Problem: Outsized EBSD map #589

caoyi0701 · 2020-11-25T05:43:21Z

caoyi0701
Nov 25, 2020

Hi all,

I am attempting to calcuate and plot the grains of an EBSD map using the function below.

[grains,ebsd('indexed').grainId,ebsd.mis2mean] = calcGrains(ebsd('indexed'),'threshold',[1*degree, 10*degree],'boundary','tight'); ebsd(grains(grains.grainSize<=2)) = []; F = KuwaharaFilter; F.numNeighbours = 5; ebsd = smooth(ebsd('indexed'),F); [grains,ebsd('indexed').grainId,ebsd.mis2mean] = calcGrains(ebsd('indexed'),'threshold',[1*degree, 10*degree],'boundary','tight'); plot(grains)

However, the figure it yielded turns out to be strange as shown in the attached figure.

The frame of the figure is much larger than the original EBSD map.
Could anyone help fix this problem？

Best regards,
Yi Cao

Answered by ralfHielscher

Dec 1, 2020

Hi Yi,

I did some testing and assume that this problem is due to a bug in QHull, which is a library for Voronoi tessellation used by MTEX.
For me everything was fine when I used the option noQHull which causes MTEX to use a different library for this task, i.e., try

grains = calcGrains(ebsd('indexed'),'threshold',10*degree,'boundary','tight','noQHull');

Ralf.

View full answer

ralfHielscher · 2020-11-25T05:55:41Z

ralfHielscher
Nov 25, 2020
Maintainer

Hi Yi

Could you please attache your data?
Could you identify it which step during your calculations the error occurs?

Ralf.

3 replies

caoyi0701 Nov 25, 2020
Author

Hi Ralf,

Thank you for the reply.
Please see attachment for my data.
example EBSD data.zip

I selected a small region to plot the figure as shown previously, using the codes below.

`%% Rotate EBSD data
% roate the whole data set about the z-axis by 90degree
ebsd = rotate(ebsd,-90degree);
plot(ebsd)

%% Remove inaccurate orientations
figure(1)
ebsd = ebsd(ebsd.mad<1);
plot(ebsd,ebsd.mad)
mtexColorbar
%
figure(2)
plot(ebsd)

%% Select regions
% Select Bt-poor layer (BPL)
figure(3)
region1 = [-933 -17726; -2164 -17805; -3401 -17943; -4633 -17894; -5935, -18758; -7206 -19185; -7305 -19324;...
-8397 -19393; -9468 -19751; -10404 -20506; -10812 -20933; -11414 -20981; -11656 -21251; -12103 -21271; -12327 -20981;...
-12803 -20704; -13121 -20465; -13518 -20346; -14409 -20482; -15260 -20777; -17250 -21126;-17250 -26142;...
-14550 -25874; -12508 -25705; -10990 -25334; -9201 -24963; -7582 -24355; -5894 -23950; -3712 -23324;-1012 -23006];
ebsd = ebsd(inpolygon(ebsd,region1))
plot(ebsd)`

When plotting the EBSD map, i.e., plot(ebsd), the figure is okay. But the problem occurs when plotting the grains, using plot(grains).

Best regards,
Yi Cao

ralfHielscher Nov 25, 2020
Maintainer

Hi Cia,

unfortunately I was not able to reproduce your error. The are two problems with you code:

no grains are computed that could be plotted
after restricting to the region the ebsd variable is empty

Ralf.

caoyi0701 Nov 26, 2020
Author

Hi Ralf,

I attached the complete code of my script here, which I tested. I hope it can work.

`%% Import Script for EBSD Data
%
% This script was automatically created by the import wizard. You should
% run the whoole script or parts of it in order to import your data. There
% is no problem in making any changes to this script.

%% Specify Crystal and Specimen Symmetries

% crystal symmetry
CS = {...
'notIndexed',...
crystalSymmetry('321', [4.9 4.9 5.5], 'X||a*', 'Y||b', 'Z||c*', 'mineral', 'Quartz', 'color', [0 1 0]),...
crystalSymmetry('-1', [8.2 13 14], [93.51,115.91,90.66]degree, 'X||a', 'Z||c', 'mineral', 'Bytownite', 'color', [0 0 1]),...
crystalSymmetry('4/mmm', [4.6 4.6 3], 'mineral', 'Rutile', 'color', [1 0 0]),...
crystalSymmetry('12/m1', [5.3 9.3 10], [90,100.23,90]degree, 'X||a', 'Y||b*', 'Z||c', 'mineral', 'Biotite', 'color', [0.85 0.65 0.13]),...
crystalSymmetry('m-3m', [12 12 12], 'mineral', 'Almandine', 'color', [1 0.75 0.8]),...
crystalSymmetry('-3', [5.1 5.1 14], 'X||a*', 'Y||b', 'Z||c*', 'mineral', 'Ilmenite', 'color', [0 0.39 0]),...
crystalSymmetry('m-3m', [8.4 8.4 8.4], 'mineral', 'Magnetite', 'color', [0.55 0 0.83])};

% plotting convention
setMTEXpref('xAxisDirection','east');
setMTEXpref('zAxisDirection','outOfPlane');

%% Specify File Names

% path to files
pname = 'C:\Users\DELL\Desktop\example.EBSD.data\example EBSD data';

% which files to be imported
fname = [pname '\example EBSD data.cpr'];

%% Import the Data

% create an EBSD variable containing the data
ebsd = EBSD.load(fname,CS,'interface','crc',...
'convertSpatial2EulerReferenceFrame');

%% Rotate EBSD data
% roate the whole data set about the z-axis by 80degree
ebsd = rotate(ebsd,-90degree);
plot(ebsd)

%% Remove inaccurate orientations
figure(1)
ebsd = ebsd(ebsd.mad<1);
plot(ebsd,ebsd.mad)
mtexColorbar
%
figure(2)
plot(ebsd)

%% Select regions
% Select Bt-poor layer (BPL)
figure(3)
region1 = [-933 -17726; -2164 -17805; -3401 -17943; -4633 -17894; -5935, -18758; -7206 -19185; -7305 -19324;...
-8397 -19393; -9468 -19751; -10404 -20506; -10812 -20933; -11414 -20981; -11656 -21251; -12103 -21271; -12327 -20981;...
-12803 -20704; -13121 -20465; -13518 -20346; -14409 -20482; -15260 -20777; -17250 -21126;-17250 -26142;...
-14550 -25874; -12508 -25705; -10990 -25334; -9201 -24963; -7582 -24355; -5894 -23950; -3712 -23324;-1012 -23006];
ebsd = ebsd(inpolygon(ebsd,region1))
plot(ebsd)

%% Calculate grains
[grains,ebsd('indexed').grainId,ebsd.mis2mean] = calcGrains(ebsd('indexed'),'threshold',[1degree, 10degree],'boundary','tight');
ebsd(grains(grains.grainSize<=2)) = [];
%[grains,ebsd('indexed').grainId,ebsd.mis2mean] = calcGrains(ebsd('indexed'),'threshold',[1degree, 10degree],'boundary','tight');
F = KuwaharaFilter;
F.numNeighbours = 5;
ebsd = smooth(ebsd('indexed'),F);
[grains,ebsd('indexed').grainId,ebsd.mis2mean] = calcGrains(ebsd('indexed'),'threshold',[1degree, 10degree],'boundary','tight');
% Smooth grains
grains_smoothed = smooth(grains,4); % "grains_smoothed_temp" is raw constructed grains; it is used for merging twin boundaries
plot(grains_smoothed)
`

All the best,
Yi

kilir · 2020-11-25T20:14:44Z

kilir
Nov 25, 2020
Collaborator

If I remember correctly, some older version of mtex had a bug after smoothing where under certain conditions some coordinates were placed at funny conditions - but that's maybe +1/2 year ago. Do you use a recent version?
Rüdiger

1 reply

caoyi0701 Nov 26, 2020
Author

Hi Rüdiger,

Thank you for the reply. I am using the latest version of MTEX, ver. 5.5.0.

Yi

kilir · 2020-11-29T12:36:00Z

kilir
Nov 29, 2020
Collaborator

Hi Yi,
your region seems to be a bit ill defined, hence one cannot reproduce your issue right way. I think in your no fully correct mixture of ebsd and ebsd('indexed')` some things may go wrong: Using the following works for me:

CS = {... 
  'notIndexed',...
  crystalSymmetry('321', [4.9 4.9 5.5], 'X||a*', 'Y||b', 'Z||c*', 'mineral', 'Quartz-new', 'color', [0.53 0.81 0.98]),...
  crystalSymmetry('-1', [8.2 13 14], [93.51,115.91,90.66]*degree, 'X||a*', 'Z||c', 'mineral', 'Bytownite', 'color', [0.56 0.74 0.56]),...
  crystalSymmetry('4/mmm', [4.6 4.6 3], 'mineral', 'Rutile', 'color', [0.85 0.65 0.13]),...
  crystalSymmetry('12/m1', [5.3 9.3 10], [90,100.23,90]*degree, 'X||a*', 'Y||b*', 'Z||c', 'mineral', 'Biotite', 'color', [0.94 0.5 0.5]),...
  crystalSymmetry('m-3m', [12 12 12], 'mineral', 'Almandine', 'color', [0 0 0.55]),...
  crystalSymmetry('-3', [5.1 5.1 14], 'X||a*', 'Y||b', 'Z||c*', 'mineral', 'Ilmenite', 'color', [0 0.39 0]),...
  crystalSymmetry('m-3m', [8.4 8.4 8.4], 'mineral', 'Magnetite', 'color', [0.55 0 0])};

% plotting convention
setMTEXpref('xAxisDirection','east');
setMTEXpref('zAxisDirection','intoPlane');
fname = ['example EBSD data.crc'];

ebsd = EBSD.load(fname,CS,'interface','crc',...
  'convertEuler2SpatialReferenceFrame');
ebsd = rotate(ebsd,-90*degree);

region1 = [-933 -17726; -2164 -17805; -3401 -17943; -4633 -17894; -5935, -18758; -7206 -19185; -7305 -19324;...
-8397 -19393; -9468 -19751; -10404 -20506; -10812 -20933; -11414 -20981; -11656 -21251; -12103 -21271; -12327 -20981;...
-12803 -20704; -13121 -20465; -13518 -20346; -14409 -20482; -15260 -20777; -17250 -21126;-17250 -26142;...
-14550 -25874; -12508 -25705; -10990 -25334; -9201 -24963; -7582 -24355; -5894 -23950; -3712 -23324;-1012 -23006];

region1 = [-region1(:,1) region1(:,2)];

plot(ebsd)
hold on
plot(region1(:,1),region1(:,2))
hold off

ebsd = ebsd(inpolygon(ebsd,region1))

[grains,ebsd.grainId,ebsd.mis2mean] = calcGrains(ebsd,'threshold',[1*degree, 10*degree],'boundary','tight');
ebsd(grains(grains.grainSize<=2)) = [];
F = KuwaharaFilter;
F.numNeighbours = 5;
ebsd = smooth(ebsd,F);
[grains,ebsd.grainId,ebsd.mis2mean] = calcGrains(ebsd,'threshold',[1*degree, 10*degree],'boundary','tight');
grains_smoothed = smooth(grains,4);
plot(grains_smoothed)

Cheers,
Rüdiger

7 replies

caoyi0701 Dec 1, 2020
Author

Hi Rüdiger,

Thank you very much for your patient help.

I used the alternative approach you provided and it works well for now. But I also found that after removing the high MAD data points using ebsd = ebsd(ebsd.mad<1);, the result still has an error.

For a comparison, I attached the results of both with and without high MAD data points removal.

Phase map with all MAD points:

Phase map with only low MAD points:

Nevertheless, this result is good enough for my purpose; and I am looking forward to an update on this calcGrains function in the future.
Thank you again for your kind help.

Best wishes,
Yi

kilir Dec 1, 2020
Collaborator

Hi,
Did you try to fix your nonIndexed points after removing those pixels?
Cherrs,
Rüdiger

caoyi0701 Dec 1, 2020
Author

Hi Rüdiger,

Yes, I did. I run the following codes ebsd = ebsd.gridify; ebsd(isnan(ebsd.phaseId)).phaseId = 1; after removing the high MAD pixels using ebsd = ebsd(ebsd.mad<1);. The result turned out to be which I attached in my previous reply.

Best wishes,
Yi

kilir Dec 1, 2020
Collaborator

Same issue as you create non existent pixels, ebsd(ebsd.mad<1).phaseId=1; works for me.

Cheers,
Rüdiger

caoyi0701 Dec 1, 2020
Author

Hi Rüdiger,

The code ebsd(ebsd.mad<1).phaseId=1 also works for me. But does it set the low mad pixels (mad<1) as notIndexed or non-existent pixels? When I try the code ebsd(ebsd.mad>1).phaseId=1, the result is the same as before.

Best wishes,
Yi

ralfHielscher · 2020-12-01T16:47:06Z

ralfHielscher
Dec 1, 2020
Maintainer

Hi Yi,

I did some testing and assume that this problem is due to a bug in QHull, which is a library for Voronoi tessellation used by MTEX.
For me everything was fine when I used the option noQHull which causes MTEX to use a different library for this task, i.e., try

grains = calcGrains(ebsd('indexed'),'threshold',10*degree,'boundary','tight','noQHull');

Ralf.

1 reply

caoyi0701 Dec 2, 2020
Author

Hi Ralf,

Thanks a lot for your solution. The code also works fine for me.

Best wishes,
Yi

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Problem: Outsized EBSD map #589

caoyi0701 Nov 25, 2020

Replies: 4 comments · 12 replies

ralfHielscher Nov 25, 2020 Maintainer

caoyi0701 Nov 25, 2020 Author

ralfHielscher Nov 25, 2020 Maintainer

caoyi0701 Nov 26, 2020 Author

kilir Nov 25, 2020 Collaborator

caoyi0701 Nov 26, 2020 Author

kilir Nov 29, 2020 Collaborator

caoyi0701 Dec 1, 2020 Author

kilir Dec 1, 2020 Collaborator

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kilir Dec 1, 2020 Collaborator

caoyi0701 Dec 1, 2020 Author

ralfHielscher Dec 1, 2020 Maintainer

caoyi0701 Dec 2, 2020 Author

caoyi0701
Nov 25, 2020

Replies: 4 comments 12 replies

ralfHielscher
Nov 25, 2020
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caoyi0701 Nov 25, 2020
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caoyi0701 Nov 26, 2020
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kilir
Nov 25, 2020
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caoyi0701 Nov 26, 2020
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kilir
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caoyi0701 Dec 1, 2020
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kilir Dec 1, 2020
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caoyi0701 Dec 1, 2020
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kilir Dec 1, 2020
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