% dopOSCCI function Tree (3rd June 2011)
% - provide a diagram of dopOSCCI functions
%
% -------------------------------------------------------------------------
%     'dopOSCCI' summarises functional transcranial Doppler ultrasonography
%     (fTCD) data.  The primary function of the software is to assess the
%     hemispheric lateralization of cognitive function.
%
%     Copyright (C) 2011 the Chancellor, Masters and Scholars of the
%     University of Oxford.
% 
%     This program is free software: you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published by
%     the Free Software Foundation, either version 3 of the License, or
%     (at your option) any later version.
% 
%     This program is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License for more details.
% 
%     You should have received a copy of the GNU General Public License
%     along with this program.  If not, see <http://www.gnu.org/licenses/> 
%     or write to the Free Software Foundation, Inc., 51 Franklin Street,
%     Fifth Floor, Boston, MA 02110-1301, USA.
%
%     Authors: Nic Badcock, Georgina Holt, Anneka Holden, & Dorothy Bishop.
%       contact: nicholas.badcock@gmail.com
%
%     Type 'dopOSCCIlicense' for license details or see dopOSCCIlicense.txt
%
%% dopOSCCI func Tree
%
% please note: 
%   dopOSCCIdebug is used constantly but has not been included in the diagram
%
%   | - < - |
%   |       |
% dopOSCCI  |
%   |       |
%   |--> dopOSCCIgui (these don't run automatically)
%   |       |
%   |       |--> dopOSCCIdef
%   |       |
%   |       |--> dopOSCCIgetFileList
%   |       |       | 
%   |       |       |--> getTXfileList
%   |       |       |       |
%   |       |       |       |--> isTXmatchTW
%   |       |       |               |
%   |       |       |               |--> isTX
%   |       |       | 
%   |       |       |--> getEXPfileList
%   |       |               |
%   |       |               |--> isEXP
%   |       |
%   |       |--> dopOSCCIeventCheck
%   |       |
%   |       |--> dopScrnFileCreate
%   |       |       | 
%   |       |       |--> dopOSCCIgetFileList 
%   |       |               |
%   |       |               |--> (see above)
%   |       |
%   |       |--> dopGrpFileCreate
%   |       |       | 
%   |       |       |--> dopOSCCIgetFileList
%   |       |               |
%   |       |               |--> (see above)
%   |       |
%   |       |--> dopBehFileCreate
%   |       |       | 
%   |       |       |--> dopOSCCIgetFileList
%   |       |               |
%   |       |               |--> (see above)
%   |       |
%   |       |--> dopSesFileCreate
%   |               | 
%   |               |--> dopOSCCIgetFileList
%   |                       |
%   |                       |--> (see above)
%   |       
%   |--> dopOSCCIrun
%           |
%           |--> dopOSCCIdef
%           |       | 
%           |       |--> dopSaveDirBase
%           |       |       |
%           |       |       |--> dopSaveDirDescription 
%           |       |
%           |       |--> dopOSCCIeventCheck
%           |
%           |--> dopOSCCIsetup
%           |       |
%           |       |--> dopSaveNotes
%           |       |
%           |       |--> dopOSCCIgetFileList
%           |       |       |
%           |       |       |--> (see above)
%           |       |
%           |       |--> dopGrpSet
%           |       |       |
%           |       |       |--> dopGrpChk 
%           |       |               |
%           |       |               |--> dopGrpFileRead
%           |       | 
%           |       |--> dopScrnSet
%           |       |       |
%           |       |       |--> dopScrnChk 
%           |       |               |
%           |       |               |--> dopScrnFileRead
%           |       | 
%           |       |--> dopBehSet
%           |       |       |
%           |       |       |--> dopBehChk 
%           |       |               |
%           |       |               |--> dopBehFileRead
%           |       | 
%           |       |--> dopSessionSet
%           |       |       |
%           |       |       |--> dopSesChk 
%           |       |       |       |
%           |       |       |       |--> dopSessionFileRead
%           |       |       |
%           |       |       |--> dopSessionReset
%           |       | 
%           |       |--> dopSaveDirSetup
%           |       |
%           |       |--> dopSkipNotes
%           |
%           |--> dopOSCCIsummary
%           |       |
%           |       |--> dopSelectFile
%           |       |       |
%           |       |       |--> dopSaveNotes
%           |       |
%           |       |--> dopGetData
%           |       |       |
%           |       |       |-->dopProcessRawDataFile
%           |       |               |
%           |       |               |--> readTWfromTX
%           |       |               |       |
%           |       |               |       |--> txRead
%           |       |               |       |       |
%           |       |               |       |       |--> dec2ch
%           |       |               |       |
%           |       |               |       |--> twRead
%           |       |               |
%           |       |               |--> dopEXPread
%           |       |               |
%           |       |               |--> dopFindRawMarkers
%           |       |               |
%           |       |               |--> dopRawHBmarks
%           |       |               |
%           |       |               |--> dopRawChEqual
%           |       |               |
%           |       |               |--> dopRawHBcor
%           |       |
%           |       |--> dopEventData
%           |       |       |
%           |       |       |--> dopEventMarks (find the appropriate markers)
%           |       |       |
%           |       |       |--> dopEventStack (stack the data into events/trials)
%           |       |       |
%           |       |       |--> dopEventStack - 2nd time for raw data
%           |       |       |
%           |       |       |--> dopEventFilter (create filter for base and poi selection
%           |       |       |
%           |       |       |--> dopEventActRej (creates epoch screen based upon activation rejection values, see dopTaskDef)
%           |       |       |
%           |       |       |--> dopEventBaseCorrect (runs baseline correction adjustment)
%           |       |       |
%           |       |       |--> dopEventAverage (calculates average activation of left & right channels)
%           |       |       |
%           |       |       |--> dopEventDifference (calculates difference between the left and right doppler channels)
%           |       |       |
%           |       |       |--> dopEventScreen (creates event/epoch screening array)
%           |       |
%           |       |
%           |       |--> dopEpochScreen
%           |       |
%           |       |--> dopIndexFilters
%           |       |
%           |       |--> dopDataCalc
%           |       |       |
%           |       |       |--> dopDataIndexCalcSetup
%           |       |       |       |
%           |       |       |       |--> dopDataIndexCalc
%           |       |       |
%           |       |       |--> dopDataDropCalcSetup
%           |       |       |       |
%           |       |       |       |--> dopDataDropCalc
%           |       |       |
%           |       |       |--> dopDataLIcalcSetup
%           |       |       |       |
%           |       |       |       |--> dopDataLICalc
%           |       |       |
%           |       |       |--> dopDataSplitHalfCalcSetup
%           |       |               |
%           |       |               |--> dopDataLICalc (same as above)
%           |       |
%           |       |--> dopBehSummary
%           |       |       |
%           |       |       |--> dopDataIndexCalcSetup
%           |       |       |       |
%           |       |       |       |--> dopDataIndexCalc
%           |       |       |
%           |       |       |--> dopDataLIcalcSetup
%           |       |               |
%           |       |               |--> dopDataLICalc
%           |       |
%           |       |--> dopSaveSum
%           |       |
%           |       |--> dopGraphDataSave
%           |       |
%           |       |--> dopGraph
%           |       |       |
%           |       |       |--> dopGraph1Raw
%           |       |       |
%           |       |       |--> dopGraph2Norm
%           |       |       |
%           |       |       |--> dopGraph3laterality
%           |       |       |
%           |       |       |--> dopGraphSave
%           |       |
%           |       |--> dopSumReport
%           |       |       |
%           |       |       |--> dopSkipNotes
%           |       |
%           |       |--> dopSessionCollect
%           |               |
%           |               |--> dopDataCalc
%           |               |
%           |               |--> dopBehSummary
%           |               |
%           |               |--> dopSaveSum
%           |               |
%           |               |--> dopGraphDataSave
%           |               |
%           |               |--> dopGraph
%           |               |
%           |               |--> dopSumReport
%           |               |
%           |               |--> dopSessionReset
%           |       
%           |--> dopOSCCIfinish
%                   |
%                   |--> dopOverallDataFinish
%                   |       |
%                   |       |--> dopOverallDataRead
%                   |       |
%                   |       |--> dopGraphDataFileInfo
%                   |       |
%                   |       |--> dopOverallDataVert
%                   |       |
%                   |       |--> dopOverallDataCalc
%                   |       |       |
%                   |       |       |--> dopDataIndexCalc
%                   |       |       |
%                   |       |       |--> dopDataLICalc
%                   |       |
%                   |       |--> dopOverallCalcSave
%                   |       |
%                   |       |--> dopGraph
%                   |
%                   |--> dopOSCCIsave
%                   |
%                   |--> dopSaveNotes
%                   |
%                   |--> dopOSCCIalert
%

help dopOSCCIfuncTree; % displays above in the command window
