From 7d76945d0ecc4da50831fd84945a3398e916e153 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 31 Jul 2023 14:03:16 -0400
Subject: [PATCH] [FIX] handle nan and and datetimes when printing tables
 (#605)

* fix bugs in tables and datetimes

* skip on windows
---
 +bids/+util/tsvwrite.m            | 27 ++++++++++++++++------
 tests/tests_utils/test_tsvwrite.m | 37 ++++++++++++++++++++++++++++++-
 2 files changed, 56 insertions(+), 8 deletions(-)

diff --git a/+bids/+util/tsvwrite.m b/+bids/+util/tsvwrite.m
index 57124f8b..494a12c4 100644
--- a/+bids/+util/tsvwrite.m
+++ b/+bids/+util/tsvwrite.m
@@ -7,16 +7,16 @@ function tsvwrite(filename, var)
   %   tsvwrite(f, var)
   %
   % :param filename:
-  % :type filename: string
+  % :type  filename: string
+  %
   % :param var:
-  % :type var: data array or structure
+  % :type  var: data array or structure
   %
   %
   % Based on spm_save.m from SPM12.
   %
-  %
+
   % (C) Copyright 2018 Guillaume Flandin, Wellcome Centre for Human Neuroimaging
-  %
   % (C) Copyright 2018 BIDS-MATLAB developers
 
   delim = sprintf('\t');
@@ -55,6 +55,7 @@ function tsvwrite(filename, var)
         var = num2cell(var);
       end
 
+      var = convert_datetimes(var);
       var = cellfun(@(x) num2str(x, 16), var, 'UniformOutput', false);
       var = strtrim(var);
       var(cellfun(@(x) strcmp(x, 'NaN'), var)) = {'n/a'};
@@ -64,9 +65,10 @@ function tsvwrite(filename, var)
     write_to_file(filename, var, delim);
 
   elseif isa(var, 'table')
-    writetable(var, filename, ...
-               'FileType', 'text', ...
-               'Delimiter', delim);
+    header = var.Properties.VariableNames;
+    var = table2cell(var);
+    var = cat(1, header, var);
+    bids.util.tsvwrite(filename, var);
 
   else
     error('Unknown data type.');
@@ -75,6 +77,17 @@ function tsvwrite(filename, var)
 
 end
 
+function var = convert_datetimes(var)
+  if bids.internal.is_octave
+    return
+  end
+  is_datetime = find(cellfun(@(x) isdatetime(x), var(:)));
+  for i = 1:numel(is_datetime)
+    idx = is_datetime(i);
+    var{idx} = char(var{idx}, 'yyyy-MM-dd''T''HH:mm:ss.SSS'); % bids-compliant datetime
+  end
+end
+
 function write_to_file(filename, var, delim)
 
   fid = fopen(filename, 'Wt');
diff --git a/tests/tests_utils/test_tsvwrite.m b/tests/tests_utils/test_tsvwrite.m
index 0d4ef5ce..587f6976 100644
--- a/tests/tests_utils/test_tsvwrite.m
+++ b/tests/tests_utils/test_tsvwrite.m
@@ -6,6 +6,41 @@
   initTestSuite;
 end
 
+function test_datetime_in_table()
+  % TODO fix line issue on windows
+  if bids.internal.is_octave() || ispc()
+    moxunit_throw_test_skipped_exception('no datetime in Octave and line issue in windows');
+  end
+  x = '201401010000';
+  acq_time = datetime(x, 'InputFormat', 'yyyyMMddHHmm');
+  sub_id = {'foo'};
+  patients = table(sub_id, acq_time);
+  file = fullfile(tempname(), 'foo.tsv');
+  bids.util.mkdir(fileparts(file));
+  bids.util.tsvwrite(file, patients);
+
+  FID = fopen(file, 'r');
+  C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
+  assertEqual(C{2}{2}, '2014-01-01T00:00:00.000');
+end
+
+function test_nan_in_table()
+  % TODO fix line issue on windows
+  if bids.internal.is_octave()  || ispc()
+    moxunit_throw_test_skipped_exception('no table in Octave and line issue in windows');
+  end
+  sub_id = {'foo'; 'bar'};
+  age = [25; nan];
+  patients = table(sub_id, age);
+  file = fullfile(tempname(), 'foo.tsv');
+  bids.util.mkdir(fileparts(file));
+  bids.util.tsvwrite(file, patients);
+
+  FID = fopen(file, 'r');
+  C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
+  assertEqual(C{2}{3}, 'n/a');
+end
+
 function test_tsvwrite_basic()
 
   pth = fileparts(mfilename('fullpath'));
@@ -67,7 +102,7 @@ function test_tsvwrite_basic()
 
   FID = fopen(tsv_file, 'r');
   C = textscan(FID, '%s%s', 'Delimiter', '\t', 'EndOfLine', '\n');
-  assertEqual(C{1}{2}, 'n/a'); %
+  assertEqual(C{1}{2}, 'n/a');
 
   delete(tsv_file);