defdap.hrdic module

class defdap.hrdic.Map(*args, **kwargs)

Bases: Map

Class to encapsulate DIC map data and useful analysis and plotting methods.

format

Software name.

Type:

str

version

Software version.

Type:

str

binning

Sub-window size in pixels.

Type:

int

xdim

Size of map along x (from header).

Type:

int

ydim

Size of map along y (from header).

Type:

int

shape

Size of map (after cropping, like *Dim).

Type:

tuple

corrVal

Correlation value.

Type:

numpy.ndarray

ebsd_map

EBSD map linked to DIC map.

Type:

defdap.ebsd.Map

highlight_alpha

Alpha (transparency) of grain highlight.

Type:

float

bseScale

Size of a pixel in the correlated images.

Type:

float

path

File path.

Type:

str

fname

File name.

Type:

str

crop_dists

Crop distances (default all zeros).

Type:

numpy.ndarray

data

Must contain after loading data (maps):

coordinatenumpy.ndarray

X and Y coordinates

displacementnumpy.ndarray

X and Y displacements

Generated data:

fnumpy.ndarray

Components of the deformation gradient (0=x, 1=y).

enumpy.ndarray

Components of the green strain (0=x, 1=y).

max_shearnumpy.ndarray

Max shear component np.sqrt(((e11 - e22) / 2.)**2 + e12**2).

Derived data:

Grain list data to map data from all grains

Type:

defdap.utils.Datastore

MAPNAME = 'hrdic'

property original_shape

property crystal_sym

load_data(file_name, data_type=None)

Load DIC data from file.

Parameters:

• file_name (pathlib.Path) – Name of file including extension.

• data_type (str, {'Davis', 'OpenPIV'}) – Type of data file.

load_corr_val_data(file_name, data_type=None)

Load correlation value for DIC data

Parameters:

• file_name (pathlib.Path or str) – Path to file.

• data_type (str, {'DavisImage'}) – Type of data file.

retrieve_name()

Gets the first name assigned to the a map, as a string

set_scale(scale)

Sets the scale of the map.

Parameters:

scale (float) – Length of pixel in original BSE image in micrometres.

property scale

Returns the number of micrometers per pixel in the DIC map.

print_stats_table(percentiles, components)

Print out a statistics table for a DIC map

Parameters:

• percentiles (list of float) – list of percentiles to print i.e. 0, 50, 99.

• components (list of str) – list of map components to print i.e. e, f, max_shear.

set_crop(*, left=None, right=None, top=None, bottom=None, update_homog_points=False)

Set a crop for the DIC map.

Parameters:

• left (int) – Distance to crop from left in pixels (formally xMin)

• right (int) – Distance to crop from right in pixels (formally xMax)

• top (int) – Distance to crop from top in pixels (formally yMin)

• bottom (int) – Distance to crop from bottom in pixels (formally yMax)

• update_homog_points (bool, optional) – If true, change homologous points to reflect crop.

crop(map_data, binning=None)

Crop given data using crop parameters stored in map i.e. cropped_data = DicMap.crop(DicMap.data_to_crop).

Parameters:

• map_data (numpy.ndarray) – Bap data to crop.

• binning (int) – True if mapData is binned i.e. binned BSE pattern.

link_ebsd_map(ebsd_map, transform_type='affine', **kwargs)

Calculates the transformation required to align EBSD dataset to DIC.

Parameters:

• ebsd_map (defdap.ebsd.Map) – EBSD map object to link.

• transform_type (str, optional) – affine, piecewiseAffine or polynomial.

• kwargs – All arguments are passed to estimate method of the transform.

check_ebsd_linked()

Check if an EBSD map has been linked.

Returns:

Returns True if EBSD map linked.

Return type:

bool

Raises:

Exception – If EBSD map not linked.

warp_to_dic_frame(map_data, **kwargs)

Warps a map to the DIC frame.

Parameters:

• map_data (numpy.ndarray) – Data to warp.

• kwargs – All other arguments passed to defdap.experiment.Experiment.warp_map().

Returns:

Map (i.e. EBSD map data) warped to the DIC frame.

Return type:

numpy.ndarray

generate_threshold_mask(mask, dilation=0, preview=True)

Generate a dilated mask, based on a boolean array and previews the appication of this mask to the max shear map.

Parameters:

• mask (numpy.array(bool)) – A boolean array where points to be removed are True

• dilation (int, optional) – Number of pixels to dilate the mask by. Useful to remove anomalous points around masked values. No dilation applied if not specified.

• preview (bool) – If true, show the mask and preview the masked effective shear strain map.

Examples

To remove data points in dic_map where max_shear is above 0.8, use:

>>> mask = dic_map.data.max_shear > 0.8

To remove data points in dic_map where e11 is above 1 or less than -1, use:

>>> mask = (dic_map.data.e[0, 0] > 1) | (dic_map.data.e[0, 0] < -1)

To remove data points in dic_map where corrVal is less than 0.4, use:

>>> mask = dic_map.corr_val < 0.4

Note: correlation value data needs to be loaded seperately from the DIC map, see defdap.hrdic.load_corr_val_data()

apply_threshold_mask()

Apply mask to all DIC map data by setting masked values to nan.

set_pattern(img_path, window_size)

Set the path to the image of the pattern.

Parameters:

• path (str) – Path to image.

• window_size (int) – Size of pixel in pattern image relative to pixel size of DIC data i.e 1 means they are the same size and 2 means the pixels in the pattern are half the size of the dic data.

load_pattern()

plot_grain_av_max_shear(**kwargs)

Plot grain map with grains filled with average value of max shear. This uses the max shear values stored in grain objects, to plot other data use plotGrainAv().

Parameters:

kwargs – All arguments are passed to defdap.base.Map.plot_grain_data_map().

find_grains(algorithm=None, min_grain_size=10)

Finds grains in the DIC map.

Parameters:

• algorithm (str {'warp', 'floodfill'}) – Use floodfill or warp algorithm.

• min_grain_size (int) – Minimum grain area in pixels for floodfill algorithm.

grain_inspector(vmax=0.1, correction_angle=0, rdr_line_length=3)

Run the grain inspector interactive tool.

Parameters:

• vmax (float) – Maximum value of the colour map.

• correction_angle (float) – Correction angle in degrees to subtract from measured angles to account for small rotation between DIC and EBSD frames. Approximately the rotation component of affine transform.

• rdr_line_length (int) – Length of lines perpendicular to slip trace used to calculate RDR.

class defdap.hrdic.Grain(grain_id, dicMap, group_id)

Bases: Grain

Class to encapsulate DIC grain data and useful analysis and plotting methods.

dicMap

DIC map this grain is a member of

Type:

defdap.hrdic.Map

ownerMap

DIC map this grain is a member of

Type:

defdap.hrdic.Map

maxShearList

List of maximum shear values for grain.

Type:

list

ebsd_grain

EBSD grain ID that this DIC grain corresponds to.

Type:

defdap.ebsd.Grain

ebsd_map

EBSD map that this DIC grain belongs to.

Type:

defdap.ebsd.Map

points_list

Start and end points for lines drawn using defdap.inspector.GrainInspector.

Type:

numpy.ndarray

groups_list

Groups, angles and slip systems detected for lines drawn using defdap.inspector.GrainInspector.

data

Must contain after creating:

pointlist of tuples

(x, y) in cropped map

Generated data:

Derived data:

Map data to list data from the map the grain is part of

Type:

defdap.utils.Datastore

plot_max_shear(**kwargs)

Plot a maximum shear map for a grain.

Parameters:

kwargs – All arguments are passed to defdap.base.plot_grain_data().

Return type:

defdap.plotting.GrainPlot

property ref_ori

Returns average grain orientation.

Return type:

defdap.quat.Quat

property slip_traces

Returns list of slip trace angles based on EBSD grain orientation.

Return type:

list

calc_slip_traces(slip_systems=None)

Calculates list of slip trace angles based on EBSD grain orientation.

Parameters:

slip_systems (defdap.crystal.SlipSystem, optional) –

calc_slip_bands(grain_map_data, thres=None, min_dist=None)

Use Radon transform to detect slip band angles.

Parameters:

• grain_map_data (numpy.ndarray) – Data to find bands in.

• thres (float, optional) – Normalised threshold for peaks.

• min_dist (int, optional) – Minimum angle between bands.

Returns:

Detected slip band angles

Return type:

list(float)

class defdap.hrdic.BoundarySet(dic_map, points, lines)

Bases: object

classmethod from_ebsd_boundaries(dic_map, ebsd_boundaries)

property image