869 pspm get smr empty channels

doc/PsPM_Developers_Guide.lyx

@@ -29400,7 +29400,8 @@ In the line 1-5 of a markdown file,
 
 \begin_layout Standard
 \begin_inset Graphics
-	filename /Users/teddy/Desktop/Screenshot 2025-02-06 at 14.51.44.png
+	filename Figures/screenshot-000.png
+	scale 50
 
 \end_inset
 
@@ -29468,7 +29469,7 @@ The second line is the title of this webpage.
 
 \begin_layout Standard
 \begin_inset Graphics
-	filename /Users/teddy/Desktop/Screenshot 2025-02-06 at 15.14.02.png
+	filename Figures/screenshot-002.png
 	width 90text%
 
 \end_inset
@@ -29612,7 +29613,7 @@ toc-date.html
 
 \begin_layout Standard
 \begin_inset Graphics
-	filename /Users/teddy/Desktop/Screenshot 2025-02-07 at 03.32.35.png
+	filename Figures/screenshot-004.png
 	width 95text%
 
 \end_inset

doc/PsPM_Manual.lyx

@@ -5584,7 +5584,12 @@ Here,
 \end_layout
 
 \begin_layout Paragraph
-CED Spike
+CED Spike 
+\end_layout
+
+\begin_layout Standard
+When importing SMR files,
+ channels that are empty are still imported as empty channels rather than being removed.
 \end_layout
 
 \begin_layout Paragraph

src/pspm_get_smr.m

@@ -7,7 +7,7 @@
 % ● Arguments
 %   *  datafile : the data file to be imported. 
 %   ┌───import
-%   ├───channel : X
+%   ├───channel : the number of the channel to load.
 %   └───denoise : for marker channels in CED spike format (recorded as 'level'),
 %                 only retains markers with duration longer than the value given here (in ms).
 % ● Outputs
@@ -44,17 +44,10 @@
     errorflag(channel)=1;
     chandata{channel}=[];
     chanhead{channel}.title='';
+    chanhead{channel}.kind = -1 ;
   end
 end
 fclose(fid);
-% 2.5 delete empty channels
-if ~isempty(errorflag)
-  ind=find(errorflag);
-  for channel=ind(end:-1:1)
-    chandata(channel)=[];
-    chanhead(channel)=[];
-  end
-end
 warning on;
 %% 3 extract individual channels
 % 3.1 loop through import jobs
@@ -75,7 +68,11 @@
   sourceinfo.channel{iImport, 1} = sprintf('Channel %02.0f: %s', channel, chanhead{channel}.title);
   % 3.1.2 convert to waveform or get sample rate for wave channel types
   if strcmpi(settings.channeltypes(import{iImport}.typeno).data, 'wave')
-    if chanhead{channel}.kind == 1 % waveform
+    if  chanhead{channel}.kind == -1 % empty channel      
+      import{iImport}.data = zeros(1,0);
+      import{iImport}.units = '';
+      import{iImport}.sr   = 1;
+    elseif chanhead{channel}.kind == 1 % waveform
       import{iImport}.data = chandata{channel};
       import{iImport}.sr   = 1./chanhead{channel}.sampleinterval;
     elseif chanhead{channel}.kind == 3 % timestamps
@@ -100,7 +97,12 @@
     end
     % extract, and possibly denoise event channels
   elseif strcmpi(settings.channeltypes(import{iImport}.typeno).data, 'events')
-    if chanhead{channel}.kind == 1 % waveform
+    if  chanhead{channel}.kind == -1 % empty channel
+      import{iImport}.marker = 'continuous'  ; % or ''
+      import{iImport}.data = zeros(1,0);
+      import{iImport}.units = 'event';  
+      import{iImport}.sr = 1;  
+    elseif chanhead{channel}.kind == 1 % waveform
       import{iImport}.marker = 'continuous';
       import{iImport}.data = chandata{channel};
       import{iImport}.sr   = 1./chanhead{channel}.sampleinterval;

test/pspm_get_smr_test.m

@@ -13,14 +13,15 @@ function define_testcases(this)
       % testcase 1
       this.testcases{1}.pth = 'ImportTestData/spike/AEC_11.smr';
       this.testcases{1}.import{1} = struct('type', 'scr'   , 'channel', 1);
-      this.testcases{1}.import{2} = struct('type', 'marker', 'channel', 2);
-      this.testcases{1}.import{3} = struct('type', 'marker', 'channel', 3);
+      this.testcases{1}.import{2} = struct('type', 'marker', 'channel', 2);% empty
+      this.testcases{1}.import{3} = struct('type', 'marker', 'channel', 3);% empty
       this.testcases{1}.import{4} = struct('type', 'marker', 'channel', 4);
       this.testcases{1}.import{5} = struct('type', 'marker', 'channel', 5);
       this.testcases{1}.import{6} = struct('type', 'marker', 'channel', 6);
       this.testcases{1}.import{7} = struct('type', 'marker', 'channel', 7);
-      % this.testcases{1}.import{8} = struct('type', 'marker', 'channel', 8);
-      % this.testcases{1}.import{9} = struct('type', 'marker', 'channel', 9);
+      this.testcases{1}.import{8} = struct('type', 'marker', 'channel', 8);
+      this.testcases{1}.import{9} = struct('type', 'marker', 'channel', 9);
+      this.testcases{1}.import{10} = struct('type', 'marker', 'channel', 10);% empty
       % testcase 2
       this.testcases{2}.pth = 'ImportTestData/spike/Spike_SCR_Marker.smr';
       this.testcases{2}.import{1} = struct('type', 'scr'   , 'channel', 1);