Differences

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--- plotcurves [2010/06/19 19:00] – added GUI reference jochen
+++ plotcurves [2011/05/27 15:54] (current) – added additional keyboard commands jochen
@@ Line 24: / Line 24: @@
 % this filters channel 1 into a new channel (10)
-% all parameters are default, the post-filtering cut-off is set to 0.5s
+% all parameters are default, the post-filtering cut-off is set to 0.2s
-gsr.Filter(1, struct('dest', 10, 'post', 0.5));</code>
+gsr.Filter(1, struct('dest', 10, 'post', 0.2));</code>
 ===== Function reference ('help plotcurves') =====
@@ Line 36: / Line 36: @@
         obj         xff object with plotable data or SxC double data
         opts        optional settings
+         .cuediff   difference between cue and onset (only useful if
+                    fixed interval!; default: -2)
          .curves    Cx2 cell array with names and a 1x3 double array
                     containing [channelnumber, onset, offset]
-                    for multiple curves, the mean will be computed
+                    - for curves in a set, the mean/std. error is computed
-         .freq      data sampling frequency (if not in object)
+                    - onset and offset are given in seconds
-         .resfreq   resampling frequency
+         .dchannel  data channel (for onset detection, default: 1)
+         .dfilt     detection filter length (in seconds, default: 0.5)
+         .dminlat   minimum detection latency (after one point, def: 0.5)
+         .freq      data sampling frequency (if not in object, def: 100)
+         .ochannel  onset channel number (will add curves, default: [])
+         .odchannel original data channel (allows to filter effect)
+         .onsets    Ox1 onset vector in seconds
+         .owin      1x2 onset window in seconds (default: [-2, 18])
          .sets      Sx2 cell array with names and lists of curve indices
-         .spot      Sx1 cell array with Cx1 X or Cx2 x/y coordinates
+         .spot      Sx1 cell array with Cx1 X or Cx2 x/y time-points
-         .spotcol   Sx3 RGB color (either [0 .. 255] or [0 .. 1])
          .spotnames Sx1 cell array with strings
          .spottype  Sx1 cell array with either of
-                    {'free'}, 'max', 'min', 'minmax'
+                    'cue', {'free'}, 'max', 'min', 'minmax', 'onset'
          .var       1xV struct with fields
            .calc    either of 'dx', {'dy'}, 'mean', 'std', 'var', 'x', 'y'
+           .name    variable name
            .spot    1x1 or 1x2 index into S
            .trans   apply additional transformation to each value, one of
                     {'none'}, 'log', 'log+1', 'sqrt'
-         .varnames
   Output fields:
@@ Line 59: / Line 67: @@
         varc        computed variables
         spot        updated spots
-        sets        updates sets (new indices)</file>
+        sets        updates sets (new indices)
+  Note: where appropriate, the options are taken from obj.RunTimeVars
+        if not specified in the call!</file>
 ===== GUI =====
@@ Line 82: / Line 93: @@
   * '''d''' key -> decrease zoom (de-magnify)
   * '''f''' key -> toggle force-to-curve checkbox
+  * '''i''' / '''o''' keys -> toggle whether this curve (onset) is included (i) or omitted (o) from averages
   * '''m''' key -> increase zoom (magnify)
+  * '''p''' key -> places a currently highlighted marker at a peak (max or min, depending on data)
   * '''r''' key -> reset axes limits (to initial curve setting)
   * '''u''' key -> toggle use-curve checkbox
@@ Line 157: / Line 170: @@
 <code matlab plotcurves_withonsets.m>% data is in object gsr and already preprocessed
-% we define three spots of interest:
+% for this example we define four (!) spots of interest:
+% - cue (time of stimulus minus 2 secs)
 % - onset (time of stimulus),
 % - delay of response (minimum before peak),
 % - and peak of response (amplitude)
-spotnames = {'onset', 'delay', 'peak'};
+spotnames = {'cue', 'onset', 'delay', 'peak'};
-spottype = {'onset', 'min', 'max'};
+spottype = {'cue', 'onset', 'min', 'max'};
 % the spot values are set to empty arrays with size 0x2!
 % this tells plotcurves to autodetect...
-spot = {zeros(0,2), zeros(0,2), zeros(0, 2)};
+spot = {zeros(0,2), zeros(0,2), zeros(0,2), zeros(0, 2)};
+% then we define the variables of interest:
+% NOTE: since we have a CUE spot, all spot indices shift by one!
+% - Latency (defined as x-diff between onset and delay)
+% - Response time (defined as x-diff between delay and peak)
+% - Base amplitude (defined as y-value at delay)
+% - Peak amplitude (defined as y-value at peak)
+% - Peak-to-peak response amplitude (defined as y-diff between delay and peak)
+% additionally, we define that for the response amplitude, the log+1 transform
+% should be applied after we're done
+vars = struct( ...
+    'name', {'Latency', 'Resp. time', 'Base ampl.', 'Peak ampl.', 'Resp. ampl.'}, ...
+    'calc', {'dx', 'dx', 'y', 'y', 'dy'}, ...
+    'spot', {[2, 3], [3, 4], [3], [4], [3, 4]}, ...
+    'trans', {'none', 'none', 'none', 'none', 'log+1'});
 % re-using the variables definition from above, options:
@@ Line 172: / Line 201: @@
 % - original data is in channel 1 (pre-filter)
 % - onsets are coded in channel 8 (0Volts nothing, 5 Volts boxes)
+% - cue onffset is 2 seconds
+% - thus, the window is increased! [-4, 20]
 % - variables and spots as defined
 pcopts = struct( ...
@@ Line 177: / Line 208: @@
     'odchannel', 1, ...
     'ochannel',  8, ...
+    'cuediff',   2, ...
+    'owin',      [-4, 20],...
     'var',       vars, ...
     'spot',      {spot}, ...
@@ Line 184: / Line 217: @@
 % now we call plotcurves
 plotcurves(gsr, pcopts);</code>
+===== Output =====
+The function outputs the following variables:
+  * sel (boolean vector with curve selection, copied from use-curve checkbox)
+  * varc (number-of-curves - by - number-of-variables double table)
+  * spot (1 - by - number-of-spots cell array with coordinates of spots)
+  * sets (updated list of sets, that is to say with correct indices, only if sets defined!)
+In addition to this, the final options and configuration (when the dialog was closed) is stored in the gsr object under ''.RunTimeVars.plotcurves''.