Reuben hill/updates

DIGIGUI.prj

@@ -1,5 +1,5 @@
 <deployment-project plugin="plugin.ezdeploy" plugin-version="1.0">
-  <configuration build-checksum="222460721" file="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI\DIGIGUI.prj" location="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI" name="DIGIGUI" preferred-package-location="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI\DIGIGUI\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
+  <configuration build-checksum="187533882" file="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI\DIGIGUI.prj" location="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI" name="DIGIGUI" preferred-package-location="C:\Users\Reuben\Documents\GitHub\Polhemus-GUI\DIGIGUI\for_redistribution" preferred-package-type="package.type.exe" target="target.ezdeploy.standalone" target-name="Application Compiler">
     <param.appname>DIGIGUI</param.appname>
     <param.icon>${PROJECT_ROOT}\DIGIGUI_resources\icon.ico</param.icon>
     <param.icons>
@@ -8,12 +8,12 @@
       <file>${PROJECT_ROOT}\DIGIGUI_resources\icon_24.png</file>
       <file>${PROJECT_ROOT}\DIGIGUI_resources\icon_16.png</file>
     </param.icons>
-    <param.version>1.2</param.version>
+    <param.version>1.3</param.version>
     <param.authnamewatermark>Reuben Nixon-Hill</param.authnamewatermark>
     <param.email>reuben.w.hill@gmail.com</param.email>
     <param.company />
     <param.summary>A graphical user interface for use with the Polhemus Patriot Digitiser at a baud rate of 115200.</param.summary>
-    <param.description>Version 1.2.1.
+    <param.description>Version 1.3.0-gamma2.
 Copyright © 2023 Reuben Nixon-Hill, MATLAB® © 1984 - 2016 The MathWorks, Inc.
 This package is licenced under the MIT Licence (see LICENCE.txt) and was created using MATLAB® compiler.</param.description>
     <param.screenshot />
@@ -38,9 +38,9 @@ This package is licenced under the MIT Licence (see LICENCE.txt) and was created
     <param.web.mcr.name>DIGIGUI_web</param.web.mcr.name>
     <param.package.mcr.name>DIGIGUI_mcr</param.package.mcr.name>
     <param.no.mcr.name>MyAppInstaller_app</param.no.mcr.name>
-    <param.windows.command.prompt>true</param.windows.command.prompt>
-    <param.create.log>false</param.create.log>
-    <param.log.file>log</param.log.file>
+    <param.windows.command.prompt>false</param.windows.command.prompt>
+    <param.create.log>true</param.create.log>
+    <param.log.file>log.txt</param.log.file>
     <unset>
       <param.company />
       <param.screenshot />
@@ -61,25 +61,30 @@ This package is licenced under the MIT Licence (see LICENCE.txt) and was created
       <param.package.mcr />
       <param.no.mcr />
       <param.no.mcr.name />
-      <param.windows.command.prompt />
-      <param.create.log />
     </unset>
     <fileset.main>
       <file>${PROJECT_ROOT}\DIGIGUI.m</file>
     </fileset.main>
     <fileset.resources>
-      <file>${PROJECT_ROOT}\DIGIGUI.fig</file>
-      <file>${PROJECT_ROOT}\refpts_landmarks.mat</file>
-      <file>${PROJECT_ROOT}\scalpSurfaceMesh.mat</file>
+      <file>${PROJECT_ROOT}\default_atlas\atlas_landmarks.mat</file>
+      <file>${PROJECT_ROOT}\default_atlas\CoordinateTransform.m</file>
+      <file>${PROJECT_ROOT}\default_atlas\mesh.mat</file>
+      <file>${PROJECT_ROOT}\default_settings.mat</file>
+      <file>${PROJECT_ROOT}\savedLocationNames.mat</file>
     </fileset.resources>
     <fileset.package>
+      <file>${PROJECT_ROOT}\default_atlas</file>
+      <file>${PROJECT_ROOT}\expected_coordinates_example.txt</file>
       <file>${PROJECT_ROOT}\LICENCE.txt</file>
       <file>${PROJECT_ROOT}\Locations Example.txt</file>
       <file>${PROJECT_ROOT}\Readme.txt</file>
     </fileset.package>
     <fileset.depfun>
       <file>${PROJECT_ROOT}\affine_trans_RJC.m</file>
       <file>${PROJECT_ROOT}\affinemap.m</file>
+      <file>${PROJECT_ROOT}\checkmark.tif</file>
+      <file>${PROJECT_ROOT}\DIGIGUI.fig</file>
+      <file>${PROJECT_ROOT}\doubletapdialog.m</file>
       <file>${PROJECT_ROOT}\FindPatriotSerial.m</file>
     </fileset.depfun>
     <build-deliverables>

Polhemus_Headmesh_Process.m

@@ -1,6 +1,6 @@
 % Head mesh transformation sequence for polhemus gui
 % landmarks = Inion, Nasion, Ar, Al, Cz measured with Polhemus
-% pts = landmarks of atlas (from refpts_landmarks.mat)
+% pts = landmarks of atlas (from default_atlas/atlas_landmarks.mat)
 % mesh = adult atlas scalp mesh
 
 [A,B] = affinemap(pts,landmarks);

README.md

@@ -13,6 +13,6 @@ For more information see the comments in `DIGIGUI.m`.
 
 This has been designed for use with MATLAB compiler using the `DIGIGUI.prj` file.
 
-Copyright (C) 2022 Reuben W. Nixon-Hill (formerly Reuben W. Hill)
+Copyright (C) 2023 Reuben W. Nixon-Hill (formerly Reuben W. Hill)
 
 This package is licenced under the MIT Licence (see LICENCE.txt).

default_atlas/CoordinateTransform.m

@@ -0,0 +1,65 @@
+%This function outputs a vector to transform inion to origin
+%also outputs rotation transformation matrix to allign the head model to
+%intuitive coordinates.
+%To apply to row vector, the vector should be multiplied by the transpose
+%with the vector on the left
+function [Matrix,vector] = CoordinateTransform(landmarks)
+  %calculate lengths between vectors
+
+  %these are the untransformed reference points, defined here in case I want
+  %to use them
+  Nasion = landmarks(1,:);
+  Inion = landmarks(2,:);
+  Ar = landmarks(3,:);
+  Al = landmarks(4,:);
+  Cz = landmarks(5,:);
+
+  %------TRANSLATION-------
+
+  %translate inion to origion
+  vector = -Inion;
+
+  %translate Al
+  Al = Al + vector;
+
+  %------ROTATE AL TO Y AXIS-------
+
+  %calculate rotation to y axis
+  AlToYAxisRot = vrrotvec(Al,[0,1,0]);
+
+  %convert to rotation matrix
+  AlToYAxisMatrix = vrrotvec2mat(AlToYAxisRot);
+
+  %repmat
+  % Apply translation and rotation to points
+  for k = 1:5
+      landmarks(k,:) = landmarks(k,:)+vector;
+      landmarks(k,:) = landmarks(k,:)*AlToYAxisMatrix';
+  end
+
+  %------ROTATE AR TO XY PLANE ABOUT INION-AL AXIS-------
+
+  % find angle to rotate nasion into XY plane about the new y axis
+  [ArToXYRotAngle,~] = cart2pol(landmarks(3,1),landmarks(3,3));
+
+  %Find second rotation matrix
+  ArToXYMatrix = vrrotvec2mat([0,1,0,ArToXYRotAngle]);
+
+  % Apply second rotation to points
+  for k = 1:5
+      landmarks(k,:) = landmarks(k,:)*ArToXYMatrix';
+  end
+
+  %------FINAL ROTATION ABOUT AL-AR AXIS TO ALLIGN INION AND NASION-------
+
+  %find angle of nasion to xy plane
+  [~,NasionToXYRotAngle,~] = cart2sph(landmarks(1,1),landmarks(1,2),landmarks(1,3));
+  %define vector to rotate around (the line joining AL and AR)
+  NasionRotVector = landmarks(4,:) - landmarks(3,:);
+  %find rotation matrix
+  NasionToXYRotMatrix = vrrotvec2mat([NasionRotVector, NasionToXYRotAngle]);
+
+  %------OUTPUT FINAL MATRIX-------
+  Matrix = NasionToXYRotMatrix*ArToXYMatrix*AlToYAxisMatrix;
+
+end

doubletapdialog.m

@@ -0,0 +1,64 @@
+function [choice, enabled] = doubletapdialog(currentchoice, currentenabled)
+
+    d = dialog('Position',[300 300 260 180],'Name','Double tap');
+
+    checkbox = uicontrol('Parent', d, ...
+            'Style', 'checkbox', ...
+            'String', 'Enable double tap error?', ...
+            'Position', [68 70 200 170], ...
+            'Value', currentenabled, ...
+            'Callback', @checkbox_callback);
+
+    slider = uicontrol('Parent',d,...
+           'Style','slider',...
+           'Position',[31 60 200 25],...
+           'Min',0,...
+           'Max',1,...
+           'Value', currentchoice,...
+           'Callback',@slider_callback);
+
+    txt = uicontrol('Parent',d,...
+           'Style','text',...
+           'Position',[31 100 210 30],...
+           'String', sprintf('Use slider to set error distance.\nCurrent value: %0.2g cm.', currentchoice));
+
+    fun = @(~,e)set(txt,'String',sprintf('Use slider to set error distance.\nCurrent value: %0.2g cm.', get(e.AffectedObject,'Value')));
+
+    addlistener(slider, 'Value', 'PostSet', fun);
+
+    btn = uicontrol('Parent',d,...
+           'Position',[99 20 70 25],...
+           'String','Close',...
+           'Callback','delete(gcf)');
+
+    choice = currentchoice;
+    enabled = currentenabled;
+
+    if currentenabled
+        set(txt,'Enable','on');
+        set(slider,'Enable','on');
+    else
+        set(txt,'Enable','off');
+        set(slider,'Enable','off');
+    end
+
+    % Wait for d to close before running to completion
+    uiwait(d);
+
+
+    function slider_callback(slider,event)
+        choice = slider.Value;
+    end
+
+    function checkbox_callback(checkbox,event)
+        enabled = checkbox.Value;
+        if enabled
+            set(txt,'Enable','on');
+            set(slider,'Enable','on');
+        else
+            set(txt,'Enable','off');
+            set(slider,'Enable','off');
+        end
+    end
+
+end

expected_coordinates_example.txt

@@ -0,0 +1,5 @@
+Location,X,Y,Z
+Nasion,15.0,0,0
+Ar,0,0,0
+Example Pt 1,20.0,0,0
+Tolerance,10,NaN,NaN