plot a crystal definition
Syntax: viewCrystal(cdef)
In the simplest form, the crystal is displayed with all facets being
present. The facets are colored according to their face groups. The plot also contains
a legend that annotates the facet colors. The required fields of the
struct cdef are: A and groupMappingMatrix (see obtainCrystal).
h = viewCrystal returns the patch handles of the plotted crystal.
viewCrystal(cdef, h) or viewCrystal(cdef, hC) uses the given h- or
hC-vector to plot the crystal.
viewCrystal(.., 'optionName', optionValue) accepts a list of options to
adjust the behavior of this function:
colorbar - switches the colorbar legend on (1) and off (0).
Default: 1
colormap - is either a string for the selected colormap or a matrix
with predefined colors (see 'doc colormap'). Default:
'jet'
option - an option struct that is handed to viewPolytope (see
viewPolytop for details. Default: []
zerotol - zerotol is used to identify values that are close to zero
by zero. Default: elkZerotol
See also: obtainCrystal0001 function patchHandleVector = viewCrystal(cdef, h, varargin) 0002 % plot a crystal definition 0003 % 0004 % Syntax: viewCrystal(cdef) 0005 % 0006 % In the simplest form, the crystal is displayed with all facets being 0007 % present. The facets are colored according to their face groups. The plot also contains 0008 % a legend that annotates the facet colors. The required fields of the 0009 % struct cdef are: A and groupMappingMatrix (see obtainCrystal). 0010 % 0011 % h = viewCrystal returns the patch handles of the plotted crystal. 0012 % 0013 % viewCrystal(cdef, h) or viewCrystal(cdef, hC) uses the given h- or 0014 % hC-vector to plot the crystal. 0015 % 0016 % viewCrystal(.., 'optionName', optionValue) accepts a list of options to 0017 % adjust the behavior of this function: 0018 % colorbar - switches the colorbar legend on (1) and off (0). 0019 % Default: 1 0020 % colormap - is either a string for the selected colormap or a matrix 0021 % with predefined colors (see 'doc colormap'). Default: 0022 % 'jet' 0023 % option - an option struct that is handed to viewPolytope (see 0024 % viewPolytop for details. Default: [] 0025 % zerotol - zerotol is used to identify values that are close to zero 0026 % by zero. Default: elkZerotol 0027 % 0028 % See also: obtainCrystal 0029 0030 % The elk-library: convex geometry applied to crystallization modeling. 0031 % Copyright (C) 2012 Alexander Reinhold 0032 % 0033 % This program is free software: you can redistribute it and/or modify it 0034 % under the terms of the GNU General Public License as published by the 0035 % Free Software Foundation, either version 3 of the License, or (at your 0036 % option) any later version. 0037 % 0038 % This program is distributed in the hope that it will be useful, but 0039 % WITHOUT ANY WARRANTY; without even the implied warranty of 0040 % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU 0041 % General Public License for more details. 0042 % 0043 % You should have received a copy of the GNU General Public License along 0044 % with this program. If not, see <http://www.gnu.org/licenses/>. 0045 0046 %% Input handling 0047 if ~exist('h', 'var') || isempty(h) 0048 h = ones([size(cdef.A, 1), 1]); 0049 end 0050 if size(h,1) == 1, h = h';end 0051 if length(h) == size(cdef.A, 1) 0052 % everything OK 0053 elseif length(h) == size(cdef.groupMappingMatrix, 2) 0054 h = cdef.groupMappingMatrix * h; 0055 else 0056 error('elk:crystal:wrongInput', ... 0057 'The input vector must either be an h- or an hC-vector'); 0058 end 0059 nGroup = size(cdef.groupMappingMatrix, 2); 0060 0061 %% Options handling 0062 [colorMap, f_colorbar, plotOptionStruct, zerotol, millerStringOption] = ... 0063 mapOption(varargin, ... 0064 'colormap', 'jet', ... 0065 'colorbar', 1, ... 0066 'option', struct([]), ... 0067 'zerotol', elkZerotol, ... 0068 'millerStringOption', {'{', 1}); 0069 0070 %% plot crystal 0071 hrep.A = cdef.A; 0072 hrep.h = h; 0073 patchHandleVector = viewPolytope(hrep, 'option', plotOptionStruct); 0074 0075 %% find facet numbers 0076 patchIsFacet = zeros(1, length(patchHandleVector)); 0077 for iPatch = 1:length(patchHandleVector) 0078 % m vertices in an m times 3 matrix. 0079 vertices = [get(patchHandleVector(iPatch), 'XData'), ... 0080 get(patchHandleVector(iPatch), 'YData'), ... 0081 get(patchHandleVector(iPatch), 'ZData')]'; 0082 filter = ones([size(cdef.A, 1), 1]); 0083 for i_vertex = 1:size(vertices, 2) 0084 filter = filter & isZero(cdef.A*vertices(:,i_vertex) - h, zerotol); 0085 end 0086 if sum(filter) == 1 0087 patchIsFacet(iPatch) = find(filter); 0088 else 0089 %error('facet of patch can not be identified: either not unique or not existing'); 0090 end 0091 end 0092 0093 %% annotation handling 0094 % switch annotation 0095 % case 'single' 0096 % for i_patch = 1:length(patch_facet) 0097 % if patch_facet(i_patch)==0, ann_str{i_patch} = '';continue;end; 0098 % ann_str{i_patch} = '('; 0099 % for j = 1:3 0100 % ann_str{i_patch} = [ann_str{i_patch} num2str(cdef.mil_complete(patch_facet(i_patch), j))]; 0101 % if j < 3,ann_str{i_patch} = [ann_str{i_patch} ','];end; 0102 % end 0103 % ann_str{i_patch} = [ann_str{i_patch} ')']; 0104 % end 0105 % case 'groups' 0106 % for i_patch = 1:length(patch_facet) 0107 % if patch_facet(i_patch)==0, ann_str{i_patch} = '';continue;end; 0108 % group = find(cdef.groupMappingMatrix(patch_facet(i_patch), :)); 0109 % ann_str{i_patch} = '\{'; 0110 % for j = 1:3 0111 % ann_str{i_patch} = [ann_str{i_patch} num2str(cdef.mil_defined(group, j))]; 0112 % if j < 3,ann_str{i_patch} = [ann_str{i_patch} ','];end; 0113 % end 0114 % ann_str{i_patch} = [ann_str{i_patch} '\}']; 0115 % end 0116 % case iscell(annotation) 0117 % switch length(annotation) 0118 % case size(G, 1) 0119 % case size(G, 2) 0120 % otherwise 0121 % error('with strings given in annotation, the number of labels should match the number of facets or the number of facet groups'); 0122 % end 0123 % otherwise 0124 % for i_patch = 1:length(patch_facet) 0125 % ann_str{i_patch} = ''; 0126 % end 0127 % end 0128 % 0129 % % make annotation 0130 % for i_patch = 1:length(patch_facet) 0131 % if patch_facet(i_patch)==0,continue;end; 0132 % %X = cdef.A(patch_facet(i_patch), :) * h(patch_facet(i_patch)) * 1.1; 0133 % vertices = [get(h_patches(i_patch), 'XData'), ... 0134 % get(h_patches(i_patch), 'YData'), ... 0135 % get(h_patches(i_patch), 'ZData')]'; 0136 % X = mean(vertices, 2)' + cdef.A(patch_facet(i_patch), :) * max(... 0137 % [get(gca, 'XLim'), get(gca, 'YLim'), get(gca, 'ZLim')]... 0138 % ) / 10000; 0139 % h_tmp = text(X(1), X(2), X(3), ann_str{i_patch}); 0140 % end 0141 0142 %% apply colors 0143 set(gca, 'Color', 'none'); 0144 0145 % assign color-data to patches 0146 for iPatch = 1:length(patchIsFacet) 0147 if patchIsFacet(iPatch)==0 0148 group = size(cdef.groupMappingMatrix, 2) + 1; 0149 set(patchHandleVector(iPatch), 'linestyle', 'none'); 0150 else 0151 group = find(cdef.groupMappingMatrix(patchIsFacet(iPatch), :)); 0152 end 0153 set(patchHandleVector(iPatch), 'CData', nGroup - group + 1, 'FaceColor', 'flat', ... 0154 'CDataMapping', 'direct'); 0155 end 0156 0157 % set limits of c-axis 0158 set(gca, 'CLim', [0.5, size(cdef.groupMappingMatrix, 2) + 0.5]); 0159 0160 % determine colormap 0161 if ischar(colorMap) 0162 eval(['colorMap = colormap(' colorMap '(size(cdef.groupMappingMatrix, 2)));']); 0163 end 0164 colorMap = colorMap(end:-1:1, :); 0165 0166 % apply colormap 0167 colormap(colorMap); 0168 0169 % draw colorbar 0170 if f_colorbar 0171 handleColorBar = colorbar; 0172 % label colorbar 0173 for j = 1:size(cdef.groupMappingMatrix, 2) 0174 if length(millerStringOption) == 2 0175 labelColorBar{nGroup - j + 1} = convertMillerToString(... 0176 cdef.millerDefined(j,:), millerStringOption{1}, millerStringOption{2}); 0177 elseif length(millerStringOption) == 1 && ~iscell(millerStringOption{1}) 0178 labelColorBar{nGroup - j + 1} = millerStringOption{1}; 0179 elseif length(millerStringOption) == 1 && iscell(millerStringOption{1}) 0180 labelColorBar{nGroup - j + 1} = millerStringOption{1}{j}; 0181 end 0182 end 0183 set(handleColorBar, 'YTick', 1:size(cdef.groupMappingMatrix, 2), 'YTickLabel', labelColorBar); 0184 end 0185 0186 if nargout == 0 0187 clear patchHandleVector 0188 end