From 8f304318b3b99dd22fa32bf94652193882fdfc3c Mon Sep 17 00:00:00 2001
From: Nicola Vigano <nicola.vigano@esrf.fr>
Date: Wed, 9 Mar 2016 12:30:10 +0100
Subject: [PATCH] GtEBSDView: improved to accept and use the EBSD data
structure
Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>
---
zUtil_TomoUtils/GtEBSDView.m | 102 ++++++++++++++++++++++++++---------
1 file changed, 76 insertions(+), 26 deletions(-)
diff --git a/zUtil_TomoUtils/GtEBSDView.m b/zUtil_TomoUtils/GtEBSDView.m
index 5c03d380..1af6555f 100644
--- a/zUtil_TomoUtils/GtEBSDView.m
+++ b/zUtil_TomoUtils/GtEBSDView.m
@@ -1,9 +1,10 @@
classdef GtEBSDView < GtBaseGuiElem
properties
+ ebsd = [];
end
methods
- function self = GtEBSDView(ebsd_map, varargin)
+ function self = GtEBSDView(ebsd_str, varargin)
% GTVOLVIEW/GTVOLVIEW Constructor
self = self@GtBaseGuiElem();
@@ -11,24 +12,16 @@ classdef GtEBSDView < GtBaseGuiElem
self.conf.cmap = 'gray';
- if (isstruct(ebsd_map))
- ebsd = ebsd_map;
- ebsd_map = ebsd.map_r;
-
- ebsd_mask = ebsd.mask;
- phase_id = ebsd.phase_id;
- else
- ebsd_mask = [];
- phase_id = 1;
+ if (~isstruct(ebsd_str))
+ error('GtEBSDView:wrong_argument', ...
+ 'Only an EBSD data structure is accepted')
end
- self.conf.ebsd_map = ebsd_map;
- self.conf.mask = ebsd_mask;
+ self.ebsd = ebsd_str;
self.conf.ipf_axis = [];
- self.conf.phase_id = phase_id;
self.conf.horDim = 1;
self.conf.verDim = 2;
- [dim(1), dim(2), dim(3)] = size(self.conf.ebsd_map);
+ [dim(1), dim(2), dim(3)] = size(self.ebsd.map_r);
self.conf.dim = dim(1:2);
self.conf.hordisplay = [1 self.conf.dim(1)];
self.conf.verdisplay = [1 self.conf.dim(2)];
@@ -59,7 +52,7 @@ classdef GtEBSDView < GtBaseGuiElem
% GTVOLVIEW/GETVOLVALUE Returns the value for the given point, from the
% volume stored in the object
roundedPoint = round(point);
- r_vec = obj.conf.ebsd_map(roundedPoint(1), roundedPoint(2), :);
+ r_vec = obj.ebsd.map_r(roundedPoint(1), roundedPoint(2), :);
r_vec = reshape(r_vec, 1, 3);
end
@@ -84,11 +77,11 @@ classdef GtEBSDView < GtBaseGuiElem
function initParams(self, arguments)
initParams@GtBaseGuiElem(self, arguments)
- bad_voxels_mask = any(abs(self.conf.ebsd_map) > eps('single'), 3);
- if (isempty(self.conf.mask))
- self.conf.mask = bad_voxels_mask;
+ bad_voxels_mask = any(abs(self.ebsd.map_r) > eps('single'), 3);
+ if (isempty(self.ebsd.mask))
+ self.ebsd.mask = bad_voxels_mask;
else
- self.conf.mask = self.conf.mask & bad_voxels_mask;
+ self.ebsd.mask = self.ebsd.mask & bad_voxels_mask;
end
end
@@ -186,8 +179,8 @@ classdef GtEBSDView < GtBaseGuiElem
set(obj.conf.h_im, 'UIContextMenu', obj.conf.h_context_menu);
% Copy pixel info in context menu
- cbk = @(src, evt)copy3DPixInfoToClipboard(obj);
obj.conf.h_menu_items = {};
+ cbk = @(src, evt)copy3DPixInfoToClipboard(obj);
obj.conf.h_menu_items{end+1} = uimenu(obj.conf.h_context_menu, ...
'Label', 'Copy pixel 3D info', ...
'Callback', cbk);
@@ -195,6 +188,14 @@ classdef GtEBSDView < GtBaseGuiElem
obj.conf.h_menu_items{end+1} = uimenu(obj.conf.h_context_menu, ...
'Label', 'Copy grain Average R-vector info', ...
'Callback', cbk);
+ cbk = @(src, evt)segmentGrain(obj);
+ obj.conf.h_menu_items{end+1} = uimenu(obj.conf.h_context_menu, ...
+ 'Label', 'Segment grain to file...', ...
+ 'Callback', cbk);
+ cbk = @(src, evt)extractBandContrastOfGrain(obj);
+ obj.conf.h_menu_items{end+1} = uimenu(obj.conf.h_context_menu, ...
+ 'Label', 'Extract grain Band Contrast to file...', ...
+ 'Callback', cbk);
end
function resetUiComponents(obj)
@@ -230,7 +231,7 @@ classdef GtEBSDView < GtBaseGuiElem
else
point = round(self.getPixel());
end
- [grain_r_vecs, grain_mask] = gtDefEBSDSegmentGrainFromSeed(self.conf.ebsd_map, self.conf.mask, point);
+ [grain_r_vecs, grain_mask] = gtDefEBSDSegmentGrainFromSeed(self.ebsd.map_r, self.ebsd.mask, point);
grain_r_vecs = gtDefDmvol2Gvdm(permute(grain_r_vecs, [1 2 4 3]));
avg_r_vec = sum(grain_r_vecs(:, grain_mask(:)), 2) ./ sum(grain_mask(:));
clipString = sprintf('(%d, %d) [%g, %g, %g]', point, avg_r_vec');
@@ -240,6 +241,55 @@ classdef GtEBSDView < GtBaseGuiElem
clipboard('copy', clipString);
end
+ function segmentGrain(self)
+ if (isfield(self.conf, 'clicked_point') && ~isempty(self.conf.clicked_point))
+ point = round(self.conf.clicked_point);
+ else
+ point = round(self.getPixel());
+ end
+ [grain_r_vecs, grain_mask, grain_bb] = gtDefEBSDSegmentGrainFromSeed(self.ebsd.map_r, self.ebsd.mask, point);
+
+ filter = {'*.mat', 'MATLAB Files (*.mat)'};
+ [filename, pathname] = uiputfile( ...
+ filter, 'Select file...', ...
+ fullfile('EBSD', 'grain_seg.mat'));
+
+ grain_struct = struct( ...
+ 'R_vectors', grain_r_vecs, ...
+ 'mask', grain_mask, ...
+ 'bb', grain_bb); %#ok<NASGU>
+
+ if (filename)
+ save(fullfile(pathname, filename), '-struct', 'grain_struct', '-v7.3');
+ end
+ end
+
+ function extractBandContrastOfGrain(self)
+ if (isfield(self.conf, 'clicked_point') && ~isempty(self.conf.clicked_point))
+ point = round(self.conf.clicked_point);
+ else
+ point = round(self.getPixel());
+ end
+ [~, grain_mask, grain_bb] = gtDefEBSDSegmentGrainFromSeed(self.ebsd.map_r, self.ebsd.mask, point);
+
+ grain_lims = grain_bb([1 2 1 2]) + [1 1 grain_bb(3:4)];
+ grain_bc = self.ebsd.bc(grain_lims(1):grain_lims(3), grain_lims(2):grain_lims(4));
+
+ grain_struct = struct( ...
+ 'band_contrast', grain_bc, ...
+ 'mask', grain_mask, ...
+ 'bb', grain_bb); %#ok<NASGU>
+
+ filter = {'*.mat', 'MATLAB Files (*.mat)'};
+ [filename, pathname] = uiputfile( ...
+ filter, 'Select file...', ...
+ fullfile('EBSD', 'grain_bc.mat'));
+
+ if (filename)
+ save(fullfile(pathname, filename), '-struct', 'grain_struct', '-v7.3');
+ end
+ end
+
function doUpdateDisplay(obj)
% GTVOLVIEW/DOUPDATEDISPLAY Function that actually updates all the
% visualized GUI components of the GUI element
@@ -288,17 +338,17 @@ classdef GtEBSDView < GtBaseGuiElem
% transformations on them, to adapt to the requested visualization needs
p = gtLoadParameters();
- cryst_system = p.cryst(self.conf.phase_id).crystal_system;
- cryst_spacegroup = p.cryst(self.conf.phase_id).spacegroup;
+ cryst_system = p.cryst(self.ebsd.phase_id).crystal_system;
+ cryst_spacegroup = p.cryst(self.ebsd.phase_id).spacegroup;
symm = gtCrystGetSymmetryOperators(cryst_system, cryst_spacegroup);
- indx = find(self.conf.mask);
+ indx = find(self.ebsd.mask);
- r_vecs = reshape(self.conf.ebsd_map, [], 3);
+ r_vecs = reshape(self.ebsd.map_r, [], 3);
r_vecs = r_vecs(indx, :);
[cmap, ~, ~] = gtIPFCmap( ...
- self.conf.phase_id, self.conf.ipf_axis, ...
+ self.ebsd.phase_id, self.conf.ipf_axis, ...
'r_vectors', r_vecs, ...
'crystal_system', cryst_system, ...
'background', false, ...
--
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