From ebfa4616a83761a705113f72e3683cd1a9f5631d Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Fri, 26 Apr 2024 17:08:10 +0200
Subject: [PATCH 1/7] enable INPUT import in import_eyelink

---
 src/Import/eyelink/import_eyelink.m | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/src/Import/eyelink/import_eyelink.m b/src/Import/eyelink/import_eyelink.m
index ed81f0bf..1fc36c6c 100644
--- a/src/Import/eyelink/import_eyelink.m
+++ b/src/Import/eyelink/import_eyelink.m
@@ -267,7 +267,8 @@
 eblink_indices = find(strncmp(messages, 'EBLINK', numel('EBLINK')));
 ssacc_indices = find(strncmp(messages, 'SSACC', numel('SSACC')));
 esacc_indices = find(strncmp(messages, 'ESACC', numel('ESACC')));
-msg_indices = strncmp(messages, 'MSG', numel('MSG'));
+msg_indices = strncmp(messages, 'MSG', numel('MSG')) | ...
+    strncmp(messages, 'INPUT', numel('INPUT'));
 for name = {'RECCFG', 'ELCLCFG', 'GAZE_COORDS', 'THRESHOLDS', 'ELCL_', 'PUPIL_DATA_TYPE', '!MODE'}
   msg_indices = msg_indices & ~contains(messages, name);
 end
@@ -433,7 +434,7 @@
   extra = setdiff(beg_indices, end_indices);
   for idx = extra
     parts = split(messages{idx});
-    which_eye = parts{2}
+    which_eye = parts{2};
     beg_time = str2num(parts{3});
     end_time = session_end_time;
 

From b96dae93ddbd6d0b769835f1f08a6880869425e5 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Sat, 27 Apr 2024 13:50:08 +0200
Subject: [PATCH 2/7] improvements to marker import

---
 src/Import/eyelink/import_eyelink.m | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/Import/eyelink/import_eyelink.m b/src/Import/eyelink/import_eyelink.m
index 1fc36c6c..59bea1ca 100644
--- a/src/Import/eyelink/import_eyelink.m
+++ b/src/Import/eyelink/import_eyelink.m
@@ -311,14 +311,15 @@
   msgline = messages{idx};
   parts = split(msgline);
   time = str2num(parts{2});
-  if ismember(time,markers.times)
-    warning('ID:markers_with_same_timestamp',['PsPM found markers with same timestamps.',...
-      'Only the first one will be imported.'])
-  elseif time <= session_end_time
+  % if ismember(time,markers.times)
+  %   warning('ID:markers_with_same_timestamp',['PsPM found markers with same timestamps.',...
+  %     'Only the first one will be imported.'])
+  %   keyboard
+  % elseif time <= session_end_time
     markers.markers(bsearch(timecol, time)) = true;
     markers.times(end + 1, 1) = time;
     markers.names{end + 1, 1} = cell2mat(join(parts(3:end), ' '));
-  end
+  % end
 end
 
 % set data columns

From 03e74b40c94d4f10df863074d05291abe9561e23 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Mon, 29 Apr 2024 18:09:58 +0200
Subject: [PATCH 3/7] allow analog input into eyetracker to be converted to
 markers

---
 src/Import/eyelink/import_eyelink.m | 45 +++++++++------------
 src/pspm_get_eyelink.m              | 63 ++++++++---------------------
 2 files changed, 35 insertions(+), 73 deletions(-)

diff --git a/src/Import/eyelink/import_eyelink.m b/src/Import/eyelink/import_eyelink.m
index 59bea1ca..c0c4291f 100644
--- a/src/Import/eyelink/import_eyelink.m
+++ b/src/Import/eyelink/import_eyelink.m
@@ -22,9 +22,8 @@
 %                           - ymin: y coordinate of top left corner of screen in pixels.
 %                           - xmax: x coordinate of bottom right corner of screen in pixels.
 %                           - ymax: y coordinate of bottom right corner of screen in pixels.
-%                       markers: Array of the same size as data columns. An entry is 1 if there is
-%                                marker at that time.
-%                       markerinfos: Structure with the following fields:
+%                       markers: Sample number of any detected marker
+%                       markerinfo: Structure with the following fields:
 %                           - name: Cell array of marker name.
 %                           - value: Index of the marker name to an array containing
 %                                    unique marker names.
@@ -52,7 +51,7 @@
 
 % write outputs
 % -------------
-markers_sess = create_marker_val_fields(markers_sess);
+markers_sess = create_marker_val_fields(markers_sess); % create marker values from unique names
 for sn = 1:numel(dataraw)
   data{sn}.raw = dataraw{sn};
   data{sn}.channels = data{sn}.raw(:, chan_info{sn}.col_idx);
@@ -71,20 +70,20 @@
   data{sn}.gaze_coords.ymax = chan_info{sn}.ymax;
   data{sn}.elcl_proc = chan_info{sn}.elcl_proc;
 
-  data{sn}.markers = markers_sess{sn}.markers;
-  data{sn}.markerinfos.name = markers_sess{sn}.names;
-  data{sn}.markerinfos.value = markers_sess{sn}.vals;
+  data{sn}.markers = markers_sess{sn}.times;
+  data{sn}.markerinfo.name = markers_sess{sn}.names;
+  data{sn}.markerinfo.value = markers_sess{sn}.vals;
 end
 data{end + 1} = combine_markers(markers_sess);
 
 session_end_times = calc_session_end_times(messages);
 for i = 1:numel(data) - 1
-  [data{i}.markers, data{i}.markerinfos] = remove_markers_beyond_end(...
-    data{i}.markers, data{i}.markerinfos, markers_sess{i}.times, session_end_times{i});
+  [data{i}.markers, data{i}.markerinfo] = remove_markers_beyond_end(...
+    data{i}.markers, data{i}.markerinfo, markers_sess{i}.times, session_end_times{i});
 end
 end
 
-function [markers_out, markerinfos_out] = remove_markers_beyond_end(markers, markerinfos, markertimes, sess_end_time)
+function [markers_out, markerinfos_out] = remove_markers_beyond_end(markers, markerinfo, markertimes, sess_end_time)
 mask = markertimes <= sess_end_time;
 
 marker_indices = find(markers);
@@ -93,7 +92,7 @@
   markers_out(marker_indices(end)) = 0;
 end
 
-markerinfos_out = markerinfos;
+markerinfos_out = markerinfo;
 markerinfos_out.name = markerinfos_out.name(mask);
 markerinfos_out.value = markerinfos_out.value(mask);
 end
@@ -267,6 +266,8 @@
 eblink_indices = find(strncmp(messages, 'EBLINK', numel('EBLINK')));
 ssacc_indices = find(strncmp(messages, 'SSACC', numel('SSACC')));
 esacc_indices = find(strncmp(messages, 'ESACC', numel('ESACC')));
+% according to information from Yanfang, MSG refers to ethernet input using
+% python eyelink library, and INPUT to analog (?) input
 msg_indices = strncmp(messages, 'MSG', numel('MSG')) | ...
     strncmp(messages, 'INPUT', numel('INPUT'));
 for name = {'RECCFG', 'ELCLCFG', 'GAZE_COORDS', 'THRESHOLDS', 'ELCL_', 'PUPIL_DATA_TYPE', '!MODE'}
@@ -304,22 +305,14 @@
 end
 
 % construct markers
-markers.markers = false(size(dataraw, 1), 1);
 markers.times = [];
 markers.names = {};
 for idx = msg_indices
   msgline = messages{idx};
   parts = split(msgline);
   time = str2num(parts{2});
-  % if ismember(time,markers.times)
-  %   warning('ID:markers_with_same_timestamp',['PsPM found markers with same timestamps.',...
-  %     'Only the first one will be imported.'])
-  %   keyboard
-  % elseif time <= session_end_time
-    markers.markers(bsearch(timecol, time)) = true;
-    markers.times(end + 1, 1) = time;
-    markers.names{end + 1, 1} = cell2mat(join(parts(3:end), ' '));
-  % end
+  markers.times(end + 1, 1) = time;
+  markers.names{end + 1, 1} = cell2mat(join(parts(3:end), ' '));
 end
 
 % set data columns
@@ -463,11 +456,11 @@
 for i = 1:numel(markers_sess)
   all_marker_names = [all_marker_names; markers_sess{i}.names];
 end
-all_markers_struct.times = [];
-all_markers_struct.vals = [];
-all_markers_struct.names = all_marker_names;
+all_markers_struct.markers = [];
+all_markers_struct.markerinfo.vals = [];
+all_markers_struct.markerinfo.names = all_marker_names;
 for i = 1:numel(markers_sess)
-  all_markers_struct.times = [all_markers_struct.times; markers_sess{i}.times];
-  all_markers_struct.vals = [all_markers_struct.vals; markers_sess{i}.vals];
+  all_markers_struct.markers = [all_markers_struct.markers; markers_sess{i}.times];
+  all_markers_struct.markerinfo.vals = [all_markers_struct.markerinfo.vals; markers_sess{i}.vals];
 end
 end
diff --git a/src/pspm_get_eyelink.m b/src/pspm_get_eyelink.m
index ec5a880f..7ebee98d 100644
--- a/src/pspm_get_eyelink.m
+++ b/src/pspm_get_eyelink.m
@@ -74,12 +74,12 @@
 
 % iterate through data and fill up channel list as long as there is no
 % marker channel. if there is any marker channel, the settings accordingly
-% markerinfos, markers and marker type.
+% markerinfo, markers and marker type.
 % -------------------------------------------------------------------------
 
 % ensure sessions have the same samplerate
-%separate marker_data from real data
-all_markers = data{numel(data)};
+% separate marker_data from real data
+all_markers = data{end};
 data = data(1:numel(data)-1);
 sr = cell2mat(cellfun(@(d) d.sampleRate, data, 'UniformOutput', false));
 eyesObs = cellfun(@(d) d.eyesObserved, data, 'UniformOutput', false);
@@ -92,9 +92,9 @@
   % samplerate
   sampleRate = data{1}.sampleRate;
   % markers
-  markers = data{1}.markers;
-  % markerinfos
-  markerinfos = data{1}.markerinfos;
+  markers = data{1}.markers/sampleRate;
+  % markerinfo
+  markerinfo = data{1}.markerinfo;
   % units
   units = data{1}.units;
 else
@@ -103,10 +103,6 @@
   last_time = data{1}.raw(1,1);
 
   channels = [];
-  markers = [];
-
-  mi_value = [];
-  mi_name = {};
 
   n_cols = size(data{1}.channels, 2);
   counter = 1;
@@ -126,25 +122,8 @@
     n_diff = round((start_time - last_time)*sr/1000);
     if n_diff > 0
 
-      % channels and markers
+      % channels 
       channels(counter:(counter+n_diff-1),1:n_cols) = NaN(n_diff, n_cols);
-      markers(counter:(counter+n_diff-1), 1) = zeros(n_diff,1);
-
-      % markerinfos
-      mi_value(end + 1 : end + n_diff, 1) = zeros(n_diff,1);
-      mi_name( end + 1 : end + n_diff, 1) = {'0'};
-
-      % find if there are markers in the breaks
-      break_markers_idx = all_markers.times>=last_time & all_markers.times<=start_time;
-      tmp_times = all_markers.times(break_markers_idx);
-      tmp_vals  = all_markers.vals(break_markers_idx);
-      tmp_names = all_markers.names(break_markers_idx);
-
-      % calculate, weher to insert missing markers
-      tmp_marker_idx = round((tmp_times- last_time)*sr/1000)-1 + counter;
-      markers(tmp_marker_idx,1) = 1;
-      mi_value(tmp_marker_idx,1) = tmp_vals;
-      mi_name(tmp_marker_idx,1) = tmp_names;
       counter = counter + n_diff;
     end
 
@@ -152,25 +131,22 @@
 
     % channels and markers
     channels(counter:(counter+n_data-1),1:n_cols) = data{c}.channels;
-    markers(counter:(counter+n_data-1),1) = data{c}.markers;
-
-    % markerinfos
-    n_markers = numel(data{c}.markerinfos.value);
-    mi_value(end + 1 : end + n_markers, 1) = data{c}.markerinfos.value;
-    mi_name( end + 1 : end + n_markers, 1) = data{c}.markerinfos.name;
 
     counter = counter + n_data;
     last_time = end_time;
   end
 
-  markerinfos.name = mi_name;
-  markerinfos.value = mi_value;
-
   % units (they should be for all channels the same)
   units = data{1}.units;
 
   % samplerate
   sampleRate = sr;
+
+  % markers
+  markers = all_markers.markers/sampleRate;
+  % markerinfo
+  markerinfo = all_markers.markerinfo;
+
 end
 
 
@@ -204,17 +180,10 @@
   end
 
   if strcmpi(import{k}.type, 'marker')
-    import{k}.marker = 'continuous';
-    import{k}.sr     = sampleRate;
+    import{k}.marker = 'timestamps';
+    import{k}.sr     = 1;
     import{k}.data   = markers;
-    % marker info is read and set (in this instance) but
-    % imported data cannot be read at the moment (in later instances)
-    import{k}.markerinfo = markerinfos;
-
-    % by default use 'all' flank for translation from continuous to events
-    if ~isfield(import{k},'flank')
-      import{k}.flank = 'all';
-    end
+    import{k}.markerinfo = markerinfo;
   else
     % determine channel id from channeltype - eyelink specific
     % thats why channel ids will be ignored!

From b1c410c68dbe6f15b8f672075b8740b07b2f5a86 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Mon, 29 Apr 2024 20:09:47 +0200
Subject: [PATCH 4/7] updates

---
 src/Import/eyelink/import_eyelink.m | 22 +++++++++-------------
 src/pspm_get_eyelink.m              |  4 ++--
 test/import_eyelink_test.m          |  2 +-
 3 files changed, 12 insertions(+), 16 deletions(-)

diff --git a/src/Import/eyelink/import_eyelink.m b/src/Import/eyelink/import_eyelink.m
index c0c4291f..eed5c96b 100644
--- a/src/Import/eyelink/import_eyelink.m
+++ b/src/Import/eyelink/import_eyelink.m
@@ -79,19 +79,15 @@
 session_end_times = calc_session_end_times(messages);
 for i = 1:numel(data) - 1
   [data{i}.markers, data{i}.markerinfo] = remove_markers_beyond_end(...
-    data{i}.markers, data{i}.markerinfo, markers_sess{i}.times, session_end_times{i});
+    data{i}.markers, data{i}.markerinfo, session_end_times{i}, data{1}.raw(1,1));
 end
+[data{end}.markers, data{end}.markerinfo] = remove_markers_beyond_end(...
+    data{end}.markers, data{end}.markerinfo, session_end_times{end}, data{1}.raw(1,1));
 end
 
-function [markers_out, markerinfos_out] = remove_markers_beyond_end(markers, markerinfo, markertimes, sess_end_time)
-mask = markertimes <= sess_end_time;
-
-marker_indices = find(markers);
-markers_out = markers;
-if any(~mask)
-  markers_out(marker_indices(end)) = 0;
-end
-
+function [markers_out, markerinfos_out] = remove_markers_beyond_end(markers, markerinfo, sess_end_time, first_sess_start)
+mask = (markers <= sess_end_time) & (markers > first_sess_start);
+markers_out = markers(mask);
 markerinfos_out = markerinfo;
 markerinfos_out.name = markerinfos_out.name(mask);
 markerinfos_out.value = markerinfos_out.value(mask);
@@ -457,10 +453,10 @@
   all_marker_names = [all_marker_names; markers_sess{i}.names];
 end
 all_markers_struct.markers = [];
-all_markers_struct.markerinfo.vals = [];
-all_markers_struct.markerinfo.names = all_marker_names;
+all_markers_struct.markerinfo.value = [];
+all_markers_struct.markerinfo.name = all_marker_names;
 for i = 1:numel(markers_sess)
   all_markers_struct.markers = [all_markers_struct.markers; markers_sess{i}.times];
-  all_markers_struct.markerinfo.vals = [all_markers_struct.markerinfo.vals; markers_sess{i}.vals];
+  all_markers_struct.markerinfo.value = [all_markers_struct.markerinfo.value; markers_sess{i}.vals];
 end
 end
diff --git a/src/pspm_get_eyelink.m b/src/pspm_get_eyelink.m
index 7ebee98d..f22ca36f 100644
--- a/src/pspm_get_eyelink.m
+++ b/src/pspm_get_eyelink.m
@@ -92,7 +92,7 @@
   % samplerate
   sampleRate = data{1}.sampleRate;
   % markers
-  markers = data{1}.markers/sampleRate;
+  markers = (data{1}.markers-data{1}.raw(1,1))/sampleRate;
   % markerinfo
   markerinfo = data{1}.markerinfo;
   % units
@@ -143,7 +143,7 @@
   sampleRate = sr;
 
   % markers
-  markers = all_markers.markers/sampleRate;
+  markers = (all_markers.markers-data{1}.raw(1,1))/sampleRate;
   % markerinfo
   markerinfo = all_markers.markerinfo;
 
diff --git a/test/import_eyelink_test.m b/test/import_eyelink_test.m
index c1acdb6c..37519efa 100644
--- a/test/import_eyelink_test.m
+++ b/test/import_eyelink_test.m
@@ -62,7 +62,7 @@ function test_import_eyelink_on_file(this, filepath)
           sn = sn + 1;
           sample_idx = 1;
           msg_idx = 1;
-          msgtimes = data{sn}.raw(data{sn}.markers, 1);
+          msgtimes = data{sn}.raw(data{sn}.markers-data{sn}.raw(1,1)+1, 1);
           this.verifyEqual(data{sn}.sampleRate, to_num(parts{5}));
           this.verifyEqual(lower(data{sn}.eyesObserved), lower(parts{8}));
           eyesObserved = parts{8};

From b62a189e76684229708c61c5d9ba170d48425a1e Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Tue, 30 Apr 2024 15:00:56 +0200
Subject: [PATCH 5/7] fixes

---
 src/pspm_get_eyelink.m     | 7 ++++---
 test/import_eyelink_test.m | 4 ++--
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/pspm_get_eyelink.m b/src/pspm_get_eyelink.m
index f22ca36f..98950d07 100644
--- a/src/pspm_get_eyelink.m
+++ b/src/pspm_get_eyelink.m
@@ -136,14 +136,15 @@
     last_time = end_time;
   end
 
-  % units (they should be for all channels the same)
+  % units (they should be the same for all sessions)
   units = data{1}.units;
 
   % samplerate
   sampleRate = sr;
 
-  % markers
-  markers = (all_markers.markers-data{1}.raw(1,1))/sampleRate;
+  % markers (time stamps are in ms; convert to seconds)
+  markers = (all_markers.markers-data{1}.raw(1,1))/1000;
+
   % markerinfo
   markerinfo = all_markers.markerinfo;
 
diff --git a/test/import_eyelink_test.m b/test/import_eyelink_test.m
index 37519efa..3edcc06f 100644
--- a/test/import_eyelink_test.m
+++ b/test/import_eyelink_test.m
@@ -62,7 +62,7 @@ function test_import_eyelink_on_file(this, filepath)
           sn = sn + 1;
           sample_idx = 1;
           msg_idx = 1;
-          msgtimes = data{sn}.raw(data{sn}.markers-data{sn}.raw(1,1)+1, 1);
+          msgtimes = data{sn}.markers;
           this.verifyEqual(data{sn}.sampleRate, to_num(parts{5}));
           this.verifyEqual(lower(data{sn}.eyesObserved), lower(parts{8}));
           eyesObserved = parts{8};
@@ -146,7 +146,7 @@ function test_import_eyelink_on_file(this, filepath)
           % check if current message and its time is correct
           message = parts(3:end);
           message = message{1};
-          this.verifyEqual(message, data{sn}.markerinfos.name{msg_idx});
+          this.verifyEqual(message, data{sn}.markerinfo.name{msg_idx});
           this.verifyEqual(to_num(parts{2}), msgtimes(msg_idx));
           msg_idx = msg_idx + 1;
         end

From 7850352ee85c015367f5d5eee5302f665eebd168 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Tue, 30 Apr 2024 15:22:14 +0200
Subject: [PATCH 6/7] update comments

---
 src/Import/eyelink/import_eyelink.m | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/Import/eyelink/import_eyelink.m b/src/Import/eyelink/import_eyelink.m
index eed5c96b..15f94186 100644
--- a/src/Import/eyelink/import_eyelink.m
+++ b/src/Import/eyelink/import_eyelink.m
@@ -262,8 +262,8 @@
 eblink_indices = find(strncmp(messages, 'EBLINK', numel('EBLINK')));
 ssacc_indices = find(strncmp(messages, 'SSACC', numel('SSACC')));
 esacc_indices = find(strncmp(messages, 'ESACC', numel('ESACC')));
-% according to information from Yanfang, MSG refers to ethernet input using
-% python eyelink library, and INPUT to analog (?) input
+% MSG refers to ethernet input using python eyelink library, and INPUT to 
+% parallel/serial port input
 msg_indices = strncmp(messages, 'MSG', numel('MSG')) | ...
     strncmp(messages, 'INPUT', numel('INPUT'));
 for name = {'RECCFG', 'ELCLCFG', 'GAZE_COORDS', 'THRESHOLDS', 'ELCL_', 'PUPIL_DATA_TYPE', '!MODE'}

From 7524bd19aa683bf344cce2c4baaf0fd41379c407 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Thu, 2 May 2024 17:52:55 +0200
Subject: [PATCH 7/7] (re)move auxiliary functions

---
 .../eyelink}/set_blinks_saccades_to_nan.m     |   6 +-
 src/backroom/blink_saccade_filtering.m        |  35 ------
 src/pspm_blink_saccade_filt.m                 | 110 ------------------
 src/pspm_get_eyelink.m                        |   8 +-
 src/pspm_get_smi.m                            |   4 +-
 src/pspm_get_viewpoint.m                      |   4 +-
 test/pspm_test.m                              |   1 -
 test/pspm_test_github_actions.m               |   1 -
 test/set_blinks_saccades_to_nan_test.m        |   4 +-
 9 files changed, 13 insertions(+), 160 deletions(-)
 rename src/{backroom => Import/eyelink}/set_blinks_saccades_to_nan.m (95%)
 delete mode 100644 src/backroom/blink_saccade_filtering.m
 delete mode 100644 src/pspm_blink_saccade_filt.m

diff --git a/src/backroom/set_blinks_saccades_to_nan.m b/src/Import/eyelink/set_blinks_saccades_to_nan.m
similarity index 95%
rename from src/backroom/set_blinks_saccades_to_nan.m
rename to src/Import/eyelink/set_blinks_saccades_to_nan.m
index 3cd17998..d17d2be1 100644
--- a/src/backroom/set_blinks_saccades_to_nan.m
+++ b/src/Import/eyelink/set_blinks_saccades_to_nan.m
@@ -27,7 +27,11 @@
     %
     %   - all elements in right data columns (except blink/saccade) that correspond to right
     %     blink or saccade rows are set to NaN
-    if nargin == 3
+%__________________________________________________________________________
+%
+% (C) 2019 Eshref Yozdemir
+
+if nargin == 3
         fn_is_left = @(x) strcmp(x(end-1:end), '_l');
     end
 
diff --git a/src/backroom/blink_saccade_filtering.m b/src/backroom/blink_saccade_filtering.m
deleted file mode 100644
index 78faac4b..00000000
--- a/src/backroom/blink_saccade_filtering.m
+++ /dev/null
@@ -1,35 +0,0 @@
-function [out_data_mat] = blink_saccade_filtering(data_mat, column_names, mask_chans, n_samples, fn_is_left)
-    if nargin == 4
-        fn_is_left = @(x) strcmp(x(end-1:end), '_l');
-    end
-
-    out_data_mat = expand_mask_chans(data_mat, column_names, mask_chans, n_samples);
-    out_data_mat = set_blinks_saccades_to_nan(out_data_mat, column_names, mask_chans);
-end
-
-function data = expand_mask_chans(data, column_names, mask_chans, offset)
-    for chan = mask_chans
-        col_idx = find(strcmpi(column_names, chan{1}));
-        data(:, col_idx) = expand_mask(data(:, col_idx), offset);
-    end
-end
-
-function mask = expand_mask(mask, offset)
-    diffmask = diff(mask);
-    indices_to_expand_towards_left = find(diffmask == 1) + 1;
-    indices_to_expand_towards_right = find(diffmask == (-1));
-
-    for ii = 1:numel(indices_to_expand_towards_left)
-        idx = indices_to_expand_towards_left(ii);
-        begidx = max(1, idx - offset);
-        endidx = max(1, idx - 1);
-        mask(begidx : endidx) = true;
-    end
-    ndata = numel(mask);
-    for ii = 1:numel(indices_to_expand_towards_right)
-        idx = indices_to_expand_towards_right(ii);
-        begidx = min(ndata, idx + 1);
-        endidx = min(ndata, idx + offset);
-        mask(begidx : endidx) = true;
-    end
-end
diff --git a/src/pspm_blink_saccade_filt.m b/src/pspm_blink_saccade_filt.m
deleted file mode 100644
index ff6c487e..00000000
--- a/src/pspm_blink_saccade_filt.m
+++ /dev/null
@@ -1,110 +0,0 @@
-function [sts, out_channel] = pspm_blink_saccade_filt(fn, discard_factor, options)
-% ● Description
-%   pspm_blink_saccade_filt perform blink-saccade filtering on a given file containing
-%   pupil data. This function extends each blink and/or saccade period towards the
-%   beginning and the end of the signal by an amount specified by the user.
-% ● Format
-%   [sts, out_channel] = pspm_blink_saccade_filt(fn, discard_factor, options)
-% ● Arguments
-%              fn: [string] Path to the PsPM file which contains
-%                  the pupil data.
-%  discard_factor: [numeric] Factor used to determine the number of
-%                  samples right before and right after a blink/saccade
-%                  period to discard. This value is multiplied by the
-%                  sampling rate of the recording to determine the
-%                  number of samples to discard from one end. Therefore,
-%                  for each blink/saccade period, 2*this_value*SR many
-%                  samples are discarded in total, and effectively
-%                  blink/saccade period is extended.
-%                  This value also corresponds to the duration of
-%                  samples to discard on one end in seconds. For example,
-%                  when it is 0.01, we discard 10 ms worth of data on
-%                  each end of every blink/saccade period.
-%         options:
-%        .channel: [numeric/string, optional, default:0]
-%                  Channel ID to be preprocessed.
-%                  By default preprocesses all the pupil and gaze channels.
-% .channel_action: [string, optional, accept:'add'/'replace', default:'add']
-%                  Defines whether corrected data should be added or the
-%                  corresponding preprocessed channel should be replaced.
-% ● History
-%   Written in 2020 by Eshref Yozdemir (University of Zurich)
-
-global settings;
-if isempty(settings), pspm_init; end
-sts = -1;
-if nargin == 2
-  options = struct();
-end
-options = pspm_options(options, 'blink_saccade_filt');
-if options.invalid; return; end
-if ~isnumeric(discard_factor)
-  warning('ID:invalid_input', 'discard_factor must be numeric');
-  return
-end
-[lsts, ~, data] = pspm_load_data(fn);
-if lsts ~= 1
-  return
-end
-[lsts, ~, data_user] = pspm_load_data(fn, options.channel);
-if lsts ~= 1
-  return
-end
-data_user = keep_pupil_gaze_channels(data_user);
-%% build matrixes and lists
-data_mat = {};
-column_names = {};
-mask_channels = {};
-for i = 1:numel(data)
-  channeltype = data{i}.header.chantype;
-  if strncmp(channeltype, 'blink', numel('blink')) || ...
-      strncmp(channeltype, 'saccade', numel('saccade'))
-    mask_channels{end + 1} = channeltype;
-    data_mat{end + 1} = data{i}.data;
-    column_names{end + 1} = channeltype;
-  end
-end
-n_mask_channels = numel(data_mat);
-for i = 1:numel(data_user)
-  channeltype = data_user{i}.header.chantype;
-  should_add = options.channel ~= 0 || ...
-    strncmp(channeltype, 'pupil', numel('pupil')) || ...
-    strncmp(channeltype, 'gaze', numel('gaze'));
-  if should_add
-    data_mat{end + 1} = data_user{i}.data;
-    column_names{end + 1} = data_user{i}.header.chantype;
-  end
-end
-data_mat = cell2mat(data_mat);
-%% perform filtering
-addpath(pspm_path('backroom'));
-sr = data{1}.header.sr;
-samples_to_discard = round(sr * discard_factor);
-out_mat = blink_saccade_filtering(data_mat, column_names, mask_channels, samples_to_discard);
-rmpath(pspm_path('backroom'));
-%% write back
-for i = 1:numel(data_user)
-  data_user{i}.data = out_mat(:, n_mask_channels + i);
-end
-channel_str = options.channel;
-if isnumeric(channel_str)
-  channel_str = num2str(channel_str);
-end
-o.msg.prefix = sprintf('Blink saccade filtering :: Input channel: %s', channel_str);
-[lsts, out_id] = pspm_write_channel(fn, data_user, options.channel_action, o);
-if lsts ~= 1
-  return
-end
-out_channel = out_id.channel;
-sts = 1;
-return
-%% keep_pupil_gaze_channels
-function [out_cell] = keep_pupil_gaze_channels(in_cell)
-out_cell = {};
-for i = 1:numel(in_cell)
-  channel = lower(in_cell{i}.header.chantype);
-  if contains(channel, 'pupil') || contains(channel, 'gaze')
-    out_cell{end + 1} = in_cell{i};
-  end
-end
-
diff --git a/src/pspm_get_eyelink.m b/src/pspm_get_eyelink.m
index 98950d07..2aad77d9 100644
--- a/src/pspm_get_eyelink.m
+++ b/src/pspm_get_eyelink.m
@@ -50,7 +50,6 @@
 % expand blink/saccade channels with offset
 % set data channels with blinks/saccades to NaN
 % -------------------------------------------------------------------------
-addpath(pspm_path('backroom'));
 for i = 1:numel(data)-1
   if strcmpi(data{i}.eyesObserved, settings.eye.char.l)
     mask_chans = {'blink_l', 'saccade_l'};
@@ -61,16 +60,13 @@
   else
     warning('ID:invalid_input', ['No valid eye marker is detected, please check input channels.']);
   end
-  expand_factor = 0;
 
-  data{i}.channels = blink_saccade_filtering(...
+  data{i}.channels = set_blinks_saccades_to_nan(...
     data{i}.channels, ...
     data{i}.channel_header, ...
-    mask_chans, ...
-    expand_factor * data{i}.sampleRate ...
+    mask_chans ...
     );
 end
-rmpath(pspm_path('backroom'));
 
 % iterate through data and fill up channel list as long as there is no
 % marker channel. if there is any marker channel, the settings accordingly
diff --git a/src/pspm_get_smi.m b/src/pspm_get_smi.m
index 26a24a35..a89815a5 100644
--- a/src/pspm_get_smi.m
+++ b/src/pspm_get_smi.m
@@ -119,7 +119,7 @@
   if ~assert_sessions_are_one_after_another(data); return; end
 end
 [data_concat, markers, mi_values, mi_names] = concat_sessions(data);
-addpath(pspm_path('backroom'));
+addpath(pspm_path('Import','eyelink'));
 chan_struct = data{1}.channel_columns;
 eyes_observed = lower(data{1}.eyesObserved);
 if strcmpi(eyes_observed, settings.lateral.char.l)
@@ -134,7 +134,7 @@
   chan_struct,...
   mask_chans,...
   @(x) contains(x, 'L '));
-rmpath(pspm_path('backroom'));
+rmpath(pspm_path('Import','eyelink'));
 sampling_rate = data{1}.sampleRate;
 units = data{1}.units;
 raw_columns = data{1}.raw_columns;
diff --git a/src/pspm_get_viewpoint.m b/src/pspm_get_viewpoint.m
index f9ec090d..978b5255 100644
--- a/src/pspm_get_viewpoint.m
+++ b/src/pspm_get_viewpoint.m
@@ -103,7 +103,7 @@
 screen_size = data{1}.screenSize;
 viewing_dist = data{1}.viewingDistance;
 
-addpath(pspm_path('backroom'));
+addpath(pspm_path('Import', 'eyelink'));
 if strcmpi(eyes_observed, settings.lateral.char.l)
   mask_chans = {'blink_l', 'saccade_l'};
 elseif strcmpi(eyes_observed, settings.lateral.char.r)
@@ -112,7 +112,7 @@
   mask_chans = {'blink_l', 'blink_r', 'saccade_l', 'saccade_r'};
 end
 data_concat = set_blinks_saccades_to_nan(data_concat, chan_struct, mask_chans, @(x) strcmp(x(end-1:end), '_l'));
-rmpath(pspm_path('backroom'));
+rmpath(pspm_path('Import', 'eyelink'));
 
 num_import_cells = numel(import);
 for k = 1:num_import_cells
diff --git a/test/pspm_test.m b/test/pspm_test.m
index b4d0825e..463e4bff 100644
--- a/test/pspm_test.m
+++ b/test/pspm_test.m
@@ -22,7 +22,6 @@ function pspm_test(varargin)
   TestSuite.fromClass(?pspm_align_channels_test), ...
   TestSuite.fromClass(?pspm_bf_data_test), ...
   TestSuite.fromClass(?pspm_bf_test), ...
-  TestSuite.fromClass(?pspm_blink_saccade_filt_test), ...
   TestSuite.fromClass(?pspm_convert_gaze_test), ...
   TestSuite.fromClass(?pspm_convert_unit_test), ...
   TestSuite.fromClass(?pspm_dcm_test), ...
diff --git a/test/pspm_test_github_actions.m b/test/pspm_test_github_actions.m
index caf10ae0..f167732c 100644
--- a/test/pspm_test_github_actions.m
+++ b/test/pspm_test_github_actions.m
@@ -21,7 +21,6 @@ function pspm_test_github_actions(varargin)
   TestSuite.fromClass(?pspm_align_channels_test), ...
   TestSuite.fromClass(?pspm_bf_data_test), ...
   TestSuite.fromClass(?pspm_bf_test), ...
-  TestSuite.fromClass(?pspm_blink_saccade_filt_test), ...
   TestSuite.fromClass(?pspm_convert_gaze_test), ...
   TestSuite.fromClass(?pspm_convert_unit_test), ...
   TestSuite.fromClass(?pspm_check_python_test), ...
diff --git a/test/set_blinks_saccades_to_nan_test.m b/test/set_blinks_saccades_to_nan_test.m
index f8ecb246..06ce456e 100644
--- a/test/set_blinks_saccades_to_nan_test.m
+++ b/test/set_blinks_saccades_to_nan_test.m
@@ -11,7 +11,7 @@
   end
   methods(TestClassSetup)
     function add(this)
-      addpath(pspm_path('backroom'));
+      addpath(pspm_path('Import', 'eyelink'));
     end
   end
   methods(Test)
@@ -71,7 +71,7 @@ function test_both_eyes(this)
   end
   methods(TestClassTeardown)
     function remove(this)
-      addpath(pspm_path('backroom'));
+      addpath(pspm_path('Import', 'eyelink'));
     end
   end
 end
\ No newline at end of file