added NOHELPINFO to some files, modified help info of other files a l…

…ittle, related to #9
mmagnuski · Aug 16, 2014 · 288f9b6 · 288f9b6 · mmagnuski · Aug 16, 2014
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Showing 34 changed files with 102 additions and 20 deletions.
diff --git a/ICAw_ep_proc_GUI.m b/ICAw_ep_proc_GUI.m
@@ -1,4 +1,6 @@
 function varargout = ICAw_ep_proc_GUI(varargin)
+
+% NOHELPINFO
 % ICAW_EP_PROC_GUI MATLAB code for ICAw_ep_proc_GUI.fig
 %      ICAW_EP_PROC_GUI, by itself, creates a new ICAW_EP_PROC_GUI or raises the existing
 %      singleton*.

diff --git a/ICAw_epoch_proc.m b/ICAw_epoch_proc.m
@@ -5,6 +5,8 @@
 % optionally remove additional epochs after IC
 % removal and add channels to badchan structure
 
+% BRANCH
+% CHECK
 
 % checking for 'laststep':
 cnt = true;

diff --git a/ICAw_find.m b/ICAw_find.m
@@ -1,6 +1,7 @@
 function r = ICAw_find(ICAw, lookfor, varargin)
 
 % r = ICAw_find(ICAw, lookfor)
+% 
 % Looks for a specific ICAw entry (or entries)
 % and returns their adress in vector r.
 %

diff --git a/ICAw_find_r.m b/ICAw_find_r.m
@@ -1,8 +1,9 @@
 function r = ICAw_find_r(ICAw, fld, val)
 
 % r = ICAw_find_r(ICAw, fld, val)
+%
 % looks for a record that has field 'fld'
-% filled with value 'val'.
+% set to value 'val'.
 % Returns all indices that fulfill these
 % constaints.
 

diff --git a/ICAw_getrej.m b/ICAw_getrej.m
@@ -1,14 +1,16 @@
 function outlist = ICAw_getrej(ICAw, r, varargin)
 
 % rejlist = ICAw_getrej(ICAw, r)
+%
 % returns a list of markings that are present for a given file
 % rejlist.name - displayed name of the marking
 % rejlist.color - color of the marking
 % rejlist.value - value of the marking (what is being marked)
 
 % CHANGE
 % [ ] clear up ICAw_getrej
-% [ ] ICAw_checkfields takes up about 80% of execution time
+% [ ] profile and change/rewrite
+% [X] ICAw_checkfields takes up about 80% of execution time
 %     - should we resign from ICAw_checkfields?
 %     it shouldn't be called so often...
 

diff --git a/ICAw_getversions.m b/ICAw_getversions.m
@@ -1,5 +1,6 @@
 function versions = ICAw_getversions(ICAw, r)
 
+% FIXHELPINFO
 % provides info about versions in cell matrix
 % first row: version field; second row: version
 % name

diff --git a/ICAw_gui_choose_chan.m b/ICAw_gui_choose_chan.m
@@ -1,5 +1,7 @@
 function [f] = ICAw_gui_choose_chan(chan_names, chan_sel, varargin)
 
+% NOHELPINFO
+
 color = [0.85 0.90 0.95];
 if nargin > 2
     color = varargin{1};

diff --git a/ICAw_gui_epoch.m b/ICAw_gui_epoch.m
@@ -1,4 +1,6 @@
 function varargout = ICAw_gui_epoch(varargin)
+
+% NOHELPINFO
 % ICAW_GUI_EPOCH
 %
 % See also: GUIDE, GUIDATA, GUIh

diff --git a/ICAw_gui_upd_txt.m b/ICAw_gui_upd_txt.m
@@ -1,5 +1,7 @@
 function ICAw_gui_upd_txt(ICAw, r, h)
 
+% NOHELPINFO
+
 ICAw_txt = {'filename: '; 'badchans: '; 'rejected comps: ';...
     'comments: '};
 

diff --git a/ICAw_gui_upd_txt2.m b/ICAw_gui_upd_txt2.m
@@ -1,5 +1,7 @@
 function ICAw_gui_upd_txt2(addinf, h)
 
+% NOHELPINFO
+
 % ICAw_txt = {'filename: '; 'badchans: '; 'rejected comps: ';...
 %     'comments: '};
 ICAw_txt2 = {'all ifrej comps num: '; 'current comp: '; 'comps left: ';...

diff --git a/ICAw_isbase.m b/ICAw_isbase.m
@@ -1,6 +1,6 @@
 function [isICAw, moreinfo] = ICAw_isbase(somevar)
 
-% PARTIALHELPINFO
+% FIXHELPINFO
 % determines whether given variable is 
 % an ICAw structure
 

diff --git a/ICAw_loadbase.m b/ICAw_loadbase.m
@@ -6,6 +6,9 @@
 % interface to matlab load() function
 % WARNING! NON-UNIVERSAL
 
+% CHANGE
+% BRANCH
+% NOT-USED
 
 Drop = false;
 PTH = 'Dropbox\DANE\MGR\EEG';

diff --git a/ICAw_mainversion.m b/ICAw_mainversion.m
@@ -1,5 +1,7 @@
 function ICAw = ICAw_mainversion(ICAw, rr)
 
+% NOHELPINFO
+
 % if no - create
 % else - give back(?)
 

diff --git a/ICAw_moverej.m b/ICAw_moverej.m
@@ -1,6 +1,7 @@
 function ICAw = ICAw_moverej(ICAw, r, epoch_info, perc, varargin)
 
 % ICAw = ICAw_moverej(ICAw, epoch_info, perc, varargin)
+%
 % Moves rejections from onesecepoch to any other
 % event-based epoching.
 % ICAw - the database
@@ -9,7 +10,8 @@
 %              and new epoch above (and equal to) which
 %              the new epoch is rejected
 
-% copy bad windows to bad epochs:
+% ADD some tests and options...
+% TEST thoroughly
 
 % load original (unepoched) file:
 % eeg_path('add');

diff --git a/ICAw_newrejtype.m b/ICAw_newrejtype.m
@@ -1,6 +1,6 @@
 function ICAw = ICAw_newrejtype(ICAw, newtypes)
 
-% NOHELP
+% NOHELPINFO
 
 if isempty(newtypes)
     ex = evalin('base', 'exist(''TMPNEWREJ'', ''var'');');
@@ -17,8 +17,8 @@
 % CHANGE - this should be only performed
 %          for consistency checks one time
 %          (at the beginning)
-%          !! use persistent option :)
-rejt = ICAw_scanrejtypes(ICAw);
+%          !! use persistent option?
+rejt = ICAw_scanrejtypes(ICAw); % <-- consider moving this to C maybe...
 
 % take only userrem types:
 urem = strcmp('userrem', rejt.infield);

diff --git a/ICAw_nonrej.m b/ICAw_nonrej.m
@@ -1,6 +1,6 @@
 function nonrejid = ICAw_nonrej(ICAw, r, varargin)
 
-% help description coming soon
+% NOHELPINFO
 
 % TODOs:
 % [ ] - the function should check segment by itself

diff --git a/ICAw_onechan_comp.m b/ICAw_onechan_comp.m
@@ -1,6 +1,7 @@
 function ICAw = ICAw_onechan_comp(ICAw, r)
 
 % ICAw = ICAw_onechan_comp(ICAw);
+% 
 % adds a field ica_onechan to ICAw
 % structure that contains ICs that
 % are most probably explaining only
@@ -10,6 +11,9 @@
 % component)
 %
 
+% BRANCH
+% CHANGE - this does not work that well, should be changed
+
 opt.sd = 4;
 opt.multip_more = 3;
 

diff --git a/ICAw_path.m b/ICAw_path.m
@@ -1,6 +1,7 @@
 function pth = ICAw_path(PTH, varargin)
 
 % pth = ICAw_path(PTH);
+% 
 % goes through path strings in PTH and
 % finds pth - the string that is a valid
 % directory on the current computer.

diff --git a/ICAw_refield.m b/ICAw_refield.m
@@ -1,13 +1,19 @@
 function ICAw = ICAw_refield(ICAw, fieldfrom, fieldto)
 
-% this function changes field names in ICAw structure
-% for now it simply works as if it was renaming the
+% ICAw = ICAw_refield(ICAw, fieldfrom, fieldto)
+% 
+% this function renames fields in ICAw structure.
+% fieldfrom fileds are renamed to fieldto fields
+% respectively.
+% 
+% Currently it simply works by renaming the
 % fields - so renaming 'core' fields of ICAw (like
 % 'removed' will cause ICAw to break - this will be
 % later changed so that the fields cannot be renamed
 % using this function)
 
-% ADD - not possible to rename core fields?
+% FIXHELPINFO - add examples
+% CHANGE, ADD - not possible to rename core fields?
 
 flds = fieldnames(ICAw);
 fldpos = find(strcmp(fieldfrom, flds));

diff --git a/ICAw_rejICAw2EEG.m b/ICAw_rejICAw2EEG.m
@@ -1,5 +1,7 @@
 function EEG = ICAw_rejICAw2EEG(ICAw, r, EEG, prerej)
 
+% NOHELPINFO
+
 % taking care of rejections
 % in and out from ICAw/EEG
 ICAw_present = true;

diff --git a/ICAw_rejTMP.m b/ICAw_rejTMP.m
@@ -1,5 +1,7 @@
 function [ICAw, EEG] = ICAw_rejTMP(ICAw, r, EEG, TMPREJ)
 
+% NOHELPINFO
+
 % taking care of rejections
 % in and out from ICAw/EEG
 ICAw_present = true;

diff --git a/ICAw_rem_marks.m b/ICAw_rem_marks.m
@@ -1,4 +1,6 @@
-function ICAw = ICAw_rem_marks(ICAw);
+function ICAw = ICAw_rem_marks(ICAw)
+
+% NOHELPINFO
 
 not = {'color', 'name'};
 

diff --git a/ICAw_runCleanLine.m b/ICAw_runCleanLine.m
@@ -1,8 +1,15 @@
 function ICAw = ICAw_runCleanLine(ICAw)
 
-% runs CleanLine for file with field usecleanline set
-% to true. Updates ICAw structure
-% add new filepath argument?
+% ICAw = ICAw_runCleanLine(ICAw)
+%
+% runs CleanLine for records where field 
+% usecleanline is set to true. 
+% Updates ICAw structure.
+% FIXHELPINFO - add info about creation of
+%               \CleanLine\ folder etc.
+
+% CHANGE - add new filepath argument?
+% CHANGE - other options? (parameter scan?)
 
 % TODOs:
 % [ ] check for datainfo.cleanline - if true do not run (?)

diff --git a/ICAw_scan4patterns.m b/ICAw_scan4patterns.m
@@ -1,5 +1,7 @@
 function pattern = ICAw_scan4patterns(DIR, pat, varargin)
 
+% NOHELPINFO
+
 %%
 % default parameters
 verbose = true;

diff --git a/ICAw_scanrejtypes.m b/ICAw_scanrejtypes.m
@@ -1,6 +1,6 @@
 function rejt = ICAw_scanrejtypes(ICAw)
 
-% NOHELP
+% NOHELPINFO
 
 % TODOs:
 % [ ] this is not a particulary fast way to check this

diff --git a/ICAw_search_by_tag.m b/ICAw_search_by_tag.m
@@ -1,10 +1,13 @@
 function tags = ICAw_search_by_tag(ICAw, r, varargin)
 
 % tags = ICAw_search_by_tag(ICAw, r);
+% 
 % searches given ICAw record for component
 % tags (that is text of format '[tag_text]'
 % present in component notes.
 
+% CHECK ICAw_search_by_tag vs ICAw_tag_search
+
 % check if ICA_desc has any info:
 if ~femp(ICAw(r), 'ICA_desc')
     error(['ICA_desc field (the field that contains',...

diff --git a/ICAw_sorter.m b/ICAw_sorter.m
@@ -1,7 +1,12 @@
 function ICAw = ICAw_sorter(ICAw)
 
+% NOHELPINFO
 % sort fields of ICAw:
 
+% CHANGE - once eegDb field structure is settled upon
+%          this function should be changed to reflect
+%          that structure
+
 fldord = {'subjectcode'; 'filename'; 'filepath'; 'datainfo';...
     'tasktype'; 'badchan'; 'filter'; 'usecleanline'; 'onesecepoch'; 'winlen';
     'distance'; 'epoch_events'; 'epoch_limits';...

diff --git a/ICAw_start.m b/ICAw_start.m
@@ -1,7 +1,9 @@
 function ICAw_start(PTH, varargin)
 
 % function for starting your work with ICAw
-%
+% FIXHELPINFO
+
+% CHECK, CHANGE this function and to a stable, relatively final form
 
 % TODOs:
 % [ ] add some more options

diff --git a/ICAw_sub2r.m b/ICAw_sub2r.m
@@ -1,5 +1,7 @@
 function sub2r = ICAw_sub2r(ICAw, varargin)
 
+% sub2r = ICAw_sub2r(ICAw, varargin)
+%
 % ICAw_sub2r() retruns cell matrix
 % subjects X 2 representing for each
 % subject (first column) registries of 
@@ -23,7 +25,7 @@
 %         this subject
 % 
 % Usage 2:
-% sub2r = ICAw_sub2r(ICAw);
+% sub2r = ICAw_sub2r(ICAw, s);
 %
 % where :
 % ICAw  - ICAw structure (as used by ICAw
@@ -35,6 +37,10 @@
 %
 % coded by M. Magnuski, august, 2013
 
+% CHANGE - check for subjectcode etc.
+% NOTUSED - possibly this is not used in the
+%           core eegDb
+
 %% defaults
 sub = false;
 

diff --git a/ICAw_testfiles.m b/ICAw_testfiles.m
@@ -1,8 +1,12 @@
 function log = ICAw_testfiles(ICAw)
 
 % log = ICAw_testfiles(ICAw)
-% tests for file presence of all ICAw records
-% (checks whether .set file is present)
+%
+% tests for file presence in all ICAw records
+% (checks whether .set file referenced by 
+% filepath and filename is present)
+% log is a boolean vector where true means 
+% that the file was present
 
 len = length(ICAw);
 log = false(1, len);

diff --git a/ICAw_updatetonewformat.m b/ICAw_updatetonewformat.m
@@ -1,5 +1,6 @@
 function ICAw = ICAw_updatetonewformat(ICAw)
 
+% OUTDATED
 % updates ICAw structure to its most current form
 
 

diff --git a/ICAw_updateversion.m b/ICAw_updateversion.m
@@ -1,11 +1,16 @@
 function ICAw = ICAw_updateversion(ICAw, r, verf)
 
+% ICAw = ICAw_updateversion(ICAw, r, verf)
+%
 % ICAw_updateversion updates version whose
 % field or name has been given
 % that is it updates the version field of a
 % given ICAw(r) registry with its current main
 % content that is the contents of ICAw(r)
 % nonempty fields
+% 
+% FIXHELPINFO
+% verf is not explained - version field name?
 
 
 %% check version field:

diff --git a/ICAw_ver2EEG.m b/ICAw_ver2EEG.m
@@ -1,10 +1,14 @@
 function EEG = ICAw_ver2EEG(ICAw, r, EEG)
 
+% EEG = ICAw_ver2EEG(ICAw, r, EEG)
 % transports current version to EEG.etc.recov
 % this is for the interface to know later whether
 % currently recovered EEG corresponds to currently
 % active version
 
+% CHANGE - this may not be the best way
+%          to do it...
+
 % current version:
 cvf = ICAw(r).versions.current;
 cv = ICAw(r).versions.(cvf);

diff --git a/ICAw_vers_compare.m b/ICAw_vers_compare.m
@@ -1,5 +1,7 @@
 function iseq = ICAw_vers_compare(ver01, ver02)
 
+% NOHELPINFO
+
 % compare non-empty fields of databases
 ign = {'subjectcode', 'tasktype', 'filename', 'filepath',...
     'datainfo', 'session', 'versions', 'version_name', ...