From 6fa45813555e77e80a4bcb07837fb645ccb7c551 Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <jean-yves.tinevez@pasteur.fr>
Date: Fri, 24 Jul 2020 15:26:32 +0200
Subject: [PATCH] Better version of find_contour.
One call to pdist per run. Speed-up ~ x8.
---
src/@deproj/find_countour.m | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
diff --git a/src/@deproj/find_countour.m b/src/@deproj/find_countour.m
index a5cae48..47920b8 100644
--- a/src/@deproj/find_countour.m
+++ b/src/@deproj/find_countour.m
@@ -4,9 +4,12 @@ function P2 = find_countour( P )
P2 = NaN( size( P ) );
current = 1;
+ D = squareform( pdist ( P ) );
+ D( D == 0 ) = Inf;
+
% Start point
- ps = P( 1, : );
- set_visited( 1 )
+ id = 1;
+ ps = P( id, : );
P2( current, : ) = ps;
current = current + 1;
@@ -16,9 +19,10 @@ function P2 = find_countour( P )
done = current == size( P, 1 );
- id = find_next_point( ps );
+ prev_id = id;
+ id = find_next_point( id );
ps = P( id, : );
- set_visited( id )
+ set_visited( prev_id )
P2( current, : ) = ps;
current = current + 1;
@@ -26,11 +30,12 @@ function P2 = find_countour( P )
function set_visited( id )
- P( id, : ) = NaN;
+ D( id, : ) = Inf;
+ D( :, id ) = Inf;
end
- function id = find_next_point( p0 )
- [ ~, id ] = pdist2( P, p0, 'Euclidean', 'Smallest', 1 );
+ function id = find_next_point( id )
+ [ ~, id ] = min( D( :, id ) );
end
end
--
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