function gephus

%% STARTUP BOILERPLATE 
%Set up a wait bar to show the progress.
wb = waitbarWithCancel(0, 'Starting ephus...', 'Name', 'Loading software...');
pos = get(wb, 'Position');
pos(2) = pos(2) - pos(4);
set(wb, 'Position', pos);

%% CONFIG EPHYS/ACQUIRER/STIM  (DEVICES/CHANNELS) --> Please adjust!

%Amplifier objects for ephys
patch{1} = multi_clamp('text_file_location', 'C:\MATLAB6p1\work\Physiology\MClamp700BChannel1.txt', 'scaledOutputBoardID', 1, 'scaledOutputChannelID', 0, ...
    'vComBoardID', 1, 'vComChannelID', 0, 'channel', 1, 'name', '700B-1');

patch{2} = multi_clamp('text_file_location', 'C:\MATLAB6p1\work\Physiology\MClamp700BChannel2.txt', 'scaledOutputBoardID', 1, 'scaledOutputChannelID', 4, ...
    'vComBoardID', 1, 'vComChannelID', 1, 'channel', 2, 'name', '700B-2');

%Acquirer channels 
acqChannelNames = {'photodiode1'};
acqBoardIDs =   [2];
acqChanIDs =    [0];

%Stimulator channels 
stimChannelNames = {'pockelsCell' 'shutter0' 'xMirror' 'yMirror' 'shutter1' 'ao5' 'ao6' 'ao7'};
stimBoardIDs = [3 3 3 3 3 3 3 3];
stimChanIDs =  [0 1 2 3 4 5 6 7];

%% CONFIG VARS --> Please adjust!
triggerOrigin = '/dev1/port0/line0'; %Corresponds to EXSTRB on a BNC2090 on connector 0 for a PCI-6259 board.
triggerDest = 'PFI0';

xsgStartDirectory = 'C:\Data\';

xVideoScaleFactor =  2625;
yVideoScaleFactor = 1980;

%% TIMING/CLOCK CONFIG --> Adjust with care...
%Set up the triggering.   
acqJob = daqjob('acquisition');
scopeJob = daqjob('scope');
setTriggerOrigin(acqJob, '/dev1/port0/line0');
setTriggerOrigin(scopeJob, '/dev1/port0/line0');
setTriggerDestination(acqJob, 'PFI0');
setTriggerDestination(scopeJob, 'PFI0');

%% START PROGRAMS --> Add/remove/configure with care...
if waitbarUpdate(0.0, wb, 'Starting experimentSavingGui...'); return; end
xsg = openprogram(progmanager,{'xsg', 'experimentSavingGui'});
setLocalBatch(progmanager, xsg, 'directory',xsgStartDirectory);
setLocal(progmanager,xsg,'autosave',0);  %turns off autosave

if waitbarUpdate(0.1, wb, 'Starting ephys...'); return; end
ep = openprogram(progmanager,'ephys',patch);

if waitbarUpdate(0.16, wb,  'Starting ephysScopeAccessory...'); return; end
openprogram(progmanager,'ephysScopeAccessory',patch);

if waitbarUpdate(0.24, wb,  'Starting stimulator...'); return; end
stim = openprogram(progmanager, 'stimulator');
stim_addChannels(stim,stimChannelNames,stimBoardIDs,stimChanIDs);

if waitbarUpdate(0.32, wb, 'Starting acquirer...');return;end
acq = openprogram(progmanager,'acquirer');
acq_addChannels(acq,acqChannelNames,acqBoardIDs,acqChanIDs);

if waitbarUpdate(0.48, wb, 'Starting pulseJacker...');return;end
openprogram(progmanager, 'pulseJacker',{ep,stim});

if waitbarUpdate(0.52, wb, 'Starting userFcns...');return;end
openprogram(progmanager, 'userFcns');

if waitbarUpdate(0.56, wb, 'Starting autonotes...');return;end
openprogram(progmanager, 'autonotes');

if waitbarUpdate(0.60, wb, 'Starting headerGui...');return;end
openprogram(progmanager, 'headerGUI');

if waitbarUpdate(0.64, wb, 'Starting HotSwitch...');return;end
openprogram(progmanager,{'hotswitch', 'hotswitch', 'hotswitch', 'hs_config', 'hs_config'});

if waitbarUpdate(.68, wb, 'Starting photodiode configuration...');return;end
pdiodeConfig = openprogram(progmanager, {'photodiode' 'photodiodeConfiguration'},'photodiode1');

if waitbarUpdate(0.76, wb, 'Starting mapper...');return;end
mapper = openprogram(progmanager, 'mapper','xMirror','yMirror','pockelsCell','shutter0',pdiodeConfig);
setLocalBatch(progmanager, mapper, 'xVideoScaleFactor', xVideoScaleFactor, 'yVideoScaleFactor', xVideoScaleFactor);

%% DEVELOPER-CREATED USERFCNS --> Adjust with care...
%These userFcns allow developers to customize Ephus to specific applications 

if waitbarUpdate(0.84, wb, 'Setting up default (built-in) userFcns...');return;end

userFcnCBM = getUserFcnCBM;

fprintf(1, 'Default UserFcn mappings:\n');
%userFcns for LSPS/mapping customization
addCallback(userFcnCBM, 'xsg:NewCell', @mapper_newCell_userFcn, 'userFcns_mapper_newCell_userFcn','verbose');
addCallback(userFcnCBM, 'ephys:SamplesAcquired', @mapper_userFcn_ephysSamplesAcquired_display, 'userFcns_mapper_userFcn_ephysSamplesAcquired_display','verbose');
addCallback(userFcnCBM, 'ephys:SamplesAcquired', @mapper_userFcn_ephysSamplesAcquired_updateMirrorPosition, 'userFcns_mapper_userFcn_ephysSamplesAcquired_updateMirrorPosition','verbose');
addCallback(userFcnCBM, 'mapper:MapStart', @mapper_userFcn_mapStart_display, 'userFcns_mapper_userFcn_mapStart_display','verbose');
addCallback(userFcnCBM, 'mapper:MapStop', @mapper_userFcn_mapStop_display, 'userFcns_mapper_userFcn_mapStop_display','verbose');
addCallback(userFcnCBM, 'mapper:MouseStart', @mapper_userFcn_mouseStart_updateMirrorPosition, 'userFcns_mapper_userFcn_mouseStart_updateMirrorPosition','verbose');
addCallback(userFcnCBM, 'mapper:PreGrabVideo', @loadImage4Mapper, 'userFcns_loadImage4Mapper','verbose');
addCallback(userFcnCBM, 'mapper:PostGrabVideo', @unloadImage4Mapper, 'userFcns_unloadImage4Mapper','verbose');

fprintf(1, '----------------------------\n');

%% USER-CREATED USERFCNS --> Please add!
%Add userFcns here to customize Ephus yourself
%userFcns can also be added via userFcns GUI, and saved to configuration sets

if waitbarUpdate(0.86, wb, 'Setting up user-made userFcns...');return;end
fprintf(1, 'User-created UserFcn mappings:\n');
% add here!
fprintf(1, '----------------------------\n');


%% ENDING BOILERPLATE
%Load a configuration (if requested).
if waitbarUpdate(0.88, wb, 'Loading configuration...');return;end
loadConfigurations(progmanager);
fprintf(1, '\nLoading Completed.\n\n');

delete(wb); %Kill the waitbar.
fprintf(1, '\n\n-----------------------------------\n-----------------------------------\n\n\n\n\n\n\n\n');