From bf51ffb50ed727a21a2b4392148251e08dfe49d4 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Sun, 13 Aug 2023 16:50:26 +0200
Subject: [PATCH] bugfixes

---
 src/pspm_interp1.m |  9 ++++-----
 src/pspm_sf.m      | 40 +++++++++++++++++++++++++---------------
 src/pspm_sf_dcm.m  |  9 +++++----
 3 files changed, 34 insertions(+), 24 deletions(-)

diff --git a/src/pspm_interp1.m b/src/pspm_interp1.m
index 86b1e5aae..9e9154844 100644
--- a/src/pspm_interp1.m
+++ b/src/pspm_interp1.m
@@ -69,11 +69,10 @@
 end
 X_body = X(index_non_nan_full(1):index_non_nan_full(end));
 % processing body
-index = 1:length(X_body);
-index_nan = index(isnan(X_body) | index_missing(index_non_nan_full(1):index_non_nan_full(end))) ;
-index_non_nan = 1 - index_nan;
-if ~isempty(index_nan)
-  X_body_interp = interp1(index_non_nan,X_body(index_non_nan),index_nan);
+index_nan = zeros(size(X_body));
+index_nan(isnan(X_body) | index_missing(index_non_nan_full(1):index_non_nan_full(end))) = 1;
+if any(index_nan)
+  X_body_interp = interp1(find(~index_nan),X_body(~index_nan), (1:numel(X_body))');
 else
   X_body_interp = X_body;
 end
diff --git a/src/pspm_sf.m b/src/pspm_sf.m
index beb3cec24..3cf6e4f42 100644
--- a/src/pspm_sf.m
+++ b/src/pspm_sf.m
@@ -227,6 +227,9 @@
   % 3.5 Get missing epochs --
   if ~isempty(model.missing{iFile})
     [~, missing{iFile}] = pspm_get_timing('missing', model.missing{iFile}, 'seconds');
+    model.missing_data = zeros(size(y{2}));
+    missing_index = pspm_time2index(missing{iFile}, sr(datatype(k)));
+    model.missing_data((missing_index(:,1)+1):(missing_index(:,2)+1)) = 1;
   else
     missing{iFile} = [];
   end
@@ -247,9 +250,9 @@
         return;
       end
     end
+    % use first marker channel
+    events{iFile} = ndata{1}.data(:);
   end
-  % use first marker channel
-  events{iFile} = data{1}.data(:);
 
 
   for iEpoch = 1:size(epochs{iFile}, 1)
@@ -263,17 +266,23 @@
         case 'samples'
           win = round(epochs{iFile}(iEpoch, :) * sr(datatype(k)) / sr(1));
         case 'markers'
-          win = round(events(epochs{iFile}(iEpoch, :)) * sr(datatype(k)));
+          win = round(events{iFile}(epochs{iFile}(iEpoch, :)) * sr(datatype(k)));
         case 'whole'
           win = [1 numel(y{datatype(k)})];
       end
       if any(win > numel(y{datatype(k)}) + 1) || any(win < 0)
         warning('\nEpoch %2.0f outside of file %s ...', iEpoch, model.modelfile{iFile});
+        inv_flag = 0;
       else
+        inv_flag = 1;
         % correct issues with using 'round'
         win(1) = max(win(1), 1);
         win(2) = min(win(2), numel(y{datatype(k)}));
       end
+      if diff(win) < 4
+          warning('\nEpoch %2.0f contains insufficient data ...', iEpoch);
+          inv_flag = 0;
+      end
       % 3.6.1 collect information --
       sf.model{k}(iEpoch).modeltype = method{k};
       sf.model{k}(iEpoch).boundaries = squeeze(epochs{iFile}(iEpoch, :));
@@ -283,23 +292,24 @@
       %
       escr = y{datatype(k)}(win(1):win(end));
       sf.model{k}(iEpoch).data = escr;
-      if any(missing{iFile})
-        model.missing_data = zeros(size(escr));
-        missing_index = pspm_time2index(missing, sr(datatype(k)));
-        model.missing_data((missing_index{iFile}(:,1)+1):(missing_index{iFile}(:,2)+1)) = 1;
-      end
+      
       % 3.6.2 do the analysis and collect results --
-      if any(missing{iFile})
-        model_analysis = struct('scr', escr, 'sr', sr(datatype(k)), 'missing_data', model.missing_data);
+      if ~isempty(model.missing{iFile})
+        model_analysis = struct('scr', escr, 'sr', sr(datatype(k)), 'missing_data', model.missing_data(win(1):win(end)));
       else
         model_analysis = struct('scr', escr, 'sr', sr(datatype(k)));
       end
-      invrs = fhandle{k}(model_analysis, options);
-      if any(strcmpi(method{k}, {'dcm', 'mp'}))
-        sf.model{k}(iEpoch).inv     = invrs;
+       if inv_flag ~= 0
+           invrs = fhandle{k}(model_analysis, options);
+           sf.model{k}(iEpoch).inv = invrs;
+       else
+           sf.model{k}(iEpoch).inv = [];
+       end
+     if inv_flag == 0
+         sf.stats(iEpoch, k) = NaN;
+     elseif any(strcmpi(method{k}, {'dcm', 'mp'}))
         sf.stats(iEpoch, k)         = invrs.f;
-      else
-        sf.model{k}(iEpoch).stats   = invrs;
+     else
         sf.stats(iEpoch, k)         = invrs;
       end
     end
diff --git a/src/pspm_sf_dcm.m b/src/pspm_sf_dcm.m
index 2df113ac7..1d27f2076 100644
--- a/src/pspm_sf_dcm.m
+++ b/src/pspm_sf_dcm.m
@@ -150,12 +150,13 @@
 flag_missing_too_long = 0;
 if any(diff(miss_epoch, 1, 2)/model.sr > 0)
   if any(diff(miss_epoch, 1, 2)/model.sr > options.missingthresh)
-    warning_message = ['Imported data includes too long miss epoches (over ',...
-      num2str(options.missingthresh), 's), thus estimation has been skipped.'];
+    warning_message = ['Epoch includes missing data of more than ',...
+      num2str(options.missingthresh), ' s, thus estimation has been skipped. ', ...
+      'Please adjust options.missingthresh to proceed if you wish.'];
     flag_missing_too_long = 1;
   else
-    warning_message = ['Imported data includes miss epoches (over ',...
-      num2str(options.missingthresh), 's), but the trial has been allowed. ',...
+    warning_message = ['Epoch includes missing data of less than ',...
+      num2str(options.missingthresh), ' s, hence estimation is proceeding. ', ...
       'Please adjust options.missingthresh to skip if you wish.'];
   end
   warning('ID:missing_data', warning_message);