Small changes and bug fixes in matching GUI. Changes in the help but not in...

Small changes and bug fixes in matching GUI. Changes in the help but not in the code for gtFedRotationMatrixComp.m and gtMathsRotationMatrixComp.m .

git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@265 4c865b51-4357-4376-afb4-474e03ccb993

3_pairmatchingGUI/gtMatchCalculateProjectionPath.m

@@ -27,7 +27,7 @@ refreshdata(handles.Fullim_CentA,'caller');
 
 
 % Points out of plane
-projAmirrZ = (labAmirr-labgeo.detrefpos)*labgeo.detnorm'/labgeo.pixelsizeu;
+projAmirrZ = (labAmirr-labgeo.detrefpos)*(-labgeo.detnorm')/labgeo.pixelsizeu;
 
 % Points along projection A-A'-B in 3D
 if ~isempty(handles.Fullim_ProjLine3D)

3_pairmatchingGUI/gtMatchFilterPairs.m

@@ -11,16 +11,18 @@ end
 set(handles.Text_Progress,'String','Updating...')
 gtMatchSetBusy(handles,'on');
 
-filtind = handles.pairs.error <= handles.ErrorFilter;
+% Indices with an error smaller than the error filter 
+handles.pairs.filterr = handles.pairs.error <= handles.ErrorFilter;
+
+% Combine the theta and error filters
+handles.pairs.filtind = (handles.pairs.filterr & handles.pairs.filttheta);
 
-handles.pairs.filtind = filtind;
 
 % Copy all fields from pairs to pairsfilt
 fn = fieldnames(handles.pairs);
 for ii = 1:length(fn)
-    handles.pairsfilt.(fn{ii}) = handles.pairs.(fn{ii})(filtind,:);
+    handles.pairsfilt.(fn{ii}) = handles.pairs.(fn{ii})(handles.pairs.filtind,:);
 end
-handles.pairsfilt = rmfield(handles.pairsfilt,'filtind');
 
 
 % Update Eta-Theta figure in other GUI

3_pairmatchingGUI/gtMatchFindPairCandidates.m

@@ -283,6 +283,7 @@ gtMatchUpdateStatistics(handles);
 
 % Display result, no. of pairs
 pairstext    = get(handles.Text_PairsResults,'String');
+pairstext{1} = num2str(iw);
 pairstext{2} = num2str(length(handles.pairs.indA));
 set(handles.Text_PairsResults,'String',pairstext);
 

3_pairmatchingGUI/gtMatchGUIMain.m

@@ -253,7 +253,7 @@ histtheta = NaN;
 refreshdata(handles.GUIEtaTheta.HistHandle,'caller')
 
 % Reset results display
-pairtext{1} = '';
+pairtext{1} = '0000';
 pairtext{2} = '0000'; 
 pairtext{3} = '0000'; 
 set(handles.Text_PairsResults,'String',pairtext);
@@ -399,21 +399,7 @@ function ThetaLims_Push_Add_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 
-% Check input
-if handles.ThetaLimLastLow >= handles.ThetaLimLastHigh
-  return
-end
-
-% Add new values to array
-handles.ThetaLimits(end+1,1:2) = [handles.ThetaLimLastLow, handles.ThetaLimLastHigh];
-
-% Change string in list box
-set(handles.ThetaLims_Listbox,'String',num2str(handles.ThetaLimits));
-
-% Update theta limits in figure
-handles = gtMatchUpdateThetaFilterDisplay(handles);
-
-guidata(hObject,handles);
+gtMatchUpdateThetaFilter(handles,'add');
 
 
 
@@ -423,28 +409,7 @@ function ThetaLims_Push_Delete_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 
-if isempty(handles.ThetaLimits)
-    return
-end
-
-% Current index in list
-ind = get(handles.ThetaLims_Listbox,'Value'); 
-
-% Delete currently selected limits
-handles.ThetaLimits(ind,:) = [];
-set(handles.ThetaLims_Listbox,'Value',1); 
-
-% Set string
-if isempty(handles.ThetaLimits)
-    set(handles.ThetaLims_Listbox,'String','!! None !!');
-else
-    set(handles.ThetaLims_Listbox,'String',num2str(handles.ThetaLimits));
-end
-
-% Update theta limits in figure
-handles = gtMatchUpdateThetaFilterDisplay(handles);
-
-guidata(hObject,handles);
+gtMatchUpdateThetaFilter(handles,'delete');
 
 
 
@@ -454,22 +419,7 @@ function ThetaLims_Push_Change_Callback(hObject, eventdata, handles)
 % eventdata  reserved - to be defined in a future version of MATLAB
 % handles    structure with handles and user data (see GUIDATA)
 
-% Check input
-if handles.ThetaLimLastLow >= handles.ThetaLimLastHigh
-  return
-end
-
-% Change values in array
-ind = get(handles.ThetaLims_Listbox,'Value');  % current index in list
-handles.ThetaLimits(ind,1:2) = [handles.ThetaLimLastLow, handles.ThetaLimLastHigh];
-
-% Change string in list box
-set(handles.ThetaLims_Listbox,'String',num2str(handles.ThetaLimits));
-
-% Update theta limits in figure
-handles = gtMatchUpdateThetaFilterDisplay(handles);
-
-guidata(hObject,handles);
+gtMatchUpdateThetaFilter(handles,'change');
 
 
 

3_pairmatchingGUI/gtMatchInitialize.m

@@ -390,7 +390,7 @@ spottext{3} = handles.nof_spotsB;
 set(handles.Text_SpotsResults,'String',spottext);
 
 % Pair results    
-pairtext{1} = '';
+pairtext{1} = '0000';
 pairtext{2} = '0000'; 
 pairtext{3} = '0000'; 
 set(handles.Text_PairsResults,'String',pairtext);

3_pairmatchingGUI/gtMatchInitializeGUIPairFigure.m

@@ -185,8 +185,9 @@ set(handles.Radio_RotAxis,'Value',get(handles.Radio_RotAxis,'Max'));
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % Get transformation matrix lab2det
-[~,labgeo.lab2det] = gtGeoLab2Det([0 0 0 ],labgeo,1);
-       
+%[~,labgeo.lab2det] = gtGeoLab2Det([0 0 0],labgeo,1);
+[origxyz,labgeo.lab2det] = gtGeoLab2Det([0 0 0],labgeo,0);
+  
 % Scaling for quivers
 scale = 0.5;
 
@@ -198,14 +199,21 @@ if mainhandles.plot3D
         handles.rotaxisendsz,'LineStyle','-.','Color',[1 1 0],...
         'Parent',handles.Axes_Full,'LineWidth',2);
 
-    % Use transformation matrix; add some Z coordinate
-    transmat = [labgeo.lab2det, labgeo.detnorm'/labgeo.pixelsizeu];
-
-    % Origin of plotted vectors
-    origuvz = [1 1 0];
+    % Use lab2det  transformation matrix to get U,V coordinates. To display
+    % everything relative to the image coordinate system, addition of a Z 
+    % coordinate is needed. In order to keep this new reference right-handed,
+    % the Z coordinate direction is defined negative from detnorm 
+    % and the scaling is chosen reasonably as:
+    transmat = [labgeo.lab2det, -labgeo.detnorm'/labgeo.pixelsizeu];
 
     % Not that if linux (X client) font settings are not correct, some 
     % fonts may not show up and plotting may get extremely slow. 
+
+    
+    % Detector orientation
+    
+    % Origin of plotted vectors
+    origuvz = [1 1 0];
     
     dirvec = labgeo.detdiru*transmat;
     handles.Fullim_BaseVectors(1) = quiver3(origuvz(1),origuvz(2),origuvz(3),...
@@ -224,9 +232,14 @@ if mainhandles.plot3D
         'VerticalAlignment','Top');
 
     
-    % Origin of plotted vectors
-    origuvz = [labgeo.detsizeu, labgeo.detsizev]/2;
-    origuvz(3) = labgeo.detsizeu/2;
+    % Origin of plotted vectors for rotdir, beamdir, Lab axes
+    origuvz([1 2]) = origxyz([1 2]);
+    origuvz(3)= ([0 0 0] - labgeo.detrefpos)*(-labgeo.detnorm')/labgeo.pixelsizeu;
+    
+    % Lab origin
+    handles.Fullim_BaseVectors(15) = plot3(origuvz(1),origuvz(2),origuvz(3), ...
+        'mo','LineWidth',2,'Parent',handles.Axes_Full);
+
     
     % Rotdir
     dirvec = labgeo.rotdir*transmat;
@@ -247,7 +260,7 @@ if mainhandles.plot3D
         'String','Beamdir','Color','r','FontSize',14,'Parent',handles.Axes_Full,...
         'VerticalAlignment','Top','HorizontalAlignment','Right');
     
-    
+   
     % Lab axes
     dirvec = [1 0 0]*transmat;
     handles.Fullim_BaseVectors(9) = quiver3(origuvz(1),origuvz(2),origuvz(3),...
@@ -281,13 +294,12 @@ else
     
     % Use transformation matrix
     transmat = labgeo.lab2det;
-   
+
+    % Detector orientation
+
     % Origin of plotted vectors
     origuv = [1 1];
     
-    % It looks like that font size 12 doesn't show up
-    % (problem may be related to linux settings)
-    
     dirvec = labgeo.detdiru*transmat;
     handles.Fullim_BaseVectors(1) = quiver(origuv(1),origuv(2),...
         dirvec(1),dirvec(2),...
@@ -304,9 +316,13 @@ else
         'String','Detdirv','Color','w','FontSize',14,'Parent',handles.Axes_Full,...
         'VerticalAlignment','Top','HorizontalAlignment','Left');
     
-    % Origin of plotted vectors
-    origuv = [labgeo.detsizeu, labgeo.detsizev]/2;
-    
+    % Origin of plotted vectors for rotdir, beamdir, Lab axes
+    origuv = origxyz([1 2]);
+
+    % Lab origin
+    handles.Fullim_BaseVectors(15) = plot3(origuv(1),origuv(2), ...
+        'mo','LineWidth',2,'Parent',handles.Axes_Full);
+
     % Rotdir
     dirvec = labgeo.rotdir*transmat;
     handles.Fullim_BaseVectors(5) = quiver(origuv(1),origuv(2),...

3_pairmatchingGUI/gtMatchLoadDifspotData.m

@@ -63,6 +63,10 @@ allsp.pairid = NaN(length(allsp.ind),1);
 % Initial no. of pairs
 handles.nof_pairs_ini = mym(sprintf('SELECT count(*) FROM %s',handles.pairtable));
 
+disp('Number of Friedel pairs already present in database:')
+disp(handles.nof_pairs_ini)
+
+
 % Display status
 if handles.nof_pairs_ini > 0
     set(handles.Text_PairtableEmpty,'String','NOT EMPTY!')
@@ -111,8 +115,19 @@ if handles.nof_pairs_ini > 0
                               handles.parameters.acq.nproj;
 
         if (ps.phasetype(ii) && ps.thetatype(ii))
-            ps.hkl(ii,:) = handles.parameters.cryst(ps.phasetype(ii)).hkl(:,ps.thetatype(ii));
+            
+            tmphkl = handles.parameters.cryst(ps.phasetype(ii)).hkl(:,ps.thetatype(ii));
+            
+            if size(tmphkl,1)==3
+                ps.hkl(ii,:) = tmphkl;
+            elseif size(tmphkl,1)==4
+                ps.hkl(ii,:) = tmphkl([1 2 4]);
+            else
+                error('Expected format for field hkl is 3xn or 4xn.')
+            end
+                
             ps.hklunique(ii,1) = true;
+            
         else
             ps.hkl(ii,:) = [NaN NaN NaN];
             ps.hklunique(ii,1) = false;
@@ -127,9 +142,13 @@ if handles.nof_pairs_ini > 0
 
     end
    
-    handles.pairs     = ps;
-    handles.pairsfilt = ps;
-    
+    handles.pairs           = ps;
+    handles.pairs.filttheta = true(size(handles.pairs.indA));
+    handles.pairs.filterr   = true(size(handles.pairs.indA));
+    handles.pairs.filtind   = true(size(handles.pairs.indA));
+
+    handles.pairsfilt = handles.pairs;
+   
 end
 
 handles.allsp = allsp;

3_pairmatchingGUI/gtMatchRankCandidates.m

@@ -166,6 +166,9 @@ handles.pairs.centAV = handles.allsp.centv(handles.pairs.indA);
 handles.pairs.centBU = handles.allsp.centu(handles.pairs.indB);
 handles.pairs.centBV = handles.allsp.centv(handles.pairs.indB);
 
+handles.pairs.filttheta = true(size(handles.pairs.indA));
+handles.pairs.filterr   = true(size(handles.pairs.indA));
+handles.pairs.filtind   = true(size(handles.pairs.indA));
 
 
 % Copy pairid-s into allsp:

3_pairmatchingGUI/gtMatchRotAxisProjection.m

@@ -85,8 +85,8 @@ if nargout > 1
     % Note that there will be a distortion in this 3D figure compared to 
     % reality, if the pixel sizes are different or detdiru and detdirv are 
     % not orthogonal. It is only for plotting over the detector image.
-    endpointsz(1) = (end1lab - labgeo.detrefpos)*labgeo.detnorm'/labgeo.pixelsizeu;
-    endpointsz(2) = (end2lab - labgeo.detrefpos)*labgeo.detnorm'/labgeo.pixelsizeu;
+    endpointsz(1) = (end1lab - labgeo.detrefpos)*(-labgeo.detnorm')/labgeo.pixelsizeu;
+    endpointsz(2) = (end2lab - labgeo.detrefpos)*(-labgeo.detnorm')/labgeo.pixelsizeu;
 
 end
 

3_pairmatchingGUI/gtMatchSplitSpotData.m

@@ -7,7 +7,8 @@ function handles = gtMatchSplitSpotData(handles)
 % analysed independently in other functions.
 %
 
-rangeA = ceil(handles.matchpars.thr_max_offset);
+% Image range for subgroups A:
+rangeA = max(ceil(handles.matchpars.thr_max_offset),1);
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

3_pairmatchingGUI/gtMatchUpdateThetaFilter.m

+function gtMatchUpdateThetaFilter(handles,op)
+
+% Updates the theta range values in handles.ThetaLimits if changed by the user 
+% via the GUI. Calls other functions to update the graphical display of 
+% the theta ranges and the pairs in the eta-theta plot that pass the filter.
+
+
+% Check input
+if handles.ThetaLimLastLow >= handles.ThetaLimLastHigh
+  return
+end
+
+
+switch op
+    
+    case 'add'
+    % Add new values to array
+    handles.ThetaLimits(end+1,1:2) = [handles.ThetaLimLastLow, handles.ThetaLimLastHigh];
+
+    case 'delete'
+    if isempty(handles.ThetaLimits)
+        return
+    end
+    % Current index in list
+    ind = get(handles.ThetaLims_Listbox,'Value');
+    % Delete currently selected limits
+    handles.ThetaLimits(ind,:) = [];
+    set(handles.ThetaLims_Listbox,'Value',1);
+
+    case 'change'
+    % Current index in list
+    ind = get(handles.ThetaLims_Listbox,'Value');
+    % Change limits
+    handles.ThetaLimits(ind,1:2) = [handles.ThetaLimLastLow, handles.ThetaLimLastHigh];
+
+end
+
+
+% Change string in list box
+if isempty(handles.ThetaLimits)
+    set(handles.ThetaLims_Listbox,'String','!! None !!');
+else
+    set(handles.ThetaLims_Listbox,'String',num2str(handles.ThetaLimits));
+end
+
+
+% Update theta limits in figure
+handles = gtMatchUpdateThetaFilterDisplay(handles);
+
+
+% Apply filter to pairs
+tmpfilt = false(size(handles.pairs.theta,1),size(handles.ThetaLimits,1));
+for ii = 1:size(handles.ThetaLimits,1)
+   tmpfilt(:,ii) = ((handles.ThetaLimits(ii,1) <= handles.pairs.theta)...
+       & (handles.pairs.theta <= handles.ThetaLimits(ii,2)));
+end
+
+handles.pairs.filttheta = any(tmpfilt,2);
+
+
+% Update eta-theta and text display
+handles = gtMatchFilterPairs(handles);
+
+
+% Update GUI data
+guidata(handles.figure1,handles);
+
+
+

7_fed/geometry/gtFedRotationMatrixComp.m

 function rotmatcomp = gtFedRotationMatrixComp(rotdir)
 % rotmatcomp = gtFedRotationMatrixComp(rotdir)
 %
-% Gives the matrices to compose a rotation matrix according to Rodrigues'
-% rotation formula:
+% Given an arbitrary rotation axis in 3D space, returns the three matrices
+% in Rodrigues's formula. The matrices can be used to compose the rotation 
+% tensor. Considers right-handed rotation for a positive angle.
+%
+% To be used with COLUMN VECTORS, MULTIPLY FROM THE LEFT side! 
+% Multiplication of row vectors from the right gives the wrong result!
+%
+% Rodrigues's rotation formula describes a linear combination of
+% matrices with only cos(om) and only sin(om) dependent terms:
 %   S = Sconst + Scos*cos(om) + Ssin*sin(om)
-%     S:  rotation matrix: nlab = S*nsam
+%     S:  rotation matrix: columnvector_rotated = S*columnvector
 %     om: right-handed rotation angle
 %
 % INPUT
-%   rotdir - rotation axis direction in LAB coordinates
+%   rotdir - rotation axis direction in LAB coordinates (3,1)
 %
 % OUTPUT
-%   rotmatcomp.const = Sconst
-%   rotmatcomp.cos   = Scos
-%   rotmatcomp.sin   = Ssin
+%   rotmatcomp.const = matrix Sconst (3,3)
+%   rotmatcomp.cos   = matrix Scos   (3,3)
+%   rotmatcomp.sin   = matrix Ssin   (3,3)
 %
 
 if size(rotdir) ~= [3,1]
-	error('Input rotdir has to be a 3x1 coloumn vector.')
+	error('Input rotdir has to be a 3x1 column vector.')
 end
 
 
-if rotdir == [0; 0; 0] % no rotation (polychromatic case)
+if rotdir == [0; 0; 0] % no rotation (e.g. polychromatic case)
 	
 	rotmatcomp.const = [1 0 0; 0 1 0; 0 0 1];
 	rotmatcomp.cos   = [0 0 0; 0 0 0; 0 0 0];
@@ -32,8 +39,8 @@ else  % monochromatic case
 	rotmatcomp.const = rotdir*rotdir';
 	rotmatcomp.cos   = eye(3) - rotmatcomp.const;
 	rotmatcomp.sin   = [ 0         -rotdir(3)  rotdir(2);...
-		rotdir(3)          0 -rotdir(1);...
-		-rotdir(2)  rotdir(1)          0];
+		                 rotdir(3)          0 -rotdir(1);...
+		                -rotdir(2)  rotdir(1)          0];
 	
 end
 

zUtil_Maths/gtMathsRotationMatrixComp.m

@@ -5,10 +5,14 @@
 % in Rodrigues's formula. The matrices can be used to compose the rotation 
 % tensor. Considers right-handed rotation for a positive angle.
 %
+% To be used with ROW VECTORS, MULTIPLY FROM THE RIGHT side! 
+% Multiplication of column vectors from the left gives the wrong result!
+%
 % Rodrigues's rotation formula describes a linear combination of
 % matrices with only cos(om) and only sin(om) dependent terms:
 %   Srot = Sconst + Scos*cos(om) + Ssin*sin(om)
-%     Srot: is the rotation tensor for a row vector: vec_rotated = vec*Srot
+%     Srot: rotation tensor for a row vector:
+%             rowvector_rotated = rowvector*Srot
 %     om  : rotation angle 
 %
 % INPUT
@@ -16,9 +20,9 @@
 %            rotation (1,3)
 %
 % OUTPUT
-%   rotmatcomp.const = Sconst matrix
-%   rotmatcomp.cos   = Scos matrix
-%   rotmatcomp.sin   = Ssin matrix 
+%   rotmatcomp.const = matrix Sconst (3,3)
+%   rotmatcomp.cos   = matrix Scos   (3,3)
+%   rotmatcomp.sin   = matrix Ssin   (3,3) 
 %
 
 function rotmatcomp = gtMathsRotationMatrixComp(rotdir)