From aba66fe8007d4d2c91d60cb71c4943b071374cd8 Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Mon, 30 Sep 2024 07:39:26 +0200
Subject: [PATCH 1/7] made pspm_expand_epochs and added to pspm_remove

---
 src/pspm_expand_epochs.m | 147 +++++++++++++++++++++++++++++++++++++++
 src/pspm_remove_epochs.m |  27 ++++++-
 2 files changed, 172 insertions(+), 2 deletions(-)
 create mode 100644 src/pspm_expand_epochs.m

diff --git a/src/pspm_expand_epochs.m b/src/pspm_expand_epochs.m
new file mode 100644
index 000000000..dff0a1d37
--- /dev/null
+++ b/src/pspm_expand_epochs.m
@@ -0,0 +1,147 @@
+function [sts, ep_exp] = pspm_expand_epochs(epoches, expansion, options)
+
+% fn passt nicht zu missing epochs
+%   [sts, channel_index]   = pspm_expand_epochs( {data_fn,  channel},    expansion , options)
+%   [sts, output_file]     = pspm_expand_epochs( missing_epochs_fn,      expansion , options)
+%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,         expansion , options) %
+%   options.mode =  'datafile'
+%                   'missing_ep_file'
+%                   'missing_ep'
+
+global settings
+if isempty(settings)
+  pspm_init;
+end
+
+sts = -1;
+
+if nargin < 3
+  warning('ID:invalid_input', 'Not enough input arguments');
+  return;
+end
+
+switch options.mode
+    % missing epochs
+    case 'missing_ep'
+        % Directly expand the given epochs
+        [sts, ep_exp] = expand(epoches, expansion);
+        return;
+
+    % missing epoches file
+    case 'missing_ep_file'
+        % Load missing epochs from file
+        data = load(epoches);  % Load the file without specifying a variable
+        
+        % Assuming the file contains a variable called 'epochs', access it
+        % Right name?
+        if isfield(data, 'epochs')
+            missing_epochs = data.epochs;
+        else
+            error('File does not contain variable ''epochs''.');
+            return;
+        end
+
+        if isempty(missing_epochs)
+            error('Failed to load missing epochs from file.');
+            return;
+        end
+
+        % Expand the loaded epochs
+        [sts, ep_exp] = expand(missing_epochs, expansion);
+        if sts == -1
+            error('Failed to expand epochs.');
+        end
+
+        % Save expanded missing epoch to a new file with 'e' prefix
+        [pathstr, name, ext] = fileparts(epoches);
+        output_file = fullfile(pathstr, ['e' name ext]);
+        save(output_file, 'ep_exp'); % should i save it as epoch???
+        disp(['Expanded epochs saved to: ', output_file]);
+
+        sts = 0;
+        return;
+
+
+    case 'datafile' % rename!!
+
+        % Load channel data
+        datafile = epoches{1};
+        channel  = epoches{2};
+        [lsts, ~, data] = pspm_load_data(datafile, channel);
+        if lsts == -1
+            error('Failed to load data from file.');
+        end
+
+        channel_data = data{1};
+        sr = channel_data.header.sr;
+
+        % Find NaN indices
+        nan_indices = isnan(channel_data.data);
+
+        % Convert NaN indices to epochs
+        nan_epochs = pspm_logical2epochs(nan_indices, sr);
+
+        % Expand the epochs
+        [sts, ep_exp] = expand(nan_epochs, expansion);
+        if sts == -1
+            error('Failed to expand epochs.');
+        end
+
+        % Convert expanded epochs back to logical indices
+        expanded_indices = pspm_epochs2logical(ep_exp, numel(channel_data.data), sr);
+
+        % Set data to NaN at expanded indices
+        channel_data.data(expanded_indices) = NaN;
+
+        % Save the data back to the file
+        [sts, out] = pspm_write_channel(datafile, {channel_data}, 'replace'); % add to options 'newfile'?
+        varargout{2} = 23 % channel_data.data;
+        return;
+
+
+    otherwise
+        error('Unknown mode in options.');
+        return;
+end
+
+end
+
+
+function [sts, ep_exp] = expand(ep, expansion)
+% Helper function to expand epochs by the specified pre and post times
+% and merge overlapping epochs.
+% Also ensures that no epoch starts before time 0.
+
+% Initialize status
+sts = -1;
+
+% Check if epochs matrix and expansion vector are valid
+if isempty(ep) || numel(expansion) ~= 2
+    error('Invalid input to expand function.');
+    return;
+end
+
+% Expand epochs
+pre = expansion(1);
+post = expansion(2);
+expanded_epochs_temp = [ep(:,1) - pre, ep(:,2) + post];
+
+% 
+% Ensure that the start of any epoch is not negative
+expanded_epochs_temp(expanded_epochs_temp(:,1) < 0, 1) = 0; % or <1???
+
+% Merge overlapping epochs
+ep_exp = expanded_epochs_temp(1, :);  % Start with the first epoch
+for i = 2:size(expanded_epochs_temp, 1)
+    % If the current epoch overlaps with the previous, merge them
+    if ep_exp(end, 2) >= expanded_epochs_temp(i, 1)
+        ep_exp(end, 2) = max(ep_exp(end, 2), expanded_epochs_temp(i, 2));
+    else
+        % Otherwise, add the current epoch as a new row
+        ep_exp = [ep_exp; expanded_epochs_temp(i, :)];
+    end
+end
+
+% Success
+sts = 0;
+end
diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index 3236a1a47..491dfdf7d 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -12,14 +12,17 @@
 %                 be in seconds. This parameter is passed to pspm_get_timing().
 %   * timeunits:  timeunits of the epochfile.
 %   ┌───options
-%   └─.channel_action:
+%   └─.channel_action: [pre, post]
 %                 ['add'/'replace'] Defines whether new channels should be added or
 %                 corresponding channels should be replaced. The default value is 'add'.
+%     .expand_epochs: 
+%                    Expand epochs by 0.5 seconds before and after        
 % ● Output
 %   * channel_index: index of channel containing the processed data
 % ● History
 %   Introduced in PsPM 4.0
 %   Written in 2016 by Tobias Moser (University of Zurich)
+%   Maintained in 2024 by Bernhard Agoué von Raußendorf
 
 global settings
 if isempty(settings)
@@ -36,7 +39,7 @@
 elseif nargin < 4
   options = struct();
 end
-options = pspm_options(options, 'remove_epochs');
+options = pspm_options(options, 'remove_epochs'); % change!!! [0,0]
 if options.invalid
   return
 end
@@ -51,6 +54,26 @@
   return;
 end
 
+
+
+expansion = options.expand_epochs;
+
+if numel(expansion) ~= 2
+    error('Expansion must be a 2-element vector [pre, post].');
+end
+% Expand the epochs
+
+[sts, ep_exp] = pspm_expand_epochs(ep, expansion, 'missing_ep');
+if psts == -1
+    return;
+end
+
+
+
+
+
+
+
 n_ep = size(ep, 1);
 n_data = numel(data);
 for i_data = 1:n_data

From 0285c103c47fc9d1b93458d12d9f6008fe3b94f5 Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Sun, 6 Oct 2024 23:55:25 +0200
Subject: [PATCH 2/7] pspm_expand_epochs varagin structure

---
 src/pspm_expand_epochs.m | 188 +++++++++++++++++++++++----------------
 src/pspm_remove_epochs.m |   9 +-
 2 files changed, 117 insertions(+), 80 deletions(-)

diff --git a/src/pspm_expand_epochs.m b/src/pspm_expand_epochs.m
index dff0a1d37..b9ffa4a26 100644
--- a/src/pspm_expand_epochs.m
+++ b/src/pspm_expand_epochs.m
@@ -1,9 +1,9 @@
-function [sts, ep_exp] = pspm_expand_epochs(epoches, expansion, options)
+function [sts, ep_exp] = pspm_expand_epochs(varargin)
 
 % fn passt nicht zu missing epochs
-%   [sts, channel_index]   = pspm_expand_epochs( {data_fn,  channel},    expansion , options)
 %   [sts, output_file]     = pspm_expand_epochs( missing_epochs_fn,      expansion , options)
-%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,         expansion , options) %
+%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,         expansion , options) 
+%   [sts, channel_index]   = pspm_expand_epochs( filename,  channel,    expansion , options)
 %   options.mode =  'datafile'
 %                   'missing_ep_file'
 %                   'missing_ep'
@@ -20,100 +20,125 @@
   return;
 end
 
-switch options.mode
-    % missing epochs
-    case 'missing_ep'
-        % Directly expand the given epochs
-        [sts, ep_exp] = expand(epoches, expansion);
-        return;
 
-    % missing epoches file
-    case 'missing_ep_file'
-        % Load missing epochs from file
-        data = load(epoches);  % Load the file without specifying a variable
-        
-        % Assuming the file contains a variable called 'epochs', access it
-        % Right name?
-        if isfield(data, 'epochs')
-            missing_epochs = data.epochs;
-        else
-            error('File does not contain variable ''epochs''.');
-            return;
-        end
 
-        if isempty(missing_epochs)
-            error('Failed to load missing epochs from file.');
-            return;
-        end
 
-        % Expand the loaded epochs
-        [sts, ep_exp] = expand(missing_epochs, expansion);
-        if sts == -1
-            error('Failed to expand epochs.');
-        end
+if nargin == 3
+    
+    expansion = varargin{2};
+    options   = varargin{3};
 
-        % Save expanded missing epoch to a new file with 'e' prefix
-        [pathstr, name, ext] = fileparts(epoches);
-        output_file = fullfile(pathstr, ['e' name ext]);
-        save(output_file, 'ep_exp'); % should i save it as epoch???
-        disp(['Expanded epochs saved to: ', output_file]);
+    switch options.mode
+        % missing epochs
+        case 'missing_ep'
+            % Directly expand the given epochs
+            epochs = varargin{1};
+            [ests, ep_exp] = expand(epochs, expansion);
 
-        sts = 0;
-        return;
+            if ests == -1
+                error("Failed to expand epochs.");
+                return;
+            end 
+            
+            sts = 1;
+            return;
 
+            % missing epoches file
+        case 'missing_ep_file'
+            % Load missing epochs from file
+            filename = varargin{1};
+
+            [lsts, epochs] = pspm_get_timing('file', filename);
+           
+            
+            if lsts == -1
+                error("Epoch could not be loaded");
+                return;
+            end 
+
+            % Expand the loaded epochs
+            [ests, ep_exp] = expand(epochs.epochs, expansion);
+            if ests == -1
+                error('Failed to expand epochs.');
+                return;
+            end
+
+            % Save expanded missing epoch to a new file with 'e' prefix
+            [pathstr, name, ext] = fileparts(filename);
+            output_file = fullfile(pathstr, ['e' name ext]);
+            save(output_file, 'ep_exp'); % should i save it as epoch???
+            disp(['Expanded epochs saved to: ', output_file]);
+
+            sts = 1;
+            return;
+    end
+end
 
-    case 'datafile' % rename!!
+if nargin == 4 %&& options.mode == 'datafile' % rename!!
+   
+    % Load channel data
+    filename = varargin{1};
+    channel  = varargin{2};
+    expansion = varargin{3};
+    [lsts, ~, data] = pspm_load_data(filename, channel);
+    if lsts == -1
+        error('Failed to load data from file.');
+        return;
+    end
 
-        % Load channel data
-        datafile = epoches{1};
-        channel  = epoches{2};
-        [lsts, ~, data] = pspm_load_data(datafile, channel);
-        if lsts == -1
-            error('Failed to load data from file.');
-        end
+    channel_data = data{1};
+    sr = channel_data.header.sr;
 
-        channel_data = data{1};
-        sr = channel_data.header.sr;
+    % Find NaN indices
+    nan_indices = isnan(channel_data.data);
 
-        % Find NaN indices
-        nan_indices = isnan(channel_data.data);
+    % Convert NaN indices to epochs
+    nan_epochs = pspm_logical2epochs(nan_indices, sr);
 
-        % Convert NaN indices to epochs
-        nan_epochs = pspm_logical2epochs(nan_indices, sr);
+    % Expand the epochs
+    [ests, ep_exp] = expand(nan_epochs, expansion);
+    if ests == -1
+        error('Failed to expand epochs.');
+    end
 
-        % Expand the epochs
-        [sts, ep_exp] = expand(nan_epochs, expansion);
-        if sts == -1
-            error('Failed to expand epochs.');
-        end
+    % Convert expanded epochs back to logical indices
+    expanded_indices = pspm_epochs2logical(ep_exp, numel(channel_data.data), sr);
 
-        % Convert expanded epochs back to logical indices
-        expanded_indices = pspm_epochs2logical(ep_exp, numel(channel_data.data), sr);
+    % Set data to NaN at expanded indices
+    channel_data.data(logical(expanded_indices)) = NaN;
 
-        % Set data to NaN at expanded indices
-        channel_data.data(expanded_indices) = NaN;
+    % Save the data back to the file
+    opt = struct();
+    [wsts, ~] = pspm_write_channel(filename, {channel_data}, 'replace',opt); % add to options 'newfile'?
+     % channel_data.data;
 
-        % Save the data back to the file
-        [sts, out] = pspm_write_channel(datafile, {channel_data}, 'replace'); % add to options 'newfile'?
-        varargout{2} = 23 % channel_data.data;
-        return;
+    if wsts == -1
+        error('Failed to write the new channel.');
+        return
+    end
 
+    sts = 1;
+    return;
 
-    otherwise
-        error('Unknown mode in options.');
-        return;
+
+else
+    error('Unknown mode in options.'); 
+    return;
 end
 
+
 end
 
 
-function [sts, ep_exp] = expand(ep, expansion)
+
+function [ests, ep_exp] = expand(ep, expansion)
 % Helper function to expand epochs by the specified pre and post times
 % and merge overlapping epochs.
 % Also ensures that no epoch starts before time 0.
 
-% Initialize status
-sts = -1;
+% Initialize status of expand
+ests = -1;
+ep_exp = [];
 
 % Check if epochs matrix and expansion vector are valid
 if isempty(ep) || numel(expansion) ~= 2
@@ -126,9 +151,23 @@
 post = expansion(2);
 expanded_epochs_temp = [ep(:,1) - pre, ep(:,2) + post];
 
-% 
+%
 % Ensure that the start of any epoch is not negative
-expanded_epochs_temp(expanded_epochs_temp(:,1) < 0, 1) = 0; % or <1???
+
+[ksts, expanded_epochs_temp] = pspm_get_timing('epochs',expanded_epochs_temp , 'seconds') ;
+if ksts == -1 
+    error('Offsets must be larger than onsets')
+    return
+end
+
+% If there is only one epoch, no need for merging
+if size(expanded_epochs_temp, 1) == 1
+    ep_exp = expanded_epochs_temp;
+    ests = 1;
+    return;
+end
+
+
 
 % Merge overlapping epochs
 ep_exp = expanded_epochs_temp(1, :);  % Start with the first epoch
@@ -142,6 +181,5 @@
     end
 end
 
-% Success
-sts = 0;
+ests = 1;
 end
diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index 491dfdf7d..7b725542c 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -12,11 +12,10 @@
 %                 be in seconds. This parameter is passed to pspm_get_timing().
 %   * timeunits:  timeunits of the epochfile.
 %   ┌───options
-%   └─.channel_action: [pre, post]
-%                 ['add'/'replace'] Defines whether new channels should be added or
-%                 corresponding channels should be replaced. The default value is 'add'.
-%     .expand_epochs: 
-%                    Expand epochs by 0.5 seconds before and after        
+%   └─.channel_action: ['add'/'replace'] Defines whether new channels should be added or
+%                      corresponding channels should be replaced. The default value is 'add'.
+%   └─.expand_epochs:  [pre, post]
+%                              
 % ● Output
 %   * channel_index: index of channel containing the processed data
 % ● History

From a4b6010eaf467c998c1a6b528fdc44cdc565627e Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Tue, 12 Nov 2024 14:46:22 +0100
Subject: [PATCH 3/7] changed error handeling

---
 src/pspm_expand_epochs.m | 111 ++++++++++++++++++++++++++-------------
 src/pspm_remove_epochs.m |   8 +--
 2 files changed, 79 insertions(+), 40 deletions(-)

diff --git a/src/pspm_expand_epochs.m b/src/pspm_expand_epochs.m
index b9ffa4a26..e2571a145 100644
--- a/src/pspm_expand_epochs.m
+++ b/src/pspm_expand_epochs.m
@@ -1,12 +1,20 @@
 function [sts, ep_exp] = pspm_expand_epochs(varargin)
-
-% fn passt nicht zu missing epochs
-%   [sts, output_file]     = pspm_expand_epochs( missing_epochs_fn,      expansion , options)
-%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,         expansion , options) 
-%   [sts, channel_index]   = pspm_expand_epochs( filename,  channel,    expansion , options)
+% ● Description
+%
+% ● Format
+%   fn passt nicht zu missing epochs
+%   [sts, output_file]     = pspm_expand_epochs( missing_epochs_fn,  expansion , options)
+%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,     expansion , options) 
+%   [sts, channel_index]   = pspm_expand_epochs( filename,  channel, expansion , options)
+% ● Arguments 
 %   options.mode =  'datafile'
 %                   'missing_ep_file'
-%                   'missing_ep'
+%                   'missing_epochs'
+%   expansion = [pre , post] or [pre ; post]
+%
+% ● History
+%   Written in 2024 by Bernhard Agoué von Raußendorf
+
 
 global settings
 if isempty(settings)
@@ -14,13 +22,28 @@
 end
 
 sts = -1;
+ep_exp = [];
 
-if nargin < 3
-  warning('ID:invalid_input', 'Not enough input arguments');
+if nargin < 3 || nargin > 4
+  warning('ID:invalid_input', 'Not enough or to many input arguments');
   return;
 end
 
 
+% Checks if expantion vector is the valid
+if nargin == 3 
+    if numel(varargin{2})  ~= 2 || ~isnumeric(varargin{2})
+        warning('Invalid input to expand vector musst be 1x2 or 2x1.');
+        return;
+    end
+end
+if nargin == 4 
+    if numel(varargin{3}) ~= 2 || ~isnumeric(varargin{3})
+      warning('Invalid input to expand vector musst be 1x2 or 2x1.');
+      return;
+    end
+end
+
 
 
 if nargin == 3
@@ -30,43 +53,63 @@
 
     switch options.mode
         % missing epochs
-        case 'missing_ep'
+        case 'missing_epochs'
             % Directly expand the given epochs
+            
             epochs = varargin{1};
+            
+            [gsts, epochs] = pspm_get_timing('epochs',epochs,'seconds');
+            if gsts < 1
+                warning('Invaled epochs.')
+                return
+            end     
+            
+            % Checks if epoch is empty bc pspm_get_timing returns sts = 1
+            if isempty(epochs)
+                warning('Invaled epochs.')
+                return
+            end
+
+
+
             [ests, ep_exp] = expand(epochs, expansion);
 
-            if ests == -1
-                error("Failed to expand epochs.");
+            if ests < 1
+                warning('Failed to expand epochs.');
                 return;
             end 
             
             sts = 1;
             return;
 
-            % missing epoches file
+            
         case 'missing_ep_file'
             % Load missing epochs from file
             filename = varargin{1};
 
             [lsts, epochs] = pspm_get_timing('file', filename);
-           
+            if isempty(epochs)
+                warning('Invaled epochs.')
+                return
+            end
             
-            if lsts == -1
-                error("Epoch could not be loaded");
+            if lsts < 1
+                warning('Epoch could not be loaded');
                 return;
-            end 
+            end
 
+           
             % Expand the loaded epochs
-            [ests, ep_exp] = expand(epochs.epochs, expansion);
-            if ests == -1
-                error('Failed to expand epochs.');
+            [ests, epochs] = expand(epochs.epochs, expansion);
+            if ests < 1
+                warning('Failed to expand epochs.');
                 return;
             end
 
             % Save expanded missing epoch to a new file with 'e' prefix
             [pathstr, name, ext] = fileparts(filename);
             output_file = fullfile(pathstr, ['e' name ext]);
-            save(output_file, 'ep_exp'); % should i save it as epoch???
+            save(output_file, 'epochs'); 
             disp(['Expanded epochs saved to: ', output_file]);
 
             sts = 1;
@@ -81,8 +124,8 @@
     channel  = varargin{2};
     expansion = varargin{3};
     [lsts, ~, data] = pspm_load_data(filename, channel);
-    if lsts == -1
-        error('Failed to load data from file.');
+    if lsts < 1
+        warning('Failed to load data from file.');
         return;
     end
 
@@ -97,7 +140,7 @@
 
     % Expand the epochs
     [ests, ep_exp] = expand(nan_epochs, expansion);
-    if ests == -1
+    if ests < 1
         error('Failed to expand epochs.');
     end
 
@@ -112,8 +155,8 @@
     [wsts, ~] = pspm_write_channel(filename, {channel_data}, 'replace',opt); % add to options 'newfile'?
      % channel_data.data;
 
-    if wsts == -1
-        error('Failed to write the new channel.');
+    if wsts < 1
+        warning('Failed to write the new channel.');
         return
     end
 
@@ -122,7 +165,7 @@
 
 
 else
-    error('Unknown mode in options.'); 
+    warning('Unknown mode in options.'); 
     return;
 end
 
@@ -140,23 +183,19 @@
 ests = -1;
 ep_exp = [];
 
-% Check if epochs matrix and expansion vector are valid
-if isempty(ep) || numel(expansion) ~= 2
-    error('Invalid input to expand function.');
-    return;
-end
+
 
 % Expand epochs
 pre = expansion(1);
 post = expansion(2);
 expanded_epochs_temp = [ep(:,1) - pre, ep(:,2) + post];
 
-%
-% Ensure that the start of any epoch is not negative
 
+% Ensure that the start of epoch is not neg. but 0
 [ksts, expanded_epochs_temp] = pspm_get_timing('epochs',expanded_epochs_temp , 'seconds') ;
-if ksts == -1 
-    error('Offsets must be larger than onsets')
+
+if ksts < 1 
+    warning('Offsets must be larger than onsets')
     return
 end
 
@@ -182,4 +221,4 @@
 end
 
 ests = 1;
-end
+end
\ No newline at end of file
diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index 7b725542c..4a87fa4ca 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -44,12 +44,12 @@
 end
 [lsts, ~, data, filestruct] = pspm_load_data(datafile, channel);
 pos_of_channels = filestruct.posofchannels;
-if lsts == -1
+if lsts < 1
   return;
 end
 
 [lsts, ep] = pspm_get_timing('epochs', epochfile, 'seconds');
-if lsts == -1
+if lsts < 1
   return;
 end
 
@@ -63,7 +63,7 @@
 % Expand the epochs
 
 [sts, ep_exp] = pspm_expand_epochs(ep, expansion, 'missing_ep');
-if psts == -1
+if psts < 1
     return;
 end
 
@@ -100,4 +100,4 @@
 % save data to file
 [sts, out] = pspm_write_channel(datafile, data, options.channel_action, ...
     struct('channel', pos_of_channels));
-outchanel = out.channel;
+outchanel = out.channel;
\ No newline at end of file

From 311361535d448c24431cad0c7ec5b1a4ea1d1ac0 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Thu, 14 Nov 2024 09:58:20 +0100
Subject: [PATCH 4/7] streamline pspm_expand_epochs

---
 src/pspm_expand_epochs.m | 280 +++++++++++++++------------------------
 src/pspm_options.m       |   4 +
 2 files changed, 112 insertions(+), 172 deletions(-)

diff --git a/src/pspm_expand_epochs.m b/src/pspm_expand_epochs.m
index e2571a145..ca1a3bc96 100644
--- a/src/pspm_expand_epochs.m
+++ b/src/pspm_expand_epochs.m
@@ -1,131 +1,104 @@
-function [sts, ep_exp] = pspm_expand_epochs(varargin)
+function [sts, out] = pspm_expand_epochs(varargin)
 % ● Description
-%
+% pspm_expand_epochs expands epochs in time, and merges overlapping epochs. 
+% This is useful in processing missing data epochs. The function can take 
+% a missing epochs file and creates a new file with the original name 
+% prepended with 'e', a matrix of missing epochs, or a PsPM data file with 
+% missing data in a given channel.
 % ● Format
-%   fn passt nicht zu missing epochs
-%   [sts, output_file]     = pspm_expand_epochs( missing_epochs_fn,  expansion , options)
-%   [sts, expanded_epochs] = pspm_expand_epochs( missing_epochs,     expansion , options) 
-%   [sts, channel_index]   = pspm_expand_epochs( filename,  channel, expansion , options)
+%   [sts, output_file]     = pspm_expand_epochs(epochs_fn, expansion, options)
+%   [sts, expanded_epochs] = pspm_expand_epochs(epochs, expansion, options) 
+%   [sts, channel_index]   = pspm_expand_epochs(data_fn, channel, expansion , options)
 % ● Arguments 
-%   options.mode =  'datafile'
-%                   'missing_ep_file'
-%                   'missing_epochs'
-%   expansion = [pre , post] or [pre ; post]
-%
+%   *   epochs_fn:  An epochs file as defined in pspm_get_timing.
+%   *      epochs:  A 2-column matrix with epochs onsets and offsets in seconds.
+%   *     data_fn:  A PsPM data file.
+%   *     channel:  Channel identifier accepted by pspm_load_channel.
+%   *   expansion:  A 2-element vector with positive numbers [pre, post]
+%   ┌────────────options:
+%   ├─────────.overwrite: Define if already existing files should be
+%   │                     overwritten. Default ist 0. (Only used if input
+%   │                     is epochs file.)
+%   └────.channel_action: Channel action, add / replace existing data
+%                         data (default: add)
+% ● Output
+%   *  channel_index: index of channel containing the processed data
 % ● History
+%   Introduced in PsPM 7.0
 %   Written in 2024 by Bernhard Agoué von Raußendorf
 
-
+% Initialise
+% -------------------------------------------------------------------------
 global settings
 if isempty(settings)
   pspm_init;
 end
 
 sts = -1;
-ep_exp = [];
+out = [];
 
-if nargin < 3 || nargin > 4
-  warning('ID:invalid_input', 'Not enough or to many input arguments');
+% Input checks and parsing 
+%  ------------------------------------------------------------------------
+if nargin < 2 
+  warning('ID:invalid_input', 'Not enough input arguments');
   return;
 end
 
-
-% Checks if expantion vector is the valid
-if nargin == 3 
-    if numel(varargin{2})  ~= 2 || ~isnumeric(varargin{2})
-        warning('Invalid input to expand vector musst be 1x2 or 2x1.');
-        return;
+% parse first input and determine mode
+if isnumeric(varargin{1})
+    mode = 'epochs';
+    [gsts, epochs] = pspm_get_timing('epochs', varargin{1}, 'seconds');
+    if gsts < 1
+        return
     end
-end
-if nargin == 4 
-    if numel(varargin{3}) ~= 2 || ~isnumeric(varargin{3})
-      warning('Invalid input to expand vector musst be 1x2 or 2x1.');
-      return;
+elseif ischar(varargin{1})
+    fn = varargin{1};
+    warning off
+    [gsts, epochs] = pspm_get_timing('epochs', fn, 'seconds');
+    warning on
+    if gsts == 1
+        mode = 'epochfile';
+    else
+        fprint('Assuming input is a PsPM data file ...\n');
+        mode = 'datafile';
     end
+else 
+    warning('ID:invalid_input', 'First argument must be a file name or epoch matrix.');
 end
 
-
-
-if nargin == 3
-    
+% parse remaining arguments
+if ismember(mode, {'epochs', 'epochfile'})
     expansion = varargin{2};
-    options   = varargin{3};
-
-    switch options.mode
-        % missing epochs
-        case 'missing_epochs'
-            % Directly expand the given epochs
-            
-            epochs = varargin{1};
-            
-            [gsts, epochs] = pspm_get_timing('epochs',epochs,'seconds');
-            if gsts < 1
-                warning('Invaled epochs.')
-                return
-            end     
-            
-            % Checks if epoch is empty bc pspm_get_timing returns sts = 1
-            if isempty(epochs)
-                warning('Invaled epochs.')
-                return
-            end
-
-
-
-            [ests, ep_exp] = expand(epochs, expansion);
-
-            if ests < 1
-                warning('Failed to expand epochs.');
-                return;
-            end 
-            
-            sts = 1;
-            return;
-
-            
-        case 'missing_ep_file'
-            % Load missing epochs from file
-            filename = varargin{1};
-
-            [lsts, epochs] = pspm_get_timing('file', filename);
-            if isempty(epochs)
-                warning('Invaled epochs.')
-                return
-            end
-            
-            if lsts < 1
-                warning('Epoch could not be loaded');
-                return;
-            end
+    k = 2;
+else
+    channel   = varargin{2};
+    expansion = varargin{3};
+    k = 3;
+end
 
-           
-            % Expand the loaded epochs
-            [ests, epochs] = expand(epochs.epochs, expansion);
-            if ests < 1
-                warning('Failed to expand epochs.');
-                return;
-            end
+if nargin > k
+    options = varargin{3};
+else
+    options = struct();
+end
 
-            % Save expanded missing epoch to a new file with 'e' prefix
-            [pathstr, name, ext] = fileparts(filename);
-            output_file = fullfile(pathstr, ['e' name ext]);
-            save(output_file, 'epochs'); 
-            disp(['Expanded epochs saved to: ', output_file]);
+% finalise options structure
+options = pspm_options(options, 'expand_epochs');
 
-            sts = 1;
-            return;
-    end
+% check if expansion vector is valid
+if  ~isnumeric(expansion) || numel(expansion) ~= 2
+    warning('Invalid input to expand vector musst be 1x2 or 2x1.');
+    return;
 end
 
-if nargin == 4 %&& options.mode == 'datafile' % rename!!
-   
-    % Load channel data
-    filename = varargin{1};
-    channel  = varargin{2};
-    expansion = varargin{3};
-    [lsts, ~, data] = pspm_load_data(filename, channel);
+% work on input
+% -------------------------------------------------------------------------
+
+% construct epochs from data file
+if strcmpi(mode, 'datafile')
+    
+    [lsts, ~, data] = pspm_load_data(fn, channel);
     if lsts < 1
-        warning('Failed to load data from file.');
         return;
     end
 
@@ -136,89 +109,52 @@
     nan_indices = isnan(channel_data.data);
 
     % Convert NaN indices to epochs
-    nan_epochs = pspm_logical2epochs(nan_indices, sr);
-
-    % Expand the epochs
-    [ests, ep_exp] = expand(nan_epochs, expansion);
-    if ests < 1
-        error('Failed to expand epochs.');
-    end
-
-    % Convert expanded epochs back to logical indices
-    expanded_indices = pspm_epochs2logical(ep_exp, numel(channel_data.data), sr);
-
-    % Set data to NaN at expanded indices
-    channel_data.data(logical(expanded_indices)) = NaN;
+    epochs = pspm_logical2epochs(nan_indices, sr);
 
-    % Save the data back to the file
-    opt = struct();
-    [wsts, ~] = pspm_write_channel(filename, {channel_data}, 'replace',opt); % add to options 'newfile'?
-     % channel_data.data;
-
-    if wsts < 1
-        warning('Failed to write the new channel.');
-        return
-    end
-
-    sts = 1;
-    return;
-
-
-else
-    warning('Unknown mode in options.'); 
-    return;
 end
 
-
-end
-
-
-
-function [ests, ep_exp] = expand(ep, expansion)
-% Helper function to expand epochs by the specified pre and post times
-% and merge overlapping epochs.
-% Also ensures that no epoch starts before time 0.
-
-% Initialize status of expand
-ests = -1;
-ep_exp = [];
-
-
-
-% Expand epochs
+% expand epochs
 pre = expansion(1);
 post = expansion(2);
-expanded_epochs_temp = [ep(:,1) - pre, ep(:,2) + post];
-
-
-% Ensure that the start of epoch is not neg. but 0
-[ksts, expanded_epochs_temp] = pspm_get_timing('epochs',expanded_epochs_temp , 'seconds') ;
-
+expanded_epochs_temp = [epochs(:,1) - pre, epochs(:,2) + post];
+% remove negative values and merge overlapping epochs
+[ksts, expanded_epochs] = pspm_get_timing('missing',expanded_epochs_temp , 'seconds') ;
 if ksts < 1 
-    warning('Offsets must be larger than onsets')
     return
 end
 
-% If there is only one epoch, no need for merging
-if size(expanded_epochs_temp, 1) == 1
-    ep_exp = expanded_epochs_temp;
-    ests = 1;
-    return;
-end
+% generate output
+switch mode
+    case 'epochs'
+        out = expanded_epochs;
+    
+    case 'epochfile'
+        % save expanded epochs to a new file with 'e' prefix
+            [pathstr, name, ext] = fileparts(fn);
+            output_file = fullfile(pathstr, ['e', name, ext]);
+            overwrite_final = pspm_overwrite(output_file, options.overwrite);
+            if overwrite_final == 1
+                save(output_file, 'epochs'); 
+                fprintf(['Expanded epochs saved to file: ', output_file, '\n']);
+            end
+    
+    case 'datafile'
 
+    % Convert expanded epochs back to logical indices
+    expanded_indices = pspm_epochs2logical(expanded_epochs, numel(channel_data.data), sr);
 
+    % Set data to NaN at expanded indices
+    channel_data.data(logical(expanded_indices)) = NaN;
 
-% Merge overlapping epochs
-ep_exp = expanded_epochs_temp(1, :);  % Start with the first epoch
-for i = 2:size(expanded_epochs_temp, 1)
-    % If the current epoch overlaps with the previous, merge them
-    if ep_exp(end, 2) >= expanded_epochs_temp(i, 1)
-        ep_exp(end, 2) = max(ep_exp(end, 2), expanded_epochs_temp(i, 2));
-    else
-        % Otherwise, add the current epoch as a new row
-        ep_exp = [ep_exp; expanded_epochs_temp(i, :)];
+    % Save the data 
+    [wsts, out] = pspm_write_channel(fn, {channel_data}, options.channel_action, struct('channel', channel)); 
+    if wsts < 1
+        return
     end
+    out = out.channel;
 end
 
-ests = 1;
-end
\ No newline at end of file
+sts = 1;
+
+
+
diff --git a/src/pspm_options.m b/src/pspm_options.m
index b97dff4ab..ec95ca1e4 100644
--- a/src/pspm_options.m
+++ b/src/pspm_options.m
@@ -496,6 +496,10 @@
         % 2.48 pspm_combine_markerchannels
         options = autofill(options, 'marker_chan_num',        'marker',   '*Int*Char'       );
         options = autofill_channel_action(options);
+    case 'expand_epochs'
+        % 2.49 pspm_expand_epochs
+        options = autofill(options, 'overwrite',              2,          [0,1]             );
+        options = autofill_channel_action(options);
 end
 return
 

From 50cced7d3e8a626d31c60e186828b06a075213f8 Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Sun, 17 Nov 2024 15:32:42 +0100
Subject: [PATCH 5/7] added new pspm_expand_epochs to pspm_remove_epochs

---
 src/pspm_remove_epochs.m | 33 ++++++++++++++++++++-------------
 1 file changed, 20 insertions(+), 13 deletions(-)

diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index 4a87fa4ca..5dae6e748 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -12,8 +12,8 @@
 %                 be in seconds. This parameter is passed to pspm_get_timing().
 %   * timeunits:  timeunits of the epochfile.
 %   ┌───options
-%   └─.channel_action: ['add'/'replace'] Defines whether new channels should be added or
-%                      corresponding channels should be replaced. The default value is 'add'.
+%   ├─.channel_action: ['add'/'replace'] Defines whether new channels should be added or
+%   │                  corresponding channels should be replaced. The default value is 'add'.
 %   └─.expand_epochs:  [pre, post]
 %                              
 % ● Output
@@ -38,7 +38,7 @@
 elseif nargin < 4
   options = struct();
 end
-options = pspm_options(options, 'remove_epochs'); % change!!! [0,0]
+options = pspm_options(options, 'remove_epochs');
 if options.invalid
   return
 end
@@ -54,19 +54,25 @@
 end
 
 
+% add check for options.expand_epochs!!!
+% was ist mit commer werten??
 
-expansion = options.expand_epochs;
+% was ist mit mehren daten?? channels??
+% event and this function??
+% float epochts?
 
-if numel(expansion) ~= 2
-    error('Expansion must be a 2-element vector [pre, post].');
-end
-% Expand the epochs
+% options-> overwrite?? 
+% options -> load expansion??
 
-[sts, ep_exp] = pspm_expand_epochs(ep, expansion, 'missing_ep');
-if psts < 1
-    return;
-end
 
+if numel(options.expand_epochs) ~= 2 || ~isnumeric(options.expand_epochs)
+    warning('Expansion must be a 2-element vector [pre, post].');
+else
+    [psts, ep] = pspm_expand_epochs(ep, options.expand_epochs);
+    if psts < 1
+        return;
+    end
+end
 
 
 
@@ -98,6 +104,7 @@
   end
 end
 % save data to file
+
 [sts, out] = pspm_write_channel(datafile, data, options.channel_action, ...
     struct('channel', pos_of_channels));
-outchanel = out.channel;
\ No newline at end of file
+outchanel = out.channel; % out is channel_nr
\ No newline at end of file

From fd8dce6213f227238b7d1563487fcb6914e8046c Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Mon, 18 Nov 2024 00:37:06 +0100
Subject: [PATCH 6/7] pspm_remove_epochs with pspm_expand_epochs

---
 src/pspm_remove_epochs.m | 27 +++++++++------------------
 1 file changed, 9 insertions(+), 18 deletions(-)

diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index 5dae6e748..a43ce022f 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -54,23 +54,15 @@
 end
 
 
-% add check for options.expand_epochs!!!
-% was ist mit commer werten??
 
-% was ist mit mehren daten?? channels??
-% event and this function??
-% float epochts?
-
-% options-> overwrite?? 
-% options -> load expansion??
-
-
-if numel(options.expand_epochs) ~= 2 || ~isnumeric(options.expand_epochs)
-    warning('Expansion must be a 2-element vector [pre, post].');
-else
-    [psts, ep] = pspm_expand_epochs(ep, options.expand_epochs);
-    if psts < 1
-        return;
+if isfield(options,'expand_epochs')
+    if numel(options.expand_epochs) ~= 2 || ~isnumeric(options.expand_epochs)
+        warning('Expansion must be a 2-element vector [pre, post].');
+    else
+        [psts, ep] = pspm_expand_epochs(ep, options.expand_epochs);
+        if psts < 1
+            return;
+        end
     end
 end
 
@@ -78,7 +70,6 @@
 
 
 
-
 n_ep = size(ep, 1);
 n_data = numel(data);
 for i_data = 1:n_data
@@ -107,4 +98,4 @@
 
 [sts, out] = pspm_write_channel(datafile, data, options.channel_action, ...
     struct('channel', pos_of_channels));
-outchanel = out.channel; % out is channel_nr
\ No newline at end of file
+outchanel = out.channel;
\ No newline at end of file

From 59c2d8a20c5a22b246b06a1ce49b377c7705a0f8 Mon Sep 17 00:00:00 2001
From: Bernhard <90285552+4gwe@users.noreply.github.com>
Date: Mon, 18 Nov 2024 00:39:47 +0100
Subject: [PATCH 7/7] added comment

---
 src/pspm_remove_epochs.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pspm_remove_epochs.m b/src/pspm_remove_epochs.m
index a43ce022f..3714b8ae7 100644
--- a/src/pspm_remove_epochs.m
+++ b/src/pspm_remove_epochs.m
@@ -54,7 +54,7 @@
 end
 
 
-
+% expands the epoch if  options.expand_epochs exists
 if isfield(options,'expand_epochs')
     if numel(options.expand_epochs) ~= 2 || ~isnumeric(options.expand_epochs)
         warning('Expansion must be a 2-element vector [pre, post].');