Select EBSD data

An EBSD variable is a list of measurements. Selecting part of the specimen, one phase, or measurements that satisfy a quality condition is therefore ordinary list indexing. The result is another EBSD variable, so the same phase, position, orientation, and plotting operations apply to it. This is the EBSD version of Lists and Indexing.

Each measurement may also carry a per-pixel property, such as mean angular deviation mad or band contrast bc. A property has one value per measurement and is selected in lockstep with the map; see Properties.

plottingConvention.default('y↑→x');
mtexdata forsterite silent

close all;
plot(ebsd);

The phase map contains three indexed phases. The white points belong to the notIndexed phase, where a diffraction pattern was recorded but could not be indexed.

Selecting a phase

A mineral name used as an index restricts the list to that phase.

ebsd('Forsterite')

ans = EBSD (y↑→x)
 
 Phase   Orientations     Mineral         Color  Symmetry  Crystal reference frame
     1  152345 (100%)  Forsterite  LightSkyBlue       mmm                         
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [0 → 36550] × [0 → 16750] × [0 → 0]
 Normal vector: (0,0,1)

Two things in that display are worth noticing. The list is shorter: 152345 of the 245952 measurements are forsterite. Its class has also changed from EBSDsquare to EBSD. A selection is generally not a full rectangular grid, although every retained measurement still has its original position.

Use gridify when later code explicitly needs a matrix-shaped map. Many spatial MTEX operations reconstruct the virtual lattice internally; Square and Hex Grids explains when the stored grid shape matters.

A prefix of a mineral name works as an abbreviation. MTEX does not check that a prefix is unique, so use the full name when two phase names begin alike. Several phases are selected by grouping their names in curly brackets.

ebsd({'Fo','En'})

ans = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     1  152345 (85%)  Forsterite  LightSkyBlue       mmm                         
     2   26058 (15%)   Enstatite  DarkSeaGreen       mmm                         
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [0 → 36550] × [0 → 16750] × [0 → 0]
 Normal vector: (0,0,1)

Two names are available whatever the minerals are called. The name 'indexed' selects every point matched to a phase. The degenerate phase 'notIndexed' selects points whose diffraction pattern could not be indexed.

ebsd('indexed')

ans = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     1  152345 (81%)  Forsterite  LightSkyBlue       mmm                         
     2   26058 (14%)   Enstatite  DarkSeaGreen       mmm                         
     3   9064 (4.8%)    Diopside     Goldenrod     12/m1        X||a*, Y||b, Z||c
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [0 → 36550] × [0 → 16750] × [0 → 0]
 Normal vector: (0,0,1)

Plotting a phase selection uses the ordinary plot command.

close all;
plot(ebsd('Forsterite'),ebsd('Forsterite').orientations, ...
  'ipfDirection',zvector);

Only the forsterite footprint remains. Its colour still varies with orientation because selection changes the list, not the plotting rule; see Plot.

Restricting to a region of interest

A rectangle is specified as [xmin ymin width height] in the map units, here microns.

region = [5 2 10 5] * 10^3;

Draw the rectangle on the phase map before applying it.

close all;
plot(ebsd);
rectangle('Position',region,'EdgeColor','red','LineWidth',2);

The red rectangle crosses all three indexed phases and many notIndexed points. inpolygon tests every measurement and returns one true or false for each point.

condition = inpolygon(ebsd,region);

Logical indexing keeps the points for which the condition is true: 20301 of the 245952 measurements, about one twelfth of the map.

ebsdRegion = ebsd(condition)

ebsdRegion = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     0    4052 (20%)  notIndexed          none                                   
     1   14093 (69%)  Forsterite  LightSkyBlue       mmm                         
     2   1397 (6.9%)   Enstatite  DarkSeaGreen       mmm                         
     3    759 (3.7%)    Diopside     Goldenrod     12/m1        X||a*, Y||b, Z||c
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [5000 → 15000] × [2000 → 7000] × [0 → 0]
 Normal vector: (0,0,1)

Plot the selected region with the same phase colours.

close all;
plot(ebsdRegion);

The cropped map keeps its specimen coordinates rather than being moved to the origin. Only its extent and list membership have changed.

A region need not be rectangular. inpolygon also accepts the vertices of any closed polygon. Draw those vertices with the mouse using

poly = selectPolygon

Screening measurements by fit quality

Indexing software stores quantities that describe the pattern solution. Oxford Channel maps commonly provide the mean angular deviation mad, for which lower values mean a closer angular fit. EDAX OIM maps commonly provide a confidence index ci, for which higher values mean that the winning indexed solution is better separated from the runner-up.

These quantities are not interchangeable measures of orientation error. A threshold flags measurements for scrutiny; it does not prove that an orientation is wrong. Inspect the spatial map and the distribution before choosing a data-dependent threshold.

close all;
plot(ebsdRegion, ebsdRegion.mad);
mtexColorbar('title','mean angular deviation (degree)');
setColorRange([0 1.2]);

Most of the map sits at about 0.4°. The deep blue patches are the notIndexed points, which report 0. The yellow speckles are the worst fits in this map and lie mainly along grain boundaries, where the interaction volume can contain signal from two crystals. A histogram shows the populations more clearly.

close all;
histogram(ebsdRegion.mad);
xlabel('mean angular deviation (degree)');

The tallest bar is at zero. It is not a population of perfect fits but the notIndexed points again. The indexed measurements run from 0.1° to 1.2°, with the bulk at 0.4°. A cut at 0.8° removes the tail and keeps 96% of all points in the region.

% take measurements with MAD smaller than 0.8 degrees
ebsdCorrected = ebsdRegion(ebsdRegion.mad < 0.8)

ebsdCorrected = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     0    4052 (21%)  notIndexed          none                                   
     1   13359 (69%)  Forsterite  LightSkyBlue       mmm                         
     2   1333 (6.9%)   Enstatite  DarkSeaGreen       mmm                         
     3    676 (3.5%)    Diopside     Goldenrod     12/m1        X||a*, Y||b, Z||c
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [5000 → 15000] × [2000 → 7000] × [0 → 0]
 Normal vector: (0,0,1)

Plot the screened map with the same property on the same colour scale, so that it can be compared with the map above.

close all;
plot(ebsdCorrected, ebsdCorrected.mad);
mtexColorbar('title','mean angular deviation (degree)');
setColorRange([0 1.2]);

The yellow speckles have gone, because every measurement above 0.8° was removed. Those 881 positions are now empty and render as background.

The deep blue patches are still there, and that is the point to take from this figure. This threshold does not remove notIndexed points: they have no fit to report, so their mad is stored as 0 and passes every smaller-than test. All 4052 notIndexed points are still in the map above.

Dropping them is a separate phase selection. The deliberate output below shows how many indexed measurements remain.

ebsdCorrected('indexed')

ans = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     1   13359 (87%)  Forsterite  LightSkyBlue       mmm                         
     2   1333 (8.7%)   Enstatite  DarkSeaGreen       mmm                         
     3    676 (4.4%)    Diopside     Goldenrod     12/m1        X||a*, Y||b, Z||c
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [5000 → 15000] × [2000 → 7000] × [0 → 0]
 Normal vector: (0,0,1)

Combining selections

Conditions combine with MATLAB's elementwise AND and OR operators, or a phase name can narrow a logical selection. This example applies the region and MAD conditions together, then keeps only forsterite.

keep = inpolygon(ebsd,region) & ebsd.mad < 0.8;
goodForsterite = ebsd(keep);
goodForsterite = goodForsterite('Forsterite')

goodForsterite = EBSD (y↑→x)
 
 Phase  Orientations     Mineral         Color  Symmetry  Crystal reference frame
     1  13359 (100%)  Forsterite  LightSkyBlue       mmm                         
 
 Properties: bands, bc, bs, error, mad, oldId
 Scan unit : um
 X × Y × Z : [5000 → 15000] × [2000 → 7000] × [0 → 0]
 Normal vector: (0,0,1)

Whether notIndexed points should be dropped depends on the analysis that follows. Their locations often record cracks, poor surface preparation, unresolved phases, or difficult grain boundaries. Keep the raw variable and assign a selection to a new name so that this information is not overwritten. Filling Missing Data explains how missing orientations can be treated without pretending they were measured.

Further reading

Next

Select by Index distinguishes list position, persistent measurement id, map coordinates, and grid indices. Square and Hex Grids explains when to restore matrix shape. Continue with Grain Reconstruction before selecting whole grains rather than individual measurements.