From 546457fe2990d74625cd8be5ee66528a5ff10a84 Mon Sep 17 00:00:00 2001
From: ac_fx <arc334@drexel.edu>
Date: Sun, 12 Nov 2023 13:03:50 -0500
Subject: [PATCH] SSF clip quantiles
---
matlab/+SSF/getClipLimits.m | 9 ++++-----
matlab/+SSF/getClipQuantiles.m | 12 ++++++++++++
matlab/+SSF/go_ssf_ncd.m | 2 +-
3 files changed, 17 insertions(+), 6 deletions(-)
create mode 100644 matlab/+SSF/getClipQuantiles.m
diff --git a/matlab/+SSF/getClipLimits.m b/matlab/+SSF/getClipLimits.m
index c3d93db2..5eb239d7 100644
--- a/matlab/+SSF/getClipLimits.m
+++ b/matlab/+SSF/getClipLimits.m
@@ -29,10 +29,9 @@ parfor ff=1:length(flist)
end
kymoPixels = vertcat(kymoPixels{:});
-cl = [mean(kymoPixels)-std(kymoPixels), mean(kymoPixels)+std(kymoPixels)];
-q1 = length(find(kymoPixels<cl(1)))./length(kymoPixels);
-q2 = 1 - length(find(kymoPixels>cl(2)))./length(kymoPixels);
-pxTarget = linspace(q1,q2,254);
-clipLimits = quantile(kymoPixels,pxTarget);
+
+clip_neg = SSF.getClipQuantiles(kymoPixels(kymoPixels<0),127);
+clip_pos = SSF.getClipQuantiles(kymoPixels(kymoPixels>0),127);
+clipLimits = [clip_neg,clip_pos];
clipLimits = repmat({clipLimits},length(flist),1);
4;
diff --git a/matlab/+SSF/getClipQuantiles.m b/matlab/+SSF/getClipQuantiles.m
new file mode 100644
index 00000000..b6cf656d
--- /dev/null
+++ b/matlab/+SSF/getClipQuantiles.m
@@ -0,0 +1,12 @@
+function clipLimits = getClipQuantiles(voxels,nQuant)
+%
+% mx = mean(voxels);
+% sx = std(voxels);
+% cl = [mx-sx, mx+sx];
+% q1 = length(find(voxels<cl(1)))./length(voxels);
+% q2 = 1 - length(find(voxels>cl(2)))./length(voxels);
+% pxTarget = linspace(q1,q2,nQuant);
+% clipLimits = quantile(voxels,pxTarget);
+
+pxTarget = linspace(2.5,97.5,nQuant);
+clipLimits = prctile(voxels,pxTarget);
diff --git a/matlab/+SSF/go_ssf_ncd.m b/matlab/+SSF/go_ssf_ncd.m
index db4ad479..5a06be40 100644
--- a/matlab/+SSF/go_ssf_ncd.m
+++ b/matlab/+SSF/go_ssf_ncd.m
@@ -24,7 +24,7 @@ kymoPixels = {};
p = ljsStartParallel();
%
-if ~exist('clipLimits','var')
+if ~exist('clipLimits','var') || isempty(clipLimits)
clipLimits = SSF.getClipLimits(flist,targetChannels,nKeep,tClip);
end
%
--
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