#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# pept is a Python library that unifies Positron Emission Particle
# Tracking (PEPT) research, including tracking, simulation, data analysis
# and visualisation tools
#
# Copyright (C) 2019 Andrei Leonard Nicusan
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
# File : modular_camera.py
# License: License: GNU v3.0
# Author : Sam Manger <s.manger@bham.ac.uk>
# Date : 20.08.2019
import time
import numpy as np
from pept import LineData
from .extensions.get_pept_event import get_pept_LOR
[docs]def modular_camera(
data_file,
sample_size = None,
overlap = None,
verbose = True
):
'''Initialise PEPT LoRs from the modular camera DAQ.
Can read data from a `.da_1` file or equivalent. The file must contain
the standard datawords from the modular camera output. This will then
be automatically transformed into the standard `LineData` format
with every row being `[time, x1, y1, z1, x2, y2, z2]`, where the geometry
is derived from the C-extension. The current useable geometry is a square
layout with 4 stacks for 4 modules, separated by 250 mm.
Parameters
----------
data_file : str
A string with the (absolute or relative) path to the data file
from which the PEPT data will be read. It should include the
full file name, along with the extension (.da_1)
sample_size : int, optional
An `int`` that defines the number of lines that should be
returned when iterating over `_lines`. A `sample_size` of 0
yields all the data as one single sample. (Default is 200)
overlap : int, optional
An `int` that defines the overlap between two consecutive
samples that are returned when iterating over `_lines`.
An overlap of 0 means consecutive samples, while an overlap
of (`sample_size` - 1) means incrementing the samples by one.
A negative overlap means skipping values between samples. An
error is raised if `overlap` is larger than or equal to
`sample_size`. (Default is 0)
verbose : bool, optional
An option that enables printing the time taken for the
initialisation of an instance of the class. Useful when
reading large files (10gb files for PEPT data is not unheard
of). (Default is True)
Returns
-------
LineData
The initialised LoRs.
Raises
------
ValueError
If `overlap` >= `sample_size`. Overlap has to be smaller than
`sample_size`. Note that it can also be negative.
ValueError
If the data file does not have (N, 7) shape.
'''
if verbose:
start = time.time()
x = 10
header_buffer_size = 1000
n_events = 0
# Modular camera data reader requires 'itag' for timing. We will drop
# this column at the end of initialisation
# Row: [itag, itime, X1, Y1, Z1, X2, Y2, Z2]
lines = np.zeros([sample_size, 8])
with open(data_file, "rb") as f:
# Skip over the header and handshake word
f.seek(header_buffer_size)
word = f.read(4)
if word.hex() == 'cefacefa':
# Skip two words
word = f.read(4)
word = f.read(4)
itime = 0
itag = 0
# BufTime = 0
# nBuf = 0
while word != b'' and (n_events < sample_size):
word = f.read(4)
# Handshake word
if word.hex() == 'cefacefa':
# Skip two words
word = f.read(4)
word = f.read(4)
if word != b'':
word = int.from_bytes(word, "little")
lines[n_events, :] = get_pept_LOR(
word, itag, itime
) # C function
itag = lines[n_events, 1]
itime = lines[n_events, 1]
n_events = n_events + 1
if (n_events % x) == 0:
print("Got ", n_events, "\n")
x = x * 10
# Remove 'zero' lines
lines = lines[np.all(lines, axis = 1)]
# Drop itag column
lines = np.delete(lines, 0, axis=1)
if verbose:
end = time.time()
print(f"\nInitialised the PEPT data in {end - start:3.3f} s.\n")
return LineData(lines, sample_size = sample_size, overlap = overlap)