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JFatermansJFatermans
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Update on model selection (MAP)
-Minor overall changes have been implemented in the GUI -Functionality of the model-selection procedure by the maximum a posteriori (MAP) probability rule has been improved -StatSTEM manual has been thoroughly updated
1 parent 31cc9b7 commit a324e2f

34 files changed

Lines changed: 850 additions & 494 deletions

‎Examples/Example_Graphene_MAP_input.mat‎

5.91 KB
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Examples/ExamplePtIr.mat renamed to Examples/Example_PtIr.mat

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‎Examples/Example_SrTiO3_MAP_output.mat‎

1.01 MB
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‎Examples/SrTiO.mat‎

-87.2 KB
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‎Examples/exp_graphene.mat‎

-6 KB
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‎GUI/LeftPanels/Fit Model/Advanced/panelModelOptions.m‎

Lines changed: 39 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
%--------------------------------------------------------------------------
1010
% This file is part of StatSTEM
1111
%
12-
% Copyright: 2018, EMAT, University of Antwerp
12+
% Copyright: 2020, EMAT, University of Antwerp
1313
% Author: K. H. W. van den Bos, J. Fatermans
1414
% License: Open Source under GPLv3
1515
% Contact: sandra.vanaert@uantwerpen.be
@@ -18,7 +18,7 @@
1818
panel = struct;
1919

2020
% Start by defining the name
21-
panel.name = 'Fitting options';
21+
panel.name = 'Options';
2222

2323
panel.row = struct;
2424
%% Define buttons, etc row per row (don't put too much buttons per row for size limitations)
@@ -28,82 +28,83 @@
2828
panel.row(1).option1 = textfield('name','Max. # columns:','width',100);
2929

3030
panel.row(1).option2 = editfield('name','','width',62,'enable',1,...
31-
'tooltip','Define the maximum number of columns in the image','input','input','equalTo','input.MaxColumns');
31+
'input','input','equalTo','input.MaxColumns');
3232

3333

34-
panel.row(2).option1 = textfield('name','# Test points:','width',100);
34+
% panel.row(2).option1 = textfield('name','# Test points:','width',100);
35+
%
36+
% panel.row(2).option2 = editfield('name','','width',62,'enable',1,...
37+
% 'tooltip','Define the number of initial random starting coordinates per model evaluation','input','input','equalTo','input.testpoints');
3538

36-
panel.row(2).option2 = editfield('name','','width',62,'enable',1,...
37-
'tooltip','Define the number of initial random starting coordinates per model evaluation','input','input','equalTo','input.testpoints');
3839

40+
panel.row(2).option1 = textfield('name','Min. background:','width',100);
41+
42+
panel.row(2).option2 = editfield('name','','width',62,'enable',1,...
43+
'input','input','equalTo','input.zetamin');
3944

40-
panel.row(3).option1 = textfield('name','Min. x-coord.:','width',100);
4145

42-
panel.row(3).option2 = editfield('name','','width',42,'enable',1,...
43-
'tooltip','Define the minimum x-coordinate','input','input','equalTo','input.beta_xmin');
46+
panel.row(3).option1 = textfield('name','Max. background:','width',100);
4447

45-
panel.row(3).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
48+
panel.row(3).option2 = editfield('name','','width',62,'enable',1,...
49+
'input','input','equalTo','input.zetamax');
4650

4751

48-
panel.row(4).option1 = textfield('name','Max. x-coord.:','width',100);
52+
panel.row(4).option1 = textfield('name','Min. width.:','width',100);
4953

5054
panel.row(4).option2 = editfield('name','','width',42,'enable',1,...
51-
'tooltip','Define the maximum x-coordinate','input','input','equalTo','input.beta_xmax');
55+
'input','input','equalTo','input.rhomin');
5256

5357
panel.row(4).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
5458

5559

56-
panel.row(5).option1 = textfield('name','Min. y-coord.:','width',100);
60+
panel.row(5).option1 = textfield('name','Max. width:','width',100);
5761

5862
panel.row(5).option2 = editfield('name','','width',42,'enable',1,...
59-
'tooltip','Define the minimum y-coordinate','input','input','equalTo','input.beta_ymin');
63+
'input','input','equalTo','input.rhomax');
6064

6165
panel.row(5).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
6266

6367

64-
panel.row(6).option1 = textfield('name','Max. y-coord.:','width',100);
68+
panel.row(6).option1 = textfield('name','Min. intensity:','width',100);
6569

66-
panel.row(6).option2 = editfield('name','','width',42,'enable',1,...
67-
'tooltip','Define the maximum y-coordinate','input','input','equalTo','input.beta_ymax');
70+
panel.row(6).option2 = editfield('name','','width',62,'enable',1,...
71+
'input','input','equalTo','input.etamin');
6872

69-
panel.row(6).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
7073

74+
panel.row(7).option1 = textfield('name','Max. intensity:','width',100);
7175

72-
panel.row(7).option1 = textfield('name','Min. width.:','width',100);
76+
panel.row(7).option2 = editfield('name','','width',62,'enable',1,...
77+
'input','input','equalTo','input.etamax');
7378

74-
panel.row(7).option2 = editfield('name','','width',42,'enable',1,...
75-
'tooltip','Define the minimum column width','input','input','equalTo','input.rhomin');
7679

77-
panel.row(7).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
78-
79-
80-
panel.row(8).option1 = textfield('name','Max. width:','width',100);
80+
panel.row(8).option1 = textfield('name','Min. x-coord.:','width',100);
8181

8282
panel.row(8).option2 = editfield('name','','width',42,'enable',1,...
83-
'tooltip','Define the maximum column width','input','input','equalTo','input.rhomax');
83+
'input','input','equalTo','input.beta_xmin');
8484

8585
panel.row(8).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
8686

8787

88-
panel.row(9).option1 = textfield('name','Min. intensity:','width',100);
88+
panel.row(9).option1 = textfield('name','Max. x-coord.:','width',100);
89+
90+
panel.row(9).option2 = editfield('name','','width',42,'enable',1,...
91+
'input','input','equalTo','input.beta_xmax');
8992

90-
panel.row(9).option2 = editfield('name','','width',62,'enable',1,...
91-
'tooltip','Define the minimum column intensity','input','input','equalTo','input.etamin');
93+
panel.row(9).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
9294

9395

94-
panel.row(10).option1 = textfield('name','Max. intensity:','width',100);
96+
panel.row(10).option1 = textfield('name','Min. y-coord.:','width',100);
9597

96-
panel.row(10).option2 = editfield('name','','width',62,'enable',1,...
97-
'tooltip','Define the maximum column intensity','input','input','equalTo','input.etamax');
98+
panel.row(10).option2 = editfield('name','','width',42,'enable',1,...
99+
'input','input','equalTo','input.beta_ymin');
98100

101+
panel.row(10).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
99102

100-
panel.row(11).option1 = textfield('name','Min. background:','width',100);
101103

102-
panel.row(11).option2 = editfield('name','','width',62,'enable',1,...
103-
'tooltip','Define the minimum pixel value of the background','input','input','equalTo','input.zetamin');
104+
panel.row(11).option1 = textfield('name','Max. y-coord.:','width',100);
104105

105-
panel.row(12).option1 = textfield('name','Max. background:','width',100);
106+
panel.row(11).option2 = editfield('name','','width',42,'enable',1,...
107+
'input','input','equalTo','input.beta_ymax');
106108

107-
panel.row(12).option2 = editfield('name','','width',62,'enable',1,...
108-
'tooltip','Define the maximum pixel value of the background','input','input','equalTo','input.zetamax');
109+
panel.row(11).option3 = editfield('name',char(197),'width',20,'enable',0,'alignment','c');
109110

‎GUI/LeftPanels/Fit Model/panelFitModelSelection.m‎

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@
99
%--------------------------------------------------------------------------
1010
% This file is part of StatSTEM
1111
%
12-
% Copyright: 2018, EMAT, University of Antwerp
12+
% Copyright: 2020, EMAT, University of Antwerp
1313
% Author: J. Fatermans
1414
% License: Open Source under GPLv3
1515
% Contact: sandra.vanaert@uantwerpen.be
@@ -25,8 +25,11 @@
2525
% Define buttons, etc for the first row per option. Each row has a maximum
2626
% width of 162 pixels
2727

28-
panel.row(1).option1 = pushbutton('name','Run model selection','width',162,'tooltip','Perform model order selection',...
29-
'func','MAP_back_samerho','input','input.coordinates','output',{'output';'outputMAP'},'fitting',1,'figEnd','Model','figOptEnd',{'Fitted coordinates'});
28+
% panel.row(1).option1 = pushbutton('name','Run model selection','width',162,'tooltip','Perform model-order selection',...
29+
% 'func','MAP','input','input.coordinates','output',{'output';'outputMAP'},'fitting',1,'figEnd','Model','figOptEnd',{'Fitted coordinates'});
30+
31+
panel.row(1).option1 = pushbutton('name','Run model selection','width',162,'tooltip','Perform model-order selection',...
32+
'func','MAP','input','input','output',{'output';'outputMAP'},'fitting',1,'figEnd','Model','figOptEnd',{'Fitted coordinates'});
3033

3134
panel.row(2).option1 = pushbutton('name','Abort fitting routine','width',162,'func','abortFit','input','input');
3235

‎GUI/LeftPanels/Preparation/panelAddRemove.m‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@
1818
panel = struct;
1919

2020
% Start by defining the name
21-
panel.name = 'Add/Remove Peaks';
21+
panel.name = 'Add/Remove peaks';
2222

2323
panel.row = struct;
2424
%% Define buttons, etc row per row (don't put too much buttons per row for size limitations)

‎GUI/LeftPanels/Preparation/panelImgPar.m‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -39,11 +39,11 @@
3939
'func','selectPartImage','input','input.obs','output','input',...
4040
'figStart','Observation','figOptStart',{'Input coordinates'},'reshowFigEnd',true);
4141

42-
panel.row(3).option1 = pushbutton('name','Flip contrast image','width',162,...
42+
panel.row(3).option1 = pushbutton('name','Flip image contrast','width',162,...
4343
'func','flipContrastImage','input','input.obs','output','input',...
4444
'figStart','Observation','figOptStart',{'Input coordinates'},'reshowFigEnd',true);
4545

46-
panel.row(4).option1 = pushbutton('name','Make image background','width',162,...
46+
panel.row(4).option1 = pushbutton('name','Replace image background','width',162,...
4747
'func','makeBack','input','input.obs','output','input','tooltip','Make part of the image equal to a background value',...
4848
'figStart','Observation','figEnd','Observation','figOptEnd',{'Input coordinates'},'reshowFigEnd',true);
4949

‎GUI/LeftPanels/Preparation/panelImpPeak.m‎

Lines changed: 0 additions & 29 deletions
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