From 442a49fc0378ab591baba7ce822699a000b09824 Mon Sep 17 00:00:00 2001
From: Waddah Moghram <waddah.moghram@gmail.com>
Date: Thu, 7 Mar 2019 11:25:33 -0600
Subject: [PATCH 1/2] Update setROIfromForcemap.m

Unable to open ROI is stage drift stage was not done. Error  in opening reference frame
---
 software/setROIfromForcemap.m | 24 ++++++++++++++++++------
 1 file changed, 18 insertions(+), 6 deletions(-)

diff --git a/software/setROIfromForcemap.m b/software/setROIfromForcemap.m
index 6bb59a6..d4b3e22 100644
--- a/software/setROIfromForcemap.m
+++ b/software/setROIfromForcemap.m
@@ -34,12 +34,18 @@
     displProc = tfmPackage.getProcess(2);
 end
 displField=displProc.loadChannelOutput;
-% SDC proc
-try
-    SDCProc = tfmPackage.getProcess(1);
-catch
+% % SDC proc---------------
+% % Lines below commented out and corrected by Waddah Moghram on 2/18/2019
+% try
+%     SDCProc = tfmPackage.getProcess(1);
+% catch
+%     SDCProc = tfmPackage.getProcess(2);
+% end
+SDCProc = tfmPackage.getProcess(1);
+if isempty(SDCProc)                     % No Stage Drift Step was Done
     SDCProc = tfmPackage.getProcess(2);
 end
+%-----------------------
 % Get force map
 % try
 %     tMap = load(forceProc.outFilePaths_{2});
@@ -63,7 +69,10 @@
 %     tMap = load(forceProc.outFilePaths_{2});
 %     tMap = tMap.tMap;
 % end
-refFrame = double(imread(SDCProc.outFilePaths_{2,1}));
+%---------------- Corrected by Waddah Moghram. Should be reference frame, not dispMaps.mat on 2/18/2019
+% refFrame = double(imread(SDCProc.outFilePaths_{2,1}));
+refFrame =  imread(SDCProc.funParams_.referenceFramePath);
+%----------------------------------
 
 % Use mask of first frame to filter bead detection
 firstMask = refFrame>0; %false(size(refFrame));
@@ -80,7 +89,10 @@
 else
     roiMask=imread(MD.roiMaskPath_);
     boundROI=bwboundaries(roiMask);
-    hold on, plot(boundROI{1}(:,2),boundROI{1}(:,1),'w')
+    % ----- if-statement added by Waddah Moghram on 2/18/2019
+    if ~isempty(boundROI)
+        hold on, plot(boundROI{1}(:,2),boundROI{1}(:,1),'w')
+    end % -------------------------
     h=imrect;
 end
 ROI_rect = wait(h);

From 99541fcc2f3cdbabd535ba8811fe8212090089bc Mon Sep 17 00:00:00 2001
From: Waddah Moghram <waddah.moghram@gmail.com>
Date: Thu, 7 Mar 2019 11:38:55 -0600
Subject: [PATCH 2/2] Update setROIfromForcemap.m

Fixes the following Error:
=====================
tfmPackage=MD.getPackage(MD.getPackageIndex('TFMPackage'));
K>> displProc
displProc =
     []
Dot indexing is not supported for variables of this type.
Error in setROIfromForcemap (line 36)
displField=displProc.loadChannelOutput;
Error in forceFieldCalculationProcessGUI>setROIfromForcemap_Callback (line 359)
    setROIfromForcemap(MD);
Error in gui_mainfcn (line 95)
        feval(varargin{:});
Error in forceFieldCalculationProcessGUI (line 62)
        gui_mainfcn(gui_State, varargin{:});
Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)forceFieldCalculationProcessGUI('setROIfromForcemap_Callback',hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback.
=====================================================
---
 software/setROIfromForcemap.m | 35 +++++++----------------------------
 1 file changed, 7 insertions(+), 28 deletions(-)

diff --git a/software/setROIfromForcemap.m b/software/setROIfromForcemap.m
index d4b3e22..82dfc06 100644
--- a/software/setROIfromForcemap.m
+++ b/software/setROIfromForcemap.m
@@ -28,19 +28,15 @@
 forceProc = tfmPackage.getProcess(4);
 p = forceProc.funParams_;
 % Load displ process
-try
-    displProc = tfmPackage.getProcess(3);
-catch
+% ---------- Modified by Waddah Moghram on 3/7/2019 
+displProc = tfmPackage.getProcess(3);
+if isempty(displProc)      % No correction to displacement step
     displProc = tfmPackage.getProcess(2);
 end
 displField=displProc.loadChannelOutput;
+%------------------------------------
 % % SDC proc---------------
-% % Lines below commented out and corrected by Waddah Moghram on 2/18/2019
-% try
-%     SDCProc = tfmPackage.getProcess(1);
-% catch
-%     SDCProc = tfmPackage.getProcess(2);
-% end
+% ----------- Lines below commented out and corrected by Waddah Moghram on 3/7/2019
 SDCProc = tfmPackage.getProcess(1);
 if isempty(SDCProc)                     % No Stage Drift Step was Done
     SDCProc = tfmPackage.getProcess(2);
@@ -69,8 +65,7 @@
 %     tMap = load(forceProc.outFilePaths_{2});
 %     tMap = tMap.tMap;
 % end
-%---------------- Corrected by Waddah Moghram. Should be reference frame, not dispMaps.mat on 2/18/2019
-% refFrame = double(imread(SDCProc.outFilePaths_{2,1}));
+%---------------- Corrected by Waddah Moghram. Should be reference frame, not dispMaps.mat on 3/7/2019
 refFrame =  imread(SDCProc.funParams_.referenceFramePath);
 %----------------------------------
 
@@ -89,7 +84,7 @@
 else
     roiMask=imread(MD.roiMaskPath_);
     boundROI=bwboundaries(roiMask);
-    % ----- if-statement added by Waddah Moghram on 2/18/2019
+    % ----- if-statement added by Waddah Moghram on 3/7/2019
     if ~isempty(boundROI)
         hold on, plot(boundROI{1}(:,2),boundROI{1}(:,1),'w')
     end % -------------------------
@@ -107,19 +102,3 @@
 % maskArray = MD.getROIMask;
 close(h2)
 disp('ROI created!')
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