From 759699c3a731f1636964b02826a4769af2911dc4 Mon Sep 17 00:00:00 2001
From: Waddah Moghram <16141123+wmoghram@users.noreply.github.com>
Date: Fri, 26 Apr 2019 04:39:36 -0500
Subject: [PATCH] Errors when no outliers are detected in first frame

MATLAB Version 9.5.0.1067069 (R2018b) Update 4
MATLAB License Number: 837756
Operating System: Microsoft Windows 7 Professional  Version 6.1 (Build 7601: Service Pack 1)
Java VM Version: Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Movie 1 - Y:\Waddah\Official TFM Videos 3\Bead 2\Displacement Control\Displacement Control Bead 2 Epi ROI\movieData.mat:

-- Step 3: Displacement Field Correction

Error using detectVectorFieldOutliersTFM (line 145)
Matrix dimensions must agree.
Error in correctMovieDisplacementField (line 140)
parfor j= 1:nFrames
Error in Process/run (line 254)
                obj.funName_(obj.getOwner(), varargin{:});
Error in packageGUI_RunFcn>userfcn_runProc_dfs (line 633)
        userData.crtPackage.processes_{procID}.run(); % throws exception
Error in packageGUI_RunFcn>start_processing_movies_in_series (line 217)
                userfcn_runProc_dfs(procID, procRun{iMovie}, handles); % user data is retrieved, updated and submitted
Error in packageGUI_RunFcn (line 162)
        movieException = start_processing_movies_in_series(movieRun,handles,movieException,procRun);
Error in packageGUI_OpeningFcn>@(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)) (line 380)
    set(handles.pushbutton_run, 'Callback', @(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)));
======================================================================================================================

MATLAB Version 9.5.0.1067069 (R2018b) Update 4
MATLAB License Number: 837756
Operating System: Microsoft Windows 7 Professional  Version 6.1 (Build 7601: Service Pack 1)
Java VM Version: Java 1.8.0_152-b16 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode
Movie 1 - Y:\Waddah\Official TFM Videos 3\Bead 2\Displacement Control\Displacement Control Bead 2 Epi ROI\movieData.mat:

-- Step 3: Displacement Field Correction

Error using >
Matrix dimensions must agree.
Error in detectVectorFieldOutliersTFM (line 145)
    idAwayVectors = distance2>neighborhood_distance | isnan(distance2);
Error in correctMovieDisplacementField (line 155)
            [outlierIndex,sparselyLocatedIdx,~,neighborhood_distance(j)] = detectVectorFieldOutliersTFM(dispMat,outlierThreshold,1);
Error in Process/run (line 254)
                obj.funName_(obj.getOwner(), varargin{:});
Error in packageGUI_RunFcn>userfcn_runProc_dfs (line 633)
        userData.crtPackage.processes_{procID}.run(); % throws exception
Error in packageGUI_RunFcn>start_processing_movies_in_series (line 217)
                userfcn_runProc_dfs(procID, procRun{iMovie}, handles); % user data is retrieved, updated and submitted
Error in packageGUI_RunFcn (line 162)
        movieException = start_processing_movies_in_series(movieRun,handles,movieException,procRun);
Error in packageGUI_OpeningFcn>@(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)) (line 380)
    set(handles.pushbutton_run, 'Callback', @(hObject,eventdata)packageGUI_RunFcn(hObject,eventdata,guidata(hObject)));
---
 software/detectVectorFieldOutliersTFM.m | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/software/detectVectorFieldOutliersTFM.m b/software/detectVectorFieldOutliersTFM.m
index e1a039f..ba3b0ed 100644
--- a/software/detectVectorFieldOutliersTFM.m
+++ b/software/detectVectorFieldOutliersTFM.m
@@ -135,13 +135,19 @@
 % elseif n==1 && fitError
 %     threshDist = 2*mean(distance2);
 % end
+
+% ----------- DeBugged by Waddah Moghram on 4/27/2019
 threshDist = nanmean(distance2)+2*nanstd(distance2);
-idxCloseVectors = distance2<threshDist & ~isnan(distance2);
-neighborhood_distance = 5*max(distance2(idxCloseVectors));%quantile(distance,0.95);%mean(distance);%size(refFrame,1)*size(refFrame,2)/length(beads);
-idAwayVectors = distance2>neighborhood_distance | isnan(distance2);
-idxCloseEnoughVectors = distance2<neighborhood_distance & ~isnan(distance2);
+idxCloseVectors = (distance2 < threshDist) & ~isnan(distance2);                      
+neighborhood_distance = 5*max(distance2(idxCloseVectors));                           %quantile(distance,0.95);%mean(distance);%size(refFrame,1)*size(refFrame,2)/length(beads); 
+if isempty(neighborhood_distance)
+   neighborhood_distance = 0;
+end
+idAwayVectors = (distance2>neighborhood_distance) | isnan(distance2);
+idxCloseEnoughVectors = (distance2<neighborhood_distance) & ~isnan(distance2);          % Fixed by Waddah Moghram on 4/26/2019. added parantheses
 dataFiltered = dataU(idxCloseEnoughVectors,:);
 idCloseEnoughVectors = find(idxCloseEnoughVectors);
+%------------------------------------
 
 % Find neighbors and distances
 % [idx,neiDist] = KDTreeBallQuery(data(:,1:2), data(:,1:2), neighborhood_distance);
@@ -208,4 +214,4 @@
 % Filter outliers using threshold
 % outlierIndex = ind(idata([idCloseVectors(r.^(1/2).*(rOri/critAng).^1.5>threshold)]));
 outlierIndex = ind(idata(idCloseEnoughVectors(r>threshold)));
-sparseIndex = ind(idata(idAwayVectors));
\ No newline at end of file
+sparseIndex = ind(idata(idAwayVectors));