From be82fe6de76e2138954a32f9b0ef22870ce4b030 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Sun, 24 Mar 2024 11:55:04 -0400
Subject: [PATCH] [ENH] add zero padding to entity labels / indices when passed
 as numbers (#680)

* pad indices when passed as numbers

* update changelog

* skip octave test
---
 +bids/File.m             | 25 ++++++++++++++++
 .vscode/settings.json    |  3 +-
 docs/source/changelog.md | 61 ++++++++++++++++++++++++++++++++++++++++
 docs/source/index.rst    |  1 +
 tests/test_bids_file.m   | 36 ++++++++++++++++++++++++
 5 files changed, 125 insertions(+), 1 deletion(-)
 create mode 100644 docs/source/changelog.md

diff --git a/+bids/File.m b/+bids/File.m
index c88fa2e1..223e086c 100644
--- a/+bids/File.m
+++ b/+bids/File.m
@@ -172,6 +172,8 @@
 
     verbose = false
 
+    padding = 2
+
   end
 
   properties (SetAccess = private)
@@ -188,11 +190,13 @@
       args.addParameter('use_schema', false, @islogical);
       args.addParameter('tolerant', obj.tolerant, @islogical);
       args.addParameter('verbose', obj.verbose, @islogical);
+      args.addParameter('padding', obj.padding, @isnumeric);
 
       args.parse(varargin{:});
 
       obj.tolerant = args.Results.tolerant;
       obj.verbose = args.Results.verbose;
+      obj.padding = args.Results.padding;
 
       if args.Results.use_schema
         obj.schema = bids.Schema();
@@ -224,6 +228,11 @@
         obj.bids_file_error('emptySuffix', 'no suffix specified');
       end
 
+      if isfield(f_struct, 'entities')
+        f_struct.entities = obj.pad_indices(f_struct.entities);
+        obj.entities = f_struct.entities;
+      end
+
       if isfield(f_struct, 'modality')
         obj.modality = f_struct.modality;
       end
@@ -241,6 +250,21 @@
       obj = obj.update();
     end
 
+    function structure = pad_indices(obj, structure)
+      fields = fieldnames(structure);
+      pattern = ['%0', num2str(obj.padding), '.0f'];
+      if obj.padding <= 0
+        pattern = '%0.0f';
+      end
+      for i = 1:numel(fields)
+        if isnumeric(structure.(fields{i}))
+          structure.(fields{i}) = sprintf(pattern, ...
+                                          structure.(fields{i}));
+        end
+      end
+
+    end
+
     %% Getters
     function value = get.bids_path(obj)
       if obj.changed
@@ -577,6 +601,7 @@
           obj.extension = spec.ext;
         end
         if isfield(spec, 'entities')
+          spec.entities = obj.pad_indices(spec.entities);
           spec.entities = obj.normalize_entities(spec.entities);
           entities = fieldnames(spec.entities); %#ok<*PROPLC>
           for i = 1:numel(entities)
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 9e80844a..b3e8da67 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -4,5 +4,6 @@
         "fileMatch": ["model-*_smdl.json"],
         "url": "https://raw.githubusercontent.com/bids-standard/stats-models/gh-pages/BIDSStatsModel.json"
         }
-    ]
+    ],
+    "esbonio.sphinx.confDir": ""
 }
diff --git a/docs/source/changelog.md b/docs/source/changelog.md
new file mode 100644
index 00000000..49529ab9
--- /dev/null
+++ b/docs/source/changelog.md
@@ -0,0 +1,61 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+<!--
+### Added
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+-->
+
+## [Unreleased]
+
+### Added
+
+* [ENH] Add zero padding when numbers are passed for indices to `bids.File` or `bids.File.rename` #680 by @Remi-Gau
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+
+## [v0.2.0]
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
+
+## [v0.1.0]
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+### Security
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 228951c6..0aad4f3d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -26,6 +26,7 @@ To see how to install BIDS-Matlab, please check
    schema
    performance
    dev_doc
+   changelog
 
 
 Indices and tables
diff --git a/tests/test_bids_file.m b/tests/test_bids_file.m
index ac70d0c2..7e57b5a0 100644
--- a/tests/test_bids_file.m
+++ b/tests/test_bids_file.m
@@ -17,6 +17,8 @@
 
 function test_no_entity_warning
 
+  skip_if_octave('mixed-string-concat warning thrown');
+
   assertWarning(@()bids.File('TStatistic.nii', 'verbose', true), ...
                 'File:noEntity');
 
@@ -391,6 +393,40 @@ function test_change()
 
 end
 
+function test_zero_padding
+
+  entities = struct('sub', 1, ...
+                    'task', 'faceRecognition', ...
+                    'ses', 3, ...
+                    'run', 2);
+  filename.suffix = 'bold';
+  filename.ext = '.nii';
+  filename.entities = entities;
+  file = bids.File(filename, 'use_schema', true);
+  assertEqual(file.filename, 'sub-01_ses-03_task-faceRecognition_run-02_bold.nii');
+
+  file = bids.File(filename, 'use_schema', true, 'padding', 3);
+  assertEqual(file.filename, 'sub-001_ses-003_task-faceRecognition_run-002_bold.nii');
+
+  file = bids.File(filename, 'use_schema', true, 'padding', 0);
+  assertEqual(file.filename, 'sub-1_ses-3_task-faceRecognition_run-2_bold.nii');
+
+end
+
+function test_zero_padding_spec
+
+  input_filename = 'sub-01_task-faceRecognition_bold.nii';
+  file = bids.File(input_filename, 'use_schema', false);
+
+  spec.entities.res = 2;
+
+  file = file.rename('spec', spec);
+
+  output_filename = 'sub-01_task-faceRecognition_res-02_bold.nii';
+  assertEqual(file.filename, output_filename);
+
+end
+
 function test_bids_file_remove_entities()
 
   % GIVEN