denoising module-first part: Java-Matlab interface for LCPCA denoising
 
 ### Fixed
 - replace `datestr(now)` with `datetime('now')` in line with [MATLAB recommendation](https://mathworks.com/help/matlab/matlab_prog/replace-discouraged-instances-of-serial-date-numbers-and-date-strings.html)
 - fix crash if input images have different matrix sizes, and warn
 - make B1-map creation using 3DEPI SE/STE and AFI methods fall back to defaults without sidecar files, rather than crash
 - Modify the filenames as files are copied to RFsensCalc to prevent overwriting in further processing
 - batch interface now enforces the number of B1 input images correctly for B1 mapping methods which only need two images.
+- fix error if optimization toolbox not present during NLLS R2* calculation
 
 ## [v0.6.1]
 ### Fixed

config/hmri_denoising_defaults.m

@@ -0,0 +1,19 @@
+function hmri_denoising_defaults
+
+%init the global variable which carries the params
+global hmri_def;
+
+%Enter denoising default values as: hmri_def.denoising.(denoising-protocol).(default-value)
+
+%The default values for lcpca denoising protocol
+%all optional parameters turned off
+hmri_def.denoising.lcpca_denoise.mag_input = {}; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.phase_input = {}; %%optional-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.output_path=''; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.min_dimension= 0; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.max_dimension = -1; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.unwrap = false; %%optional
+hmri_def.denoising.lcpca_denoise.rescale_phs = false; %%optional
+hmri_def.denoising.lcpca_denoise.process_2d=false; %%optional
+hmri_def.denoising.lcpca_denoise.use_rmt=false; %%optional
+end

config/local/hmri_local_denoising_defaults.m

@@ -0,0 +1,16 @@
+%init the global variable which carries the params
+global hmri_def;
+
+%Enter denoising default values as: hmri_def.denoising.(denoising-protocol).(default-value)
+
+%The default values for lcpca denoising protocol
+%all optional parameters turned off
+hmri_def.denoising.lcpca_denoise.mag_input = {}; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.phase_input = {}; %%optional-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.output_path=''; %%required-null initialize here input with GUI
+hmri_def.denoising.lcpca_denoise.min_dimension= 0; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.max_dimension = -1; %%required-initialize here 
+hmri_def.denoising.lcpca_denoise.unwrap = false; %%optional
+hmri_def.denoising.lcpca_denoise.rescale_phs = false; %%optional
+hmri_def.denoising.lcpca_denoise.process_2d=false; %%optional
+hmri_def.denoising.lcpca_denoise.use_rmt=false; %%optional

hmri_calc_R2s.m

@@ -147,6 +147,18 @@
         beta(2:end,:)=exp(beta(2:end,:));
 
     case {'nlls_ols','nlls_wls1','nlls_wls2','nlls_wls3'}
+        %lsqcurvefit uses optimization toolbox
+        %Check both for the toolbox and/or an active license for it
+        %Error if one of them is missing
+        versionStruct = ver;
+        versionCell = {versionStruct.Name};
+        ver_status = any(ismember(versionCell, 'Optimization Toolbox'));
+        [license_status,~] = license('checkout', 'Optimization_toolbox');
+        if ver_status==0 || license_status==0
+            error('hmri:NoOptimToolbox', "The methods 'nlls_ols','nlls_wls1','nlls_wls2','nlls_wls3' require Optimization Toolbox: either this toolbox and/or its license is missing." + ...
+                " Please use another method which does not need the Optimization Toolbox such as 'ols','wls1','wls2','wls3'. ")
+        end
+
         % Check for NLLS case, where specification of the log-linear 
         % initialisation method is in the method string following a hyphen
         r=regexp(lower(method),'^nlls_(.*)$','tokens');
@@ -167,7 +179,7 @@
         end
 
         expDecay=@(x,D) (D(:,2:end)*x(2:end)).*exp(x(1)*D(:,1));
-        
+
         % Loop over voxels
         parfor n=1:size(y,2)
             beta(:,n)=lsqcurvefit(@(x,D)expDecay(x,D),beta0(:,n),D,y(:,n),[],[],opt);