The xarray.Dataset strucuture for AITA

xarrayaita is a dataset accessor for xarray. In this section we explain what is the minimal construction you need to build and what are the functions that you can apply through this xarrayaita

The minimal structure of xarrayaita

import xarrayaita.loadData_aita as lda #here are some function to build xarrayaita structure
import xarrayaita.aita as xa

import numpy as np
import matplotlib.pyplot as plt
import matplotlib.cm as cm
import xarray as xr

Load data to show an exemple.

# path to data and microstructure
path_data='orientation_test.dat'
path_micro='micro_test.bmp'

In this case we use a constructor function that takes as input :

  1. a .dat file that is an output from G50 fabric analyser. If you have another analyser it should be easy to implement another constructor function.

  2. a .bmp that is the microstructure image that must have been processed elsewhere in order to extract the grain boundaries from the orientation image (grain boundaries are the white pixel). This input can be left empty

help(lda.aita5col)
Help on function aita5col in module xarrayaita.loadData_aita:

aita5col(adr_data, micro_adress=0)
    Function to load the data from G50 analyser that have 5 columns
    
    :param adr_data: path to the data
    :type adr_data: str
    :param micro_adress: path to microstructure file (black and white image where grains boundaries are white) `.bmp`
    :type micro_adress: str
data=lda.aita5col(path_data,path_micro)

xarray.Dataset

The data structure is a regular xarray.Dataset. Therefore it can be used as one. (Pas clair!)

Specific function can be applied to it :

data.xa.FUNCTION

You can visualise what is stored in your xarray.Dataset using :

data
<xarray.Dataset>
Dimensions:      (uvecs: 2, x: 1000, y: 2500)
Coordinates:
  * x            (x) float64 0.0 0.02 0.04 0.06 0.08 ... 19.92 19.94 19.96 19.98
  * y            (y) float64 49.98 49.96 49.94 49.92 49.9 ... 0.06 0.04 0.02 0.0
Dimensions without coordinates: uvecs
Data variables:
    orientation  (y, x, uvecs) float64 2.395 0.6451 5.377 ... 0.6098 0.6473
    quality      (y, x) int64 0 90 92 93 92 92 94 94 ... 96 96 96 96 96 97 97 96
    micro        (y, x) float64 0.0 0.0 0.0 0.0 0.0 0.0 ... 0.0 0.0 0.0 0.0 0.0
    grainId      (y, x) int64 1 1 1 1 1 1 1 1 1 1 1 1 ... 1 1 1 1 1 1 1 1 1 1 1
Attributes:
    date:       Thursday, 19 Nov 2015, 11:24 am
    unit:       millimeters
    step_size:  0.02
    path_dat:   orientation_test.dat

There is 4 xarray.DataArray variables :

  1. orientation : that store the orientation of each pixel. It is store as azimuth and colatitude. (see figure below) It is meant to be use with xarrayuvecs DataArray.

  2. quality : that is the quality factor given by the analyser (between \([0,100]\)).

  3. micro : it is the microstrucure image given as input.

  4. grainId : it is a labelling of the microstrucure where each pixel within the same grain as a unique label.

This is the minimal structure to use xarrayaita function.

Visualisation of the variable

Every Data variable can be plotted using a regular xarray plot function

Orientation variable

The data are stored as azimuth and colatitude

plt.figure(figsize=(10,10))
plt.subplot(1,2,1)
data.orientation[:,:,0].plot()
plt.axis('equal')
plt.title('azimuth')
plt.subplot(1,2,2)
data.orientation[:,:,1].plot()
plt.axis('equal')
plt.title('colatitude')
Text(0.5, 1.0, 'colatitude')
../_images/The_dataset_structure_13_1.png

Quality variable

plt.figure(figsize=(5,10))
data.quality.plot(cmap=cm.gray)
plt.axis('equal')
plt.title('quality')
Text(0.5, 1.0, 'quality')
../_images/The_dataset_structure_15_1.png

GrainID variable

plt.figure(figsize=(5,10))
data.grainId.plot()
plt.axis('equal')
plt.title('grainId')
Text(0.5, 1.0, 'grainId')
../_images/The_dataset_structure_17_1.png

If you prefer to look at Bunge Euler angles you can extract them using uvecs

All the variable are visible in your xarray.Dataset

The function within xarrayaita

xa.filter

It only affects the orientation value. When the data.quality variable is below the given value val the orienation value is replace by a nan.

help(xa.aita.filter)
Help on function filter in module xarrayaita.aita:

filter(self, val)
    Put nan value in orientation file
data.aita.filter(75)
plt.figure(figsize=(10,10))
plt.subplot(1,2,1)
data.orientation[:,:,0].plot()
plt.axis('equal')
plt.title('azimuth')
plt.subplot(1,2,2)
data.orientation[:,:,1].plot()
plt.axis('equal')
plt.title('colatitude')
Text(0.5, 1.0, 'colatitude')
../_images/The_dataset_structure_24_1.png

Symmetry transformation

fliplr

Flip the data with a horizontal mirror.

help(xa.aita.fliplr)
Help on function fliplr in module xarrayaita.aita:

fliplr(self)
    flip left right the data and rotate the orientation
    
    May be it is more a routation around the 0y axis of 180 degree

rot180

help(xa.aita.rot180)
Help on function rot180 in module xarrayaita.aita:

rot180(self)
    rotate 180 degre around Oz the data and rotate the orientation