Merge pull request #64 from kschan0214/dev1.2.2.4

Dev1.2.2.4

README.md

@@ -41,7 +41,10 @@ If you have a more general question regarding the usage of SEPIA and/or other QS
 
 For full update log, please visit https://sepia-documentation.readthedocs.io/en/latest/getting_started/Release-note.html.
 
-### 1.2.2.3 (current master)
+### 1.2.2.4 (current master)
+* Fix bug when importing SEPIA pipeline configuration files (sepia_config.m) to the GUI for using VSHARP and FANSI
+
+### 1.2.2.3 (current efde35b)
 * Fix bug when using BIDS compatible directory input where magnitude images did not utilise the rescale slope and intercept to obtain the true values for R2* mapping
 
 ### 1.2.2.2 (current e53fd99)

gui_func/callback/config/get_num_as_string.m

@@ -43,7 +43,8 @@
     indicatorE_idx 	= regexp(A,end_indicator);
 
     % get all characters between the indicators
-    str = A(indicatorS_idx(find(indicatorS_idx > str_end_idx, 1 ))+1:indicatorE_idx(find(indicatorE_idx > str_end_idx, 1 ))-1);
+    % 20230329 KC: fixed bug when the value/string is separated by white  space
+    str = A(indicatorS_idx(find(indicatorS_idx > str_end_idx, 1 ))+1:indicatorE_idx(find(indicatorE_idx > indicatorS_idx(find(indicatorS_idx > str_end_idx, 1 ))+1, 1 ))-1);
 
     % remove all white space for scalar quantity
     if isScalarString

gui_func/callback/config/get_set_bfr_vsharp.m

@@ -37,12 +37,32 @@ function get_set_bfr_vsharp(h,mode,input)
         % max radius
         pattern_curr    = str_pattern{1};
         val             = get_num_as_string(config_txt, pattern_curr, '[', ':');
+        if isempty(val)
+            % in case of machine generated config file
+            val             = get_num_as_string(config_txt, pattern_curr, '[', '\s');
+        end
         set_non_nan_value(action_handle{1},'String',val)
 
         % min radius
-        val             = get_num_as_string(config_txt, pattern_curr, ':', ']');
-        idx             = regexp(val,':');
-        val             = val(idx+1:end);
+        % 20230329: bug fix for sepiaIO auto-generated pipeline configuration file
+        try
+            val             = get_num_as_string(config_txt, pattern_curr, ':', ']');
+            idx             = regexp(val,':');
+            val             = val(idx+1:end);
+        catch
+            idx_open        = regexp(config_txt,'[');
+            idx_close       = regexp(config_txt,']');
+            idx_pattern     = regexp(config_txt,pattern_curr);
+
+            idx_first       = find(idx_open>idx_pattern);
+            idx_last        = find(idx_close>idx_pattern);
+
+            val_text        = config_txt(idx_open(idx_first):idx_close(idx_last));
+            val_num         = str2num(val_text);
+
+            val             = min(val_num);
+        end
+
         set_non_nan_value(action_handle{2},'String',val)
 
 end

gui_func/callback/config/get_set_qsm_fansi.m

@@ -131,7 +131,7 @@ function get_set_qsm_fansi(h,mode,input)
         % trigger popup callback to switch method panel
         feval(action_handle{k}.Callback{1},action_handle{k},[],{action_handle{k+1},action_handle{k+2}},1);
 
-        for k = 10:11
+        for k = 11:12
             pattern_curr    = str_pattern{k};
             val             = get_num_as_string(config_txt, pattern_curr, '=', ';');
             set_non_nan_value(action_handle{k},'String',val);

sepia.m

@@ -44,6 +44,7 @@
 % Date modified: 27 Jan 2020 (v0.8.1)
 % Date modified: 12 June 2021 (v1.0)
 % Date modified: 3 August 2022 (v1.1)
+% Date modified: 3 April 2023 (v1.2.2.4)
 %
 function sepia 
 
@@ -370,7 +371,7 @@ function PushbuttonStart_Callback(source,eventdata)
 
 function PushbuttonLoadConfig_Callback(source,eventdata)
 
-global h
+global h tooltip fieldString
 
 % only read m file
 [config_filename,pathDir] = uigetfile({'*.m'},'Select a SEPIA config file');
@@ -382,6 +383,18 @@ function PushbuttonLoadConfig_Callback(source,eventdata)
 
 tab = h.StepsPanel.dataIO.Parent.Title;
 
+% Tab specific strings and tooltips
+tooltip.input_dir{1} = 'Directory contains phase (*ph*.nii*), magnitude (*mag*.nii) & header (*header*.mat) (& mask, *mask*nii*) files';
+tooltip.input_dir{2} = 'Directory contains the total field map (*fieldmap*.nii*) and SEPIA header (*header*.mat)';
+tooltip.input_dir{3} = 'Directory contains the local field map (*localfield*.nii*) (depending on QSM algorithm, additional file(s) may also be needed, e.g. *mag*.nii* and *weights*.nii*)';
+
+fieldString.inputData1{1}= 'or Phase:';
+fieldString.inputData1{2}= 'or Fieldmap:';
+fieldString.inputData1{3}= 'or Local field:';
+
+fieldString.inputData3{1}= '    Weights:';
+fieldString.inputData3{2}= '    Noise SD:';
+
 switch tab
 
     % QSM one-stop station tab

sepia_universal_variables.m

@@ -14,7 +14,7 @@
 % DO NOT change the order of the entities, add a new one at the end instead
 %
 %% Version
-SEPIA_version = 'v1.2.2.3';
+SEPIA_version = 'v1.2.2.4';
 
 %% PATH
 SEPIA_HOME = fileparts(mfilename('fullpath'));