missing function for pairmatch - sample shifts

Signed-off-by: Wolfgang Ludwig <wolfgang.ludwig@esrf.fr>

3_pairmatchingGUI/gtMatchGetSampleShifts.m

+function [shifts_lab, shifts_sam, abspos, relpos] = gtMatchGetSampleShifts(parameters, omega_values, varargin)
+%   function [shifts_lab, shifts_sam, abspos, relpos] = gtMatchGetSampleShifts(parameters, omega_values)
+%
+    conf.display = false;
+    conf.offset_pos = 0;
+    conf = parse_pv_pairs(conf, varargin);
+
+    if (~exist('parameters', 'var') || isempty(parameters))
+        parameters=gtLoadParameters;
+    end
+    
+    tot_proj = 2 * parameters.acq.nproj;
+    omstep   = 360 / tot_proj;
+    refon    = parameters.acq.refon;
+    ref_grps = tot_proj/refon;
+
+    filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, conf.offset_pos);
+    info     = edf_info(filename);
+    offset   = [info.motor.samtx, info.motor.samty, info.motor.samtz];
+
+    shifts_lab  = zeros(tot_proj, 3);
+    shifts_sam  = zeros(tot_proj, 3);
+    refpos      = zeros(ref_grps, 3);
+    rotcomp = gtMathsRotationMatrixComp(parameters.labgeo.rotdir, 'row');
+
+    for ii = 1 : ref_grps
+        filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, (ii-1) * refon);
+        info = edf_info(filename);
+        abspos(ii, :) = [info.motor.samtx, info.motor.samty, info.motor.samtz];
+        relpos(ii, :) = abspos(ii, :) - offset;
+        for jj = 1 : refon
+            im_num = (ii - 1) * refon + jj - 1;
+            omega = omstep * im_num;
+            rottens = gtMathsRotationTensor(omega, rotcomp);
+            shifts_lab(im_num + 1, :) = relpos(ii, :) * rottens * eye(3);
+            shifts_sam(im_num + 1, :) = relpos(ii, :);
+        end
+    end
+    % handle 360 degree image after scan
+    filename = sprintf('%s/0_rawdata/Orig/%s%04d.edf', parameters.acq.dir, parameters.acq.name, tot_proj);
+    info = edf_info(filename);
+    abspos(ref_grps + 1, :) = [info.motor.samtx, info.motor.samty, info.motor.samtz];
+    relpos(ref_grps + 1, :) = abspos(ref_grps + 1, :) - offset;
+    shifts_lab(tot_proj + 1, :) = relpos(ref_grps + 1, :) * eye(3);
+    shifts_sam(tot_proj + 1, :) = relpos(ref_grps + 1, :);
+
+    if (exist('omega_values', 'var') & ~isempty(omega_values))
+        % set NaN entries in omega to 0;
+        nans = isnan(omega_values);
+        omega_values(nans) = 0;
+        % transform into image_numbers
+        im_num = round(omega_values / omstep) + 1;
+        shifts_lab = shifts_lab(im_num, :);
+        shifts_sam = shifts_sam(im_num, :);
+        refgrp = floor(im_num / refon) + 1;
+        abspos = abspos(refgrp, :);
+        relpos = relpos(refgrp, :);
+    end
+    if conf.display
+        figure;
+        plot(shifts_lab(:, 1)', shifts_lab(:, 2)', '*')
+    end
+end
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