From ea294214a05f0f7c59d576ad1593f9ed3c11fc01 Mon Sep 17 00:00:00 2001
From: Jean-Yves TINEVEZ <jean-yves.tinevez@pasteur.fr>
Date: Thu, 16 Jul 2020 21:13:04 +0200
Subject: [PATCH] Methods to plot the distorsion caused by the projection.
---
src/@deproj/add_plot_distorsion_area.m | 12 +++++++
src/@deproj/add_plot_distorsion_perimeter.m | 12 +++++++
src/@deproj/deproj.m | 9 ++++++
src/@deproj/plot_distorsions.m | 36 +++++++++++++++++++++
4 files changed, 69 insertions(+)
create mode 100644 src/@deproj/add_plot_distorsion_area.m
create mode 100644 src/@deproj/add_plot_distorsion_perimeter.m
create mode 100644 src/@deproj/plot_distorsions.m
diff --git a/src/@deproj/add_plot_distorsion_area.m b/src/@deproj/add_plot_distorsion_area.m
new file mode 100644
index 0000000..66737dc
--- /dev/null
+++ b/src/@deproj/add_plot_distorsion_area.m
@@ -0,0 +1,12 @@
+function hts = add_plot_distorsion_area( obj, ax )
+%ADD_PLOT_DISTORSION_AREA Add the tissue plot colored with the error on
+%cell area caused by the projection.
+
+ epicells = obj.epicells;
+ areas = vertcat( epicells.area );
+ uncorr_areas = vertcat( epicells.uncorrected_area );
+ err = 1 - uncorr_areas ./ areas;
+
+ hts = add_plot_variable( obj, 100. * err, ax );
+end
+
diff --git a/src/@deproj/add_plot_distorsion_perimeter.m b/src/@deproj/add_plot_distorsion_perimeter.m
new file mode 100644
index 0000000..c46f72d
--- /dev/null
+++ b/src/@deproj/add_plot_distorsion_perimeter.m
@@ -0,0 +1,12 @@
+function hts = add_plot_distorsion_perimeter( obj, ax )
+%ADD_PLOT_DISTORSION_PERIMETER Add the tissue plot colored with the error on
+%cell perimeter caused by the projection.
+
+ epicells = obj.epicells;
+ perims = vertcat( epicells.perimeter );
+ uncorr_perims = vertcat( epicells.uncorrected_perimeter );
+ err = 1 - uncorr_perims ./ perims;
+
+ hts = add_plot_variable( obj, 100. * err, ax );
+end
+
diff --git a/src/@deproj/deproj.m b/src/@deproj/deproj.m
index 29c33a1..0bead4f 100644
--- a/src/@deproj/deproj.m
+++ b/src/@deproj/deproj.m
@@ -37,6 +37,9 @@ classdef deproj
% Figure with the cells area and perimeter.
[ hf, ax1, ax2 ] = plot_sizes( obj, scale_bar_length )
+ % Figure with the error on uncorrected cells area and perimeter.
+ [ hf, ax1, ax2 ] = plot_distorsions( obj, scale_bar_length )
+
%% Helpers.
% They are public in case of.
@@ -78,6 +81,12 @@ classdef deproj
% Add the tissue plot colored with the cell perimeter.
hts = add_plot_perimeter( obj, ax )
+
+ % Add the tissue plot colored with the error on cell area caused by the projection.
+ hts = add_plot_distorsion_area( obj, ax )
+
+ % Add the tissue plot colored with the error on cell perimeter caused by the projection.
+ hts = add_plot_distorsion_perimeter( obj, ax )
end
diff --git a/src/@deproj/plot_distorsions.m b/src/@deproj/plot_distorsions.m
new file mode 100644
index 0000000..3eaf8d8
--- /dev/null
+++ b/src/@deproj/plot_distorsions.m
@@ -0,0 +1,36 @@
+function [ hf, ax1, ax2 ] = plot_distorsions( obj, scale_bar_length )
+%PLOT_DISTORSIONS Figure with the error on uncorrected cells area and perimeter.
+
+ if nargin < 2
+ scale_bar_length = 10;
+ end
+
+ hf = figure( 'Position', [ 1204 20 600 650 ] );
+
+ ax1 = subplot( 2, 1, 1 );
+ hold on
+ axis equal
+ add_plot_distorsion_area( obj, ax1 );
+ colorbar
+
+ ax2 = subplot( 2, 1, 2 );
+ hold on
+ axis equal
+ add_plot_distorsion_perimeter( obj, ax2 );
+ colorbar
+
+ add_plot_scalebar( obj, scale_bar_length, ax2 );
+
+ axis( ax1, 'off' )
+ axis( ax2, 'off' )
+
+ title( ax1, 'Error on cell area (%)', ...
+ 'FontWeight', 'normal', ...
+ 'Interpreter', 'none' )
+ title( ax2, 'Error on cell perimeter (%)', ...
+ 'FontWeight', 'normal', ...
+ 'Interpreter', 'none' )
+
+ linkaxes( [ ax2 ax1 ] )
+end
+
--
GitLab