def __init__(self, fpath, unused_detector=23, phi=None):
""" Extract useful data from raw .nxs file.
Deletes data from unused detector. Allows definition of az_angle (phi)
if the unused detector is not 23. Prepares the file for peak/profile
analysis.
Args:
fpath (str): Path to NeXus file
unused_detector (int): Unused detector (normally 23)
phi (ndarray, list): Re-define phi if detector order is mixed
"""
self.fpath = fpath
f = h5py.File(fpath, 'r')
# Use scan command to find number of dimensions and the order in which
# they were acquired. Important/useful for plotting!
scan_command = f['entry1/scan_command'][()][0]
dims = re.findall(b'ss2_\w+', scan_command)
self.ndim = len(dims)
all_dims = [b'ss2_x', b'ss2_y', b'ss2_z']
dims = dims + [dim for dim in all_dims if dim not in dims]
co_ords = []
for dim in dims:
co_ords.append(dimension_fill(f, dim.decode("utf-8")))
self.d1, self.d2, self.d3 = co_ords
# Remove unused detector - resulting detector array is almost certainly
# arrayed in ascending order from from -np.pi to 0 (phi). Option exists
# to specify the order if this isn't true.
self.q = f['entry1/EDXD_elements/edxd_q'][()]
self.q = np.delete(self.q, unused_detector, 0)
self.I = f['entry1/EDXD_elements/data'][()]
self.I = np.delete(self.I, unused_detector, -2)
self.phi = np.linspace(-np.pi, 0, 23) if phi is None else phi
self.analysis_state = 'integrated'
self.detector = i12_energy()
def __init__(self, fpath, unused_detector=23, phi=None):
""" Extract useful data from raw .nxs file.
Deletes data from unused detector. Allows definition of az_angle (phi)
if the unused detector is not 23. Prepares the file for peak/profile
analysis.
Args:
fpath (str): Path to NeXus file
unused_detector (int): Unused detector (normally 23)
phi (ndarray, list): Re-define phi if detector order is mixed
"""
self.fpath = fpath
f = h5py.File(fpath, 'r')
# Use scan command to find number of dimensions and the order in which
# they were acquired. Important/useful for plotting!
scan_command = f['entry1/scan_command'][()][0]
dims = re.findall(b'ss2_\w+', scan_command)
self.ndim = len(dims)
all_dims = [b'ss2_x', b'ss2_y', b'ss2_z']
dims = dims + [dim for dim in all_dims if dim not in dims]
co_ords = []
for dim in dims:
co_ords.append(dimension_fill(f, dim.decode("utf-8")))
self.d1, self.d2, self.d3 = co_ords
# Remove unused detector - resulting detector array is almost certainly
# arrayed in ascending order from from -np.pi to 0 (phi). Option exists
# to specify the order if this isn't true.
self.q = f['entry1/EDXD_elements/edxd_q'][()]
self.q = np.delete(self.q, unused_detector, 0)
self.I = f['entry1/EDXD_elements/data'][()]
self.I = np.delete(self.I, unused_detector, -2)
self.phi = np.linspace(-np.pi, 0, 23) if phi is None else phi
self.analysis_state = 'integrated'
self.detector = i12_energy()
def __init__(self, folder, fend='mca', fname=None, phi=[0, np.pi / 2]):
"""
Takes a folder containing .mca data files from ED detectors and merges
the data while associating it with spatial information. The I data
can then be analysed (peak_fit/strain calculations).
Args:
folder (str): Folder containing the files for analysis
"""
fname = '{}.h5'.format(os.path.split(folder)[1])
self.fpath = os.path.join(folder, fname)
self.phi = np.array(phi)
co_ords, self.I = mca_array(folder, fend)
(self.d1, self.d2, self.d3), self.dims = dim_fill(co_ords)
self.ndim = len(self.dims)
# Not sure how data will be presented, but this can be remedied.
E = np.linspace(0, 4095, 4096)
q1 = e_to_q(0.07 + 0.07493 * E + 4.422e-8 * E,
5.10541851 * np.pi / 180)
q2 = e_to_q(0.1453 + 0.07483 * E + 9.026e-8 * E,
4.9718601 * np.pi / 180)
#E = np.vstack((q1, q2))
self.q = np.vstack((q1, q2))
# Create az_slice 'specific' q values - to work with edxd data
#self.q = np.repeat(q[None, :], self.phi.size, axis=0)
self.analysis_state = 'integrated'
# Temporary - extract from ai!
self.detector = i12_energy()
#folder = os.path.expanduser(r'~/Dropbox/Python/nc_ni/')
#test = EDID15(folder)
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from mock import patch
import numpy as np
import matplotlib.pyplot as plt
from pyxpb.detectors import i12_energy
i12 = i12_energy()
i12.add_material('Fe')
def test_intensity_profiles():
phi = np.pi / 3.2
profile_0 = i12.intensity(phi,
background=0,
x_axis='q',
strain_tensor=(0.2, 0.2, 0.3))
profile_180 = i12.intensity(phi - np.pi,
background=0,
x_axis='q',
strain_tensor=(0.2, 0.2, 0.3))
assert np.allclose(profile_0[1]['Fe'], profile_180[1]['Fe'])
# Test a few combinations of parameters
i12.intensity(0,
background=0,
x_axis='energy',
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from mock import patch
import numpy as np
from pyxpb.detectors import i12_energy
i12 = i12_energy()
i12.add_material('Fe')
def test_intensity_profiles():
phi = np.pi / 3.2
profile_0 = i12.intensity(phi, background=0, x_axis='q',
strain_tensor=(0.2, 0.2, 0.3))
profile_180 = i12.intensity(phi-np.pi, background=0, x_axis='q',
strain_tensor=(0.2, 0.2, 0.3))
assert np.allclose(profile_0[1]['Fe'], profile_180[1]['Fe'])
# Test a few combinations of parameters
i12.intensity(0, background=0, x_axis='energy',
strain_tensor=(0.2, 0.2, 0.3))
i12.intensity([0, np.pi/7], background=0, x_axis='energy',
strain_tensor=(0., 0., 0.))
def test_all_intensity():
