From 7a9aeccd9a9affe9d04d956490e1508b4a0fe4c7 Mon Sep 17 00:00:00 2001
From: ernesto-vidal <61276100+ernesto-vidal@users.noreply.github.com>
Date: Tue, 15 Nov 2022 13:12:16 +0000
Subject: [PATCH] Add available landmarks to NIRS SD3D output (#40)

* Include cranial landmarks in .nirs file

The saving function write_NIRS was missing the cranial landmarks in the SD3D structure

* Added comments to write_NIRS

write_NIRS was modified to include landmarks and comments were added to clarify changes

* Update write_NIRS.m

Cranial landmark names were missing in the SD3D structure, this has been amended.
---
 +lumofile/read_lufr.m  |  2 +-
 +lumofile/write_NIRS.m | 17 +++++++++++++++++
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/+lumofile/read_lufr.m b/+lumofile/read_lufr.m
index abfed7a..21c725b 100644
--- a/+lumofile/read_lufr.m
+++ b/+lumofile/read_lufr.m
@@ -798,7 +798,7 @@
 
 
 % Load layout or take from the user
-if isempty(layout_override) & (n_layouts == 0)
+if isempty(layout_override) && (n_layouts == 0)
   
   % The user has nor provided a layout, we must use the embedded data if it exists
   % enum.groups(gidx + 1).layout = [];
diff --git a/+lumofile/write_NIRS.m b/+lumofile/write_NIRS.m
index 6483492..fe87c20 100644
--- a/+lumofile/write_NIRS.m
+++ b/+lumofile/write_NIRS.m
@@ -210,6 +210,23 @@
   
 end
 
+% Add Landmarks to SD3D
+%
+SD3D.Landmarks = zeros(size(layout.landmarks,1),3);
+SD3D.LandmarksNames = cell(1,size(layout.landmarks,1));
+for li = 1:size(layout.landmarks,1)
+    SD3D.Landmarks(li,1) = layout.landmarks(li).coords_3d.x;
+    SD3D.Landmarks(li,2) = layout.landmarks(li).coords_3d.y;
+    SD3D.Landmarks(li,3) = layout.landmarks(li).coords_3d.z;
+    
+% Add Landmarks names
+    SD3D.LandmarksNames{li} = layout.landmarks(li).name;
+    
+end
+
+
+
+
 % Build MeasList
 %
 SD.MeasList = zeros(size(glch,1), 4);