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Alex updates and additions #2

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584588e
Added CalcGrainSize and modified fine_twin_gbs
Brustaf Mar 14, 2022
c3d407b
Truncate_Ebsd_Function
Brustaf Mar 14, 2022
6258c16
Updated Functions
Brustaf Jun 21, 2022
4b4b192
Script Updates
Brustaf Aug 12, 2022
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90 changes: 62 additions & 28 deletions Examples/Basics/Basics.m
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Original file line number Diff line number Diff line change
Expand Up @@ -3,29 +3,19 @@
% Shows the simplest method for reconstructing the Austenite phase
% from an EBSD scan of Martensite
% ======================================================================= %

% Create "AF96.ang" file from provided sample data if not already made
if size(dir('Af96.ang'),1) == 0
data = h5read("../../Resources/EBSD/EBSD.hdf5","/AF96_small/AF001");
header = h5readatt("../../Resources/EBSD/EBSD.hdf5","/AF96_small",'header');
f = fopen('AF96.txt','w');
fprintf(f,header);
fclose(f);
writematrix(data','AF96.txt','delimiter',' ','WriteMode','append')
movefile AF96.txt AF96.ang
end
tic

% load some metadata about folder locations and do a flight check
Mart2Aust_Parent_folder = "C:\Users\agerlt\workspace\Mart2Aust";
Mart2Aust_Parent_folder = "C:\Users\ALEBRUS\Desktop\Software\Matlab\Mart2Aust-main";
meta.Data_folder = Mart2Aust_Parent_folder + filesep +'Resources'+...
filesep + 'EBSD'+ filesep +'AF96_small';
meta.MTEX_folder = Mart2Aust_Parent_folder + filesep + 'MTEX';
meta.MTEX_folder = Mart2Aust_Parent_folder + filesep + 'Mart2Aust' + filesep + 'MTEX';
meta.Functions_folder = Mart2Aust_Parent_folder + filesep + 'Mart2Aust';
meta.current_folder = string(pwd);
meta.MTEX_Version = "mtex-5.7.0";
addpath(genpath(meta.Functions_folder));

check_AusRecon_loaded;
% check_AusRecon_loaded;
try
disp(['Compatable MTEX version ', check_MTEX_version(meta.MTEX_Version), ' detected'])
catch
Expand All @@ -34,6 +24,8 @@
addpath(meta.MTEX_folder + filesep + meta.MTEX_Version);
startup_mtex
end
setMTEXpref('xAxisDirection','east')
setMTEXpref('zAxisDirection','outOfPlane')
clear Aus_Recon_Parent_folders split_loc f data header Mart2Aust_Parent_folder


Expand All @@ -45,40 +37,82 @@

% Load default reconstruction options and file location
options = load_options("default");
fname = dir('AF96.ang');
% Use these two choices to generate some other location information
name = split(string(fname.name),'.');
name = name(end-1);
location = [fname.folder, filesep, fname.name];
pname = 'C:\Users\ALEBRUS\Documents\Microstructure_Work\Exxon_2022\Data';
fname = '55-HR_EBSD1.ang';
tname = fullfile(pname,fname);

% Load a Martensite/Austenite Orientation Relationship and MDF halfwidth
% that was previously measured on this scan (remove this line to recalculate
% the values. See some of the other examples for more details on defining
% and calculating the orientation relationship)
options.OR_ksi = [2.9057 7.7265 8.2255];
options.OR_noise = 0.0281;
%% Alter Default Options
% options.OR_ksi = [2.7 9.2 9.4];
% % options.OR_ksi = [2.4284 8.6749 8.8738];
% % options.OR_ksi = [3.89,8.84,9.17];
% options.OR_noise = 0.029;
% options.RGC_in_plane_m = 6;
% options.RGC_in_plane_b = 12;
% options.RGC_post_pre_m = 1.75e-1;
% options.RGC_post_pre_b = 0.6;
% options.OR_sampling_size = 2000;

% load the ebsd
original_ebsd = EBSD.load(location, ...
options.OR_plot_PAG_Mart_Guess = 1;
options.OR_plot_ODF_of_PAG_OR_guess = 1;

%% Load EBSD and Format for Reconstruction
% Load original ebsd
original_ebsd = EBSD.load(tname, ...
'convertEuler2SpatialReferenceFrame','setting 2');

% Truncate ebsd if flagged
truncate = 1;
if truncate
ebsd = truncate_ebsd(original_ebsd,10,125,7,107);
else
ebsd = original_ebsd;
end

% Not all scans list phases in the same order: this command fixes that
ebsd = prep_for_Recon(original_ebsd,options);
clear original_ebsd
ebsd = prep_for_Recon(ebsd,options);

% clear original_ebsd
% at this point, we have identical scans with the following phase IDs:
% 0 : Unindexed
% 1 : Untransformed Parent (High temperature, or HT)
% 2 : Transformed Child (Low Temperature, or LR)
% 3 : Reconstructed Parent (starts empty) (Reconstructed, or R)

%% Auto OR Computation

% Determine the Orientation Relationship, if not already given
CS_HT =ebsd.CSList{1};
CS_LT =ebsd.CSList{2};
CS_HT = ebsd.CSList{1};
CS_LT = ebsd.CSList{2};
[ebsd.opt.OR,ebsd.opt.HW,~] = AutoOR_estimation(ebsd,options);

%% Calculate Misorientation Distribution Function

% Determine the Misorientation Distribution function for the LT phase
[ebsd.opt.LT_MDF,ebsd.opt.psi] = calc_LT_MDF(CS_HT, CS_LT, ebsd.opt.HW, ebsd.opt.OR);

%% Perform Reconstruction
tic

[Recon_ebsd, Recon_Likelihood] = Call_Reconstruction_Austin(ebsd,options);

[a,AusGrns,E2627,E112_13] = CalcGrainSize(Recon_ebsd,3,1);

Recon_Time = toc/60;
%%
tic
options.RGC_in_plane_m = 5;
options.RGC_in_plane_b = 3;
options.RGC_post_pre_m = 1.75e-1;
options.RGC_post_pre_b = 2;

% Perform the actual Reconstruction
Recon_ebsd = Call_Reconstruction(ebsd,options);
[Recon_ebsdOrig, Recon_LikelihoodOrig] = Call_Reconstruction(ebsd,options);
Recon_TimeOrig = toc/60;
%% Segment Variants

% Segment the variants using the low temp and high temp maps
variant_int_map = variants(ebsd, Recon_ebsd,options);
6 changes: 3 additions & 3 deletions Mart2Aust/Core/AutoOR_estimation.m
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@

%% search the low temp phase (Phase 2) for acceptably close PAG
% for first iteration, make the entire scan searchable
searchable_ebsd = ebsd(ebsd.phaseId == 2);
searchable_ebsd = ebsd;
for iteration = 1:10
% NOTE TO FUTURE USERS: The first step in this code is to use the MTEX
% calcgrain tool to find likely martensite grains, then merge grains
Expand Down Expand Up @@ -66,7 +66,7 @@
%to the leftovers-only search, JIC. Feel free to try either way.
%% Method 1: Search all unused areas
% find indices of a possible grain
[Aus_Grain_Ids,~,AusOr] = HT_grain_guess(searchable_ebsd);
[Aus_Grain_Ids,~,AusOr] = HT_grain_guess_Alex(searchable_ebsd);
% extract the expected grain and leave the remainder for future searches
grain_ebsd = searchable_ebsd(Aus_Grain_Ids);
searchable_ebsd(Aus_Grain_Ids) = [];
Expand All @@ -89,6 +89,7 @@
martensite=martensite(keep(1:options.OR_sampling_size));
else
end

% plot the martensite pole figure and grain if desired
if options.OR_plot_PAG_Mart_Guess == 1
figure();
Expand Down Expand Up @@ -142,7 +143,6 @@
%leftover can ignore
austenite_prior_odf=uniformODF(CS_HT,SS);


prior_pars=struct;
prior_pars.ksi_prior_mu=ksi_prior_mu;
prior_pars.ksi_prior_sigma=ksi_prior_sigma;
Expand Down
33 changes: 25 additions & 8 deletions Mart2Aust/Core/Call_Reconstruction.m
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
function HT_ebsd = Call_Reconstruction(orig_ebsd,options,LT_MDF)
function [HT_ebsd, GlobOP_wts] = Call_Reconstruction(orig_ebsd,options,LT_MDF)
% Do the actual reconstruction from the low temp to the high temp phase

% Pre-flight stuff:
Expand All @@ -23,7 +23,7 @@

% Now do the actual reconstruction as a seperate function (helps avoid
% accidental overwrites and removes pre-flight parameters)
recon_ebsd = Reconstruct_HT_grains(LT_ebsd,...
[recon_ebsd, RecOP_wts] = Reconstruct_HT_grains(LT_ebsd,...
neigh_list,...
IP_wts,...
options);
Expand All @@ -34,10 +34,15 @@
HT_ebsd = orig_ebsd;
HT_ebsd(orig_ebsd.phaseId == 2).orientations = temp_ebsd.orientations;
HT_ebsd(orig_ebsd.phaseId == 2).phaseId = recon_ebsd.phaseId;

% Set likelihood for entire ebsd data set, regardless of the phase. Those
% specific likelihood values can be later extracted using ebsd('phase').id
GlobOP_wts = zeros(length(orig_ebsd),1);
GlobOP_wts(orig_ebsd.isIndexed) = RecOP_wts;
end


function LT_ebsd = Reconstruct_HT_grains(LT_ebsd,neigh_list,IP_wts,options)
function [LT_ebsd,RecOP_wts] = Reconstruct_HT_grains(LT_ebsd,neigh_list,IP_wts,options)
%Reconstruct_HT_grains perform the actual reconstruction
% performs a 'while ' loop that progressively cuts out possible grains
% until eithr there is nothing left to cut, or the algorithm starts
Expand All @@ -51,6 +56,9 @@
%%figure()
%%plot(Active_Ebsd,Active_Ebsd.orientations)

% Alex add on: Global Likelihood
RecOP_wts = zeros(length(LT_ebsd),1);

while continue_recon == 1
% checks to break out of while loop
if iterations > options.max_recon_attempts || bad_cut_counter > 10
Expand All @@ -61,7 +69,7 @@
disp('=========================================\n')
continue
end
if sum(LT_ebsd.phaseId == 2) == 0
if sum(LT_ebsd.phaseId == 2) < 4
continue_recon = false;
disp('\n=========================================')
disp('reconstruction completed successfully!')
Expand All @@ -71,7 +79,12 @@

%% ======== Step 1 ======== %%
% Find a likely high temp grain orientation to attempt to cut out.
Guess_ID = randsample(1:length(Active_Ebsd),1,true,Active_Ebsd.ci);
try
Guess_ID = randsample(1:length(Active_Ebsd),1,true,Active_Ebsd.ci);
catch
Guess_ID = randsample(1:length(Active_Ebsd),1,true);
end

HT_guess_ori = Active_Ebsd(Guess_ID).orientations;

% Using that guess, make a rough cut to find a likely HT grain.If the
Expand Down Expand Up @@ -102,7 +115,7 @@
% if the grain made it this far, reset the counters and do 5 graph
% cuts (1 for the parent, 4 for the twins) to find the parent/twin areas
bad_cut_counter = 0;
[PT_ID_stack] = Seperate_Twins(proposed_grain, neigh_list, IP_wts, PT_oris,options);
[PT_ID_stack,LocOP_wts] = Seperate_Twins(proposed_grain, neigh_list, IP_wts, PT_oris,options);
% Use this data to overwrite the orientation and phase data in LT_ebsd
for i = 1:size(PT_oris,1)
mask = PT_ID_stack(i,1:end);
Expand All @@ -113,6 +126,7 @@
IDs_to_assign = proposed_grain(mask).id;
LT_ebsd(ismember(LT_ebsd.id, IDs_to_assign)).orientations = PT_oris(i);
LT_ebsd(ismember(LT_ebsd.id, IDs_to_assign)).phase = 3;
RecOP_wts(ismember(LT_ebsd.id, IDs_to_assign)) = LocOP_wts(mask);
end

% Prune out any orphaned pixels
Expand Down Expand Up @@ -292,6 +306,7 @@
[~,~,cs,~]=maxflow(FP_digraph,N+1,N+2);
cs(cs>length(Rough_Guess)) = [];
proposed_grain = Rough_Guess(cs);

% Code for debugging to show the cut out area. NOTE: this is not a grain,
% Its just a region of the scan that likely has at least one complete grain
% in it
Expand All @@ -307,7 +322,7 @@
end


function [Parent_and_Twin_IDs] = Seperate_Twins(proposed_grain, neigh_list, IP_wts, PT_oris,options)
function [Parent_and_Twin_IDs,LocOP_wts] = Seperate_Twins(proposed_grain, neigh_list, IP_wts, PT_oris,options)
% Given we have a for sure parent grain, check to see if parts would make
% more sense as a twin or as part of the parent.

Expand Down Expand Up @@ -338,6 +353,7 @@
mx = (bg_likelyhoods*options.RGC_post_pre_m);
b = options.RGC_post_pre_b;
OP_Parent_wts = mx + b;
LocOP_wts = OP_Parent_wts;
clear Parent_variants Parent_odf bg_likelyhoods mx b

for i = 2:size(PT_oris,1)
Expand Down Expand Up @@ -375,6 +391,8 @@
% save out the mask of the cut
% yes_mask = [1:N].*ismember([1:N],cs);
Parent_and_Twin_IDs(i,1:end) = ismember((1:N),cs);
% Establish OP weights for completed parent and twins
LocOP_wts(ismember((1:N),cs)) = OP_twin_wts(cs);
% find the already assigned orientations, set their in-plane weights to
% zero so they won't get pulled out again.
assigned =(1:N).*(sum(Parent_and_Twin_IDs,1)>0);
Expand Down Expand Up @@ -503,4 +521,3 @@
% neighborhood) change options.degree_of_connections_for_neighborhood
% from 2 to 1.


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