From d3f339a2f7bf4b72c6698351b72183552b04efce Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sat, 26 Aug 2023 11:18:32 -0400
Subject: [PATCH] [ENH] remove atlas and update res and den metadata (#622)

* rm atlas and update res and den metadata

* fix
---
 +bids/derivatives_json.m                      | 22 ++-----------------
 .../BIDS_Matlab_03_filenames_and_metadata.m   |  2 +-
 tests/test_derivatives_json.m                 | 19 ++--------------
 3 files changed, 5 insertions(+), 38 deletions(-)

diff --git a/+bids/derivatives_json.m b/+bids/derivatives_json.m
index 8319a113..75a11387 100644
--- a/+bids/derivatives_json.m
+++ b/+bids/derivatives_json.m
@@ -69,38 +69,20 @@
 
     %% entity related content
     if any(ismember(fieldnames(p.entities), 'res'))
-      try
-        content.Resolution = {{ struct(p.entities.res, 'REQUIRED if "res" entity') }};
-      catch
-        bids.internal.error_handling(mfilename(), 'invalidFieldname', ....
-                                     sprintf('Invalid field name for entity res-%s', ...
-                                             p.entities.res), ...
-                                     true, ...
-                                     true);
-      end
+      content.Resolution = p.entities.res;
     end
 
     if any(ismember(fieldnames(p.entities), 'den'))
-      try
-        content.Density = {{ struct(p.entities.den, 'REQUIRED if "den" entity') }};
-      catch
-        bids.internal.error_handling(mfilename(), 'invalidFieldname', ....
-                                     sprintf('Invalid field name for entity den-%s', ...
-                                             p.entities.den), ...
-                                     true, ...
-                                     true);
-      end
+      content.Density = p.entities.den;
     end
 
     %% suffix related content
     if any(ismember(p.suffix, {'dseg', 'probseg'}))
       content.Manual = {{'OPTIONAL'}};
-      content.Atlas = {{'OPTIONAL'}};
     end
 
     if any(ismember(p.suffix, {'mask'}))
       content.RawSources = {{'REQUIRED'}};
-      content.Atlas = {{'OPTIONAL'}};
       content.Type = {{'OPTIONAL'}};
     end
 
diff --git a/demos/notebooks/BIDS_Matlab_03_filenames_and_metadata.m b/demos/notebooks/BIDS_Matlab_03_filenames_and_metadata.m
index 04ebdbba..9471d236 100644
--- a/demos/notebooks/BIDS_Matlab_03_filenames_and_metadata.m
+++ b/demos/notebooks/BIDS_Matlab_03_filenames_and_metadata.m
@@ -143,4 +143,4 @@
 json = bids.derivatives_json('sub-01_ses-test_task-faceRecognition_res-r2pt0_space-IXI549Space_desc-brain_mask.nii');
 json.filename;
 json.content;
-json.content.Resolution{1}{1};
+json.content.Resolution;
diff --git a/tests/test_derivatives_json.m b/tests/test_derivatives_json.m
index 30280834..32470e76 100644
--- a/tests/test_derivatives_json.m
+++ b/tests/test_derivatives_json.m
@@ -22,19 +22,6 @@ function test_derivatives_json_basic()
 
 end
 
-function test_derivatives_json_entity_as_number()
-
-  if bids.internal.is_octave()
-    moxunit_throw_test_skipped_exception('Octave:mixed-string-concat warning thrown');
-  end
-
-  filename = 'sub-01_ses-test_task-faceRecognition_run-02_res-2_bold.nii';
-
-  assertWarning(@() bids.derivatives_json(filename), ...
-                'derivatives_json:invalidFieldname');
-
-end
-
 function test_derivatives_json_force()
 
   %% force to create default content
@@ -57,8 +44,8 @@ function test_derivatives_json_preproc()
 
   content = expected_content();
 
-  content.Resolution = {{ struct('hi', 'REQUIRED if "res" entity') }};
-  content.Density = {{ struct('lo', 'REQUIRED if "den" entity') }};
+  content.Resolution = 'hi';
+  content.Density = 'lo';
 
   expected.content = content;
   expected.filename = 'sub-01_task-faceRecognition_res-hi_den-lo_desc-preproc_bold.json';
@@ -76,7 +63,6 @@ function test_derivatives_json_segmentation()
 
   content = expected_content();
   content.Manual = {{'OPTIONAL'}};
-  content.Atlas = {{'OPTIONAL'}};
 
   expected.content = content;
   expected.filename = 'sub-01_desc-T1w_dseg.json';
@@ -94,7 +80,6 @@ function test_derivatives_json_mask()
 
   content = expected_content();
   content.RawSources = {{'REQUIRED'}};
-  content.Atlas = {{'OPTIONAL'}};
   content.Type = {{'OPTIONAL'}};
 
   expected.content = content;