detgeo: another round of fixes

(thanks to Lorenzo for spotting some of them once again)

Signed-off-by: Nicola Vigano <nicola.vigano@esrf.fr>

1_preprocessing/gtFillCrystFields.m

@@ -278,7 +278,7 @@ function parameters = sfGetReflectionInfoFromFable(parameters, phase_id)
     disp('Using fable calculation of theoretical reflections')
     disp('The only missing information is the intensity')
     % reflection list
-    list = gtCrystCalculateReflections(parameters.cryst(phase_id), parameters.labgeo, parameters.acq.energy, 'reflections_');
+    list = gtCrystCalculateReflections(parameters.cryst(phase_id), parameters.detgeo, parameters.acq.energy, 'reflections_');
     parameters.cryst(phase_id) = gtAddMatFile(parameters.cryst(phase_id), list, true, false, false, false, false);
 
     clear list

1_preprocessing/gtPreprocessing.m

@@ -200,7 +200,7 @@ else
     if strcmpi(check,'y')
         parameters.acq.rotu = gtFindRotationAxis(parameters.acq,bbdir);
         parameters.acq.rotx = parameters.acq.rotu;
-        parameters.labgeo.detrefpos(2) = -(parameters.acq.rotu - parameters.acq.xdet / 2) * parameters.acq.pixelsize;
+        parameters.detgeo.detrefpos(2) = -(parameters.acq.rotu - parameters.acq.xdet / 2) * parameters.detgeo.pixelsizeu;
     end
     save(parameters_name,'parameters');
 

2_difspot/gtSegmentationInitialise.m

@@ -42,9 +42,9 @@ totproj = totproj-1;
 
 % One quarter of detector, 10 images
 set(handles.u_start, 'string', '1')
-set(handles.u_end, 'string', num2str(round(parameters.labgeo.detsizeu/2)))
+set(handles.u_end, 'string', num2str(round(parameters.detgeo.detsizeu/2)))
 set(handles.v_start, 'string', '1')
-set(handles.v_end, 'string', num2str(round(parameters.labgeo.detsizev/2)))
+set(handles.v_end, 'string', num2str(round(parameters.detgeo.detsizev/2)))
 set(handles.image_start, 'string', num2str(round(totproj/2)))
 set(handles.image_end, 'string', num2str(round(totproj/2)+9))
 % start with the first image

zUtil_Cryst/gtCrystCalculateReflections.m

-function list = gtCrystCalculateReflections(cryst, labgeo, energy, filename)
+function list = gtCrystCalculateReflections(cryst, detgeo, energy, filename)
 % GTCRYSTCALCULATEREFLECTIONS  Calculate the reflections list using python 
 %                              from xfab library in fable
-%     list = gtCrystCalculateReflections(cryst, labgeo, energy, [filename])
+%     list = gtCrystCalculateReflections(cryst, detgeo, energy, [filename])
 %     -------------------------------------------------------------------
 %     List of theoretical reflections for a given crystal system and spacegroup
 %
@@ -30,9 +30,9 @@ function list = gtCrystCalculateReflections(cryst, labgeo, energy, filename)
 latticepar = cryst.latticepar;
 sg = cryst.spacegroup;
 
-tmp = labgeo.detanglemin/2; % theta
+tmp = detgeo.detanglemin/2; % theta
 minsintl = min(0.0001, sind(tmp)/gtConvEnergyToWavelength(energy));
-tmp = labgeo.detanglemax/2;
+tmp = detgeo.detanglemax/2;
 maxsintl = sind(tmp)/gtConvEnergyToWavelength(energy);
 
 if ~exist('filename','var') || isempty(filename)

zUtil_Geo/gtGeoDiffVecInLab.m

+function [diffvec, labAXYZ, theta] = gtGeoDiffVecInLab(detAUV, labBXYZ, labgeo)
+% FUNCTION [diffvec, labAXYZ, theta] = gtGeoDiffVecInLab(detAUV, labBXYZ, labgeo)
 %
-% FUNCTION [diffvec,labAXYZ,theta] = gtGeoDiffVecInLab(detAUV,labBXYZ,labgeo)
-%
-% Given a set of points A on the detector with their Detector coordinates 
-% U,V, and another set of points B with their Lab coordinates X,Y,Z,
+% Given a set of points A on the detector with their Detector coordinates
+% U, V, and another set of points B with their Lab coordinates X, Y, Z,
 % the function returns the corresponding diffraction vectors in the Lab
-% reference. The diffraction vectors indicate the direction of the 
+% reference. The diffraction vectors indicate the direction of the
 % diffracted beam paths.
-% It also returns the Bragg angles and the Lab coordinates of points A. 
+% It also returns the Bragg angles and the Lab coordinates of points A.
 %
-% INPUT  detAUV  - Detector coordinates U,V of the points A (n,2)
-%        labBXYZ - Lab coordinates X,Y,Z of points B (n,3)      
+% INPUT  detAUV  - Detector coordinates U, V of the points A (n, 2)
+%        labBXYZ - Lab coordinates X, Y, Z of points B (n, 3)
 %
 %        Geometry parameters in Lab coordinates:
 %
 %        labgeo.rotpos   - rotation axis position (row vector)
 %        labgeo.rotdir   - rotation axis direction (unit row vector)
-%        labgeo.detorig  - position of detector origin (row vector)
-%        labgeo.detdiru  - detector U direction (unit row vector)
-%        labgeo.detdirv  - detector V direction (unit row vector)
-%	     labgeo.pixelsizeu - pixel size U (same unit as position values)
-%	     labgeo.pixelsizev - pixel size V (same unit as position values)
+%        detgeo.detorig  - position of detector origin (row vector)
+%        detgeo.detdiru  - detector U direction (unit row vector)
+%        detgeo.detdirv  - detector V direction (unit row vector)
+%        detgeo.pixelsizeu - pixel size U (same unit as position values)
+%        detgeo.pixelsizev - pixel size V (same unit as position values)
 %
 % OUTPUT diffvec - Lab coordinates of the normalised diffraction vectors;
-%                  direction points from points B to A (n,3)
-%        labAXYZ - Lab coordinates of points A (n,3)
-%        theta   - Bragg angles theta in degrees (n,1)
+%                  direction points from points B to A (n, 3)
+%        labAXYZ - Lab coordinates of points A (n, 3)
+%        theta   - Bragg angles theta in degrees (n, 1)
 %
 
-function [diffvec,labAXYZ,theta] = gtGeoDiffVecInLab(detAUV,labBXYZ,labgeo)
-
-% Coordinate transformation from Detector to Lab
-labAXYZ = gtGeoDet2Lab(detAUV,labgeo,0);
-
-% Diffraction vectors from labXYZ to point A: 
-diffvec = labAXYZ - labBXYZ;
+    % Coordinate transformation from Detector to Lab
+    labAXYZ = gtGeoDet2Lab(detAUV, labgeo, 0);
 
-% Normalise diffvec-s (seems the fastest way for nx3 vectors):
-dnorm = sqrt(diffvec(:,1).^2 + diffvec(:,2).^2 + diffvec(:,3).^2) ;
+    % Diffraction vectors from labXYZ to point A:
+    diffvec = labAXYZ - labBXYZ;
 
-diffvec(:,1) = diffvec(:,1)./dnorm ; 
-diffvec(:,2) = diffvec(:,2)./dnorm ;
-diffvec(:,3) = diffvec(:,3)./dnorm ;
+    % Normalise diffvec-s (seems the fastest way for nx3 vectors):
+    dnorm = sqrt(diffvec(:, 1) .^ 2 + diffvec(:, 2) .^ 2 + diffvec(:, 3) .^2 );
 
+    diffvec(:, 1) = diffvec(:, 1) ./ dnorm;
+    diffvec(:, 2) = diffvec(:, 2) ./ dnorm;
+    diffvec(:, 3) = diffvec(:, 3) ./ dnorm;
 
-if nargout == 3
-
-    % Use the dot products of beamdir and diffvec to get theta
-    theta  = 0.5*acosd(diffvec*labgeo.beamdir');
 
+    if (nargout == 3)
+        % Use the dot products of beamdir and diffvec to get theta
+        theta  = 0.5 * acosd(diffvec * labgeo.beamdir');
+    end
 end
 
-

zUtil_Geo/gtGeoLab2Det.m

-function [detUV,lab2det] = gtGeoLab2Det(labXYZ,labgeo,freevec_flag)
-%
-% FUNCTION [detUV,lab2det] = gtGeoLab2Det(labXYZ,labgeo,freevec_flag)
+function [detUV, lab2det] = gtGeoLab2Det(labXYZ, detgeo, freevec_flag)
+% FUNCTION [detUV, lab2det] = gtGeoLab2Det(labXYZ, detgeo, freevec_flag)
 %
 % LAB -> DETECTOR coordinate transformation using arbitrary geometry.
 %
@@ -8,51 +7,46 @@ function [detUV,lab2det] = gtGeoLab2Det(labXYZ,labgeo,freevec_flag)
 % Detector coordinates. If labXYZ is not in the detector plane, 
 % its perpendicular projection onto the detector plane will be used.
 %
-% INPUT  labXYZ - array of LAB coordinates (n,3)
+% INPUT  labXYZ - array of LAB coordinates (n, 3)
 %
 %        Geometry parameters given in LAB coordinates:
-%        labgeo.detorig    - position of detector origin: pixel {0,0};
-%                            size (1,3)
-%        labgeo.detdiru    - detector U direction (unit row vector)
-%        labgeo.detdirv    - detector V direction (unit row vector)
-%        labgeo.pixelsizeu - pixel size U (same unit as position)
-%        labgeo.pixelsizev - pixel size V (same unit as position)
+%        detgeo.detorig    - position of detector origin: pixel {0, 0};
+%                            size (1, 3)
+%        detgeo.detdiru    - detector U direction (unit row vector)
+%        detgeo.detdirv    - detector V direction (unit row vector)
+%        detgeo.pixelsizeu - pixel size U (same unit as position)
+%        detgeo.pixelsizev - pixel size V (same unit as position)
 %
 %        freevec_flag      - 1 for free vectors, 0 for bound vectors
 %
-% OUTPUT detUV             - detector coordinates in pixels (n,2)
-%        lab2det           - transformation matrix from Lab to Detector (3,2)
+% OUTPUT detUV             - detector coordinates in pixels (n, 2)
+%        lab2det           - transformation matrix from Lab to Detector (3, 2)
 %
 
+    if isfield(detgeo, 'lab2det')
+        lab2det = detgeo.lab2det;
+    else
+        % Determine the det2lab transformation matrix from geometry.
+        % The u, v basis may not be orthonormal, not like the Lab reference which
+        % is an orthonormal basis by definition. Therefore here the decomposition
+        % of labXYZ into u and v vectors needs to be done adequately.
+        % The transformation matrix lab2det is the same as the pseudo-inverse
+        % of det2lab.
+        u = detgeo.detdiru;
+        v = detgeo.detdirv;
+        uv = u*v';
 
-if isfield(labgeo,'lab2det')
-    lab2det = labgeo.lab2det;
-else
-    % Determine the det2lab transformation matrix from geometry.
-    % The u,v basis may not be orthonormal, not like the Lab reference which
-    % is an orthonormal basis by definition. Therefore here the decomposition
-    % of labXYZ into u and v vectors needs to be done adequately.
-    % The transformation matrix lab2det is the same as the pseudo-inverse
-    % of det2lab.
-    u = labgeo.detdiru;
-    v = labgeo.detdirv;
-    uv = u*v';
-        
-    a = (u-v*uv)/(1-uv*uv);
-    b = v-a*uv;
-   
-    lab2det = [a/labgeo.pixelsizeu; b/labgeo.pixelsizev]';
-end
-
-
-% New coordinates
+        a = (u - v * uv) / (1 - uv * uv);
+        b = v - a * uv;
 
-if freevec_flag  % free vectors
-    
-    detUV = labXYZ*lab2det;
+        lab2det = [a / detgeo.pixelsizeu; b / detgeo.pixelsizev]';
+    end
 
-else  % offset vectors
+    % New coordinates
 
-    detUV = (labXYZ - labgeo.detorig(ones(size(labXYZ,1),1),:)) * lab2det;
-    
+    if (freevec_flag)  % free vectors
+        detUV = labXYZ * lab2det;
+    else  % offset vectors
+        detUV = (labXYZ - detgeo.detorig(ones(size(labXYZ, 1), 1), :)) * lab2det;
+    end
 end