combined_orientation.py

import os
import sys

import numpy as np
import pickle
from tqdm import tqdm as report_progress

import matplotlib
# matplotlib.use('Qt5Agg')
matplotlib.use('pgf')
import matplotlib.pyplot as plt


import hyperspy.api as hs
from pyxem.signals.indexation_results import IndexationResults

from common import result_object_file_info
from parameters import parameters_parse


matplotlib.rcParams['text.usetex'] = True
matplotlib.rcParams['pgf.rcfonts'] = False
matplotlib.rcParams['image.interpolation'] = 'none'


def save_figure(signal, filename, padding=(0.05, 0.05, 1, 1), size=(2.5, 2.5), **kwargs):
    plot = hs.plot.plot_images(signal,
            label=None,
            suptitle=None,
            tight_layout=True,
            padding={'left': padding[0], 'bottom': padding[1], 'right': padding[2], 'top': padding[3]},
            **kwargs)[0]
    plot.figure.set_size_inches(size)

    plot.figure.savefig(filename + '.pdf')
    plot.figure.savefig(filename + '.pgf')
    # plt.show()

def combine_indexation_results(object_infos):
    total_width  = max((info['x_stop'] for info in object_infos))
    total_height = max((info['y_stop'] for info in object_infos))

    combined_indexation_results_data = None

    for object_info in object_infos:
        print('Tile {}:{}  {}:{} (of {} {})'.format(
            object_info['x_start'], object_info['x_stop'],
            object_info['y_start'], object_info['y_stop'],
            total_width, total_height))

        with open(object_info['filename'], 'rb') as f:
            indexation_results_data = pickle.load(f)

        if combined_indexation_results_data is None:
            combined_indexation_results_data = np.zeros((total_height, total_width, *indexation_results_data.shape[2:4]))

        combined_indexation_results_data[
                object_info['y_start']:object_info['y_stop'],
                object_info['x_start']:object_info['x_stop']] = indexation_results_data

    return IndexationResults(combined_indexation_results_data)


def combine_orientations(result_directory):
    parameters = parameters_parse(os.path.join(result_directory, 'metadata.txt'))
    methods = [
            method.strip() for method in parameters['methods'].split(',')
            if parameters['__save_method_{}'.format(method.strip())] == 'object']

    object_infos = result_object_file_info(result_directory)
    if 'template_match' in object_infos:
        indexation_results = combine_indexation_results(object_infos['template_match'])

        crystal_map = indexation_results.get_crystallographic_map()
        crystal_map.save_mtex_map('mtex_test.csv')
        phase_map = crystal_map.get_phase_map()
        orientation_map = crystal_map.get_orientation_map()

        phase_map.metadata.General.title = 'Phase map'
        phase_map.axes_manager.signal_axes[0].name = '$x$'
        phase_map.axes_manager.signal_axes[1].name = '$y$'
        orientation_map.axes_manager.signal_axes[0].name = '$x$'
        orientation_map.axes_manager.signal_axes[1].name = '$y$'
        save_figure(phase_map, os.path.join(result_directory, 'phase_map'), scalebar='all', colorbar=False)
        save_figure(orientation_map, os.path.join(result_directory, 'orientation_map'),
                padding=(0.1, 0.05, 1, 1),
                scalebar='all')



        # dp = hs.load('D:/Dokumenter/MTNANO/Prosjektoppgave/SPED_data_GaAs_NW/gen/Julie_180510_SCN45_FIB_a_three_phase_single_area.hdf5')
        # dp.axes_manager.signal_axes[0].scale = 0.032
        # dp.axes_manager.signal_axes[1].scale = 0.032
        # dp.axes_manager.signal_axes[0].offset = -72*0.032
        # dp.axes_manager.signal_axes[1].offset = -72*0.032
        # print(dp.axes_manager)
        # from pyxem.libraries.diffraction_library import load_DiffractionLibrary
        # diffraction_library_cache_filename = os.path.join(
            # parameters['output_dir'],
            # 'tmp/diffraction_library_{}.pickle'.format(parameters['shortname']))
        # library = load_DiffractionLibrary(diffraction_library_cache_filename, safety=True)
        # indexation_results.plot_best_matching_results_on_signal(dp, ['zb', 'wz'], library)
        # crystal_map.get_reliability_map_phase().plot()
        # crystal_map.get_reliability_map_orientation().plot()
        # plt.show()

        # print(crystal_map.axes_manager)
        # print(crystal_map.data)


if __name__ == '__main__':
    hs.preferences.General.nb_progressbar = False
    hs.preferences.General.show_progressbar = False
    result_directory = sys.argv[1]
    combine_orientations(result_directory)