some changes for gtCrystComputeExperimentalFamilyIntensities_v2

Signed-off-by: Zheheng Liu <zheheng.liu@esrf.fr>

zUtil_Cryst/gtCrystComputeExperimentalFamilyIntensities_v2.m

-function [fams_ints, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystComputeExperimentalFamilyIntensities_v2(phase_id, p, det_ind, varargin)
+function [fams_ints, fams_intsp, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystComputeExperimentalFamilyIntensities_v2(phase_id, p, det_ind, varargin)
 % FUNCTION GTCRYSTCOMPUTEEXPERIMENTALFAMILYINTENSITIES_V2
-% [fams_ints, fams_intsp, usable, fams_counts] = gtCrystComputeExperimentalFamilyIntensities_v2(phase_id, p, det_ind, varargin)
+% [fams_ints, fams_intsp, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystComputeExperimentalFamilyIntensities_v2(phase_id, p, det_ind, varargin)
 % INPUTS:
 %         phase_id       = <int>      Phase ID. The default is 1.
 %         p              = <struct>   The parameter structure.
 %         det_ind        = <int>      Detector index. The default is 1.
 % OPTIONAL INPUTS:
-%         only_selected  = <bool>     If true, only selected spots will be
-%                                     considered. (The default is false)
-%         deselect_annealing_twin_shared_spots
-%                        = <bool>     If true, the spots shared by
-%                                     annealing twins will be deselected.
+%         fams_ints_norm = <int>      Estimate the intensity of each hkl
+%                                     family by [1]: median spot intensity,
+%                                     or 2: average spot intensity.
+%         only_selected  = <bool>     [true]: only use selected spots;
+%                                     false: use all the included spots.
+%         use_spot2grain = <bool>     [true]: deselect the shared spots
+%                                     indicated by spot2grain.mat;
+%         mu_att         = <double>   Attenuation coefficient. If empty,
+%                                     absorption volume will be used.
+%         flat_image     =            Flat image used for direct beam profile.
+%                                     If empty, it will be generated automatically.
+%         gr_ids         = <int>      ID of used grains.
+%         usedfam        = <bool>     Used hkl families.
+%      fams_counts_thres = <int>      For each grain, only if the spots are
+%                                     more than this threshold, the hkl
+%                                     family will be used. Default: 4
+%         abs_vol        =            Absorption volume.
 %
 % 06-09-2021 by Zheheng. (based on Nicola's function gtCrystComputeExperimentalFamilyIntensities)
     if (~exist('phase_id', 'var') || isempty(phase_id))
@@ -25,11 +37,9 @@ function [fams_ints, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystCompu
 
     conf = struct(...
         'fams_ints_norm', 1, ... % 0 and 1 are median, 2 is average
-        'use_nullspace', true, ...
         'only_selected', true, ... % To use included spots or only use selected spots
         'use_spot2grain', true, ... % deselect the shared spots indicated by spot2grain.mat
         'mu_att', [], ... % 32.2686 cm^-1 43.57keV Ni
-        'verbose', false, ...
         'flat_image', [], ...
         'gr_ids', [], ...
         'usedfam', [], ...
@@ -47,12 +57,6 @@ function [fams_ints, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystCompu
         num_grains = numel(conf.gr_ids);
     end
 
-%     if conf.deselect_annealing_twin_shared_spots
-%         clusters = sfTwinClusters(conf.gr_ids, tot_grains, sample.phases{phase_id}.clusters);
-%     else
-%         clusters = num2cell(conf.gr_ids);
-%     end
-
     fams_ints = nan(num_grains, numel(p.cryst(phase_id).int));
 
     fams_counts = zeros(num_grains, numel(p.cryst(phase_id).int));
@@ -150,6 +154,7 @@ function [fams_ints, fams_ints_raw, usable, fams_counts, gr_vols] = gtCrystCompu
     [fams_ints, gr_vols] = gtMathsEstimateCoefVecFromIncompDataMatByNullSpace(fams_ints');
     % fams_ints contain 1/sin(2theta), which is part of Lorentz factor.
     fams_ints = fams_ints' ./ sind(2 * p.cryst(phase_id).theta(1:numel(fams_ints)));
+    fams_intsp = fams_ints(p.cryst(phase_id).thetatypesp);
 
     fprintf('Theoretical Intensities:\n');
     disp(p.cryst(phase_id).int / norm(p.cryst(phase_id).int));