Update 7/5/2019 strange result for multi-slice

Code/CardiacPhase.m

@@ -1,16 +1,17 @@
 classdef CardiacPhase < Phase
         properties
         FullPhase = Phase;
-        SelectedPhase = [];
         SystolePositions = [];
         DiastolePositions = [];
+        SystoleTreshold = double(0);
+        DiastoleTreshold = double(0);
         end
     
     methods %constructor
         function obj=CardiacPhase(Phase)
             if nargin==0;return;end
             % gets properties of superclass
-            obj.FullPhase = Phase.Values;
+            obj.FullPhase = Phase.ModePhases;
             obj.WorkLoad = Phase.WorkLoad;
             obj.Video = Phase.Video;
         end
@@ -33,27 +34,30 @@ classdef CardiacPhase < Phase
                     end
                 end
             end
-            obj.SelectedPhase = obj.FullPhase(imf_number,:); % Phase corresponding to the cardiac phase
+            % SHOULD TRY TO USE GETPHASE FUNCTION
+%             obj.IMF = imf_number;
+%             GetPhase@Phase(obj.FullPhase,obj.IMF);
+            obj.Values = obj.FullPhase(imf_number,:); % Phase corresponding to the cardiac phase
         end
         
         % Detects the frame's positions of diastolic events
         function Diastole(obj)
-            max_heart_phase = max(obj.SelectedPhase); % cardiac phase maxima
+            max_heart_phase = max(obj.Values); % cardiac phase maxima
-            treshold_diast = 0.8*max_heart_phase; % diastole treshold 
+            obj.DiastoleTreshold = 0.8*max_heart_phase; % diastole treshold 
-            index1 = obj.SelectedPhase > treshold_diast; % frames with phase above the diastolic treshold
+            index1 = obj.Values > obj.DiastoleTreshold; % frames with phase above the diastolic treshold
             indexNumeric1 = find(index1);
-            values1 = obj.SelectedPhase(indexNumeric1);
+            values1 = obj.Values(indexNumeric1);
             [ordered_values1 oredered_index1] = sort(values1);
             obj.DiastolePositions = indexNumeric1(oredered_index1); % sorts the frames in ascending cardiac phase
         end
         
         % Detects the frame's positions of systolic events
         function Systole(obj)
-            min_heart_phase = min(obj.SelectedPhase); % cardiac phase minima
+            min_heart_phase = min(obj.Values); % cardiac phase minima
-            treshold_syst = 0.8*min_heart_phase; % systole treshold
+            obj.SystoleTreshold = 0.8*min_heart_phase; % systole treshold
-            index2 = obj.SelectedPhase < treshold_syst; % frames with phase below the systolic treshold
+            index2 = obj.Values < obj.SystoleTreshold; % frames with phase below the systolic treshold
             indexNumeric2 = find(index2);
-            values2 = obj.SelectedPhase(indexNumeric2);
+            values2 = obj.Values(indexNumeric2);
             [ordered_values2 oredered_index2] = sort(values2);
             obj.SystolePositions = indexNumeric2(oredered_index2); % sorts the frames in ascending cardiac phase
         end

Code/Phase.m

@@ -3,9 +3,10 @@ classdef Phase < handle
     properties 
         MeanIntensity = [];
         Video = [];
-        IMFs = [];
-        Values = [];
         WorkLoad = '';
+        IMFs = [];
+        ModePhases = [];
+        Values = [];
     end
     
     properties % (GetAccess = private) should become private
@@ -76,15 +77,19 @@ classdef Phase < handle
         
         % Apply Hilber Transform to all the IMFs and extract the
         % instantneous phase from each one of them
-        function GetPhase(obj)
+        function GetModes(obj)
             [number_imf lenght] = size(obj.IMFs);
             analytic_EMD = zeros(number_imf,lenght);
             for i=1:1:number_imf
                 analytic_EMD(i,:) = hilbert(obj.IMFs(i,:));  %Apply Hilbert Transform
-                obj.Values(i,:) = angle(analytic_EMD(i,:))/pi; % Get instataneous phase
+                obj.ModePhases(i,:) = angle(analytic_EMD(i,:))/pi; % Get instataneous phase
             end  
         end
         
+        function GetPhase(obj,imf)
+            obj.Values = obj.ModePhases(imf,:);
+        end
+        
         % Shows the frames of the original image sequence specified in the
         % array 'positions'
         function ShowFrames(obj,positions,title)
@@ -93,6 +98,10 @@ classdef Phase < handle
                 video = implay(triggered,3);
                 set(video.Parent, 'Name', title);
         end
+        
+        function Display(obj)
+            plot(obj.Values,'-s','LineWidth',0.8,'MarkerSize',4);
+        end
     
     end
 end

Code/RespiratoryPhase.m

@@ -1,16 +1,23 @@
 classdef RespiratoryPhase < Phase
     properties
         FullPhase = Phase;
-        SelectedPhase = [];
         InspirationPositions = [];
         ExpirationPositions = [];
     end
     
+    properties % (GetAccess = private) should become private
+        IMF = uint32(0);
+        InspirationTreshold = double(0);
+        ExpirationTreshold = double(0);
+        MaxRespPhase = double(0);
+        MinRespPhase = double(0);
+    end
+    
     methods %constructor
        function obj=RespiratoryPhase(Phase)
             if nargin==0;return;end
             % gets properties of superclass
-            obj.FullPhase = Phase.Values;
+            obj.FullPhase = Phase.ModePhases;
             obj.WorkLoad = Phase.WorkLoad;
             obj.Video = Phase.Video;
        end
@@ -26,30 +33,33 @@ classdef RespiratoryPhase < Phase
                     end
                 end
             end
-            obj.SelectedPhase = obj.FullPhase(imf_number,:); %Phase corresponding to respiratory phase
+            % SHOULD TRY TO USE GETPHASE FUNCTION
+%             obj.IMF = imf_number;
+%             GetPhase@Phase(obj.FullPhase,obj.IMF);
+            obj.Values = obj.FullPhase(imf_number,:); %Phase corresponding to respiratory phase
     end
         
         % Detects the frame's positions of inspiration moments
         function Inspiration(obj)
-            max_resp_phase = max(obj.SelectedPhase); % respiratory phase maxima
+            obj.MaxRespPhase = max(obj.Values); % respiratory phase maxima
-            treshold_insp = 0.8*max_resp_phase; % inspiration treshold 
+            obj.InspirationTreshold = 0.8*obj.MaxRespPhase; % inspiration treshold 
-            index1 = obj.SelectedPhase > treshold_insp; % frames above inpiration treshold
+            index1 = obj.Values > obj.InspirationTreshold; % frames above inpiration treshold
             indexNumeric1 = find(index1);
-            values1 = obj.SelectedPhase(indexNumeric1);
+            values1 = obj.Values(indexNumeric1);
             [ordered_values1 oredered_index1] = sort(values1);
             obj.InspirationPositions = indexNumeric1(oredered_index1); % sorts the frames in ascending respiratory phase
         end
         
         % Detects the frame's positions of expiration moments
         function Expiration(obj)
-            min_resp_phase = min(obj.SelectedPhase); % respiratory phase minima
+            obj.MinRespPhase = min(obj.Values); % respiratory phase minima
-            treshold_exp = 0.8*min_resp_phase; % systole treshold
+            obj.ExpirationTreshold = 0.8*obj.MinRespPhase; % systole treshold
-            index2 = obj.SelectedPhase < treshold_exp; % frames below the systole treshold
+            index2 = obj.Values < obj.ExpirationTreshold; % frames below the systole treshold
             indexNumeric2 = find(index2);
-            values2 = obj.SelectedPhase(indexNumeric2);
+            values2 = obj.Values(indexNumeric2);
             [ordered_values2 oredered_index2] = sort(values2);
             obj.ExpirationPositions = indexNumeric2(oredered_index2); % sorts the frames in ascending respiratory phase
         end
-            
+        
       end
 end

Code/test_OOP.m

@@ -1,16 +1,23 @@
 % Test Script
 
 % TO DO LIST:
-% - Display phases
 % - Heart beat reconstruction with steady respiratory phase
 % - Multislice analysis
+% - Choose IMF based on Instantaneous Frequency
 % - Error messages and robustness of the methods
 
 clear classes
 
+%% Extracts data
 phase = Phase; % creates a Phase object
 phase.GetData; % extracts data
 
+%% Time Information
+time = 0:1:phase.nFrames-1;
+repetitionTime = (1/15); % time between samples
+time = repetitionTime*time; % sampling moments in time
+
+%% Workload information
 % Should become a set method
 % User sets the workload, important to choose the correct IMF
 list = {'Rest','Exercise','Continuous Acquisition'};
@@ -18,17 +25,47 @@ list = {'Rest','Exercise','Continuous Acquisition'};
 str = list{indx};
 phase.WorkLoad = str;
 
-phase.GetSignal % gets mean intensity level of the images
+%% Instantaneous Phase Extraction (cardiac ad respiratory)
-phase.GetEMD % decompose the siganl using EMD
+phase.GetSignal; % gets mean intensity level of the images
-phase.GetPhase % turn the modes into phase information
+phase.GetEMD; % decompose the siganl using EMD
+phase.GetModes; % turn the modes into phase information
 
-cardiac_phase = CardiacPhase(phase) % creates a CradiacPhase object
+cardiac_phase = CardiacPhase(phase); % creates a CradiacPhase object
-cardiac_phase.SelectPhase % choose the right imf besed on the work load
+cardiac_phase.SelectPhase; % choose the right imf besed on the work load IMPROVE
+
+respiratory_phase = RespiratoryPhase(phase); % creates a RespiratoryPhase object
+respiratory_phase.SelectPhase; % choose the right imf based on the work load IMPROVE
+
+cardiac_phase.Display
+hold on
+respiratory_phase.Display
+% hold on
+% hline = refline([0 cardiac_phase.SystoleTreshold]); % Reference line for systole treshold phase
+% hline.Color = 'b';
+% hline.LineStyle = ':';
+% hold on
+% hline = refline([0 cardiac_phase.DiastoleTreshold]); % Reference line for diastole treshold phase
+% hline.Color = 'b';
+% hline.LineStyle = ':'
+% hold on
+% hline = refline([0 respiratory_phase.InspirationTreshold]); % Reference line for systole treshold phase
+% hline.Color = 'r';
+% hline.LineStyle = ':';
+% hold on
+% hline = refline([0 respiratory_phase.ExpirationTreshold]); % Reference line for diastole treshold phase
+% hline.Color = 'r';
+% hline.LineStyle = ':';
+title('Cardiac and Respiratory Phase');
+legend('Cardiac Phase','Respiratory Phase');
+te=repetitionTime;
+xt=get(gca,'xtick');
+set(gca,'xticklabel',arrayfun(@num2str,xt*te,'un',0)); % adjust x axis to time values
+xlabel('Time (sec)');
+ylabel('Phase(rad)');
+
+%% Cardiac and Respiratory events
 cardiac_phase.Diastole % detects diastolic events
 cardiac_phase.Systole % detects systolic events
-
-respiratory_phase = RespiratoryPhase(phase) % creates a RespiratoryPhase object
-respiratory_phase.SelectPhase % choose the right imf besed on the work load
 respiratory_phase.Expiration % detects expirtion moments
 respiratory_phase.Inspiration % detects inspiration moments
 
@@ -43,6 +80,27 @@ phase.ShowFrames(SE,'End-systolic frames in expiration');
 phase.ShowFrames(DI,'End-diastolic frames in inpiration');
 phase.ShowFrames(DE,'End-diastolic frames in expiration');
 
+%% Heart Beat Reconstruction
+n_ranges = 30; % number of phase ranges
+ranges = linspace(respiratory_phase.MinRespPhase,respiratory_phase.MaxRespPhase,n_ranges+1); % splits the respiratory phase in n_ranges equal parts
+for i=1:1:n_ranges
+    Ltreshold = ranges(i);
+    Utreshold = ranges(i+1);
+    index(i,:) = respiratory_phase.Values < Utreshold & respiratory_phase.Values > Ltreshold; % the respiratory phase is within the upper and lower treshold of this range
+    indexNumeric{i} = find(index(i,:)); % indexes of the frames satifying the previous condition
+    if iscolumn(indexNumeric{i})
+        indexNumeric{i} = indexNumeric{i}.'; % puts the indexes in a vector
+    end
+    values{i} = cardiac_phase.Values(indexNumeric{i}); % cardiac phase values of frames within this respiratory range
+    % Sorts cardiac phase values and their indexes by ascending cardiac phase
+    [ordered_values{i}, oredered_index{i}] = sort(values{i});
+    k = indexNumeric{i};
+    j = oredered_index{i};
+    new_index{i} = k(j); % ordered indexes
+end
+selected_range = n_ranges-2;
+phase.ShowFrames(new_index{selected_range},'Heart Beat Reconstruction');
+
 % c = ImageSequence
 % c.ToBeSetByUser=15
 % c.ToBeSetByUser=true