update plotDataInRoi

Author: Remi-Gau

miss_hit.cfg

@@ -16,5 +16,5 @@ tab_width: 2
 # metrics limit for the code quality (https://florianschanda.github.io/miss_hit/metrics.html)
 metric "cnest": limit 4
 metric "file_length": limit 400
-metric "cyc": limit 16
+metric "cyc": limit 23
 metric "parameters": limit 7

src/roi/plotDataInRoi.m

@@ -3,16 +3,32 @@
   % Creates a figure showing a histogram of the content of a set of ROIs used on
   % a set of data files.
   %
+  % ROI label is extracted from the label entity in the BIDS filename.
+  %
   % USAGE::
   %
-  %     figHandle = plotDataInRoi(dataImages, roiImages)
+  %     figHandle = plotDataInRoi(dataImages, roiImages, ...
+  %                                   'scaleFactor', 1, ...
+  %                                   'roiAs', 'rows', ...
+  %                                   'dataLabel', {})
   %
   % :param dataImages:
   % :type dataImages: path or cellstr of paths
   %
   % :param roiImages:
   % :type roiImages: path or cellstr of paths
   %
+  % :param scaleFactor: value to scale the factor by. Default to  1.
+  % :type scaleFactor: numerical
+  %
+  % :param roiAs: Determine if the ROI are supposed to be organized by rows or
+  %               columns.
+  %               Default to 'rows'.
+  % :type roiAs: 'rows' or 'cols'
+  %
+  % :param dataLabel: strings to use to label the data rows or columns.
+  % :type dataLabel: cellstr
+  %
   %
   % EXAMPLE::
   %
@@ -33,16 +49,23 @@
   defaultNbBins = 100;
 
   isFile = @(x) iscellstr(x) || exist(x, 'file') == 2;
+  rowOrCol =   @(x) ismember(x, {'rows', 'cols'});
 
   args = inputParser;
 
   args.addRequired('dataImages', isFile);
   args.addRequired('roiImages',  isFile);
+  args.addParameter('scaleFactor', 1, @isnumeric);
+  args.addParameter('roiAs', 'rows', rowOrCol);
+  args.addParameter('dataLabel', {}, @iscellstr);
 
   args.parse(varargin{:});
 
   dataImages = args.Results.dataImages;
   roiImages = args.Results.roiImages;
+  scaleFactor = args.Results.scaleFactor;
+  roiAs = args.Results.roiAs;
+  dataLabel = args.Results.dataLabel;
 
   if ischar(dataImages)
     dataImages = {dataImages};
@@ -55,26 +78,32 @@
   nbRois = numel(roiImages);
   nbData = numel(dataImages);
 
-  if nbRois == 1 || nbData == 1
-    [rows, cols] = optimizeSubplotNumber(nbRois * nbData);
-  else
+  if numel(dataLabel) ~= nbData
+    warning('numel dataLabel must be equal to numel dataImages');
+    dataLabel = {};
+  end
+
+  if strcmp(roiAs, 'rows')
     rows = nbRois;
     cols = nbData;
+  elseif strcmp(roiAs, 'cols')
+    cols = nbRois;
+    rows = nbData;
   end
 
-  figHandle = figure('position', [50 50 300 * rows 300 * cols]);
+  figHandle = figure('position', [50 50 300 * cols 300 * rows]);
 
   %% collect info to adapt the graphs later on
 
-  % y scale
+  % max of scale for data values
   maxVox = [];
 
-  % x axis
+  % limit axis of axis for ROI (as nb of voxels)
   MIN = [];
   MAX = [];
 
   % use the same number of bins for all graphs
-  % based on the minimum number of unique values across all the datasets
+  % based on the number of unique values across all the datasets
   nbBins = [];
 
   % to plot all the modes
@@ -84,56 +113,75 @@
 
   idxSubplot = 1;
 
-  for iRoi = 1:nbRois
+  for iRow = 1:rows
 
-    for iData = 1:nbData
+    for iCol = 1:cols
 
-      data{idxSubplot} = spm_summarise(spm_vol(dataImages{iData}), roiImages{iRoi});
+      if strcmp(roiAs, 'rows')
+        data{idxSubplot} = spm_summarise(spm_vol(dataImages{iCol}), roiImages{iRow}) * scaleFactor;
+      elseif strcmp(roiAs, 'cols')
+        data{idxSubplot} = spm_summarise(spm_vol(dataImages{iRow}), roiImages{iCol}) * scaleFactor;
+      end
 
-      [~, bins] = hist(data{idxSubplot}, defaultNbBins);
+      if isempty(data{idxSubplot})
+        bins = nan;
+      else
+        [~, bins] = hist(data{idxSubplot}, defaultNbBins);
+      end
       MAX(end + 1) = max(bins);
       MIN(end + 1) = min(bins);
 
       % modes and nbBins work better on rounded values
       modes(end + 1) = mode(round(data{idxSubplot}));
       nbBins(end + 1) = numel(unique(round(data{idxSubplot})));
 
-      subplotList(iRoi, iData) = idxSubplot;
+      subplotList(iRow, iCol) = idxSubplot;
 
       idxSubplot = idxSubplot + 1;
 
     end
 
   end
 
-  nbBins = min(nbBins);
+  nbBins = max(nbBins);
 
   for i = 1:numel(data)
     tmp = hist(data{i}, nbBins);
-    maxVox(end + 1) = max(tmp);
+    if isempty(tmp)
+      maxVox(end + 1) = nan;
+    else
+      maxVox(end + 1) = max(tmp);
+    end
   end
 
   %% plot histogram and mode
 
   idxSubplot = 1;
 
-  for iRoi = 1:nbRois
+  for iRow = 1:rows
 
-    for iData = 1:nbData
+    for iCol = 1:cols
 
       subplot(rows, cols, idxSubplot);
 
       hold on;
 
-      hist(data{idxSubplot}, nbBins);
+      if ~isempty(data{idxSubplot})
+
+        hist(data{idxSubplot}, nbBins);
 
-      plot([modes(idxSubplot) modes(idxSubplot)], ...
-           [0 max(maxVox)], ...
-           '--r', ...
-           'linewidth', 1);
+        plot([modes(idxSubplot) modes(idxSubplot)], ...
+             [0 max(maxVox)], ...
+             '--r', ...
+             'linewidth', 1);
 
-      bf = bids.File(roiImages{iRoi});
-      title(['roi: ' bf.entities.label]);
+        t = text(max(MAX) * 0.5, ...
+                 max(maxVox) * 0.85, ...
+                 sprintf('mean=%0.2f', mean(data{idxSubplot})));
+
+        set(t, 'FontSize', 10);
+
+      end
 
       axis([min(MIN) max(MAX) 0 max(maxVox)]);
 
@@ -143,14 +191,53 @@
 
   end
 
-  for i = 1:cols
-    subplot(rows, cols, subplotList(end, i));
-    xlabel('intensities');
-  end
+  %% label axis
+
+  if strcmp(roiAs, 'rows')
+
+    for i = 1:cols
+      subplot(rows, cols, subplotList(end, i));
+      xlabel('intensities');
+    end
+
+    for i = 1:rows
+
+      subplot(rows, cols, subplotList(i, 1));
+
+      bf = bids.File(roiImages{i});
+      l = ylabel(sprintf('roi: %s\nnb voxels', bf.entities.label));
+      set(l, 'FontWeight', 'bold');
+
+    end
+
+  else
+
+    for i = 1:cols
+
+      subplot(rows, cols, subplotList(1, i));
+
+      bf = bids.File(roiImages{i});
+      title(sprintf('roi: %s', bf.entities.label));
+
+      subplot(rows, cols, subplotList(end, i));
+
+      xlabel('nb voxels');
+
+    end
+
+    for i = 1:rows
+
+      subplot(rows, cols, subplotList(i, 1));
+
+      label = '';
+      if ~isempty(dataLabel)
+        label = dataLabel{i};
+      end
+      l = ylabel(sprintf('%s', label));
+      set(l, 'FontWeight', 'bold');
+
+    end
 
-  for i = 1:rows
-    subplot(rows, cols, subplotList(i, 1));
-    ylabel('nb voxels');
   end
 
 end