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380 lines
58 KiB
Matlab
380 lines
58 KiB
Matlab
import beamline.identify_eaccount
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import beamline.radial_integ
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import io.spec_read
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import utils.get_fil_trans
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import utils.get_gas_trans
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import utils.pixel_to_q
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% EDIT HERE:
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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% where the data is saved (Data10, Data20, p-account)
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raw_data = '~/Data10';
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e_account = identify_eaccount;
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%uncomment for using during online analysis in the e-account
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BasePath = raw_data;
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%uncomment for using during offline analysis
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% BasePath= sprintf('%s/%s', raw_data, e_account);
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%_____________________________________________________________
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% needed for flux calculation using bim2
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use_bim2 = 1;
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% Remember to activate Elletra
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scan_dark=43; % scan with closed shutter (set offset in Elettra device such that counts are almost zero)
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scan=44; % scan with open shutter and BIM2 diode in the beam
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air_path = 10; % air path distance between the exposure box window and the sample in mm
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Elettra_bitmode = 24;
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Elettra_range = 2.5e-3; %[A]
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%_____________________________________________________________
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% needed for flux calculation using the glassy carbon L14
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use_GCL14 = 1;
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%glassy carbon
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Glassy_carbon=34; % the scan number of glassy carbon
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%air scattering
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Air = 42; %scan number of air scattering
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DB = 42; %direct beam, use air scattering in case there is no direct beam measurement
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%parameters for calculating the flux
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DetDist_mm = 2.1397e3; %in mm
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used_bs = 1; % 1 for diode in the beam stop
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% 2 for cyberstar diode
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%_____________________________________________________________
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% also scale WAXS data?
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use_WAXS = 0; % 1 to scale the WAXS data, 0 not used
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%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
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%% calculations
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if use_bim2
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% calculation
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%read the spec files
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S=spec_read(BasePath,'ScanNr',scan);
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S_dark=spec_read(BasePath,'ScanNr',scan_dark);
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%read the energy in keV
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energy = S_dark.mokev;
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%other important parameters
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epsilon_Si=3.66; % energy required to generate an electron-hole pair in Si [eV]
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e_charge=1.6e-19; %electron change [C]
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% from http://henke.lbl.gov/optical_constants/filter2.html, considering
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% mica KAl3Si3O11.8H1.8F0.2 Density=2.76 Thickness= 4. microns
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% 4 um mica at the exposure box exit
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[val, ~ ] = get_fil_trans( 'mica', energy, 4);
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trans_factor_d1 = val(2);
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%calculate the transmission of the air path
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% between the exposure box exit and the sample
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%from http://henke.lbl.gov/optical_constants/gastrn2.html considering
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% air N1.562O.42C.0003Ar.0094 Pressure=760 torr. T = 297 K, Path = 1 cm
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[ val ] = get_gas_trans('air', energy, air_path/10,760, 297 );
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ap_trans = val(2);
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% from http://henke.lbl.gov/optical_constants/filter2.html, considering
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% Silicon Density=2.33 Thickness= 10. microns
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% contributes positively to the calculated flux
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t_d1=10; % thickness Si sensor in microns
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[ val, ~ ] = get_fil_trans( 'Si', energy, t_d1);
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trans_si = val(2);
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%calculate the counts difference between open and closed shutter
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counts_d1 = mean(S.transd) - mean(S_dark.transd); %photons
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fprintf('The average counts at the transmission diode is %7.2f photons \n',counts_d1)
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%calculate the current
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curr_d1 = counts_d1 * Elettra_range/(2^(Elettra_bitmode-1));
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fprintf('The current at the transmission diode is %7.2f microA \n',curr_d1*1e6)
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%calculate the flux
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flux_BIM2= ((curr_d1 * epsilon_Si)/(e_charge* (energy*1e3) *(1-trans_si)))*(trans_factor_d1 * ap_trans);
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fprintf('The flux based on bim2 is %7.2e photons/s \n',flux_BIM2)
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end
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%%
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if use_GCL14
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% determination of the flux
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%thickness of the sample
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thickness_L14 = 0.1; % in cm for L14
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%calculate the relative transmittance
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%load the diode value for the air
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S_air = spec_read(BasePath,'ScanNr',Air);
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%scale in case the exposure times are different
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exp_time = S_air.sec(1,1);
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scale_air = 1/exp_time;
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%read the scep data for the glassy carbon sample
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S = spec_read(BasePath,'ScanNr',Glassy_carbon);
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energy = S.mokev; % in kev
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pixel_size = 0.172; % in mm
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%normalize the measurement to the correct
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exp_time = S.sec(1,1);
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scale_GC = 1/exp_time;
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%calculation of transmittance
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if used_bs == 1
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transmittance = (mean(S.diode)/mean(S.bpm4i))/(mean(S_air.diode)/mean(S_air.bpm4i));
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elseif used_bs == 2
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transmittance = (mean(S.cyb)/mean(S.bpm4i))/(mean(S_air.cyb)/mean(S_air.bpm4i));
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else
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error('Please inform the beam stop used in used_bs');
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end
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%define the name of the measurement
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scan_num = Glassy_carbon;
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if scan_num > 9999
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init = floor(scan_num/10000)*10000;
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last_number = init+9999;
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filename = sprintf('%s/analysis/radial_integration/S%05d-%05d/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, init, last_number, e_account, scan_num);
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else
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filename = sprintf('%s/analysis/radial_integration/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, e_account, scan_num);
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if exist(filename, 'file') ~= 2
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init = floor(scan_num/10000)*10000;
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last_number = init+9999;
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filename = sprintf('%s/analysis/radial_integration/S%05d-%05d/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, init, last_number, e_account, scan_num);
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end
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end
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Data_GC = importdata(filename);
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I_GC_m = mean(Data_GC.I_all,3);
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I_GC_m = sum(I_GC_m.*Data_GC.norm_sum,2)./sum(Data_GC.norm_sum, 2);
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q_GC_m = pixel_to_q(Data_GC.radius, pixel_size, DetDist_mm, energy);
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%estimate the direct beam measurement
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S_DB = spec_read(BasePath,'ScanNr',DB);
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%scale in case the exposure times are different
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exp_time = S_DB.sec(1,1);
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scale_DB = 1/exp_time;
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%plot the measured standard
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scan_num = DB;
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if scan_num > 9999
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init = floor(scan_num/10000)*10000;
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last_number = init+9999;
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filename = sprintf('%s/analysis/radial_integration/S%05d-%05d/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, init, last_number, e_account, scan_num);
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else
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filename = sprintf('%s/analysis/radial_integration/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, e_account, scan_num);
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if exist(filename, 'file') ~= 2
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init = floor(scan_num/10000)*10000;
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last_number = init+9999;
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filename = sprintf('%s/analysis/radial_integration/S%05d-%05d/%s_1_%05d_00000_00000_integ.mat', ...
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BasePath, init, last_number, e_account, scan_num);
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end
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end
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Data_DB = importdata(filename);
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I_DB= mean(Data_DB.I_all,3);
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I_DB = sum(I_DB.*Data_DB.norm_sum,2)./sum(Data_DB.norm_sum, 2);
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%hold on;
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%q_GC_m = (q_GC_m*10);
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%normalize by the exposure time
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I_GC_m = ((((I_GC_m*scale_GC)*1/transmittance )-(I_DB*scale_DB))*1/thickness_L14);
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%compare to calibrated standard
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%values provided for the calibrated Glassy carbon sample
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q_GC_c = 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9349;0.0688300976069800;0.0671026054992115;0.0661618440460318;0.0653930304940334;0.0636208596998396;0.0639784034222365;0.0635229980704250;0.0623671078908284;0.0636393741862071;0.0611647215570232;0.0613685831463423;0.0602813250585447;0.0599577571307978;0.0593124415473514;0.0589698604148216;0.0579031515354112;0.0576563734653825;0.0576102970273536;0.0562779062829001;0.0565768260968255;0.0564576134285343;0.0547751054008383;0.0538450533243285;0.0536064668509639;0.0533224619491000;0.0518254662023279;0.0523011630072659;0.0516270561189482;0.0517028170452727;0.0499300632458147;0.0510264266766338;0.0502485827312818;0.0505876790311235;0.0502110242476833;0.0500473147949757;0.0491911407345692;0.0476975090423956;0.0483856879935516;0.0469366149549049;0.0453442993889730;0.0462023027358431;0.0463876562848192;0.0453418296004854;0.0444586257598817;0.0445587267898697;0.0451806253054321;0.0443530800112586;0.0441915944442830;0.0445684958026137;0.0418947171411499;0.0441932722684921;0.0445756131632978;0.0436317802141775;0.0427427454263860;0.0426922927217532;0.0415835282106632;0.0411889052039778;0.0410213188276570;0.0422992472442955;0.0412247369996285;0.0411719078579223;0.0407179272032039;0.0402909378390404;0.0397923907599835;0.0400005482577337;0.0386561450792916;0.0390622401845554;0.0386415696772356;0.0390949596575275;0.0386859596994390;0.0384390111146331;0.0383528156908703;0.0389125312182718;0.0375412660102177;0.0365562411844043;0.0401222106537155;0.0375443465195469;0.0370207350895898;0.0385787683121572;0.0363112885761093;0.0376749688091075;0.0380773846718442;0.0365970300223128;0.0353199987716234;0.0366100764337691;0.0347705940290818;0.0359591666134441;0.0341095252262050;0.0359824512084458;0.0362504606412126;0.0346785880250509;0.0368545668631960;0.0350404429632715;0.0347629248751471;0.0358759237820286;0.0337229423357313;0.0351449217310496;0.0345992732995441;0.0370188029009108;0.0336262016120379;0.0377555442233060;0.0351219932628978;0.0368512970054316;0.0360720304482021;0.0311529300960851;0.0305857332354005;0.0335578236015645;0.0270776921474693;0.0344479515485556;0.0376524121577235;0.0359300145802958;0.0309831285148927;0.0366590293688815;0.0388807887245713;0.0354092897313060];
|
||
|
||
|
||
|
||
%determine the factor to scale the intensity in absolute scale
|
||
C = [];
|
||
%create a vector to fit the region from q 0.07 to 0.08 A
|
||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
q_range = [q_GC_c(1):0.01:q_GC_m(end-1000)]; %good region for 2 and 7 m flight tube
|
||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
for i = 1:length(q_range)
|
||
[~, index_m] = min(abs(q_GC_m - q_range(i)));
|
||
[~, index_c] = min(abs(q_GC_c - q_range(i)));
|
||
C = [C I_GC_c(index_c)/I_GC_m(index_m)]; %determined in cm/s
|
||
end
|
||
dev_SAXS = std(C);
|
||
C_SAXS = mean(C);
|
||
calibration_factor_SAXS = C_SAXS; %in s/photons
|
||
|
||
|
||
if (use_WAXS)
|
||
scan_num = Glassy_carbon;
|
||
if scan_num > 9999
|
||
init = floor(scan_num/10000)*10000;
|
||
last_number = init+9999;
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, init, last_number, e_account, scan_num);
|
||
else
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, e_account, scan_num);
|
||
if exist(filename, 'file') ~= 2
|
||
init = floor(scan_num/10000)*10000;
|
||
last_number = init+9999;
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, init, last_number, e_account, scan_num);
|
||
end
|
||
end
|
||
WAXS_GC = importdata(filename);
|
||
I_GC_WAXS= median(squeeze(WAXS_GC.I_all),2);
|
||
scan_num = DB;
|
||
if scan_num > 9999
|
||
init = floor(scan_num/10000)*10000;
|
||
last_number = init+9999;
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, init, last_number, e_account, scan_num);
|
||
else
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, e_account, scan_num);
|
||
if exist(filename, 'file') ~= 2
|
||
init = floor(scan_num/10000)*10000;
|
||
last_number = init+9999;
|
||
filename = sprintf('%s/analysis/radial_integration_waxs/%s_2_%05d_00000_00000_integ.mat',...
|
||
BasePath, init, last_number, e_account, scan_num);
|
||
end
|
||
end
|
||
Data_DB_WAXS= importdata(filename);
|
||
I_DB_WAXS = median(squeeze(Data_DB_WAXS.I_all),2);
|
||
q_GC_WAXS = WAXS_GC.q;
|
||
I_GC_WAXS = ((((I_GC_WAXS*scale_GC)*1/transmittance )-(I_DB_WAXS*scale_DB))*1/thickness_L14);
|
||
|
||
%determine the factor to scale the intensity in absolute scale
|
||
C=[];
|
||
%create a vector to fit the region from q 0.07 to 0.08 A
|
||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
q_range = [q_GC_WAXS(1):0.01:q_GC_WAXS(300) ]; %good region for 2 and 7 m flight tube
|
||
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
|
||
for i = 1:length(q_range)
|
||
[~, index_m] = min(abs(q_GC_WAXS - q_range(i)));
|
||
[~, index_c] = min(abs(q_GC_c - q_range(i)));
|
||
C = [C I_GC_c(index_c)/I_GC_WAXS(index_m)]; %determined in cm/s
|
||
end
|
||
dev_WAXS = std(C);
|
||
C_WAXS = mean(C);
|
||
calibration_factor_WAXS = C_WAXS; %in s/photons
|
||
else
|
||
calibration_factor_WAXS=1;
|
||
dev_WAXS = 0;
|
||
C_WAXS = 1;
|
||
end
|
||
|
||
|
||
%calculate the efficiency of the detector
|
||
% from http://henke.lbl.gov/optical_constants/filter2.html, considering
|
||
%silicon Si Density=2.33 Thickness=320. microns
|
||
[ val, ~ ] = get_fil_trans( 'Si', energy, 320);
|
||
TransmissionSi1 = val(2);
|
||
p = 1-(TransmissionSi1);
|
||
|
||
%contribution from the FT windows to the flux
|
||
% from http://henke.lbl.gov/optical_constants/filter2.html, considering
|
||
% mica KAl3Si3O11.8H1.8F0.2 Density=2.76 Thickness= 7. microns
|
||
[ val, ~ ] = get_fil_trans( 'mica', energy, 7);
|
||
mica = val(2);
|
||
|
||
%from http://henke.lbl.gov/optical_constants/filter2.html, considering
|
||
% mylar C10H8O4 Density=1.43 Thickness=300. microns
|
||
[ val, ~ ] = get_fil_trans( 'mylar', energy, 300);
|
||
mylar = val(2);
|
||
|
||
% define the length of the air path in mm
|
||
% remove the air path in vacuum from the DetDist_mm
|
||
% values from https://intranet.psi.ch/CSAXS/NewFlightTube
|
||
if DetDist_mm < 5e3
|
||
air_path = DetDist_mm - 2051.5; %for 2m flight tube in mm
|
||
else
|
||
air_path = DetDist_mm - 7030.2; %for 3m flight tube in mm
|
||
end
|
||
|
||
%calculate the transmission of the air path
|
||
|
||
%from http://henke.lbl.gov/optical_constants/gastrn2.html considering
|
||
%N1.562O.42C.0003Ar.0094 Pressure=760. T = 297 K, Path = 1 cm
|
||
% air N1.562O.42C.0003Ar.0094 Pressure=760 torr. T = 297 K, Path = 1 cm
|
||
[ val ] = get_gas_trans('air', energy, air_path/10,760, 297 );
|
||
ap_trans = val(2);
|
||
|
||
|
||
%define the solid angle: we consider the first pixel close to the beam stop
|
||
%as it would have the highest intensity
|
||
angle = (atan(pixel_size/DetDist_mm)); %in radians
|
||
sol_angle = angle^2; %in steradian (sr): square radians
|
||
|
||
%plot the comparison
|
||
loglog(q_GC_c, I_GC_c,'k', 'LineWidth', 4);
|
||
hold on
|
||
I_GC_m = I_GC_m*calibration_factor_SAXS; % in cm-1
|
||
loglog(q_GC_m, I_GC_m, 'r', 'LineWidth', 2);
|
||
|
||
if (use_WAXS)
|
||
loglog(q_GC_WAXS, I_GC_WAXS*C_WAXS, 'LineWidth', 2);
|
||
end
|
||
|
||
xlabel('Scattering vector q (A^{-1})');
|
||
ylabel('Differential scattering cross section (cm^{-1})');
|
||
axis tight
|
||
grid on;
|
||
|
||
if (use_WAXS)
|
||
legend('Standard GCL14', sprintf('Corrected SAXS GCL14 x %.2d',C_SAXS ), ...
|
||
sprintf('Corrected WAXS GCL14 x %.2d',C_WAXS ), 'Location','southwest')
|
||
else
|
||
legend('Standard GCL14', sprintf('Corrected SAXS GCL14 x %.2d',C_SAXS ),...
|
||
'Location','southwest')
|
||
end
|
||
|
||
set(gca,'fontsize',12)
|
||
|
||
%calculate the flux
|
||
positive_cont = (mica * mylar * ap_trans * p);
|
||
flux_GC = 1/(calibration_factor_SAXS*sol_angle * positive_cont); %flux in photons/s
|
||
|
||
|
||
%display the results
|
||
fprintf('The approximated flux from GCL14 is %5.2e photons/s \n', flux_GC);
|
||
fprintf('The calibration factor for corrected intensity is C_{SAXS} = %.2d ± %.2d. \n ', calibration_factor_SAXS, dev_SAXS);
|
||
if (use_WAXS)
|
||
fprintf('The calibration factor for corrected intensity is C_{WAXS} = %.2d ± %.2d. \n ', calibration_factor_WAXS, dev_WAXS);
|
||
end
|
||
end
|
||
|
||
%*-----------------------------------------------------------------------*
|
||
%| |
|
||
%| Except where otherwise noted, this work is licensed under a |
|
||
%| Creative Commons Attribution-NonCommercial-ShareAlike 4.0 |
|
||
%| International (CC BY-NC-SA 4.0) license. |
|
||
%| |
|
||
%| Copyright (c) 2017 by Paul Scherrer Institute (http://www.psi.ch) |
|
||
%| |
|
||
%| Author: CXS group, PSI |
|
||
%*-----------------------------------------------------------------------*
|
||
% You may use this code with the following provisions:
|
||
%
|
||
% If the code is fully or partially redistributed, or rewritten in another
|
||
% computing language this notice should be included in the redistribution.
|
||
%
|
||
% If this code, or subfunctions or parts of it, is used for research in a
|
||
% publication or if it is fully or partially rewritten for another
|
||
% computing language the authors and institution should be acknowledged
|
||
% in written form in the publication: “Data processing was carried out
|
||
% using the “cSAXS matlab package” developed by the CXS group,
|
||
% Paul Scherrer Institut, Switzerland.”
|
||
% Variations on the latter text can be incorporated upon discussion with
|
||
% the CXS group if needed to more specifically reflect the use of the package
|
||
% for the published work.
|
||
%
|
||
% A publication that focuses on describing features, or parameters, that
|
||
% are already existing in the code should be first discussed with the
|
||
% authors.
|
||
%
|
||
% This code and subroutines are part of a continuous development, they
|
||
% are provided “as they are” without guarantees or liability on part
|
||
% of PSI or the authors. It is the user responsibility to ensure its
|
||
% proper use and the correctness of the results. |