[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