New.m

function varargout = New(varargin)
% NEW MATLAB code for New.fig
%      NEW, by itself, creates a new NEW or raises the existing
%      singleton*.
%
%      H = NEW returns the handle to a new NEW or the handle to
%      the existing singleton*.
%
%      NEW('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in NEW.M with the given input arguments.
%
%      NEW('Property','Value',...) creates a new NEW or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before New_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to New_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help New

% Last Modified by GUIDE v2.5 01-Apr-2016 20:50:42

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @New_OpeningFcn, ...
                   'gui_OutputFcn',  @New_OutputFcn, ...
                   'gui_LayoutFcn',  [] , ...
                   'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before New is made visible.
function New_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to New (see VARARGIN)

global Y Z;
Y = '';
Z = 1;


% Choose default command line output for New
handles.output = hObject;

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes New wait for user response (see UIRESUME)
% uiwait(handles.figure1);



% --- Outputs from this function are returned to the command line.
function varargout = New_OutputFcn(hObject, eventdata, handles) 
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;



% --- Executes on button press in pushbutton1.
function pushbutton1_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
x = uigetdir();
% display(x);
% start(x);
if(x ~= 0)
    set(handles.edit3,'String',x);
end;



function edit2_Callback(hObject, eventdata, handles)
% hObject    handle to edit2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit2 as text
%        str2double(get(hObject,'String')) returns contents of edit2 as a double

Y = get(hObject,'String');
display(get(hObject,'String'));



% --- Executes during object creation, after setting all properties.
function edit2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



% --- Executes on button press in pushbutton4.
function pushbutton4_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton4 (se e GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
x  = get(handles.edit3,'String');

    

% Our code 
%----------------------------------------------------------------
%----------------------------------------------------------------

system('rm -rf /Users/nikhilthakur/Desktop/results/*') %Remove previous images
s = strcat(x,'/*.tif');
s1 = strcat(x,'/');
% src = dir('/Users/nikhilthakur/Desktop/samples/sample_set_1/*.png');
src = dir(s);

number_of_samples = length(src);
set(handles.edit2,'String',number_of_samples);


%display(number_of_samples);
%fprintf('Program paused. Press enter to continue.\n');
%pause;

porosities = double(length(src));
ssas = double(length(src));
% permeas = double(length(src));
str = get(handles.popupmenu2,'Value');
if(str==1)
    b = 'square';
elseif(str==2)
    b = 'octagon';
else
    b = ' disk';
end

%display(b);        

y = get(handles.popupmenu4,'Value');
if(y==1)
    c = 1;
elseif(y==2)
    c = 2;
elseif(y==3)
    c = 3;
elseif(y==4)
    c = 4;
elseif(y==5)
    c = 5; 
elseif(y==6)
    c = 6;     
else
    c = 7;
end

%display(c); 
count=1;

for i = 1 : length(src)
    filename = strcat(s1,src(i).name);
    display(filename);
    I = imread(filename);
    % Compute properties
    if (get(handles.radiobutton1,'Value') == get(hObject,'Max'))
        [porosities(i),ssas(i)] = RGB(I,b,c,count);
        count=count+1;
    else
        [porosities(i),ssas(i)] = YCbCr(I,b,c,count);
        count=count+1;
    end
end


% Unitless
%display(porosities);
avg_porosity = sum(porosities)/length(porosities);
%display(avg_porosity);
set(handles.edit4,'String',num2str(avg_porosity));
fprintf('Porosty Unitless.\n');


%fprintf('Program paused. Press enter to continue.\n');
%pause;
avg_ssa = sum(ssas)/length(ssas);
%display(avg_ssa);
set(handles.edit5,'String',num2str(avg_ssa));
fprintf('Specific Surface area in cm^-1.\n');


%fprintf('Program paused. Press enter to continue.\n');
%pause;
% Tortuosity estiation using its relationships with porosity
for i=1:length(porosities)
    to(i) = tortuosity(porosities(i)/100);
end    
[tor] = tortuosity(avg_porosity/100);
avg_tortuosity = sum(tor)/length(tor);
set(handles.edit8,'String',num2str(avg_tortuosity));
fprintf('Tortuosity Unitless.\n');


%fprintf('Program paused. Press enter to continue.\n');
%pause;
% Permeability Estimation
% Unit:mD(Milli Darcies/m^2/cm^2)
for i=1:length(porosities)
    per(i) = permea(ssas(i),porosities(i)/100,to(i));
end
avg_p = sum(per)/length(per);
fprintf('Permeability in cm^2.\n');
set(handles.edit6,'String',num2str(avg_p));




%fprintf('Program paused. Press enter to continue.\n');
%pause;
% Bulk Density using its relationship with porosity
fprintf('Bulk Density in cm^-3.\n');
D = (2.156 - (avg_porosity/100))/0.756;
set(handles.edit9,'String',num2str(D));


figure(1)
plot(porosities,per,'ok','MarkerFaceColor','r');
xlabel('Porosity(%)');
ylabel('Permebility(cm^2)');


figure(2)
plot(porosities,ssas,'ok','MarkerFaceColor','b');
xlabel('Porosity(%)');
ylabel('Specific Surface Area(cm^-1)');

figure(3)
plot(ssas,per,'ok','MarkerFaceColor','g');
xlabel('Specific Surface Area(cm^-1)');
ylabel('Permeability(cm^2');



% function uibuttongroup2_SelectionChangedFcn(hObject1, eventdata1, handles1)
%     % hObject    handle to the selected object in uibuttongroup2 
%     % eventdata  reserved - to be defined in a future version of MATLAB
%     % handles    structure with handles and user data (see GUIDATA)
%     persistent a;
%     switch get(eventdata1.NewValue,'Tag')
%         case 'radiobutton1'
%             a = 1;
%         case 'radiobutton2'
%             a = 2;
%     end

%-----------------------------------------------------------------
%-----------------------------------------------------------------


function edit3_Callback(hObject, eventdata, handles)
% hObject    handle to edit3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit3 as text
%        str2double(get(hObject,'String')) returns contents of edit3 as a double



% --- Executes during object creation, after setting all properties.
function edit3_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit3 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit4_Callback(hObject, eventdata, handles)
% hObject    handle to edit4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit4 as text
%        str2double(get(hObject,'String')) returns contents of edit4 as a double
%set(handles.edit4,'Integer',avg_porosity);



% --- Executes during object creation, after setting all properties.
function edit4_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit5_Callback(hObject, eventdata, handles)
% hObject    handle to edit5 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit5 as text
%        str2double(get(hObject,'String')) returns contents of edit5 as a double


% --- Executes during object creation, after setting all properties.
function edit5_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit5 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit6_Callback(hObject, eventdata, handles)
% hObject    handle to edit6 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit6 as text
%        str2double(get(hObject,'String')) returns contents of edit6 as a double


% --- Executes during object creation, after setting all properties.
function edit6_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit6 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit8_Callback(hObject, eventdata, handles)
% hObject    handle to edit8 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit8 as text
%        str2double(get(hObject,'String')) returns contents of edit8 as a double



% --- Executes during object creation, after setting all properties.
function edit8_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit8 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit9_Callback(hObject, eventdata, handles)
% hObject    handle to edit9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit9 as text
%        str2double(get(hObject,'String')) returns contents of edit9 as a double



% --- Executes during object creation, after setting all properties.
function edit9_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



function edit10_Callback(hObject, eventdata, handles)
% hObject    handle to edit10 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of edit10 as text
%        str2double(get(hObject,'String')) returns contents of edit10 as a double



% --- Executes during object creation, after setting all properties.
function edit10_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit10 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end



% --- Executes on button press in pushbutton7.
function pushbutton7_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton7 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%open(get(handles.edit3,'String'));
g = horzcat('open ',get(handles.edit3,'String'));
system(g);




% --- Executes on button press in radiobutton1.
function radiobutton1_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton1


% --- Executes on button press in radiobutton2.
function radiobutton2_Callback(hObject, eventdata, handles)
% hObject    handle to radiobutton2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of radiobutton2


% --- Executes during object creation, after setting all properties.
function uibuttongroup2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uibuttongroup2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called


% --- Executes when selected object is changed in uibuttongroup2.


% --- Executes on selection change in popupmenu2.
function popupmenu2_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu2 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu2


% --- Executes during object creation, after setting all properties.
function popupmenu2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on selection change in popupmenu4.
function popupmenu4_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns popupmenu4 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu4


% --- Executes during object creation, after setting all properties.
function popupmenu4_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu4 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in pushbutton8.
function pushbutton8_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton8 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
close all;
system('rm -rf /Users/nikhilthakur/Desktop/results/*')


% --- Executes on button press in pushbutton9.
function pushbutton9_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton9 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

z = horzcat('open ','/Users/nikhilthakur/Desktop/results');
system(z);