Merge pull request #398 from bids-standard/improve_constant

[ENH] improve diagnostic to be able to split by suffix

+bids/+internal/plot_diagnostic_table.m

@@ -15,16 +15,7 @@ function plot_diagnostic_table(diagnostic_table, headers, yticklabel, fig_name)
 
  end
 
- % prepare x tick labels
- for col = 1:numel(headers)
- xticklabel{col} = [headers{col}.modality];
- if isfield(headers{col}, 'task')
- xticklabel{col} = sprintf('%s - task: %s', headers{col}.modality, headers{col}.task);
- end
- if length(xticklabel{col}) > 43
- xticklabel{col} = [xticklabel{col}(1:40) '...'];
- end
- end
+ xticklabel = create_x_tick_label(headers);
 
  nb_rows = size(diagnostic_table, 1);
  nb_cols = size(diagnostic_table, 2);
@@ -52,9 +43,7 @@ function plot_diagnostic_table(diagnostic_table, headers, yticklabel, fig_name)
  % y axis
  set(gca, 'yTick', 1:nb_rows);
 
- if nb_rows < 50
- set(gca, 'yTickLabel', yticklabel);
- end
+ set(gca, 'yTickLabel', yticklabel);
 
  box(gca, 'on');
 
@@ -111,3 +100,39 @@ function plot_diagnostic_table(diagnostic_table, headers, yticklabel, fig_name)
  title(fig_name);
 
 end
+
+function xticklabel = create_x_tick_label(headers)
+
+ for col = 1:numel(headers)
+
+ if iscell(headers{col}.modality)
+ xticklabel{col} = headers{col}.modality{1};
+ else
+ xticklabel{col} = headers{col}.modality;
+ end
+
+ xticklabel = append_entity_to_label(headers, xticklabel, col, 'task');
+
+ xticklabel = append_entity_to_label(headers, xticklabel, col, 'suffix');
+
+ if length(xticklabel{col}) > 43
+ xticklabel{col} = [xticklabel{col}(1:40) '...'];
+ end
+
+ end
+
+end
+
+function label = append_entity_to_label(headers, label, col, entity)
+
+ if isfield(headers{col}, entity)
+
+ if iscell(headers{col}.(entity))
+ headers{col}.(entity) = headers{col}.(entity){1};
+ end
+
+ label{col} = sprintf(['%s - ' entity ': %s'], label{col}, headers{col}.(entity));
+
+ end
+
+end

+bids/diagnostic.m

@@ -1,4 +1,4 @@
-function diagnostic_table = diagnostic(varargin)
+function [diagnostic_table, sub_ses, headers] = diagnostic(varargin)
  %
  % Creates a summary figure listing the number of files for each subject / session and
  % and imaging modality (possiblty split by task)
@@ -41,7 +41,7 @@
  % (C) Copyright 2021 BIDS-MATLAB developers
 
  default_BIDS = pwd;
- default_schema = true;
+ default_schema = false;
  default_filter = struct();
  default_split = {''};
  default_output_path = '';
@@ -65,11 +65,9 @@
 
  subjects = bids.query(BIDS, 'subjects', filter);
 
- modalities = bids.query(BIDS, 'modalities', filter);
-
- headers = get_headers(BIDS, modalities, filter, args.Results.split_by);
+ headers = get_headers(BIDS, filter, args.Results.split_by);
 
- diagnostic_table = nan(numel(subjects), numel(modalities));
+ diagnostic_table = nan(numel(subjects), numel(headers));
  % events_table = nan(numel(subjects), numel(tasks));
 
  row = 1;
@@ -102,6 +100,9 @@
  if isfield(headers{i_col}, 'task')
  this_filter.task = headers{i_col}.task;
  end
+ if isfield(headers{i_col}, 'suffix')
+ this_filter.suffix = headers{i_col}.suffix;
+ end
 
  files = bids.query(BIDS, 'data', this_filter);
 
@@ -141,28 +142,49 @@
 
 end
 
-function headers = get_headers(BIDS, modalities, filter, split_by)
+function headers = get_headers(BIDS, filter, split_by)
  %
  % Get the headers to include in the output table
  %
 
+ % TODO will probably need to use a recursive way to build the header list
+
  headers = {};
+
+ modalities = bids.query(BIDS, 'modalities', filter);
+
  for i_modality = 1:numel(modalities)
 
- if ismember('task', split_by) && ...
-  ismember(modalities(i_modality), {'func', 'eeg', 'meg', 'ieeg', 'pet', 'beh'})
+ this_filter = filter;
+ this_filter.modality = modalities(i_modality);
 
- this_filter = filter;
- this_filter.modality = modalities(i_modality);
- tasks = bids.query(BIDS, 'tasks', this_filter);
+ this_header = struct('modality', {modalities(i_modality)});
+
+ if ismember('suffix', split_by)
+
+ suffixes = bids.query(BIDS, 'suffixes', this_filter);
+
+ for i_suffix = 1:numel(suffixes)
+
+ this_filter.suffix = suffixes(i_suffix);
+
+ this_header.suffix = suffixes(i_suffix);
+
+ if ismember('task', split_by)
+ headers = add_task_based_headers(BIDS, headers, this_filter, this_header, split_by);
+ else
+ headers{end + 1} = this_header;
+ end
 
- for i_task = 1:numel(tasks)
- headers{end + 1} = struct('modality', modalities(i_modality), ...
- 'task', tasks(i_task));
  end
 
  else
- headers{end + 1} = struct('modality', modalities(i_modality));
+
+ if ismember('task', split_by)
+ headers = add_task_based_headers(BIDS, headers, this_filter, this_header, split_by);
+ else
+ headers{end + 1} = this_header;
+ end
 
  end
 
@@ -177,3 +199,18 @@
  this_filter.ses = ses;
  end
 end
+
+function headers = add_task_based_headers(BIDS, headers, this_filter, this_header, split_by)
+
+ if ismember('task', split_by)
+
+ tasks = bids.query(BIDS, 'tasks', this_filter);
+
+ for i_task = 1:numel(tasks)
+ this_header.task = tasks(i_task);
+ headers{end + 1} = this_header;
+ end
+
+ end
+
+end

+bids/query.m

@@ -159,7 +159,7 @@
  bids.internal.error_handling(mfilename(), 'unknownQuery', msg, false, true);
  end
 
- bids_entities = schema_entities();
+ % bids_entities = schema_entities();
 
  BIDS = bids.layout(BIDS);
 
@@ -175,7 +175,7 @@
  % Get optional target option for metadata query
  [target, options] = get_target(query, options);
 
- result = perform_query(BIDS, query, options, subjects, modalities, target, bids_entities);
+ result = perform_query(BIDS, query, options, subjects, modalities, target);
 
  %% Postprocessing output variable
  switch query
@@ -341,7 +341,7 @@ case cat(2, {'suffixes', 'suffixes', 'extensions', 'prefixes'}, valid_entity_qu
 
 end
 
-function result = perform_query(BIDS, query, options, subjects, modalities, target, bids_entities)
+function result = perform_query(BIDS, query, options, subjects, modalities, target)
 
  % Initialise output variable
  result = {};
@@ -366,13 +366,13 @@ case cat(2, {'suffixes', 'suffixes', 'extensions', 'prefixes'}, valid_entity_qu
  end
 
  result = update_result(query, options, result, this_subject, ...
- this_modality, target, bids_entities);
+ this_modality, target);
 
  end
 
  end
 
- result = update_result_with_root_content(query, options, result, BIDS, bids_entities);
+ result = update_result_with_root_content(query, options, result, BIDS);
 
 end
 
@@ -387,7 +387,6 @@ case cat(2, {'suffixes', 'suffixes', 'extensions', 'prefixes'}, valid_entity_qu
  this_subject = varargin{4};
  this_modality = varargin{5};
  target = varargin{6};
- bids_entities = varargin{7};
 
  d = this_subject.(this_modality);
 
@@ -441,7 +440,7 @@ case cat(2, {'suffixes', 'suffixes', 'extensions', 'prefixes'}, valid_entity_qu
 
  case valid_entity_queries()
 
- result = update_if_entity(query, result, d(k), bids_entities);
+ result = update_if_entity(query, result, d(k));
 
  case {'suffixes', 'prefixes'}
  field = query(1:end - 2);
@@ -459,7 +458,7 @@ case valid_entity_queries()
  end
 end
 
-function result = update_result_with_root_content(query, options, result, BIDS, bids_entities)
+function result = update_result_with_root_content(query, options, result, BIDS)
 
  d = BIDS.root;
 
@@ -493,7 +492,7 @@ case valid_entity_queries()
 
  case valid_entity_queries()
 
- result = update_if_entity(query, result, d(k), bids_entities);
+ result = update_if_entity(query, result, d(k));
 
  case {'suffixes', 'prefixes'}
  field = query(1:end - 2);
@@ -513,7 +512,7 @@ case valid_entity_queries()
  value = schema.content.objects.entities;
 end
 
-function result = update_if_entity(query, result, dk, bids_entities)
+function result = update_if_entity(query, result, dk)
 
  if ismember(query, short_valid_entity_queries())
  field = query(1:end - 1);
@@ -522,6 +521,7 @@ case valid_entity_queries()
  field = 'atlas';
 
  elseif ismember(query, long_valid_entity_queries())
+ bids_entities = schema_entities();
  field = bids_entities.(query(1:end - 1)).entity;
 
  else

tests/test_diagnostic.m

@@ -22,7 +22,9 @@ function test_diagnostic_basic()
  BIDS = bids.layout(deblank(examples(i, :)));
 
  diagnostic_table = bids.diagnostic(BIDS, 'output_path', pwd);
+ diagnostic_table = bids.diagnostic(BIDS, 'split_by', {'suffix'}, 'output_path', pwd);
  diagnostic_table = bids.diagnostic(BIDS, 'split_by', {'task'}, 'output_path', pwd);
+ diagnostic_table = bids.diagnostic(BIDS, 'split_by', {'task', 'suffix'}, 'output_path', pwd);
 
  end