Topotomo import: fixes to previous commit

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

4_grains/gtGrainTopotomoUpdateParameters.m

@@ -12,6 +12,8 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
         c = tic();
         xmlfname = fullfile(p.acq.dir, '0_rawdata', 'Orig', [p.acq.name '.xml']);
         acq_xml = gtLoadAcquisitionXML(xmlfname, false, false);
+
+        % We now have to handle the fact that it is a legacy datastructure
         p.acq(1).motors = acq_xml.motors;
         base_acq = make_parameters(2);
         base_acq = base_acq.acq;
@@ -23,14 +25,26 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
     end
 
     acq_tt = p.acq(1);
-    acq_tt.type = 'topotomo';
 
     fprintf(' - Reading Topotomo acquisition parameters..')
     c = tic();
     topotomo_xml = gtLoadAcquisitionXML(scan_xml, false, false);
     acq_tt = gtAddMatFile(acq_tt, topotomo_xml, true, false, false);
+    acq_tt.type = 'topotomo'; % The XML tends to set it to 360degree
     acq_tt = gtAcqDefaultParameters(acq_tt);
+    acq_tt.collection_dir = tt_scan_dir;
     fprintf('\b\b: Done in %g seconds.\n', toc(c))
+    if (acq_tt.energy < 0)
+        disp(' ')
+        warning('Energy reported by the XML file is: %d, parsing info file...', acq_tt.energy)
+        info_file = fullfile(tt_scan_dir, [acq_tt.name '.info']);
+        fid = fopen(info_file);
+        info_line = fgetl(fid);
+        fclose(fid);
+        energy = regexp(info_line, 'Energy=\s*(?<value>.+)', 'names', 'once');
+        acq_tt.energy = str2double(energy.value);
+        disp(' ')
+    end
 
     dct_samt = [p.acq(1).motors.samtx, p.acq(1).motors.samty, p.acq(1).motors.samtz];
     tt_samt = [acq_tt.motors.samtx, acq_tt.motors.samty, acq_tt.motors.samtz];
@@ -44,7 +58,6 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
     % samr X and Y reversed, because the first on the right is the one
     % applied first when doing SAM->LAB
     acq_tt.sample_tilts = tt_samr - dct_samr;
-    acq_tt.sample_tilts
 
     acq_tt.range_basetilt = range_basetilt;
     acq_tt.nproj_basetilt = nproj_basetilt;
@@ -56,14 +69,15 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
 
     p.detgeo(det_ind) = detgeo_tt;
     p.recgeo(det_ind) = p.recgeo(1);
+    p.recgeo(det_ind).voxsize = mean([detgeo_tt.pixelsizeu, detgeo_tt.pixelsizev]) * [1, 1, 1];
 
-    if (~isempty(pl_ind))
-        p.acq(det_ind).pl_ind = pl_ind;
-    else
+    if (isempty(pl_ind))
         fprintf(' - Guessing Topotomo pl_ind, with respect to DCT (for the range: [%g, %g])..', range_basetilt)
         c = tic();
         % Trying to detect the tilts
-        p.diffractometer(det_ind) = gtGeoDiffractometerDefinition('esrf_id11', 'axes_rotation_offset', dct_diffrz_start);
+        p.diffractometer(det_ind) = gtGeoDiffractometerDefinition('esrf_id11', ...
+            'axes_rotation_offset', dct_diffrz_start, ...
+            'shifts_sam_stage', acq_tt.sample_shifts);
 
         diff = p.diffractometer(det_ind);
         tilts = p.acq(det_ind).sample_tilts;
@@ -75,6 +89,7 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
         angle = gtMathsVectorsAnglesDeg(diff.axes_rotation, pl_labd, false);
         fprintf('\b\b: Done in %g seconds.\n', toc(c))
         [~, pl_ind] = min(angle);
-        fprintf('   + Chosen pl_ind:  %d (%g deg)\n', pl_ind, angle(pl_ind))
+        fprintf('   + Chosen pl_ind: %d (%g deg)\n', pl_ind, angle(pl_ind))
     end
+    p.acq(det_ind).pl_ind = pl_ind;
 end
\ No newline at end of file

zUtil_Geo/gtGeoDiffractometerDefinition.m

 function diff = gtGeoDiffractometerDefinition(types, varargin)
     diff = struct( ...
-        'axes_basetilt', {zeros(1, 3)}, ...
-        'axes_rotation', {zeros(1, 3)}, ...
-        'axes_sam_tilt', {zeros(0, 3)}, ... % They are applied in reverse order (last->first) for SAM->LAB transformations in gtGeoDiffractometerTensor
-        'origin_basetilt', {zeros(1, 3)}, ...
-        'origin_rotation', {zeros(1, 3)}, ...
-        'origin_sam_tilt', {zeros(0, 3)}, ...
-        'limits_sam_tilt', {zeros(0, 2)}, ...
-        'shifts_sam_stage', {zeros(0, 3)} );
-
-    conf = struct( ...
+        'axes_basetilt', zeros(1, 3), ...
+        'axes_rotation', zeros(1, 3), ...
+        'axes_sam_tilt', zeros(0, 3), ... % They are applied in reverse order (last->first) for SAM->LAB transformations in gtGeoDiffractometerTensor
+        'origin_basetilt', zeros(1, 3), ...
+        'origin_rotation', zeros(1, 3), ...
+        'origin_sam_tilt', zeros(0, 3), ...
+        'limits_sam_tilt', zeros(0, 2), ...
+        'shifts_sam_stage', zeros(0, 3), ...
         'axes_rotation_offset', [], ...
-        'axes_sam_tilt_offset', []);
-    conf = parse_pv_pairs(conf, varargin);
+        'axes_sam_tilt_offset', [] );
 
-    if (iscell(types))
-        diff(2:numel(types)) = diff;
-        for ii = 1:numel(types)
-            diff(ii) = gtAcqDiffractometerDefinition(types{ii});
-        end
-    else
-        switch (lower(types))
-            case 'esrf_id11'
-                diff.axes_basetilt = [0, 1, 0];
-                diff.axes_rotation = [0, 0, 1];
-                diff.axes_sam_tilt = [0, 1, 0; 1, 0, 0];
-                diff.origin_sam_tilt = [0, 0, 0; 0, 0, 0];
-                diff.limits_sam_tilt = [-15, 15; -20 20];
+    diff = parse_pv_pairs(diff, varargin);
 
-                if (~isempty(conf.axes_sam_tilt_offset))
-                    rot = eye(3);
-                    for ii = (size(diff.axes_sam_tilt, 1)-1):-1:1
-                        rotcomp = gtMathsRotationMatrixComp(diff.axes_sam_tilt(ii, :), 'row');
-                        rot_ii = gtMathsRotationTensor(conf.axes_sam_tilt_offset(ii), rotcomp);
-                        rot = rot * rot_ii;
-                    end
-                    diff.axes_sam_tilt = diff.axes_sam_tilt * rot;
-                end
+    switch (lower(types))
+        case 'esrf_id11'
+            diff.axes_basetilt = [0, 1, 0];
+            diff.axes_rotation = [0, 0, 1];
+            diff.axes_sam_tilt = [0, 1, 0; 1, 0, 0];
+            diff.origin_sam_tilt = [0, 0, 0; 0, 0, 0];
+            diff.limits_sam_tilt = [-15, 15; -20 20];
+        otherwise
+            error('gtAcqDiffractometerDefinition:wrong_argument', ...
+                'Unknown diffractometer: %s', types)
+    end
 
-                if (~isempty(conf.axes_rotation_offset))
-                    rotcomp = gtMathsRotationMatrixComp(diff.axes_rotation, 'row');
-                    rot = gtMathsRotationTensor(conf.axes_rotation_offset, rotcomp);
-                    diff.axes_sam_tilt = diff.axes_sam_tilt * rot;
-                end
-            otherwise
-                error('gtAcqDiffractometerDefinition:wrong_argument', ...
-                    'Unknown diffractometer: %s', types)
+    if (~isempty(diff.axes_sam_tilt_offset))
+        rot = eye(3);
+        for ii = (size(diff.axes_sam_tilt, 1)-1):-1:1
+            rotcomp = gtMathsRotationMatrixComp(diff.axes_sam_tilt(ii, :), 'row');
+            rot_ii = gtMathsRotationTensor(diff.axes_sam_tilt_offset(ii), rotcomp);
+            rot = rot * rot_ii;
         end
+        diff.axes_sam_tilt = diff.axes_sam_tilt * rot;
+
+        rotcomp = gtMathsRotationMatrixComp(diff.axes_sam_tilt(end, :), 'row');
+        rot_ii = gtMathsRotationTensor(diff.axes_sam_tilt_offset(end), rotcomp);
+        rot = rot_ii * rot;
+        diff.shifts_sam_stage = diff.shifts_sam_stage * rot;
+    end
+
+    if (~isempty(diff.axes_rotation_offset))
+        rotcomp = gtMathsRotationMatrixComp(diff.axes_rotation, 'row');
+        rot = gtMathsRotationTensor(diff.axes_rotation_offset, rotcomp);
+        diff.axes_sam_tilt = diff.axes_sam_tilt * rot;
+        diff.shifts_sam_stage = diff.shifts_sam_stage * rot;
     end
 end