[FIX] display error when impossible slice timing values are given

.pre-commit-config.yaml

@@ -103,5 +103,10 @@ repos:
     types: [dockerfile]
     entry: ghcr.io/hadolint/hadolint hadolint
 
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.2.4
+  hooks:
+  - id: codespell
+
 ci:
   skip: [hadolint-docker]

bidspm.m

@@ -82,7 +82,11 @@
     opt.dir.output = args.Results.output_dir;
     opt.dryRun = false;
     opt.verbosity = 3;
-    bugReport(opt, ME);
+    if isempty(which('bugReport'))
+      rethrow(ME);
+    else
+      bugReport(opt, ME);
+    end
     returnCode = 1;
   end
 end

docs/source/examples/preprocess.md

@@ -5,7 +5,7 @@ using statistical parametric mapping
 (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
 https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
 using MATLAB 9.4.0.813654 (R2018a)
-on a unix computer (Linux version 5.15.0-53-generic (buildd@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
+on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
 ).
 .
 

docs/source/examples/stats.md

@@ -5,7 +5,7 @@ using statistical parametric mapping
 (SPM12 - 7771; Wellcome Center for Neuroimaging, London, UK;
 https://www.fil.ion.ucl.ac.uk/spm; RRID:SCR_007037)
 using MATLAB 9.4.0.813654 (R2018a)
-on a unix computer (Linux version 5.15.0-53-generic (buildd@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
+on a unix computer (Linux version 5.15.0-53-generic (build@lcy02-amd64-047) (gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #59-Ubuntu SMP Mon Oct 17 18:53:30 UTC 2022
 ).
 
 The input data were the preprocessed BOLD images in IXI549Space space for the task " facerepetition ".

lib/mancoreg/mancoreg.m

@@ -51,7 +51,7 @@ function mancoreg(varargin)
   % and "reset transformation" button (12.1.2004, JH)
   %
   % Version 1.0.3
-  % Added: Made compatible with SPM5 and corrected "Yawn" (altho I like it)
+  % Added: Made compatible with SPM5 and corrected "Yawn" (although I like it)
 
   global st mancoregvar
 

lib/panel-2.14/demo/demopanelA.m

@@ -84,7 +84,7 @@
 % mitigate this is to export at a higher DPI, but that makes
 % for a very large figure file. an alternative is to ask
 % panel to render at a higher DPI but then to smooth back
-% down to the specfied resolution. you'll have to wait a few
+% down to the specified resolution. you'll have to wait a few
 % seconds for the result, since rendering at these sizes
 % takes time. here, we'll smooth by factor 2. since this
 % takes a little while, i don't usually do this until i'm

lib/panel-2.14/panel.m

@@ -2382,7 +2382,7 @@ function pack(p, varargin)
           p.m_children(end + 1) = child;
         end
 
-        % recurse (further argumens are passed on)
+        % recurse (further arguments are passed on)
         if ~isempty(args)
           child_packdim = flippackdim(p.packdim);
           edges = 'hv';
@@ -5027,10 +5027,10 @@ function restoreAxisState(h, store)
 
 end
 
-function b = isofsize(value, siz)
+function b = isofsize(value, size_)
 
   sz = size(value);
-  b = length(sz) == length(siz) && all(sz == siz);
+  b = length(sz) == length(size_) && all(sz == size_);
 
 end
 

lib/utils/cprintf.m

@@ -333,7 +333,7 @@
           style = style(~debugIdx);
       end
 
-      % Check if the remaining style sting is a numeric vector
+      % Check if the remaining style string is a numeric vector
       %styleNum = str2num(style); %#ok<ST2NM>  % not good because style='text' is evaled!
       %if ~isempty(styleNum)
       if any(style==' ' | style==',' | style==';')

lib/utils/resize_img.m

@@ -23,7 +23,7 @@ function resize_img(imnames, Voxdim, BB, ismask)
   % This version doesn't check spm_flip_analyze_images -- the handedness of
   % the output image and matrix should match those of the input.
 
-  % DONWLOADED FROM ON THE 2021 02 17
+  % DOWNLOADED FROM ON THE 2021 02 17
   % https://blogs.warwick.ac.uk/nichols/entry/spm5_gem_3/
 
   % Check spm version:
@@ -99,8 +99,8 @@ function resize_img(imnames, Voxdim, BB, ismask)
 
     % output image
     VO            = V;
-    [pth, nam, ext] = fileparts(V.fname);
-    VO.fname      = fullfile(pth, ['r' nam ext]);
+    [pth, name, ext] = fileparts(V.fname);
+    VO.fname      = fullfile(pth, ['r' name ext]);
     VO.dim(1:3)   = imgdim(1:3);
     VO.mat        = mat;
     VO = spm_create_vol(VO);

lib/utils/unfold.m

@@ -7,7 +7,7 @@ function unfold(input, varargin)
     %   unfold(SC, name, show, file_id)
     %
     %
-    % :param SC: vairable to show the content of.
+    % :param SC: variable to show the content of.
     % :type SC: structure or cell
     %
     % If SC is a structure it recursively shows the name of SC and
@@ -17,10 +17,10 @@ function unfold(input, varargin)
     %
     % It uses the caller's workspace variable name as the name of SC.
     %
-    % :param name: can be used isntead of the name of SC.
+    % :param name: can be used instead of the name of SC.
     % :type name: string
     %
-    % :param show: if ``false`` only the fieldnames and their sizes are  shown,
+    % :param show: if ``false`` only the fieldnames and their size_es are  shown,
     %              if ``true`` the contents are shown also.
     % :type show: boolean
     %
@@ -97,11 +97,11 @@ function unfold(input, varargin)
             for i = 1:NF
 
                 if NS > 1
-                    siz = size(input);
+                    size_ = size_e(input);
                     if show
-                        name_i = [name '(' indToStr(siz, h) ').' F{i}];
+                        name_i = [name '(' indToStr(size_, h) ').' F{i}];
                     else
-                        name_i = [name '(' indToStr(siz, NS) ').'  F{i}];
+                        name_i = [name '(' indToStr(size_, NS) ').'  F{i}];
                     end
                 else
                     name_i = [name '.' F{i}];
@@ -116,7 +116,7 @@ function unfold(input, varargin)
                             printKeyToScreen(name_i, file_id);
                             fprintf(file_id, ' =\t{};');
                         else
-                            siz = size(input(h).(F{i}));
+                            size_ = size_e(input(h).(F{i}));
                             NC = numel(input(h).(F{i}));
                             if show
                                 jmax = NC;
@@ -125,9 +125,9 @@ function unfold(input, varargin)
                             end
                             for j = 1:jmax
                                 if show
-                                    name_j = [name_i '{' indToStr(siz, j) '}'];
+                                    name_j = [name_i '{' indToStr(size_, j) '}'];
                                 else
-                                    name_j = [name_i '{' indToStr(siz, NC) '}'];
+                                    name_j = [name_i '{' indToStr(size_, NC) '}'];
                                 end
                                 printKeyToScreen(name_j, file_id);
                                 if show
@@ -153,9 +153,9 @@ function unfold(input, varargin)
             fprintf(file_id, ' =\t{};');
         else
             % recursively display cell
-            siz = size(input);
+            size_ = size_e(input);
             for i = 1:numel(input)
-                name_i = [name '{' indToStr(siz, i) '}'];
+                name_i = [name '{' indToStr(size_, i) '}'];
                 unfold(input{i}, name_i, show, file_id);
             end
         end
@@ -209,20 +209,20 @@ function printValueToScreen(input, file_id)
 
 % local functions
 % --------------------------------------------------------------------------
-function str = indToStr(siz, ndx)
+function str = indToStr(size_, ndx)
 
-    n = length(siz);
+    n = length(size_);
     % treat vectors and scalars correctly
     if n == 2
-        if siz(1) == 1
-            siz = siz(2);
+        if size_(1) == 1
+            size_ = size_(2);
             n = 1;
-        elseif siz(2) == 1
-            siz = siz(1);
+        elseif size_(2) == 1
+            size_ = size_(1);
             n = 1;
         end
     end
-    k = [1 cumprod(siz(1:end - 1))];
+    k = [1 cumprod(size_(1:end - 1))];
     ndx = ndx - 1;
     str = '';
     for i = n:-1:1

src/preproc/utils/getAcquisitionTime.m

@@ -16,20 +16,24 @@
   % SPM accepts slice time acquisition as inputs for slice order
   % (simplifies things when dealing with multiecho data)
 
-  sliceOrder = unique(sliceOrder);
-
-  acquisitionTime = repetitionTime - (repetitionTime / numel(sliceOrder));
+  acquisitionTime = computeAcquisitionTime(sliceOrder, repetitionTime);
 
   % ceil to avoid making this too brittle
-  if any(sliceOrder >= ceil(acquisitionTime * 1000) / 1000)
+  if any(sliceOrder > ceil(acquisitionTime * 100) / 100)
+    sliceOrder = bids.internal.create_unordered_list(num2str(sliceOrder));
     msg = sprintf(['Acquisition time cannot be < to any slice timing value:\n\n', ...
                    'Current values:', ...
                    '\n- acquisition time: %f', ...
-                   '\n- slice timing: ' pattern], ...
+                   '\n- slice timing %s'], ...
                   acquisitionTime, ...
                   sliceOrder);
     id = 'sliceTimingSuperiorToAcqTime';
     logger('ERROR', msg, 'id', id, 'filename', mfilename());
   end
 
 end
+
+function acquisitionTime = computeAcquisitionTime(sliceOrder, repetitionTime)
+  sliceOrder = unique(sliceOrder);
+  acquisitionTime = repetitionTime - (repetitionTime / numel(sliceOrder));
+end

tests/tests_preproc/utils/test_getAcquisitionTime.m

@@ -0,0 +1,79 @@
+function test_suite = test_getAcquisitionTime %#ok<*STOUT>
+  % (C) Copyright 2023 bidspm developers
+  try % assignment of 'localfunctions' is necessary in Matlab >= 2016
+    test_functions = localfunctions(); %#ok<*NASGU>
+  catch % no problem; early Matlab versions can use initTestSuite fine
+  end
+  initTestSuite;
+end
+
+function test_getAcquisitionTime_basic()
+
+  repetitionTime = 1.5;
+  sliceOrder = repmat([0.5475, 0,    0.3825, 0.055, 0.4375, 0.11, ...
+                       0.4925, 0.22, 0.6025, 0.275, 0.6575, 0.3275, ...
+                       0.71,   0.165], ...
+                      1, 3)';
+
+  acquisitionTime = getAcquisitionTime(sliceOrder, repetitionTime);
+
+  assertElementsAlmostEqual(acquisitionTime, 1.3929, 'absolute', 1e-4);
+
+end
+
+function test_getAcquisitionTime_error()
+
+  repetitionTime = 1.5;
+  sliceOrder = repmat([0.5475, 0,    0.3825, 0.055, 0.4375, 0.11, ...
+                       0.4925, 0.22, 0.6025, 0.275, 0.6575, 0.3275, ...
+                       0.71,   1.49], ...
+                      1, 3)';
+
+  assertExceptionThrown(@() getAcquisitionTime(sliceOrder, repetitionTime), ...
+                        'getAcquisitionTime:sliceTimingSuperiorToAcqTime');
+
+end
+
+function test_getAcquisitionTime_bug_967()
+  % https://github.com/cpp-lln-lab/bidspm/issues/967
+
+  repetitionTime = 2;
+  sliceOrder = [0
+                0.0575
+                0.115
+                0.1725
+                0.23
+                0.2875
+                0.345
+                0.4025
+                0.46
+                0.5175
+                0.575
+                0.6325
+                0.69
+                0.745
+                0.8025
+                0.86
+                0.9175
+                0.975
+                1.0325
+                1.09
+                1.1475
+                1.205
+                1.2625
+                1.32
+                1.3775
+                1.435
+                1.4925
+                1.55
+                1.6075
+                1.665
+                1.7225
+                1.7775
+                1.835
+                1.8925
+                1.95];
+
+  getAcquisitionTime(sliceOrder, repetitionTime);
+
+end