Better handle sample shifts correction (activate in p.acq)

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

3_pairmatchingGUI/gtMatchGetSampleShifts.m

@@ -19,17 +19,6 @@ function [shifts_lab, shifts_sam, abspos, relpos] = gtMatchGetSampleShifts(param
 
     filename = sprintf('%s/%s%04d.edf', base_dir, acq_name, conf.offset_pos);
 
-    % Let's handle some special case
-    if (~exist(filename, 'file'))
-        if (~exist('omega_values', 'var') || isempty(omega_values))
-            omega_values = 0;
-        end
-        shifts_lab = zeros(numel(omega_values), 3);
-        shifts_sam = zeros(numel(omega_values), 3);
-        abspos = zeros(numel(omega_values), 3);
-        relpos = zeros(numel(omega_values), 3);
-        return
-    end
     info     = edf_info(filename);
     offset   = [info.motor.samtx, info.motor.samty, info.motor.samtz];
 

3_pairmatchingGUI/gtMatchInitialize.m

@@ -29,6 +29,8 @@ end
 
 check = inputwdefault('Do you want to reset all the parameters for matching? [y/n]', 'n');
 if (strcmpi(check, 'y'))
+     mym(sprintf('truncate %s', parameters.acq.pair_tablename));
+     %mym(sprintf('truncate %s', parameters.acq.calib_tablename));
      parameters.match = gtMatchDefaultParametersGUI();
      parameters.match.thetalimits = 0.5 * ...
          [parameters.labgeo.detanglemin, parameters.labgeo.detanglemax];
@@ -85,8 +87,12 @@ handles.matchparnames = parnames;
 %%% "update_ref_pos"... leading to sample displacements at reference
 %%% positions
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-handles.shifts = gtMatchGetSampleShifts(parameters);
-
+if isfield(parameters.acq, 'correct_sample_shifts')
+    handles.shifts = gtMatchGetSampleShifts(parameters);
+else
+    tot_proj = gtAcqTotNumberOfImages(parameters);
+    handles.shifts = zeros(tot_proj, 3);
+end
 
 % Get parameters description
 parlist = build_list_v2();

4_grains/GtThreshold.m

@@ -503,8 +503,8 @@ classdef GtThreshold < handle
 
             threshold_val = meanvol - par_thr.percentile/100 * stdvol;
 
-            %seed = round([size(vol, 1), size(vol, 2), size(vol, 3)] / 2);
-            seed = vol > maxvol * 0.7;
+            seed = round([size(vol, 1), size(vol, 2), size(vol, 3)] / 2);
+            %seed = vol > maxvol * 0.7;
             grain_seg = obj.segmentAndDoMorph(grain_rec, threshold_val, ...
                 par_thr.do_morph_recon, seed);
         end

zUtil_DB/gtDBCreateCalibrationTable_v3.m

@@ -11,9 +11,10 @@ function gtDBCreateCalibrationTable_v3(name)
 
 fprintf('Working on %s\n',name);
 
-mym('close')
-mym('open','mysql.esrf.fr','gtadmin','gtadmin')
-mym('use graintracking')
+gtDBConnect;
+%mym('close')
+%mym('open','mysql.esrf.fr','gtadmin','gtadmin')
+%mym('use graintracking')
 
 tablename_calibration=sprintf('%scalibration',name);
 

zUtil_Deformation/Gt6DReconstructionAlgorithmFactory.m

@@ -849,18 +849,25 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
             labgeo = self.parameters.labgeo;
             samgeo = self.parameters.samgeo;
 
+            om = zeros(numel(ab_sel), num_ors);
+
+            for ii_o = 1:num_ors
+                om(:, ii_o) = ors_allblobs(ii_o).omega(ab_sel);
+            end
+            if isfield(self.parameters.acq, 'correct_sample_shifts')
+                    [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, om(:));
+            else
+                    shifts_sam = zeros(numel(om(:)), 3);
+            end
             % Dimensions are: <blobs x uv x edges x orientations>
             uv_tab = zeros(num_blobs, 2, 8, num_ors);
             for ii_o = 1:num_ors
                 dveclab_t = ors_allblobs(ii_o).dvec(ab_sel, :)';
 
-                om = ors_allblobs(ii_o).omega(ab_sel);
-                [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, om);
-
-                % It only works if there are no offsets in the tilt axes
                 rot_l2s = ors_allblobs(ii_o).srot(:, :, ab_sel);
                 rot_s2l = permute(rot_l2s, [2 1 3]);
-                gcsam_v = ref_gr.center(ones(1, size(rot_l2s, 3)), :) + shifts_sam;
+                shifts_sam_ii_o = shifts_sam((ii_o - 1) * numel(ab_sel) +1 : ii_o * numel(ab_sel), :);
+                gcsam_v = ref_gr.center(ones(1, size(rot_l2s, 3)), :) + shifts_sam_ii_o;
 
                 ii_e = 1;
 
@@ -1018,27 +1025,33 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
 
             ab_sel = ond(inc(sel));
 
-            num_orients = numel(ors_allblobs);
+            num_ors = numel(ors_allblobs);
+            om = zeros(numel(ab_sel), num_ors);
 
-            geoms = cell(num_orients, 1);
-            for ii_o = 1:num_orients
+            for ii_o = 1:num_ors
+                om(:, ii_o) = ors_allblobs(ii_o).omega(ab_sel);
+            end
+            if isfield(self.parameters.acq, 'correct_sample_shifts')
+                    [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, om(:));
+            else
+                    shifts_sam = zeros(numel(om(:)), 3);
+            end
+            geoms = cell(num_ors, 1);
+            for ii_o = 1:num_ors
                 dvec_sam = ors_allblobs(ii_o).dvecsam(ab_sel, :);
                 rot_w_l2s = ors_allblobs(ii_o).srot(:, :, ab_sel);
 
-                % account for sample shifts relative to rotation axis
-                [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, ors_allblobs(ii_o).omega(ab_sel));
-
                 % Dimensions are: <blobs x uv x [min, max]>
                 proj_or_lims = projs_uv_lims(:, :, :, ii_o);
                 bb_bls_uv = [proj_or_lims(:, :, 1), proj_or_lims(:, :, 2) - proj_or_lims(:, :, 1) + 1];
-
+                shifts_sam_ii_o = shifts_sam((ii_o - 1) * numel(ab_sel) +1 : ii_o * numel(ab_sel), :);
                 proj_geom = gtGeoProjForReconstruction(...
                     dvec_sam, rot_w_l2s, ref_gr.center, bb_bls_uv, [], ...
                     self.parameters.detgeo(det_ind), ...
                     self.parameters.labgeo, ...
                     self.parameters.samgeo, ...
                     self.parameters.recgeo(self.det_index(1)), ...
-                    'ASTRA_grain', shifts_sam);
+                    'ASTRA_grain', shifts_sam_ii_o);
 
                 if (self.volume_downscaling > 1)
                     proj_geom(:, 4:12) = proj_geom(:, 4:12) / self.volume_downscaling;
@@ -1151,7 +1164,11 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                     self.parameters.labgeo, self.parameters.samgeo, true);
 
                 % accounting for sample shifts relative to rotation axis
-                [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, ors_allblobs(ii_o).omega(ab_sel(ind_of_blob)));
+                if isfield(self.parameters.acq, 'correct_sample_shifts')
+                    [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, ors_allblobs(ii_o).omega(ab_sel(ind_of_blob)));
+                else
+                    shifts_sam = zeros(numel(ors_allblobs(ii_o).omega(ab_sel(ind_of_blob))), 3);
+                end
 
                 % Dimensions are: <blobs x uv x [min, max]>
                 proj_or_lims = projs_uv_lims(:, :, :, ii_o);
@@ -1262,7 +1279,11 @@ classdef Gt6DReconstructionAlgorithmFactory < handle
                     self.parameters.labgeo, self.parameters.samgeo, true);
 
                 % accounting for sample shifts relative to rotation axis
-                [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, ors_allblobs(ii_o).omega(ab_sel(ind_of_blob)));
+                if isfield(self.parameters.acq, 'correct_sample_shifts')
+                    [~, shifts_sam] = gtMatchGetSampleShifts(self.parameters, ors_allblobs(ii_o).omega(ab_sel(ind_of_blob)));
+                else
+                    shifts_sam = zeros(numel(ors_allblobs(ii_o).omega(ab_sel(ind_of_blob))), 3);
+                end
 
                 % Dimensions are: <blobs x uv x [min, max]>
                 proj_or_lims = projs_uv_lims(:, :, :, ii_o);