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IAH public
DeProj
Commits
d0cd038e
Commit
d0cd038e
authored
Jul 15, 2020
by
Jean-Yves TINEVEZ
Browse files
Plot tissue local curvature with a nice colormap.
parent
f915ca9a
Changes
8
Hide whitespace changes
Inline
Side-by-side
RunExample.m
View file @
d0cd038e
...
...
@@ -68,8 +68,11 @@ dpr = deproj.from_heightmap( ...
inpaint_zeros
,
...
prune_zeros
);
%% Plot
euler angle
s.
%% Plot
morphological parameter
s.
close
all
plot_fit_plane
(
dpr
);
% plot_fit_plane( dpr );
% plot_fit_ellipse( dpr );
[
hf
,
ax1
,
ax2
,
ax3
]
=
plot_curvatures
(
dpr
);
src/@deproj/add_plot_curvature_gauss.m
0 → 100644
View file @
d0cd038e
function
hts
=
add_plot_curvature_gauss
(
obj
,
ax
)
%ADD_PLOT_CURVATURE_GAUSS Add the tissue plot colored with the Gaussian curvature.
epicells
=
obj
.
epicells
;
curvs
=
vertcat
(
epicells
.
curvatures
);
gauss_curv
=
curvs
(
:,
2
);
hts
=
add_plot_variable
(
obj
,
gauss_curv
,
ax
);
end
src/@deproj/add_plot_curvature_k1.m
0 → 100644
View file @
d0cd038e
function
hts
=
add_plot_curvature_k1
(
obj
,
ax
)
%ADD_PLOT_CURVATURE_K1 Add the tissue plot colored with the first principal curvature.
epicells
=
obj
.
epicells
;
curvs
=
vertcat
(
epicells
.
curvatures
);
k1_curv
=
curvs
(
:,
3
);
hts
=
add_plot_variable
(
obj
,
k1_curv
,
ax
);
end
src/@deproj/add_plot_curvature_k2.m
0 → 100644
View file @
d0cd038e
function
hts
=
add_plot_curvature_k2
(
obj
,
ax
)
%ADD_PLOT_CURVATURE_K2 Add the tissue plot colored with the first principal curvature.
epicells
=
obj
.
epicells
;
curvs
=
vertcat
(
epicells
.
curvatures
);
k2_curv
=
curvs
(
:,
4
);
hts
=
add_plot_variable
(
obj
,
k2_curv
,
ax
);
end
src/@deproj/add_plot_curvature_mean.m
0 → 100644
View file @
d0cd038e
function
hts
=
add_plot_curvature_mean
(
obj
,
ax
)
%ADD_PLOT_CURVATURE_MEAN Add the tissue plot colored with the mean curvature.
epicells
=
obj
.
epicells
;
curvs
=
vertcat
(
epicells
.
curvatures
);
mean_curv
=
curvs
(
:,
1
);
hts
=
add_plot_variable
(
obj
,
mean_curv
,
ax
);
end
src/@deproj/cmap_seismic.m
0 → 100644
View file @
d0cd038e
function
cmap
=
cmap_seismic
()
%CMAP_SEISMIC Returns the seismic colormap.
cmap
=
[
0
0
0.4980
0
0
0.5142
0
0
0.5304
0
0
0.5466
0
0
0.5628
0
0
0.5790
0
0
0.5952
0
0
0.6114
0
0
0.6276
0
0
0.6438
0
0
0.6600
0
0
0.6762
0
0
0.6923
0
0
0.7085
0
0
0.7247
0
0
0.7409
0
0
0.7571
0
0
0.7733
0
0
0.7895
0
0
0.8057
0
0
0.8219
0
0
0.8381
0
0
0.8543
0
0
0.8705
0
0
0.8867
0
0
0.9028
0
0
0.9190
0
0
0.9352
0
0
0.9514
0
0
0.9676
0
0
0.9838
0
0
1.0000
0.0104
0.0104
1.0000
0.0208
0.0208
1.0000
0.0312
0.0312
1.0000
0.0417
0.0417
1.0000
0.0521
0.0521
1.0000
0.0625
0.0625
1.0000
0.0729
0.0729
1.0000
0.0833
0.0833
1.0000
0.0938
0.0938
1.0000
0.1042
0.1042
1.0000
0.1146
0.1146
1.0000
0.1250
0.1250
1.0000
0.1354
0.1354
1.0000
0.1458
0.1458
1.0000
0.1562
0.1562
1.0000
0.1667
0.1667
1.0000
0.1771
0.1771
1.0000
0.1875
0.1875
1.0000
0.1979
0.1979
1.0000
0.2083
0.2083
1.0000
0.2188
0.2188
1.0000
0.2292
0.2292
1.0000
0.2396
0.2396
1.0000
0.2500
0.2500
1.0000
0.2604
0.2604
1.0000
0.2708
0.2708
1.0000
0.2812
0.2812
1.0000
0.2917
0.2917
1.0000
0.3021
0.3021
1.0000
0.3125
0.3125
1.0000
0.3229
0.3229
1.0000
0.3333
0.3333
1.0000
0.3438
0.3438
1.0000
0.3542
0.3542
1.0000
0.3646
0.3646
1.0000
0.3750
0.3750
1.0000
0.3854
0.3854
1.0000
0.3958
0.3958
1.0000
0.4062
0.4062
1.0000
0.4167
0.4167
1.0000
0.4271
0.4271
1.0000
0.4375
0.4375
1.0000
0.4479
0.4479
1.0000
0.4583
0.4583
1.0000
0.4688
0.4688
1.0000
0.4792
0.4792
1.0000
0.4896
0.4896
1.0000
0.5000
0.5000
1.0000
0.5104
0.5104
1.0000
0.5208
0.5208
1.0000
0.5312
0.5312
1.0000
0.5417
0.5417
1.0000
0.5521
0.5521
1.0000
0.5625
0.5625
1.0000
0.5729
0.5729
1.0000
0.5833
0.5833
1.0000
0.5938
0.5938
1.0000
0.6042
0.6042
1.0000
0.6146
0.6146
1.0000
0.6250
0.6250
1.0000
0.6354
0.6354
1.0000
0.6458
0.6458
1.0000
0.6562
0.6562
1.0000
0.6667
0.6667
1.0000
0.6771
0.6771
1.0000
0.6875
0.6875
1.0000
0.6979
0.6979
1.0000
0.7083
0.7083
1.0000
0.7188
0.7188
1.0000
0.7292
0.7292
1.0000
0.7396
0.7396
1.0000
0.7500
0.7500
1.0000
0.7604
0.7604
1.0000
0.7708
0.7708
1.0000
0.7812
0.7812
1.0000
0.7917
0.7917
1.0000
0.8021
0.8021
1.0000
0.8125
0.8125
1.0000
0.8229
0.8229
1.0000
0.8333
0.8333
1.0000
0.8438
0.8438
1.0000
0.8542
0.8542
1.0000
0.8646
0.8646
1.0000
0.8750
0.8750
1.0000
0.8854
0.8854
1.0000
0.8958
0.8958
1.0000
0.9062
0.9062
1.0000
0.9167
0.9167
1.0000
0.9271
0.9271
1.0000
0.9375
0.9375
1.0000
0.9479
0.9479
1.0000
0.9583
0.9583
1.0000
0.9688
0.9688
1.0000
0.9792
0.9792
1.0000
0.9896
0.9896
1.0000
1.0000
1.0000
1.0000
1.0000
0.9922
0.9922
1.0000
0.9844
0.9844
1.0000
0.9766
0.9766
1.0000
0.9688
0.9688
1.0000
0.9609
0.9609
1.0000
0.9531
0.9531
1.0000
0.9453
0.9453
1.0000
0.9375
0.9375
1.0000
0.9297
0.9297
1.0000
0.9219
0.9219
1.0000
0.9141
0.9141
1.0000
0.9062
0.9062
1.0000
0.8984
0.8984
1.0000
0.8906
0.8906
1.0000
0.8828
0.8828
1.0000
0.8750
0.8750
1.0000
0.8672
0.8672
1.0000
0.8594
0.8594
1.0000
0.8516
0.8516
1.0000
0.8438
0.8438
1.0000
0.8359
0.8359
1.0000
0.8281
0.8281
1.0000
0.8203
0.8203
1.0000
0.8125
0.8125
1.0000
0.8047
0.8047
1.0000
0.7969
0.7969
1.0000
0.7891
0.7891
1.0000
0.7812
0.7812
1.0000
0.7734
0.7734
1.0000
0.7656
0.7656
1.0000
0.7578
0.7578
1.0000
0.7500
0.7500
1.0000
0.7422
0.7422
1.0000
0.7344
0.7344
1.0000
0.7266
0.7266
1.0000
0.7188
0.7188
1.0000
0.7109
0.7109
1.0000
0.7031
0.7031
1.0000
0.6953
0.6953
1.0000
0.6875
0.6875
1.0000
0.6797
0.6797
1.0000
0.6719
0.6719
1.0000
0.6641
0.6641
1.0000
0.6562
0.6562
1.0000
0.6484
0.6484
1.0000
0.6406
0.6406
1.0000
0.6328
0.6328
1.0000
0.6250
0.6250
1.0000
0.6172
0.6172
1.0000
0.6094
0.6094
1.0000
0.6016
0.6016
1.0000
0.5938
0.5938
1.0000
0.5859
0.5859
1.0000
0.5781
0.5781
1.0000
0.5703
0.5703
1.0000
0.5625
0.5625
1.0000
0.5547
0.5547
1.0000
0.5469
0.5469
1.0000
0.5391
0.5391
1.0000
0.5312
0.5312
1.0000
0.5234
0.5234
1.0000
0.5156
0.5156
1.0000
0.5078
0.5078
1.0000
0.5000
0.5000
1.0000
0.4922
0.4922
1.0000
0.4844
0.4844
1.0000
0.4766
0.4766
1.0000
0.4688
0.4688
1.0000
0.4609
0.4609
1.0000
0.4531
0.4531
1.0000
0.4453
0.4453
1.0000
0.4375
0.4375
1.0000
0.4297
0.4297
1.0000
0.4219
0.4219
1.0000
0.4141
0.4141
1.0000
0.4062
0.4062
1.0000
0.3984
0.3984
1.0000
0.3906
0.3906
1.0000
0.3828
0.3828
1.0000
0.3750
0.3750
1.0000
0.3672
0.3672
1.0000
0.3594
0.3594
1.0000
0.3516
0.3516
1.0000
0.3438
0.3438
1.0000
0.3359
0.3359
1.0000
0.3281
0.3281
1.0000
0.3203
0.3203
1.0000
0.3125
0.3125
1.0000
0.3047
0.3047
1.0000
0.2969
0.2969
1.0000
0.2891
0.2891
1.0000
0.2812
0.2812
1.0000
0.2734
0.2734
1.0000
0.2656
0.2656
1.0000
0.2578
0.2578
1.0000
0
0
0.9844
0
0
0.9689
0
0
0.9533
0
0
0.9377
0
0
0.9222
0
0
0.9066
0
0
0.8911
0
0
0.8755
0
0
0.8599
0
0
0.8444
0
0
0.8288
0
0
0.8132
0
0
0.7977
0
0
0.7821
0
0
0.7665
0
0
0.7510
0
0
0.7354
0
0
0.7199
0
0
0.7043
0
0
0.6887
0
0
0.6732
0
0
0.6576
0
0
0.6420
0
0
0.6265
0
0
0.6109
0
0
0.5953
0
0
0.5798
0
0
0.5642
0
0
0.5487
0
0
0.5331
0
0
0.5175
0
0
0.5020
0
0
];
end
src/@deproj/deproj.m
View file @
d0cd038e
...
...
@@ -72,7 +72,7 @@ classdef deproj
end
%% Public static methods: builders.
%% Public static methods: builders
& util
.
methods
(
Access
=
public
,
Hidden
=
false
,
Static
=
true
)
% Returns the Z position of points taken from a height-map.
...
...
@@ -84,6 +84,9 @@ classdef deproj
invert_z
,
...
inpaint_zeros
,
...
prune_zeros
);
% Returns the seismic colormap.
cmap
=
cmap_seismic
();
end
%% Private static methods: utilities.
...
...
src/@deproj/plot_curvatures.m
0 → 100644
View file @
d0cd038e
function
[
hf
,
ax1
,
ax2
,
ax3
]
=
plot_curvatures
(
obj
,
scale_bar_length
)
%PLOT_CURVATURES Figure with the local curvaure for a collection of epicells.
if
nargin
<
2
scale_bar_length
=
10
;
end
hf
=
figure
(
'Position'
,
[
1204
20
600
1000
]
);
ax1
=
subplot
(
3
,
1
,
1
);
hold
on
axis
equal
add_plot_curvature_mean
(
obj
,
ax1
);
ax2
=
subplot
(
3
,
1
,
2
);
hold
on
axis
equal
add_plot_curvature_k1
(
obj
,
ax2
);
ax3
=
subplot
(
3
,
1
,
3
);
hold
on
axis
equal
add_plot_curvature_k2
(
obj
,
ax3
);
% Collect min & max.
cl1
=
get
(
ax1
,
'CLim'
);
cl2
=
get
(
ax2
,
'CLim'
);
cl3
=
get
(
ax3
,
'CLim'
);
min1
=
cl1
(
1
);
max1
=
cl1
(
2
);
min2
=
cl2
(
1
);
max2
=
cl2
(
2
);
min3
=
cl3
(
1
);
max3
=
cl3
(
2
);
minc
=
max
(
abs
(
[
min1
,
min2
,
min3
]
)
);
maxc
=
max
(
abs
(
[
max1
,
max2
,
max3
]
)
);
ml
=
max
(
[
minc
,
maxc
]
);
set
(
ax1
,
'CLim'
,
[
-
ml
,
ml
]
)
set
(
ax2
,
'CLim'
,
[
-
ml
,
ml
]
)
set
(
ax3
,
'CLim'
,
[
-
ml
,
ml
]
)
cmap
=
deproj
.
cmap_seismic
();
colormap
(
ax1
,
cmap
)
colormap
(
ax2
,
cmap
)
colormap
(
ax3
,
cmap
)
colorbar
(
ax3
,
'Location'
,
'EastOutside'
)
add_plot_scalebar
(
obj
,
scale_bar_length
,
ax3
);
axis
(
ax1
,
'off'
)
axis
(
ax2
,
'off'
)
axis
(
ax3
,
'off'
)
title
(
ax1
,
'Local mean curvature'
,
...
'FontWeight'
,
'normal'
)
title
(
ax2
,
'First principal curvature'
,
...
'FontWeight'
,
'normal'
)
title
(
ax3
,
'Second principal curvature'
,
...
'FontWeight'
,
'normal'
)
linkaxes
(
[
ax3
ax2
ax1
]
)
end
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