From 46d4a11eb3f41a680defa132e558f23192b15dd2 Mon Sep 17 00:00:00 2001
From: ncguilbeault <ncguilbeault@gmail.com>
Date: Wed, 19 Feb 2025 21:58:58 +0000
Subject: [PATCH 1/2] Fixed issue when constructing density estimation without
 passing kernel limit parameter.

---
 .../Configuration/PointProcessModelConfiguration.cs          | 5 +++++
 .../Encoder/ClusterlessMarkEncoder.cs                        | 4 +++-
 src/PointProcessDecoder.Core/Encoder/SortedSpikeEncoder.cs   | 1 +
 src/PointProcessDecoder.Core/PointProcessModel.cs            | 2 ++
 4 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/src/PointProcessDecoder.Core/Configuration/PointProcessModelConfiguration.cs b/src/PointProcessDecoder.Core/Configuration/PointProcessModelConfiguration.cs
index 2325383..5454099 100644
--- a/src/PointProcessDecoder.Core/Configuration/PointProcessModelConfiguration.cs
+++ b/src/PointProcessDecoder.Core/Configuration/PointProcessModelConfiguration.cs
@@ -97,6 +97,11 @@ public class PointProcessModelConfiguration
     /// </summary>
     public double? SigmaRandomWalk { get; set; }
 
+    /// <summary>
+    /// The kernel limit of the model.
+    /// </summary>
+    public int? KernelLimit { get; set; }
+
     /// <summary>
     /// The scalar type of the model.
     /// </summary>
diff --git a/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs b/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
index 1149482..954ef22 100644
--- a/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
+++ b/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
@@ -98,6 +98,7 @@ public ClusterlessMarkEncoder(
                 _observationEstimation = new KernelDensity(
                     bandwidth: observationBandwidth, 
                     dimensions: _stateSpace.Dimensions, 
+                    kernelLimit: kernelLimit,
                     device: device,
                     scalarType: scalarType
                 );
@@ -106,7 +107,8 @@ public ClusterlessMarkEncoder(
                 {
                     _markEstimation[i] = new KernelDensity(
                         bandwidth: bandwidth, 
-                        dimensions: jointDimensions, 
+                        dimensions: jointDimensions,
+                        kernelLimit: kernelLimit,
                         device: device,
                         scalarType: scalarType
                     );
diff --git a/src/PointProcessDecoder.Core/Encoder/SortedSpikeEncoder.cs b/src/PointProcessDecoder.Core/Encoder/SortedSpikeEncoder.cs
index a205c00..d00e4f5 100644
--- a/src/PointProcessDecoder.Core/Encoder/SortedSpikeEncoder.cs
+++ b/src/PointProcessDecoder.Core/Encoder/SortedSpikeEncoder.cs
@@ -112,6 +112,7 @@ private static IEstimation GetEstimationMethod(
             EstimationMethod.KernelDensity => new KernelDensity(
                 bandwidth: bandwidth, 
                 dimensions: dimensions, 
+                kernelLimit: kernelLimit,
                 device: device,
                 scalarType: scalarType
             ),
diff --git a/src/PointProcessDecoder.Core/PointProcessModel.cs b/src/PointProcessDecoder.Core/PointProcessModel.cs
index fb92527..32e1ff8 100644
--- a/src/PointProcessDecoder.Core/PointProcessModel.cs
+++ b/src/PointProcessDecoder.Core/PointProcessModel.cs
@@ -181,6 +181,7 @@ public PointProcessModel(
             DistanceThreshold = distanceThreshold,
             IgnoreNoSpikes = ignoreNoSpikes,
             SigmaRandomWalk = sigmaRandomWalk,
+            KernelLimit = kernelLimit,
             ScalarType = scalarType
         };
     }
@@ -272,6 +273,7 @@ public override void Save(string basePath)
             distanceThreshold: configuration.DistanceThreshold,
             ignoreNoSpikes: configuration.IgnoreNoSpikes,
             sigmaRandomWalk: configuration.SigmaRandomWalk,
+            kernelLimit: configuration.KernelLimit,
             device: device,
             scalarType: configuration.ScalarType
         );

From 8a11304166245236ebf75138102bdf25d1c7fce0 Mon Sep 17 00:00:00 2001
From: ncguilbeault <ncguilbeault@gmail.com>
Date: Sun, 23 Feb 2025 17:14:28 +0000
Subject: [PATCH 2/2] Made channel estimates readonly

---
 src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs b/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
index 954ef22..e228a59 100644
--- a/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
+++ b/src/PointProcessDecoder.Core/Encoder/ClusterlessMarkEncoder.cs
@@ -34,7 +34,7 @@ public class ClusterlessMarkEncoder : ModelComponent, IEncoder
     private Tensor _markIntensities = empty(0);
     private Tensor _channelIntensities = empty(0);
     private Tensor _observationDensity = empty(0);
-    private Tensor[] _channelEstimates = [];
+    private readonly Tensor[] _channelEstimates = [];
 
     private Tensor _spikeCounts = empty(0);
     private Tensor _samples = empty(0);