From 6dc23cc82883c8fc62823b8ce86d54f0fdeb9fc6 Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <tinevez@pasteur.fr>
Date: Mon, 6 Jul 2020 14:12:39 +0200
Subject: [PATCH] Reorganize processing in a mother class 'deproj'.
This class mainly manages a collection of epicells, has
static methods for its creation from images, and has some
methods for plotting things.
---
RunExample.m | 122 +++---------------
src/{ => @deproj}/add_plot_euler_alpha.m | 5 +-
src/{ => @deproj}/add_plot_euler_beta.m | 5 +-
src/{ => @deproj}/add_plot_euler_gamma.m | 5 +-
src/{ => @deproj}/add_plot_id.m | 9 +-
src/{ => @deproj}/add_plot_scalebar.m | 7 +-
src/{ => @deproj}/add_plot_variable.m | 6 +-
src/@deproj/deproj.m | 74 +++++++++++
src/@deproj/from_heightmap.m | 153 +++++++++++++++++++++++
src/{ => @deproj}/get_z.m | 2 +-
src/{ => @deproj}/mask_to_objects.m | 0
src/{ => @deproj}/plot_fit_ellipse.m | 11 +-
src/{ => @deproj}/plot_fit_plane.m | 14 ++-
src/@epicell/epicell.m | 5 +-
src/@epicell/fit_ellipse_3d.m | 2 +-
15 files changed, 291 insertions(+), 129 deletions(-)
rename src/{ => @deproj}/add_plot_euler_alpha.m (70%)
rename src/{ => @deproj}/add_plot_euler_beta.m (70%)
rename src/{ => @deproj}/add_plot_euler_gamma.m (58%)
rename src/{ => @deproj}/add_plot_id.m (54%)
rename src/{ => @deproj}/add_plot_scalebar.m (91%)
rename src/{ => @deproj}/add_plot_variable.m (65%)
create mode 100644 src/@deproj/deproj.m
create mode 100644 src/@deproj/from_heightmap.m
rename src/{ => @deproj}/get_z.m (91%)
rename src/{ => @deproj}/mask_to_objects.m (100%)
rename src/{ => @deproj}/plot_fit_ellipse.m (61%)
rename src/{ => @deproj}/plot_fit_plane.m (72%)
diff --git a/RunExample.m b/RunExample.m
index 7cf67f2..511f016 100755
--- a/RunExample.m
+++ b/RunExample.m
@@ -31,129 +31,45 @@ heightmap_filename = 'HeightMap-2.tif';
% Physical size of a pixel in X and Y. This will be used to report sizes in
% µm.
pixel_size = 0.183; % µm
+units = 'µm';
% Z spacing.
% How many µm bewtween each Z-slices. We need this to convert the
% height-map values, that stores the plane of interest, into µm.
voxel_depth = 1.; % µm
+
% Try to remove objects that have a Z position equal to 0. Normally this
% value reports objects that are out of the region-of-interest.
prune_zeros = true;
+inpaint_zeros = true;
+
+% Invert z for plotting.
+invert_z = true;
-%% Read a mask file and convert it to objects.
+%% Read files.
% ImageJ mask.
fprintf('Opening mask image: %s\n', mask_filename )
I = imread( fullfile( root_folder, mask_filename ) );
-% The conversion can take up to 30s for a 1000 x 1000 mask image.
-fprintf('Converting mask to objects.\n' )
-tic
-% We will downsample later: for now we will need all the pixels to have a
-% robust estimate of the ellipse and plane fit.
-downsample = false;
-[ objects, junction_graph ] = mask_to_objects( I, downsample );
-n_objects = numel( objects );
-n_junctions = numel( junction_graph.Nodes );
-fprintf('Converted a %d x %d mask in %.1f seconds. Found %d objects and %d junctions.\n', ...
- size(I,1), size(I,2), toc, n_objects, n_junctions )
-
-%% Compute some scale of an object radius.
-
-% Median area (pixel units)
-med_area = median(arrayfun( @(s) polyarea( s.boundary(:,1), s.boundary(:,2) ), ...
- objects ) ); % pixels^2
-
-object_scale = 2 * sqrt( med_area )/ pi; % pixel units
-
-fprintf('Typical object scale: %.1f pixels or %.2f µm.\n', ...
- object_scale, object_scale * pixel_size )
-
-
-%% Scale to physical coordinates.
-
-% Scale junction XY coordinates to µm.
-junction_graph.Nodes.Centroid( :, 1:2 ) = junction_graph.Nodes.Centroid( :, 1:2 ) * pixel_size;
-
-% Scale object XY boundary to µm.
-for i = 1 : n_objects
- objects( i ).boundary = objects( i ).boundary * pixel_size;
- objects( i ).center = objects( i ).center * pixel_size;
-end
-
-%% Load the height-map and add the Z coordinates to objects.
-
fprintf('Opening height-map image: %s\n', heightmap_filename )
H = imread( fullfile( root_folder, heightmap_filename ) );
-if prune_zeros
- mask = H == 0;
- H = regionfill( H, mask );
- H( H == 0 ) = NaN;
-end
-
-% Smooth the height-map over a scale smaller than a cell.
-H = imgaussfilt( H, object_scale );
-
-% For junction.
-z_junction = get_z( junction_graph.Nodes.Centroid, H, pixel_size, voxel_depth );
-
-% For objects.
-for i = 1 : n_objects
- z_obj = get_z( objects( i ).boundary, H, pixel_size, voxel_depth );
- objects( i ).boundary = [ objects( i ).boundary z_obj ];
- objects( i ).center(3) = mean( z_obj );
-end
-
-%% Possibly remove the junctions and cells found at z = 0.
-
-if prune_zeros
-
- bad_junctions = find( z_junction == 0 | isnan( z_junction ) );
- junction_graph = junction_graph.rmnode( bad_junctions );
- z_junction( bad_junctions ) = [];
-
- fprintf( 'Removed %d junctions at Z=0.\n', numel( bad_junctions ) )
-
- objects_to_prune = false( n_objects, 1 );
- for i = 1 : numel( objects )
- o = objects( i );
- if any( isnan( o.boundary(:) ) ) || ~isempty( intersect( bad_junctions, o.junctions ) )
- objects_to_prune( i ) = true;
- end
- end
-
- objects( objects_to_prune ) = [];
- fprintf( 'Removed %d objects touching these junctions.\n', sum( objects_to_prune ) )
-
- n_objects = numel( objects );
- n_junctions = numel( junction_graph.Nodes );
-
-end
-
-%% Invert Z position for plotting.
-
-max_z = max( z_junction );
-z_junction = max_z - z_junction;
-junction_graph.Nodes.Centroid = [ junction_graph.Nodes.Centroid z_junction ];
-
-for i = 1 : n_objects
- objects( i ).boundary( :, 3 ) = max_z - objects( i ).boundary( :, 3 );
- objects( i ).center( 3 ) = max_z - objects( i ).center( 3 );
-end
-
-%% Create epicell instances.
-
-epicells = repmat( epicell, n_objects, 1 );
-for i = 1 : n_objects
- o = objects( i );
- epicells( i ) = epicell( o.boundary, o.junctions, i );
-end
+%% Create deproj instance.
+
+dpr = deproj.from_heightmap( ...
+ I, ...
+ H, ...
+ pixel_size, ...
+ voxel_depth, ...
+ units, ...
+ invert_z, ...
+ inpaint_zeros, ...
+ prune_zeros );
%% Plot euler angles.
close all
-plot_fit_plane( epicells );
-
+plot_fit_plane( dpr );
diff --git a/src/add_plot_euler_alpha.m b/src/@deproj/add_plot_euler_alpha.m
similarity index 70%
rename from src/add_plot_euler_alpha.m
rename to src/@deproj/add_plot_euler_alpha.m
index 83ccfa7..f20cce6 100644
--- a/src/add_plot_euler_alpha.m
+++ b/src/@deproj/add_plot_euler_alpha.m
@@ -1,6 +1,7 @@
-function hts = add_plot_euler_alpha( ax, epicells )
+function hts = add_plot_euler_alpha( obj, ax )
%ADD_PLOT_EULER_ALPHA Add the tissue plot colored with the 1st euler angle.
+ epicells = obj.epicells;
angles = vertcat( epicells.euler_angles );
alphas = rad2deg( angles( :, 1 ) );
@@ -8,6 +9,6 @@ function hts = add_plot_euler_alpha( ax, epicells )
neg_alphas = alphas < 0;
alphas( neg_alphas ) = 180 + alphas( neg_alphas );
- hts = add_plot_variable( ax, { epicells.boundary }, alphas );
+ hts = add_plot_variable( obj, alphas, ax );
end
diff --git a/src/add_plot_euler_beta.m b/src/@deproj/add_plot_euler_beta.m
similarity index 70%
rename from src/add_plot_euler_beta.m
rename to src/@deproj/add_plot_euler_beta.m
index a359f4b..0689723 100644
--- a/src/add_plot_euler_beta.m
+++ b/src/@deproj/add_plot_euler_beta.m
@@ -1,6 +1,7 @@
-function hts = add_plot_euler_beta( ax, epicells )
+function hts = add_plot_euler_beta( obj, ax )
%ADD_PLOT_EULER_BETA Add the tissue plot colored with the 2nd euler angle.
+ epicells = obj.epicells;
angles = vertcat( epicells.euler_angles );
betas = rad2deg( angles( :, 2 ) );
@@ -8,6 +9,6 @@ function hts = add_plot_euler_beta( ax, epicells )
large_betas = betas > 90;
betas( large_betas ) = 180 - betas( large_betas );
- hts = add_plot_variable( ax, { epicells.boundary }, betas );
+ hts = add_plot_variable( obj, betas, ax );
end
diff --git a/src/add_plot_euler_gamma.m b/src/@deproj/add_plot_euler_gamma.m
similarity index 58%
rename from src/add_plot_euler_gamma.m
rename to src/@deproj/add_plot_euler_gamma.m
index fcab772..2965905 100644
--- a/src/add_plot_euler_gamma.m
+++ b/src/@deproj/add_plot_euler_gamma.m
@@ -1,8 +1,9 @@
-function hts = add_plot_euler_gamma( ax, epicells )
+function hts = add_plot_euler_gamma( obj, ax )
%ADD_PLOT_EULER_GAMMA Add the tissue plot colored with the 3rd euler angle.
+ epicells = obj.epicells;
angles = vertcat( epicells.euler_angles );
gammas = rad2deg( angles( :, 3 ) );
- hts = add_plot_variable( ax, { epicells.boundary }, gammas );
+ hts = add_plot_variable( obj, gammas, ax );
end
diff --git a/src/add_plot_id.m b/src/@deproj/add_plot_id.m
similarity index 54%
rename from src/add_plot_id.m
rename to src/@deproj/add_plot_id.m
index 7345bea..e4acb12 100644
--- a/src/add_plot_id.m
+++ b/src/@deproj/add_plot_id.m
@@ -1,12 +1,15 @@
-function hts = add_plot_id( epicells, ax )
+function hts = add_plot_id( obj, ax )
%ADD_PLOT_ID Add the epicell ids to the specified plot axes.
+ epicells = obj.epicells;
n_objects = numel( epicells );
hts = NaN( n_objects, 1 );
for i = 1 : n_objects
- o = objects( i );
- hts(i ) = text( ax, o.center(1), o.center(2), o.center(3) + 0.5, num2str( o.id ), ...
+ o = epicells( i );
+ hts(i ) = text( ax, ...
+ o.center(1), o.center(2), o.center(3) + 0.5, ...
+ num2str( o.id ), ...
'HorizontalAlignment', 'center', ...
'VerticalAlignment', 'middle' );
end
diff --git a/src/add_plot_scalebar.m b/src/@deproj/add_plot_scalebar.m
similarity index 91%
rename from src/add_plot_scalebar.m
rename to src/@deproj/add_plot_scalebar.m
index 0e11918..56a9d91 100644
--- a/src/add_plot_scalebar.m
+++ b/src/@deproj/add_plot_scalebar.m
@@ -1,10 +1,13 @@
-function [ hsb, ht ] = add_plot_scalebar( ax, epicells, length, units )
+function [ hsb, ht ] = add_plot_scalebar( obj, length, ax )
%ADD_PLOT_SCALEBAR Add a scale-bar to the plot.
% We used the collection of epicells to determine a sensible position.
POS_RATIO = 0.10; % of width to position the bar
THICKNESS_RATIO = 0.02;
-
+
+ epicells = obj.epicells;
+ units = obj.units;
+
p = vertcat( epicells.boundary );
minp = double( min( p ) );
maxp = double( max( p ) );
diff --git a/src/add_plot_variable.m b/src/@deproj/add_plot_variable.m
similarity index 65%
rename from src/add_plot_variable.m
rename to src/@deproj/add_plot_variable.m
index 6573e1f..1a89b60 100644
--- a/src/add_plot_variable.m
+++ b/src/@deproj/add_plot_variable.m
@@ -1,7 +1,9 @@
-function hts = add_plot_variable( ax, boundaries, values )
+function hts = add_plot_variable( obj, values, ax )
%ADD_PLOT_VARIABLE Plots the boundaries as patches, colored by the specified values.
- n_objects = numel( boundaries );
+ epicells = obj.epicells;
+ boundaries = { epicells.boundary };
+ n_objects = numel( boundaries );
hts = NaN( n_objects, 1 );
for i = 1 : n_objects
diff --git a/src/@deproj/deproj.m b/src/@deproj/deproj.m
new file mode 100644
index 0000000..caec79a
--- /dev/null
+++ b/src/@deproj/deproj.m
@@ -0,0 +1,74 @@
+classdef deproj
+ %DEPROJ Manage a collection of epicells.
+
+ properties
+ epicells
+ units
+ end
+
+ methods
+ function obj = deproj( epicells, units )
+ obj.epicells = epicells;
+ obj.units = units;
+ end
+ end
+
+ %% Plotting routines.
+ methods
+
+ %% Generate figures.
+
+ % Figure with the local plan orientation for a collection of epicells.
+ [ hf, ax1, ax2, ax3 ] = plot_fit_plane( obj, scale_bar_length )
+
+ % Plot the 2D ellipses on the tissue surface.
+ [ hf, hc, he ] = plot_fit_ellipse( obj, scale_bar_length )
+
+ %% Helpers.
+ % They are public in case of.
+
+ % Add the tissue plot colored with the 1st euler angle.
+ hts = add_plot_euler_alpha( obj, ax )
+
+ % Add the tissue plot colored with the 2nd euler angle.
+ hts = add_plot_euler_beta( obj, ax )
+
+ % Add the tissue plot colored with the 3rd euler angle.
+ hts = add_plot_euler_gamma( obj, ax )
+
+ % Add the epicell ids to the specified plot axes.
+ hts = add_plot_id( obj, ax )
+
+ % Add a scale-bar to the plot.
+ [ hsb, ht ] = add_plot_scalebar( obj, length, ax )
+
+ % Plots the boundaries as patches, colored by the specified values.
+ hts = add_plot_variable( obj, values, ax )
+ end
+
+ %% Public static methods: builders.
+ methods ( Access = public, Hidden = false, Static = true )
+
+ % Returns the Z position of points taken from a height-map.
+ obj = from_heightmap( I, ...
+ H, ...
+ pixel_size, ...
+ voxel_depth, ...
+ units, ...
+ invert_z, ...
+ inpaint_zeros, ...
+ prune_zeros );
+ end
+
+ %% Private static methods: utilities.
+ methods ( Access = private, Hidden = true, Static = true )
+
+ % Returns the Z position of points taken from a height-map.
+ z_coords = get_z( P, H, pixel_size, voxel_depth )
+
+ % Returns the cells from a BW image with ridges.
+ [ objects, junction_graph ] = mask_to_objects( I, downsample )
+
+ end
+end
+
diff --git a/src/@deproj/from_heightmap.m b/src/@deproj/from_heightmap.m
new file mode 100644
index 0000000..54e8408
--- /dev/null
+++ b/src/@deproj/from_heightmap.m
@@ -0,0 +1,153 @@
+function obj = from_heightmap( ...
+ I, ...
+ H, ...
+ pixel_size, ...
+ voxel_depth, ...
+ units, ...
+ invert_z, ...
+ inpaint_zeros, ...
+ prune_zeros )
+%FROM_HEIGTHMAP Returns a deproj oebjct built from segmentatio and height-map.
+
+ %% Default values for some parameters.
+
+ if nargin < 8
+ prune_zeros = true;
+ end
+ if nargin < 7
+ inpaint_zeros = true;
+ end
+ if nargin < 6
+ invert_z = false;
+ end
+ if nargin < 5
+ units = 'pixels';
+ end
+ if nargin < 4
+ voxel_depth = 1.;
+ end
+ if nargin < 3
+ pixel_size = 1.;
+ end
+
+ %% Load objects from segmentation mask.
+
+ fprintf('Converting mask to objects.\n' )
+ tic
+ % We will downsample later: for now we will need all the pixels to have
+ % a robust estimate of the ellipse and plane fit.
+ downsample = false;
+ [ objects, junction_graph ] = deproj.mask_to_objects( I, downsample );
+ n_objects = numel( objects );
+ n_junctions = numel( junction_graph.Nodes );
+ fprintf('Converted a %d x %d mask in %.1f seconds. Found %d objects and %d junctions.\n', ...
+ size(I,1), size(I,2), toc, n_objects, n_junctions )
+
+
+ %% Compute some scale of an object radius.
+
+ % Median area (pixel units)
+ med_area = median(arrayfun( @(s) polyarea( s.boundary(:,1), s.boundary(:,2) ), ...
+ objects ) ); % pixels^2
+
+ object_scale = 2 * sqrt( med_area )/ pi; % pixel units
+
+ fprintf('Typical object scale: %.1f pixels or %.2f µm.\n', ...
+ object_scale, object_scale * pixel_size )
+
+
+ %% Scale to physical coordinates.
+
+ % Scale junction XY coordinates to µm.
+ junction_graph.Nodes.Centroid( :, 1:2 ) = junction_graph.Nodes.Centroid( :, 1:2 ) * pixel_size;
+
+ % Scale object XY boundary to µm.
+ for i = 1 : n_objects
+ objects( i ).boundary = objects( i ).boundary * pixel_size;
+ objects( i ).center = objects( i ).center * pixel_size;
+ end
+
+ %% Load the height-map and add the Z coordinates to objects.
+
+ fprintf('Collecting Z coordinates.\n' )
+ tic
+
+ if inpaint_zeros
+ mask = H == 0;
+ H = regionfill( H, mask );
+ end
+
+ if prune_zeros
+ H( H == 0 ) = NaN;
+ end
+
+ % Smooth the height-map over a scale smaller than a cell.
+ H = imgaussfilt( H, object_scale );
+
+ % For junction.
+ z_junction = deproj.get_z( junction_graph.Nodes.Centroid, H, pixel_size, voxel_depth );
+
+ % For objects.
+ for i = 1 : n_objects
+ z_obj = deproj.get_z( objects( i ).boundary, H, pixel_size, voxel_depth );
+ objects( i ).boundary = [ objects( i ).boundary z_obj ];
+ objects( i ).center(3) = mean( z_obj );
+ end
+
+ fprintf('Done in %.1f seconds.\n', toc )
+
+
+ %% Possibly remove the junctions and cells found at z = 0.
+
+ if prune_zeros
+
+ bad_junctions = find( z_junction == 0 | isnan( z_junction ) );
+ junction_graph = junction_graph.rmnode( bad_junctions );
+ z_junction( bad_junctions ) = [];
+
+ fprintf( 'Removed %d junctions at Z=0.\n', numel( bad_junctions ) )
+
+ objects_to_prune = false( n_objects, 1 );
+ for i = 1 : numel( objects )
+ o = objects( i );
+ if any( isnan( o.boundary(:) ) ) || ~isempty( intersect( bad_junctions, o.junctions ) )
+ objects_to_prune( i ) = true;
+ end
+ end
+
+ objects( objects_to_prune ) = [];
+ fprintf( 'Removed %d objects touching these junctions.\n', sum( objects_to_prune ) )
+
+ n_objects = numel( objects );
+
+ end
+
+ %% Invert Z position for plotting.
+
+ if invert_z
+ max_z = max( z_junction );
+ z_junction = max_z - z_junction;
+ junction_graph.Nodes.Centroid = [ junction_graph.Nodes.Centroid z_junction ];
+
+ for i = 1 : n_objects
+ objects( i ).boundary( :, 3 ) = max_z - objects( i ).boundary( :, 3 );
+ objects( i ).center( 3 ) = max_z - objects( i ).center( 3 );
+ end
+ end
+
+ %% Create epicell instances.
+
+ fprintf('Computing morphological descriptors of all objects.\n' )
+ tic
+
+ epicells = repmat( epicell, n_objects, 1 );
+ for i = 1 : n_objects
+ o = objects( i );
+ epicells( i ) = epicell( o.boundary, o.junctions, i );
+ end
+
+ obj = deproj( epicells, units );
+
+ fprintf('Done in %.1f seconds.\n', toc )
+
+end
diff --git a/src/get_z.m b/src/@deproj/get_z.m
similarity index 91%
rename from src/get_z.m
rename to src/@deproj/get_z.m
index 0904e2f..9f23e3d 100644
--- a/src/get_z.m
+++ b/src/@deproj/get_z.m
@@ -1,5 +1,5 @@
function z_coords = get_z( P, H, pixel_size, voxel_depth )
-%GET_Z Returns the Z position of points taken from a height-map
+%GET_Z Returns the Z position of points taken from a height-map.
% - P is a Nx2 list of points, in physical coordinates.
% - H is the height map, encoding the z plane of interest for all X & Y.
% - pixel_size: convert pixel coordinates to physical coordinates.
diff --git a/src/mask_to_objects.m b/src/@deproj/mask_to_objects.m
similarity index 100%
rename from src/mask_to_objects.m
rename to src/@deproj/mask_to_objects.m
diff --git a/src/plot_fit_ellipse.m b/src/@deproj/plot_fit_ellipse.m
similarity index 61%
rename from src/plot_fit_ellipse.m
rename to src/@deproj/plot_fit_ellipse.m
index e459166..7fe5d27 100644
--- a/src/plot_fit_ellipse.m
+++ b/src/@deproj/plot_fit_ellipse.m
@@ -1,5 +1,10 @@
-function [ hf, hc, he ] = plot_fit_ellipse( epicells )
-%PLOT_FIT_ELLIPSE Summary of this function goes here
+function [ hf, hc, he ] = plot_fit_ellipse( obj, scale_bar_length )
+%PLOT_FIT_ELLIPSE Plot the 2D ellipses on the tissue surface.
+
+ epicells = obj.epicells;
+ if nargin < 2
+ scale_bar_length = 10;
+ end
hf = figure( 'Position', [ 1204 20 600 500 ] );
hold on
@@ -19,7 +24,7 @@ function [ hf, hc, he ] = plot_fit_ellipse( epicells )
end
set( he, 'Color', 'k' )
- add_plot_scalebar( gca, epicells, 10, 'µm' );
+ add_plot_scalebar( obj, scale_bar_length, gca );
end
diff --git a/src/plot_fit_plane.m b/src/@deproj/plot_fit_plane.m
similarity index 72%
rename from src/plot_fit_plane.m
rename to src/@deproj/plot_fit_plane.m
index de98557..c3d488a 100644
--- a/src/plot_fit_plane.m
+++ b/src/@deproj/plot_fit_plane.m
@@ -1,29 +1,33 @@
-function [ hf, ax1, ax2, ax3 ] = plot_fit_plane( epicells )
+function [ hf, ax1, ax2, ax3 ] = plot_fit_plane( obj, scale_bar_length )
%PLOT_FIT_PLANE Figure with the local plan orientation 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_euler_alpha( ax1, epicells );
+ add_plot_euler_alpha( obj, ax1 );
colormap( ax1, 'hsv' )
colorbar(ax1)
ax2 = subplot( 3, 1, 2 );
hold on
axis equal
- add_plot_euler_beta( ax2, epicells );
+ add_plot_euler_beta( obj, ax2 );
colorbar(ax2)
ax3 = subplot( 3, 1, 3 );
hold on
axis equal
- add_plot_euler_gamma( ax3, epicells );
+ add_plot_euler_gamma( obj, ax3 );
colormap( ax3, 'hsv' )
colorbar(ax3)
- add_plot_scalebar( ax3, epicells, 10, 'µm' );
+ add_plot_scalebar( obj, scale_bar_length, ax3 );
linkaxes( [ ax3 ax2 ax1 ] )
axis( ax1, 'off' )
diff --git a/src/@epicell/epicell.m b/src/@epicell/epicell.m
index 2040133..7a5fdd1 100644
--- a/src/@epicell/epicell.m
+++ b/src/@epicell/epicell.m
@@ -43,7 +43,7 @@ classdef epicell
% Morphological descriptors on non-downsampled boundary.
p = epicell.centered_points( boundary );
obj.euler_angles = epicell.fit_plane( p );
- obj.ellipse_fit = fit_ellipse( p, obj.euler_angles );
+ obj.ellipse_fit = epicell.fit_ellipse_3d( p, obj.euler_angles );
end
function h = plot_patch_2d( obj, val )
@@ -149,8 +149,7 @@ classdef epicell
end
- %% Public static methods: utilities.
-
+ %% Public static methods: utilities.
methods ( Access = public, Hidden = false, Static = true )
% Convert euler angles to rotation matrix.
R = euleurZXZ2rot( E )
diff --git a/src/@epicell/fit_ellipse_3d.m b/src/@epicell/fit_ellipse_3d.m
index fe153c4..5f54f98 100644
--- a/src/@epicell/fit_ellipse_3d.m
+++ b/src/@epicell/fit_ellipse_3d.m
@@ -28,7 +28,7 @@ function [ f3d, v ] = fit_ellipse_3d( p, E, method )
if nargin < 2
[ ~, ~, v ] = svd( p );
else
- v = euleurZXZ2rot( E );
+ v = epicell.euleurZXZ2rot( E );
end
% Rotate the points into the principal axes frame.
--
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