From a1d47c39f99c8e3edc92b929f25f55dc6ef858b6 Mon Sep 17 00:00:00 2001
From: TianbiZhang <73138336+TianbiZhang@users.noreply.github.com>
Date: Wed, 22 Nov 2023 18:17:11 -0800
Subject: [PATCH] Reflection-DED EBSD codes - small fixes

Fixed analyze code; changed a variable in EBSP_PCSearch from 0 to false to avoid an error.
---
 modules/ded_ebsd/Cu_Mapping_Analysis_2Passes.m |  8 ++++----
 modules/ded_ebsd/Si_LineScan_Analysis.m        | 14 ++++++--------
 modules/indexing/EBSP_PCSearch.m               |  2 +-
 3 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/modules/ded_ebsd/Cu_Mapping_Analysis_2Passes.m b/modules/ded_ebsd/Cu_Mapping_Analysis_2Passes.m
index 59499db..9347b56 100644
--- a/modules/ded_ebsd/Cu_Mapping_Analysis_2Passes.m
+++ b/modules/ded_ebsd/Cu_Mapping_Analysis_2Passes.m
@@ -23,10 +23,10 @@
 home;
 
 %% start up Astro etc.
-InputUser.Astro_loc = 'C:\Users\billy\Documents\GitHub\AstroEBSD';
-InputUser.location_mtex='E:\MATLAB\mtex-5.8.0\';
-run(fullfile(InputUser.Astro_loc,'start_AstroEBSD.m'));
-run(fullfile(InputUser.location_mtex,'startup.m'));
+InputUser.location_mtex="C:\Users\billy\Documents\MATLAB\mtex-5.10.0";
+run(fullfile(InputUser.location_mtex, "startup_mtex.m"));
+InputUser.Astro_loc = "C:\Users\billy\Documents\MATLAB\AstroEBSD-main";
+run(fullfile(InputUser.Astro_loc, "start_AstroEBSD.m"));
 
 %% location of patterns
 pattern_loc='C:\Users\billy\OneDrive - UBC\PhD\TKD\20230807_Cu_EBSD';
diff --git a/modules/ded_ebsd/Si_LineScan_Analysis.m b/modules/ded_ebsd/Si_LineScan_Analysis.m
index ac22d8d..f751149 100644
--- a/modules/ded_ebsd/Si_LineScan_Analysis.m
+++ b/modules/ded_ebsd/Si_LineScan_Analysis.m
@@ -20,13 +20,11 @@
 home;
 
 %% start astro & mtex - please edit the paths!
-
-InputUser.Astro_loc = 'C:\Users\billy\Documents\GitHub\AstroEBSD';
-InputUser.location_mtex='E:\MATLAB\mtex-5.8.0\';
-run(fullfile(InputUser.Astro_loc,'start_AstroEBSD.m'));
-run(fullfile(InputUser.location_mtex,'startup.m'));
-
-pattern_loc = 'C:\Users\billy\OneDrive - UBC\PhD\TKD\20230804_Si_EBSD\Vertscan';
+InputUser.location_mtex="C:\Users\billy\Documents\MATLAB\mtex-5.10.0";
+run(fullfile(InputUser.location_mtex, "startup_mtex.m"));
+InputUser.Astro_loc = "C:\Users\billy\Documents\MATLAB\AstroEBSD-main";
+run(fullfile(InputUser.Astro_loc, "start_AstroEBSD.m"));
+pattern_loc = "C:\Users\billy\OneDrive - UBC\PhD\TKD\20230804_Si_EBSD\Vertscan";
 
 %% Enter pattern information and set up indexing
 eangs=[176.81 19.31 225.90]*pi/180; %demo
@@ -57,7 +55,7 @@
 
 %% Pattern I/O
 num_pat_ini = 1;
-num_pat_end = 1;
+num_pat_end = 20;
 pattern_root = 'Spot';
 num_pats = num_pat_end - num_pat_ini + 1;
 
diff --git a/modules/indexing/EBSP_PCSearch.m b/modules/indexing/EBSP_PCSearch.m
index 95cc844..9ba902b 100644
--- a/modules/indexing/EBSP_PCSearch.m
+++ b/modules/indexing/EBSP_PCSearch.m
@@ -9,7 +9,7 @@
 %set up the GA - needs the global optimisation toolbox
 PC_GA_options = optimoptions('ga');
 PC_GA_options.FunctionTolerance=1E-3;
-PC_GA_options.UseParallel=0;
+PC_GA_options.UseParallel=false;
 PC_GA_options.MaxGenerations=15;
 PC_GA_options.PopulationSize=30;
 PC_GA_options.MaxStallGenerations=20;