defdap.ebsd module¶

class defdap.ebsd.Map(fileName, dataType=None)[source]¶

Bases: defdap.base.Map

Class to encapsulate an EBSD map and useful analysis and plotting methods.

step_size¶

Step size in micron.

Type:: float

phases¶

List of phases.

Type:: list of defdap.crystal.Phase

boundaries¶

Map of boundaries. -1 for a boundary, 0 otherwise.

Type:: numpy.ndarray

phaseBoundaries¶

Map of phase boundaries. -1 for boundary, 0 otherwise.

Type:: numpy.ndarray

grains¶

Map of grains. Grain numbers start at 1 here but everywhere else grainID starts at 0. Regions that are smaller than the minimum grain size are given value -2. Remnant boundary points are -1.

Type:: numpy.ndarray

misOri¶

Map of misorientation.

Type:: numpy.ndarray

misOriAxis¶

Map of misorientation axis components.

Type:: list of numpy.ndarray

origin¶

Map origin (x, y). Used by linker class where origin is a homologue point of the maps.

Type:: tuple(int)

data¶

Must contain after loading data (maps):

phasenumpy.ndarray: 1-based, 0 is non-indexed points
euler_anglenumpy.ndarray: stored as (3, yDim, xDim) in radians

Derived data:

orientationnumpy.ndarray of defdap.quat.Quat: Quaterion for each point of map. Shape (yDim, xDim).
KAMnumpy.ndarray: Kernal average misorientaion map.
GNDnumpy.ndarray: GND scalar map.
Nye_tensornumpy.ndarray: 3x3 Nye tensor at each point.

Type:: defdap.utils.Datastore

loadData(fileName, dataType=None)[source]¶

Load in EBSD data from file.

Parameters:

fileName (str) – Path to EBSD file, including name, excluding extension.
dataType (str, {'OxfordBinary', 'OxfordText'}) – Format of EBSD data file.

save(file_name, data_type=None, file_dir='')[source]¶

Save EBSD map to file.

Parameters:

file_name (str) – Name of file to save to, it must not already exist.
data_type (str, {'OxfordText'}) – Format of EBSD data file to save.
file_dir (str) – Directory to save the file to.

property crystalSym¶

Crystal symmetry of the primary phase.

Returns:: Crystal symmetry
Return type:: str

property cOverA¶

C over A ratio of the primary phase

Returns:: C over A ratio if hexagonal crystal structure otherwise None
Return type:: float or None

property numPhases¶

property primaryPhase¶

Primary phase of the EBSD map.

Returns:: Primary phase
Return type:: defdap.crystal.Phase

property scale¶

plotBandContrastMap(**kwargs)[source]¶

Plot band contrast map

kwargs: All arguments are passed to defdap.plotting.MapPlot.create().

Returns:
Return type:: defdap.plotting.MapPlot

plotEulerMap(phases=None, **kwargs)[source]¶

Plot an orientation map in Euler colouring

Parameters:

phases (list of int) – Which phases to plot for
kwargs – All arguments are passed to defdap.plotting.MapPlot.create().

Returns:

Return type:

defdap.plotting.MapPlot

plotIPFMap(direction, backgroundColour=None, phases=None, **kwargs)[source]¶

Plot a map with points coloured in IPF colouring, with respect to a given sample direction.

Parameters:

direction (np.array len 3) – Sample directiom.
backgroundColour (np.array len 3) – Colour of background (i.e. for phases not plotted).
phases (list of int) – Which phases to plot IPF data for.
kwargs – Other arguments passed to defdap.plotting.MapPlot.create().

Returns:

Return type:

defdap.plotting.MapPlot

plotPhaseMap(**kwargs)[source]¶

Plot a phase map.

Parameters:: kwargs – All arguments passed to defdap.plotting.MapPlot.create().
Returns:
Return type:: defdap.plotting.MapPlot

calc_kam()[source]¶: Calculates Kernel Average Misorientaion (KAM) for the EBSD map, based on a 3x3 kernel. Crystal symmetric equivalences are not considered. Stores result as KAM.

plotKamMap(**kwargs)[source]¶

Plot Kernel Average Misorientaion (KAM) for the EBSD map.

Parameters:: kwargs – All arguments are passed to defdap.plotting.MapPlot.create().
Returns:
Return type:: defdap.plotting.MapPlot

calc_nye()[source]¶: Calculates Nye tensor and related GND density for the EBSD map. Stores result as Nye_tensor and GND. Uses the crystal symmetry of the primary phase.

plotGNDMap(**kwargs)[source]¶

Plots a map of geometrically necessary dislocation (GND) density

Parameters:: kwargs – All arguments are passed to defdap.plotting.MapPlot.create().
Returns:
Return type:: defdap.plotting.MapPlot

checkDataLoaded()[source]¶

Checks if EBSD data is loaded

Returns:: True if data loaded
Return type:: bool

buildQuatArray()[source]¶: Build quaternion array

filterData(misOriTol=5)[source]¶

findBoundaries(boundDef=10)[source]¶

Find grain and phase boundaries

Parameters:: boundDef (float) – Critical misorientation.

buildNeighbourNetwork()[source]¶: Construct a list of neighbours

plotPhaseBoundaryMap(dilate=False, **kwargs)[source]¶

Plot phase boundary map.

Parameters:

dilate (bool) – If true, dilate boundary.
kwargs – All other arguments are passed to defdap.plotting.MapPlot.create().

Returns:

Return type:

defdap.plotting.MapPlot

plotBoundaryMap(**kwargs)[source]¶

Plot grain boundary map.

Parameters:: kwargs – All arguments are passed to defdap.plotting.MapPlot.create().
Returns:
Return type:: defdap.plotting.MapPlot

findGrains(minGrainSize=10)[source]¶

Find grains and assign IDs.

Parameters:: minGrainSize (int) – Minimum grain area in pixels.

plotGrainMap(**kwargs)[source]¶

Plot a map with grains coloured.

Parameters:: kwargs – All arguments are passed to defdap.plotting.MapPlot.create().
Returns:
Return type:: defdap.plotting.MapPlot

floodFill(x, y, grainIndex, points_left)[source]¶

Flood fill algorithm that uses the x and y boundary arrays to fill a connected area around the seed point. The points are inserted into a grain object and the grain map array is updated.

Parameters:

x (int) – Seed point x for flood fill
y (int) – Seed point y for flood fill
grainIndex (int) – Value to fill in grain map
points_left (numpy.ndarray) – Boolean map of the points that have not been assigned a grain yet

Returns:

currentGrain – New grain object with points added

Return type:

defdap.ebsd.Grain

calcGrainAvOris()[source]¶: Calculate the average orientation of grains.

calcGrainMisOri(calcAxis=False)[source]¶

Calculate the misorientation within grains.

Parameters:: calcAxis (bool) – Calculate the misorientation axis if True.

plotMisOriMap(component=0, **kwargs)[source]¶

Plot misorientation map.

Parameters:

component (int, {0, 1, 2, 3}) – 0 gives misorientation, 1, 2, 3 gives rotation about x, y, z
kwargs – All other arguments are passed to defdap.plotting.MapPlot.create().

Returns:

Return type:

defdap.plotting.MapPlot

calcAverageGrainSchmidFactors(loadVector, slipSystems=None)[source]¶

Calculates Schmid factors for all slip systems, for all grains, based on average grain orientation.

Parameters:

loadVector – Loading vector, e.g. [1, 0, 0].
slipSystems (list, optional) – Slip planes to calculate Schmid factor for, maximum of all planes calculated if not given.

plotAverageGrainSchmidFactorsMap(planes=None, directions=None, **kwargs)[source]¶

Plot maximum Schmid factor map, based on average grain orientation (for all slip systems unless specified).

Parameters:

planes (list, optional) – Plane ID(s) to consider. All planes considered if not given.
directions (list, optional) – Direction ID(s) to consider. All directions considered if not given.
kwargs – All other arguments are passed to defdap.plotting.MapPlot.create().

Returns:

Return type:

defdap.plotting.MapPlot

class defdap.ebsd.Grain(grainID, ebsdMap)[source]¶

Bases: defdap.base.Grain

Class to encapsulate a grain in an EBSD map and useful analysis and plotting methods.

ebsdMap¶

EBSD map this grain is a member of.

Type:: defdap.ebsd.Map

ownerMap¶

EBSD map this grain is a member of.

Type:: defdap.ebsd.Map

phaseID¶

Type:: int

phase¶

Type:: defdap.crystal.Phase

quatList¶

List of quats.

Type:: list

misOriList¶

MisOri at each point in grain.

Type:: list

misOriAxisList¶

MisOri axes at each point in grain.

Type:: list

refOri¶

Average ori of grain

Type:: defdap.quat.Quat

averageMisOri¶: Average misOri of grain.

averageSchmidFactors¶

List of list Schmid factors (grouped by slip plane).

Type:: list

slipTraceAngles¶

Slip trace angles in screen plane.

Type:: list

slipTraceInclinations¶

Angle between slip plane and screen plane.

Type:: list

property plotDefault¶

property crystalSym¶: Temporary

addPoint(coord, quat)[source]¶

Append a coordinate and a quat to a grain.

Parameters:

coord (tuple) – (x,y) coordinate to append
quat (defdap.quat.Quat) – Quaternion to append.

calcAverageOri()[source]¶: Calculate the average orientation of a grain.

buildMisOriList(calcAxis=False)[source]¶

Calculate the misorientation within given grain.

Parameters:: calcAxis (bool) – Calculate the misorientation axis if True.

plotRefOri(direction=array([0, 0, 1]), **kwargs)[source]¶

Plot the average grain orientation on an IPF.

Parameters:

direction (numpy.ndarray) – Sample direction for IPF.
kwargs – All other arguments are passed to defdap.quat.Quat.plotIPF().

Returns:

Return type:

defdap.plotting.PolePlot

plotOriSpread(direction=array([0, 0, 1]), **kwargs)[source]¶

Plot all orientations within a given grain, on an IPF.

Parameters:

direction (numpy.ndarray) – Sample direction for IPF.
kwargs – All other arguments are passed to defdap.quat.Quat.plotIPF().

Returns:

Return type:

defdap.plotting.PolePlot

plotUnitCell(fig=None, ax=None, plot=None, **kwargs)[source]¶

Plot an unit cell of the average grain orientation.

Parameters:

fig (matplotlib.figure.Figure) – Matplotlib figure to plot on
ax (matplotlib.figure.Figure) – Matplotlib figure to plot on
plot (defdap.plotting.PolePlot) – defdap plot to plot the figure to.
kwargs – All other arguments are passed to defdap.quat.Quat.plotUnitCell().

plotMisOri(component=0, **kwargs)[source]¶

Plot misorientation map for a given grain.

Parameters:

component (int, {0, 1, 2, 3}) – 0 gives misorientation, 1, 2, 3 gives rotation about x, y, z.
kwargs – All other arguments are passed to defdap.ebsd.plotGrainData().

Returns:

Return type:

defdap.plotting.GrainPlot

calcAverageSchmidFactors(loadVector, slipSystems=None)[source]¶

Calculate Schmid factors for grain, using average orientation.

Parameters:

loadVector (numpy.ndarray) – Loading vector, i.e. [1, 0, 0]
slipSystems (list, optional) – Slip planes to calculate Schmid factor for. Maximum for all planes used if not set.

property slipTraces¶

Returns list of slip trace angles.

Returns:: Slip trace angles based on grain orientation in calcSlipTraces.
Return type:: list

printSlipTraces()[source]¶: Print a list of slip planes (with colours) and slip directions

calcSlipTraces(slipSystems=None)[source]¶

Calculates list of slip trace angles based on grain orientation.

Parameters:: slipSystems (defdap.crystal.SlipSystem, optional) –

class defdap.ebsd.BoundarySegment(ebsdMap, grain1, grain2)[source]¶

Bases: object

addBoundaryPoint(point, kind, ownerGrain)[source]¶

boundaryPointPairs(kind)[source]¶: Return pairs of points either side of the boundary. The first point is always in grain1

property boundaryPointPairsX¶: Return pairs of points either side of the boundary. The first point is always in grain1

property boundaryPointPairsY¶: Return pairs of points either side of the boundary. The first point is always in grain1

property boundaryLines¶: Return line points along this boundary segment

misorientation()[source]¶

static boundary_points_to_lines(*, boundary_points_x=None, boundary_points_y=None)[source]¶

class defdap.ebsd.Linker(ebsd_maps)[source]¶

Bases: object

Class for linking multiple EBSD maps of the same region for analysis of deformation.

ebsd_maps¶

List of ebsd.Map objects that are linked.

Type:: list(ebsd.Map)

links¶

List of grain link. Each link is stored as a tuple of grain IDs (one from each map stored in same order of maps).

Type:: list(tuple(int))

plots¶

List of last opened plot of each map.

Type:: list(plotting.MapPlot)

set_origin(**kwargs)[source]¶

Interacive tool to set origin of each EBSD map.

Parameters:: kwargs – Keyword arguments passed to defdap.ebsd.Map.plotDefault()

click_set_origin(event, plot)[source]¶

Event handler for clicking to set origin of map.

Parameters:

event – Click event.
plot (defdap.plotting.MapPlot) – Plot to capture clicks from.

start_linking()[source]¶: Start interactive grain linking process of each EBSD map.

click_grain_guess(event, plot)[source]¶

Guesses grain position in other maps, given click on one.

Parameters:

event – Click handler.
plot (defdap.plotting.Plot) – Plot to capture clicks from.

make_link(event, plot)[source]¶: Make a link between the EBSD maps after clicking.

reset_links()[source]¶: Reset links.

set_ref_ori_from_master()[source]¶: Loop over each map (not first/reference) and each link. Sets refOri of linked grains to refOri of grain in first map.

update_misori(calc_axis=False)[source]¶

Recalculate misorientation for linked grain (not for first map)

Parameters:: calc_axis (bool) – Calculate the misorientation axis if True.