From ff428e9943d4d33f8db1e8bdcee19b2516379979 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 14:45:53 +0100
Subject: [PATCH 01/43] funciton name correction

---
 Browsing Functions/AtlasTransformBrowser.m | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 5cf501c..a93b803 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -1,4 +1,4 @@
-function f = allenAtlasBrowser(f, templateVolume, annotationVolume, structureTree, slice_figure, save_location, save_suffix, plane)
+function f = AtlasTransformBrowser(f, templateVolume, annotationVolume, structureTree, slice_figure, save_location, save_suffix, plane)
 % ------------------------------------------------
 % Browser for the allen atlas ccf data in matlab.
 % ------------------------------------------------
@@ -359,7 +359,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
                 template_point = 1; template_points_shown = 0;
                 updateBoundaries(f,ud, allData); ud = get(f, 'UserData');
             end
-        else; disp('transform point mode OFF');    
+        else; disp('transform point mode OFF');
         end     
 % a -- toggle viewing of annotation boundaries  
     case 'a' 
@@ -432,7 +432,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             ud.slice_at_shift_start = ud_slice.slice_num;
             ud.slice_shift = 0;
         end
-        disp('switch scroll mode -- scroll along slice images')     
+        disp('switch scroll mode -- scroll along slice images')
 % h -- toggle viewing of histology / histology overlay
     case 'h'
         disp('  ');
@@ -732,7 +732,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
   
 % scroll through slices (left arrow pressed)
 elseif ud.scrollMode == 3
-  set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+        set(ud.pointHands_for_transform(:), 'Visible', 'off');
   ud.showOverlay = 0;
   delete(ud.overlayAx); ud.overlayAx = [];  
   ud_slice = get(slice_figure, 'UserData');
@@ -776,7 +776,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
             ud.current_pointList_for_transform = transform_data.transform_points{1};
             ud_slice.pointList = transform_data.transform_points{2};
         else
-            ud_slice.pointList = [];           
+            ud_slice.pointList = [];
         end
         set(slice_figure, 'UserData', ud_slice);
         

From 5d6e40916bcf4238f4385c60369faaf662c49d75 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 14:49:32 +0100
Subject: [PATCH 02/43] load and show saved slice points

---
 Browsing Functions/sliceBrowser.m | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index e190b6e..9711a15 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -45,6 +45,9 @@ function sliceClickCallback(im, keydata)
 f = get(get(im, 'Parent'), 'Parent');
 ud = get(f, 'UserData');
 
+if isempty(ud.pointHands)
+    ud.pointHands = gobjects(0);
+end
 
 if ud.getPoint
     clickX = round(keydata.IntersectionPoint(1));
@@ -127,7 +130,13 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
     file_transformations = fullfile(ud.processed_images_folder, 'transformations\\' ,...
                             [processed_image_name(1:end-4) '_transform_data.mat']);
 
-    set(ud.pointHands(:), 'Visible', 'off'); 
+    try
+        delete(findobj(ud.im.Parent, 'Type','line','color',[0 0.5 0],'Marker','o')); % delete all the circles
+    end
+
+    ud.pointHands = gobjects(0);
+    % set(ud.pointHands(:), 'Visible', 'off'); %TODO WHY hiding? Maybe you
+    % want to delete/initialize them? ud is from fig.UserData
     ud.pointList = [];
     
     if exist(file_transformations,'file')
@@ -136,6 +145,9 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
         transform_data = transform_data.save_transform;
         if ~isempty(transform_data.transform_points{2})
             ud.pointList = transform_data.transform_points{2};
+            for i = 1:size(ud.pointList,1)
+                ud.pointHands(end+1) = plot(ud.sliceAx, ud.pointList(i,1), ud.ref_size(1) - ud.pointList(i,2), 'ro', 'color', [0 .5 0],'linewidth',2,'markers',4);
+            end
             title_ending = ' (transform points loaded)';
         end       
     end

From 0f801272106f69aa4e88877d70022c5cb2f68d51 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 14:56:15 +0100
Subject: [PATCH 03/43] show scroll mode as XLabel

---
 Browsing Functions/AtlasTransformBrowser.m | 37 +++++++++++++++++++---
 1 file changed, 33 insertions(+), 4 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 5cf501c..ad41e47 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -79,6 +79,15 @@
 set(f, 'WindowScrollWheelFcn', @(src,evt)updateSlice(f, evt, allData, slice_figure, save_location))
 set(f, 'WindowButtonMotionFcn',@(f,k)fh_wbmfcn(f, allData, slice_figure, save_location)); % Set the motion detector.
 
+ud.atlasAx.XLabel.Visible = 'on';
+if strcmp(ud.plane,'coronal')
+    xlabel(ud.atlasAx, 'Scroll slices along A/P axis')
+elseif strcmp(ud.plane,'sagittal')
+    xlabel(ud.atlasAx, 'Scroll slices along M/L axis')
+elseif strcmp(ud.plane,'transverse')
+    xlabel(ud.atlasAx, 'Scroll slices along D/V axis')
+end
+
 % display user controls in the console
 function display_controls(plane)
 fprintf(1, '\n Controls: \n');
@@ -359,7 +368,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
                 template_point = 1; template_points_shown = 0;
                 updateBoundaries(f,ud, allData); ud = get(f, 'UserData');
             end
-        else; disp('transform point mode OFF');    
+        else; disp('transform point mode OFF');
         end     
 % a -- toggle viewing of annotation boundaries  
     case 'a' 
@@ -402,29 +411,47 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
         ud.scrollMode = 1;
         if strcmp(ud.plane,'coronal')
             disp('switch scroll mode -- tilt D/V')
+            xlabel(ud.atlasAx, 'Scroll to tilt D/V')
+
         elseif strcmp(ud.plane,'sagittal')
             disp('switch scroll mode -- tilt D/V')
+            xlabel(ud.atlasAx, 'Scroll to tilt D/V')
+
         elseif strcmp(ud.plane,'transverse')
             disp('switch scroll mode -- tilt M/L')
+            xlabel(ud.atlasAx, 'Scroll to tilt M/L')
+
         end
     case 'rightarrow' % scroll angles along A/P axis
         ud.scrollMode = 2;
         if strcmp(ud.plane,'coronal')
             disp('switch scroll mode -- tilt M/L')
+            xlabel(ud.atlasAx, 'Scroll to tilt M/L')
+
         elseif strcmp(ud.plane,'sagittal')
             disp('switch scroll mode -- tilt A/P')
+            xlabel(ud.atlasAx, 'Scroll to tilt A/P')
+
         elseif strcmp(ud.plane,'transverse')
             disp('switch scroll mode -- tilt A/P')
+            xlabel(ud.atlasAx, 'Scroll to tilt A/P')
+
         end
         
     case 'downarrow' % scroll along A/P axis
         ud.scrollMode = 0;
         if strcmp(ud.plane,'coronal')
             disp('switch scroll mode -- scroll along A/P axis')
+            xlabel(ud.atlasAx, 'Scroll slices along A/P axis')
+
         elseif strcmp(ud.plane,'sagittal')
             disp('switch scroll mode -- scroll along M/L axis')
+            xlabel(ud.atlasAx, 'Scroll slices along M/L axis')
+
         elseif strcmp(ud.plane,'transverse')
             disp('switch scroll mode -- scroll along D/V axis')
+            xlabel(ud.atlasAx, 'Scroll slices along D/V axis')
+
         end
     case 'leftarrow' % scroll along A/P axis
         ud.scrollMode = 3;
@@ -432,7 +459,9 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             ud.slice_at_shift_start = ud_slice.slice_num;
             ud.slice_shift = 0;
         end
-        disp('switch scroll mode -- scroll along slice images')     
+        disp('switch scroll mode -- scroll along slice images')
+        xlabel(ud.atlasAx, 'Scroll along slice images')
+
 % h -- toggle viewing of histology / histology overlay
     case 'h'
         disp('  ');
@@ -732,7 +761,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
   
 % scroll through slices (left arrow pressed)
 elseif ud.scrollMode == 3
-  set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+        set(ud.pointHands_for_transform(:), 'Visible', 'off');
   ud.showOverlay = 0;
   delete(ud.overlayAx); ud.overlayAx = [];  
   ud_slice = get(slice_figure, 'UserData');
@@ -776,7 +805,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
             ud.current_pointList_for_transform = transform_data.transform_points{1};
             ud_slice.pointList = transform_data.transform_points{2};
         else
-            ud_slice.pointList = [];           
+            ud_slice.pointList = [];
         end
         set(slice_figure, 'UserData', ud_slice);
         

From 575599bd12b75ad3aaa0b20241b7fef6a41bcf2c Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 15:01:59 +0100
Subject: [PATCH 04/43] use graphic objects

---
 Browsing Functions/AtlasTransformBrowser.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 5cf501c..eca9bc4 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -36,7 +36,8 @@
 ud.probe_view_mode = false;
 ud.currentProbe = 0; ud.ProbeColors = [1 1 1; 1 .75 0;  .3 1 1; .4 .6 .2; 1 .35 .65; .7 .7 1; .65 .4 .25; .7 .95 .3; .7 0 0; .5 0 .6; 1 .6 0]; 
 ud.ProbeColor =  {'white','gold','turquoise','fern','bubble gum','overcast sky','rawhide', 'green apple','red','purple','orange'};
-ud.getPoint_for_transform =false; ud.pointList_for_transform = zeros(0,2); ud.pointHands_for_transform = [];
+ud.getPoint_for_transform =false; ud.pointList_for_transform = zeros(0,2); 
+ud.pointHands_for_transform = gobjects(0);
 ud.current_pointList_for_transform = zeros(0,2); ud.curr_slice_num = 1;
 ud.clicked = false;
 ud.showAtlas = false;

From e9e1f10476cd90521f4ed4680dd13dd1c6dc9a2d Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 15:04:26 +0100
Subject: [PATCH 05/43] load and show saved atlas points

---
 Browsing Functions/AtlasTransformBrowser.m | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index eca9bc4..22e8050 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -775,6 +775,16 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
         
         if ~isempty(transform_data.transform_points{1}) && ~isempty(transform_data.transform_points{2})
             ud.current_pointList_for_transform = transform_data.transform_points{1};
+            delete(ud.pointHands_for_transform);% delete them %TODO not working
+            ud.pointHands_for_transform = gobjects(0);% initialize
+            for i = 1:size(ud.current_pointList_for_transform,1)
+                ud.pointHands_for_transform(i) = plot(ud.atlasAx, ...
+                    ud.current_pointList_for_transform(i,1), ...
+                    ud.current_pointList_for_transform(i,2), ...
+                    'ro', 'color', [.7 .3 .3],'LineWidth',2,'markers',4);
+            end
+            set(ud.pointHands_for_transform(end),'color', [0 .9 0]);
+
             ud_slice.pointList = transform_data.transform_points{2};
         else
             ud_slice.pointList = [];           

From 2d8497dde2d2f20aced4bf72c7e7e6dcd8b10d6c Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 25 Jul 2022 15:19:42 +0100
Subject: [PATCH 06/43] chabge ud.pointHands_for_transform to grahic objects
 error handling

---
 Browsing Functions/AtlasTransformBrowser.m | 44 +++++++++++++++++-----
 1 file changed, 35 insertions(+), 9 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 22e8050..efd1992 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -355,12 +355,27 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             if ~size(ud.current_pointList_for_transform,1)% ) (ud.curr_slice_num ~= (ud.slice_at_shift_start+ud.slice_shift) ||  && ~ud.loaded 
                 ud.curr_slice_num = ud.slice_at_shift_start+ud.slice_shift; %ud_slice.slice_num;
                 ud.current_pointList_for_transform = zeros(0,2);
+                try
                 set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+                catch
+                end
                 num_hist_points = size(ud_slice.pointList,1);
                 template_point = 1; template_points_shown = 0;
                 updateBoundaries(f,ud, allData); ud = get(f, 'UserData');
+            else
+                try
+                set(ud.pointHands_for_transform(:), 'Visible', 'on'); 
+                catch
+                end
+            end
+        else; disp('transform point mode OFF');
+            % hide transform points
+
+            try 
+                set(ud.pointHands_for_transform(:), 'Visible', 'off');
+            catch
             end
-        else; disp('transform point mode OFF');    
+
         end     
 % a -- toggle viewing of annotation boundaries  
     case 'a' 
@@ -433,7 +448,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             ud.slice_at_shift_start = ud_slice.slice_num;
             ud.slice_shift = 0;
         end
-        disp('switch scroll mode -- scroll along slice images')     
+        disp('switch scroll mode -- scroll along slice images')
 % h -- toggle viewing of histology / histology overlay
     case 'h'
         disp('  ');
@@ -631,13 +646,13 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             
             % Try to delete only the most recent point
             ud.current_pointList_for_transform = ud.current_pointList_for_transform(1:end-1,:);
-            ud_slice.pointList = ud_slice.pointList(1:end-1,:); 
+            ud_slice.pointList = ud_slice.pointList(1:end-1,:); %TODO this should be accompanied by deleting circles on Slive Viewer
             set(slice_figure, 'UserData', ud_slice);
-            if ud.pointHands_for_transform
+            if ~isempty(ud.pointHands_for_transform)
                 % remove circle for most revent point
-                set(ud.pointHands_for_transform(end), 'Visible', 'off');
+                set(ud.pointHands_for_transform(end), 'Visible', 'off');%TODO why hiding rather than deleting???
                 ud.pointHands_for_transform = ud.pointHands_for_transform(1:end-1); 
-                if ud.pointHands_for_transform
+                if  ~isempty(ud.pointHands_for_transform)
                     % recolor points
                     set(ud.pointHands_for_transform(end), 'color', [0 .9 0]);
                 end
@@ -733,7 +748,10 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
   
 % scroll through slices (left arrow pressed)
 elseif ud.scrollMode == 3
-  set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+    try
+        set(ud.pointHands_for_transform(:), 'Visible', 'off');
+    catch
+    end
   ud.showOverlay = 0;
   delete(ud.overlayAx); ud.overlayAx = [];  
   ud_slice = get(slice_figure, 'UserData');
@@ -787,7 +805,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
 
             ud_slice.pointList = transform_data.transform_points{2};
         else
-            ud_slice.pointList = [];           
+            ud_slice.pointList = [];
         end
         set(slice_figure, 'UserData', ud_slice);
         
@@ -811,6 +829,8 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
         % if no transform, just show reference
         ud.histology_overlay = 0;
         ud.current_pointList_for_transform = zeros(0,2);
+        delete(ud.pointHands_for_transform);% delete them %TODO not working
+        ud.pointHands_for_transform = gobjects(0);% initialize
         set(ud.im, 'CData', ud.ref);
         ud.curr_im = ud.ref; set(f, 'UserData', ud);   
         set(ud.text,'Visible','off');
@@ -845,7 +865,10 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
         updateOverlay(f, allData, ann, slice_figure, save_location);
     end  
     ud.ref = uint8(reference_slice);
-    set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+%     try 
+%         set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+%     catch
+%     end
     ud.offset_map = zeros(ud.ref_size); 
     set(f, 'UserData', ud);
     
@@ -1071,7 +1094,10 @@ function atlasClickCallback(im, keydata, slice_figure, save_location)
     end
     ud.pointList_for_transform(end+1, :) = [clickX, clickY];
     ud.current_pointList_for_transform(end+1, :) = [clickX, clickY];
+    try
     set(ud.pointHands_for_transform(:), 'color', [.7 .3 .3]);
+    catch
+    end
     ud.pointHands_for_transform(end+1) = plot(ud.atlasAx, clickX, clickY, 'ro', 'color', [0 .9 0],'LineWidth',2,'markers',4);    
         
     ud.slice_at_shift_start = ud_slice.slice_num;

From 5ca2bc2f96ce1aaf266eeb1d02c3dd9ece092149 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 19 Oct 2022 15:31:08 +0100
Subject: [PATCH 07/43] show/hide point counter for slice

---
 Browsing Functions/sliceBrowser.m | 41 ++++++++++++++++++++++++-------
 1 file changed, 32 insertions(+), 9 deletions(-)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index 9711a15..5df5fab 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -11,8 +11,8 @@ function sliceBrowser(slice_figure, processed_images_folder, f, reference_size)
 ud_slice.break = 0; 
 ud_slice.slice_num = 1;
 ud_slice.key = 1; 
-ud_slice.pointList = []; 
-ud_slice.pointHands = [];
+ud_slice.pointList = [];  % point coordinates
+ud_slice.pointHands = []; % graphic objects
 ud_slice.getPoint = 0;
 ud_slice.ref_size = reference_size(2:3);
 
@@ -23,6 +23,10 @@ function sliceBrowser(slice_figure, processed_images_folder, f, reference_size)
 set(ud_slice.sliceAx, 'HitTest', 'off');
 ud_slice.im = plotTVslice(zeros(ud_slice.ref_size, 'uint8'));
 
+ud_slice.pointsText = annotation('textbox', [0.88 0.03 0.1 0.05], ...
+    'String', '0 point', 'EdgeColor', 'none', 'Color', 'k', 'HorizontalAlignment', 'right');
+ud_slice.pointsText.Visible = 'off';
+
 % create functions needed to interact with the figure
 set(ud_slice.im, 'ButtonDownFcn', @(slice_figure,k)sliceClickCallback(slice_figure, k));
 set(slice_figure, 'KeyPressFcn', @(slice_figure, keydata)SliceAtlasHotkeyFcn(slice_figure, keydata, f));
@@ -38,6 +42,9 @@ function sliceBrowser(slice_figure, processed_images_folder, f, reference_size)
 % set up first slice image
 ud_slice = updateSliceImage(ud_slice);
 
+set(slice_figure, 'UserData', ud_slice);
+
+
 % ------------------------------------------------    
 % Clicking function to register transform points  
 % ------------------------------------------------
@@ -60,6 +67,8 @@ function sliceClickCallback(im, keydata)
         ud.pointList = []; 
         set(ud.pointHands(:), 'Visible', 'off');     
      end
+
+     ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));
     
 end
 set(f, 'UserData', ud);
@@ -91,14 +100,28 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
 %     ud.pointList = [];    
     
     % Try to delete only most recent point
-    set(ud.pointHands(end), 'Visible', 'off'); 
-    ud.pointHands = ud.pointHands(1:end-1); 
-    ud.pointList = ud.pointList(1:end-1,:); 
-    disp('transform point deleted')
+    if isempty(ud.pointHands)
+        disp('There is no transform point to delete.')
+    else
+        set(ud.pointHands(end), 'Visible', 'off'); 
+        ud.pointHands = ud.pointHands(1:end-1);
+        ud.pointList = ud.pointList(1:end-1,:);
+        disp('transform point deleted')
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));
+
+    end
 % t -- transform point mode
 elseif strcmp(keydata.Key,'t')
     ud.getPoint = ~ud.getPoint;
-        if ud.getPoint; disp('transform point mode!'); end
+    if ud.getPoint
+        disp('transform point mode!'); 
+        set(ud.pointHands(:), 'Visible', 'on')
+        ud.pointsText.Visible = 'on';
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));    
+    else
+        ud.pointsText.Visible = 'off';
+        set(ud.pointHands(:), 'Visible', 'off')
+    end
 else
 % otherwise -- call function to atlas browser       
     figure(f);
@@ -135,8 +158,6 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
     end
 
     ud.pointHands = gobjects(0);
-    % set(ud.pointHands(:), 'Visible', 'off'); %TODO WHY hiding? Maybe you
-    % want to delete/initialize them? ud is from fig.UserData
     ud.pointList = [];
     
     if exist(file_transformations,'file')
@@ -151,4 +172,6 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
             title_ending = ' (transform points loaded)';
         end       
     end
+    set(ud.pointHands(:), 'Visible', 'off'); %Hide because not in 't' mode
+
     title(['Slice Viewer -- Slice ' num2str(ud.slice_num) '/' num2str(ud.total_num_files) title_ending])    

From 3cafbbbf528149aa8b17fbcc2be2bcd8dffa43e4 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 19 Oct 2022 15:31:30 +0100
Subject: [PATCH 08/43] show/hide point counter for atlas

---
 Browsing Functions/AtlasTransformBrowser.m | 24 +++++++++++++++++++++-
 1 file changed, 23 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 9b34253..ad39268 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -70,6 +70,10 @@
 ud.angleText = annotation('textbox', [.7 0.95 0.4 0.05], ...
     'EdgeColor', 'none', 'Color', 'k');
 
+ud.pointsText = annotation('textbox', [0.88 0.03 0.1 0.05], ...
+    'String', '0 point', 'EdgeColor', 'none', 'Color', 'k', 'HorizontalAlignment', 'right');
+ud.pointsText.Visible = 'off';
+
 allData.tv = templateVolume;
 allData.av = annotationVolume;
 allData.st = structureTree;
@@ -358,6 +362,10 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
         if ud.getPoint_for_transform
             disp('transform point mode on'); 
 
+            % set(ud.pointHands_for_transform(:), 'Visible', 'on') %TODO
+            ud.pointsText.Visible = 'on';
+            ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
             ud.currentProbe = 0;
 
             % launch transform point mode
@@ -382,6 +390,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
 
             try 
                 set(ud.pointHands_for_transform(:), 'Visible', 'off');
+                ud.pointsText.Visible = 'off';
             catch
             end
 
@@ -535,11 +544,18 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
                     ud.curr_im = ud.curr_slice_trans;
                 end
             % if wrong number of points clicked
-            catch
+            catch mexc1
+                if mexc1.identifier == "images:geotrans:requiredNonCollinearPoints"
+                    disp(['Unable to transform -- ', mexc1.message])
+
+                else
+
                 ref_mode = true;
                 disp(['Unable to transform -- ' num2str(size(ud_slice.pointList,1)) ...
                      ' slice points and ' num2str(size(ud.current_pointList_for_transform,1)) ' reference points']);
                 key_letter = 'h'; 
+
+                end
             end
         end
         % if not doing transform, just show reference atlas
@@ -687,6 +703,8 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             end
             
             disp('transform point deleted');
+            ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
             
         elseif ud.currentProbe
             ud.pointList{ud.currentProbe,1} = ud.pointList{ud.currentProbe,1}(1:end-1,:);
@@ -1133,6 +1151,10 @@ function atlasClickCallback(im, keydata, slice_figure, save_location)
     ud.curr_slice_num = ud.slice_at_shift_start+ud.slice_shift;
     ud.loaded = 0;
     ud.clicked = true;
+
+    ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
+
 end
 set(f, 'UserData', ud);
 

From 13d6c1bb6759fccbb577323b1e4875b7e85aacca Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 19 Oct 2022 16:14:27 +0100
Subject: [PATCH 09/43] point counter behaviour

---
 Browsing Functions/sliceBrowser.m | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index 5df5fab..654dc81 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -172,6 +172,11 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
             title_ending = ' (transform points loaded)';
         end       
     end
-    set(ud.pointHands(:), 'Visible', 'off'); %Hide because not in 't' mode
-
+    if ud.getPoint
+        set(ud.pointHands(:), 'Visible', 'on');
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));        
+    else
+        set(ud.pointHands(:), 'Visible', 'off'); %Hide because not in 't' mode
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));        
+    end
     title(['Slice Viewer -- Slice ' num2str(ud.slice_num) '/' num2str(ud.total_num_files) title_ending])    

From 8b43f40b7380abec41edd529b4ecbeb790ac4169 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 19 Oct 2022 16:34:54 +0100
Subject: [PATCH 10/43] point counter behaviour

---
 Browsing Functions/AtlasTransformBrowser.m | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index ad39268..ff5e18b 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -852,6 +852,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
             ud_slice.pointList = transform_data.transform_points{2};
         else
             ud_slice.pointList = [];
+            ud.pointHands_for_transform = gobjects(0);
         end
         set(slice_figure, 'UserData', ud_slice);
         
@@ -868,6 +869,9 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
         ud.curr_slice_num = ud.slice_at_shift_start+ud.slice_shift;
         
         ud.histology_overlay = 1;
+
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
         
         set(ud.text,'Visible','off');
         fill([5 5 250 250],[5 50 50 5],[0 0 0]); ud.text(end+1) = text(5,15,['Slice ' num2str(ud.slice_at_shift_start+ud.slice_shift)],'color','white');
@@ -880,7 +884,9 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
         set(ud.im, 'CData', ud.ref);
         ud.curr_im = ud.ref; set(f, 'UserData', ud);   
         set(ud.text,'Visible','off');
-        fill([5 5 250 250],[5 50 50 5],[0 0 0]); ud.text(end+1) = text(5,15,['Slice ' num2str(ud.slice_at_shift_start+ud.slice_shift) ' - no transform'],'color','white');        
+        fill([5 5 250 250],[5 50 50 5],[0 0 0]); ud.text(end+1) = text(5,15,['Slice ' num2str(ud.slice_at_shift_start+ud.slice_shift) ' - no transform'],'color','white'); 
+        ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
     end  
         
 end  

From 98cc667394a4b8c8e164fbab78a62eef3a580a34 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 19 Oct 2022 17:44:30 +0100
Subject: [PATCH 11/43] points show status

---
 Browsing Functions/AtlasTransformBrowser.m | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index ff5e18b..297760c 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -855,7 +855,13 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
             ud.pointHands_for_transform = gobjects(0);
         end
         set(slice_figure, 'UserData', ud_slice);
-        
+
+        if ud.getPoint_for_transform
+            set(ud.pointHands_for_transform, 'Visible', 'on')
+        else
+            set(ud.pointHands_for_transform, 'Visible', 'off')
+        end
+
         % load allen ref location
         ud.currentSlice = transform_data.allen_location{1}; ud.currentAngle = transform_data.allen_location{2};
 

From 9e614f55f7d53eee9ebef79088bb22d4b3fa744f Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 31 Oct 2022 17:05:54 +0000
Subject: [PATCH 12/43] Better action. But perhaps there is a bug about coronal
 sections?

---
 Browsing Functions/AtlasTransformBrowser.m | 5 +++++
 Browsing Functions/sliceBrowser.m          | 6 +++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 297760c..f307164 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -190,6 +190,11 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
                         
             disp(['probe point mode -- selecting probe ' num2str(ud.currentProbe) ' (' ud.ProbeColor{ud.currentProbe} ')']); 
             ud.getPoint_for_transform = false; 
+            try
+                set(ud.pointHands_for_transform(:), 'Visible', 'off');
+                ud.pointsText.Visible = 'off';
+            catch
+            end
             
             % show Transformed Slice & Probage Viewer, if not already showing
             if ~ud.slice_at_shift_start; add = 1; else; add = 0; end
diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index 654dc81..df8ac47 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -61,7 +61,8 @@ function sliceClickCallback(im, keydata)
     clickY = round(keydata.IntersectionPoint(2));
 
     ud.pointList(end+1, :) = [clickX, ud.ref_size(1) - clickY];
-    ud.pointHands(end+1) = plot(ud.sliceAx, clickX, clickY, 'ro', 'color', [0 .5 0],'linewidth',2,'markers',4);    
+    set(ud.pointHands,'Color',[.7 .3 .3])
+    ud.pointHands(end+1) = plot(ud.sliceAx, clickX, clickY, 'o', 'color', [0 .9 0],'linewidth',2,'markers',4);
     
      if clickX < 100 && (ud.ref_size(1) - clickY) < 100 % if click in corner, break
         ud.pointList = []; 
@@ -134,6 +135,7 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
 
 
 function ud = updateSliceImage(ud)
+    %TODO occasionally pointList has more items than pointHands
 
     title_ending = '';
     
@@ -169,6 +171,8 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
             for i = 1:size(ud.pointList,1)
                 ud.pointHands(end+1) = plot(ud.sliceAx, ud.pointList(i,1), ud.ref_size(1) - ud.pointList(i,2), 'ro', 'color', [0 .5 0],'linewidth',2,'markers',4);
             end
+            set(ud.pointHands(end),'color', [0 .9 0]);
+
             title_ending = ' (transform points loaded)';
         end       
     end

From f2eafc61dc204475d340a453dcf9a4fd9b401bed Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 1 Feb 2023 18:00:38 +0000
Subject: [PATCH 13/43] deletion of points

---
 Browsing Functions/AtlasTransformBrowser.m | 10 +++++++---
 Browsing Functions/sliceBrowser.m          |  4 ++--
 2 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index f307164..1af1bb0 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -483,7 +483,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             xlabel(ud.atlasAx, 'Scroll slices along D/V axis')
 
         end
-    case 'leftarrow' % scroll along A/P axis
+    case 'leftarrow' % scroll along along slice images
         ud.scrollMode = 3;
         if ~ud.slice_at_shift_start
             ud.slice_at_shift_start = ud_slice.slice_num;
@@ -694,8 +694,12 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
 %             disp('current transform erased');
             
             % Try to delete only the most recent point
+            if isempty(ud.pointHands_for_transform)
+                disp('There is no transform point to delete.')
+            else
+
             ud.current_pointList_for_transform = ud.current_pointList_for_transform(1:end-1,:);
-            ud_slice.pointList = ud_slice.pointList(1:end-1,:); %TODO this should be accompanied by deleting circles on Slive Viewer
+                ud_slice.pointList = ud_slice.pointList(1:end-1,:); %TODO this should be accompanied by deleting circles on Slice Viewer
             set(slice_figure, 'UserData', ud_slice);
             if ~isempty(ud.pointHands_for_transform)
                 % remove circle for most revent point
@@ -709,7 +713,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             
             disp('transform point deleted');
             ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
-
+            end
             
         elseif ud.currentProbe
             ud.pointList{ud.currentProbe,1} = ud.pointList{ud.currentProbe,1}(1:end-1,:);
diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index df8ac47..0e5199a 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -104,7 +104,7 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
     if isempty(ud.pointHands)
         disp('There is no transform point to delete.')
     else
-        set(ud.pointHands(end), 'Visible', 'off'); 
+        set(ud.pointHands(end), 'Visible', 'off'); %TODO isn't this better to be deleted? But if you do, you have a problem for callbacks        
         ud.pointHands = ud.pointHands(1:end-1);
         ud.pointList = ud.pointList(1:end-1,:);
         disp('transform point deleted')
@@ -156,7 +156,7 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
                             [processed_image_name(1:end-4) '_transform_data.mat']);
 
     try
-        delete(findobj(ud.im.Parent, 'Type','line','color',[0 0.5 0],'Marker','o')); % delete all the circles
+        delete(findobj(ud.im.Parent, 'Type','line','Marker','o')); % delete all the circles
     end
 
     ud.pointHands = gobjects(0);

From ef13d6b7b31b9943b0bae2207bb53c6bb9bf9f62 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 1 Feb 2023 18:01:01 +0000
Subject: [PATCH 14/43] causing a bug of mismatching numbers of points

---
 Browsing Functions/AtlasTransformBrowser.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 1af1bb0..2618458 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -863,7 +863,8 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
             ud_slice.pointList = [];
             ud.pointHands_for_transform = gobjects(0);
         end
-        set(slice_figure, 'UserData', ud_slice);
+        % set(slice_figure, 'UserData', ud_slice);
+        %TODO causing a bug of mismatching numbers of points
 
         if ud.getPoint_for_transform
             set(ud.pointHands_for_transform, 'Visible', 'on')

From 5207316ac629821226df80bedc552a2c2c605b73 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 1 Feb 2023 18:01:45 +0000
Subject: [PATCH 15/43] Not sure why points need to be hidden when moving along
 an axis or tilting

---
 Browsing Functions/AtlasTransformBrowser.m | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 2618458..197cd6d 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -1003,7 +1003,7 @@ function updateSlice(f, evt, allData, slice_figure, save_location)
   end  
 
   ud.ref = uint8(angle_slice);
-  set(ud.pointHands_for_transform(:), 'Visible', 'off'); 
+  % set(ud.pointHands_for_transform(:), 'Visible', 'off'); %TODO is this needed???
 end
 
 

From 8ad7313c738e969163483d45ea4c9dca5da9b367 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Sat, 3 Jun 2023 09:44:37 +0100
Subject: [PATCH 16/43] color change and beep for warning

---
 Browsing Functions/AtlasTransformBrowser.m | 29 ++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 197cd6d..7e2857a 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -713,6 +713,21 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             
             disp('transform point deleted');
             ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
+
+            if abs(length(ud.pointHands_for_transform) - length(ud_slice.pointHands)) >= 2
+                beep
+                if length(ud.pointHands_for_transform) - length(ud_slice.pointHands) >= 2
+                    ud.pointsText.Color = 'red';
+                    ud_slice.pointsText.Color = 'blue';
+                else
+                    ud.pointsText.Color = 'blue';
+                    ud_slice.pointsText.Color = 'red';
+                end
+            else
+                ud.pointsText.Color = 'black';
+                ud_slice.pointsText.Color = 'black';
+            end 
+
             end
             
         elseif ud.currentProbe
@@ -1176,6 +1191,20 @@ function atlasClickCallback(im, keydata, slice_figure, save_location)
 
     ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
 
+    if abs(length(ud.pointHands_for_transform) - length(ud_slice.pointHands)) >= 2
+        beep
+        if length(ud.pointHands_for_transform) - length(ud_slice.pointHands) >= 2
+            ud.pointsText.Color = 'red';
+            ud_slice.pointsText.Color = 'blue';
+
+        else
+            ud.pointsText.Color = 'blue';
+            ud_slice.pointsText.Color = 'red';            
+        end
+    else
+        ud.pointsText.Color = 'black';
+        ud_slice.pointsText.Color = 'black';
+    end    
 
 end
 set(f, 'UserData', ud);

From e913028507b4082bbbb69be5b1bbdfcb5457fa1f Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 3 Aug 2023 16:52:39 +0100
Subject: [PATCH 17/43]  sliceBrowser.m Browsing Functions 
 AtlasTransformBrowser.m Browsing Functions

---
 Browsing Functions/AtlasTransformBrowser.m |  2 +-
 Browsing Functions/sliceBrowser.m          | 35 +++++++++++++++++-----
 2 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 7e2857a..af86a1d 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -715,7 +715,7 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands_for_transform));
 
             if abs(length(ud.pointHands_for_transform) - length(ud_slice.pointHands)) >= 2
-                beep
+                % beep
                 if length(ud.pointHands_for_transform) - length(ud_slice.pointHands) >= 2
                     ud.pointsText.Color = 'red';
                     ud_slice.pointsText.Color = 'blue';
diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index 0e5199a..d8bc290 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -60,16 +60,25 @@ function sliceClickCallback(im, keydata)
     clickX = round(keydata.IntersectionPoint(1));
     clickY = round(keydata.IntersectionPoint(2));
 
-    ud.pointList(end+1, :) = [clickX, ud.ref_size(1) - clickY];
+    % ud.pointList(end+1, :) = [clickX, ud.ref_size(1) - clickY]; % often pointList is shorter than pointHands
     set(ud.pointHands,'Color',[.7 .3 .3])
     ud.pointHands(end+1) = plot(ud.sliceAx, clickX, clickY, 'o', 'color', [0 .9 0],'linewidth',2,'markers',4);
-    
-     if clickX < 100 && (ud.ref_size(1) - clickY) < 100 % if click in corner, break
-        ud.pointList = []; 
-        set(ud.pointHands(:), 'Visible', 'off');     
-     end
 
-     ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));
+    % make sure what you see are what you have
+    phx = zeros(length(ud.pointHands), 1);
+    phy = zeros(length(ud.pointHands), 1);
+    for i = 1:length(ud.pointHands)
+        phx(i) = ud.pointHands(i).XData;
+        phy(i) = ud.pointHands(i).YData;
+    end
+    ud.pointList = [phx, ud.ref_size(1) - phy]; %TODO
+
+    if clickX < 100 && (ud.ref_size(1) - clickY) < 100 % if click in corner, break
+        ud.pointList = [];
+        set(ud.pointHands(:), 'Visible', 'off');
+    end
+
+    ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));
     
 end
 set(f, 'UserData', ud);
@@ -106,7 +115,17 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
     else
         set(ud.pointHands(end), 'Visible', 'off'); %TODO isn't this better to be deleted? But if you do, you have a problem for callbacks        
         ud.pointHands = ud.pointHands(1:end-1);
-        ud.pointList = ud.pointList(1:end-1,:);
+        
+        % make sure the length of ud.pointHands and the rows of ud.pointList match
+        % make sure what you see are what you have
+        phx = zeros(length(ud.pointHands), 1);
+        phy = zeros(length(ud.pointHands), 1);
+        for i = 1:length(ud.pointHands)
+            phx(i) = ud.pointHands(i).XData;
+            phy(i) = ud.pointHands(i).YData;
+        end
+        ud.pointList = [phx, ud.ref_size(1) - phy];
+
         disp('transform point deleted')
         ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));
 

From 4de3d02dd2eafc33333b3772ad87b56177cec1fd Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 3 Aug 2023 16:52:55 +0100
Subject: [PATCH 18/43] depth correction

---
 Browsing Functions/accf2pxs_mm.m     | 20 ++++++++++
 Browsing Functions/allenCCF2pxs_mm.m | 18 +++++++++
 Browsing Functions/apdvml2info.m     | 56 ++++++++++++++++++++++++++++
 3 files changed, 94 insertions(+)
 create mode 100644 Browsing Functions/accf2pxs_mm.m
 create mode 100644 Browsing Functions/allenCCF2pxs_mm.m
 create mode 100644 Browsing Functions/apdvml2info.m

diff --git a/Browsing Functions/accf2pxs_mm.m b/Browsing Functions/accf2pxs_mm.m
new file mode 100644
index 0000000..ded57e6
--- /dev/null
+++ b/Browsing Functions/accf2pxs_mm.m	
@@ -0,0 +1,20 @@
+function y_mm = accf2pxs_mm(x_mm)
+% convert Allen Common Coordinates into standard values (Paxinos and Franklin)
+% x_mm   Allen Common Coordinates
+%     if this is scaler, x_mm should be depth
+%     if this is n x 3 array, x_mm is an array of the same (or similar) size
+% y_mm Paxinos and Franklin coordinates
+
+if size(x_mm,2) ==1 
+    y_mm = 0.921 * x_mm - 0.834; % global
+    % y = 0.908 * x - 0.957; % local
+
+elseif size(x_mm,2) == 3
+    % assume that the 2nd column is the DV
+    y_mm = x_mm;
+    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834; % global
+    % y(:,2) = 0.908 * x(:,2) - 0.957;  % local
+
+else
+    error('unexpected size')
+end
\ No newline at end of file
diff --git a/Browsing Functions/allenCCF2pxs_mm.m b/Browsing Functions/allenCCF2pxs_mm.m
new file mode 100644
index 0000000..999221e
--- /dev/null
+++ b/Browsing Functions/allenCCF2pxs_mm.m	
@@ -0,0 +1,18 @@
+function y_mm = accf2pxs_mm(x_mm)
+% convert Allen Common Coordinates into standard values (Paxinos and Franklin)
+% x_mm   Allen Common Coordinates 
+% y_mm Paxinos and Franklin coordinates
+
+if size(x_mm,2) ==1 
+    y_mm = 0.921 * x_mm - 0.834; % global
+    % y = 0.908 * x - 0.957; % local
+
+elseif size(x_mm,2) == 3
+    % assume that the 2nd column is the DV
+    y_mm = x_mm;
+    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834; % global
+    % y(:,2) = 0.908 * x(:,2) - 0.957;  % local
+
+else
+    error('unexpected size')
+end
\ No newline at end of file
diff --git a/Browsing Functions/apdvml2info.m b/Browsing Functions/apdvml2info.m
new file mode 100644
index 0000000..8735ce2
--- /dev/null
+++ b/Browsing Functions/apdvml2info.m	
@@ -0,0 +1,56 @@
+function Tapdvml = apdvml2info(apdvml_points, av, st)
+% apdvml_points has three columns for ap, dv, and ml
+% bregma is 1 x 3 in size
+% atlas_resolution in mm
+% av  1320 ,800, 1140
+% st
+%
+% see also
+% Analyze_Clicked_Points.m
+
+% generate needed values
+bregma = allenCCFbregma(); % bregma position in reference data space
+atlas_resolution = 0.010; % mm
+
+
+ap = -(apdvml_points(:,1)-bregma(1))*atlas_resolution;
+dv = (apdvml_points(:,2)-bregma(2))*atlas_resolution;
+ml = (apdvml_points(:,3)-bregma(3))*atlas_resolution;
+
+% roi_location_curr = [ap dv ml];
+
+% initialize array of region annotations
+roi_annotation_curr = cell(size(apdvml_points,1),3);
+
+% loop through every point to get ROI locations and region annotations
+tf_rows = true(size(apdvml_points,1),1);
+for point = 1:size(apdvml_points,1)
+
+    % find the annotation, name, and acronym of the current ROI pixel
+    depth = ceil(apdvml_points(point,2));
+    if depth >= 1
+
+        ann = av(ceil(apdvml_points(point,1)), ...
+            depth, ... %NOTE this can take the value of 0 and cause an error (must be >= 1)
+            ceil(apdvml_points(point,3)));
+        name = st.safe_name{ann};
+        acr = st.acronym{ann};
+
+        roi_annotation_curr{point,1} = ann;
+        roi_annotation_curr{point,2} = name;
+        roi_annotation_curr{point,3} = acr;
+
+    else
+        % ignore this point, too dorsal
+        roi_annotation_curr{point,1} = NaN;
+        roi_annotation_curr{point,2} = '';
+        roi_annotation_curr{point,3} = '';
+
+    end
+
+end
+
+Tapdvml = [table(ap, dv, accf2pxs_mm(dv), ml, 'VariableNames',{'ap_mm','dv_mm', 'dv_mm_paxinos', 'ml_mm'}), ...
+    cell2table(roi_annotation_curr, 'VariableNames', {'annotation', 'name', 'acronym'})];
+
+end
\ No newline at end of file

From f522cf993e2ddf64eb88c26bd5f994e41b174b47 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Fri, 4 Aug 2023 17:40:17 +0100
Subject: [PATCH 19/43] bug fix
 https://github.com/cortex-lab/allenCCF/issues/70

---
 Browsing Functions/AtlasTransformBrowser.m | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index af86a1d..78cd002 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -779,8 +779,9 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
         disp('atlas location saved')
         
         % save transformed histology image
-        current_slice_image = imread(fullfile(save_location, [slice_name '.tif']));
-%         current_slice_image = flip(get(ud_slice.im, 'CData'),1);
+        % current_slice_image = imread(fullfile(save_location, [slice_name '.tif']));%TODO no imreisze() used, size mismatch creates a huge error in transform
+        current_slice_image = flip(get(ud_slice.im, 'CData'),1);
+
         R = imref2d(size(ud.ref));
         curr_slice_trans = imwarp(current_slice_image, ud.transform, 'OutputView',R);
         imwrite(curr_slice_trans, fullfile(folder_transformations, [slice_name '_transformed.tif']))

From 6f73199a9e57716beb37f824af2816579d87ee14 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Tue, 15 Aug 2023 14:28:05 +0100
Subject: [PATCH 20/43] C:\Users\phar0528\OneDrive -
 Nexus365\Private_Dropbox\Projects\allenCCF\Browsing
 Functions\plot_and_compute_probe_positions_from2.m

---
 .../plot_and_compute_probe_positions_from2.m  | 376 ++++++++++++++++++
 1 file changed, 376 insertions(+)
 create mode 100644 Browsing Functions/plot_and_compute_probe_positions_from2.m

diff --git a/Browsing Functions/plot_and_compute_probe_positions_from2.m b/Browsing Functions/plot_and_compute_probe_positions_from2.m
new file mode 100644
index 0000000..80475a7
--- /dev/null
+++ b/Browsing Functions/plot_and_compute_probe_positions_from2.m	
@@ -0,0 +1,376 @@
+function [probes, fwireframe, fwireframe2, fig_probes, T_probes, Tapdvml_contacts, T_borders] ...
+    = plot_and_compute_probe_positions_from2(av, st, subject_id, plane,...
+    processed_images_folder, probe_save_name_suffix,probes_to_analyze, probe_lengths,...
+    active_probe_length, probe_radius)
+% Create 3D plot for probe positions, 2D plots for brain structures along
+% each probe, and return tables for structure names and coordinates
+%
+%
+% SYNTAX
+% [] = plot_and_compute_probe_positions(fwireframe, black_brain, probes, subject_id, plane,...
+%    use_tip_to_get_reference_probe_length, probe_insertion_direction)
+% [D] = func1(A,B)
+% [D] = func1(____,'Param',value)
+%
+% longer description may come here
+%
+% INPUT ARGUMENTS
+% av          uint16
+%             3 dimensional array of integers representing the different
+%             brain regions in the model space
+%
+% st          table
+%
+% subject_id  char
+%             Animal name
+%
+% plane       'coronal' | 'sagittal' | 'transverse'
+%
+% processed_images_folder
+%             char
+%
+% probe_save_name_suffix
+%             char
+%             Needed to access stored data
+%
+% probes_to_analyze
+%             'all' | a row vector of positive integers specifying probes
+%             
+
+% B           0 (default) | non-negative integers
+%             (Optional) Description about B comes here.
+% 
+%
+% OPTIONAL PARAMETER/VALUE PAIRS
+% 'C'         'on' (default) | 'off'
+%             (Optional) Description about 'C' comes here.
+%
+%
+% OUTPUT ARGUMENTS
+% D           cell array 
+%             Description about D comes here.
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 09-Aug-2023 11:12:42
+%
+% See also
+% doc
+
+
+
+% load the reference brain annotations
+% if ~exist('av','var') || ~exist('st','var')
+%     disp('loading reference atlas...')
+%     av = readNPY(annotation_volume_location);
+%     st = loadStructureTree(structure_tree_location);
+% end
+
+arguments
+
+    av (:,:,:) uint16
+    st (:, 22) table
+    subject_id (1, :) char
+    plane (1, :) char {mustBeMember(plane,{'coronal','sagittal','transverse'})}
+    processed_images_folder (1, :) char {mustBeFolder}
+    probe_save_name_suffix (1, :) char
+    probes_to_analyze % 'all' | A vector of integer indices for probes
+    probe_lengths {mustBeVector}
+    active_probe_length (1,1)
+    probe_radius (1,1)
+
+end
+
+
+scaling_factor = false;
+show_region_table = true;
+black_brain = true;
+probe_insertion_direction = 'down';
+show_parent_category = false; 
+distance_past_tip_to_plot = .5;
+
+
+
+% select the plane for the viewer
+if strcmp(plane,'coronal')
+    av_plot = av;
+elseif strcmp(plane,'sagittal')
+    av_plot = permute(av,[3 2 1]);
+elseif strcmp(plane,'transverse')
+    av_plot = permute(av,[2 3 1]);
+end
+
+% load probe points
+probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
+ProbeColors = .75*[1.3 1.3 1.3; 1 .75 0;  .3 1 1; .4 .6 .2; 1 .35 .65; .7 .7 .9; .65 .4 .25; .7 .95 .3; .7 0 0; .6 0 .7; 1 .6 0]; 
+% order of colors: {'white','gold','turquoise','fern','bubble gum','overcast sky','rawhide', 'green apple','red','purple','orange'};
+fwireframe = [];
+
+% % scale active_probe_length appropriately
+% active_probe_length = active_probe_length*100;
+
+% determine which probes to analyze
+if strcmp(probes_to_analyze,'all')
+    probes = 1:size(probePoints.pointList.pointList,1);
+else
+    probes = probes_to_analyze;
+end 
+
+
+
+%%
+
+% create a new figure with wireframe
+fwireframe = plotBrainGrid([], [], fwireframe, black_brain);
+hold on; 
+fwireframe.InvertHardcopy = 'off';
+
+fwireframe2 = plotBrainGrid([], [], fwireframe, black_brain); %TODO what is this one for?????????
+hold on;
+fwireframe2.InvertHardcopy = 'off';
+
+fig_probes = gobjects(1,length(probes));
+borders_table = cell(1,length(probes)) %TODO
+t_size = [size(probePoints.pointList.pointList,1),1];
+T_probes = table(repmat(string(subject_id), t_size),...
+    strings(t_size), ...
+    NaN(t_size),...
+    strings(t_size), ...
+    NaN(t_size),...
+    NaN(t_size),...
+    NaN(t_size),...
+    NaN(t_size),...
+    NaN(t_size),...
+    NaN(t_size),...
+    strings(t_size), ...    
+    'VariableNames',{'subject_id','session_id','probe_id','probe_AB',...
+        'depth_reported_um','depth_from_ACCF_um','scaling', ...
+        'scaling2',...
+        'tip_active_um', 'top_active_um', 'probe_note'});
+T_probes.probe_id(probes') = probes';
+T_probes.probe_lengths(probes) = probe_lengths(probes)' * 1000;
+
+
+c_Tapdvml_contacts = cell(length(probes),1);
+
+for selected_probe = probes
+
+    % get the probe points for the currently analyzed probe
+    if strcmp(plane,'coronal')
+        curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [3 2 1]);
+    elseif strcmp(plane,'sagittal')
+        curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 2 3]);
+    elseif strcmp(plane,'transverse')
+        curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 3 2]);
+    end
+
+    assert(size(curr_probePoints,1) ==2, 'Only accepts 2 points (the tip and surface) per probe')
+
+    % get user-defined probe length from experiment
+    if length(probe_lengths) > 1
+        probe_length = probe_lengths(selected_probe);
+    else
+        probe_length = probe_lengths;
+    end
+
+    % get the scaling-factor method to use
+    if scaling_factor
+        use_tip_to_get_reference_probe_length = false;
+        reference_probe_length = probe_length * scaling_factor;
+        disp(['probe scaling of ' num2str(scaling_factor) ' determined by user input']);
+    else
+        use_tip_to_get_reference_probe_length = true;
+        disp(['getting probe scaling from histology data...']);
+    end
+
+    % get line of best fit through points
+    % m is the mean value of each dimension; p is the eigenvector for largest eigenvalue
+    [m,p,s] = best_fit_line(curr_probePoints(:,1), curr_probePoints(:,2), curr_probePoints(:,3)); %TODO
+    if isnan(m(1))
+        disp(['no points found for probe ' num2str(selected_probe)])
+        continue
+    end
+
+    % ensure proper orientation: want 0 at the top of the brain and positive distance goes down into the brain
+    if p(2)<0
+        p = -p;
+    end
+
+
+    % determine "origin" at top of brain -- step upwards along tract direction until tip of brain / past cortex
+    ann = 10;
+    out_of_brain = false;
+    while ~(ann==1 && out_of_brain) % && distance_stepped > .5*active_probe_length)
+        m = m-p; % step 10um, backwards up the track
+        ann = av(round(m(1)),round(m(2)),round(m(3))); %until hitting the top
+        if strcmp(st.safe_name(ann), 'root')
+            % make sure this isn't just a 'root' area within the brain
+            m_further_up = m - p*20; % is there more brain 200 microns up along the track?
+            ann_further_up = av(round(max(1,m_further_up(1))),round(max(1,m_further_up(2))),round(max(1,m_further_up(3))));
+            if strcmp(st.safe_name(ann_further_up), 'root')
+                out_of_brain = true;
+            end
+        end
+    end
+    %NOTE m is now the highest point
+
+    %% focus on wireframe plot
+    figure(fwireframe);
+
+    % plot probe points
+    hp = plot3(curr_probePoints(:,1), curr_probePoints(:,3),...
+        curr_probePoints(:,2), '.','linewidth',2, 'color',[ProbeColors(selected_probe,:) .2],'markers',10);
+
+    % plot brain entry point
+    plot3(m(1), m(3), m(2), 'r*','linewidth',1)
+
+    % use the deepest clicked point as the tip of the probe, if no scaling provided (scaling_factor = false)
+    if use_tip_to_get_reference_probe_length
+        % find length of probe in reference atlas space
+        if strcmp(probe_insertion_direction, 'down')
+            [depth, tip_index] = max(curr_probePoints(:,2));
+        elseif strcmp(probe_insertion_direction, 'up')
+            [depth, tip_index] = min(curr_probePoints(:,2));
+        end
+        reference_probe_length_tip = sqrt(sum((curr_probePoints(tip_index,:) - m).^2));
+
+        % and the corresponding scaling factor
+        shrinkage_factor = (reference_probe_length_tip / 100) / probe_length;
+
+        % display the scaling
+        disp(['probe length of ' num2str(reference_probe_length_tip/100) ...
+            ' mm in reference atlas space compared to a reported ' num2str(probe_length) ' mm']);
+        disp(['probe scaling of ' num2str(shrinkage_factor)]); disp(' ');
+
+        T_probes.depth_from_ACCF_um(selected_probe) = reference_probe_length_tip/100 * 1000; 
+        T_probes.scaling(selected_probe) = shrinkage_factor; 
+
+        % plot line the length of the probe in reference space
+        probe_length_histo = round(reference_probe_length_tip);
+        % probe_length_histo is the distance from the tip to the surface
+        % measured in Allen CCF space.
+
+        % if scaling_factor is user-defined as some number, use it to plot the length of the probe
+    else
+        probe_length_histo = round(reference_probe_length * 100);
+    end
+
+    % find the percent of the probe occupied by electrodes
+    % percent_of_tract_with_active_sites = min([active_probe_length*100 / (probe_length*100), 1.0]); %TODO here probe_length is used, but this should be ignored
+    % active_site_start = probe_length_histo*(1-percent_of_tract_with_active_sites);
+
+    %NOTE ignore the probe_length. Use probe_length_histo instead.
+    percent_of_tract_with_active_sites = min([active_probe_length*100 / probe_length_histo, 1.0]); 
+    active_site_start = probe_length_histo*(1-percent_of_tract_with_active_sites);
+    active_probe_position = round([active_site_start  probe_length_histo]); %TODO use this?
+
+    % plot line the length of the active probe sites in reference space
+    plot3(m(1)+p(1)*[active_probe_position(1) active_probe_position(2)], ...
+        m(3)+p(3)*[active_probe_position(1) active_probe_position(2)], ...
+        m(2)+p(2)*[active_probe_position(1) active_probe_position(2)], ...
+        'Color', ProbeColors(selected_probe,:), 'LineWidth', 1);
+    % plot line the length of the entire probe in reference space
+    plot3(m(1)+p(1)*[1 probe_length_histo], m(3)+p(3)*[1 probe_length_histo], m(2)+p(2)*[1 probe_length_histo], ...
+        'Color', ProbeColors(selected_probe,:), 'LineWidth', 1, 'LineStyle',':');
+
+
+    %% ----------------------------------------------------------------
+    % Get and plot brain region labels along the extent of each probe
+    % ----------------------------------------------------------------
+
+    % convert error radius into mm
+    error_length = round(probe_radius / 10);
+
+    % find and regions the probe goes through, confidence in those regions, and plot them
+    borders_table{selected_probe} = plotDistToNearestToTip(m, p, av_plot, st, probe_length_histo, ...
+        error_length, active_site_start, distance_past_tip_to_plot, ...
+        show_parent_category, show_region_table, plane); % plots confidence score based on distance to nearest region along probe
+    title(['Probe ' num2str(selected_probe)],'color',ProbeColors(selected_probe,:))
+
+    T_probes.tip_active_um(selected_probe) = probe_length_histo *10; %TODO
+    T_probes.top_active_um(selected_probe) = active_site_start * 10; %TODO
+
+    fig_probes(selected_probe) = gcf;
+
+
+    %%%% coordinates, cf. Analyze_Clicked_Points.m
+    %
+    % m is the brain entry point
+
+    Tapdvml_m = apdvml2info(m, av, st, plane);
+
+    Tapdvml_tip = apdvml2info(curr_probePoints(tip_index,:), av, st, plane);
+
+    % measure the distance 
+
+    tip2surface_mm = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+        (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
+        (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+
+    tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+        (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
+        (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+    
+    top_active = (m * active_probe_length + ...
+        curr_probePoints(tip_index,:) * (tip2surface_mm - active_probe_length))...
+        /tip2surface_mm;
+
+    % obtained the information for all the 384 channels
+
+
+    a = [linspace(curr_probePoints(tip_index,1), top_active(1), 192)', ...
+        linspace(curr_probePoints(tip_index,2), top_active(2), 192)', ...
+        linspace(curr_probePoints(tip_index,3), top_active(3), 192)'];
+    probe_contact_points = zeros(384, 3);
+    for i = 1:192
+        probe_contact_points(2*i-1,:) = a(i,:);
+        probe_contact_points(2*i,:) = a(i,:);
+    end
+    clear a
+
+    c_t_contacts = cell(384,1);
+
+    theta = acos(p(2)); % Assuming p(2) corresponds to the DV direction
+
+    for i = 1:384
+        c_t_contacts{i} = apdvml2info(probe_contact_points(i,:), av, st, plane);
+        c_t_contacts{i}.contact_id = repmat(i,height(c_t_contacts{i}));
+        c_t_contacts{i}.probe_id = repmat(selected_probe,height(c_t_contacts{i}));
+        c_t_contacts{i}.depth_mm = tip2surface_mm - 0.020 * floor((i-1)/2);
+        
+        % Project the depth along the line
+        projected_depth_mm = c_t_contacts{i}.depth_mm * cos(theta);
+
+        % Convert using the transformation for the chosen plane
+        projected_depth_mm_paxinos = accf2pxs_mm(projected_depth_mm, plane, 'distance');
+
+        c_t_contacts{i}.depth_mm_paxinos = projected_depth_mm_paxinos;
+    end
+
+    c_Tapdvml_contacts{selected_probe} = vertcat(c_t_contacts{:});
+    clear c_t_contacts
+
+    pause(.05)
+end
+
+
+Tapdvml_contacts = vertcat(c_Tapdvml_contacts{:});
+Tapdvml_contacts.probe_AB = strings(height(Tapdvml_contacts), 1);
+Tapdvml_contacts.session_id = strings(height(Tapdvml_contacts), 1);
+Tapdvml_contacts.subject_id = strings(height(Tapdvml_contacts), 1);
+
+
+T_borders = [];
+for i = probes
+    borders_table{i}.probe_id = repmat(i,height(borders_table{i}),1);
+    T_borders = [T_borders; join(borders_table{i}, T_probes(i,:))];
+end
+
+i = T_borders.Properties.VariableNames == "upperBorder";
+T_borders.Properties.VariableNames{i} = 'upperBorder_um';
+
+i = T_borders.Properties.VariableNames == "lowerBorder";
+T_borders.Properties.VariableNames{i} = 'lowerBorder_um';
+

From 5d827e9a30db77b6cf71cb230f213c2b9a0e3371 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Tue, 15 Aug 2023 14:28:33 +0100
Subject: [PATCH 21/43] getting there

---
 Browsing Functions/accf2pxs_mm.m | 96 ++++++++++++++++++++++++++------
 Browsing Functions/apdvml2info.m | 14 ++++-
 2 files changed, 91 insertions(+), 19 deletions(-)

diff --git a/Browsing Functions/accf2pxs_mm.m b/Browsing Functions/accf2pxs_mm.m
index ded57e6..37b107e 100644
--- a/Browsing Functions/accf2pxs_mm.m	
+++ b/Browsing Functions/accf2pxs_mm.m	
@@ -1,20 +1,84 @@
-function y_mm = accf2pxs_mm(x_mm)
-% convert Allen Common Coordinates into standard values (Paxinos and Franklin)
-% x_mm   Allen Common Coordinates
-%     if this is scaler, x_mm should be depth
-%     if this is n x 3 array, x_mm is an array of the same (or similar) size
-% y_mm Paxinos and Franklin coordinates
+function y_mm = accf2pxs_mm(x_mm, plane, numtype)
+% convert Allen Common Coordinates into standard values (Paxinos and Franklin, 2012, 4th edition)
+%
+% SYNTAX
+% y_mm = accf2pxs_mm(x_mm, plane)
+%
+% INPUT ARGUMENTS
+% x_mm        Allen Common Coordinates
+%             if this is scaler, x_mm should be depth.
+%             if this is n x 3 array, x_mm is an array of the same (or similar) size
+%
+% plane       'coronal' | 'sagittal' | 'transverse'
+%
+% numtype     'coordinate' (defalut) |  'distance'
+%
+% OUTPUT ARGUMENTS
+% y_mm        Paxinos and Franklin coordinates
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 09-Aug-2023 11:06:59
+%
+% See also
+% apdvml2info
 
-if size(x_mm,2) ==1 
-    y_mm = 0.921 * x_mm - 0.834; % global
-    % y = 0.908 * x - 0.957; % local
+arguments
+ x_mm 
+ plane (1,1) string {mustBeMember(plane, {'coronal','sagittal','transverse'})}
+ numtype (1,1) string {mustBeMember(numtype, {'coordinate','distance'})} = "coordinate"
 
-elseif size(x_mm,2) == 3
-    % assume that the 2nd column is the DV
-    y_mm = x_mm;
-    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834; % global
-    % y(:,2) = 0.908 * x(:,2) - 0.957;  % local
+end
 
-else
-    error('unexpected size')
+
+switch plane
+
+    case "coronal"
+        if size(x_mm,2) ==1
+            switch numtype
+                case "coordinate"
+                    y_mm = 0.825 * x_mm - 0.131;
+                case "distance"
+                    y_mm = 0.825 * x_mm ; 
+            end
+
+        elseif size(x_mm,2) == 3
+
+            % assume that the 2nd column is the DV
+            y_mm = x_mm;
+            switch numtype
+                case "coordinate"
+                    y_mm(:,2) = 0.825 * x_mm(:,2) - 0.131;
+                case "distance"
+                    y_mm = 0.825 * x_mm(:,2) ;
+            end
+        else
+            error('unexpected size')
+        end        
+    case "sagittal"
+        if size(x_mm,2) ==1
+            switch numtype
+                case "coordinate"
+                    y_mm = 0.921 * x_mm - 0.834;
+                case "distance"
+                    y_mm = 0.921 * x_mm ;
+            end
+        elseif size(x_mm,2) == 3
+            % assume that the 2nd column is the DV
+            y_mm = x_mm;
+            switch numtype
+                case "coordinate"
+                    y_mm(:,2) = 0.921 * x_mm(:,2) - 0.834;
+                case "distance"
+                    y_mm = 0.921 * x_mm(:,2) ;
+            end
+        else
+            error('unexpected size')
+        end
+    case "transverse"
+        error("not implemented yet")
+    otherwise
+        error("wrong input for 'plane'")
 end
\ No newline at end of file
diff --git a/Browsing Functions/apdvml2info.m b/Browsing Functions/apdvml2info.m
index 8735ce2..4b88cc9 100644
--- a/Browsing Functions/apdvml2info.m	
+++ b/Browsing Functions/apdvml2info.m	
@@ -1,4 +1,4 @@
-function Tapdvml = apdvml2info(apdvml_points, av, st)
+function Tapdvml = apdvml2info(apdvml_points, av, st, plane)
 % apdvml_points has three columns for ap, dv, and ml
 % bregma is 1 x 3 in size
 % atlas_resolution in mm
@@ -6,7 +6,15 @@
 % st
 %
 % see also
-% Analyze_Clicked_Points.m
+% Analyze_Clicked_Points.m, accf2pxs_mm
+
+arguments
+    apdvml_points (:,3)
+    av
+    st
+    plane (1,1) string {mustBeMember(plane, {'coronal','sagittal','transverse'})}
+end
+
 
 % generate needed values
 bregma = allenCCFbregma(); % bregma position in reference data space
@@ -50,7 +58,7 @@
 
 end
 
-Tapdvml = [table(ap, dv, accf2pxs_mm(dv), ml, 'VariableNames',{'ap_mm','dv_mm', 'dv_mm_paxinos', 'ml_mm'}), ...
+Tapdvml = [table(ap, dv, accf2pxs_mm(dv, plane), ml, 'VariableNames',{'ap_mm','dv_mm', 'dv_mm_paxinos', 'ml_mm'}), ...
     cell2table(roi_annotation_curr, 'VariableNames', {'annotation', 'name', 'acronym'})];
 
 end
\ No newline at end of file

From 9099b37ffb3e36bcba576296312eb7d4b68844e6 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 17 Aug 2023 15:24:54 +0100
Subject: [PATCH 22/43] mask_boundaries prep_Tavdvml_contacts

---
 Browsing Functions/mask_boundaries.m       | 66 +++++++++++++++++
 Browsing Functions/prep_Tapdvml_contacts.m | 84 ++++++++++++++++++++++
 2 files changed, 150 insertions(+)
 create mode 100644 Browsing Functions/mask_boundaries.m
 create mode 100644 Browsing Functions/prep_Tapdvml_contacts.m

diff --git a/Browsing Functions/mask_boundaries.m b/Browsing Functions/mask_boundaries.m
new file mode 100644
index 0000000..239132e
--- /dev/null
+++ b/Browsing Functions/mask_boundaries.m	
@@ -0,0 +1,66 @@
+function boundary_mask = mask_boundaries(av, margin_radius_um)
+% mask_boundaries will return a 3D array of logical which defines the mask
+% for structural boundaries
+%
+% SYNTAX
+% mask_boundaries(av, margin_radius_um)
+%
+% INPUT ARGUMENTS
+% av          the 3D array provided from Allen Brain Institute as Allen CCF
+%             Grid interval is 10 um (micrometers)
+%
+% margin_radius_um
+%             positive number
+%             Boundary margin as a radius in um (micrometers)
+%
+%
+% OUTPUT ARGUMENTS
+% boundary_mask  
+%             logical
+%             The same size as av.
+%             Voxels within margin_radius_um from boundaries are labelled
+%             as true. Otherwise the values are false.
+%
+%
+% EXAMPLE
+% boundary_mask = mask_boundaries(av, 20)
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 16-Aug-2023 11:22:57
+%
+% See also
+% doc
+
+
+arguments
+    av (:, :, :) uint16
+    margin_radius_um (1,1) {mustBePositive}
+end
+
+% Initialize boundary_mask
+boundary_mask = false(size(av));
+
+% Convert margin_um to grid units
+margin_units = round(margin_radius_um / 10);
+
+% Iterate through each voxel in av
+for x = 1:size(av, 1)
+    tic
+    for y = 1:size(av, 2)
+        for z = 1:size(av, 3)
+            % Check neighbors in all three dimensions
+            neighbors = av(max(1, x-margin_units):min(size(av, 1), x+margin_units), ...
+                          max(1, y-margin_units):min(size(av, 2), y+margin_units), ...
+                          max(1, z-margin_units):min(size(av, 3), z+margin_units));
+            
+            % If any neighbor has a different value, mark as boundary
+            if any(neighbors(:) ~= av(x, y, z))
+                boundary_mask(x, y, z) = true;
+            end
+        end
+    end
+    toc
+end
\ No newline at end of file
diff --git a/Browsing Functions/prep_Tapdvml_contacts.m b/Browsing Functions/prep_Tapdvml_contacts.m
new file mode 100644
index 0000000..0f6e574
--- /dev/null
+++ b/Browsing Functions/prep_Tapdvml_contacts.m	
@@ -0,0 +1,84 @@
+function Tapdvml_contacts = prep_Tapdvml_contacts(T_probes, Tapdvml_contacts)
+% short description comes here
+%
+% SYNTAX
+% Tapdvml_contacts = prep_Tapdvml_contacts(T_probes)
+%
+% longer description may come here
+%
+% INPUT ARGUMENTS
+% T_probes     table
+%             Rows for probes (+ optic fibers)
+%             With the following variables:
+%                probe_id          
+%                probe_AB          
+%                session_id        
+%                subject_id        
+%                probe_note        
+%                upward_from_tip_um
+%                upward_from_tim_um
+%
+% Tapdvml_contacts 
+%             table
+%
+%
+% OUTPUT ARGUMENTS
+% Tapdvml_contacts
+%             table
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 17-Aug-2023 09:51:42
+%
+% See also
+% doc
+
+arguments
+    T_probes table
+    Tapdvml_contacts table
+end
+
+for i = 1:height(T_probes)
+
+    tf = Tapdvml_contacts.probe_id == i;
+    Tapdvml_contacts.session_id(tf) = string(T_probes.session_id(i));
+    Tapdvml_contacts.probe_AB(tf) = string(T_probes.probe_AB(i));
+    Tapdvml_contacts.probe_note(tf) = string(T_probes.probe_note(i));
+    
+end
+
+
+% Bregma's coordinates in grid units
+
+bregma = allenCCFbregma();
+bregma_ml = bregma(1);
+bregma_dv = bregma(2);
+bregma_ap = bregma(3);
+
+%load boundary_mask
+load('\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\boundary_mask_20um_radius.mat', 'boundary_mask') % boundary_mask
+
+% Add a new column 'name_with_margin' to Tapdvml_contacts
+Tapdvml_contacts.name_with_margin = Tapdvml_contacts.name;
+
+% Iterate through each row in Tapdvml_contacts
+for i = 1:height(Tapdvml_contacts)
+    % Convert the coordinates to grid units and adjust based on bregma
+    ml = round(Tapdvml_contacts.ml_mm(i) * 100 + bregma_ml);
+    dv = round(Tapdvml_contacts.dv_mm(i) * 100 + bregma_dv);
+    ap = round(Tapdvml_contacts.ap_mm(i) * 100 + bregma_ap);
+    
+    if dv < 0
+        dv = 1;
+    end
+
+    if ap < 0
+        ap = 1;
+    end
+    % Check the boundary_mask array
+    if boundary_mask(ml, dv, ap)
+        Tapdvml_contacts.name_with_margin(i) = {'boundary'};
+    end
+end

From 47d559738ef4433afd95126d3308901c3afaa6c9 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Fri, 6 Oct 2023 11:05:49 +0100
Subject: [PATCH 23/43] removing fwireframe2

---
 .../plot_and_compute_probe_positions_from2.m  | 46 ++++++++++++-------
 Browsing Functions/prep_Tapdvml_contacts.m    |  4 +-
 2 files changed, 32 insertions(+), 18 deletions(-)

diff --git a/Browsing Functions/plot_and_compute_probe_positions_from2.m b/Browsing Functions/plot_and_compute_probe_positions_from2.m
index 80475a7..312c928 100644
--- a/Browsing Functions/plot_and_compute_probe_positions_from2.m	
+++ b/Browsing Functions/plot_and_compute_probe_positions_from2.m	
@@ -1,4 +1,4 @@
-function [probes, fwireframe, fwireframe2, fig_probes, T_probes, Tapdvml_contacts, T_borders] ...
+function [probes, fwireframe, fig_probes, T_probes, Tapdvml_contacts, T_borders] ...
     = plot_and_compute_probe_positions_from2(av, st, subject_id, plane,...
     processed_images_folder, probe_save_name_suffix,probes_to_analyze, probe_lengths,...
     active_probe_length, probe_radius)
@@ -35,20 +35,38 @@
 %
 % probes_to_analyze
 %             'all' | a row vector of positive integers specifying probes
-%             
-
-% B           0 (default) | non-negative integers
-%             (Optional) Description about B comes here.
-% 
 %
-% OPTIONAL PARAMETER/VALUE PAIRS
-% 'C'         'on' (default) | 'off'
-%             (Optional) Description about 'C' comes here.
+% probe_lengths 
+%              vector
+%              A vector of the depths of the deepest points for all the
+%              probes. Previously in the original SharpTrack, this
+%              information was used to calculate the depth, but now this is
+%              much less important.
+%
+% active_probe_length
+%              Should be 3.84 mm for Neuropixels 1.0 probes
+% 
+% probe_radius scalar
+%              in micrometers
 %
 %
 % OUTPUT ARGUMENTS
-% D           cell array 
-%             Description about D comes here.
+% probes
+% 
+% fwireframe figure
+% 
+% fig_probes figure
+%            
+% 
+% T_probes   table
+%            Summary for probe penetrations
+%
+% Tapdvml_contacts
+%            table
+%            A table containig whereabouts of all the recording contacts
+%
+% T_borders  table
+%            Modified from original SharpTrack output
 %
 % Written by Kouichi C. Nakamura Ph.D.
 % MRC Brain Network Dynamics Unit
@@ -57,7 +75,7 @@
 % 09-Aug-2023 11:12:42
 %
 % See also
-% doc
+% apdvml2info
 
 
 
@@ -127,10 +145,6 @@
 hold on; 
 fwireframe.InvertHardcopy = 'off';
 
-fwireframe2 = plotBrainGrid([], [], fwireframe, black_brain); %TODO what is this one for?????????
-hold on;
-fwireframe2.InvertHardcopy = 'off';
-
 fig_probes = gobjects(1,length(probes));
 borders_table = cell(1,length(probes)) %TODO
 t_size = [size(probePoints.pointList.pointList,1),1];
diff --git a/Browsing Functions/prep_Tapdvml_contacts.m b/Browsing Functions/prep_Tapdvml_contacts.m
index 0f6e574..17acdb0 100644
--- a/Browsing Functions/prep_Tapdvml_contacts.m	
+++ b/Browsing Functions/prep_Tapdvml_contacts.m	
@@ -70,11 +70,11 @@
     dv = round(Tapdvml_contacts.dv_mm(i) * 100 + bregma_dv);
     ap = round(Tapdvml_contacts.ap_mm(i) * 100 + bregma_ap);
     
-    if dv < 0
+    if dv <= 0
         dv = 1;
     end
 
-    if ap < 0
+    if ap <= 0
         ap = 1;
     end
     % Check the boundary_mask array

From 9d6ddba7b637e4851adda58f5b5f4720791e2835 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Fri, 6 Oct 2023 11:06:04 +0100
Subject: [PATCH 24/43] Checking the status

---
 Browsing Functions/sliceBrowser.m      | 49 ++++++++++++++++++++++++--
 Histology Functions/HistologyBrowser.m | 44 ++++++++++++++++++++++-
 Histology Functions/SliceFlipper.m     | 45 +++++++++++++++++++++--
 3 files changed, 133 insertions(+), 5 deletions(-)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index d8bc290..a875484 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -27,6 +27,8 @@ function sliceBrowser(slice_figure, processed_images_folder, f, reference_size)
     'String', '0 point', 'EdgeColor', 'none', 'Color', 'k', 'HorizontalAlignment', 'right');
 ud_slice.pointsText.Visible = 'off';
 
+check_file_status(ud_slice)
+
 % create functions needed to interact with the figure
 set(ud_slice.im, 'ButtonDownFcn', @(slice_figure,k)sliceClickCallback(slice_figure, k));
 set(slice_figure, 'KeyPressFcn', @(slice_figure, keydata)SliceAtlasHotkeyFcn(slice_figure, keydata, f));
@@ -82,6 +84,7 @@ function sliceClickCallback(im, keydata)
     
 end
 set(f, 'UserData', ud);
+end
 
 % ------------------------
 % react to keyboard press
@@ -151,7 +154,7 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
 
 
 set(fig, 'UserData', ud);
-
+end
 
 function ud = updateSliceImage(ud)
     %TODO occasionally pointList has more items than pointHands
@@ -202,4 +205,46 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
         set(ud.pointHands(:), 'Visible', 'off'); %Hide because not in 't' mode
         ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));        
     end
-    title(['Slice Viewer -- Slice ' num2str(ud.slice_num) '/' num2str(ud.total_num_files) title_ending])    
+    title(['Slice Viewer -- Slice ' num2str(ud.slice_num) '/' num2str(ud.total_num_files) title_ending])
+
+end
+
+end
+
+
+function check_file_status(ud_slice)
+
+proc_file_names = [string({ud_slice.processed_images.name})]';
+processed_images_folder = ud_slice.processed_images_folder;
+
+
+T_files = table(proc_file_names, zeros(length(proc_file_names),1),'VariableNames',{'file_names','status'});
+
+if isfile(fullfile(processed_images_folder, 'file_status.mat'))
+
+    S = load(fullfile(processed_images_folder, 'file_status.mat'));
+    for i = 1:height(T_files)
+        % apply saved values for the existing images
+        T_files.status(i) = S.T_files{S.T_files.file_names == T_files.file_names(i) , 2};
+    end
+
+else
+    error('You have to run HistologyBrowser first for the image %s', this_image_name)    
+
+end
+
+T_files.Properties.VariableDescriptions = ["",...
+    "0, raw; 1, HistologyBrowser; 2, SliceFlipper"];
+
+for i = 1:height(T_files)
+    switch T_files.status(i) 
+        case 0
+            error('You have to run HistologyBrowser and SliceFlipper for the image %s', this_image_name)
+        case 1
+            error('You have to run SliceFlipper for the image %s', this_image_name)      
+        case 2
+            % good to go!
+    end
+end
+
+end
diff --git a/Histology Functions/HistologyBrowser.m b/Histology Functions/HistologyBrowser.m
index c8058f4..319e8a1 100644
--- a/Histology Functions/HistologyBrowser.m	
+++ b/Histology Functions/HistologyBrowser.m	
@@ -41,6 +41,7 @@ function HistologyBrowser(histology_figure, save_folder, image_folder, image_fil
 ud.adjusted_image = original_image;
 
 imwrite(ud.adjusted_image, fullfile(ud.save_folder, [image_file_names{ud.file_num}(1:end-4) ud.file_name_suffix '.tif']))
+update_file_status(ud, image_file_names, ud.file_num, 1);
 
 set(histology_figure, 'UserData', ud);
 
@@ -96,11 +97,13 @@ function HistologyHotkeyFcn(fig, keydata, image_file_names, use_already_downsamp
         case 's' % save image
             disp(['saving processed image ' num2str(ud.file_num)]);
             imwrite(ud.adjusted_image, fullfile(ud.save_folder, [image_file_names{ud.file_num}(1:end-4) ud.file_name_suffix '.tif']))
+            update_file_status(ud, image_file_names, ud.file_num, 1);            
             imshow(ud.adjusted_image)
         case 'leftarrow' % save image and move to previous image
             disp(['saving processed image ' num2str(ud.file_num)]);
             imwrite(ud.adjusted_image, fullfile(ud.save_folder, [image_file_names{ud.file_num}(1:end-4) ud.file_name_suffix '.tif']))
-        
+            update_file_status(ud, image_file_names, ud.file_num, 1);
+
             if ud.file_num > 1
                 ud.file_num = ud.file_num - 1;
                 move_on = true;
@@ -110,6 +113,7 @@ function HistologyHotkeyFcn(fig, keydata, image_file_names, use_already_downsamp
         case 'rightarrow' % save image and move to next image
             disp(['saving processed image ' num2str(ud.file_num)]);
             imwrite(ud.adjusted_image, fullfile(ud.save_folder, [image_file_names{ud.file_num}(1:end-4) ud.file_name_suffix '.tif']))
+            update_file_status(ud, image_file_names, ud.file_num, 1);
              
             if ud.file_num < ud.num_files;
                 ud.file_num = ud.file_num + 1;
@@ -138,6 +142,7 @@ function HistologyHotkeyFcn(fig, keydata, image_file_names, use_already_downsamp
 
         % save immediately
         imwrite(ud.adjusted_image, fullfile(ud.save_folder, [image_file_names{ud.file_num}(1:end-4) ud.file_name_suffix '.tif']))
+        update_file_status(ud, image_file_names, ud.file_num, 1);
 
     end
 else % if pressing commands while adjusting contrast
@@ -158,4 +163,41 @@ function HistologyHotkeyFcn(fig, keydata, image_file_names, use_already_downsamp
 
 set(fig, 'UserData', ud);
 
+end
+
+function update_file_status(ud, image_file_names, K, status)
+
+    proc_file_names = strings(length(image_file_names),1);
+    for i = 1:length(image_file_names)
+        proc_file_names{i} = [image_file_names{i}(1:end-4) ud.file_name_suffix '.tif'];
+    end
+    T_files = table(proc_file_names, zeros(length(image_file_names),1),'VariableNames',{'file_names','status'});
+
+    if isfile(fullfile(ud.save_folder, 'file_status.mat'))
+
+        S = load(fullfile(ud.save_folder, 'file_status.mat'));
+        for i = 1:height(T_files)
+            % apply saved values for the existing images
+            if nnz(S.T_files.file_names == string(T_files.file_names{i})) == 1
+                T_files.status(i) = S.T_files{S.T_files.file_names == string(T_files.file_names{i}) , 2};
+            elseif nnz(S.T_files.file_names == string(T_files.file_names{i})) > 1
+                warning('multiple hits')
+            else
+                % ignore
+            end
+        end
+
+    end
+    T_files.Properties.VariableDescriptions = ["",...
+        "0, raw; 1, HistologyBrowser; 2, SliceFlipper"];
+
+    T_files.status(K) = status;
+
+    save(fullfile(ud.save_folder, 'file_status.mat'),'T_files')
+
+end
+
+
+
 
+end
\ No newline at end of file
diff --git a/Histology Functions/SliceFlipper.m b/Histology Functions/SliceFlipper.m
index c8ba7e8..0f75ea6 100644
--- a/Histology Functions/SliceFlipper.m	
+++ b/Histology Functions/SliceFlipper.m	
@@ -52,12 +52,14 @@ function SliceCropHotkeyFcn(keydata, slice_figure, folder_processed_images)
 
 switch lower(keydata.Key)   
     case 'leftarrow' % save and previous slice
-        imwrite(ud.current_slice_image, fullfile(folder_processed_images, ud.processed_image_name))        
+        imwrite(ud.current_slice_image, fullfile(folder_processed_images, ud.processed_image_name))
+        update_file_status(folder_processed_images, ud, 2) %TODO
         ud.slice_num = ud.slice_num - 1*(ud.slice_num>1);
         ud = load_next_slice(ud,folder_processed_images);
 
     case 'rightarrow' % save and next slice      
         imwrite(ud.current_slice_image, fullfile(folder_processed_images, ud.processed_image_name))
+        update_file_status(folder_processed_images, ud, 2) %TODO
         ud.slice_num = ud.slice_num + 1*(ud.slice_num < length(ud.processed_image_names));
         ud = load_next_slice(ud,folder_processed_images);
         
@@ -136,6 +138,8 @@ function SliceCropHotkeyFcn(keydata, slice_figure, folder_processed_images)
 
 set(slice_figure, 'UserData', ud);
 
+end
+
 function ud = load_next_slice(ud,folder_processed_images)
     ud.processed_image_name = ud.processed_image_names{ud.slice_num};
     ud.current_slice_image = imread(fullfile(folder_processed_images, ud.processed_image_name));
@@ -157,7 +161,8 @@ function SliceCropHotkeyFcn(keydata, slice_figure, folder_processed_images)
     ud.rotate_angle = 0;
     
     imwrite(ud.current_slice_image, fullfile(folder_processed_images, ud.processed_image_name)) 
-
+    update_file_status(folder_processed_images, ud, 2) %TODO
+end
 
 % function to rotate slice by scrolling
 function SliceScrollFcn(fig, evt)
@@ -173,5 +178,41 @@ function SliceScrollFcn(fig, evt)
 
 set(fig, 'UserData', ud);
 
+end
+
+end
+
+
+function update_file_status(folder_processed_images, ud, status)
 
+proc_file_names = ud.processed_image_names;
+this_image_name = ud.processed_image_name;
 
+K = find(proc_file_names == string(this_image_name));
+
+T_files = table(proc_file_names', zeros(length(proc_file_names),1),'VariableNames',{'file_names','status'});
+
+if isfile(fullfile(folder_processed_images, 'file_status.mat'))
+
+    S = load(fullfile(folder_processed_images, 'file_status.mat'));
+    for i = 1:height(T_files)
+        % apply saved values for the existing images
+        T_files.status(i) = S.T_files{S.T_files.file_names == string(T_files.file_names{i}) , 2};
+    end
+
+end
+T_files.Properties.VariableDescriptions = ["",...
+    "0, raw; 1, HistologyBrowser; 2, SliceFlipper"];
+
+switch T_files.status(K)
+    case 0
+        error('You have to run HistologyBrowser first for the image %s', this_image_name)
+    case 1
+        T_files.status(K) = status;
+    case 2
+        T_files.status(K) = status;
+end
+
+save(fullfile(folder_processed_images, 'file_status.mat'),'T_files')
+
+end

From 3e71d98dfe6c0d8f22a35dbcdd656ac17de232f2 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 9 Oct 2023 14:45:46 +0100
Subject: [PATCH 25/43] file status checker behaviour updated If all the images
 have been processed, MATLAB will ask you whether to proceed (Yes) or skip
 (No).

---
 Histology Functions/HistologyBrowser.m | 33 ++++++++++++++++++++++-
 Histology Functions/SliceFlipper.m     | 36 +++++++++++++++++++++++---
 2 files changed, 65 insertions(+), 4 deletions(-)

diff --git a/Histology Functions/HistologyBrowser.m b/Histology Functions/HistologyBrowser.m
index 319e8a1..104f698 100644
--- a/Histology Functions/HistologyBrowser.m	
+++ b/Histology Functions/HistologyBrowser.m	
@@ -33,6 +33,14 @@ function HistologyBrowser(histology_figure, save_folder, image_folder, image_fil
 ud.channel = min( 3, size(image,3));
 original_image = image(:,:,1:ud.channel)*gain;
 
+out = update_file_status(ud, image_file_names, 0, 0);
+if out == 0
+    fprintf("Aborted\n")
+    close();
+    return
+end
+
+
 imshow(original_image);
 title(['Adjusting channel ' num2str(ud.channel) ' on image ' num2str(ud.file_num) ' / ' num2str(ud.num_files)],...
                     'color',[1==ud.channel 2==ud.channel 3==ud.channel])
@@ -165,7 +173,7 @@ function HistologyHotkeyFcn(fig, keydata, image_file_names, use_already_downsamp
 
 end
 
-function update_file_status(ud, image_file_names, K, status)
+function out = update_file_status(ud, image_file_names, K, status)
 
     proc_file_names = strings(length(image_file_names),1);
     for i = 1:length(image_file_names)
@@ -191,10 +199,33 @@ function update_file_status(ud, image_file_names, K, status)
     T_files.Properties.VariableDescriptions = ["",...
         "0, raw; 1, HistologyBrowser; 2, SliceFlipper"];
 
+    if K == 0 % check this for the first run only
+        if ~any(T_files.status == 0)
+            answer  = questdlg("All the files have been processed by HistologyBrowser. Would you like to do it again?",...
+                "HistologyBrowser",...
+                "Yes", "No", "No");
+
+            switch answer
+                case "Yes"
+                    % proceed
+                    out = 1;
+                    return
+                case "No"
+                    % quit the function
+                    out = 0;
+                    return
+            end
+        end
+
+        out = 1;
+        return
+    end
+
     T_files.status(K) = status;
 
     save(fullfile(ud.save_folder, 'file_status.mat'),'T_files')
 
+    out = 1;
 end
 
 
diff --git a/Histology Functions/SliceFlipper.m b/Histology Functions/SliceFlipper.m
index 0f75ea6..78891dd 100644
--- a/Histology Functions/SliceFlipper.m	
+++ b/Histology Functions/SliceFlipper.m	
@@ -21,7 +21,15 @@ function SliceFlipper(slice_figure, folder_processed_images, reference_size)
 title(['Slice ' num2str(ud.slice_num) ' / ' num2str(ud.total_num_files)])
 set(slice_figure, 'UserData', ud);
 
-     
+
+out = update_file_status(folder_processed_images, ud, 0); %TODO
+if out == 0
+    fprintf("Aborted\n")
+    close();
+    return
+end
+
+
 
 % key function for slice
 set(slice_figure, 'KeyPressFcn', @(slice_figure,keydata)SliceCropHotkeyFcn(keydata, slice_figure, folder_processed_images));
@@ -183,7 +191,7 @@ function SliceScrollFcn(fig, evt)
 end
 
 
-function update_file_status(folder_processed_images, ud, status)
+function out = update_file_status(folder_processed_images, ud, status)
 
 proc_file_names = ud.processed_image_names;
 this_image_name = ud.processed_image_name;
@@ -204,6 +212,28 @@ function update_file_status(folder_processed_images, ud, status)
 T_files.Properties.VariableDescriptions = ["",...
     "0, raw; 1, HistologyBrowser; 2, SliceFlipper"];
 
+if status == 0 % check this for the first run only
+    if all(T_files.status == 2)
+        answer  = questdlg("All the files have been processed by SliceFlipper. Would you like to do it again?",...
+            "HistologyBrowser",...
+            "Yes", "No", "No");
+
+        switch answer
+            case "Yes"
+                % proceed
+                out = 1;
+                return
+            case "No"
+                % quit the function
+                out = 0;
+                return
+        end
+    end
+
+    out = 1;
+    return
+end
+
 switch T_files.status(K)
     case 0
         error('You have to run HistologyBrowser first for the image %s', this_image_name)
@@ -214,5 +244,5 @@ function update_file_status(folder_processed_images, ud, status)
 end
 
 save(fullfile(folder_processed_images, 'file_status.mat'),'T_files')
-
+out = 1;
 end

From 0c9123447ff9aec667e0dc128cf63211c3354f3a Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Tue, 10 Oct 2023 10:58:53 +0100
Subject: [PATCH 26/43] last point is set green when deleting the points

---
 Browsing Functions/sliceBrowser.m | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index a875484..1f5a94a 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -128,6 +128,8 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
             phy(i) = ud.pointHands(i).YData;
         end
         ud.pointList = [phx, ud.ref_size(1) - phy];
+        set(ud.pointHands(end),'color', [0 .9 0]);
+
 
         disp('transform point deleted')
         ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));

From bdcd3fb7649c31a1b0c8d7eb56a8a23183be205f Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Tue, 10 Oct 2023 15:25:10 +0100
Subject: [PATCH 27/43] minor bug fix

---
 Browsing Functions/sliceBrowser.m | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/Browsing Functions/sliceBrowser.m b/Browsing Functions/sliceBrowser.m
index 1f5a94a..45cf0aa 100644
--- a/Browsing Functions/sliceBrowser.m	
+++ b/Browsing Functions/sliceBrowser.m	
@@ -128,8 +128,9 @@ function SliceAtlasHotkeyFcn(fig, keydata, f)
             phy(i) = ud.pointHands(i).YData;
         end
         ud.pointList = [phx, ud.ref_size(1) - phy];
-        set(ud.pointHands(end),'color', [0 .9 0]);
-
+        if ~isempty(ud.pointHands)
+            set(ud.pointHands(end),'color', [0 .9 0]);
+        end
 
         disp('transform point deleted')
         ud.pointsText.String = sprintf('%d point(s)', length(ud.pointHands));

From eeb4136b900bb821a9c48926f510b46fd04580b8 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 30 Oct 2023 16:10:21 +0000
Subject: [PATCH 28/43] renamed the function

---
 ...ot_and_compute_probe_positions_from_ccf.m} | 31 ++++++++++++-------
 1 file changed, 19 insertions(+), 12 deletions(-)
 rename Browsing Functions/{plot_and_compute_probe_positions_from2.m => plot_and_compute_probe_positions_from_ccf.m} (93%)

diff --git a/Browsing Functions/plot_and_compute_probe_positions_from2.m b/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m
similarity index 93%
rename from Browsing Functions/plot_and_compute_probe_positions_from2.m
rename to Browsing Functions/plot_and_compute_probe_positions_from_ccf.m
index 312c928..9e1f441 100644
--- a/Browsing Functions/plot_and_compute_probe_positions_from2.m	
+++ b/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m	
@@ -1,5 +1,5 @@
-function [probes, fwireframe, fig_probes, T_probes, Tapdvml_contacts, T_borders] ...
-    = plot_and_compute_probe_positions_from2(av, st, subject_id, plane,...
+function [probes, fwireframe, fig_probes, Tapdvml_contacts, T_borders, p] ...
+    = plot_and_compute_probe_positions_from_ccf(av, st, subject_id, plane,...
     processed_images_folder, probe_save_name_suffix,probes_to_analyze, probe_lengths,...
     active_probe_length, probe_radius)
 % Create 3D plot for probe positions, 2D plots for brain structures along
@@ -7,7 +7,7 @@
 %
 %
 % SYNTAX
-% [] = plot_and_compute_probe_positions(fwireframe, black_brain, probes, subject_id, plane,...
+% [] = plot_and_compute_probe_positions_from_ccf(fwireframe, black_brain, probes, subject_id, plane,...
 %    use_tip_to_get_reference_probe_length, probe_insertion_direction)
 % [D] = func1(A,B)
 % [D] = func1(____,'Param',value)
@@ -56,10 +56,6 @@
 % fwireframe figure
 % 
 % fig_probes figure
-%            
-% 
-% T_probes   table
-%            Summary for probe penetrations
 %
 % Tapdvml_contacts
 %            table
@@ -68,6 +64,9 @@
 % T_borders  table
 %            Modified from original SharpTrack output
 %
+% p          array with 3 columns
+%            eigen vectors for the largest eigen values            
+%
 % Written by Kouichi C. Nakamura Ph.D.
 % MRC Brain Network Dynamics Unit
 % University of Oxford
@@ -123,7 +122,11 @@
 % load probe points
 probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
 ProbeColors = .75*[1.3 1.3 1.3; 1 .75 0;  .3 1 1; .4 .6 .2; 1 .35 .65; .7 .7 .9; .65 .4 .25; .7 .95 .3; .7 0 0; .6 0 .7; 1 .6 0]; 
-% order of colors: {'white','gold','turquoise','fern','bubble gum','overcast sky','rawhide', 'green apple','red','purple','orange'};
+
+ProbeColors255 = uint8(255 * ProbeColors);
+order_of_colors = ["white","gold","turquoise","fern","bubble gum","overcast sky","rawhide", "green apple","red","purple","orange"]';
+T_colors = table(order_of_colors, ProbeColors255); % useful when managing multiple probes
+
 fwireframe = [];
 
 % % scale active_probe_length appropriately
@@ -146,8 +149,9 @@
 fwireframe.InvertHardcopy = 'off';
 
 fig_probes = gobjects(1,length(probes));
-borders_table = cell(1,length(probes)) %TODO
+borders_table = cell(1,length(probes)); %TODO
 t_size = [size(probePoints.pointList.pointList,1),1];
+
 T_probes = table(repmat(string(subject_id), t_size),...
     strings(t_size), ...
     NaN(t_size),...
@@ -157,12 +161,13 @@
     NaN(t_size),...
     NaN(t_size),...
     NaN(t_size),...
-    NaN(t_size),...
     strings(t_size), ...    
     'VariableNames',{'subject_id','session_id','probe_id','probe_AB',...
         'depth_reported_um','depth_from_ACCF_um','scaling', ...
-        'scaling2',...
-        'tip_active_um', 'top_active_um', 'probe_note'});
+        'tip_active_um', 'top_active_um', 'probe_note', ...
+        });
+P = zeros([size(probePoints.pointList.pointList,1),3]);
+
 T_probes.probe_id(probes') = probes';
 T_probes.probe_lengths(probes) = probe_lengths(probes)' * 1000;
 
@@ -260,6 +265,7 @@
 
         T_probes.depth_from_ACCF_um(selected_probe) = reference_probe_length_tip/100 * 1000; 
         T_probes.scaling(selected_probe) = shrinkage_factor; 
+        P(selected_probe,:) = p; % eigenvector for largest eigenvalue
 
         % plot line the length of the probe in reference space
         probe_length_histo = round(reference_probe_length_tip);
@@ -388,3 +394,4 @@
 i = T_borders.Properties.VariableNames == "lowerBorder";
 T_borders.Properties.VariableNames{i} = 'lowerBorder_um';
 
+p = P; %rename
\ No newline at end of file

From 347b83703cfbfdc79ed8a006778fcbef673b6b9b Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 6 Nov 2023 15:04:11 +0000
Subject: [PATCH 29/43] p and m

---
 Browsing Functions/apdvml2info.m              | 30 +++++++
 Browsing Functions/apdvml_mm2ccf.m            | 90 +++++++++++++++++++
 ...lot_and_compute_probe_positions_from_ccf.m |  7 +-
 3 files changed, 125 insertions(+), 2 deletions(-)
 create mode 100644 Browsing Functions/apdvml_mm2ccf.m

diff --git a/Browsing Functions/apdvml2info.m b/Browsing Functions/apdvml2info.m
index 4b88cc9..2ddb266 100644
--- a/Browsing Functions/apdvml2info.m	
+++ b/Browsing Functions/apdvml2info.m	
@@ -5,6 +5,36 @@
 % av  1320 ,800, 1140
 % st
 %
+% SYNTAX
+% Tapdvml = apdvml2info(apdvml_points, av, st, plane)
+%
+% INPUT ARGUMENTS
+% apdvml_points
+%             n by 3 array
+%             [ap, dv, ml]
+%             Allen CCF coordinates in 10 micrometers.
+%
+% av          uint16 (1320 x 800 x 1140)
+%             3D array for structure delineation
+%
+% st          table
+%             For structures
+%
+% plane       'coronal' | 'sagittal' | 'transverse'
+%
+% OUTPUT ARGUMENTS
+% Tapdvml     table
+%             Including output ap_mm, dv_mm, and ml_mm
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 06-Nov-2023 14:41:14
+%
+% See also
+% apdvml_mm2ccf
+
 % see also
 % Analyze_Clicked_Points.m, accf2pxs_mm
 
diff --git a/Browsing Functions/apdvml_mm2ccf.m b/Browsing Functions/apdvml_mm2ccf.m
new file mode 100644
index 0000000..427af1f
--- /dev/null
+++ b/Browsing Functions/apdvml_mm2ccf.m	
@@ -0,0 +1,90 @@
+function Tccf = apdvml_mm2ccf(apdvml_mm)%, av, st, plane)
+% Opposite of apdvml2info.
+% Convert coordinates in mm back to Allen CCF coodinates in 10 micrometers
+%
+% SYNTAX
+% v = apdvml_mm2ccf(apdvml_mm)
+%
+%
+% INPUT ARGUMENTS
+% apdvml_mm   n by 3 array
+%             [ap_mm, dv_mm, ml_mm]
+%             a coordinate in mm
+%
+% % av          uint16 (1320 x 800 x 1140)
+% %             3D array for structure delineation
+% %
+% % st          table
+% %             For structures
+% %
+% % plane       'coronal' | 'sagittal' | 'transverse'
+%
+% OUTPUT ARGUMENTS
+% Tccf        table
+%             including Allen CCF coordinates in 10 micrometers.
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 06-Nov-2023 14:35:03
+%
+% See also
+% apdvml2info
+
+
+arguments
+    apdvml_mm (:,3)
+    % av
+    % st
+    % plane (1,1) string {mustBeMember(plane, {'coronal','sagittal','transverse'})}
+end
+
+% generate needed values
+bregma = allenCCFbregma(); % bregma position in reference data space
+atlas_resolution = 0.010; % mm
+
+
+%TODO
+
+ap = (- apdvml_mm(:,1))/atlas_resolution + bregma(1);
+dv = (apdvml_mm(:,2))/atlas_resolution + bregma(2);
+ml = (apdvml_mm(:,3))/atlas_resolution + bregma(3);
+
+% roi_location_curr = [ap dv ml];
+
+% % initialize array of region annotations
+% roi_annotation_curr = cell(size(apdvml_points,1),3);
+% 
+% % loop through every point to get ROI locations and region annotations
+% tf_rows = true(size(apdvml_mm,1),1);
+% for point = 1:size(apdvml_mm,1)
+% 
+%     % find the annotation, name, and acronym of the current ROI pixel
+%     depth = ceil(apdvml_points(point,2));
+%     if depth >= 1
+% 
+%         ann = av(ceil(apdvml_points(point,1)), ...
+%             depth, ... %NOTE this can take the value of 0 and cause an error (must be >= 1)
+%             ceil(apdvml_points(point,3)));
+%         name = st.safe_name{ann};
+%         acr = st.acronym{ann};
+% 
+%         roi_annotation_curr{point,1} = ann;
+%         roi_annotation_curr{point,2} = name;
+%         roi_annotation_curr{point,3} = acr;
+% 
+%     else
+%         % ignore this point, too dorsal
+%         roi_annotation_curr{point,1} = NaN;
+%         roi_annotation_curr{point,2} = '';
+%         roi_annotation_curr{point,3} = '';
+% 
+%     end
+% 
+% end
+
+Tccf = table(ap, dv, ml, 'VariableNames',{'ap_mm','dv_mm', 'ml_mm'});%, ...
+    %cell2table(roi_annotation_curr, 'VariableNames', {'annotation', 'name', 'acronym'})];
+
+end
\ No newline at end of file
diff --git a/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m b/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m
index 9e1f441..16b6996 100644
--- a/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m	
+++ b/Browsing Functions/plot_and_compute_probe_positions_from_ccf.m	
@@ -1,4 +1,4 @@
-function [probes, fwireframe, fig_probes, Tapdvml_contacts, T_borders, p] ...
+function [probes, fwireframe, fig_probes, Tapdvml_contacts, T_borders, p, m] ...
     = plot_and_compute_probe_positions_from_ccf(av, st, subject_id, plane,...
     processed_images_folder, probe_save_name_suffix,probes_to_analyze, probe_lengths,...
     active_probe_length, probe_radius)
@@ -167,6 +167,7 @@
         'tip_active_um', 'top_active_um', 'probe_note', ...
         });
 P = zeros([size(probePoints.pointList.pointList,1),3]);
+M = zeros([size(probePoints.pointList.pointList,1),3]);
 
 T_probes.probe_id(probes') = probes';
 T_probes.probe_lengths(probes) = probe_lengths(probes)' * 1000;
@@ -266,6 +267,7 @@
         T_probes.depth_from_ACCF_um(selected_probe) = reference_probe_length_tip/100 * 1000; 
         T_probes.scaling(selected_probe) = shrinkage_factor; 
         P(selected_probe,:) = p; % eigenvector for largest eigenvalue
+        M(selected_probe,:) = m; % highest point
 
         % plot line the length of the probe in reference space
         probe_length_histo = round(reference_probe_length_tip);
@@ -394,4 +396,5 @@
 i = T_borders.Properties.VariableNames == "lowerBorder";
 T_borders.Properties.VariableNames{i} = 'lowerBorder_um';
 
-p = P; %rename
\ No newline at end of file
+p = P; %rename
+m = M;
\ No newline at end of file

From cc91f663b48268e6a47b284259483b60541fb211 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 6 Nov 2023 15:53:24 +0000
Subject: [PATCH 30/43] bug fix

---
 Browsing Functions/prep_Tapdvml_contacts.m | 1 +
 1 file changed, 1 insertion(+)

diff --git a/Browsing Functions/prep_Tapdvml_contacts.m b/Browsing Functions/prep_Tapdvml_contacts.m
index 17acdb0..aaf8924 100644
--- a/Browsing Functions/prep_Tapdvml_contacts.m	
+++ b/Browsing Functions/prep_Tapdvml_contacts.m	
@@ -44,6 +44,7 @@
 
     tf = Tapdvml_contacts.probe_id == i;
     Tapdvml_contacts.session_id(tf) = string(T_probes.session_id(i));
+    Tapdvml_contacts.subject_id(tf) = string(T_probes.subject_id(i));
     Tapdvml_contacts.probe_AB(tf) = string(T_probes.probe_AB(i));
     Tapdvml_contacts.probe_note(tf) = string(T_probes.probe_note(i));
     

From eaa68f355a339e2d536d52537adda83b94816d04 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 13 Nov 2023 11:23:48 +0000
Subject: [PATCH 31/43] Create updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 542 ++++++++++++++++++
 1 file changed, 542 insertions(+)
 create mode 100644 Browsing Functions/updown_probe_with_slider.m

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
new file mode 100644
index 0000000..04468c8
--- /dev/null
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -0,0 +1,542 @@
+function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
+    task_dir_name, imaging_session_dir, image_folder_name, depth_level)
+
+arguments
+    session_id (1,1) string
+    probeAB (1,1) string {mustBeMember(probeAB,["ProbeA","ProbeB"])}
+    plane (1,1) string {mustBeMember(plane,["coronal","sagittal", "transverse"])}
+    sessions_dir (1,1) string  {mustBeFolder}
+    task_dir_name (1,1) string
+    imaging_session_dir (1,1) string  {mustBeFolder}
+    image_folder_name (1,1) string
+    depth_level (1,1) double {mustBePositive, mustBeInteger} = 6
+end
+
+sorter_output_dir = fullfile(sessions_dir, task_dir_name,  ...
+    session_id, "processed\kilosort", probeAB, "sorter_output");
+
+recording_cell_metrics_path = fullfile(sorter_output_dir, "recording.cell_metrics.cellinfo.mat");
+s = load(recording_cell_metrics_path);
+recording_cell_metrics = s.cell_metrics;
+
+opts = detectImportOptions(Tapdvml_contacts_path);
+opts = setvartype(opts, 'session_id', 'string');
+
+Tapdvml_contacts = readtable(Tapdvml_contacts_path, opts );
+
+% Tborders_table = readtable(borders_table_path);
+
+T_probes=  readtable(Tprobes_path);
+
+if ~ ismember('p_1',T_probes.Properties.VariableNames) || ...
+        ~ ismember('p_2',T_probes.Properties.VariableNames) ||...
+        ~ ismember('p_3',T_probes.Properties.VariableNames)
+    warning('The eigen vectors p is not found in T_probes. You cannot update the Tapdvml_contacts.')
+end
+
+
+%% Figure
+
+ufig = uifigure(Position=[800, 150, 720, 1080]);
+
+uax1 = uiaxes(ufig);
+uax1.PositionConstraint = 'innerposition';
+uax1.Position=[100, 150, 350, 800];
+ylabel(uax1, 'Dsitance from the tip (mm)')
+uax1.XTick =[];
+
+uax2 = uiaxes(ufig);
+uax2.PositionConstraint = 'innerposition';
+uax2.Position=[448, 150, 80, 800];
+uax2.YTickLabel =[];
+uax2.XTick =[];
+
+
+uax3 = uiaxes(ufig);
+uax3.PositionConstraint = 'innerposition';
+uax3.Position=[525, 150, 120, 800];
+uax3.YTickLabel =[];
+uax3.XTick =[];
+
+
+tickdir([uax1,uax2, uax3], 'out')
+ticklengthcm([uax1,uax2, uax3], 0.2)
+
+% usl1 = uislider(ufig, Orientation='vertical' , Limits=[-50, 50]);
+% usl1.Position = [50, 200, 3, 300];
+
+bg1 = uibuttongroup(ufig, Title='Move');
+bg1.Position = [20, 150, 70, 200];
+
+bt1 = uibutton(bg1, "Text","+5", "ButtonPushedFcn", @(src, event) move_vertically(uax1, 5));
+bt1.Position = [10, 140, 50, 30];
+
+bt2 = uibutton(bg1, "Text","+1", "ButtonPushedFcn", @(src, event) move_vertically(uax1, 1));
+bt2.Position = [10, 110, 50, 30];
+
+bt3 = uibutton(bg1, "Text","-1", "ButtonPushedFcn", @(src, event) move_vertically(uax1, -1));
+bt3.Position = [10, 40, 50, 30];
+
+bt4 = uibutton(bg1, "Text","-5", "ButtonPushedFcn", @(src, event) move_vertically(uax1, -5));
+bt4.Position = [10, 10, 50, 30];
+
+bt6 = uibutton(bg1, "Text","0", "ButtonPushedFcn", @(src, event) move_back_to_original(uax1));
+bt6.Position = [10, 75, 50, 30];
+
+
+bt7 = uibutton(ufig, "Text","Save", "ButtonPushedFcn", @(src, event) save_updown_to_table(uax1));
+bt7.Position = [150, 30, 300, 50];
+
+tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.5 0.1],  'String', session_id +"/" + probeAB,...
+    HorizontalAlignment='center',FontSize=18,LineStyle='none');
+
+
+%% Plot cells
+n = length(recording_cell_metrics.firingRate);
+
+x_val = rand(n,1);
+
+y = recording_cell_metrics.maxWaveformCh * 0.010; % mm
+
+c = recording_cell_metrics.firingRate;
+
+sc1 = scatter(uax3, x_val, y, 36, c, LineWidth=1.5);
+uax3.Color = 'k';
+
+ylim(uax3, [-0.100, 3.940])
+
+cb1 =colorbar(uax3,'eastoutside');
+ylabel(cb1,'Mean firing rates (spikes/s)' )
+cb1.Label.FontSize = 14;
+cb1.TickDirection = 'out';
+ticklengthcm(cb1, 0.2)
+
+
+%% Moving average of five channels
+% 
+% SDF like plot with Gaussian kernel convolution is better
+cla(uax2,'reset')
+
+movingaverageval = zeros(384,1);
+
+for i = 1:384
+
+    % moving average of five channels
+    chans = i - 1 : i + 3;
+    ind = ismember(recording_cell_metrics.maxWaveformCh, chans);
+    movingaverageval(i) = mean(recording_cell_metrics.firingRate(ind));
+
+end
+
+isc1 = imagesc(uax2, 1, (1:384)'*0.01, movingaverageval);
+
+uax2.YDir = 'normal';
+ylim(uax2, [-0.100, 3.940])
+uax2.XTick =[];
+
+uax2.Color = 'k';
+
+uax3.CLim = uax2.CLim; % same color scale
+
+
+%% Read the Allen CCF data
+% directory of reference atlas files
+annotation_volume_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\annotation_volume_10um_by_index.npy";
+structure_tree_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\structure_tree_safe_2017.csv";
+template_volume_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\template_volume_10um.npy";
+
+% load the reference brain and region annotations
+if ~exist('av','var') || ~exist('st','var') || ~exist('tv','var')
+    disp('loading reference atlas...')
+    av = readNPY(annotation_volume_location);
+    st = loadStructureTree(structure_tree_location);
+    tv = readNPY(template_volume_location);
+end
+
+
+probeAB = "ProbeA";
+
+switch probeAB
+    case "ProbeA"
+        probeAB_short = "A";
+    case "ProbeB"
+        probeAB_short = "B";
+    otherwise
+
+end
+
+tf = T_probes.session_id == session_id & T_probes.probe_AB == probeAB_short;
+
+probe_id = T_probes{tf, "probe_id"};
+
+
+depth = 6;
+
+Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
+
+%%
+anc = preallocatestruct(["index", "anc_id", "anc_name", "anc_color_hex", "anc_color_255", "anc_color"], [height(Tapdvml_contacts_this), 1]);
+% profile on
+st.name = regexprep(st.name, '["'']',''); % remove clutters
+
+f = waitbar(0,'1','Name','Approximating pi...',...
+    'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
+
+for i = 1:height(Tapdvml_contacts_this) % SLOW
+    waitbar( i/height(Tapdvml_contacts_this), f, ...
+        fprintf("%d of %d", i, height(Tapdvml_contacts_this)))
+    name = Tapdvml_contacts_this.name{i};
+    [anc(i)] = find_name_for_depth(st, depth_level, name); %TODO stopped working for i = 61, i = 1327
+end
+% profile viewer
+
+delete(f)
+
+%%
+Tanc = struct2table(anc, AsArray=true);
+
+Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
+
+
+% Sample data
+anc_id = Tapdvml_contacts_this.anc_id;
+
+anc_name = Tapdvml_contacts_this.anc_name;
+
+anc_color = Tapdvml_contacts_this.anc_color;
+
+
+anc_id_diff = diff(anc_id);
+
+start_ind = [1; find(anc_id_diff) + 1];
+
+end_ind = [start_ind(2:end) - 1; length(anc_id)];
+
+block_names = anc_name(start_ind);
+
+block_colors = anc_color(start_ind, :);
+
+
+Tblocks = table(block_names, start_ind, end_ind, block_colors, ...
+    VariableNames={'block_names', 'start_ind','end_ind', 'block_colors'});
+
+
+%% Plot structures
+cla(uax1)
+
+uax1.Color = 'k';
+
+for i = 1:height(Tblocks)
+    X = [0 1 1 0];
+    Y = [Tblocks{i,'start_ind'}-0.5, Tblocks{i,'start_ind'}-0.5,...
+         Tblocks{i,'end_ind'}+0.5, Tblocks{i,'end_ind'}+0.5]/100; % in mm
+    patch(uax1, X, Y, Tblocks.block_colors(i,:));
+    text(uax1, 0.5, mean([Tblocks{i,'start_ind'}, Tblocks{i,'end_ind'}])/100, ...
+        Tblocks.block_names(i),...
+        'FontSize',14,...
+        'HorizontalAlignment','center', Clipping='on');
+end
+
+ylim(uax1, [-0.100, 3.940])
+
+uax1.YLabel.FontSize = 14;
+
+
+
+function move_back_to_original(uax1)
+
+if isfield(uax1.UserData, 'YLim_shift_mm')
+    ch = uax1.Children;
+
+    for i = 1:length(ch)
+        step = - uax1.UserData.YLim_shift_mm;
+
+        if isa(ch(i),'matlab.graphics.primitive.Text')
+            ch(i).Position(2) = ch(i).Position(2) + step;
+
+        elseif isa(ch(i),'matlab.graphics.primitive.Patch')
+            ch(i).YData = ch(i).YData + step;
+
+        end
+
+    end
+
+    uax1.UserData.YLim_shift_mm = 0;
+else
+    %nothing to do
+end
+
+end
+
+
+function move_vertically(uax1, step)
+
+% arguments
+%     uax1(1,1)
+%     step (1,1) {mustBeInteger}
+% end
+
+ch = uax1.Children;
+
+for i = 1:length(ch)
+
+    if isa(ch(i),'matlab.graphics.primitive.Text')
+        ch(i).Position(2) = ch(i).Position(2) + step*0.01;
+
+    elseif isa(ch(i),'matlab.graphics.primitive.Patch')
+        ch(i).YData = ch(i).YData + step*0.01;
+
+    end
+
+end
+
+if isfield(uax1.UserData, 'YLim_shift_mm')
+    uax1.UserData.YLim_shift_mm = uax1.UserData.YLim_shift_mm + step*0.01;
+else
+    uax1.UserData.YLim_shift_mm = step*0.01;
+end
+
+end
+
+
+
+function save_updown_to_table(uax1, ~) 
+
+if isempty(uax1.UserData)
+    disp('The probe has not moved on GUI yet. No change made.')
+    return
+else
+    if isfield(uax1.UserData, 'YLim_shift_mm')
+        %TODO move
+    else
+        disp('YLim_shift_mm is not found. No change made.')
+        return
+    end
+end
+
+
+%TODO save the backup
+
+assert(endsWith(Tapdvml_contacts_path,'.xlsx'))
+
+assert(isfile(Tapdvml_contacts_path))
+
+f_info = dir(Tapdvml_contacts_path);
+
+dt = datetime(f_info.date, 'InputFormat', 'dd-MMM-yyyy HH:mm:ss');
+
+dt.Format = 'yyyy-MM-dd_HH-mm-ss';
+suffix = string(dt);
+
+new_file_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + ".xlsx");
+
+original_backup_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + "_original.xlsx");
+
+if isfile(original_backup_path)
+    % save a backup file
+
+    copyfile(Tapdvml_contacts_path, new_file_path)
+
+else
+    % this is the first time you change the Excel file
+    % save a backup file
+
+    copyfile(Tapdvml_contacts_path, original_backup_path)
+
+end
+
+%% Job
+see plot_and_compute_probe_positions_from_ccf.m
+% I need the eigen vector, to be saved in T_probes?
+
+switch probeAB
+    case "ProbeA"
+        probeAB_ = "A";
+    case "ProbeB"
+        probeAB_ = "B";
+    case "optic fiber"
+        probeAB_ = "optic fiber";
+end
+
+% eigen vector
+tf = T_probes.session_id == session_id & ...
+    T_probes.probe_AB == probeAB_;
+
+assert(nnz(tf) == 1)
+
+p = T_probes{T_probes.session_id == session_id & ...
+    T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
+
+m = T_probes{T_probes.session_id == session_id & ...
+    T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
+
+%TODO what columns to change or add???
+
+processed_images_folder = fullfile(image_folder, 'processed');
+
+probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
+
+% get the probe points for the currently analyzed probe
+if strcmp(plane,'coronal')
+    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [3 2 1]);
+elseif strcmp(plane,'sagittal')
+    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 2 3]);
+elseif strcmp(plane,'transverse')
+    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 3 2]);
+end
+
+% m is the brain entry point
+
+%TODO modifiy the m and curr_probePoints(tip_index,:) by YLim_shift_mm
+% p is in 10 µm
+
+if strcmp(probe_insertion_direction, 'down')
+    [depth, tip_index] = max(curr_probePoints(:,2));
+elseif strcmp(probe_insertion_direction, 'up')
+    [depth, tip_index] = min(curr_probePoints(:,2));
+end
+
+% curr_probePoints(tip_index,:) either to get it from the ProbePoints or
+% from Tapdvml_contacts.xlsx (convert ap_mm, dv_mm, ml_mm back to allen coordinates)
+% opposite of apdvml2info
+
+
+% Tapdvml_contacts.session_id
+
+% tip_mm = 
+
+YLim_shift_mm = uax1.UserData.YLim_shift_mm;
+new_cp = curr_probePoints(tip_index,:) - YLim_shift_mm*100; % minus to move up
+
+
+Tapdvml_m = apdvml2info(m, av, st, plane);
+
+Tapdvml_tip = apdvml2info(new_cp, av, st, plane);
+
+
+
+% measure the distance 
+
+tip2surface_mm = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+    (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
+    (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+
+tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+    (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
+    (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+
+top_active = (m * active_probe_length + ...
+    curr_probePoints(tip_index,:) * (tip2surface_mm - active_probe_length))...
+    /tip2surface_mm;
+
+% obtained the information for all the 384 channels
+
+
+a = [linspace(curr_probePoints(tip_index,1), top_active(1), 192)', ...
+    linspace(curr_probePoints(tip_index,2), top_active(2), 192)', ...
+    linspace(curr_probePoints(tip_index,3), top_active(3), 192)'];
+probe_contact_points = zeros(384, 3);
+for i = 1:192
+    probe_contact_points(2*i-1,:) = a(i,:);
+    probe_contact_points(2*i,:) = a(i,:);
+end
+clear a
+
+c_t_contacts = cell(384,1);
+
+theta = acos(p(2)); % Assuming p(2) corresponds to the DV direction
+
+for i = 1:384
+    c_t_contacts{i} = apdvml2info(probe_contact_points(i,:), av, st, plane);
+    c_t_contacts{i}.contact_id = repmat(i,height(c_t_contacts{i}));
+    c_t_contacts{i}.probe_id = repmat(selected_probe,height(c_t_contacts{i}));
+    c_t_contacts{i}.depth_mm = tip2surface_mm - 0.020 * floor((i-1)/2);
+    
+    % Project the depth along the line
+    projected_depth_mm = c_t_contacts{i}.depth_mm * cos(theta);
+
+    % Convert using the transformation for the chosen plane
+    projected_depth_mm_paxinos = accf2pxs_mm(projected_depth_mm, plane, 'distance');
+
+    c_t_contacts{i}.depth_mm_paxinos = projected_depth_mm_paxinos;
+end
+
+c_Tapdvml_contacts{selected_probe} = vertcat(c_t_contacts{:});
+clear c_t_contacts
+
+%TODO writetable()
+
+keyboard()
+
+end
+
+end
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+function [anc, this] = find_name_for_depth(st, depth, name)
+
+arguments
+    st table
+    depth (1,1) double {mustBeInteger,mustBeNonnegative}
+    name (1,1) string
+end
+
+st.name = regexprep(st.name, '["'']','');
+
+id = st.id(st.name == name);
+
+
+cstr = arrayfun(@(x) strsplit(x, "/"), string(st.structure_id_path),'UniformOutput',false);
+
+% remove empty string ""
+
+% cemp = cellfun(@(x) x == "" , cstr,'UniformOutput',false);
+
+for j = 1:size(cstr,1) % i = 741
+    % fprintf("j = %d\n",j)
+    % cstr{i}(cemp{i}) = [];
+    % v = zeros(1,length(cstr{i}),'int32');
+    % for j = 1:length(cstr{i})
+    %     fprintf("j = %d\n",j)
+    %     v(j) = int32(str2double(cstr{i}(j)));
+    % end
+    % cstr{i} = v;
+
+    if cstr{j}(1) == ""
+        cstr{j}(1) = [];
+    end
+    if cstr{j}(end) == ""
+        cstr{j}(end) = [];
+    end    
+    cstr{j} = arrayfun(@(x) int32(str2double(x)), cstr{j});%SUPER SLOW
+
+end
+
+
+st.structure_id_path_vec = cstr;
+
+
+anc_id_path = st.structure_id_path_vec{st.id == id};
+if length(anc_id_path) <= depth
+    anc.anc_id = anc_id_path(end);
+else
+    anc.anc_id = anc_id_path(depth + 1);
+end
+
+anc.anc_name = string(st.name(st.id == anc.anc_id));
+anc.anc_color_hex = string(st.color_hex_triplet(st.id == anc.anc_id,:));
+anc.anc_color_255 = [hex2dec(anc.anc_color_hex{1}(1:2)), hex2dec(anc.anc_color_hex{1}(3:4)), hex2dec(anc.anc_color_hex{1}(5:6))];
+anc.anc_color = anc.anc_color_255/255;
+anc.index = st.index(st.id == anc.anc_id,:);
+
+this.id = id;
+this.name = name;
+this.color_hex = string(st.color_hex_triplet(st.id == id,:));
+this.color_255 = [hex2dec(this.color_hex{1}(1:2)), hex2dec(this.color_hex{1}(3:4)), hex2dec(this.color_hex{1}(5:6))];
+this.color = this.color_255/255;
+
+
+end
+
+

From d273bb3de86f8cb0dbf3ee991ea97a432a7eacaf Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 13 Nov 2023 11:55:41 +0000
Subject: [PATCH 32/43] Update updown_probe_with_slider.m

bug fixes
---
 Browsing Functions/updown_probe_with_slider.m | 81 +++++++++----------
 1 file changed, 40 insertions(+), 41 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 04468c8..61db6ae 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -1,5 +1,5 @@
 function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
-    task_dir_name, imaging_session_dir, image_folder_name, depth_level)
+    task_dir_name, imaging_session_dir, image_folder_name, active_probe_length, depth_level)
 
 arguments
     session_id (1,1) string
@@ -9,6 +9,7 @@ function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
     task_dir_name (1,1) string
     imaging_session_dir (1,1) string  {mustBeFolder}
     image_folder_name (1,1) string
+    active_probe_length (1,1) double = 3.84 % in mm
     depth_level (1,1) double {mustBePositive, mustBeInteger} = 6
 end
 
@@ -170,8 +171,6 @@ function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
 probe_id = T_probes{tf, "probe_id"};
 
 
-depth = 6;
-
 Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
 
 %%
@@ -278,13 +277,13 @@ function move_vertically(uax1, step)
 
 ch = uax1.Children;
 
-for i = 1:length(ch)
+for j = 1:length(ch)
 
-    if isa(ch(i),'matlab.graphics.primitive.Text')
-        ch(i).Position(2) = ch(i).Position(2) + step*0.01;
+    if isa(ch(j),'matlab.graphics.primitive.Text')
+        ch(j).Position(2) = ch(j).Position(2) + step*0.01;
 
-    elseif isa(ch(i),'matlab.graphics.primitive.Patch')
-        ch(i).YData = ch(i).YData + step*0.01;
+    elseif isa(ch(j),'matlab.graphics.primitive.Patch')
+        ch(j).YData = ch(j).YData + step*0.01;
 
     end
 
@@ -370,8 +369,6 @@ function save_updown_to_table(uax1, ~)
 m = T_probes{T_probes.session_id == session_id & ...
     T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
 
-%TODO what columns to change or add???
-
 processed_images_folder = fullfile(image_folder, 'processed');
 
 probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
@@ -421,24 +418,24 @@ function save_updown_to_table(uax1, ~)
     (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
     (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
 
-tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
-    (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
-    (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+% tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+%     (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
+%     (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
 
 top_active = (m * active_probe_length + ...
-    curr_probePoints(tip_index,:) * (tip2surface_mm - active_probe_length))...
+    new_cp * (tip2surface_mm - active_probe_length))...
     /tip2surface_mm;
 
 % obtained the information for all the 384 channels
 
 
-a = [linspace(curr_probePoints(tip_index,1), top_active(1), 192)', ...
-    linspace(curr_probePoints(tip_index,2), top_active(2), 192)', ...
-    linspace(curr_probePoints(tip_index,3), top_active(3), 192)'];
+a = [linspace(new_cp(1), top_active(1), 192)', ...
+    linspace(new_cp(2), top_active(2), 192)', ...
+    linspace(new_cp(3), top_active(3), 192)'];
 probe_contact_points = zeros(384, 3);
-for i = 1:192
-    probe_contact_points(2*i-1,:) = a(i,:);
-    probe_contact_points(2*i,:) = a(i,:);
+for j = 1:192
+    probe_contact_points(2*j-1,:) = a(j,:);
+    probe_contact_points(2*j,:) = a(j,:);
 end
 clear a
 
@@ -446,27 +443,39 @@ function save_updown_to_table(uax1, ~)
 
 theta = acos(p(2)); % Assuming p(2) corresponds to the DV direction
 
-for i = 1:384
-    c_t_contacts{i} = apdvml2info(probe_contact_points(i,:), av, st, plane);
-    c_t_contacts{i}.contact_id = repmat(i,height(c_t_contacts{i}));
-    c_t_contacts{i}.probe_id = repmat(selected_probe,height(c_t_contacts{i}));
-    c_t_contacts{i}.depth_mm = tip2surface_mm - 0.020 * floor((i-1)/2);
+for j = 1:384
+    c_t_contacts{j} = apdvml2info(probe_contact_points(j,:), av, st, plane);
+    c_t_contacts{j}.contact_id = repmat(j,height(c_t_contacts{j}));
+    c_t_contacts{j}.probe_id = repmat(selected_probe,height(c_t_contacts{j}));
+    c_t_contacts{j}.depth_mm = tip2surface_mm - 0.020 * floor((j-1)/2);
     
     % Project the depth along the line
-    projected_depth_mm = c_t_contacts{i}.depth_mm * cos(theta);
+    projected_depth_mm = c_t_contacts{j}.depth_mm * cos(theta);
 
     % Convert using the transformation for the chosen plane
     projected_depth_mm_paxinos = accf2pxs_mm(projected_depth_mm, plane, 'distance');
 
-    c_t_contacts{i}.depth_mm_paxinos = projected_depth_mm_paxinos;
+    c_t_contacts{j}.depth_mm_paxinos = projected_depth_mm_paxinos;
 end
 
-c_Tapdvml_contacts{selected_probe} = vertcat(c_t_contacts{:});
+Tapdvml_contacts_new = vertcat(c_t_contacts{:});
 clear c_t_contacts
 
-%TODO writetable()
+%% update the relevant rows of Tapdvml_contacts
+
+%% update values
+for j = 1:height(Tapdvml_contacts_new)
+    probe_id = Tapdvml_contacts_new{j,"probe_id"};
+    contact_id = Tapdvml_contacts_new{j,"contact_id"};
+
+    cols = ["ap_mm","dv_mm","dv_mm_paxinos","ml_mm","annotation","name","acronym","contact_id","probe_id","depth_mm","depth_mm_paxinos"];
+    Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id ...
+        & Tapdvml_contacts.contact_id == contact_id,  cols) = ...
+        Tapdvml_contacts_new(j, cols);   
+end
+
+writetable(Tapdvml_contacts, "Tapdvml_contacts.xlsx",'FileType','spreadsheet')
 
-keyboard()
 
 end
 
@@ -491,17 +500,7 @@ function save_updown_to_table(uax1, ~)
 
 % remove empty string ""
 
-% cemp = cellfun(@(x) x == "" , cstr,'UniformOutput',false);
-
-for j = 1:size(cstr,1) % i = 741
-    % fprintf("j = %d\n",j)
-    % cstr{i}(cemp{i}) = [];
-    % v = zeros(1,length(cstr{i}),'int32');
-    % for j = 1:length(cstr{i})
-    %     fprintf("j = %d\n",j)
-    %     v(j) = int32(str2double(cstr{i}(j)));
-    % end
-    % cstr{i} = v;
+for j = 1:size(cstr,1) 
 
     if cstr{j}(1) == ""
         cstr{j}(1) = [];

From d52e20ceef54d6faf5963a2af86065c3ce229857 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 13 Nov 2023 13:01:42 +0000
Subject: [PATCH 33/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 81 +++++++++++++------
 1 file changed, 58 insertions(+), 23 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 61db6ae..4e334dc 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -1,16 +1,39 @@
-function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
-    task_dir_name, imaging_session_dir, image_folder_name, active_probe_length, depth_level)
+function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_dir,...
+    task_dir_name, imaging_session_dir, image_folder_name, depth_level, ...
+    active_probe_length, probe_insertion_direction)
+% Move up and down a probe using a slider to match the anatomical borders
+% to the changes in the firing rates of neurons
+%
+% EXAMPLE USAGE
+% session_id = "kms058-2023-03-25-184034"
+% probeAB ="ProbeA";
+% plane = "sagittal";
+% sessions_dir = "\\ettina\Magill_Lab\Julien\Data\head-fixed\by_sessions";
+% task_dir_name = "reaching_go_spout_bar_nov22"
+% imaging_session_dir = "\\ettina\Magill_Lab\Kouichi Nakamura\Analysis\Images from Otto\20230406 kms058";
+% image_folder_name = 'RGB_ignore';
+% 
+% % load the reference brain and region annotations
+% if ~exist('av','var') || ~exist('st','var') || ~exist('tv','var')
+%     disp('loading reference atlas...')
+%     av = readNPY(annotation_volume_location);
+%     st = loadStructureTree(structure_tree_location);
+%     tv = readNPY(template_volume_location);
+% end
 
 arguments
-    session_id (1,1) string
-    probeAB (1,1) string {mustBeMember(probeAB,["ProbeA","ProbeB"])}
-    plane (1,1) string {mustBeMember(plane,["coronal","sagittal", "transverse"])}
-    sessions_dir (1,1) string  {mustBeFolder}
-    task_dir_name (1,1) string
-    imaging_session_dir (1,1) string  {mustBeFolder}
-    image_folder_name (1,1) string
-    active_probe_length (1,1) double = 3.84 % in mm
+    av uint16
+    st table
+    session_id (1,1) string % eg. "kms058-2023-03-25-184034"
+    probeAB (1,1) string {mustBeMember(probeAB,["ProbeA","ProbeB"])} % eg. "ProbeA"
+    plane (1,1) string {mustBeMember(plane,["coronal","sagittal", "transverse"])} % eg. "sagittal"
+    sessions_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Julien\Data\head-fixed\by_sessions"
+    task_dir_name (1,1) string % eg. "reaching_go_spout_bar_nov22"
+    imaging_session_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Kouichi Nakamura\Analysis\Images from Otto\20230406 kms058"
+    image_folder_name (1,1) string = "RGB"
     depth_level (1,1) double {mustBePositive, mustBeInteger} = 6
+    active_probe_length (1,1) double = 3.84 % in mm
+    probe_insertion_direction (1,1) string {mustBeMember(probe_insertion_direction, ["down","up"])} = "down"
 end
 
 sorter_output_dir = fullfile(sessions_dir, task_dir_name,  ...
@@ -20,6 +43,17 @@ function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
 s = load(recording_cell_metrics_path);
 recording_cell_metrics = s.cell_metrics;
 
+image_folder =fullfile(imaging_session_dir, image_folder_name);  %TODO
+
+probe_save_name_suffix = '_probe';
+
+Tapdvml_contacts_path = fullfile(imaging_session_dir, "Tapdvml_contacts.xlsx");
+
+% borders_table_path= fullfile(imaging_session_dir, "borders_table.xlsx");
+
+Tprobes_path= fullfile(imaging_session_dir, "T_probes.xlsx");
+
+
 opts = detectImportOptions(Tapdvml_contacts_path);
 opts = setvartype(opts, 'session_id', 'string');
 
@@ -178,7 +212,7 @@ function updown_probe_with_slider(session_id, probeAB, plane, sessions_dir,...
 % profile on
 st.name = regexprep(st.name, '["'']',''); % remove clutters
 
-f = waitbar(0,'1','Name','Approximating pi...',...
+f = waitbar(0,'1','Name','Analysing structure hierarchy...',...
     'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
 
 for i = 1:height(Tapdvml_contacts_this) % SLOW
@@ -247,14 +281,14 @@ function move_back_to_original(uax1)
 if isfield(uax1.UserData, 'YLim_shift_mm')
     ch = uax1.Children;
 
-    for i = 1:length(ch)
+    for j = 1:length(ch)
         step = - uax1.UserData.YLim_shift_mm;
 
-        if isa(ch(i),'matlab.graphics.primitive.Text')
-            ch(i).Position(2) = ch(i).Position(2) + step;
+        if isa(ch(j),'matlab.graphics.primitive.Text')
+            ch(j).Position(2) = ch(j).Position(2) + step;
 
-        elseif isa(ch(i),'matlab.graphics.primitive.Patch')
-            ch(i).YData = ch(i).YData + step;
+        elseif isa(ch(j),'matlab.graphics.primitive.Patch')
+            ch(j).YData = ch(j).YData + step;
 
         end
 
@@ -345,7 +379,7 @@ function save_updown_to_table(uax1, ~)
 end
 
 %% Job
-see plot_and_compute_probe_positions_from_ccf.m
+% see plot_and_compute_probe_positions_from_ccf.m
 % I need the eigen vector, to be saved in T_probes?
 
 switch probeAB
@@ -374,12 +408,13 @@ function save_updown_to_table(uax1, ~)
 probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
 
 % get the probe points for the currently analyzed probe
+
 if strcmp(plane,'coronal')
-    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [3 2 1]);
+    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [3 2 1]);
 elseif strcmp(plane,'sagittal')
-    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 2 3]);
+    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 2 3]);
 elseif strcmp(plane,'transverse')
-    curr_probePoints = probePoints.pointList.pointList{selected_probe,1}(:, [1 3 2]);
+    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 3 2]);
 end
 
 % m is the brain entry point
@@ -446,7 +481,7 @@ function save_updown_to_table(uax1, ~)
 for j = 1:384
     c_t_contacts{j} = apdvml2info(probe_contact_points(j,:), av, st, plane);
     c_t_contacts{j}.contact_id = repmat(j,height(c_t_contacts{j}));
-    c_t_contacts{j}.probe_id = repmat(selected_probe,height(c_t_contacts{j}));
+    c_t_contacts{j}.probe_id = repmat(probe_id,height(c_t_contacts{j}));
     c_t_contacts{j}.depth_mm = tip2surface_mm - 0.020 * floor((j-1)/2);
     
     % Project the depth along the line
@@ -474,8 +509,8 @@ function save_updown_to_table(uax1, ~)
         Tapdvml_contacts_new(j, cols);   
 end
 
-writetable(Tapdvml_contacts, "Tapdvml_contacts.xlsx",'FileType','spreadsheet')
-
+writetable(Tapdvml_contacts, fullfile(imaging_session_dir,"Tapdvml_contacts.xlsx"),'FileType','spreadsheet')
+frpint("Tapdvml_contacts.xlsx has been updated.\n")
 
 end
 

From beb8d6462cd34ef8a4584285abc97fb20912785d Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 13 Nov 2023 15:57:03 +0000
Subject: [PATCH 34/43] Update AtlasTransformBrowser.m

fprintf to report probe points number
---
 Browsing Functions/AtlasTransformBrowser.m | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/AtlasTransformBrowser.m b/Browsing Functions/AtlasTransformBrowser.m
index 78cd002..553fb4f 100644
--- a/Browsing Functions/AtlasTransformBrowser.m	
+++ b/Browsing Functions/AtlasTransformBrowser.m	
@@ -653,7 +653,8 @@ function hotkeyFcn(f, slice_figure, keydata, allData, save_location, save_suffix
             disp('transform loaded -- press ''l'' again now to load probe points');
         else % load probe points
             if ~size(ud.pointList{1,1},1)
-                probe_points = load(fullfile(save_location, ['probe_points' save_suffix]));  disp('probe points loaded')
+                probe_points = load(fullfile(save_location, ['probe_points' save_suffix]));  
+                fprintf('%d probe points loaded\n', length(probe_points.pointList.pointList))
                 ud.pointList = probe_points.pointList.pointList;
                 ud.pointHands = probe_points.pointList.pointHands;
             else

From 68a06810d94036b6a435b19a2fd6de39bfdea31a Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 13 Nov 2023 17:10:01 +0000
Subject: [PATCH 35/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 68 ++++++++++++++++---
 1 file changed, 60 insertions(+), 8 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 4e334dc..6e986e8 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -36,6 +36,14 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
     probe_insertion_direction (1,1) string {mustBeMember(probe_insertion_direction, ["down","up"])} = "down"
 end
 
+%TODO add button to go next and previous probe
+%TODO use probe_id
+% related, use animal_id
+% make session_id, probeAB
+
+%TODO what if optic fiber data is chosen?
+
+
 sorter_output_dir = fullfile(sessions_dir, task_dir_name,  ...
     session_id, "processed\kilosort", probeAB, "sorter_output");
 
@@ -49,15 +57,29 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 Tapdvml_contacts_path = fullfile(imaging_session_dir, "Tapdvml_contacts.xlsx");
 
+original_backup_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_original.xlsx");
+
 % borders_table_path= fullfile(imaging_session_dir, "borders_table.xlsx");
 
 Tprobes_path= fullfile(imaging_session_dir, "T_probes.xlsx");
 
+YLim_shift_mm_path = fullfile(imaging_session_dir,"YLim_shift_mm.mat");
 
 opts = detectImportOptions(Tapdvml_contacts_path);
 opts = setvartype(opts, 'session_id', 'string');
 
-Tapdvml_contacts = readtable(Tapdvml_contacts_path, opts );
+YLim_shift_mm = [];
+if isfile(original_backup_path)
+    Tapdvml_contacts = readtable(original_backup_path, opts );
+    
+    if isfile(YLim_shift_mm_path)
+        S = load(YLim_shift_mm_path); % YLim_shift_mm
+        YLim_shift_mm = S.YLim_shift_mm;
+        clear S
+    end
+else
+    Tapdvml_contacts = readtable(Tapdvml_contacts_path, opts );
+end
 
 % Tborders_table = readtable(borders_table_path);
 
@@ -80,6 +102,11 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 ylabel(uax1, 'Dsitance from the tip (mm)')
 uax1.XTick =[];
 
+if ~isempty(YLim_shift_mm)
+    assert(isequal(size(YLim_shift_mm), [1 1]))
+    uax1.UserData.YLim_shift_mm = YLim_shift_mm;
+end
+
 uax2 = uiaxes(ufig);
 uax2.PositionConstraint = 'innerposition';
 uax2.Position=[448, 150, 80, 800];
@@ -209,7 +236,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 %%
 anc = preallocatestruct(["index", "anc_id", "anc_name", "anc_color_hex", "anc_color_255", "anc_color"], [height(Tapdvml_contacts_this), 1]);
-% profile on
+
 st.name = regexprep(st.name, '["'']',''); % remove clutters
 
 f = waitbar(0,'1','Name','Analysing structure hierarchy...',...
@@ -217,16 +244,17 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 for i = 1:height(Tapdvml_contacts_this) % SLOW
     waitbar( i/height(Tapdvml_contacts_this), f, ...
-        fprintf("%d of %d", i, height(Tapdvml_contacts_this)))
+        sprintf("%d of %d", i, height(Tapdvml_contacts_this))) %TODO not shown properly
     name = Tapdvml_contacts_this.name{i};
     [anc(i)] = find_name_for_depth(st, depth_level, name); %TODO stopped working for i = 61, i = 1327
 end
-% profile viewer
 
 delete(f)
 
 %%
 Tanc = struct2table(anc, AsArray=true);
+%TODO save a cache file??
+
 
 Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
 
@@ -274,6 +302,22 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 uax1.YLabel.FontSize = 14;
 
+% move items after initialiation
+if isfield(uax1.UserData, 'YLim_shift_mm')
+    uax1.UserData.YLim_shift_mm
+
+    ch = uax1.Children;
+
+    for i = 1:length(ch)
+        if isa(ch(i),'matlab.graphics.primitive.Text')
+            ch(i).Position(2) = ch(i).Position(2) + YLim_shift_mm;
+
+        elseif isa(ch(i),'matlab.graphics.primitive.Patch')
+            ch(i).YData = ch(i).YData + YLim_shift_mm;
+
+        end
+    end
+end
 
 
 function move_back_to_original(uax1)
@@ -363,10 +407,8 @@ function save_updown_to_table(uax1, ~)
 
 new_file_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + ".xlsx");
 
-original_backup_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + "_original.xlsx");
-
 if isfile(original_backup_path)
-    % save a backup file
+    % save a backup file for the latest
 
     copyfile(Tapdvml_contacts_path, new_file_path)
 
@@ -439,6 +481,14 @@ function save_updown_to_table(uax1, ~)
 
 YLim_shift_mm = uax1.UserData.YLim_shift_mm;
 new_cp = curr_probePoints(tip_index,:) - YLim_shift_mm*100; % minus to move up
+%TODO in case the probe has already moved prevously, YLim_shift_mm won't be
+% accurate
+%
+% always read both the original and the latest Excel
+% YLim_shift_mm should represent the gap from the original
+
+%GOOD always read the original Excel and saved value of YLim_shift_mm
+% YLim_shift_mm should represent the gap from the original
 
 
 Tapdvml_m = apdvml2info(m, av, st, plane);
@@ -510,7 +560,9 @@ function save_updown_to_table(uax1, ~)
 end
 
 writetable(Tapdvml_contacts, fullfile(imaging_session_dir,"Tapdvml_contacts.xlsx"),'FileType','spreadsheet')
-frpint("Tapdvml_contacts.xlsx has been updated.\n")
+fprintf("Tapdvml_contacts.xlsx has been updated with %.3f mm shift from the original.\n", YLim_shift_mm)
+% save the value of YLim_shift_mm
+save(YLim_shift_mm_path, 'YLim_shift_mm');
 
 end
 

From 226124e4717ba7fe1b945bbb1f847775f820f570 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 16 Nov 2023 10:01:03 +0000
Subject: [PATCH 36/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 43 +++++++------------
 1 file changed, 16 insertions(+), 27 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 6e986e8..29564a5 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -37,9 +37,6 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 end
 
 %TODO add button to go next and previous probe
-%TODO use probe_id
-% related, use animal_id
-% make session_id, probeAB
 
 %TODO what if optic fiber data is chosen?
 
@@ -51,7 +48,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 s = load(recording_cell_metrics_path);
 recording_cell_metrics = s.cell_metrics;
 
-image_folder =fullfile(imaging_session_dir, image_folder_name);  %TODO
+image_folder =fullfile(imaging_session_dir, image_folder_name);
 
 probe_save_name_suffix = '_probe';
 
@@ -149,9 +146,6 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 bt7 = uibutton(ufig, "Text","Save", "ButtonPushedFcn", @(src, event) save_updown_to_table(uax1));
 bt7.Position = [150, 30, 300, 50];
 
-tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.5 0.1],  'String', session_id +"/" + probeAB,...
-    HorizontalAlignment='center',FontSize=18,LineStyle='none');
-
 
 %% Plot cells
 n = length(recording_cell_metrics.firingRate);
@@ -234,6 +228,10 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
 
+tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
+    sprintf("%s/%s (%d)", session_id, probeAB, probe_id),...
+    HorizontalAlignment='center',FontSize=18,LineStyle='none');
+
 %%
 anc = preallocatestruct(["index", "anc_id", "anc_name", "anc_color_hex", "anc_color_255", "anc_color"], [height(Tapdvml_contacts_this), 1]);
 
@@ -244,17 +242,15 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 for i = 1:height(Tapdvml_contacts_this) % SLOW
     waitbar( i/height(Tapdvml_contacts_this), f, ...
-        sprintf("%d of %d", i, height(Tapdvml_contacts_this))) %TODO not shown properly
+        sprintf("%d of %d", i, height(Tapdvml_contacts_this)));
     name = Tapdvml_contacts_this.name{i};
-    [anc(i)] = find_name_for_depth(st, depth_level, name); %TODO stopped working for i = 61, i = 1327
+    [anc(i)] = find_name_for_depth(st, depth_level, name);
 end
 
 delete(f)
 
 %%
 Tanc = struct2table(anc, AsArray=true);
-%TODO save a cache file??
-
 
 Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
 
@@ -384,7 +380,7 @@ function save_updown_to_table(uax1, ~)
     return
 else
     if isfield(uax1.UserData, 'YLim_shift_mm')
-        %TODO move
+        % move
     else
         disp('YLim_shift_mm is not found. No change made.')
         return
@@ -392,7 +388,7 @@ function save_updown_to_table(uax1, ~)
 end
 
 
-%TODO save the backup
+%% save the backup
 
 assert(endsWith(Tapdvml_contacts_path,'.xlsx'))
 
@@ -461,7 +457,7 @@ function save_updown_to_table(uax1, ~)
 
 % m is the brain entry point
 
-%TODO modifiy the m and curr_probePoints(tip_index,:) by YLim_shift_mm
+% modifiy the m and curr_probePoints(tip_index,:) by YLim_shift_mm
 % p is in 10 µm
 
 if strcmp(probe_insertion_direction, 'down')
@@ -481,23 +477,16 @@ function save_updown_to_table(uax1, ~)
 
 YLim_shift_mm = uax1.UserData.YLim_shift_mm;
 new_cp = curr_probePoints(tip_index,:) - YLim_shift_mm*100; % minus to move up
-%TODO in case the probe has already moved prevously, YLim_shift_mm won't be
-% accurate
-%
-% always read both the original and the latest Excel
-% YLim_shift_mm should represent the gap from the original
-
-%GOOD always read the original Excel and saved value of YLim_shift_mm
+%NOTE always read the original Excel and saved value of YLim_shift_mm
 % YLim_shift_mm should represent the gap from the original
 
-
 Tapdvml_m = apdvml2info(m, av, st, plane);
 
 Tapdvml_tip = apdvml2info(new_cp, av, st, plane);
 
 
 
-% measure the distance 
+%% measure the distance 
 
 tip2surface_mm = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
     (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
@@ -511,8 +500,7 @@ function save_updown_to_table(uax1, ~)
     new_cp * (tip2surface_mm - active_probe_length))...
     /tip2surface_mm;
 
-% obtained the information for all the 384 channels
-
+%% obtain the information for all the 384 channels
 
 a = [linspace(new_cp(1), top_active(1), 192)', ...
     linspace(new_cp(2), top_active(2), 192)', ...
@@ -553,14 +541,15 @@ function save_updown_to_table(uax1, ~)
     probe_id = Tapdvml_contacts_new{j,"probe_id"};
     contact_id = Tapdvml_contacts_new{j,"contact_id"};
 
-    cols = ["ap_mm","dv_mm","dv_mm_paxinos","ml_mm","annotation","name","acronym","contact_id","probe_id","depth_mm","depth_mm_paxinos"];
+    cols = ["ap_mm","dv_mm","dv_mm_paxinos","ml_mm","annotation",...
+        "name","acronym","contact_id","probe_id","depth_mm","depth_mm_paxinos"];
     Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id ...
         & Tapdvml_contacts.contact_id == contact_id,  cols) = ...
         Tapdvml_contacts_new(j, cols);   
 end
 
 writetable(Tapdvml_contacts, fullfile(imaging_session_dir,"Tapdvml_contacts.xlsx"),'FileType','spreadsheet')
-fprintf("Tapdvml_contacts.xlsx has been updated with %.3f mm shift from the original.\n", YLim_shift_mm)
+fprintf("Tapdvml_contacts.xlsx has been updated with %.3f mm shift from the original for %s of %s (%d).\n", YLim_shift_mm, probeAB, session_id, probe_id)
 % save the value of YLim_shift_mm
 save(YLim_shift_mm_path, 'YLim_shift_mm');
 

From 277ba723b86a68ac966e9d77572c4da5f3e8e92e Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 16 Nov 2023 16:44:43 +0000
Subject: [PATCH 37/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 512 ++++++++++--------
 1 file changed, 286 insertions(+), 226 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 29564a5..99665fa 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -5,6 +5,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 % to the changes in the firing rates of neurons
 %
 % EXAMPLE USAGE
+%
 % session_id = "kms058-2023-03-25-184034"
 % probeAB ="ProbeA";
 % plane = "sagittal";
@@ -41,6 +42,8 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 %TODO what if optic fiber data is chosen?
 
 
+
+
 sorter_output_dir = fullfile(sessions_dir, task_dir_name,  ...
     session_id, "processed\kilosort", probeAB, "sorter_output");
 
@@ -60,32 +63,90 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 Tprobes_path= fullfile(imaging_session_dir, "T_probes.xlsx");
 
-YLim_shift_mm_path = fullfile(imaging_session_dir,"YLim_shift_mm.mat");
+%YLim_shift_mm_path = fullfile(imaging_session_dir,"YLim_shift_mm.mat"); %TODO
+Y_shift_path = fullfile(imaging_session_dir,"T_Y_shift.mat"); %TODO
+
+
+
+
+
+% Tborders_table = readtable(borders_table_path);
+
+T_probes=  readtable(Tprobes_path);
+
+if ~ ismember('p_1',T_probes.Properties.VariableNames) || ...
+        ~ ismember('p_2',T_probes.Properties.VariableNames) ||...
+        ~ ismember('p_3',T_probes.Properties.VariableNames)
+    warning('The eigen vectors p is not found in T_probes. You cannot update the Tapdvml_contacts.')
+end
+
+switch probeAB
+    case "ProbeA"
+        probeAB_short = "A";
+    case "ProbeB"
+        probeAB_short = "B";
+    otherwise
+
+end
 
+tf = T_probes.session_id == session_id & T_probes.probe_AB == probeAB_short;
+
+probe_id = T_probes{tf, "probe_id"};
+
+%% deal with the cache file
 opts = detectImportOptions(Tapdvml_contacts_path);
 opts = setvartype(opts, 'session_id', 'string');
 
 YLim_shift_mm = [];
 if isfile(original_backup_path)
+
     Tapdvml_contacts = readtable(original_backup_path, opts );
-    
-    if isfile(YLim_shift_mm_path)
-        S = load(YLim_shift_mm_path); % YLim_shift_mm
-        YLim_shift_mm = S.YLim_shift_mm;
+    Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
+
+    if isfile(Y_shift_path) % use the cache
+        S = load(Y_shift_path); % YLim_shift_mm
+
+        assert(istable(S.T_Y_shift))
+        T_Y_shift = S.T_Y_shift;
+        YLim_shift_mm = S.T_Y_shift.YLim_shift_mm(probe_id);
+        Tanc = S.T_Y_shift.Tanc{probe_id};
         clear S
+    else
+        % cache file is not found
+        Tanc_ = cell(height(T_probes), 1);
+        for i = 1:size(Tanc_,1)
+            Tanc_{i} = table();
+        end
+
+        T_Y_shift = table(zeros(height(T_probes), 1), Tanc_,...
+            'VariableNames', ["YLim_shift_mm","Tanc"]); % YLim_shift_mm and Tanc
+        clear Tanc_
+        Tanc = compute_Tanc(Tapdvml_contacts_this, st, depth_level);
+        T_Y_shift.Tanc{probe_id} = Tanc;
+        save(Y_shift_path, 'T_Y_shift');
     end
+    Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
+
 else
+    % the very first run
+
     Tapdvml_contacts = readtable(Tapdvml_contacts_path, opts );
-end
+    Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
 
-% Tborders_table = readtable(borders_table_path);
+    Tanc_ = cell(height(T_probes), 1);
+    for i = 1:size(Tanc_,1)
+        Tanc_{i} = table();
+    end
 
-T_probes=  readtable(Tprobes_path);
+    T_Y_shift = table(zeros(height(T_probes), 1), Tanc_,...
+        'VariableNames', ["YLim_shift_mm","Tanc"]); % YLim_shift_mm and Tanc
+    clear Tanc_
+    Tanc = compute_Tanc(Tapdvml_contacts_this, st, depth_level);
+    T_Y_shift.Tanc{probe_id} = Tanc;
+    save(Y_shift_path, 'T_Y_shift');
+
+    Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
 
-if ~ ismember('p_1',T_probes.Properties.VariableNames) || ...
-        ~ ismember('p_2',T_probes.Properties.VariableNames) ||...
-        ~ ismember('p_3',T_probes.Properties.VariableNames)
-    warning('The eigen vectors p is not found in T_probes. You cannot update the Tapdvml_contacts.')
 end
 
 
@@ -195,64 +256,14 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 uax3.CLim = uax2.CLim; % same color scale
 
 
-%% Read the Allen CCF data
-% directory of reference atlas files
-annotation_volume_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\annotation_volume_10um_by_index.npy";
-structure_tree_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\structure_tree_safe_2017.csv";
-template_volume_location = "\\ettina\Magill_lab\Kouichi Nakamura\Analysis\allenCCFdata\template_volume_10um.npy";
-
-% load the reference brain and region annotations
-if ~exist('av','var') || ~exist('st','var') || ~exist('tv','var')
-    disp('loading reference atlas...')
-    av = readNPY(annotation_volume_location);
-    st = loadStructureTree(structure_tree_location);
-    tv = readNPY(template_volume_location);
-end
-
-
-probeAB = "ProbeA";
-
-switch probeAB
-    case "ProbeA"
-        probeAB_short = "A";
-    case "ProbeB"
-        probeAB_short = "B";
-    otherwise
-
-end
-
-tf = T_probes.session_id == session_id & T_probes.probe_AB == probeAB_short;
-
-probe_id = T_probes{tf, "probe_id"};
-
 
-Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
+% Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
 
 tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
     sprintf("%s/%s (%d)", session_id, probeAB, probe_id),...
     HorizontalAlignment='center',FontSize=18,LineStyle='none');
 
-%%
-anc = preallocatestruct(["index", "anc_id", "anc_name", "anc_color_hex", "anc_color_255", "anc_color"], [height(Tapdvml_contacts_this), 1]);
-
-st.name = regexprep(st.name, '["'']',''); % remove clutters
-
-f = waitbar(0,'1','Name','Analysing structure hierarchy...',...
-    'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
-
-for i = 1:height(Tapdvml_contacts_this) % SLOW
-    waitbar( i/height(Tapdvml_contacts_this), f, ...
-        sprintf("%d of %d", i, height(Tapdvml_contacts_this)));
-    name = Tapdvml_contacts_this.name{i};
-    [anc(i)] = find_name_for_depth(st, depth_level, name);
-end
-
-delete(f)
-
-%%
-Tanc = struct2table(anc, AsArray=true);
-
-Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc];
+% Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc]; %TODO
 
 
 % Sample data
@@ -279,6 +290,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 
 %% Plot structures
+
 cla(uax1)
 
 uax1.Color = 'k';
@@ -294,13 +306,25 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
         'HorizontalAlignment','center', Clipping='on');
 end
 
+horzline = line(uax1, [0 1], [0 0], 'Color','r'); % distance from the tip 0 mm
+
 ylim(uax1, [-0.100, 3.940])
 
 uax1.YLabel.FontSize = 14;
 
+if isempty(uax1.UserData) || ~isfield(uax1.UserData, 'YLim_shift_mm')
+    tx2 = annotation(ufig, 'textbox', [0.2 0.03 0.3 0.1],  'String', ...
+        regexprep(sprintf("%+.2f mm", 0), '-', char(8722)),...
+        HorizontalAlignment='left',FontSize=12, LineStyle='none');
+else
+    tx2 = annotation(ufig, 'textbox', [0.2 0.03 0.3 0.1],  'String', ...
+        regexprep(sprintf("%+.2f mm", uax1.UserData.YLim_shift_mm), '-', char(8722)),...
+        HorizontalAlignment='left',FontSize=12, LineStyle='none');
+end
+
 % move items after initialiation
 if isfield(uax1.UserData, 'YLim_shift_mm')
-    uax1.UserData.YLim_shift_mm
+    % uax1.UserData.YLim_shift_mm
 
     ch = uax1.Children;
 
@@ -311,249 +335,263 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
         elseif isa(ch(i),'matlab.graphics.primitive.Patch')
             ch(i).YData = ch(i).YData + YLim_shift_mm;
 
+        elseif isa(ch(i),'matlab.graphics.primitive.Line')
+            ch(i).YData = ch(i).YData + YLim_shift_mm;            
+        
         end
     end
 end
 
 
-function move_back_to_original(uax1)
+    function move_back_to_original(uax1)
 
-if isfield(uax1.UserData, 'YLim_shift_mm')
-    ch = uax1.Children;
+        if isfield(uax1.UserData, 'YLim_shift_mm')
+            ch = uax1.Children;
+
+            for j = 1:length(ch)
+                step = - uax1.UserData.YLim_shift_mm;
 
-    for j = 1:length(ch)
-        step = - uax1.UserData.YLim_shift_mm;
+                if isa(ch(j),'matlab.graphics.primitive.Text')
+                    ch(j).Position(2) = ch(j).Position(2) + step;
 
-        if isa(ch(j),'matlab.graphics.primitive.Text')
-            ch(j).Position(2) = ch(j).Position(2) + step;
+                elseif isa(ch(j),'matlab.graphics.primitive.Patch')
+                    ch(j).YData = ch(j).YData + step;
 
-        elseif isa(ch(j),'matlab.graphics.primitive.Patch')
-            ch(j).YData = ch(j).YData + step;
+                elseif isa(ch(j),'matlab.graphics.primitive.Line')
+                    ch(j).YData = ch(j).YData + step;
+                    
+                end
 
+            end
+
+            uax1.UserData.YLim_shift_mm = 0;
+
+            tx2.String = regexprep(sprintf("%+.2f mm", uax1.UserData.YLim_shift_mm), '-', char(8722));
+        else
+            %nothing to do
         end
 
     end
 
-    uax1.UserData.YLim_shift_mm = 0;
-else
-    %nothing to do
-end
 
-end
+    function move_vertically(uax1, step)
 
+        % arguments
+        %     uax1(1,1)
+        %     step (1,1) {mustBeInteger}
+        % end
 
-function move_vertically(uax1, step)
+        ch = uax1.Children;
 
-% arguments
-%     uax1(1,1)
-%     step (1,1) {mustBeInteger}
-% end
+        for j = 1:length(ch)
 
-ch = uax1.Children;
+            if isa(ch(j),'matlab.graphics.primitive.Text')
+                ch(j).Position(2) = ch(j).Position(2) + step*0.01;
 
-for j = 1:length(ch)
+            elseif isa(ch(j),'matlab.graphics.primitive.Patch')
+                ch(j).YData = ch(j).YData + step*0.01;
 
-    if isa(ch(j),'matlab.graphics.primitive.Text')
-        ch(j).Position(2) = ch(j).Position(2) + step*0.01;
+            elseif isa(ch(j),'matlab.graphics.primitive.Line')
+                ch(j).YData = ch(j).YData + step*0.01;
 
-    elseif isa(ch(j),'matlab.graphics.primitive.Patch')
-        ch(j).YData = ch(j).YData + step*0.01;
+            end
 
-    end
+        end
 
-end
+        if isfield(uax1.UserData, 'YLim_shift_mm')
+            uax1.UserData.YLim_shift_mm = uax1.UserData.YLim_shift_mm + step*0.01;
+        else
+            uax1.UserData.YLim_shift_mm = step*0.01;
+        end
 
-if isfield(uax1.UserData, 'YLim_shift_mm')
-    uax1.UserData.YLim_shift_mm = uax1.UserData.YLim_shift_mm + step*0.01;
-else
-    uax1.UserData.YLim_shift_mm = step*0.01;
-end
+        tx2.String = regexprep(sprintf("%+.2f mm", uax1.UserData.YLim_shift_mm), '-', char(8722));
 
-end
+    end
 
 
+    function save_updown_to_table(uax1, ~)
 
-function save_updown_to_table(uax1, ~) 
+        if isempty(uax1.UserData)
+            disp('The probe has not moved on GUI yet. No change made.')
+            return
+        else
+            if isfield(uax1.UserData, 'YLim_shift_mm')
+                % move
+            else
+                disp('YLim_shift_mm is not found. No change made.')
+                return
+            end
+        end
 
-if isempty(uax1.UserData)
-    disp('The probe has not moved on GUI yet. No change made.')
-    return
-else
-    if isfield(uax1.UserData, 'YLim_shift_mm')
-        % move
-    else
-        disp('YLim_shift_mm is not found. No change made.')
-        return
-    end
-end
 
+        %% save the backup
 
-%% save the backup
+        assert(endsWith(Tapdvml_contacts_path,'.xlsx'))
 
-assert(endsWith(Tapdvml_contacts_path,'.xlsx'))
+        assert(isfile(Tapdvml_contacts_path))
 
-assert(isfile(Tapdvml_contacts_path))
+        f_info = dir(Tapdvml_contacts_path);
 
-f_info = dir(Tapdvml_contacts_path);
+        dt = datetime(f_info.date, 'InputFormat', 'dd-MMM-yyyy HH:mm:ss');
 
-dt = datetime(f_info.date, 'InputFormat', 'dd-MMM-yyyy HH:mm:ss');
+        dt.Format = 'yyyy-MM-dd_HH-mm-ss';
+        suffix = string(dt);
 
-dt.Format = 'yyyy-MM-dd_HH-mm-ss';
-suffix = string(dt);
+        new_file_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + ".xlsx");
 
-new_file_path = regexprep(Tapdvml_contacts_path, '\.xlsx$' , "_" + suffix + ".xlsx");
+        if isfile(original_backup_path)
+            % save a backup file for the latest
 
-if isfile(original_backup_path)
-    % save a backup file for the latest
+            copyfile(Tapdvml_contacts_path, new_file_path)
 
-    copyfile(Tapdvml_contacts_path, new_file_path)
+        else
+            % this is the first time you change the Excel file
+            % save a backup file
 
-else
-    % this is the first time you change the Excel file
-    % save a backup file
+            copyfile(Tapdvml_contacts_path, original_backup_path)
 
-    copyfile(Tapdvml_contacts_path, original_backup_path)
+        end
 
-end
+        %% Job
+        % see plot_and_compute_probe_positions_from_ccf.m
+        % I need the eigen vector, to be saved in T_probes?
+
+        switch probeAB
+            case "ProbeA"
+                probeAB_ = "A";
+            case "ProbeB"
+                probeAB_ = "B";
+            case "optic fiber"
+                probeAB_ = "optic fiber";
+        end
 
-%% Job
-% see plot_and_compute_probe_positions_from_ccf.m
-% I need the eigen vector, to be saved in T_probes?
+        % eigen vector
+        tf = T_probes.session_id == session_id & ...
+            T_probes.probe_AB == probeAB_;
 
-switch probeAB
-    case "ProbeA"
-        probeAB_ = "A";
-    case "ProbeB"
-        probeAB_ = "B";
-    case "optic fiber"
-        probeAB_ = "optic fiber";
-end
+        assert(nnz(tf) == 1)
 
-% eigen vector
-tf = T_probes.session_id == session_id & ...
-    T_probes.probe_AB == probeAB_;
+        p = T_probes{T_probes.session_id == session_id & ...
+            T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
 
-assert(nnz(tf) == 1)
+        m = T_probes{T_probes.session_id == session_id & ...
+            T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
 
-p = T_probes{T_probes.session_id == session_id & ...
-    T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
+        processed_images_folder = fullfile(image_folder, 'processed');
 
-m = T_probes{T_probes.session_id == session_id & ...
-    T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
+        probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
 
-processed_images_folder = fullfile(image_folder, 'processed');
+        % get the probe points for the currently analyzed probe
 
-probePoints = load(fullfile(processed_images_folder, ['probe_points' probe_save_name_suffix]));
+        if strcmp(plane,'coronal')
+            curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [3 2 1]);
+        elseif strcmp(plane,'sagittal')
+            curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 2 3]);
+        elseif strcmp(plane,'transverse')
+            curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 3 2]);
+        end
 
-% get the probe points for the currently analyzed probe
+        % m is the brain entry point
 
-if strcmp(plane,'coronal')
-    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [3 2 1]);
-elseif strcmp(plane,'sagittal')
-    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 2 3]);
-elseif strcmp(plane,'transverse')
-    curr_probePoints = probePoints.pointList.pointList{probe_id,1}(:, [1 3 2]);
-end
+        % modifiy the m and curr_probePoints(tip_index,:) by YLim_shift_mm
+        % p is in 10 µm
 
-% m is the brain entry point
+        if strcmp(probe_insertion_direction, 'down')
+            [depth, tip_index] = max(curr_probePoints(:,2));
+        elseif strcmp(probe_insertion_direction, 'up')
+            [depth, tip_index] = min(curr_probePoints(:,2));
+        end
 
-% modifiy the m and curr_probePoints(tip_index,:) by YLim_shift_mm
-% p is in 10 µm
+        % curr_probePoints(tip_index,:) either to get it from the ProbePoints or
+        % from Tapdvml_contacts.xlsx (convert ap_mm, dv_mm, ml_mm back to allen coordinates)
+        % opposite of apdvml2info
 
-if strcmp(probe_insertion_direction, 'down')
-    [depth, tip_index] = max(curr_probePoints(:,2));
-elseif strcmp(probe_insertion_direction, 'up')
-    [depth, tip_index] = min(curr_probePoints(:,2));
-end
 
-% curr_probePoints(tip_index,:) either to get it from the ProbePoints or
-% from Tapdvml_contacts.xlsx (convert ap_mm, dv_mm, ml_mm back to allen coordinates)
-% opposite of apdvml2info
+        % Tapdvml_contacts.session_id
 
+        % tip_mm =
 
-% Tapdvml_contacts.session_id
+        YLim_shift_mm = uax1.UserData.YLim_shift_mm;
+        new_cp = curr_probePoints(tip_index,:) - YLim_shift_mm*100; % minus to move up
+        %NOTE always read the original Excel and saved value of YLim_shift_mm
+        % YLim_shift_mm should represent the gap from the original
 
-% tip_mm = 
+        Tapdvml_m = apdvml2info(m, av, st, plane);
 
-YLim_shift_mm = uax1.UserData.YLim_shift_mm;
-new_cp = curr_probePoints(tip_index,:) - YLim_shift_mm*100; % minus to move up
-%NOTE always read the original Excel and saved value of YLim_shift_mm
-% YLim_shift_mm should represent the gap from the original
+        Tapdvml_tip = apdvml2info(new_cp, av, st, plane);
 
-Tapdvml_m = apdvml2info(m, av, st, plane);
 
-Tapdvml_tip = apdvml2info(new_cp, av, st, plane);
 
+        %% measure the distance
 
+        tip2surface_mm = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+            (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
+            (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
 
-%% measure the distance 
+        % tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
+        %     (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
+        %     (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
 
-tip2surface_mm = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
-    (Tapdvml_tip.dv_mm - Tapdvml_m.dv_mm)^2 + ...
-    (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+        top_active = (m * active_probe_length + ...
+            new_cp * (tip2surface_mm - active_probe_length))...
+            /tip2surface_mm;
 
-% tip2surface_mm_paxinos = sqrt((Tapdvml_tip.ap_mm - Tapdvml_m.ap_mm)^2 + ...
-%     (Tapdvml_tip.dv_mm_paxinos - Tapdvml_m.dv_mm_paxinos)^2 + ...
-%     (Tapdvml_tip.ml_mm - Tapdvml_m.ml_mm)^2);
+        %% obtain the information for all the 384 channels
 
-top_active = (m * active_probe_length + ...
-    new_cp * (tip2surface_mm - active_probe_length))...
-    /tip2surface_mm;
+        a = [linspace(new_cp(1), top_active(1), 192)', ...
+            linspace(new_cp(2), top_active(2), 192)', ...
+            linspace(new_cp(3), top_active(3), 192)'];
+        probe_contact_points = zeros(384, 3);
+        for j = 1:192
+            probe_contact_points(2*j-1,:) = a(j,:);
+            probe_contact_points(2*j,:) = a(j,:);
+        end
+        clear a
 
-%% obtain the information for all the 384 channels
+        c_t_contacts = cell(384,1);
 
-a = [linspace(new_cp(1), top_active(1), 192)', ...
-    linspace(new_cp(2), top_active(2), 192)', ...
-    linspace(new_cp(3), top_active(3), 192)'];
-probe_contact_points = zeros(384, 3);
-for j = 1:192
-    probe_contact_points(2*j-1,:) = a(j,:);
-    probe_contact_points(2*j,:) = a(j,:);
-end
-clear a
+        theta = acos(p(2)); % Assuming p(2) corresponds to the DV direction
 
-c_t_contacts = cell(384,1);
+        for j = 1:384
+            c_t_contacts{j} = apdvml2info(probe_contact_points(j,:), av, st, plane);
+            c_t_contacts{j}.contact_id = repmat(j,height(c_t_contacts{j}));
+            c_t_contacts{j}.probe_id = repmat(probe_id,height(c_t_contacts{j}));
+            c_t_contacts{j}.depth_mm = tip2surface_mm - 0.020 * floor((j-1)/2);
 
-theta = acos(p(2)); % Assuming p(2) corresponds to the DV direction
+            % Project the depth along the line
+            projected_depth_mm = c_t_contacts{j}.depth_mm * cos(theta);
 
-for j = 1:384
-    c_t_contacts{j} = apdvml2info(probe_contact_points(j,:), av, st, plane);
-    c_t_contacts{j}.contact_id = repmat(j,height(c_t_contacts{j}));
-    c_t_contacts{j}.probe_id = repmat(probe_id,height(c_t_contacts{j}));
-    c_t_contacts{j}.depth_mm = tip2surface_mm - 0.020 * floor((j-1)/2);
-    
-    % Project the depth along the line
-    projected_depth_mm = c_t_contacts{j}.depth_mm * cos(theta);
+            % Convert using the transformation for the chosen plane
+            projected_depth_mm_paxinos = accf2pxs_mm(projected_depth_mm, plane, 'distance');
 
-    % Convert using the transformation for the chosen plane
-    projected_depth_mm_paxinos = accf2pxs_mm(projected_depth_mm, plane, 'distance');
+            c_t_contacts{j}.depth_mm_paxinos = projected_depth_mm_paxinos;
+        end
 
-    c_t_contacts{j}.depth_mm_paxinos = projected_depth_mm_paxinos;
-end
+        Tapdvml_contacts_new = vertcat(c_t_contacts{:});
+        clear c_t_contacts
 
-Tapdvml_contacts_new = vertcat(c_t_contacts{:});
-clear c_t_contacts
+        %% update the relevant rows of Tapdvml_contacts
 
-%% update the relevant rows of Tapdvml_contacts
+        %% update values
+        for j = 1:height(Tapdvml_contacts_new)
+            probe_id = Tapdvml_contacts_new{j,"probe_id"};
+            contact_id = Tapdvml_contacts_new{j,"contact_id"};
 
-%% update values
-for j = 1:height(Tapdvml_contacts_new)
-    probe_id = Tapdvml_contacts_new{j,"probe_id"};
-    contact_id = Tapdvml_contacts_new{j,"contact_id"};
+            cols = ["ap_mm","dv_mm","dv_mm_paxinos","ml_mm","annotation",...
+                "name","acronym","contact_id","probe_id","depth_mm","depth_mm_paxinos"];
+            Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id ...
+                & Tapdvml_contacts.contact_id == contact_id,  cols) = ...
+                Tapdvml_contacts_new(j, cols);
+        end
 
-    cols = ["ap_mm","dv_mm","dv_mm_paxinos","ml_mm","annotation",...
-        "name","acronym","contact_id","probe_id","depth_mm","depth_mm_paxinos"];
-    Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id ...
-        & Tapdvml_contacts.contact_id == contact_id,  cols) = ...
-        Tapdvml_contacts_new(j, cols);   
-end
+        writetable(Tapdvml_contacts, fullfile(imaging_session_dir,"Tapdvml_contacts.xlsx"),'FileType','spreadsheet')
+        fprintf("Tapdvml_contacts.xlsx has been updated with %.3f mm shift from the original for %s of %s (%d).\n", YLim_shift_mm, probeAB, session_id, probe_id)
+        % save the value of YLim_shift_mm
+        T_Y_shift.YLim_shift_mm(probe_id) = YLim_shift_mm;
+        save(Y_shift_path, 'T_Y_shift');
 
-writetable(Tapdvml_contacts, fullfile(imaging_session_dir,"Tapdvml_contacts.xlsx"),'FileType','spreadsheet')
-fprintf("Tapdvml_contacts.xlsx has been updated with %.3f mm shift from the original for %s of %s (%d).\n", YLim_shift_mm, probeAB, session_id, probe_id)
-% save the value of YLim_shift_mm
-save(YLim_shift_mm_path, 'YLim_shift_mm');
 
-end
+    end
 
 end
 
@@ -615,3 +653,25 @@ function save_updown_to_table(uax1, ~)
 end
 
 
+function Tanc = compute_Tanc(Tapdvml_contacts_this, st, depth_level)
+
+anc = preallocatestruct(["index", "anc_id", "anc_name", "anc_color_hex", "anc_color_255", "anc_color"], [height(Tapdvml_contacts_this), 1]);
+
+st.name = regexprep(st.name, '["'']',''); % remove clutters
+
+f = waitbar(0,'1','Name','Analysing structure hierarchy...',...
+    'CreateCancelBtn','setappdata(gcbf,''canceling'',1)');
+
+for i = 1:height(Tapdvml_contacts_this) % SLOW
+    waitbar( i/height(Tapdvml_contacts_this), f, ...
+        sprintf("%d of %d", i, height(Tapdvml_contacts_this)));
+    name = Tapdvml_contacts_this.name{i};
+    [anc(i)] = find_name_for_depth(st, depth_level, name);
+end
+
+delete(f)
+beep();
+
+Tanc = struct2table(anc, AsArray=true);
+
+end
\ No newline at end of file

From 8effe0d8ee0783df370b8f3381c89f892f8d926a Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Thu, 16 Nov 2023 17:03:04 +0000
Subject: [PATCH 38/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 99665fa..e855aaa 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -110,6 +110,12 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
         T_Y_shift = S.T_Y_shift;
         YLim_shift_mm = S.T_Y_shift.YLim_shift_mm(probe_id);
         Tanc = S.T_Y_shift.Tanc{probe_id};
+        if isempty(Tanc)
+            Tanc = compute_Tanc(Tapdvml_contacts_this, st, depth_level);
+            T_Y_shift.Tanc{probe_id} = Tanc;
+            save(Y_shift_path, 'T_Y_shift');
+        end
+
         clear S
     else
         % cache file is not found

From ef21e009bd34aafc2cf621055cdff7d56a4d2fbd Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Fri, 17 Nov 2023 09:15:36 +0000
Subject: [PATCH 39/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 87 +++++++++++++++++--
 1 file changed, 78 insertions(+), 9 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index e855aaa..d6c1a56 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -4,6 +4,56 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 % Move up and down a probe using a slider to match the anatomical borders
 % to the changes in the firing rates of neurons
 %
+% SYNTAX
+% updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_dir,...
+%    task_dir_name, imaging_session_dir, image_folder_name, depth_level, ...
+%    active_probe_length, probe_insertion_direction)
+%
+%
+% INPUT ARGUMENTS
+% av          uint16
+%             part of Allen CCF data    
+%
+% st          table
+%             part of Allen CCF data
+%
+% session_id  string
+%             eg. "kms058-2023-03-25-184034"
+%
+% probeAB     "ProbeA" | "ProbeB"
+%
+% plane       "coronal" | "sagittal" | "transverse"
+%
+% sessions_dir
+%             folder path
+%             "\\ettina\Magill_Lab\Julien\Data\head-fixed\by_sessions"
+%
+% task_dir_name
+%             folder name
+%             "reaching_go_spout_bar_nov22"
+%
+% imaging_session_dir
+%             folder_path
+%             "\\ettina\Magill_Lab\Kouichi Nakamura\Analysis\Images from Otto\20230406 kms058"
+%
+% image_folder_name
+%             "RGB" (default)
+%             folder_name
+%
+% depth_level
+%             6 (default)
+%             The hierarchical level of the anatomical structures to be
+%             shown.
+%
+% active_probe_length
+%             3.840 (default)    
+%
+% probe_insertion_direction 
+%             "down" (default) | "up"
+%
+%
+%
+%
 % EXAMPLE USAGE
 %
 % session_id = "kms058-2023-03-25-184034"
@@ -21,6 +71,16 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 %     st = loadStructureTree(structure_tree_location);
 %     tv = readNPY(template_volume_location);
 % end
+%
+%
+% Written by Kouichi C. Nakamura Ph.D.
+% MRC Brain Network Dynamics Unit
+% University of Oxford
+% kouichi.c.nakamura@gmail.com
+% 17-Nov-2023 09:07:25
+%
+% See also
+% plot_and_compute_probe_positions_from_ccf
 
 arguments
     av uint16
@@ -241,17 +301,30 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 cla(uax2,'reset')
 
 movingaverageval = zeros(384,1);
+celldensity = zeros(384,1);
 
 for i = 1:384
 
     % moving average of five channels
-    chans = i - 1 : i + 3;
+    chans = i - 2 : i + 2;
+    
     ind = ismember(recording_cell_metrics.maxWaveformCh, chans);
+    celldensity(i) = nnz(ind)/(length(chans)*10); % cells per micrometers
     movingaverageval(i) = mean(recording_cell_metrics.firingRate(ind));
 
 end
 
-isc1 = imagesc(uax2, 1, (1:384)'*0.01, movingaverageval);
+for i = 1:384
+
+    % ten channels
+    chans = i - 4 : i + 5;
+    
+    ind = ismember(recording_cell_metrics.maxWaveformCh, chans);
+    celldensity(i) = nnz(ind)/(length(chans)*10); % cells per micrometers
+
+end
+
+isc1 = imagesc(uax2, [0 1], (1:384)'*0.01, movingaverageval);
 
 uax2.YDir = 'normal';
 ylim(uax2, [-0.100, 3.940])
@@ -261,18 +334,14 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 uax3.CLim = uax2.CLim; % same color scale
 
-
-
-% Tapdvml_contacts_this = Tapdvml_contacts(Tapdvml_contacts.probe_id == probe_id, :);
+ln1 = line(uax2, celldensity/max(celldensity), (1:384)'*0.01, 'Color', 'w');
+xlim(uax2,[0 1])
 
 tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
     sprintf("%s/%s (%d)", session_id, probeAB, probe_id),...
     HorizontalAlignment='center',FontSize=18,LineStyle='none');
 
-% Tapdvml_contacts_this = [Tapdvml_contacts_this, Tanc]; %TODO
-
-
-% Sample data
+%% 
 anc_id = Tapdvml_contacts_this.anc_id;
 
 anc_name = Tapdvml_contacts_this.anc_name;

From 22a538867e6b26cad9aae6d60d46b0df77ca3733 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 20 Nov 2023 15:04:33 +0000
Subject: [PATCH 40/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index d6c1a56..b82c23d 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -91,7 +91,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
     sessions_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Julien\Data\head-fixed\by_sessions"
     task_dir_name (1,1) string % eg. "reaching_go_spout_bar_nov22"
     imaging_session_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Kouichi Nakamura\Analysis\Images from Otto\20230406 kms058"
-    image_folder_name (1,1) string = "RGB"
+    image_folder_name (1,1) string {mustBeFolder} = "RGB"
     depth_level (1,1) double {mustBePositive, mustBeInteger} = 6
     active_probe_length (1,1) double = 3.84 % in mm
     probe_insertion_direction (1,1) string {mustBeMember(probe_insertion_direction, ["down","up"])} = "down"
@@ -546,9 +546,18 @@ function save_updown_to_table(uax1, ~)
 
         assert(nnz(tf) == 1)
 
-        p = T_probes{T_probes.session_id == session_id & ...
-            T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
-
+        try
+            p = T_probes{T_probes.session_id == session_id & ...
+                T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
+        catch ME
+            if ME.identifier == "MATLAB:table:UnrecognizedVarName"
+                error("It looks like m you have to run plot_and_compute_probe_positions_from_ccf()" ...
+                    + " and then save T_probes with p and m values. " + ...
+                    "See scr20230727_112451_SharpTrackIgnore_kms058.mlx for example.")
+            else
+                throw(ME);
+            end
+        end
         m = T_probes{T_probes.session_id == session_id & ...
             T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
 

From a2f6bd4cde8d0df582eb0812d3e7db2c6ded2529 Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Mon, 20 Nov 2023 16:06:21 +0000
Subject: [PATCH 41/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index b82c23d..310a916 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -91,7 +91,7 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
     sessions_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Julien\Data\head-fixed\by_sessions"
     task_dir_name (1,1) string % eg. "reaching_go_spout_bar_nov22"
     imaging_session_dir (1,1) string  {mustBeFolder} % eg. "\\ettina\Magill_Lab\Kouichi Nakamura\Analysis\Images from Otto\20230406 kms058"
-    image_folder_name (1,1) string {mustBeFolder} = "RGB"
+    image_folder_name (1,1) string = "RGB"
     depth_level (1,1) double {mustBePositive, mustBeInteger} = 6
     active_probe_length (1,1) double = 3.84 % in mm
     probe_insertion_direction (1,1) string {mustBeMember(probe_insertion_direction, ["down","up"])} = "down"
@@ -113,6 +113,8 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 image_folder =fullfile(imaging_session_dir, image_folder_name);
 
+assert(isfolder(image_folder), "Check the name of image_folder_name")
+
 probe_save_name_suffix = '_probe';
 
 Tapdvml_contacts_path = fullfile(imaging_session_dir, "Tapdvml_contacts.xlsx");

From 95cf48a4aa34aa5e37cd60a63aeb52035d78e73e Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Wed, 22 Nov 2023 16:41:18 +0000
Subject: [PATCH 42/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 38 +++++++++++++++++--
 1 file changed, 34 insertions(+), 4 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 310a916..2b7c001 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -19,6 +19,8 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 %
 % session_id  string
 %             eg. "kms058-2023-03-25-184034"
+%                  "JC318L-2022-12-14-164509, JC318L-2022-12-14-174050"
+%                  multiple sessions, separated by commas
 %
 % probeAB     "ProbeA" | "ProbeB"
 %
@@ -97,11 +99,22 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
     probe_insertion_direction (1,1) string {mustBeMember(probe_insertion_direction, ["down","up"])} = "down"
 end
 
+%TODO in order to move upwards, we need to load strucural data for the
+% region below the tip of the probe, eg. 1 mm beyond the tip
+% This will need p and m and retrieving the anatomical labels from st.
+
+
 %TODO add button to go next and previous probe
 
 %TODO what if optic fiber data is chosen?
 
 
+% accept multiple sessions separated by comma
+session_ids = strip(strsplit(session_id,","));
+
+if length(session_ids) > 1
+    session_id = session_ids(1);
+end
 
 
 sorter_output_dir = fullfile(sessions_dir, task_dir_name,  ...
@@ -339,10 +352,15 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 ln1 = line(uax2, celldensity/max(celldensity), (1:384)'*0.01, 'Color', 'w');
 xlim(uax2,[0 1])
 
-tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
-    sprintf("%s/%s (%d)", session_id, probeAB, probe_id),...
-    HorizontalAlignment='center',FontSize=18,LineStyle='none');
-
+if length(session_ids) > 1
+    tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
+        sprintf("%s/%s (%d)", session_ids, probeAB, probe_id),...
+        HorizontalAlignment='center',FontSize=18,LineStyle='none');
+else
+    tx1 = annotation(ufig, 'textbox', [0.2 0.85 0.8 0.1],  'String', ...
+        sprintf("%s/%s (%d)", session_id, probeAB, probe_id),...
+        HorizontalAlignment='center',FontSize=18,LineStyle='none');
+end
 %% 
 anc_id = Tapdvml_contacts_this.anc_id;
 
@@ -361,6 +379,9 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
 
 block_colors = anc_color(start_ind, :);
 
+%TODO show names for regions below the tip as well
+% may take 1- 2 hrs
+
 
 Tblocks = table(block_names, start_ind, end_ind, block_colors, ...
     VariableNames={'block_names', 'start_ind','end_ind', 'block_colors'});
@@ -381,6 +402,8 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
         Tblocks.block_names(i),...
         'FontSize',14,...
         'HorizontalAlignment','center', Clipping='on');
+
+    %TODO show names for regions below the tip as well
 end
 
 horzline = line(uax1, [0 1], [0 0], 'Color','r'); % distance from the tip 0 mm
@@ -500,6 +523,13 @@ function save_updown_to_table(uax1, ~)
             end
         end
 
+        if length(session_ids) > 1
+            %TODO
+            warning('Save for multilpe sessions not implemented yet.')
+            keyboard
+
+        end
+
 
         %% save the backup
 

From eda3c21e40eae1a5b3c8be36890c6e6148cf412a Mon Sep 17 00:00:00 2001
From: "Kouichi C. Nakamura" <kouichi.c.nakamura@gmail.com>
Date: Tue, 28 Nov 2023 15:48:32 +0000
Subject: [PATCH 43/43] Update updown_probe_with_slider.m

---
 Browsing Functions/updown_probe_with_slider.m | 26 ++++++-------------
 1 file changed, 8 insertions(+), 18 deletions(-)

diff --git a/Browsing Functions/updown_probe_with_slider.m b/Browsing Functions/updown_probe_with_slider.m
index 2b7c001..49deb6b 100644
--- a/Browsing Functions/updown_probe_with_slider.m	
+++ b/Browsing Functions/updown_probe_with_slider.m	
@@ -161,10 +161,14 @@ function updown_probe_with_slider(av, st, session_id, probeAB, plane, sessions_d
     case "ProbeB"
         probeAB_short = "B";
     otherwise
-
+        probeAB_short = "optic fiber";
 end
 
-tf = T_probes.session_id == session_id & T_probes.probe_AB == probeAB_short;
+T_probes.session_ids = (cellfun(@(x) string(strsplit(x, ', ')), ...
+    T_probes.session_id, UniformOutput=false)); % handling multiple session_ids for one probe
+
+tf = cellfun(@(x) ismember(session_id, x), T_probes.session_ids) ...
+    & T_probes.probe_AB == probeAB_short;
 
 probe_id = T_probes{tf, "probe_id"};
 
@@ -563,24 +567,11 @@ function save_updown_to_table(uax1, ~)
         % see plot_and_compute_probe_positions_from_ccf.m
         % I need the eigen vector, to be saved in T_probes?
 
-        switch probeAB
-            case "ProbeA"
-                probeAB_ = "A";
-            case "ProbeB"
-                probeAB_ = "B";
-            case "optic fiber"
-                probeAB_ = "optic fiber";
-        end
-
         % eigen vector
-        tf = T_probes.session_id == session_id & ...
-            T_probes.probe_AB == probeAB_;
-
         assert(nnz(tf) == 1)
 
         try
-            p = T_probes{T_probes.session_id == session_id & ...
-                T_probes.probe_AB == probeAB_, ["p_1","p_2","p_3"]};
+            p = T_probes{tf, ["p_1","p_2","p_3"]};
         catch ME
             if ME.identifier == "MATLAB:table:UnrecognizedVarName"
                 error("It looks like m you have to run plot_and_compute_probe_positions_from_ccf()" ...
@@ -590,8 +581,7 @@ function save_updown_to_table(uax1, ~)
                 throw(ME);
             end
         end
-        m = T_probes{T_probes.session_id == session_id & ...
-            T_probes.probe_AB == probeAB_, ["m_1","m_2","m_3"]};
+        m = T_probes{tf, ["m_1","m_2","m_3"]};
 
         processed_images_folder = fullfile(image_folder, 'processed');