From f71d554d3b3e359b356d499acdd339b0c1943010 Mon Sep 17 00:00:00 2001
From: Dominik Bach <dominik.bach@uzh.ch>
Date: Sun, 20 Aug 2023 20:44:35 +0200
Subject: [PATCH] new branch

---
 src/pspm_check_model.m | 125 +++++++++++++++++++++++++++++++++++++++++
 src/pspm_dcm.m         | 116 +++-----------------------------------
 src/pspm_glm.m         |  25 ++-------
 src/pspm_sf.m          |  29 +++-------
 4 files changed, 145 insertions(+), 150 deletions(-)
 create mode 100644 src/pspm_check_model.m

diff --git a/src/pspm_check_model.m b/src/pspm_check_model.m
new file mode 100644
index 000000000..78fef718e
--- /dev/null
+++ b/src/pspm_check_model.m
@@ -0,0 +1,125 @@
+function model = pspm_check_model(model, modeltype)
+
+% General checks
+if ~isstruct(model)
+  warning('ID:invalid_input', 'Model must be a struct.');
+  model = struct('invalid', 1);
+  return
+else
+  model.invalid = 1;
+  if isempty(model)
+    warning('ID:invalid_input', 'Model is empty.');
+    return
+  end
+end
+
+% 1. Reject missing mandatory fields common to all models
+if ~isfield(model, 'datafile')
+  warning('ID:invalid_input', 'No input data file specified.'); return;
+elseif ~isfield(model, 'modelfile')
+  warning('ID:invalid_input', 'No output model file specified.'); return;
+elseif ~isfield(model, 'timing')
+  warning('ID:invalid_input', 'No event onsets specified.'); return;
+end
+
+% 2. Reject wrong type of mandatory fields
+if ~iscell(model.datafile) && ~ischar(model.datafile)
+  warning('ID:invalid_input', 'Input data must be a cell or string.'); return;
+elseif ~ischar(model.modelfile)
+  warning('ID:invalid_input', 'Output model must be a string.'); return;
+elseif ~ischar(model.timing) && ~iscell(model.timing) && ~isstruct(model.timing)
+  warning('ID:invalid_input', 'Event definition must be a string, cell array, or (for GLM) struct.'); return;
+end
+
+% 3. Fill missing fields common to all models, and accept only allowed values
+if ~isfield(model, 'norm')
+  model.norm = 0;
+elseif ~any(ismember(model.norm, [0, 1]))
+  warning('ID:invalid_input', 'Normalisation must be specified as 0 or 1.'); return;
+end
+if ~isfield(model, 'missing')
+  model.missing = cell(nFile, 1);
+elseif ischar(model.missing) || isnumeric(model.missing)
+  model.missing = {model.missing};
+elseif ~iscell(model.missing)
+  warning('ID:invalid_input',...
+    'Missing values must be a filename, matrix, or cell array of these.');
+  return
+end
+
+% 4. Check that data files, timing, and missing values are cell arrays with
+% matching size
+if ischar(model.datafile)
+  model.datafile = {model.datafile};
+  model.timing   = {model.timing};
+end
+
+nFile = numel(model.datafile);
+if nFile ~= numel(model.timing)
+  warning('ID:number_of_elements_dont_match',...
+    'Session numbers of data files and event definitions do not match.');
+  return
+end
+if nFile ~= numel(model.missing)
+  warning('ID:number_of_elements_dont_match',...
+    'Same number of data files and missing value definitions is needed.');
+  return
+end
+
+% GLM-specific checks
+% -------------------------------------------------------------------------
+if strcmpi(modeltype, 'glm')
+    % Reject missing mandatory fields
+    if ~isfield(model, 'timeunits')
+        warning('ID:invalid_input', 'No timeunits specified.'); return;
+    end
+end
+
+
+% DCM-specific check
+% -------------------------------------------------------------------------
+if strcmpi(modeltype, 'dcm')
+    if ~ischar(model.timing) && ~iscell(model.timing)
+        warning('ID:invalid_input', 'Event definition must be a string or cell array.'); return;
+    end
+    % Fill missing fields and detect wrong values
+    if ~isfield(model, 'channel')
+        model.channel = 'scr'; % this returns the last SCR channel
+    elseif ~isnumeric(model.channel) && ~strcmp(model.channel,'scr')
+        warning('ID:invalid_input', 'Channel number must be numeric.'); return;
+    end
+    if ~isfield(model, 'constrained')
+        model.constrained = 0;
+    elseif ~any(ismember(model.constrained, [0, 1]))
+        warning('ID:invalid_input', 'Constrained model must be specified as 0 or 1.'); return;
+    end
+    if ~isfield(model, 'substhresh')
+        model.substhresh = 2;
+    elseif ~isnumeric(model.substhresh)
+        warning('ID:invalid_input', 'Subsession threshold must be numeric.');
+        return;
+    end
+end
+
+
+
+% General checks that require GLM-specific checks in case of GLM
+% -------------------------------------------------------------------------
+if ~isfield(model, 'filter')
+    if strcmpi(modeltype, 'glm')
+        model.filter = settings.glm(modno).filter;
+elseif strcmpi(modeltype, 'dcm')
+  model.filter = settings.dcm{1}.filter;
+elseif ~isfield(model.filter, 'down') || ~isnumeric(model.filter.down)
+  warning('ID:invalid_input', 'Filter structure needs a numeric ''down'' field.'); return;
+end
+
+
+% 2.7 check filter --
+
+
+
+try model.lasttrialcutoff;      catch, model.lasttrialcutoff = 7;       end
+
+
+model.invalid = 0;
\ No newline at end of file
diff --git a/src/pspm_dcm.m b/src/pspm_dcm.m
index f85524182..2f0e87391 100644
--- a/src/pspm_dcm.m
+++ b/src/pspm_dcm.m
@@ -177,82 +177,21 @@
 warnings = {};
 
 %% 2 Check input arguments & set defaults
-% 2.1 check input
-if nargin < 1
-  warning('ID:invalid_input', 'No data to work on.');
-  return
-elseif nargin < 2
-  options = struct();
-end
-if ~isfield(model, 'datafile')
-  warning('ID:invalid_input', 'No input data file specified.'); return;
-elseif ~isfield(model, 'modelfile')
-  warning('ID:invalid_input', 'No output model file specified.'); return;
-elseif ~isfield(model, 'timing')
-  warning('ID:invalid_input', 'No event onsets specified.'); return;
-end
-
-% 2.2 check faulty input
-if ~iscell(model.datafile) && ~ischar(model.datafile)
-  warning('ID:invalid_input', 'Input data must be a cell or string.'); return;
-elseif ~ischar(model.modelfile)
-  warning('ID:invalid_input', 'Output model must be a string.'); return;
-elseif ~ischar(model.timing) && ~iscell(model.timing)
-  warning('ID:invalid_input', 'Event definition must be a string or cell array.'); return;
-end
-
-% 2.3 get further input or set defaults --
-% check data channel --
-if ~isfield(model, 'channel')
-  model.channel = 'scr'; % this returns the last SCR channel
-elseif ~isnumeric(model.channel) && ~strcmp(model.channel,'scr')
-  warning('ID:invalid_input', 'Channel number must be numeric.'); return;
-end
-
-% 2.4 check normalisation --
-if ~isfield(model, 'norm')
-  model.norm = 0;
-elseif ~any(ismember(model.norm, [0, 1]))
-  warning('ID:invalid_input', 'Normalisation must be specified as 0 or 1.'); return;
-end
-
-% 2.5 check constrained model --
-if ~isfield(model, 'constrained')
-  model.constrained = 0;
-elseif ~any(ismember(model.constrained, [0, 1]))
-  warning('ID:invalid_input', 'Constrained model must be specified as 0 or 1.'); return;
-end
-
-% 2.6 check substhresh --
-if ~isfield(model, 'substhresh')
-  model.substhresh = 2;
-elseif ~isnumeric(model.substhresh)
-  warning('ID:invalid_input', 'Subsession threshold must be numeric.');
-  return;
-end
+% 2.1 check missing input --
+if nargin < 1; errmsg = 'Nothing to do.'; warning('ID:invalid_input', errmsg); return
+elseif nargin < 2; options = struct(); end
 
-% 2.7 check filter --
-if ~isfield(model, 'filter')
-  model.filter = settings.dcm{1}.filter;
-elseif ~isfield(model.filter, 'down') || ~isnumeric(model.filter.down)
-  warning('ID:invalid_input', 'Filter structure needs a numeric ''down'' field.'); return;
+% 2.2 check model
+model = pspm_check_model(model, 'dcm');
+if model.invalid
+    return
 end
 
-if ~isstruct(options)
-  warning('ID:invalid_input', '''options'' must be a struct.');
-  return;
-end
-
-
-% 2.8 set and check options ---
+% 2.3 check options (could be re-factored into pspm_options)
 options = pspm_options(options, 'dcm');
 if options.invalid
   return
 end
-
-try model.lasttrialcutoff;      catch, model.lasttrialcutoff = 7;       end
-
-% 2.9 check option fields --
 % numeric fields
 num_fields = {'depth', 'sfpre', 'sfpost', 'sffreq', 'sclpre', ...
   'sclpost', 'aSCR_sigma_offset'};
@@ -289,44 +228,6 @@
   return
 end
 
-if ischar(model.datafile)
-  model.datafile = {model.datafile};
-  model.timing   = {model.timing};
-end
-
-nFile = numel(model.datafile);
-if ~isfield(model, 'missing')
-  model.missing = cell(nFile, 1);
-elseif ischar(model.missing) || isnumeric(model.missing)
-  model.missing = {model.missing};
-elseif ~iscell(model.missing)
-  warning('ID:invalid_input',...
-    'Missing values must be a filename, matrix, or cell array of these.');
-  return
-end
-if nFile ~= numel(model.timing)
-  warning('ID:number_of_elements_dont_match',...
-    'Session numbers of data files and event definitions do not match.');
-  return
-end
-if nFile ~= numel(model.missing)
-  warning('ID:number_of_elements_dont_match',...
-    'Same number of data files and missing value definitions is needed.');
-  return
-end
-
-% 2.11 Fill model values
-try model.aSCR; catch, model.aSCR = 0; end
-try model.eSCR; catch, model.eSCR = 0; end
-try model.meanSCR; catch, model.meanSCR = 0; end
-% These parameters were set with default fallback values but will be
-% determined later by processing
-% try model.fixevents; catch, warning('model.fixevents not defined.'); end
-% try model.flexevents; catch, warning('model.flexevents not defined.'); end
-% try model.missing_data; catch, warning('model.missing_data not defined.'); end
-% These parameters do not need to have a default value and will be
-% determined later
-
 %% 3 Check, get and prepare data
 
 % split into subsessions
@@ -348,7 +249,6 @@
   sr{iSn} = data{iSn}{end}.header.sr;
   model.filter.sr = sr{iSn};
 
-
   % load and check existing missing data (if defined)
   if ~isempty(model.missing{iSn})
     [~, missing{iSn}] = pspm_get_timing('missing', ...
diff --git a/src/pspm_glm.m b/src/pspm_glm.m
index 2b05b4f51..915266358 100644
--- a/src/pspm_glm.m
+++ b/src/pspm_glm.m
@@ -158,14 +158,9 @@
 % 2.1 check missing input --
 if nargin < 1; errmsg = 'Nothing to do.'; warning('ID:invalid_input', errmsg); return
 elseif nargin < 2; options = struct(); end
+model = pspm_check_model(model, 'glm');
+
 fprintf('Computing GLM: %s ...\n', model.modelfile);
-if ~isfield(model, 'datafile')
-  warning('ID:invalid_input', 'No input data file specified.'); return;
-elseif ~isfield(model, 'modelfile')
-  warning('ID:invalid_input', 'No output model file specified.'); return;
-elseif ~isfield(model, 'timeunits')
-  warning('ID:invalid_input', 'No timeunits specified.'); return;
-end
 % 2.2 check existing --
 % whether field timing doesnt exist, field is emtpy or field is cell with empty entries
 if ~isfield(model, 'timing') || isempty(model.timing) || ...
@@ -183,11 +178,7 @@
   model.latency = 'fixed';
 end
 % 2.4 check faulty input --
-if ~ischar(model.datafile) && ~iscell(model.datafile)
-  warning('ID:invalid_input', 'Input data must be a cell or string.'); return;
-elseif ~ischar(model.modelfile)
-  warning('ID:invalid_input', 'Output model must be a string.'); return;
-elseif ~ischar(model.timing) && ~iscell(model.timing) && ~isstruct(model.timing)
+if ~ischar(model.timing) && ~iscell(model.timing) && ~isstruct(model.timing)
   warning('ID:invalid_input', 'Event onsets must be a string, cell, or struct.'); return;
 elseif ~ischar(model.timeunits) || ~ismember(model.timeunits, {'seconds', 'markers', 'samples','markervalues'})
   warning('ID:invalid_input', 'Timeunits (%s) not recognised; only ''seconds'', ''markers'' and ''samples'' are supported', model.timeunits); return;
@@ -215,12 +206,7 @@
 elseif ~isnumeric(model.channel) && ~ismember(model.channel, {settings.channeltypes.type})
   warning('ID:invalid_input', 'Channel number must be numeric.'); return;
 end
-% 2.7 check normalisation --
-if ~isfield(model, 'norm')
-  model.norm = 0;
-elseif ~ismember(model.norm, [0, 1])
-  warning('ID:invalid_input', 'Normalisation must be specified as 0 or 1.'); return;
-end
+
 % 2.8 check mean centering --
 if ~isfield(model,'centering')
   model.centering = 1;
@@ -274,9 +260,6 @@
 end
 
 %% 4 check filter
-if ~isfield(model, 'filter')
-  model.filter = settings.glm(modno).filter;
-end
 % 4.1 set default model.filter.down --
 if strcmpi(model.filter.down, 'none') || ...
     isnumeric(model.filter.down) && isnan(model.filter.down)
diff --git a/src/pspm_sf.m b/src/pspm_sf.m
index b725f6713..0d8539066 100644
--- a/src/pspm_sf.m
+++ b/src/pspm_sf.m
@@ -85,28 +85,15 @@
 end
 %% 2 Check input
 % 2.1 Check missing input --
-if nargin<1
-  warning('ID:invalid_input', 'Nothing to do.'); return;
-elseif nargin<2
-  options = struct();
-end
-if ~isfield(model, 'datafile')
-  warning('ID:invalid_input', 'No input data file specified.'); return;
-elseif ~isfield(model, 'modelfile')
-  warning('ID:invalid_input', 'No output model file specified.'); return;
-elseif ~isfield(model, 'timeunits')
-  warning('ID:invalid_input', 'No timeunits specified.'); return;
-elseif ~isfield(model, 'timing') && ~strcmpi(model.timeunits, 'file')
-  warning('ID:invalid_input', 'No epochs specified.'); return;
-end
+if nargin < 1; errmsg = 'Nothing to do.'; warning('ID:invalid_input', errmsg); return
+elseif nargin < 2; options = struct(); end
+model = pspm_check_model(model, 'sf');
+
+
+
+
 % 2.2 Check faulty input --
-if ~ischar(model.datafile) && ~iscell(model.datafile)
-  warning('ID:invalid_input', 'Input data must be a cell or string.'); return;
-elseif ~ischar(model.modelfile) && ~iscell(model.modelfile)
-  warning('ID:invalid_input', 'Output model must be a string.'); return;
-elseif ~ischar(model.timing) && ~iscell(model.timing) && ~isnumeric(model.timing)
-  warning('ID:invalid_input', 'Event onsets must be a string, cell, or struct.'); return;
-elseif ~ischar(model.timeunits) || ~ismember(model.timeunits, {'seconds', 'markers', 'samples', 'whole'})
+if ~ischar(model.timeunits) || ~ismember(model.timeunits, {'seconds', 'markers', 'samples', 'whole'})
   warning('ID:invalid_input',...
     'Timeunits (%s) not recognised; ',...
     'only ''seconds'', ''markers'', ''samples'' and ''whole'' are supported',...