From 5cac3876cd482683cd42c2fc1a27858ce580af00 Mon Sep 17 00:00:00 2001
From: stwilliams333 <stwilliamsmail@gmail.com>
Date: Wed, 14 Jun 2023 16:45:15 -0500
Subject: [PATCH] Excitation cost allowable error and error center from xml

---
 .../CostTerms/calcMuscleExcitationPenaltyCost.m             | 6 ++++--
 src/MuscleTendonPersonalization/Optimization/calcMtpCost.m  | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcMuscleExcitationPenaltyCost.m b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcMuscleExcitationPenaltyCost.m
index 5de8a3e2f..505251aee 100644
--- a/src/MuscleTendonPersonalization/Optimization/CostTerms/calcMuscleExcitationPenaltyCost.m
+++ b/src/MuscleTendonPersonalization/Optimization/CostTerms/calcMuscleExcitationPenaltyCost.m
@@ -27,13 +27,15 @@
 
 function cost = calcMuscleExcitationPenaltyCost(modeledValues, ...
     experimentalData, costTerm)
+errorCenter = valueOrAlternate(costTerm, "errorCenter", 0.5);
+maximumAllowableError = valueOrAlternate(costTerm, "maxAllowableError", 0.25);
 muscleExcitationsConstraint = modeledValues.muscleExcitationsNoTDelay(: , ...
     setdiff(1 : size(modeledValues.muscleExcitationsNoTDelay, 2), ...
     [experimentalData.synergyExtrapolation.missingEmgChannelGroups{:}]), ...
     experimentalData.numPaddingFrames + 1 : ...
     size(modeledValues.muscleExcitationsNoTDelay, 3) - ...
     experimentalData.numPaddingFrames);
-cost = 120 * (muscleExcitationsConstraint - 0.5) .^ 8;
+cost = 30 / maximumAllowableError * (muscleExcitationsConstraint - errorCenter) .^ 8;
 cost(isnan(cost))=0;
-cost = sum([sqrt(0.1) .* cost ].^ 2, 'all');
+cost = sum((sqrt(0.1) .* cost).^ 2, 'all');
 end
\ No newline at end of file
diff --git a/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m b/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
index a1783a618..7ec645d8d 100644
--- a/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
+++ b/src/MuscleTendonPersonalization/Optimization/calcMtpCost.m
@@ -76,7 +76,7 @@
                     synxModeledValues, modeledValues, experimentalData, costTerm);
             case "muscle_excitation_penalty"
                 cost = calcMuscleExcitationPenaltyCost( ...
-                    synxModeledValues, experimentalData);%, costTerm);
+                    synxModeledValues, experimentalData, costTerm);
             otherwise
                 throw(MException('', 'Cost term %s is not valid for MTP', ...
                     costTerm.type))