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2 changes: 2 additions & 0 deletions DETECTOR/fcnDefinePixels.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [input, flags] = fcnDefinePixels(input,flags,handles)
if ~flags.update.detectorgeometry; return; end
fprintf('Defining Detector Geometry... '); tic
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2 changes: 2 additions & 0 deletions DETECTOR/fcncylinder.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [P, input] = fcncylinder(input)
P = cell(1,6);
d2r = pi/180;
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2 changes: 2 additions & 0 deletions ML/ANTINEUTRINO/fcnantineutrino.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = fcnantineutrino(input,output,handles,G1,plotflag)
zv=zeros(1,10); results.xhat=zv; results.true=zv; if plotflag; try closeallexcept(handles.GUI.figure1); catch; end; tic; end

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2 changes: 2 additions & 0 deletions ML/ANTINEUTRINO/fcngetcandidates.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [C, XC, TC, EC, EFC, str] = fcngetcandidates(input,N,X,T,F,particleName)
%C=candidates, XC = candidate estimates, TC = candidate truths, EC = candidate estimate errors (xhat-xtrue)
%N=number of photons, X=xhat estimate, T=xtrue, E=error (xhat-xtrue), F=estimator failure flag, str='antineutrino'
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/E2neutronE.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function Eneutron = E2neutronE(Evis)
P = [-0.000169585232527955,0.00783271796930060,-0.167346627765554,2.19492596963189,-19.7793109964175,129.859482522855,-642.770385257028,2448.57093493363,-7265.02204696498,16885.4910975076,-30764.0514123043,43767.5233347055,-48213.5281542030,40568.9020684766,-25563.4422468919,11732.7579233951,-3777.11961099886,813.059509362973,-112.429581800018,13.4656322313572,-0.0243103851590198];

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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/doubleScatterVerification.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = doubleScatterVerification(results,input,G1,PE,handles,x,s,particle,plotflag)
MTCflag = ischecked(handles.GUI.realdataflag);
fiberCaptureFraction=.5; E2PE=input.Material(5).yield*input.cube.QEmean*fiberCaptureFraction; %MeV to PE
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnfastneutron.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = fcnfastneutron(input,output,handles,PE,G1,plotflag)
MTCflag = ischecked(handles.GUI.realdataflag);
results = []; nz = sum(output(1).N); if nz<19 || nz>1E4; return; end; if plotflag; closeallexcept(handles.GUI.figure1); end
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnneutronke.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function ke = fcnneutronke(x)
%x=[xyz t E; xyz t E];
neutronmass = 939.565378; %MeV/c^2
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnneutrontheta.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function theta = fcnneutrontheta(ke0,e)
ep = e(1); %energy of first proton hit
en = ke0; %energy of neutron before first proton hit
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnplotcone.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [X,Y,Z,conevecs] = fcnplotcone(a,b,angle)
%function plots a cone with origin 'a', pointing toward 'b', half angle 'angle'
vec = b - a;
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnplotneutronMC.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = fcnplotneutronMC(input,MC,MeVVector)
close all; clc
input.neutron = load('dEfit.mat');
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/fcnplotneutronTS.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = fcnplotneutronTS(input,MC,tsv)
if nargin==1
[fname, pname] = uigetfile('*.mat','Pick a TS file');
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2 changes: 2 additions & 0 deletions ML/FASTNEUTRON/testOrderStatistic.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = testOrderStatistic(input)
A=input.table.smearExp;

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2 changes: 2 additions & 0 deletions ML/FERMAT/fcnfermatpointvectorized.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [fx, gx, F, sourceprobability, F1] = fcnfermatpointvectorized(k,X)
%X = [xyztw...xyztw]
gx = []; %gradient
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2 changes: 2 additions & 0 deletions ML/FERMAT/fcnsolidangle.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function sa = fcnsolidangle(r,A)
%A=area of surface (units^2)
%r=radius (units)
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2 changes: 2 additions & 0 deletions ML/FERMAT/fcnsolidanglevectorized.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [fall, r] = fcnsolidanglevectorized(k,X)
%mode = 1; %1=simple, 2=reflect
np = size(X,1);
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2 changes: 2 additions & 0 deletions ML/FIBER/fiberMuonFitter.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = fiberMuonFitter(input,output,flags,PE,G1,handles,x,s,plotflag)
results=[];
[~, si] = sortrows(x,4); x=x(si,:); s=s(si,:); %sort by time
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2 changes: 2 additions & 0 deletions ML/FIBER/fiberNeutronFitter.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = fiberNeutronFitter(input,output,flags,PE,G1,handles,plotflag)
results.protonprotonflag = [0 0];
results.minangleerror = 0;
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2 changes: 2 additions & 0 deletions ML/FIBER/fitLineND.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [mu,V] = fitLineND(x,w)
%x = [n x nd] vector, nd=number dimensions
if numel(x(:,1))==1
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2 changes: 2 additions & 0 deletions ML/FIBER/weightedcov.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function C = weightedcov(x,w)
%x = NxM, weights = Nx1
[N,M]=size(x);
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2 changes: 2 additions & 0 deletions ML/GAMMA/fcnKleinNishina.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = fcnKleinNishina()
clc; clear all; close all
me = 0.510998910; %electron rest mass (MeV) or (MeV/c^2)
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2 changes: 2 additions & 0 deletions ML/GAMMA/plotSkyMap.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = plotSkyMap(F,v,angles,np,particleName)
nr = 100;
nc = 200;
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2 changes: 2 additions & 0 deletions ML/MUON/fcnmuon.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = fcnmuon(input,output,handles,photons,G1,plotflag)
results=[]; MTCflag=ischecked(handles.GUI.realdataflag); if plotflag; closeallexcept([handles.GUI.figure1, findobj('Name','Event Viewer')]); end
nz = output(1).Nsum; if nz<30 || nz>30E4; return; end
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2 changes: 2 additions & 0 deletions ML/POISSON/fcnMLenergy.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [x, fx] = fcnMLenergy(input,p0,zN,x0) %vectorized by default
if sum(zN>0)<3; x=0; fx=0; return; end
k = fcnoptimizerk(input,zN); k.reflections = 0;
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2 changes: 2 additions & 0 deletions ML/POISSON/fcnMLpoint.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [x, fx] = fcnMLpoint(input,output,x0) %vectorized by default
k = fcnoptimizerk(input,output); k.reflections = 1;
zN = k.nhpp;
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2 changes: 2 additions & 0 deletions ML/POISSON/runMLpoint.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = runMLpoint(input,output,handles,G1,plotflag)
results=[]; MTCflag = ischecked(handles.GUI.realdataflag); if MTCflag; A=input.MTC.A; ei=input.eventNumber+1; end; if plotflag; try closeallexcept(handles.GUI.figure1); catch; end; end; tic

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2 changes: 2 additions & 0 deletions ML/fcnBuffer2Memory.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [input, output] = fcnBuffer2Memory(input,flags,handles,PE)
MTCflag = ischecked(handles.GUI.realdataflag);

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2 changes: 2 additions & 0 deletions ML/fcnanalogvoltage.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [pdf, strip, pid] = fcnanalogvoltage(input,flags,PE,t,ystrip,i,addnoiseflag)
pmt = input.cube.pmt;

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2 changes: 2 additions & 0 deletions ML/fcnguessinitenergy.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function e0hat = fcnguessinitenergy(k,zN,p)
%p = sqrt(zN)'*input.cube.all.xyz/sum(sqrt(zN)); %position guess
k.reflections=0;
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2 changes: 2 additions & 0 deletions ML/fcnoptimizerk.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function k = fcnoptimizerk(input, output)
%MTCflag = ischecked(evalin('base','handles.GUI.realdataflag'));
MTC766flag = false;
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2 changes: 2 additions & 0 deletions ML/fcnoptimizerkr.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function k = fcnoptimizerkr(input,output)
%reduced version of optimizer constants using only active pixels
k = fcnoptimizerk(input,output(1).N);
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2 changes: 2 additions & 0 deletions ML/oneBookend.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function A = oneBookend(F,I,D,PEs,t0,gain)
MTC766flag=false;
if MTC766flag
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2 changes: 2 additions & 0 deletions MOMENTUM/momentum.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

clc; close; format long g

MeV = 11;
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2 changes: 2 additions & 0 deletions MOMENTUM/momentum1event.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

clc; clear; close; format long g
MeV = 4;
e = 4; %event number
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2 changes: 2 additions & 0 deletions MOMENTUM/plotPointStats.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = plotPointStats(G)

p1 = zeros(1,3);
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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/example_mtcb_commands.sh
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# Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

# LOGIN TO SERVER:
ssh -X -p 25260 m033372@mtc-b.phys.hawaii.edu

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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/fcnloadMTCQT.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [input, D, es] = fcnloadMTCQT(pathname,input,flags,handles,plotflag,ei)
if exist('ei','var') && ~isempty(ei) || flags.status.MC; MCflag=true; else MCflag=false; end
if MCflag; plotflag = 0; end; fprintf('Loading MTC data... '); tic
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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/fcnprocess1run.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [A, Cout] = fcnprocess1run(A,handles,plotflag)
try closeallexcept(handles.GUI.figure1); end %#ok<TRYNC>
if ~exist('plotflag','var') || isempty(plotflag); plotflag=false; end
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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/firstfour.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function i=firstfour(w,i)
i = i( w<(min(w)+4) );
end
2 changes: 2 additions & 0 deletions MTC/DataAnalysis/getRunCategories.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [run,category] = getRunCategories()
X = GetGoogleSpreadsheet('1LEZYzBG8Ae_jQcYmxaTPxrfccSzXTMRNtyozElfS98k');
X=X(3:end,[1 13]);
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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/lastfour.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function i=lastfour(w,i)
i = i( w>(max(w)-4) );
end
2 changes: 2 additions & 0 deletions MTC/DataAnalysis/plotAnalysis.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = plotAnalysis()
clc; clear; close all
%MTC RUNS: https://docs.google.com/spreadsheets/d/1LEZYzBG8Ae_jQcYmxaTPxrfccSzXTMRNtyozElfS98k/edit?usp=sharing
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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/removeSpikes.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function V=removeSpikes(V,threshold)
if nargin==1; threshold=50; end

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2 changes: 2 additions & 0 deletions MTC/DataAnalysis/runAnalysis.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = runAnalysis()
close all; clc; clear all %#ok<CLALL>
load M2.mat; input.MTC.A.x=[]; input.MTC.C=[]; %#ok<*STRNU>
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2 changes: 2 additions & 0 deletions MTC/Mapping/MTCSRCCH2pixelID.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function ID = MTCSRCCH2pixelID(SRCCH)
%load('MTCmapping.mat'); %X = [SRCCH PMT PMTR PMTC ASICs ASICd Si CHs FACE];
X=getmap;
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2 changes: 2 additions & 0 deletions MTC/Mapping/MTCpixelID2SRCCH.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [S, R, C, CH, PMT, PMTR, PMTC, As, Ad, Si, CHs] = MTCpixelID2SRCCH(i)
load('MTCmapping.mat'); %X = [SRCCH PMT PMTR PMTC ASICs ASICd Si CHs FACE];
%SRCCH(SRCCH(:,1)==0, 1)=102;
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2 changes: 2 additions & 0 deletions MTC/Mapping/fcnUHShigepixel2jocherpixel.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = fcnUHShigepixel2jocherpixel(input)
C_uh2j = fcnENU2NED; %x_j = C_uh2j*x_uh;
%UH - JOCHER
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2 changes: 2 additions & 0 deletions MTC/Mapping/fcnchannels2windows.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function a = fcnchannels2windows(a)
%pa = 1536x32768x5 window format (for 5 pedestals)
%pb = 786432x64x5 channel format
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2 changes: 2 additions & 0 deletions MTC/Mapping/fcnwindows2channels.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function a = fcnwindows2channels(a)
%pa = 1536x32768x5 window format (for 5 pedestals)
%pb = 786432x64x5 channel format
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2 changes: 2 additions & 0 deletions MTC/fcngmdistribution.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [mu,s,k,X] = fcngmdistribution(X)
%fits data and tells you how many normals make up the underlying mixture distribution
mu=[];
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2 changes: 2 additions & 0 deletions MTC/pedestals/convertData2Pedestals.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = convertData2Pedestals(input)
A=input.MTC.A; input.MTC.A=[]; fname=A.filename;
E = A.E-min(A.E)+1;
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2 changes: 2 additions & 0 deletions MTC/pedestals/fcnpruninglist.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [b, i] = fcnpruninglist(a)
if nargin==0; a=(1:1536)'; end

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2 changes: 2 additions & 0 deletions MTC/pedestals/subtractpedestals.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function V = subtractpedestals(pedestals,pedestalOutliers,pid,window,V)
% load('MTCpedestal') %loads X 98304x71
% pedestals = muvb(:,8:end); %#ok<NODEF> %idxm=load('MTCmapping.mat'); b=b(idxm.X(:,1),:);
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2 changes: 2 additions & 0 deletions MTC/timebase offsets 2015/fcngettimebases.m
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@@ -1,3 +1,5 @@
% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [] = fcngettimebases(input,handles,flags)
closeallexcept(handles.GUI.figure1); clc;
[pathname]=uigetdir([pwd '/*.*','MultiSelect','On'],'Select folder:');
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2 changes: 2 additions & 0 deletions NN/functions/conventionalFiberFit.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function xhat = conventionalFiberFit(I, T, threshold)
nw=size(I,2)/2; vi{1}=1:nw; vi{2}=vi{1}+nw;
if nargin==2
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2 changes: 2 additions & 0 deletions NN/functions/gatherTrainingData.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function results = gatherTrainingData(input,output,PE,G1)
% mode='trainLAPPDNTC2';
% switch mode
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2 changes: 2 additions & 0 deletions NN/functions/trainFiber64.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function trainFiber64(files)
if nargin==0
applyFlag=false;
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2 changes: 2 additions & 0 deletions NN/functions/trainNewDetector.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function []=trainNewDetector()
evalin('base','clc; clear all; close all;'); startclock=clock;

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2 changes: 2 additions & 0 deletions PHOTONS/cherenkov_magnitude.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function wlpdf = cherenkov_magnitude(wl,ir,speed)
%wl (nm)
%speed (c)
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2 changes: 2 additions & 0 deletions PHOTONS/fcnBQF.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function devis = fcnBQF(de,dx,BQF)
%converts energy to visible energy using BQF
%dx = distance travelled in mm
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2 changes: 2 additions & 0 deletions PHOTONS/fcndetectorintercept.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [p2,dt] = fcndetectorintercept(input,p1,vel)
%p1 is the vector origin, vel is the velocity vector
%endPos is the vector intercept on the detector wall, dt is the time it took to get there
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2 changes: 2 additions & 0 deletions PHOTONS/fcne2wl.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function wl = fcne2wl(e,ir) %energy (MeV)
c = 299792458; %m/s, speed of light
planck = 4.13566751691E-15; %eV*s
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2 changes: 2 additions & 0 deletions PHOTONS/fcngain2ratio.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function ratio = fcngain2ratio(gain,type)
%gain (dB)
%ratio (amplitudeOut/amplitudeIn)
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2 changes: 2 additions & 0 deletions PHOTONS/fcninsidedetector.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function i = fcninsidedetector(x, input, ec)
%x is nx3 particle position
%ec is edge cut (optional)
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2 changes: 2 additions & 0 deletions PHOTONS/fcnke2c.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function c = fcnke2c(ke,mass)
% kE in MeV
% mass in MeV
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2 changes: 2 additions & 0 deletions PHOTONS/fcnphotondeconvolution.m
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% Ultralytics πŸš€ AGPL-3.0 License - https://ultralytics.com/license

function [V, QT] = fcnphotondeconvolution(input,flags,X)
%signal = 1536x256
if isempty(X); V=X; QT=[]; return; end
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