Added a few functions

Author: adamltaylor

Diff for: collect_landmarks.m

@@ -9,20 +9,7 @@
         landmark_file_name = sprintf('%s-desc.%d.txt', leaf_folder_name, background_channel_index) ;
         landmark_file_path = fullfile(landmark_folder_path, tile_relative_path, landmark_file_name) ;
         if exist(landmark_file_path, 'file') ,
-            landmark_data = load_tabular_data(landmark_file_path) ;
-            if isempty(landmark_data) ,
-                ijk0_from_landmark_index = zeros(0,3) ;
-            else
-                flipped_ijk0_from_landmark_index = landmark_data(:,1:3) ;
-                % the landmark-detection code is run on the the raw (flipped in x and y) tiles,
-                % so need to un-flip the landmarks
-                ijk0_from_landmark_index = ...
-                    [ (tile_shape_ijk(1)-1) - flipped_ijk0_from_landmark_index(:,1) ...
-                      (tile_shape_ijk(2)-1) - flipped_ijk0_from_landmark_index(:,2) ...
-                      flipped_ijk0_from_landmark_index(:,3) ] ;
-            end
-            %foreground_p_value_from_landmark_index = landmark_data(:,4) ;
-            %imagery_value_from_landmark_index = landmark_data(:,5) ;        
+            ijk0_from_landmark_index = load_landmark_file(landmark_file_path, tile_shape_ijk) ;
         else
             fprintf('Missing (?) landmark file for tile %s\n', tile_relative_path) ;
             ijk0_from_landmark_index = zeros(0,3) ;

Diff for: figure_mip.m

@@ -0,0 +1,18 @@
+function [f, a] = figure_mip(stack_yxz)
+    mip = max(stack_yxz, [], 3) ;
+
+    c_min = double(min(min(mip))) ;
+    c_max = double(max(max(mip))) ;
+    if c_min == c_max ,
+        c_mean = c_min ;
+        c_min = c_mean - 0.5 ;
+        c_max = c_mean + 0.5 ;
+    end
+    
+    f = figure('color', 'w') ;
+    a = axes(f) ;
+    imagesc(a, mip, [c_min c_max]) ;
+    axis(a,'image') ;
+    colormap(parula(256)) ;
+    colorbar;    
+end

Diff for: file_relative_path_from_tile_relative_path.m

@@ -0,0 +1,12 @@
+function result = file_relative_path_from_tile_relative_path(relative_path, channel_index, label, extension) 
+    % E.g. '2020-12-01/01/01916' -> '2020-12-01/01/01916/01916-ngc.0.tif'
+    if ~exist('label', 'var') || isempty(label) ,
+        extension = 'ngc' ;
+    end       
+    if ~exist('extension', 'var') || isempty(extension) ,
+        extension = '.tif' ;
+    end    
+    [~, leaf_folder_name] = fileparts2(relative_path) ;
+    imagery_file_name = sprintf('%s-%s.%d%s', leaf_folder_name, label, channel_index, extension) ;
+    result = fullfile(relative_path, imagery_file_name) ;
+end

Diff for: load_landmark_file.m

@@ -0,0 +1,17 @@
+function [ijk0_from_landmark_index, foreground_p_value_from_landmark_index, imagery_value_from_landmark_index] =...
+        load_landmark_file(landmark_file_name, tile_shape_ijk)
+    landmark_data = load_tabular_data(landmark_file_name) ;
+    if isempty(landmark_data) ,
+        ijk0_from_landmark_index = zeros(0,3) ;
+    else
+        flipped_ijk0_from_landmark_index = landmark_data(:,1:3) ;
+        % the landmark-detection code is run on the the raw (flipped in x and y) tiles,
+        % so need to un-flip the landmarks
+        ijk0_from_landmark_index = ...
+            [ (tile_shape_ijk(1)-1) - flipped_ijk0_from_landmark_index(:,1) ...
+              (tile_shape_ijk(2)-1) - flipped_ijk0_from_landmark_index(:,2) ...
+              flipped_ijk0_from_landmark_index(:,3) ] ;
+    end
+    foreground_p_value_from_landmark_index = landmark_data(:,4) ;
+    imagery_value_from_landmark_index = landmark_data(:,5) ;
+end

Diff for: p_map_file_relative_path_from_relative_path.m

@@ -0,0 +1,9 @@
+function result = p_map_file_relative_path_from_relative_path(relative_path, channel_index, extension) 
+    % E.g. '2020-12-01/01/01916' -> '2020-12-01/01/01916/01916-ngc.0.tif'
+    if ~exist('extension', 'var') || isempty(extension) ,
+        extension = '.h5' ;
+    end    
+    [~, leaf_folder_name] = fileparts2(relative_path) ;
+    imagery_file_name = sprintf('%s-prob.%d%s', leaf_folder_name, channel_index, extension) ;
+    result = fullfile(relative_path, imagery_file_name) ;
+end