From c06c5629f9cf2be25bc9c818c08542fa476e0634 Mon Sep 17 00:00:00 2001
From: "Brandon Ingram (PhD Psychology Lab FT)" <bti967@student.bham.ac.uk>
Date: Sat, 11 Feb 2023 22:23:51 +0000
Subject: [PATCH] Fixed downsampling issue with Gaussian obervation model

---
 utils/analysis/getFractionalOccupancy.m |  3 ++-
 utils/analysis/getStateIntervalTimes.m  | 12 ++++++++----
 utils/analysis/getStateLifeTimes.m      | 12 ++++++++----
 utils/analysis/getSwitchingRate.m       | 12 ++++++++----
 4 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/utils/analysis/getFractionalOccupancy.m b/utils/analysis/getFractionalOccupancy.m
index eb063d9..148006f 100644
--- a/utils/analysis/getFractionalOccupancy.m
+++ b/utils/analysis/getFractionalOccupancy.m
@@ -62,7 +62,8 @@
    options.order = (sum(T) - size(Gamma,1)) / length(T);
 end
 
-if isfield(options,'tuda') && options.tuda
+if isfield(options,'tuda') && options.tuda | ...
+        isfield(options, 'order') && options.order == 0
     T = ceil(r * T);
 elseif isfield(options,'order') && options.order > 0
     T = ceil(r * T);
diff --git a/utils/analysis/getStateIntervalTimes.m b/utils/analysis/getStateIntervalTimes.m
index 95c7a54..adef3e1 100644
--- a/utils/analysis/getStateIntervalTimes.m
+++ b/utils/analysis/getStateIntervalTimes.m
@@ -54,7 +54,14 @@
     r = (options.downsample/options.Fs);
 end
 
-if isfield(options,'order') && options.order > 0
+if ~isfield(options,'order') && ~isfield(options,'embeddedlags')
+   options.order = (sum(T) - size(Gamma,1)) / length(T);
+end
+
+if isfield(options,'tuda') && options.tuda | ...
+        isfield(options, 'order') && options.order == 0
+    T = ceil(r * T);
+elseif isfield(options,'order') && options.order > 0
     T = ceil(r * T);
     T = T - options.order; 
 elseif isfield(options,'embeddedlags') && length(options.embeddedlags) > 1
@@ -62,9 +69,6 @@
     d2 = max(0,options.embeddedlags(end));
     T = T - (d1+d2);
     T = ceil(r * T);
-else
-    options.order = (sum(T) - size(Gamma,1)) / length(T); 
-    T = T - options.order; 
 end
 
 if is_vpath % viterbi path
diff --git a/utils/analysis/getStateLifeTimes.m b/utils/analysis/getStateLifeTimes.m
index 3925400..a92dac1 100644
--- a/utils/analysis/getStateLifeTimes.m
+++ b/utils/analysis/getStateLifeTimes.m
@@ -55,7 +55,14 @@
     r = (options.downsample/options.Fs);
 end
 
-if isfield(options,'order') && options.order > 0
+if ~isfield(options,'order') && ~isfield(options,'embeddedlags')
+   options.order = (sum(T) - size(Gamma,1)) / length(T);
+end
+
+if isfield(options,'tuda') && options.tuda | ...
+        isfield(options, 'order') && options.order == 0
+    T = ceil(r * T);
+elseif isfield(options,'order') && options.order > 0
     T = ceil(r * T);
     T = T - options.order; 
 elseif isfield(options,'embeddedlags') && length(options.embeddedlags) > 1
@@ -63,9 +70,6 @@
     d2 = max(0,options.embeddedlags(end));
     T = T - (d1+d2);
     T = ceil(r * T);
-else
-    options.order = (sum(T) - size(Gamma,1)) / length(T); 
-    T = T - options.order; 
 end
 
 if is_vpath % viterbi path
diff --git a/utils/analysis/getSwitchingRate.m b/utils/analysis/getSwitchingRate.m
index b3cde79..b2948a6 100644
--- a/utils/analysis/getSwitchingRate.m
+++ b/utils/analysis/getSwitchingRate.m
@@ -41,7 +41,14 @@
     r = (options.downsample/options.Fs);
 end
 
-if isfield(options,'order') && options.order > 0
+if ~isfield(options,'order') && ~isfield(options,'embeddedlags')
+   options.order = (sum(T) - size(Gamma,1)) / length(T);
+end
+
+if isfield(options,'tuda') && options.tuda | ...
+        isfield(options, 'order') && options.order == 0
+    T = ceil(r * T);
+elseif isfield(options,'order') && options.order > 0
     T = ceil(r * T);
     T = T - options.order; 
 elseif isfield(options,'embeddedlags') && length(options.embeddedlags) > 1
@@ -49,9 +56,6 @@
     d2 = max(0,options.embeddedlags(end));
     T = T - (d1+d2);
     T = ceil(r * T);
-else
-    options.order = (sum(T) - size(Gamma,1)) / length(T); 
-    T = T - options.order;     
 end
 
 if is_vpath % viterbi path