diff --git a/4_grains/gtGrainTopotomoUpdateParameters.m b/4_grains/gtGrainTopotomoUpdateParameters.m
index 4430a9137a44a21e3cc4afa1ec7a323585bad43c..9edb332970cd424bcca3e6c9cf2ad1d7dbfddc7c 100644
--- a/4_grains/gtGrainTopotomoUpdateParameters.m
+++ b/4_grains/gtGrainTopotomoUpdateParameters.m
@@ -1,14 +1,19 @@
-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
\ No newline at end of file