How to work with real data

Computing files

Before running the below commands make sure you have correctly installed and setup your environment.

Download the dataset to tmp directory (create it first). From the base folder run

laueotx realdata singlegrain 0 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000
laueotx realdata singlegrain 1 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000
laueotx realdata multigrain 0 1 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000

We will be analysing the merged output of the previous commands

fname = '../../results/realdata_fega10_v10_demo/analyze_sample__fega10_v10__merged.h5'

spot_loss, s_obs, s_mod, inds_mod, inds_obs, p_lam, s2g_mod_assign, s2g_obs_assign, s2s_mod_assign, s2s_obs_assign = plotting.load_sample(fname)

Code

a_est, x_est = plotting.load_grain_params(fname)
plotting.plotly_scatter3d_sample(a_est, x_est)

Code

omegas = range(0,360,4)

Plot grain statistics

Code

plotting.print_nspots_per_det(inds_obs[1], s2g_obs_assign, tag='detected ')
plotting.print_nspots_per_det(inds_mod[1], s2g_mod_assign, tag='model    ')

spots=detected  total      n_spots=269181 assigned  15698 [5.83%]
spots=detected  detector=0 n_spots=197047 assigned  12959 [6.58%]
spots=detected  detector=1 n_spots= 72134 assigned   2739 [3.80%]
spots=model     total      n_spots= 18889 assigned  15698 [83.11%]
spots=model     detector=0 n_spots= 15363 assigned  12959 [84.35%]
spots=model     detector=1 n_spots=  3526 assigned   2739 [77.68%]

Code

plotting.plotly_grain_stats(s2s_mod_assign, s2s_obs_assign, s2g_mod_assign, s2g_obs_assign, s_obs, s_mod, inds_mod, inds_obs)

n_grains=17

Plot prototype loss

Code

plotting.plotly_spot_loss(fname, n_max=None, xscale='linear', yscale='linear')

Plot spots for a given rotation angle

Code

plotting.plotly_scatter_spots_assignment_per_angle(s_obs=s_obs, inds_obs=inds_obs, s_mod=s_mod, inds_mod=inds_mod, spot_mod_assign=s2g_mod_assign, p_lam=p_lam, omegas=omegas, 
                                                   ind_angle=1, 
                                                   color_obs='darkgrey', 
                                                   lw=0.5, 
                                                   cmap='tab10')

Plot spots for a given grain

Code

plotting.plotly_scatter_spots_assignment_per_grain(s_obs=s_obs, inds_obs=inds_obs, s_mod=s_mod, inds_mod=inds_mod, spot_mod_assign=s2g_mod_assign, spot_obs_assign=s2g_obs_assign, p_lam=p_lam, omegas=omegas, 
                                                   ind_grain=1, 
                                                   color_obs='darkgrey', 
                                                   lw=0.5, 
                                                   cmap='tab10')

--- title: How to work with real data jupyter: python3 format: html: code-fold: true code-tools: true execute: echo: true --- ```{python} #| echo: false #| code-fold: false #| output: false import sys, os, h5py, bz2, matplotlib.pyplot as plt, importlib, itertools from tqdm.auto import tqdm, trange from collections import OrderedDict from IPython.display import set_matplotlib_formats import seaborn from ipywidgets import interactive, fixed set_matplotlib_formats('retina') plt.style.use('dark_background') # plt.style.use('default') import plotting ``` ## Computing files Before running the below commands make sure you have correctly installed and setup your environment. Download the dataset to `tmp` directory (create it first). From the base folder run ```python laueotx realdata singlegrain 0 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000 laueotx realdata singlegrain 1 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000 laueotx realdata multigrain 0 1 --conf tmp/config_realdata_fega10_v10_demo.yaml -o results/realdata_fega10_v10_demo/ --n-grid 1000 ``` We will be analysing the merged output of the previous commands ```{python} #| echo: true #| code-fold: false fname = '../../results/realdata_fega10_v10_demo/analyze_sample__fega10_v10__merged.h5' ``` ```{python} #| echo: true #| code-fold: false #| output: false spot_loss, s_obs, s_mod, inds_mod, inds_obs, p_lam, s2g_mod_assign, s2g_obs_assign, s2s_mod_assign, s2s_obs_assign = plotting.load_sample(fname) ``` ```{python} #| column: page a_est, x_est = plotting.load_grain_params(fname) plotting.plotly_scatter3d_sample(a_est, x_est) ``` ```{python} omegas = range(0,360,4) ``` ## Plot grain statistics ```{python} plotting.print_nspots_per_det(inds_obs[1], s2g_obs_assign, tag='detected ') plotting.print_nspots_per_det(inds_mod[1], s2g_mod_assign, tag='model ') ``` ```{python} #| column: page plotting.plotly_grain_stats(s2s_mod_assign, s2s_obs_assign, s2g_mod_assign, s2g_obs_assign, s_obs, s_mod, inds_mod, inds_obs) ``` ## Plot prototype loss ```{python} #| column: page plotting.plotly_spot_loss(fname, n_max=None, xscale='linear', yscale='linear') ``` ## Plot spots for a given rotation angle ```{python} #| column: page plotting.plotly_scatter_spots_assignment_per_angle(s_obs=s_obs, inds_obs=inds_obs, s_mod=s_mod, inds_mod=inds_mod, spot_mod_assign=s2g_mod_assign, p_lam=p_lam, omegas=omegas, ind_angle=1, color_obs='darkgrey', lw=0.5, cmap='tab10') ``` ## Plot spots for a given grain ```{python} #| column: page plotting.plotly_scatter_spots_assignment_per_grain(s_obs=s_obs, inds_obs=inds_obs, s_mod=s_mod, inds_mod=inds_mod, spot_mod_assign=s2g_mod_assign, spot_obs_assign=s2g_obs_assign, p_lam=p_lam, omegas=omegas, ind_grain=1, color_obs='darkgrey', lw=0.5, cmap='tab10') ```