in_out_directory_set_07_30_2018_ws1.m

function [inputdir,outputdir]=in_out_directory_set_07_30_2018_ws1(basedirname,runname)
%Set Input Output Directories

% The case for which diectories will be created
% runname2='10_14_2015_deform_whittaker_blackman';% This for image matching old processing directory 

%Creating outputdirectory structure
outputdir_main=fullfile(basedirname,'Results','final_plots',runname,'SOC_gradient');
if ~exist(outputdir_main,'dir')
    mkdir(outputdir_main);
end
outputdir{1}=fullfile(outputdir_main,'matfiles');
outputdir{2}=fullfile(outputdir_main,'figures');
if ~exist(outputdir{1},'dir')
    mkdir(outputdir{1});
end
if ~exist(outputdir{2},'dir')
    mkdir(outputdir{2});
end

% Get input directory structure

%2003B
inputdir.Pivchal03B.pranasol=fullfile(basedirname,'Results',runname,'2003B');
inputdir.Pivchal03B.davisol=fullfile(basedirname,'uncertainty_tests_Davis','uncertainty_test_2003B','2003bimages','CreateMultiframe','PIV_MP(4x64x64_87%ov)_01');
inputdir.Pivchal03B.MCdir=fullfile(basedirname,'Results',runname,'2003B');
inputdir.Pivchal03B.IMdir=fullfile(basedirname,'Results',runname,'2003B');
inputdir.Pivchal03B.pranabaseMC='PIV_scc_finalchal03_pass4_';
inputdir.Pivchal03B.pranabaseIM='PIV_scc_finalchal03_pass4_';
inputdir.Pivchal03B.davisbase='B';
inputdir.Pivchal03B.truesoldir=fullfile(basedirname,'Results','True_solution','2003B');
inputdir.Pivchal03B.truesolbase='solutiononly';

%2005B
inputdir.Pivchal05B.pranasol=fullfile(basedirname,'Results',runname,'2005B');
inputdir.Pivchal05B.davisol=fullfile(basedirname,'uncertainty_tests_Davis','uncertainty_test_2005B','Case_B','CreateMultiframe','PIV_MP(4x64x64_75%ov)');
inputdir.Pivchal05B.MCdir=fullfile(basedirname,'Results',runname,'2005B');
inputdir.Pivchal05B.IMdir=fullfile(basedirname,'Results',runname,'2005B');
inputdir.Pivchal05B.pranabaseMC='PIV_scc_chal05_diaCClsq_pass4_';
inputdir.Pivchal05B.pranabaseIM='PIV_scc_chal05_diaCClsq_pass4_';
inputdir.Pivchal05B.davisbase='B';
inputdir.Pivchal05B.truesoldir=fullfile(basedirname,'Results','True_solution','2005B');
inputdir.Pivchal05B.truesolbase='PIVchal05Btruesol';

%stagnation_flow
inputdir.stagflow.pranasol=fullfile(basedirname,'Results',runname,'stagnation_flow');
inputdir.stagflow.davisol=fullfile(basedirname,'uncertainty_tests_Davis','uncertainty_test_stagnationflow','stagnation_images','TR_PIV_MP(4x64x64_75%ov)');
inputdir.stagflow.MCdir=fullfile(basedirname,'Results',runname,'stagnation_flow');
inputdir.stagflow.IMdir=fullfile(basedirname,'Results',runname,'stagnation_flow');% New IM processing done
inputdir.stagflow.pranabaseMC='PIV_scc_finalstag_pass4_';
inputdir.stagflow.pranabaseIM='PIV_scc_finalstag_pass4_';
inputdir.stagflow.davisbase='B';
inputdir.stagflow.truesoldir=fullfile(basedirname,'Results','True_solution','stagnation_flow');
inputdir.stagflow.truesolbase='Stagtruesol';

%Vortex_Ring
inputdir.vortex.pranasol=fullfile(basedirname,'Results',runname,'Vortex_Ring');
inputdir.vortex.davisol=fullfile(basedirname,'uncertainty_tests_Davis','uncertainty_test_vortexring','Camera_01','TR_PIV_MP(4x64x64_87%ov)');
inputdir.vortex.MCdir=fullfile(basedirname,'Results',runname,'Vortex_Ring');
inputdir.vortex.IMdir=fullfile(basedirname,'Results',runname,'Vortex_Ring');
inputdir.vortex.pranabaseMC='PIV_scc_pass4_';
inputdir.vortex.pranabaseIM='PIV_scc_pass4_';
inputdir.vortex.davisbase='B';
inputdir.vortex.truesoldir=fullfile(basedirname,'Results','True_solution','Vortex_Ring');
inputdir.vortex.truesolbase='vortextruesol';

%Jetdata
inputdir.jet.pranasol=fullfile(basedirname,'Results',runname,'Jetdata');
inputdir.jet.davisol=fullfile(basedirname,'uncertainty_tests_Davis','uncertainty_test_jetflow','MS_images_F001_cropped_x_303to402_y_188to347_frame_03_501','TR_PIV_MP(4x32x32_87%ov)_nopostprocess');
inputdir.jet.MCdir=fullfile(basedirname,'Results',runname,'Jetdata');
inputdir.jet.IMdir=fullfile(basedirname,'Results',runname,'Jetdata');% New IM processing done
inputdir.jet.pranabaseMC='PIV_scc_jet_cropped_pass4_';
inputdir.jet.pranabaseIM='PIV_scc_jet_cropped_pass4_';
inputdir.jet.davisbase='B';
inputdir.jet.truesoldir=fullfile(basedirname,'Results','True_solution','Jetdata');
inputdir.jet.truesolbase='jettruesol';

end