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IAH public
DeProj
Commits
46e25fde
Commit
46e25fde
authored
Jul 24, 2020
by
Jean-Yves TINEVEZ
Browse files
Use the mesh to specify the Z position in the from_bellaiche import.
parent
53c6289f
Changes
1
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Inline
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src/@deproj/from_bellaiche.m
View file @
46e25fde
...
...
@@ -3,7 +3,7 @@ function obj = from_bellaiche( ...
frame
,
...
sides
,
...
vertices
,
...
voxel_dep
th
,
...
mesh_file_pa
th
,
...
units
)
%FROM_BELLAICHE Returns a deproj object built from the results of the tool
%from Yohannes Bellaiche lab.
...
...
@@ -13,6 +13,17 @@ function obj = from_bellaiche( ...
width
=
frame
.
imageSize
(
1
);
pixel_size
=
frame
.
scale1D
;
%% Read the mesh file.
fprintf
(
'Loading and processing the tissue mesh file.\n'
)
tic
V
=
deproj
.
ply_read
(
mesh_file_path
);
si
=
scatteredInterpolant
(
V
(:,
1
),
V
(:,
2
),
V
(:,
3
),
'linear'
,
'nearest'
);
fprintf
(
'Loaded %d vertices in %.1f seconds.\n'
,
size
(
V
,
1
),
toc
)
%% Build the junction graph.
tic
...
...
@@ -25,23 +36,22 @@ function obj = from_bellaiche( ...
node_table
=
table
();
jxy
=
vertices
.
XYs
;
% TODO
jz
=
zeros
(
size
(
jxy
,
1
),
1
);
jz
=
si
(
jxy
);
node_table
.
Centroid
=
[
jxy
jz
];
node_table
.
ID
=
vertices
.
numbers
;
junction_graph
=
graph
(
edge_table
,
node_table
,
'omitselfloops'
);
fprintf
(
'Built the junction graph with %d nodes and %d edges in %.1f seconds.\n'
,
...
junction_graph
.
numnodes
,
junction_graph
.
numedges
,
toc
)
junction_graph
.
numnodes
,
junction_graph
.
numedges
,
toc
)
%% Convert YB structure to epicells.
fprintf
(
'Converting to objects.\n'
)
tic
n_cells
=
numel
(
cells
.
contour_indices
);
fprintf
(
'Computing morphological descriptors of %d objects.\n'
,
n_cells
-
1
)
tic
% We don't go for the first one, which contains the contour of the tissue.
% Get boundary.
...
...
@@ -57,8 +67,8 @@ function obj = from_bellaiche( ...
P
=
deproj
.
find_countour
(
P
);
P
=
P
*
pixel_size
;
%
TODO
z
=
zeros
(
numel
(
x
),
1
);
%
Get Z from the mesh.
z
=
si
(
P
);
boundary
=
[
P
z
];
% Get the junction ids.
...
...
@@ -70,8 +80,10 @@ function obj = from_bellaiche( ...
end
fprintf
(
'Done in %.1f seconds.\n'
,
toc
)
obj
=
deproj
(
epicells
,
junction_graph
,
units
);
end
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