#!/usr/bin/env python
"""
.. py:currentmodule:: FileFormat.Results.XraySpectraSpecimenEmittedDetected
.. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
Read XraySpectraSpecimenEmittedDetected MCXRay results file.
"""
# Script information for the file.
__author__ = "Hendrix Demers (hendrix.demers@mail.mcgill.ca)"
__version__ = ""
__date__ = ""
__copyright__ = "Copyright (c) 2012 Hendrix Demers"
__license__ = ""
# Standard library modules.
import os.path
import csv
# Third party modules.
import numpy as np
# Local modules.
# Project modules
import pymcxray.FileFormat.Results.BaseResults as BaseResults
# Globals and constants variables.
ENERGIES_keV = "Energy (keV)"
SPECTRUM_TOTAL = "Spectra Total"
SPECTRUM_LINES = "Spectra Lines"
SPECTRUM_BREMSSTRAHLUNG = "Spectra Bremsstrahlung"
HDF5_XRAY_SPECTRA_SPECIMEN_EMITTED_DETECTED = "XraySpectraSpecimenEmittedDetected"
HDF5_ENERGIES_keV = ENERGIES_keV
HDF5_TOTAL = SPECTRUM_TOTAL
HDF5_CHARACTERISTIC = SPECTRUM_LINES
HDF5_BREMSSTRAHLUNG = SPECTRUM_BREMSSTRAHLUNG
[docs]class XraySpectraSpecimenEmittedDetected(BaseResults.BaseResults):
def __init__(self):
super(XraySpectraSpecimenEmittedDetected, self).__init__()
self.energies_keV = []
self.totals = []
self.characteristics = []
self.backgrounds = []
[docs] def read(self):
suffix = "_SpectraSpecimenEmittedDetected.csv"
filename = self.basename + suffix
filepath = os.path.join(self.path, filename)
self._read(filepath)
#self._read_fast(filepath)
def _read(self, file_path):
with open(file_path, 'r') as csvFile:
reader = csv.DictReader(csvFile, self.fieldNames)
# Skip header row
next(reader)
for row in reader:
self.energies_keV.append(float(row[ENERGIES_keV]))
self.totals.append(float(row[SPECTRUM_TOTAL]))
self.characteristics.append(float(row[SPECTRUM_LINES]))
self.backgrounds.append(float(row[SPECTRUM_BREMSSTRAHLUNG]))
def _read(self, file_path):
with open(file_path, 'r') as csvFile:
reader = csv.reader(csvFile, self.fieldNames)
# Skip header row
next(reader)
for items in reader:
self.energies_keV.append(float(items[0]))
self.totals.append(float(items[1]))
self.characteristics.append(float(items[2]))
self.backgrounds.append(float(items[3]))
def _read_fast(self, file_path):
with open(file_path, 'r') as data_file:
data = np.loadtxt(data_file, dtype=float, delimiter =',', skiprows=1)
self.energies_keV = data[:,0].tolist()
self.totals = data[:,1].tolist()
self.characteristics = data[:,2].tolist()
self.backgrounds = data[:,3].tolist()
[docs] def write_hdf5(self, hdf5_group):
hdf5_group = hdf5_group.require_group(HDF5_XRAY_SPECTRA_SPECIMEN_EMITTED_DETECTED)
hdf5_group.create_dataset(HDF5_ENERGIES_keV, data=self.energies_keV)
hdf5_group.create_dataset(HDF5_TOTAL, data=self.totals)
hdf5_group.create_dataset(HDF5_CHARACTERISTIC, data=self.characteristics)
hdf5_group.create_dataset(HDF5_BREMSSTRAHLUNG, data=self.backgrounds)
@property
def fieldNames(self):
fieldNames = []
fieldNames.append(ENERGIES_keV)
fieldNames.append(SPECTRUM_TOTAL)
fieldNames.append(SPECTRUM_LINES)
fieldNames.append(SPECTRUM_BREMSSTRAHLUNG)
return fieldNames
@property
def energies_keV(self):
return self._energies_keV
@energies_keV.setter
def energies_keV(self, energies_keV):
self._energies_keV = energies_keV
@property
def totals(self):
return self._totals
@totals.setter
def totals(self, totals):
self._totals = totals
@property
def characteristics(self):
return self._characteristics
@characteristics.setter
def characteristics(self, characteristics):
self._characteristics = characteristics
@property
def backgrounds(self):
return self._backgrounds
@backgrounds.setter
def backgrounds(self, backgrounds):
self._backgrounds = backgrounds