phasor_series.m

%% Prepare meta data
clear;
close all;

addpath('classDef');
addpath('functions');
addpath('reconstructionPatterns');

input_param.data_path         = 'E:\DDzhigaev\WorkFolder\Projects\Flexo-photovoltaics\Experiments\APS_34IDC_2018_run3\analysis\processed\Sample3__78  82  86  90  94\Copy_of_data.mat';
% input_param.data_path         = 'data_test.mat';
input_param.save_path         = fullfile('/data','netapp','dzhigd','Experiments','34_IDC_APS_STO_AFM_run3_2018','analysis','processed');
input_param.white_field_path  = fullfile('/data/netapp/dzhigd/Experiments/34_IDC_APS_STO_AFM_run3_2018/APS_34IDC_viewer','white_field_1.mat');
input_param.dark_field_path   = fullfile('/data/netapp/dzhigd/Experiments/34_IDC_APS_STO_AFM_run3_2018/APS_34IDC_viewer','dark_field_1.mat');
input_param.mask_path         = '/data/netapp/dzhigd/Experiments/34_IDC_APS_STO_AFM_run3_2018/analysis/processed/Sample1_B_pristine_mask.mat';
input_param.beamtime_id       = 'Dzhigaev1118';
input_param.sample_name       = 'test';
input_param.gpu               = 1;

% Experimental parameters
input_param.energy            = 11000;   % [eV]
input_param.sample_detector_d = 1.95;   % [m]
input_param.detector_pitch    = 55e-6; % [m]
input_param.angular_step      = -0.005; % [degree]
input_param.energy_step       = [];     % [eV]

% Experimental geometry - very important for coordinate transformations
% First two dimensions in the data is the detector plane
% The rocking curve direction goes along 3rd dimension of the data
input_param.beamline          = '34idc';
input_param.delta             = -0.795;
input_param.gamma             = -33.3149;
input_param.theta             = -0.2;
input_param.chi               = 90;
input_param.phi               = -16.1;
input_param.mu                = 0.0;
input_param.rocking_motor     = 'dphi';

% PHASOR parameters
input_param.binning           = []; % in the detector plane
input_param.metric.type       = 'both';
input_param.partial_coherence = 1;

n = 1;

for jj = 1:n
    jj    
    % Prepare PHASOR object

    % The object has to be created
    ph = Phasor(input_param);

    % just loading the mat file with cleaning from nans and recording data gaps as regions with -1 values
    ph.load_mat; 

    ph.center_data;
    
    % create support 
    % default: autocorrelation with treshold of 0.1
    % <path> : load support from outside
    ph.create_support();

    % create object 
    % default: constant amplitude of 1 multiplied by support
    % <type> : % amp  - random amplitude, constant phase
               % ph   - random phase, constant amplitude
               % amph - random phase, random amplitude
               % flat - constant amplitude
    ph.create_object('flat');

    % The package can be used in various templates of scripts going below
    % %% Simple Phase retrieval pattern

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % GPU part - common for any pattern %%%%%%%%%%%%%%%%%%
    if input_param.gpu
        ph.ram2gpu;
    end
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    %>>>>>>>>>>>>>>>>>>> Execute phasing pattern >>>>>>>>>>>>>>>>>>>>>>>>%
    tripleLoop_STO_78_94;
    % jesseClarckStandart
    %>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>%

    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    % GPU part - common for any pattern %%%%%%%%%%%%%%%%%%
    if input_param.gpu
        ph.gpu2ram;
    end
    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

    % Evaluation of results
    ph.plot_metric;

    % Remove phase only before saving, no further phasing is possible
    ph.remove_phase_ramp;
    ph.slice3d_object;
    ph.iso3d_object;

    % Save
    ph.save(string(jj));
    metric_reci(jj)  = (ph.metric.val.reciprocal(end));
    metric_sharp(jj) = (ph.metric.val.sharpness(end));
end
% figure;
% plot(metric_sharp,'-r');
% figure;
% plot(metric_reci,'-k');
% save('reconstructions\metric_reci.mat','metric_reci');