From 35da61452f1e75c2d52eefd413b00f54cb56f437 Mon Sep 17 00:00:00 2001
From: Ali Karimi <karimi.k.ali@gmail.com>
Date: Mon, 24 Apr 2023 16:16:02 +0200
Subject: [PATCH] Sepia isosurface
---
.gitignore | 1 +
code/+surface/+Scripts/sepia_writePLY.m | 3 +++
code/+surface/+genIsosurface/readVolume.m | 2 +-
code/+surface/config_V2_ACC.m | 11 +++++++++++
4 files changed, 16 insertions(+), 1 deletion(-)
create mode 100644 code/+surface/+Scripts/sepia_writePLY.m
diff --git a/.gitignore b/.gitignore
index 5f73f9d..1815c88 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,5 @@
Figures/
+data/Other/isoSurfaceGeneration/sepia/
*remoteDir.mat
*deepLayerApicalDendrite*
*layer2ApicalDendrite*
diff --git a/code/+surface/+Scripts/sepia_writePLY.m b/code/+surface/+Scripts/sepia_writePLY.m
new file mode 100644
index 0000000..4f458b5
--- /dev/null
+++ b/code/+surface/+Scripts/sepia_writePLY.m
@@ -0,0 +1,3 @@
+
+p = surface.config_V2_ACC('sepia');
+surface.genIsosurface.fromVolumeTracing(p);
\ No newline at end of file
diff --git a/code/+surface/+genIsosurface/readVolume.m b/code/+surface/+genIsosurface/readVolume.m
index b2fe8db..cf3871f 100644
--- a/code/+surface/+genIsosurface/readVolume.m
+++ b/code/+surface/+genIsosurface/readVolume.m
@@ -16,7 +16,7 @@ outdir = fullfile(volAnnotationDir,[volAnnotationFilename,'Raw']);
if ~exist(outdir,'dir')
util.mkdir(outdir)
unzip(fullfile(volAnnotationDir,[volAnnotationFilename,'.zip']), outdir);
- unzip(fullfile(outdir,'data'),outdir)
+ unzip(fullfile(outdir,'data_Volume'),outdir)
end
% WKW path of first magnification (highest resolution)
diff --git a/code/+surface/config_V2_ACC.m b/code/+surface/config_V2_ACC.m
index 3497000..2bb0d52 100644
--- a/code/+surface/config_V2_ACC.m
+++ b/code/+surface/config_V2_ACC.m
@@ -29,6 +29,17 @@ if strcmp(dataset,'acc')
'JO_ACC_Z_straightenedPosthoc_version');
p.volAnnotationName = 'ACC_volumeAnnotations';
end
+
+
+if strcmp(dataset,'sepia')
+ p.raw.voxelSize = [11.24,11.24,30];
+ p.bbox = {[0, 0, 0, 1100, 1100, 998]};
+ p.treeNames = {'Segment 1'};
+
+ p.volAnnotationDir = fullfile(p.outputDirectory,...
+ 'alik_uct_HalfBrain_5_8um_50kV_Air_LE4');
+ p.volAnnotationName = 'The_OL_volume';
+end
p.bbox = cellfun(@Util.convertWebknossosToMatlabBbox,p.bbox,...
'UniformOutput',false);
--
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