From d5f0ef7cc9fb0c0163ac8b15f2c20cbd900b9afb Mon Sep 17 00:00:00 2001
From: Julie-Fabre <julie.m.fabre@gmail.com>
Date: Wed, 5 Jun 2024 18:37:29 +0100
Subject: [PATCH] update unitmatch default params

---
 .../bc_qualityParamValuesForUnitMatch.m       |  8 +++----
 qualityMetrics/bc_updateSpatialDecaySlope.asv | 22 +++++++++++++++++++
 2 files changed, 26 insertions(+), 4 deletions(-)
 create mode 100644 qualityMetrics/bc_updateSpatialDecaySlope.asv

diff --git a/qualityMetrics/bc_qualityParamValuesForUnitMatch.m b/qualityMetrics/bc_qualityParamValuesForUnitMatch.m
index 01dd707f..fc9c4115 100644
--- a/qualityMetrics/bc_qualityParamValuesForUnitMatch.m
+++ b/qualityMetrics/bc_qualityParamValuesForUnitMatch.m
@@ -95,11 +95,11 @@
 end
 paramBC.minThreshDetectPeaksTroughs = 0.2; % this is multiplied by the max value 
 paramBC.firstPeakRatio = 1.1; % if units have an initial peak before the trough,
-
 % in a units waveform to give the minimum prominence to detect peaks using
 % matlab's findpeaks function.
-paramBC.firstPeakRatio = 1.1; % if units have an initial peak before the trough,
-
+paramBC.normalizeSpDecay = 1; % whether to normalize spatial decay points relative to 
+% maximum - this makes the spatrial decay slop calculation more invariant to the 
+% spike-sorting algorithm used
 
 % recording parametrs
 paramBC.ephys_sample_rate = 30000; % samples per second
@@ -146,7 +146,7 @@
 paramBC.somatic = 1; 
 paramBC.minWvDuration = 100; % in us
 paramBC.maxWvDuration = 800; % in us
-paramBC.minSpatialDecaySlope = -0.003;
+paramBC.minSpatialDecaySlope = -0.005;
 paramBC.maxWvBaselineFraction = 0.3;
 
 %distance metrics
diff --git a/qualityMetrics/bc_updateSpatialDecaySlope.asv b/qualityMetrics/bc_updateSpatialDecaySlope.asv
new file mode 100644
index 00000000..3c3451d0
--- /dev/null
+++ b/qualityMetrics/bc_updateSpatialDecaySlope.asv
@@ -0,0 +1,22 @@
+function bc_updateSpatialDecaySlope(kilosortSavePath, qMetricSavePath)
+
+% load in quality metrics 
+[~, qMetric] = bc_loadSavedMetrics(qMetricSavePath); 
+
+% load in relevant kilosort files 
+[~, spikeTemplates, templateWaveforms, ~, ~, ...
+    ~, ~] = bc_loadEphysData(kilosortSavePath);
+
+uniqueTemplates = unique(spikeTemplates);
+
+% update spatial decay value
+for iUnit = 1:size(uniqueTemplates,1)
+
+    thisUnit = uniqueTemplates(iUnit);
+
+    qMetric.spatialDecaySlope(iUnit) = qMetric.spatialDecaySlope(iUnit)./max(max(templateWaveforms(thisUnit, :,:)));
+end
+
+% save new metrics 
+parquetwrite([fullfile(qMetricSavePath, 'templates._bc_qMetrics.parquet')], qMetric)
+end
\ No newline at end of file