Raw only Analysis

We can generate raw output which omits any sorting and clustering, for if you want to take a quick look at the raw data.

Luna Command

./tpx3dump process -i /Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/example_data.tpx3 -o /Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/example_data.h5 --raw-only --layout single

Python Script

noindex:

Raw only processing

import os, sys
import h5py  # ensure you have `pip install h5py`
import pandas as pd  # ensure you have `pip install pandas`
from typing import *
import matplotlib.pyplot as plt
import seaborn as sns
import warnings

warnings.filterwarnings("ignore")  # suppress warnings from plotting libraries.

sns.set_context(context="talk")

# add some paths to PYTHONPATH
for directory in ["..", "."]:
    sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), directory)))

# on our system "EXAMPLE_DATA_HDF5" refers to the absolute path
# to a hdf5 file generated by luna. Replace with your own!
from env_vars_for_docs_examples import EXAMPLE_DATA_HDF5, PLOTS_DIRECTORY

# re-use functions from previous example
from ex2_read_data_time_units import TimeUnit, load_pixel_hits

TOA_UNIT = TimeUnit.Nanoseconds


def plot_toa(pixel_data: pd.DataFrame, start: int = 0, stop: int = -1, fname=None, time_units: TimeUnit = TimeUnit.Nanoseconds):
    fig = plt.figure()
    plt.plot(pixel_data["toa"].iloc[start: stop], marker=".", linestyle='none')

    plt.title(f"ToA (ns) ({start if start != 0 else ''}:{stop if stop!= '-1' else ''} data points)")
    plt.ylabel(f"{time_units}")
    plt.xlabel("Unsorted index in data stream")
    sns.despine(fig)
    if fname is None:
        fname = os.path.join(PLOTS_DIRECTORY, f"ex11_toa_{start}-{stop}.png")
    plt.savefig(fname, dpi=150, bbox_inches="tight")
    print("Plot saved to \"{}\"".format(fname))


if __name__ == "__main__":
    pixel_hits = load_pixel_hits(EXAMPLE_DATA_HDF5, TOA_UNIT)
    print(pixel_hits.head().to_string())
    plot_toa(pixel_hits, start=0, stop=50)
    plot_toa(pixel_hits, start=0, stop=500)
    plot_toa(pixel_hits, start=0, stop=5000)
    plot_toa(pixel_hits, start=0, stop=50000)

Script Output

Example Output

hdf5 datasets: ['ExposureTimeBoundaries', 'PixelHits']
            toa  cid  tot  dtoa    x    y  tof
0  1.103455e+10   -1  150    -1  143  193   -1
1  1.103455e+10   -1  200    -1  140  193   -1
2  1.103459e+10   -1  850    -1   67   92   -1
3  1.103459e+10   -1  300    -1   68   91   -1
4  1.103459e+10   -1  150    -1   67   91   -1
Plot saved to "/Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/examples_output/plots/ex11_toa_0-50.png"
Plot saved to "/Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/examples_output/plots/ex11_toa_0-500.png"
Plot saved to "/Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/examples_output/plots/ex11_toa_0-5000.png"
Plot saved to "/Users/Ciaran/atlassian-bitbucket-pipelines-runner/temp/e71169e4-520a-5b30-a5ab-ee8a44eb5fac/build/docs/source/_static/examples_output/plots/ex11_toa_0-50000.png"