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@mihelics
mihelics authored May 2, 2022
1 parent 42c3f47 commit 63ad4a8
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Showing 8 changed files with 349 additions and 94 deletions.
143 changes: 102 additions & 41 deletions source/area_histogram_plotter.m
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,18 @@ function area_histogram_plotter( strand_subscripts, lumen_radius_in_microns_rang
% Inter-positions are then binned according to statistic value. The total length of vessels in each
% bin are summed. Radius and depth are in microns, inclination in units of degrees.

is_smoothing = true ;

% % depth_bins = {[0, Inf]};
% depth_bins = {[0, Inf], [0, 100], [100, 200], [200, Inf]};
%
% number_depth_bins = length( depth_bins );
%
% colors = [ 0, 0, 0;
% 0.5, 0.75, 1;
% 1, 0.5, 0.75;
% 0.75, 1, 0.5 ];

%% inner-position strand quantities

lumen_radius_in_pixels_range = lumen_radius_in_microns_range ./ microns_per_voxel ;
Expand Down Expand Up @@ -64,23 +76,50 @@ function area_histogram_plotter( strand_subscripts, lumen_radius_in_microns_rang
% decomposing:
% delta_lengths = cell2mat( strand_delta_lengths );
inner_pos_area = cell2mat( strand_inner_pos_area );
inner_pos_radii = cell2mat( strand_inner_pos_radii );
inner_pos_z = cell2mat( strand_inner_pos_z );
inner_pos_inclinations = cell2mat( strand_inner_pos_inclinations );
inner_pos_radius = cell2mat( strand_inner_pos_radii );
inner_pos_z_pos = cell2mat( strand_inner_pos_z );
inner_pos_inclin = cell2mat( strand_inner_pos_inclinations );

radius_limits = [ min( inner_pos_radii ) - eps, max( inner_pos_radii )]; % - eps becuase error was thrown when the smallest radius object didn't make it into the 1st bin because of rounding error during exp/log transform SAM 12/1/21
%% sorting, binning
if is_smoothing, inner_pos_radius = log( inner_pos_radius ) / log( 10 ); end

radius_limits = [ min( inner_pos_radius ) - eps, ...
max( inner_pos_radius ) ]; % - eps becuase error was thrown when the smallest radius object didn't make it into the 1st bin because of rounding error during exp/log transform SAM 12/1/21
inclin_limits = [ 0, 1 ];

%% sorting, binning
[ x1, y1, dx1, dy1 ] = sort_and_bin_by_statistic( inner_pos_z, inner_pos_area, number_of_bins, z_pos_limits, false );
[ x2, y2, dx2, dy2 ] = sort_and_bin_by_statistic( inner_pos_radii, inner_pos_area, number_of_bins, radius_limits, true );
[ x3, y3, dx3, dy3 ] = sort_and_bin_by_statistic( inner_pos_inclinations, inner_pos_area, number_of_bins, inclin_limits, false );
if is_smoothing

z_pos_limits = [ min( inner_pos_z_pos ), ...
max( inner_pos_z_pos ) ];

z_pos_resolution = ( z_pos_limits( 2 ) - z_pos_limits( 1 )) / number_of_bins ;
radius_resolution = ( radius_limits( 2 ) - radius_limits( 1 )) / number_of_bins ;
inclin_resolution = ( inclin_limits( 2 ) - inclin_limits( 1 )) / number_of_bins ;

[ x1, pdf1, cdf1 ] = smooth_hist( inner_pos_z_pos , z_pos_resolution, inner_pos_area );
[ x2, pdf2, cdf2 ] = smooth_hist( inner_pos_radius, radius_resolution, inner_pos_area );
[ x3, pdf3, cdf3 ] = smooth_hist( inner_pos_inclin, inclin_resolution, inner_pos_area );

pdf = [ pdf1, pdf2, pdf3 ]';
cdf = [ cdf1, cdf2, cdf3 ]';
x = [ x1, x2, x3 ]';
y = cdf ;
dy = pdf ;
dx = zeros( size( x ));

else % binning

[ x1, y1, dx1, dy1 ] = sort_and_bin_by_statistic( inner_pos_z_pos, inner_pos_area, number_of_bins, z_pos_limits, false );
[ x2, y2, dx2, dy2 ] = sort_and_bin_by_statistic( inner_pos_radius, inner_pos_area, number_of_bins, radius_limits, true );
[ x3, y3, dx3, dy3 ] = sort_and_bin_by_statistic( inner_pos_inclin, inner_pos_area, number_of_bins, inclin_limits, false );

x = [ x1; x2; x3 ];
y = [ y1; y2; y3 ];
dx = [ dx1; dx2; dx3 ];
dy = [ dy1; dy2; dy3 ];

end

x = [ x1; x2; x3 ];
y = [ y1; y2; y3 ];
dx = [ dx1; dx2; dx3 ];
dy = [ dy1; dy2; dy3 ];

function [ x, y, dx, dy ] = sort_and_bin_by_statistic( inner_statistics, inner_pos_area, number_of_bins, statistic_limits, is_log_dist_stat )

Expand Down Expand Up @@ -149,46 +188,62 @@ function area_histogram_plotter( strand_subscripts, lumen_radius_in_microns_rang
% subplot( 1, 3, stat_i ), hold on,
subplot( 2, 3, ( histogram_style_index - 1 ) * 3 + stat_i )

if histogram_style_index == 2 % count

if stat_i == 1, ylabel( 'area [um^2]' ); end

box_plotter( x( stat_i, : ), y_zeros, dx( stat_i, : ), dy( stat_i, : ))

ylim([ 0, max( dy( : ))])

else % cumulative

if stat_i == 1, ylabel( 'cumulative area [um^2]' ); end

box_plotter( x( stat_i, : ), y_zeros, dx( stat_i, : ), y( stat_i, : ))

ylim([ 0, max( y( : ))])

if is_smoothing
if stat_i == 2 % log x axis
fxn_plotter( 10 .^ x( stat_i, : ), pdf( stat_i, : ), cdf( stat_i, : ), histogram_style_index )
else % linear x axis
fxn_plotter( x( stat_i, : ), pdf( stat_i, : ), cdf( stat_i, : ), histogram_style_index )
end
end

x_limits = [ x( stat_i, 1 ), x( stat_i, end ) + dx( stat_i, end )];
if histogram_style_index == 2 % count

xlim( x_limits )
if ~ is_smoothing
if stat_i == 1, ylabel( 'area [um^2]' ); end
else
if stat_i == 1, ylabel( 'area [um^2] / abscissa (dB) units' ); end
end

max_x_log_10 = floor( log( x_limits( 2 )) / log( 10 )) ;
min_x_log_10 = min( ceil( log( x_limits( 1 )) / log( 10 )), max_x_log_10 - 1 );
if ~ is_smoothing, box_plotter( x( stat_i, : ), y_zeros, dx( stat_i, : ), dy( stat_i, : )), end

if ~ is_smoothing, ylim([ 0, max( dy( stat_i, : ))]), end

else % cumulative

x_limits_log_10 = [ min_x_log_10, max_x_log_10 ];
if stat_i == 1, ylabel( 'area [um^2]' ); end

x_ticks = 10 .^ x_limits_log_10 ;
if ~ is_smoothing, box_plotter( x( stat_i, : ), y_zeros, dx( stat_i, : ), y( stat_i, : )), end

ylim([ 0, max( y( : ))])

end

switch stat_i
case 1, xlabel( 'depth [um]' )
case 2

if is_smoothing, x( stat_i, : ) = 10 .^ x( stat_i, : ); end

x_limits = [ x( stat_i, 1 ), x( stat_i, end ) + dx( stat_i, end )];

xlim( x_limits )

max_x_log_10 = floor( log( x_limits( 2 )) / log( 10 )) ;
min_x_log_10 = min( ceil( log( x_limits( 1 )) / log( 10 )), max_x_log_10 - 1 );

x_limits_log_10 = [ min_x_log_10, max_x_log_10 ];

x_ticks = 10 .^ x_limits_log_10 ;

xlabel( 'radius [um]' ) ...

set( gca,'xscale','log', ...
'XTickLabel', {[ '10^{', num2str( x_limits_log_10( 1 )), '}' ], ...
[ '10^{', num2str( x_limits_log_10( 2 )), '}' ] }, ...
'XTick', x_ticks, ...
'Xlim', [ min( x_ticks( 1 ), x_limits( 1 )), x_limits( 2 )] )

if is_smoothing, x( stat_i, : ) = log( x( stat_i, : )) / log( 10 ); end

case 3, xlabel( 'inclination [z component]' ), set( gca, 'Xlim', [ 0, 1 ])
end
Expand All @@ -214,14 +269,20 @@ function area_histogram_plotter( strand_subscripts, lumen_radius_in_microns_rang
% box_plotter( x, y, dx, dy )
% xlim([ bin_limits( 1 ), bin_limits( end )])

function box_plotter( x, y, dx, dy )

for ii=1:length(x), rectangle('position',[x(ii) y(ii) dx(ii) dy(ii)]), end

function box_plotter( x, y, dx, dy )

for ii=1:length(x), rectangle('position',[x(ii) y(ii) dx(ii) dy(ii)]), end

set( gca, 'FontSize', 10 )

end % FUNCTION box_plotter
set( gca, 'FontSize', 10 )

end % FUNCTION box_plotter

function fxn_plotter( x, pdf, cdf, histogram_style_index )
if histogram_style_index == 1, plot( x, cdf )
else, plot( x, pdf )
... hold on, H = area( x, pdf ); set(H(1),'FaceColor',[0.5 0.75 1], 'EdgeColor', 'none', 'FaceAlpha', 0.5 );
hold on, H = area( x, pdf ); set(H(1),'FaceColor',[0.5 0.75 1], 'EdgeColor', 'none', 'FaceAlpha', 0.5 );
end
end

end % FUNCTION
1 change: 1 addition & 0 deletions source/get_edge_metric.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

% metric = 'mean' ; % 5/16/19 1917

%% calculation
switch metric

case 'mean'
Expand Down
4 changes: 2 additions & 2 deletions source/get_edges_V300.m
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Original file line number Diff line number Diff line change
Expand Up @@ -101,8 +101,8 @@
% edge_number_tolerance = 3 ; % number of edges per vertex SAM 10/29/21 17:55 % SAM 12/24/21
% second_max_edges_per_vertex = max_edges_per_vertex ;
% radius_tolerance = 0.0801 ; % fractional change of radius from origin vertex radius
% radius_tolerance = 0.2 ; % fractional change of radius from origin vertex radius
radius_tolerance = 0.5 ; % fractional change of radius from origin vertex radius % SAM 10/27/21
radius_tolerance = 0.2 ; % fractional change of radius from origin vertex radius % SAM 4/12/21
% radius_tolerance = 0.5 ; % fractional change of radius from origin vertex radius % SAM 10/27/21
% radius_tolerance = 1 ; % SAM 12/24/21
% radius_tolerance = 1.5 ; % SAM 1/11/22
% radius_tolerance = 2/3 ; % 11/7/21 % SAM 1/21/22
Expand Down
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