Merge pull request #445 from Remi-Gau/remi-refactor_elapsed-time

[REF] refactor elapsedTime and integrate it into the code base

src/utils/elapsedTime.m

@@ -1,47 +1,63 @@
-function [startTime, runTime] = elapsedTime(input, startTime, runTime, nbIteration)
-    %
-    % USAGE::
-    %
-    %   [start, runTime] = elapsedTime(input, startTime, runTime, nbIteration)
-    %
-    %
-    % (C) Copyright 2021 CPP_SPM developers
+function [startTime, runTime] = elapsedTime(opt, action, startTime, runTime, nbIteration)
+  %
+  % USAGE::
+  %
+  %   [start, runTime] = elapsedTime(input, startTime, runTime, nbIteration)
+  %
+  %
+  % (C) Copyright 2021 CPP_SPM developers
 
-    if nargin < 3
-        runTime = [];
-    end
+  if nargin < 4
+    runTime = [];
+  end
 
-    switch input
+  switch action
 
-        case 'start'
+    case 'start'
 
-            startTime = tic;
+      startTime = tic;
 
-        case 'stop'
+    case 'stop'
 
-            fprintf('\n\n********* Done :) *********\n\n');
+      printDone(opt);
 
-            fprintf(' elapsed time is: ')
-            t=toc(startTime(end));
-            disp(datestr(datenum(0,0,0,0,0,t),'HH:MM:SS'));
+      t = toc(startTime(end));
+      msg = sprintf(' elapsed time: %s', formatDuration(t));
+      printToScreen(msg, opt);
 
-            runTime(end+1) = t;
-            ETA = mean(runTime) * (nbIteration - numel(runTime));
-            fprintf('\n ETA: ')
-            disp(datestr(datenum(0,0,0,0,0,ETA),'HH:MM:SS'));
+      runTime(end + 1) = t;
+      ETA = mean(runTime) * (nbIteration - numel(runTime));
+      msg = sprintf('\n ETA: %s', formatDuration(ETA));
+      printToScreen(msg, opt);
 
-            fprintf('\n***************************\n\n');
+      printHorizontalLine(opt, 27);
 
-        case 'globalStart'
+    case 'globalStart'
 
-            startTime = tic;
+      startTime = tic;
 
-        case 'globalStop'
+    case 'globalStop'
 
-            fprintf('\n\n********* Pipeline done :) *********\n\n');
-            fprintf('  global elapsed time is: ')
-            t=toc(startTime);
-            disp(datestr(datenum(0,0,0,0,0,t),'HH:MM:SS'));
-            fprintf('\n************************************\n\n');
+      printToScreen('\n\n********* Pipeline done :) *********\n', opt);
 
-    end
+      t = toc(opt.globalStart);
+      msg = sprintf('  global elapsed time: %s', formatDuration(t));
+      printToScreen(msg, opt);
+
+      printHorizontalLine(opt, 36);
+
+  end
+
+end
+
+function printDone(opt)
+  printToScreen('\n\n********* Done :) *********\n', opt);
+end
+
+function printHorizontalLine(opt, length)
+  printToScreen(['\n' repmat('*', 1, length) '\n\n'], opt);
+end
+
+function string = formatDuration(duration)
+  string = datestr(datenum(0, 0, 0, 0, 0, duration), 'HH:MM:SS');
+end

src/utils/printToScreen.m

@@ -6,7 +6,7 @@ function printToScreen(msg, opt)
   %
   % (C) Copyright 2021 CPP_SPM developers
 
-  if nargin < 2 || opt.verbosity
+  if nargin < 2 || ~isfield(opt, 'verbosity') || opt.verbosity
 
     fprintf(1, msg);
 

src/workflows/bidsConcatBetaTmaps.m

@@ -35,8 +35,12 @@ function bidsConcatBetaTmaps(opt, deleteIndBeta, deleteIndTmaps)
 
   RT = 0;
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -120,8 +124,12 @@ function bidsConcatBetaTmaps(opt, deleteIndBeta, deleteIndTmaps)
 
     removeBetaImgTmaps(tMaps, deleteIndBeta, deleteIndTmaps, ffxDir);
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
 end
 
 function removeBetaImgTmaps(tMaps, deleteIndBeta, deleteIndTmaps, ffxDir)

src/workflows/bidsCopyInputFolder.m

@@ -74,4 +74,6 @@ function bidsCopyInputFolder(opt, unzip)
     printToScreen('\n\n', opt);
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsCreateROI.m

@@ -133,6 +133,9 @@ function bidsCreateROI(opt)
       end
 
     end
+
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsCreateVDM.m

@@ -55,6 +55,8 @@ function bidsCreateVDM(opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
   bidsRename(opt);
 
 end

src/workflows/bidsFFX.m

@@ -41,8 +41,12 @@
     opt = createDefaultStatsModel(BIDS, opt);
   end
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -88,8 +92,12 @@
 
     end
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
 end
 
 function checks(opt, action)

src/workflows/bidsLesionAbnormalitiesDetection.m

@@ -72,6 +72,8 @@ function bidsLesionAbnormalitiesDetection(opt)
   matlabbatch = {};
   matlabbatch = setBatchLesionAbnormalitiesDetection(matlabbatch, opt, images);
 
-  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt, subLabel);
+  saveAndRunWorkflow(matlabbatch, 'LesionAbnormalitiesDetection', opt);
+
+  cleanUpWorkflow(opt);
 
 end

src/workflows/bidsLesionOverlapMap.m

@@ -36,4 +36,6 @@ function bidsLesionOverlapMap(opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsLesionSegmentation.m

@@ -19,8 +19,12 @@ function bidsLesionSegmentation(opt)
 
   [BIDS, opt] = setUpWorkflow(opt, 'lesion segmentation');
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -32,9 +36,14 @@ function bidsLesionSegmentation(opt)
 
     % copyFigures(BIDS, opt, subLabel);
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
   opt = setRenamingConfig(opt);
+
   bidsRename(opt);
 
 end

src/workflows/bidsMidbrainReslice.m

@@ -31,6 +31,8 @@ function bidsMidbrainReslice(opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
   bidsRename(opt);
 
 end

src/workflows/bidsRFX.m

@@ -78,6 +78,8 @@ function bidsRFX(action, opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
 end
 
 function checks(opt, action)

src/workflows/bidsRealignReslice.m

@@ -21,8 +21,12 @@ function bidsRealignReslice(opt)
 
   [BIDS, opt] = setUpWorkflow(opt, 'realign and reslice');
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -41,8 +45,12 @@ function bidsRealignReslice(opt)
       copyFigures(BIDS, opt, subLabel);
     end
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
   prefix = get_spm_prefix_list();
   opt.query.prefix = prefix.realign;
   bidsRename(opt);

src/workflows/bidsRealignUnwarp.m

@@ -23,8 +23,12 @@ function bidsRealignUnwarp(opt)
 
   [BIDS, opt] = setUpWorkflow(opt, 'realign and unwarp');
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -43,8 +47,12 @@ function bidsRealignUnwarp(opt)
       copyFigures(BIDS, opt, subLabel);
     end
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
   prefix = get_spm_prefix_list();
   opt.query.prefix = prefix.unwarp;
   bidsRename(opt);

src/workflows/bidsRename.m

@@ -65,4 +65,6 @@ function bidsRename(opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsResliceTpmToFunc.m

@@ -71,6 +71,8 @@ function bidsResliceTpmToFunc(opt)
 
   end
 
+  cleanUpWorkflow(opt);
+
   opt = set_spm_2_bids_defaults(opt);
   name_spec.entities.res = 'bold';
   opt.spm_2_bids = opt.spm_2_bids.add_mapping('prefix', opt.spm_2_bids.realign, ...

src/workflows/bidsResults.m

@@ -83,6 +83,8 @@
 
   end
 
+  cleanUpWorkflow(opt);
+
   cd(currentDirectory);
 
 end

src/workflows/bidsRoiBasedGLM.m

@@ -39,8 +39,12 @@ function bidsRoiBasedGLM(opt)
     opt = createDefaultStatsModel(BIDS, opt);
   end
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -134,6 +138,10 @@ function bidsRoiBasedGLM(opt)
 
     end
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsRsHrf.m

@@ -40,4 +40,6 @@
 
   end
 
+  cleanUpWorkflow(opt);
+
 end

src/workflows/bidsSTC.m

@@ -33,8 +33,12 @@ function bidsSTC(opt)
 
   [BIDS, opt] = setUpWorkflow(opt, 'slice timing correction');
 
+  runTime = [];
+
   for iSub = 1:numel(opt.subjects)
 
+    subjectStart = elapsedTime(opt, 'start');
+
     subLabel = opt.subjects{iSub};
 
     printProcessingSubject(iSub, subLabel, opt);
@@ -44,8 +48,12 @@ function bidsSTC(opt)
 
     saveAndRunWorkflow(matlabbatch, 'STC', opt, subLabel);
 
+    [~, runTime] = elapsedTime(opt, 'stop', subjectStart, runTime, numel(opt.subjects));
+
   end
 
+  cleanUpWorkflow(opt);
+
   prefix = get_spm_prefix_list;
   opt.query.prefix = prefix.stc;
   bidsRename(opt);