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nbeliyBeliy Nikitapre-commit-ci[bot]Remi-Gau
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Incorporating json into bids.File (issues #596 #371) (#597)
* First attempt to incorporate json into bids.File * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * lint * Added util function to update structures * Style and tests for util/update_struct.m * Using metadata field instead of json_struct * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Removed JSONFile subclass * Added tests for metadata for File class * Fixed spelling in doc * File: Added functions that act on individual fields * File: fixed style * Splitted File.metadada tests into smaller ones --------- Co-authored-by: Beliy Nikita <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Remi Gau <[email protected]>
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‎+bids/+util/update_struct.m‎

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Original file line numberDiff line numberDiff line change
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function js = update_struct(js, varargin)
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%
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% Updates structure with new values.
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% Can add new fields, replace field values, remove fields,
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% and append new values to a cellarray.
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%
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% Designed for manipulating json structures and will not work
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% on structarrays.
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%
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% USAGE::
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%
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% js = update_struct(key1, value1, key2, value2);
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% js = update_struct(struct(key1, value1, ...
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% key2, value2));
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%
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% Examples:
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% ---------
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% Adding and replacing existing fields:
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% update_struct(struct('a', 'val_a'),...
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% 'a', 'new_val', 'b', 'val_b')
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% struct with fields:
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% a: 'new_val'
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% b: 'val_b'
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% Removing field from structure:
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% update_struct(struct('a', 'val_a', 'b', 'val_b'),
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% 'b', [])
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% struct with fields:
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% a: 'val_a'
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% Appending values to existing field:
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% update_struct(struct('a', 'val_a', 'b', 'val_b'),
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% 'b-add', 'val_b2')
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% struct with fields:
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% a: 'val_a'
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% b: {'val_b'; 'val_b2'}
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%
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% (C) Copyright 2023 BIDS-MATLAB developers
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if numel(varargin) == 0
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% Nothing to do
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return
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end
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if numel(varargin) > 1
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key_list = varargin(1:2:end);
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val_list = varargin(2:2:end);
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elseif isstruct(varargin{1})
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key_list = fieldnames(varargin{1});
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val_list = cell(size(key_list));
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for i = 1:numel(key_list)
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val_list{i} = varargin{1}.(key_list{i});
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end
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else
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id = bids.internal.camel_case('invalidInput');
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msg = 'Not list of parameters or structure';
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bids.internal.error_handling(mfilename(), id, msg, false, true);
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end
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for ii = 1:numel(key_list)
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par_key = key_list{ii};
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try
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par_value = val_list{ii};
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% Removing field from json structure
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% Should use only empty double ([]) or any empth object?
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if isempty(par_value) && isnumeric(par_value)
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if isfield(js, par_key)
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js = rmfield(js, par_key);
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end
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continue
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end
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if bids.internal.ends_with(par_key, '-add')
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par_key = par_key(1:end - 4);
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if isfield(js, par_key)
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if ischar(js.(par_key))
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par_value = {js.(par_key); par_value}; %#ok<AGROW>
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else
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par_value = [js.(par_key); par_value]; %#ok<AGROW>
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end
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end
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end
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js(1).(par_key) = par_value;
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catch ME
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id = bids.internal.camel_case('structError');
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msg = sprintf('''%s'' (%d) -- %s', par_key, ii, ME.message);
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bids.internal.error_handling(mfilename(), id, msg, false, true);
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end
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end
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end

‎+bids/File.m‎

Lines changed: 127 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -65,6 +65,65 @@
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%
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% file = bids.File(name_spec, 'use_schema', true);
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%
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% Load metadata (supporting inheritance).
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%
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% .. code-block:: matlab
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%
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% f = bids.File('tests/data/synthetic/sub-01/anat/sub-01_T1w.nii.gz');
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%
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% Access metadata
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%
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% .. code-block:: matlab
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%
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% f.metadata()
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% struct with fields:
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% Manufacturer: 'Siemens'
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% FlipAngle: 10
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%
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% Modify metadata
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%
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% .. code-block:: matlab
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% % Adding new value
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% f = f.metadata_add('NewField', 'new value');
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% f.metadata()
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% struct with fields:
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% manufacturer: 'siemens'
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% flipangle: 10
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% NewField: 'new value'
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%
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% % Appending to existing value
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% f = f.metadata_append('NewField', 'new value 1');
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% f.metadata()
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% struct with fields:
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% manufacturer: 'siemens'
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% flipangle: 10
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% NewField: {'new value'; 'new value 1'}
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%
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% % Removing value
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% f = f.metadata_remove('NewField');
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% f.metadata()
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% struct with fields:
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% manufacturer: 'siemens'
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% flipangle: 10
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%
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% Modify several fields of metadata
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%
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% .. code-block:: matlab
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%
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% f = f.metadata_update('Description', 'source file', ...
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% 'NewField', 'new value', ...
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% 'manufacturer', []);
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% f.metadata()
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% struct with fields:
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% flipangle: 10
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% description: 'source file'
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% NewField: 'new value'
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%
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% Export metadata as json:
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%
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% .. code-block:: matlab
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%
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% f.metadata_write()
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% (C) Copyright 2021 BIDS-MATLAB developers
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@@ -90,7 +149,7 @@
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metadata_files = {} % list of metadata files related
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metadata % list of metadata for this file
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metadata = [] % list of metadata for this file
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entity_required = {} % Required entities
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@@ -707,6 +766,73 @@ function check_required_entities(obj)
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708767
end
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% Functions related to metadata manipulation
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function obj = metadata_update(obj, varargin)
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% Update stored metadata with new values passed in varargin,
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% which can be either a structure, or pairs of key-values.
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%
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% See also
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% bids.util.update_struct
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%
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% USAGE::
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%
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% f = f.metadata_update(key1, value1, key2, value2);
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% f = f.metadata_update(struct(key1, value1, ...
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% key2, value2));
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obj.metadata = bids.util.update_struct(obj.metadata, varargin{:});
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end
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786+
function obj = metadata_add(obj, field, value)
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% Add a new field (or replace existing) to the metadata structure
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obj.metadata.(field) = value;
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end
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function obj = metadata_append(obj, field, value)
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% Append new value to a metadata.(field)
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% If metadata.(field) is a chararray, it will be first
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% transformed into cellarray.
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if isfield(obj.metadata, field)
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if ischar(obj.metadata.(field))
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value = {obj.metadata.(field); value};
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else
799+
value = [obj.metadata.(field); value];
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end
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end
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obj.metadata(1).(field) = value;
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end
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function obj = metadata_remove(obj, field)
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% Removes field from metadata
807+
if isfield(obj.metadata, field)
808+
obj.metadata = rmfield(obj.metadata, field);
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end
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end
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812+
function out_file = metadata_write(obj, varargin)
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% Export current content of metadata to sidecar json with
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% same name as current file. Metadata fields can be modified
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% with new values passed in varargin, which can be either a structure,
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% or pairs of key-values. These modifications do not affect
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% current File object, and only exported into file. Use
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% bids.File.metadata_update to update current metadata.
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% Returns full path to the exported sidecar json file.
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%
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% See also
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% bids.util.update_struct
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%
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% USAGE::
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%
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% f.metadata_write(key1, value1, key2, value2);
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% f.metadata_write(struct(key1, value1, ...
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% key2, value2));
829+
[path, ~, ~] = fileparts(obj.path);
830+
out_file = fullfile(path, obj.json_filename);
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der_json = bids.util.update_struct(obj.metadata, varargin{:});
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bids.util.jsonencode(out_file, der_json, 'indent', ' ');
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end
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710836
%% Things that might go private
711837

712838
function bids_file_error(obj, id, msg)

‎tests/test_bids_file.m‎

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Original file line numberDiff line numberDiff line change
@@ -69,6 +69,83 @@ function test_get_metadata_suffixes_basic()
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7070
end
7171

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function test_metadata_update()
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% Testung updating metadata with metadata_update function
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data_dir = fullfile(fileparts(mfilename('fullpath')), 'data', 'surface_data');
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file = fullfile(data_dir, 'sub-06_space-individual_den-native_thickness.dscalar.nii');
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bf = bids.File(file);
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% Adding
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bf = bf.metadata_update('Testing', 'adding field');
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assertTrue(isfield(bf.metadata, 'Testing'));
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assertEqual(bf.metadata.Testing, 'adding field');
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% Modifying
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bf = bf.metadata_update('Testing', 'modifying field');
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assertEqual(bf.metadata.Testing, 'modifying field');
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% Removing
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bf = bf.metadata_update('Testing', []);
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assertFalse(isfield(bf.metadata, 'Testing'));
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end
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function test_metadata_add()
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data_dir = fullfile(fileparts(mfilename('fullpath')), 'data', 'surface_data');
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file = fullfile(data_dir, 'sub-06_space-individual_den-native_thickness.dscalar.nii');
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bf = bids.File(file);
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bf = bf.metadata_add('Testing', 'adding field');
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assertTrue(isfield(bf.metadata, 'Testing'));
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assertEqual(bf.metadata.Testing, 'adding field');
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end
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function test_metadata_append()
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data_dir = fullfile(fileparts(mfilename('fullpath')), 'data', 'surface_data');
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file = fullfile(data_dir, 'sub-06_space-individual_den-native_thickness.dscalar.nii');
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bf = bids.File(file);
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bf = bf.metadata_append('Testing', 'adding field1');
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bf = bf.metadata_append('Testing', 'adding field2');
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assertEqual(bf.metadata.Testing, ...
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{'adding field1'; 'adding field2'});
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% testing char to cell conversion
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bf = bf.metadata_add('Testing2', 1);
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bf = bf.metadata_append('Testing2', 2);
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assertEqual(bf.metadata.Testing2, [1; 2]);
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end
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function test_metadata_remove()
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data_dir = fullfile(fileparts(mfilename('fullpath')), 'data', 'surface_data');
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file = fullfile(data_dir, 'sub-06_space-individual_den-native_thickness.dscalar.nii');
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bf = bids.File(file);
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bf = bf.metadata_add('Testing', 'adding field');
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assertTrue(isfield(bf.metadata, 'Testing'));
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bf = bf.metadata_remove('Testing');
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assertFalse(isfield(bf.metadata, 'Testing'));
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end
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function test_metadata_write()
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data_dir = fullfile(fileparts(mfilename('fullpath')), 'data', 'surface_data');
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file = fullfile(data_dir, 'sub-06_space-individual_den-native_thickness.dscalar.nii');
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bf = bids.File(file);
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% Writing metadata
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bf.prefix = 'test_';
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out_file = bf.metadata_write();
133+
assertTrue(exist(out_file, 'file') > 0);
134+
exported_metadata = bids.util.jsondecode(out_file);
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assertEqual(bf.metadata, exported_metadata);
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teardown(out_file);
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% Writing modified metadata
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out_file = bf.metadata_write('Testing', 'exporting');
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exported_metadata = bids.util.jsondecode(out_file);
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teardown(out_file);
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assertTrue(isfield(exported_metadata, 'Testing'));
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assertFalse(isfield(bf.metadata, 'Testing'));
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bf = bf.metadata_add('Testing', 'exporting');
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assertEqual(bf.metadata, exported_metadata);
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end
148+
72149
function test_rename()
73150

74151
input_filename = 'wuasub-01_ses-test_task-faceRecognition_run-02_bold.nii';

‎tests/tests_utils/test_update_struct.m‎

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function test_suite = test_update_struct %#ok<*STOUT>
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try % assignment of 'localfunctions' is necessary in Matlab >= 2016
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test_functions = localfunctions(); %#ok<*NASGU>
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catch % no problem; early Matlab versions can use initTestSuite fine
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end
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initTestSuite;
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end
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function test_main_func()
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% testing with parameters
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js = struct([]);
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js = bids.util.update_struct(js, 'key_a', 'val_a', 'key_b', 'val_b');
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assertTrue(isfield(js, 'key_a'));
16+
assertTrue(isfield(js, 'key_b'));
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assertEqual(js.key_a, 'val_a');
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assertEqual(js.key_b, 'val_b');
19+
20+
% testing with struct
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test_struct.key_c = 'val_c';
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js = bids.util.update_struct(js, test_struct);
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assertTrue(isfield(js, 'key_c'));
25+
assertEqual(js.key_c, 'val_c');
26+
27+
% testing update and removal of field
28+
js = bids.util.update_struct(js, 'key_c', [], 'key_a', 'val_a2');
29+
assertFalse(isfield(js, 'key_c'));
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assertEqual(js.key_a, 'val_a2');
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32+
% testing concatenating as string cell
33+
js = bids.util.update_struct(js, 'key_b-add', 'val_b2');
34+
assertEqual(js.key_b, {'val_b'; 'val_b2'});
35+
36+
% testing concatenating numericals
37+
js = bids.util.update_struct(js, 'key_b-add', 3);
38+
assertEqual(js.key_b, {'val_b'; 'val_b2'; 3});
39+
end
40+
41+
function test_exceptions()
42+
% Invalid input
43+
assertExceptionThrown(@() bids.util.update_struct(struct([]), 'key_b-add'), ...
44+
'update_struct:invalidInput');
45+
assertExceptionThrown(@() bids.util.update_struct(struct([]), ...
46+
'key_b-add', [], ...
47+
'key_c'), ...
48+
'update_struct:structError');
49+
end

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