defdap.base module¶

class defdap.base.Map(file_name, data_type=None, experiment=None, increment=None, frame=None, map_name=None)[source]¶

Bases: ABC

Base class for a map. Contains common functionality for all maps.

_grains¶

List of grains.

Type:: list of defdap.base.Grain

sel_grain¶

The last selected grain

Type:: defdap.base.grain

abstract load_data(file_name, data_type=None)[source]¶

property grains¶

property x_dim¶

property y_dim¶

crop(map_data, **kwargs)[source]¶

set_homog_point(**kwargs)[source]¶

plot_grain_numbers(dilate_boundaries=False, ax=None, **kwargs)[source]¶

Plot a map with grains numbered.

Parameters:

dilate_boundaries (bool, optional) – Set to true to dilate boundaries.
ax (matplotlib.axes.Axes, optional) – axis to plot on, if not provided the current active axis is used.
kwargs (dict, optional) – Keyword arguments passed to defdap.plotting.MapPlot.add_grain_numbers()

Return type:

defdap.plotting.MapPlot

locate_grain(click_event=None, display_grain=False, **kwargs)[source]¶

Interactive plot for identifying grains.

Parameters:

click_event (optional) – Click handler to use.
display_grain (bool, optional) – If true, plot slip traces for grain selected by click.
kwargs (dict, optional) – Keyword arguments passed to defdap.base.Map.plot_default()

click_grain_id(event, plot, display_grain)[source]¶

Event handler to capture clicking on a map.

Parameters:

event – Click event.
plot (defdap.plotting.MapPlot) – Plot to capture clicks from.
display_grain (bool) – If true, plot the selected grain alone in pop-out window.

draw_line_profile(**kwargs)[source]¶

Interactive plot for drawing a line profile of data.

Parameters:: kwargs (dict, optional) – Keyword arguments passed to defdap.base.Map.plot_default()

calc_line_profile(plot, start_end, **kwargs)[source]¶

Calculate and plot the line profile.

Parameters:

plot (defdap.plotting.MapPlot) – Plot to calculate the line profile for.
start_end (array_like) – Selected points (x0, y0, x1, y1).
kwargs (dict, optional) – Keyword arguments passed to matplotlib.pyplot.plot()

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

display_neighbours(**kwargs)[source]¶

click_grain_neighbours(event, plot)[source]¶

Event handler to capture clicking and show neighbours of selected grain.

Parameters:

event – Click event.
plot (defdap.plotting.MapPlot) – Plot to monitor.

property proxigram¶

Proxigram for a map.

Returns:: Distance from a grain boundary at each point in map.
Return type:: numpy.ndarray

calc_proxigram(num_trials=500)[source]¶

Calculate distance from a grain boundary at each point in map.

Parameters:: num_trials (int, optional) – number of trials.

plot_map(map_name, component=None, **kwargs)[source]¶

Plot a map from the DIC data.

Parameters:

map_name (str) – Map data name to plot i.e. e, max_shear, euler_angle, orientation.
component (int or tuple of int or str) – Component of the map data to plot. This is either the tensor component (int or tuple of ints) or the name of a calculation to be applied e.g. ‘norm’, ‘all_euler’ or ‘IPF_x’.
kwargs – All arguments are passed to defdap.plotting.MapPlot.create().

Returns:

Plot containing map.

Return type:

defdap.plotting.MapPlot

calc_grain_average(map_data, grain_ids=- 1)[source]¶

Calculate grain average of any DIC map data.

Parameters:

map_data (numpy.ndarray) – Array of map data to grain average. This must be cropped!
grain_ids (list, optional) – grain_ids to perform operation on, set to -1 for all grains.

Returns:

Array containing the grain average values.

Return type:

numpy.ndarray

grain_data_to_map(name)[source]¶

grain_data_to_map_data(grain_data, grain_ids=- 1, bg=0)[source]¶

Create a map array with each grain filled with the given values.

Parameters:

grain_data (list or numpy.ndarray) – Grain values. This can be a single value per grain or RGB values.
grain_ids (list of int or int, optional) – IDs of grains to plot for. Use -1 for all grains in the map.
bg (int or real, optional) – Value to fill the background with.

Returns:

grain_map – Array filled with grain data values

Return type:

numpy.ndarray

plot_grain_data_map(map_data=None, grain_data=None, grain_ids=- 1, bg=0, **kwargs)[source]¶

Plot a grain map with grains coloured by given data. The data can be provided as a list of values per grain or as a map which a grain average will be applied.

Parameters:

map_data (numpy.ndarray, optional) – Array of map data. This must be cropped! Either mapData or grain_data must be supplied.
grain_data (list or np.array, optional) – Grain values. This an be a single value per grain or RGB values. You must supply either mapData or grain_data.
grain_ids (list of int or int, optional) – IDs of grains to plot for. Use -1 for all grains in the map.
bg (int or real, optional) – Value to fill the background with.
kwargs (dict, optional) – Keyword arguments passed to defdap.plotting.MapPlot.create()

Returns:

plot – Plot object created

Return type:

defdap.plotting.MapPlot

plot_grain_data_ipf(direction, map_data=None, grain_data=None, grain_ids=- 1, **kwargs)[source]¶

Plot IPF of grain reference (average) orientations with points coloured by grain average values from map data.

Parameters:

direction (numpy.ndarray) – Vector of reference direction for the IPF.
map_data (numpy.ndarray) – Array of map data. This must be cropped! Either mapData or grain_data must be supplied.
grain_data (list or np.array, optional) – Grain values. This an be a single value per grain or RGB values. You must supply either mapData or grain_data.
grain_ids (list of int or int, optional) – IDs of grains to plot for. Use -1 for all grains in the map.
kwargs (dict, optional) – Keyword arguments passed to defdap.quat.Quat.plot_ipf()

class defdap.base.Grain(grain_id, owner_map, group_id)[source]¶

Bases: ABC

Base class for a grain.

grain_id¶

Type:: int

owner_map¶

Type:: defdap.base.Map

property extreme_coords¶

Coordinates of the bounding box for a grain.

Returns:: minimum x, minimum y, maximum x, maximum y.
Return type:: int, int, int, int

centre_coords(centre_type='box', grain_coords=True)[source]¶

Calculates the centre of the grain, either as the centre of the bounding box or the grains centre of mass.

Parameters:

centre_type (str, optional, {'box', 'com'}) – Set how to calculate the centre. Either ‘box’ for centre of bounding box or ‘com’ for centre of mass. Default is ‘box’.
grain_coords (bool, optional) – If set True the centre is returned in the grain coordinates otherwise in the map coordinates. Defaults is grain.

Returns:

Coordinates of centre of grain.

Return type:

int, int

grain_outline(bg=nan, fg=0)[source]¶

Generate an array of the grain outline.

Parameters:

bg (int) – Value for points not within grain.
fg (int) – Value for points within grain.

Returns:

Bounding box for grain with nan outside the grain and given number within.

Return type:

numpy.ndarray

plot_outline(ax=None, plot_scale_bar=False, **kwargs)[source]¶

Plot the outline of the grain.

Parameters:

ax (matplotlib.axes.Axes) – axis to plot on, if not provided the current active axis is used.
plot_scale_bar (bool) – plots the scale bar on the grain if true.
kwargs (dict) – keyword arguments passed to defdap.plotting.GrainPlot.add_map()

Return type:

defdap.plotting.GrainPlot

grain_data(map_data)[source]¶

Extract this grains data from the given map data.

Parameters:: map_data (numpy.ndarray) – Array of map data. This must be cropped!
Returns:: Array containing this grains values from the given map data.
Return type:: numpy.ndarray

grain_map_data(map_data=None, grain_data=None, bg=nan)[source]¶

Extract a single grain map from the given map data.

Parameters:

map_data (numpy.ndarray) – Array of map data. This must be cropped! Either this or ‘grain_data’ must be supplied and ‘grain_data’ takes precedence.
grain_data (numpy.ndarray) – Array of data at each point in the grain. Either this or ‘mapData’ must be supplied and ‘grain_data’ takes precedence.
bg (various, optional) – Value to fill the background with. Must be same dtype as input array.

Returns:

Grain map extracted from given data.

Return type:

numpy.ndarray

grain_map_data_coarse(map_data=None, grain_data=None, kernel_size=2, bg=nan)[source]¶

Create a coarsened data map of this grain only from the given map data. Data is coarsened using a kernel at each pixel in the grain using only data in this grain.

Parameters:

map_data (numpy.ndarray) – Array of map data. This must be cropped! Either this or ‘grain_data’ must be supplied and ‘grain_data’ takes precedence.
grain_data (numpy.ndarray) – List of data at each point in the grain. Either this or ‘mapData’ must be supplied and ‘grain_data’ takes precedence.
kernel_size (int, optional) – Size of kernel as the number of pixels to dilate by i.e 1 gives a 3x3 kernel.
bg (various, optional) – Value to fill the background with. Must be same dtype as input array.

Returns:

Map of this grains coarsened data.

Return type:

numpy.ndarray

plot_grain_data(map_data=None, grain_data=None, **kwargs)[source]¶

Plot a map of this grain from the given map data.

Parameters:

map_data (numpy.ndarray) – Array of map data. This must be cropped! Either this or ‘grain_data’ must be supplied and ‘grain_data’ takes precedence.
grain_data (numpy.ndarray) – List of data at each point in the grain. Either this or ‘mapData’ must be supplied and ‘grain_data’ takes precedence.
kwargs (dict, optional) – Keyword arguments passed to defdap.plotting.GrainPlot.create()