#!/usr/bin/env python
# coding: utf-8

# This notebook is part of the `kikuchipy` documentation https://kikuchipy.org.
# Links to the documentation won't work from the notebook.

# # Change navigation and signal shapes
# 
# Patterns in an [EBSD](reference.rst#kikuchipy.signals.EBSD) or
# [EBSDMasterPattern](reference.rst#kikuchipy.signals.EBSDMasterPattern) signal
# `s` are stored in the `s.data` attribute as either [numpy.ndarray](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html) or
# [dask.array.Array](https://docs.dask.org/en/latest/array.html).
# [HyperSpy's user guide](http://hyperspy.org/hyperspy-doc/current/user_guide/signal.html#indexing)
# explains how to access, i.e. index, the data. This section details example uses
# of navigation (scan) and signal (pattern) indexing specific to EBSD and
# EBSDMasterPattern signals.
# 
# Let's import the necessary libraries, a larger Nickel EBSD test data set from
# the [kikuchipy.data](reference.rst#kikuchipy.data.nickel_ebsd_large) module
# <cite data-cite="aanes2019electron">Ånes et al. (2019)</cite>, and the Nickel
# master pattern, also from the data module

# In[ ]:


# exchange inline for qt5 for interactive plotting from the pyqt package
get_ipython().run_line_magic('matplotlib', 'inline')

import hyperspy.api as hs
import kikuchipy as kp
import matplotlib.pyplot as plt
import numpy as np

plt.rcParams["font.size"] = 15


# Use kp.load("data.h5") to load your own data
s = kp.data.nickel_ebsd_large(allow_download=True)  # External download
print(s)

s_mp = kp.data.nickel_ebsd_master_pattern_small(hemisphere="both")
print(s_mp, s_mp.projection)


# ## Crop the navigation or signal axes
# 
# A new `EBSD` or `EBSDMasterPattern` signal `s2` can be created from a region of
# interest (ROI) in another EBSD or EBSDMasterPattern signal `s` by using
# HyperSpy's navigation indexing method ``inav``. The new signal keeps the
# `metadata` and `original_metadata` of `s`. Say we, after plotting and inspecting
# the EBSD signal, want to create a new, smaller signal of the patterns within a
# rectangle defined by the upper left pattern with index (5, 7) (column, row) and
# the bottom right pattern with index (17, 23)

# In[ ]:


s2 = s.inav[5:17, 7:23]
s2


# Or, we want only the northern hemisphere of the `EBSDMasterPattern`

# In[ ]:


s_mp2 = s_mp.inav[0]
s_mp2


# Patterns can also be cropped with the signal indexing method `isig`. Say we
# wanted to remove the ten outermost pixels in our (60, 60) pixel Nickel patterns

# In[ ]:


s3 = s.isig[10:50, 10:50]
s3


# In[ ]:


fig, ax = plt.subplots(figsize=(13, 6), ncols=2)
ax[0].imshow(s.inav[10, 50].data, cmap="gray")
ax[0].set_title("Original")
ax[0].axis("off")
ax[1].imshow(s3.inav[10, 50].data, cmap="gray")
ax[1].set_title("Cropped")
ax[1].axis("off")
fig.tight_layout(w_pad=-8)


# ## Binning
# 
# A new `EBSD` signal with patterns binned e.g. by 2 can be obtained using the
# [rebin()](reference.rst#kikuchipy.signals.EBSD.rebin) method provided by
# HyperSpy, explained further in
# [their user guide](http://hyperspy.org/hyperspy-doc/current/user_guide/signal.html#rebinning),
# by passing in either the `scale` or `new_shape` parameter

# In[ ]:


print(s, s.data.dtype)


# In[ ]:


s4 = s.rebin(scale=(1, 1, 2, 2))
print(s4, s4.data.dtype)


# In[ ]:


s5 = s.rebin(new_shape=(75, 55, 30, 30))
print(s5, s5.data.dtype)


# In[ ]:


fig, ax = plt.subplots(figsize=(13, 6), ncols=2)
ax[0].imshow(s4.inav[10, 50].data, cmap="gray")
ax[0].set_title("rebin() with scale")
ax[1].imshow(s5.inav[10, 50].data, cmap="gray")
ax[1].set_title("rebin() with new_shape")
fig.tight_layout()


# Note that `rebin()` casts the data to `uint64`. This means that in this example,
# each pixel in the binned signals `s4` and `s5` takes up eight times the memory
# of pixels in the original signal `s` (`uint8`). To revert to `uint8` data type,
# we must rescale the intensities with
# [rescale_intensity()](reference.rst#kikuchipy.signals.EBSD.rescale_intensity).
# 
# This also works for `EBSDMasterPattern` signals.