Absorption reconstruction: added configuration side support for PSFs

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

5_reconstruction/gtAstraPrepareAbsorptionStack.m

@@ -23,6 +23,7 @@ function proj = gtAstraPrepareAbsorptionStack(parameters, varargin)
 conf = struct( ...
     'rot_angle', [], ...
     'rot_axis', [0 0 1], ...
+    'psf', [], ...
     'save', true, ...
     'filename', 'absorption_stack' );
 conf = parse_pv_pairs(conf, varargin);
@@ -39,12 +40,15 @@ if (isfield(parameters.rec, 'absorption'))
 else
     % Old style parameters
     warning('Old "rec" parameters')
-    rec_abs = struct(... % can be 'SIRT', '2DFBP' or '3DTV'
-        'algorithm', parameters.rec.method, ...
-        'num_iter', parameters.rec.abs_num_iter, ...
-        'interval', parameters.rec.absinterval, ...
-        'padding', 5, ...
-        'options', []);
+    % algorithm can be 'SIRT', '2DFBP' or '3DTV'
+    rec_abs = gtRecAbsorptionDefaultParameters(parameters.rec.method);
+    rec_abs.num_iter = parameters.rec.abs_num_iter;
+    rec_abs.interval = parameters.rec.absinterval;
+end
+if (~isempty(conf.psf))
+    rec_abs.psf = conf.psf;
+elseif (~isfield(rec_abs, 'psf'))
+    rec_abs.psf = [];
 end
 
 ang_incr = pi / acq.nproj;
@@ -104,10 +108,12 @@ for jj = 1:numel(imgs_nums)
     end
     [abs_img, info] = edf_read(absname, [], false, info);
 
-    stack(:, jj, :)  = -log(max(0.01,abs_img))';
+    stack(:, jj, :) = abs_img';
 
     fprintf(repmat('\b', 1, num_chars))
 end
+stack = -log(max(0.01, stack));
+
 fprintf('Done in %f seconds.\n', toc(c));
 
 % deal with the sense of the rotation
@@ -128,6 +134,7 @@ new_stack((end - rec_abs.padding + 1):end, :) = new_stack((end - rec_abs.padding
 
 proj = struct( ...
     'padding', rec_abs.padding, ...
+    'psf', rec_abs.psf, ...
     'rot_angle', conf.rot_angle, ... % Additional rotation
     'rot_axis', conf.rot_axis, ...   % Additional rotation
     'stack', new_stack, ...

5_reconstruction/gtRecAbsorptionDefaultParameters.m

@@ -8,7 +8,7 @@ function par_rec = gtRecAbsorptionDefaultParameters(algo)
         case {'SIRT', '2DFBP'}
             par_rec = struct(...
                 'algorithm', upper(algo), 'num_iter', 30, ...
-                'interval', 10, 'padding', 5, 'options', []);
+                'interval', 10, 'padding', 5, 'psf', [], 'options', []);
 
         case '3DTV'
             par_3DTV_rec_opts = struct( ...
@@ -18,7 +18,8 @@ function par_rec = gtRecAbsorptionDefaultParameters(algo)
                 'epsilon', 1e-4 ...
                 );
             par_rec = struct(...
-                'algorithm', upper(algo), 'num_iter', 30, 'interval', 10, ...
-                'padding', 5, 'options', par_3DTV_rec_opts);
+                'algorithm', upper(algo), 'num_iter', 100, ...
+                'interval', 10, 'padding', 5, 'psf', [], ...
+                'options', par_3DTV_rec_opts);
     end
 end