diff --git a/4_grains/GtThreshold.m b/4_grains/GtThreshold.m
index 4bd2d5e3daa1a8ada53749511e8ef3e28b2e5e8a..bc279809d166453f044143eb3adddede6fdbda75 100644
--- a/4_grains/GtThreshold.m
+++ b/4_grains/GtThreshold.m
@@ -15,8 +15,7 @@ classdef GtThreshold < handle
obj.conf = [];
obj.conf.verbose = true;
- obj.param = load('parameters.mat');
- obj.param = obj.param.parameters;
+ obj.param = gtLoadParameters();
par_thr = obj.getThrParams();
[par_thr, rej_params] = parse_pv_pairs(par_thr, varargin);
@@ -234,10 +233,14 @@ classdef GtThreshold < handle
fprintf('\b\b: Done.\n');
end
- function seg_struct = volumeThreshold(obj, volume, threshold, seed)
+ function seg_struct = volumeThreshold(obj, volume, threshold, seed, do_region_prop)
% GTTHRESHOLD/volumeThreshold
% segvol = volumeThreshold(obj, volume, threshold, center)
+ if (~exist('do_region_prop', 'var'))
+ do_region_prop = true;
+ end
+
if (isempty(volume))
gtError('GtThreshold:wrong_argument', ...
'Volume to segment is empty!')
@@ -253,7 +256,7 @@ classdef GtThreshold < handle
end
seg_struct = struct('vol', volume, 'shift', [0 0 0]);
- seg_struct = obj.segmentAndDoMorph(seg_struct, threshold, do_morpho, seed);
+ seg_struct = obj.segmentAndDoMorph(seg_struct, threshold, do_morpho, seed, do_region_prop);
end
end
@@ -456,9 +459,13 @@ classdef GtThreshold < handle
grain_rec.id, count, delta)
end
- function grain_seg = segmentAndDoMorph(~, grain_rec, threshold, do_morpho, seed)
+ function grain_seg = segmentAndDoMorph(~, grain_rec, threshold, do_morpho, seed, do_region_prop)
% GTTHRESHOLD/SEGMENTANDDOMORPH
+ if (~exist('do_region_prop', 'var'))
+ do_region_prop = true;
+ end
+
message = 'morphological reconstruction failed';
if (isfield(grain_rec, 'id'))
message = [message ...
@@ -481,26 +488,32 @@ classdef GtThreshold < handle
seed = zeros(0, 3);
end
- regprop = regionprops(seg_vol, 'BoundingBox', 'Area');
- if (length(regprop) > 1)
- % let's take the biggest! (usually happens without morpho)
- ind = find([regprop.Area] == max([regprop.Area]), 1);
- regprop = regprop(ind);
- end
+ if (do_region_prop)
+ regprop = regionprops(seg_vol, 'BoundingBox', 'Area');
+ if (length(regprop) > 1)
+ % let's take the biggest! (usually happens without morpho)
+ ind = find([regprop.Area] == max([regprop.Area]), 1);
+ regprop = regprop(ind);
+ end
- if isempty(regprop)
- grain_seg.seg = [];
- grain_seg.Area = [];
- grain_seg.segbb = [];
+ if isempty(regprop)
+ grain_seg.seg = [];
+ grain_seg.Area = [];
+ grain_seg.segbb = [];
+ else
+ seg_bb = regprop.BoundingBox([2 1 3 5 4 6]);
+
+ % ceil because Matlab regionprops yields "0.5" (instead of 1)
+ % for bb start values
+ grain_seg.seg = gtCrop(seg_vol, ceil(seg_bb));
+ grain_seg.Area = regprop.Area;
+ seg_bb(1:3) = grain_rec.shift + ceil(seg_bb(1:3)) - 1;
+ grain_seg.segbb = seg_bb;
+ end
else
- seg_bb = regprop.BoundingBox([2 1 3 5 4 6]);
-
- % ceil because Matlab regionprops yields "0.5" (instead of 1)
- % for bb start values
- grain_seg.seg = gtCrop(seg_vol, ceil(seg_bb));
- grain_seg.Area = regprop.Area;
- seg_bb(1:3) = grain_rec.shift + ceil(seg_bb(1:3)) - 1;
- grain_seg.segbb = seg_bb;
+ grain_seg.seg = seg_vol;
+ grain_seg.Area = [];
+ grain_seg.segbb = [0, 0, 0, size(seg_vol)];
end
grain_seg.threshold = threshold;
grain_seg.seed = seed;
diff --git a/5_reconstruction/GtGuiMultiThresholdVolume.m b/5_reconstruction/GtGuiMultiThresholdVolume.m
index f8bd5d9fda24dbc9e4124fad18aaf5f49c0f01ba..8d8abf2859d0ef97a45c6bc6aaacd9fd8bcdbbe7 100644
--- a/5_reconstruction/GtGuiMultiThresholdVolume.m
+++ b/5_reconstruction/GtGuiMultiThresholdVolume.m
@@ -14,11 +14,11 @@ classdef GtGuiMultiThresholdVolume < GtGuiThresholdGrain
end
function movedSlider(obj)
- new_thresh = get(obj.conf.h_thr_slider(1), 'Value');
+ new_thresh = get(obj.conf.h_thr_slider(1), 'Value')
set(obj.conf.h_thr_edit, 'String', num2str(obj.threshold(1)));
obj.setThresholds(new_thresh, 1);
- new_thresh = get(obj.conf.h_thr_slider(2), 'Value');
+ new_thresh = get(obj.conf.h_thr_slider(2), 'Value')
set(obj.conf.h_thr_edit, 'String', num2str(obj.threshold(2)));
obj.setThresholds(new_thresh, 2);
@@ -103,19 +103,24 @@ classdef GtGuiMultiThresholdVolume < GtGuiThresholdGrain
filter = {'*.mat', 'MATLAB Files (*.mat)';
'*.edf', 'EDF files (ESRF Data Format, *.edf)'};
[filename, pathname, filerIndex] = uiputfile(filter, 'Select file...', fullfile('5_reconstruction', 'volume_mask_multi.mat'));
+ if (isnumeric(filename) && filename == 0)
+ return;
+ end
thr = GtThreshold();
vol = zeros(size(self.conf.vol), class(self.conf.vol));
fprintf('Applying thresholds: ')
for ii = 1:numel(self.threshold)
- num_chars = fprintf('%02d/%02d', ii, numel(self.threshold));
+ num_chars = fprintf('%02d/%02d (thr: %g)', ii, numel(self.threshold), self.threshold(ii));
- partial_seg_struct = thr.volumeThreshold(self.conf.vol, self.threshold(ii));
+ partial_seg_struct = thr.volumeThreshold(self.conf.vol, self.threshold(ii), [], false);
- vol = gtPlaceSubVolume(vol, partial_seg_struct.vol, partial_seg_struct.segbb(1:3), ii);
+ vol = gtPlaceSubVolume(vol, single(partial_seg_struct.seg), partial_seg_struct.segbb(1:3), ii);
fprintf(repmat('\b', [1, num_chars]));
end
+ fprintf(repmat(' ', [1, num_chars]));
+ fprintf(repmat('\b', [1, num_chars]));
fprintf('(%02d) Done.\n', numel(self.threshold))
if (filerIndex == 1)