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postProcessing_template.m
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postProcessing_template.m
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close all;
clear;
% Enter all path without slash in the end
% ADD DEPENDENCIES - VERY IMPORTANT TO SETUP AT NEW PLACE
code_location = '/home/dzhigd/Software/preprocessing';
addpath(fullfile(code_location,'functions'));
addpath(fullfile(code_location,'classDef'));
code_location = '/home/dzhigd/Software/phasor';
% add class definitions and functions %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
addpath(genpath(fullfile(code_location,'functions')));
addpath(genpath(fullfile(code_location,'classDef')));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
scan_number = {'622-630'}; % list of changing string ids for each scan. Example: scan_number = {'1', '2', 'test'};
twin = {}; % list of changing string ids for twinned reconstruction. Can be empty. Example: twin = {'1', '2', 'test'};
for ii = 1:numel(scan_number) % loop through scan/scans
% Path to reconstruction folder with changing string ids in the place
% of %s
input_param.pre_path = sprintf('/home/dzhigd/work/projects/InZrO_TCO_films/Experiments/APS-34IDC/19112020/analysis/cohere/19112020_%s/prep/reconstructionRec-A--GAHIOlr-BST-sS-5-3-620-NM-SW',scan_number{ii});
% Path to experimental parameters.
% For the case of NanoMAX it is the path to scan file. For example:
% input_param.experimental_parameters_path = sprintf('scan_%s_merlin.mat',scan_number{ii});
input_param.experimental_parameters_path = sprintf('/home/dzhigd/work/projects/InZrO_TCO_films/Experiments/APS-34IDC/19112020/analysis/cohere/19112020_%s/conf',scan_number{ii});
% Prefix generated by the phase retrieval program
file_prefix = 'Rec-A--GAHIOlr-BST-sS-5-3-620-NM-SW-';
% SPECIFY THE BEAMLINE HERE! Options: '34idc', 'p10', 'nanomax'
input_param.experiment.beamline = '34idc';
detector_amp_reconstruction_path = [file_prefix, 'AMP.mat'];
detector_ph_reconstruction_path = [file_prefix, 'PH.mat'];
load(fullfile(input_param.pre_path,detector_amp_reconstruction_path));
a = array;
load(fullfile(input_param.pre_path,detector_ph_reconstruction_path));
% reconstructed object
input_param.object = a.*exp(1j*array);
clear array;
% Default for now
input_param.object_sampling = [1,1,1];
switch input_param.experiment.beamline
case '34idc'
% 34 ID-C, APS, Argonne
configdisp = importfile_cohere_disp(fullfile(input_param.experimental_parameters_path,'config_disp'), [2, Inf]);
% Fill it in manually otherwise
% input_param.experiment.data_path = '/home/dzhigd/work/projects/CsPbBr3_NC_BCDI_NanoMAX/data/sample0609_442/Data-A-1X1.mat';
input_param.experiment.energy = configdisp{1,3}*1000; % [eV]
input_param.experiment.sample_detector_d = configdisp{4,3}/1000; % [m]
input_param.experiment.detector_pitch = 55e-6; % [m]
input_param.experiment.angular_step = configdisp{9,3}; % [degree]
input_param.experiment.energy_step = []; % [eV]
input_param.experiment.delta = configdisp{2,3}; %
input_param.experiment.gamma = configdisp{3,3}; %
input_param.experiment.theta = configdisp{5,3}; %
input_param.experiment.chi = configdisp{6,3}; %
input_param.experiment.phi = configdisp{7,3}; %scan.motor_positions.phi(63);
input_param.experiment.mu = 0.0;
input_param.experiment.rocking_motor = 'dtheta';
input_param.experiment.d_spacing = 0e-10; % interplanar spacing for desired reflection
% Minimum requirement for imput: complex valued array, real space pitch,
% experimental parameters (for coordinate conversion)
postPhasor = PostPhasor(input_param);
postPhasor.flip(1);
case 'p10'
fioParam = getinfoFio(input_param.experimental_parameters_path);
% input_param.experiment.data_path = '/home/dzhigd/work/projects/CsPbBr3_NC_BCDI_NanoMAX/data/sample0609_442/Data-A-1X1.mat';
input_param.experiment.energy = fioParam.motorVals(2); % [eV]
input_param.experiment.sample_detector_d = fioParam.motorVals(1)/1000; % [m]
input_param.experiment.detector_pitch = 75e-6; % [m]
input_param.experiment.angular_step = (fioParam.Vector(2)-fioParam.Vector(1)); % [degree]
input_param.experiment.energy_step = []; % [eV]
input_param.experiment.beamline = 'p10';
input_param.experiment.delta = fioParam.motorVals(4); %
input_param.experiment.gamma = fioParam.motorVals(5); %
input_param.experiment.phi = fioParam.motorVals(7); %
input_param.experiment.chi = fioParam.motorVals(3); %
input_param.experiment.omega = fioParam.motorVals(6); %scan.motor_positions.phi(63);
input_param.experiment.mu = 0.0;
input_param.experiment.rocking_motor = fioParam.fastMotorName;
input_param.experiment.d_spacing = 0e-10; % interplanar spacing for desired reflection
input_param.binning = params.binning;
% Minimum requirement for imput: complex valued array, real space pitch,
% experimental parameters (for coordinate conversion)
postPhasor = PostPhasor(input_param);
postPhasor.flip(1);
postPhasor.flip(2);
case 'nanomax'
load(input_param.experimental_parameters_path);
input_param.experiment.energy = scan.motor_positions.energy; % [eV]
input_param.experiment.sample_detector_d = scan.motor_positions.radius/1e3; % [m]
input_param.experiment.detector_pitch = 55e-6; % [m]
input_param.experiment.angular_step = abs(scan.rocking_angles(2)-scan.rocking_angles(1)); % [degree]
input_param.experiment.energy_step = []; % [eV
input_param.experiment.delta = scan.motor_positions.delta;
input_param.experiment.gamma = scan.motor_positions.gamma;
input_param.experiment.gontheta = scan.motor_positions.gontheta;
input_param.experiment.chi = 90; %
input_param.experiment.gonphi = scan.motor_positions.gonphi;
input_param.experiment.rocking_motor = scan.rocking_motor;
input_param.experiment.d_spacing = 0e-10; % interplanar spacing for desired reflection
postPhasor = PostPhasor(input_param);
warning('Flipping was not tested for NanoMAX, be carefull!')
postPhasor.flip(1);
postPhasor.flip(2);
end
%% Analysis of the reconstruction
if ismember(scan_number{ii},twin)
postPhasor.twin_object;
end
% Angular corrections with respect to the center of the detector.
% Define the position of the Bragg peak
postPhasor.experiment.delta_correction = 0;
postPhasor.experiment.gamma_correction = 0;
% Angular corrections with respect to the center of the detector.
postPhasor.experiment.theta_correction = 0;
postPhasor.experiment.phi_correction = 0;
% Transformation of the phasing result to the lab coordinate system:
% x - outboard, y - up, z - along the incoming beam
% should be used to calculate strain along the measured Q-vector
postPhasor.transform2lab;
% Transformation of the phasing result to the sample coordinate system:
% x - 2nd index, y - 1st index, z - 3rd index of the array
% should be used to evaluate morphology and for easier visualzation
% postPhasor.transform2sample; % for morphology evaluation
close;
zoom_value = [2.5, 1.5, 1.5];
postPhasor.center_object;
postPhasor.create_mask(0.25);
postPhasor.calculate_displacement;
postPhasor.calculate_qVectorLab;
postPhasor.iso3dObject;
postPhasor.plot_amplitude_slice(zoom_value);
postPhasor.plot_phase_slice(zoom_value);
postPhasor.plot_displacement_slice(zoom_value);
postPhasor.calculate_strainLab;
postPhasor.iso3dStrainLab(1);
% postPhasor.slice3d_object
postPhasor.plot_strain_slice(zoom_value);
%% Saving results
% postPhasor.save_vtk;
% postPhasor.save_instance;
% postPhasor.save_all(zoom_value)
end
%%% END OF FILE %%%