Toptomo: added parameters import function

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

1_preprocessing/gtSetup_Utils/gtAcqDefaultParameters.m

@@ -5,47 +5,49 @@ function par_acq = gtAcqDefaultParameters(par_acq)
 %     -----------------------------------------
 %
 %     Version 001 15-05-2012 by LNervo
-%       Splitted from gtLoadAcquisitionXML()
-
-
-par_acq.true_detsizeu  = 2048;
-par_acq.true_detsizev  = 2048;
-
-% interlacing parameters
-% try to guess whether the scan is interlaced
-if exist([par_acq.name '0_0000.edf'], 'file')
-    par_acq.interlaced_turns = 1; % assume one extra turn is reasonable guess
-    disp('This looks like an interlaced scan! Doubling nproj...')
-    par_acq.nproj            = par_acq.nproj*2;
-else
-    par_acq.interlaced_turns = 0;
+%       Split from gtLoadAcquisitionXML()
+
+%     is_dct = ismember(lower(par_acq.type), {'360degree', '180degree', 'dct'});
+    is_dct_360 = ismember(lower(par_acq.type), {'360degree', 'dct'});
+
+    par_acq.true_detsizeu = 2048;
+    par_acq.true_detsizev = 2048;
+
+    % interlacing parameters
+    % try to guess whether the scan is interlaced
+    if (is_dct_360 && exist([par_acq.name '0_0000.edf'], 'file'))
+        par_acq.interlaced_turns = 1; % assume one extra turn is reasonable guess
+        disp('This looks like an interlaced scan! Doubling nproj...')
+        par_acq.nproj            = par_acq.nproj * 2;
+    else
+        par_acq.interlaced_turns = 0;
+    end
+
+    % mono tuned during scan? If yes, put the number of ref groups
+    par_acq.mono_tune = 0;
+    % if we have a horizontal rotation axis we turn the images during the copying process
+    par_acq.rotation_axis = 'vertical';
+    par_acq.distortion = 'none';
+
+    %   deal with flips and rotations
+    % subsequently, deal with flips and rotations, scans without direct beam
+    par_acq.flip_images = false;
+    par_acq.no_direct_beam = false;
+
+    % rotate images to the gt coordinate system !!! Help !!!
+    par_acq.rotation_direction = 'clockwise';
+    par_acq.detector_definition = 'inline';
+
+    % Images will be shifted in gtCreateFullLive to have rotation axis in center...
+    par_acq.rotu = par_acq.xdet / 2 + 0.5;
+    par_acq.rotx = par_acq.rotu;
+    par_acq.maxradius = max(par_acq.xdet, par_acq.ydet) / 2 * sqrt(2);
+    par_acq.beamchroma = 'mono';
+
+    % if it is 360degree data, we need a pair table
+    if (is_dct_360)
+        % pair tablename can be derived from the scan name
+        par_acq.pair_tablename  = [par_acq.name 'spotpairs'];
+        par_acq.calib_tablename = [par_acq.name 'paircalib'];
+    end
 end
-
-% mono tuned during scan? If yes, put the number of ref groups
-par_acq.mono_tune      = 0;
-% if we have a horizontal rotation axis we turn the images during the copying process
-par_acq.rotation_axis  = 'vertical';
-par_acq.distortion     = 'none';
-
-%   deal with flips and rotations
-% subsequently, deal with flips and rotations, scans without direct beam
-par_acq.flip_images    = false;
-par_acq.no_direct_beam = false;
-
-% rotate images to the gt coordinate system !!! Help !!!
-par_acq.rotation_direction  = 'clockwise';
-par_acq.detector_definition = 'inline';
-
-par_acq.rotu        = par_acq.xdet/2+0.5;   % Images will be shifted in gtCreateFullLive to have rotation axis in center...
-par_acq.rotx        = par_acq.rotu;
-par_acq.maxradius   = max(par_acq.xdet,par_acq.ydet)/2*sqrt(2);
-par_acq.beamchroma  = 'mono';
-
-% if it is 360degree data, we need a pair table
-if strcmpi(par_acq.type, '360degree')
-    % pair tablename can be derived from the scan name
-    par_acq.pair_tablename  = [par_acq.name 'spotpairs'];
-    par_acq.calib_tablename = [par_acq.name 'paircalib'];
-end
-
-end % end of function

1_preprocessing/gtSetup_Utils/gtLoadAcquisitionXML.m

-function acq = gtLoadAcquisitionXML(xmlfname, interactive)
+function acq = gtLoadAcquisitionXML(xmlfname, interactive, verbose)
 % FUNCTION gtLoadAcquisitionXML  Try to read the .xml file that may be present
 %     params_acq = gtLoadAcquisitionXML(xmlfname, interactive)
 %     --------------------------------------------------------
@@ -6,11 +6,16 @@ function acq = gtLoadAcquisitionXML(xmlfname, interactive)
 %     Version 002 15/05/2012 by LNervo
 %       Split acq parameters from parameters read from xml file
 
+    if (~exist('verbose', 'var') || isempty(verbose))
+        verbose = true;
+    end
     % try to read the .xml file that may be present
     acq = [];
     
     if exist(xmlfname,'file')
-        disp('Reading parameters from xml file');
+        if (verbose)
+            disp('Reading parameters from xml file');
+        end
         tmpxml = xml_read(xmlfname);
         tmpxml = tmpxml.acquisition;
 

4_grains/gtGrainTopotomoUpdateParameters.m

+function p = gtGrainTopotomoUpdateParameters(scan_xml, range_basetilt, nproj_basetilt, p, detgeo_tt, pl_ind, gr)
+    if (~exist('p', 'var') || isempty(p))
+        p = gtLoadParameters();
+    end
+
+    [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)
+    if (~isfield(p.acq(1), 'motors'))
+        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);
+        p.acq(1).motors = acq_xml.motors;
+        base_acq = make_parameters(2);
+        base_acq = base_acq.acq;
+        for ii_a = numel(p.acq):-1:1
+            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))
+    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 = gtAcqDefaultParameters(acq_tt);
+    fprintf('\b\b: Done in %g seconds.\n', toc(c))
+
+    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];
+
+    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;
+
+    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.sample_tilts
+
+    acq_tt.range_basetilt = range_basetilt;
+    acq_tt.nproj_basetilt = nproj_basetilt;
+
+    acq_tt.dist = detgeo_tt.detrefpos(1);
+
+    p.acq(end+1) = acq_tt;
+    det_ind = numel(p.acq);
+
+    p.detgeo(det_ind) = detgeo_tt;
+    p.recgeo(det_ind) = p.recgeo(1);
+
+    if (~isempty(pl_ind))
+        p.acq(det_ind).pl_ind = pl_ind;
+    else
+        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);
+
+        diff = p.diffractometer(det_ind);
+        tilts = p.acq(det_ind).sample_tilts;
+        t = gtGeoDiffractometerTensor(diff, 'sam2lab', true, 'angles_sam_tilt', tilts);
+
+        pl_samd_sign = gr.allblobs(1).pl;
+        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))
+        [~, pl_ind] = min(angle);
+        fprintf('   + Chosen pl_ind:  %d (%g deg)\n', pl_ind, angle(pl_ind))
+    end
+end
\ No newline at end of file

zUtil_Geo/gtGeoDiffractometerDefinition.m

-function diff = gtGeoDiffractometerDefinition(types)
+function diff = gtGeoDiffractometerDefinition(types, varargin)
     diff = struct( ...
         'axes_basetilt', {zeros(1, 3)}, ...
         'axes_rotation', {zeros(1, 3)}, ...
@@ -6,8 +6,14 @@ function diff = gtGeoDiffractometerDefinition(types)
         '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_rotation_offset', [], ...
+        'axes_sam_tilt_offset', []);
+    conf = parse_pv_pairs(conf, varargin);
+
     if (iscell(types))
         diff(2:numel(types)) = diff;
         for ii = 1:numel(types)
@@ -21,6 +27,22 @@ function diff = gtGeoDiffractometerDefinition(types)
                 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];
+
+                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
+
+                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)