Fwdproj of deformation volumes: updated and fixed a few small things

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

7_fed2/gtFedActiveVolumeVoxels.m

@@ -45,7 +45,7 @@ function active_vol = gtFedActiveVolumeVoxels(phase_vol, parameters_inline, vara
 
     vol_size_xyz = size(phase_vol.intvol);
 
-    det_mask = zeros(vol_size_xyz(2), vol_size_xyz(3));
+    det_mask = zeros(vol_size_xyz(2), vol_size_xyz(3), 'single');
 
     if (isempty(conf.vert_slice))
         conf.vert_slice = round(vol_size_xyz(2) / 2);
@@ -69,7 +69,7 @@ function active_vol = gtFedActiveVolumeVoxels(phase_vol, parameters_inline, vara
             det_mask(conf.vert_slice, :) = v;
         case 'line'
             % Creation of the line mask: 1 vx vertical thickness
-            det_mask(conf.vert_slice, :) = true;
+            det_mask(conf.vert_slice, :) = 1;
     end
     fprintf('\b\b: Done in %g seconds.\n', toc(c))
 

7_fed2/gtFedCreateGrainParsMasked.m

 function fedpars = gtFedCreateGrainParsMasked(grain, active_vol, dmvol, parameters, varargin)
 % [fedpars, dmvol, active_vol] = gtFedCreateGrainParsMasked(grain, grain_rec, parameters, varargin)
 
-    conf = struct(...
-        'is_real_data', [], ...
+    conf = struct( ...
         'keep_ondet', true, ...
-        'volume_super_sampling', []);
+        'volume_super_sampling', 1);
     conf = parse_pv_pairs(conf, varargin);
 
     %%%%%%%%%%%%%%%%%%%%%%%%%
@@ -31,76 +30,57 @@ function fedpars = gtFedCreateGrainParsMasked(grain, active_vol, dmvol, paramete
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     % Creation of actual fedpars structure
     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    disp('- Creating fedpars structure ...')
+    fprintf('Creating fedpars structure..')
+    c = tic();
 
     % x, y, z no. of voxels in the grain
-    fedpars.grainsize                  = size(active_vol);
-
-    % x, y, z no. of voxels in a volume element
-    fedpars.gvsize                     = fedpars.grainsize ./ size(active_vol);
+    fedpars.grainsize = size(active_vol);
 
     % Active deformation components. Total number is 9.
     % In case of rotations only (should be our case):
-    fedpars.dcomps                     = [true(1, 3) false(1, 6)];
-
-    % Origin voxel in the SAM reference
-    % Using original intensities volume size to retrieve the correct shift
-    vc = gtGeoSam2Sam(size(active_vol) / 2, parameters.recgeo(1), parameters.samgeo, false);
-    vs = [0 0 0];
-    %     vs = gtGeoSam2Sam(gr_seg.segbb(1:3), parameters.recgeo, parameters.samgeo, false);
-    fedpars.vox000sam                  = grain.center - vc + vs;
+    fedpars.dcomps = [true(1, 3), false(1, 6)];
 
     % Class of strain states
-    fedpars.gvtype                     = class(active_vol);
-
-    % Real or simulated data?
-    if (isempty(conf.is_real_data))
-        is_real = inputwdefault('Are you working with real data? [y/n]', 'y');
-        fedpars.is_real_data = ~strcmpi(is_real, 'n');
-    else
-        fedpars.is_real_data = conf.is_real_data;
-    end
+    fedpars.gvtype = class(active_vol);
 
     % Generate random deformation components
     if (~exist('dmvol', 'var') || isempty(dmvol))
-
         % Type of deformation applied
-        fedpars.deftype                = 'smooth';
         deftype = inputwdefault(['Specify the type of deformation ' ...
             'applied: smooth (s) or realistic (r):', 's']);
-
-        if (strcomp(deftype, 'r'))
-            fedpars.deftype            = 'realistic';
+        switch (lower(deftype))
+            case 'r'
+                fedpars.deftype = 'realistic';
+            otherwise
+                fedpars.deftype = 'smooth';
         end
 
         % Random strain definition mode
-        fedpars.randdefmode            = 'smooth';
         randdefmode = input(['Specify the random strain definition mode: ' ...
             'smooth (s) or interpolated (i):'], 's');
 
-        if (strcompi(randdefmode, 'i'))
-            fedpars.randdefmode        = 'interp';
+        switch (lower(randdefmode))
+            case 'i'
+                fedpars.randdefmode = 'interp';
+            otherwise
+                fedpars.randdefmode = 'smooth';
         end
 
         % Maximum absolute deformation gradient
-        fedpars.dappgradlim            = 2e-4 * ones(size(fedpars.dcomps));    % guess: verify
+        fedpars.dappgradlim = 2e-4 * ones(size(fedpars.dcomps)); % guess: verify
 
         % Maximum absolute deformation value which can be randomly generated
-        fedpars.dapplim                = 5e-3 * ones(size(fedpars.dcomps));    % guess: verify
+        fedpars.dapplim = 5e-3 * ones(size(fedpars.dcomps)); % guess: verify
     end
 
-    % ID of blobs to load for figure
-    fedpars.loadbl = [];
-
-    % Detector parameters
-    ndet = numel(parameters.detgeo);
-
     if (~conf.keep_ondet)
         grain_fwd = gtCalculateGrain(grain, parameters);
     end
 
-    for ii_det = 1:ndet
+    % Detector parameters
+    ndet = numel(parameters.detgeo);
 
+    for ii_det = 1:ndet
         if (conf.keep_ondet && isfield(grain, 'proj') && (numel(grain.proj) >= ii_det))
             if (isfield(grain.proj, 'ondet') ...
                     && (~isempty(grain.proj(ii_det).ondet)))
@@ -124,20 +104,15 @@ function fedpars = gtFedCreateGrainParsMasked(grain, active_vol, dmvol, paramete
     end
 
     % Types for blobs intensities
-    fedpars.bltype                     = 'single';
+    fedpars.bltype = 'single';
 
     % Deformation method for calculation of deformation tensor
-    fedpars.defmethod                  = 'rod_rightstretch';
-%     fedpars.defmethod                  = 'small';
+    fedpars.defmethod = 'rod_rightstretch';
 
     % Algorithm for blobs smoothing
-    fedpars.intsmoothalg               = 'none';
+    fedpars.intsmoothalg = 'none';
 
-    if (~isempty(conf.volume_super_sampling))
-        fedpars.volume_super_sampling = conf.volume_super_sampling;
-    else
-        fedpars.volume_super_sampling = 1;
-    end
+    fedpars.volume_super_sampling = conf.volume_super_sampling;
 
-    disp('Done')
+    fprintf('\b\b: Done in %g seconds.\n', toc(c))
 end