Topotomo import: updated parameters import function

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

4_grains/gtGrainTopotomoUpdateParameters.m

-function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_basetilt, p, detgeo_tt, pl_ind, gr)
+function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_basetilt, p, detgeo_tt, pl_ind, gr, varargin)
+    conf = struct('check_flips', false, 'verbose', true);
+    conf = parse_pv_pairs(conf, varargin);
+
     if (~exist('p', 'var') || isempty(p))
         p = gtLoadParameters();
     end
 
+    o = GtConditionalOutput(conf.verbose);
+
     [tt_scan_dir, ~, ~] = fileparts(scan_xml);
-    fprintf('Importing Topotomo acquisition into current DCT parameters:\n')
-    fprintf(' - Path of Topotomo scan: %s\n', tt_scan_dir)
-    fprintf(' - Path of DCT scan: %s\n', p.acq(1).dir)
+    o.fprintf('Importing Topotomo acquisition into current DCT parameters:\n')
+    o.fprintf(' - Path of Topotomo scan: %s\n', tt_scan_dir)
+    o.fprintf(' - Path of DCT scan: %s\n', p.acq(1).dir)
     if (~isfield(p.acq(1), 'motors'))
-        fprintf(' - Reading DCT motor positions..')
+        o.fprintf(' - Reading DCT motor positions..')
         c = tic();
         xmlfname = fullfile(p.acq.dir, '0_rawdata', 'Orig', [p.acq.name '.xml']);
         acq_xml = gtLoadAcquisitionXML(xmlfname, false, false);
@@ -21,19 +26,20 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
             new_acq(ii_a) = gtAddMatFile(base_acq, p.acq(ii_a), true);
         end
         p.acq = new_acq;
-        fprintf('\b\b: Done in %g seconds.\n', toc(c))
+        o.fprintf('\b\b: Done in %g seconds.\n', toc(c))
     end
 
     acq_tt = p.acq(1);
 
-    fprintf(' - Reading Topotomo acquisition parameters..')
+    o.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))
+    o.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)
@@ -46,37 +52,42 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
         disp(' ')
     end
 
-%     % Check for flips:
-%     cfg_file = fullfile(tt_scan_dir, [acq_tt.name '.cfg']);
-%     fid = fopen(cfg_file);
-%     valid = true;
-%     file_content = {};
-%     while (valid)
-%         file_content{end+1} = fgets(fid); %#ok<AGROW>
-%         valid = file_content{end} ~= -1;
-%     end
-%     fclose(fid);
-%     file_content = [file_content{:}];
-%     horz_flip = regexp(file_content, 'ccd_flip_horz\s*(?<value>\d+)', 'names', 'once');
-%     vert_flip = regexp(file_content, 'ccd_flip_vert\s*(?<value>\d+)', 'names', 'once');
-%     if (str2double(horz_flip.value))
-%         acq_tt.detroi_u_off = acq_tt.true_detsizeu - acq_tt.detroi_u_off;
-%     end
-%     if (str2double(vert_flip.value))
-%         acq_tt.detroi_v_off = acq_tt.true_detsizev - acq_tt.detroi_v_off;
-%     end
+    % Automatically checking for flips:
+    if (conf.check_flips)
+        o.fprintf(' - Checking topotomo image flips..')
+        c = tic();
+        cfg_file = fullfile(tt_scan_dir, [acq_tt.name '.cfg']);
+        fid = fopen(cfg_file);
+        valid = true;
+        file_content = {};
+        while (valid)
+            file_content{end+1} = fgets(fid); %#ok<AGROW>
+            valid = file_content{end} ~= -1;
+        end
+        fclose(fid);
+        file_content = [file_content{:}];
+        horz_flip = regexp(file_content, 'ccd_flip_horz\s*(?<value>\d+)', 'names', 'once');
+        vert_flip = regexp(file_content, 'ccd_flip_vert\s*(?<value>\d+)', 'names', 'once');
+        if (str2double(horz_flip.value))
+            acq_tt.detroi_u_off = acq_tt.true_detsizeu - acq_tt.detroi_u_off;
+        end
+        if (str2double(vert_flip.value))
+            acq_tt.detroi_v_off = acq_tt.true_detsizev - acq_tt.detroi_v_off;
+        end
+        o.fprintf('\b\b: Done in %g seconds.\n', toc(c))
+    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];
 
+    % samr X and Y reversed, because the first on the right is the one
+    % applied first when doing SAM->LAB
     dct_samr = [p.acq(1).motors.samry, p.acq(1).motors.samrx];
     tt_samr = [acq_tt.motors.samry, acq_tt.motors.samrx];
 
-    dct_diffrz_start = p.acq(1).motors.diffrz;
-
+    % Translations should be handled a bit differently, especially if there
+    % were some initial tilts in the DCT acquisition
     acq_tt.sample_shifts = tt_samt - dct_samt;
-    % 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.range_basetilt = range_basetilt;
@@ -87,18 +98,21 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
     p.acq(end+1) = acq_tt;
     det_ind = numel(p.acq);
 
+    p.diffractometer(det_ind) = gtGeoDiffractometerDefinition('esrf_id11', ...
+        'axes_rotation_offset', p.acq(1).motors.diffrz, ...
+        'shifts_sam_stage', acq_tt.sample_shifts );
+
     p.detgeo(det_ind) = detgeo_tt;
+    % It might be that the Detector definition ha to be shifted as well!!
+%     p.detgeo(det_ind).detrefpos = p.detgeo(det_ind).detrefpos + p.diffractometer(det_ind).shifts_sam_stage;
+
     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))
-        fprintf(' - Guessing Topotomo pl_ind, with respect to DCT (for the range: [%g, %g])..', range_basetilt)
+        o.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, ...
-            'shifts_sam_stage', acq_tt.sample_shifts);
-
         diff = p.diffractometer(det_ind);
         tilts = p.acq(det_ind).sample_tilts;
         t = gtGeoDiffractometerTensor(diff, 'sam2lab', 'angles_sam_tilt', tilts);
@@ -107,9 +121,9 @@ function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_bas
         pl_labd = gtGeoSam2Lab(pl_samd_sign, t, p.labgeo, p.samgeo, true);
 
         angle = gtMathsVectorsAnglesDeg(diff.axes_rotation, pl_labd, false);
-        fprintf('\b\b: Done in %g seconds.\n', toc(c))
+        o.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))
+        o.fprintf('   + Chosen pl_ind: %d (%g deg)\n', pl_ind, angle(pl_ind))
     end
     p.acq(det_ind).pl_ind = pl_ind;
 end
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