Merge pull request #9 from bassemhermila/TREES2

Add abel_tree function

.gitignore

@@ -1,2 +1,35 @@
 beta/*
-*/*.asv
+*/*.asv
+
+.MATLABDriveTag
+*.DS_Store
+
+# Windows default autosave extension
+*.asv
+
+# OSX / *nix default autosave extension
+*.m~
+
+
+# Packaged app and toolbox files
+*.mlappinstall
+*.mltbx
+
+# Generated helpsearch folders
+helpsearch*/
+
+# Simulink code generation folders
+slprj/
+sccprj/
+
+# Matlab code generation folders
+codegen/
+
+# Simulink autosave extension
+*.autosave
+
+# Simulink cache files
+*.slxc
+
+# Octave session info
+octave-workspace

metrics/abel_tree.m

@@ -0,0 +1,65 @@
+% ABEL_TREE   Euclidean length of tree segments (mean).
+% (trees package)
+%
+% abel = abel_tree (intree, options)
+% ----------------------------------
+%
+% Returns the average Euclidean distance between branch points and
+% termination points [in um].
+%
+% Input
+% -----
+% - intree   ::integer:  index of tree in trees or structured tree
+% - options  ::string:
+%     '-s'   : show
+%     {DEFAULT: ''}
+%
+% Output
+% -------
+% - abel     ::double: average Euclidean distance
+%
+% Example
+% -------
+% abel_tree  (sample_tree, '-s')
+%
+% See also len_tree
+% Uses len_tree C_tree delete_tree ver_tree
+%
+% the TREES toolbox: edit, generate, visualise and analyse neuronal trees
+% Copyright (C) 2009 - 2023  Hermann Cuntz
+
+function abel = abel_tree (intree, options)
+
+ver_tree     (intree); % verify that input is a tree structure
+
+if (nargin < 2) || isempty (options)
+    % {DEFAULT: no option}
+    options  = '';
+end
+
+iC               = C_tree (intree);
+iC (1)           = 0;
+dtree            = delete_tree (intree, find (iC));
+len              = len_tree (dtree);
+abel             = mean (len);
+
+if contains       (options, '-s') % show option
+    clf;
+    hold         on;
+    clf;
+    HP           = plot_tree (dtree, len, [], [], [], '-b');
+    set          (HP, ...
+        'edgecolor',           'none');
+    colorbar;
+    title        ( ...
+        ['ABEL: ' (num2str (round (mean (len)))) ' µm']);
+    xlabel       ('x [µm]');
+    ylabel       ('y [µm]');
+    zlabel       ('z [µm]');
+    view         (2);
+    grid         on;
+    axis         image;
+end
+
+
+