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# !/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Project: Azimuthal integration
# https://github.com/silx-kit/pyFAI
#
# Copyright (C) 2017-2018 European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
"""Jupyter helper functions
"""
__author__ = "Jerome Kieffer"
__contact__ = "Jerome.Kieffer@ESRF.eu"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "16/10/2020"
__status__ = "Production"
__docformat__ = 'restructuredtext'
import numpy
from pylab import subplots, legend
from matplotlib import lines
def display(img=None, cp=None, ai=None, label=None, sg=None, ax=None):
"""Display an image with the control points and the calibrated rings
in Jupyter notebooks
:param img: 2D numpy array with an image
:param cp: ControlPoint instance
:param ai: azimuthal integrator for iso-2th curves
:param label: name of the curve
:param sg: single geometry object regrouping img, cp and ai
:param ax: subplot object to display in, if None, a new one is created.
:return: Matplotlib subplot
"""
if ax is None:
_fig, ax = subplots()
if sg is not None:
if img is None:
img = sg.image
if cp is None:
cp = sg.control_points
if ai is None:
ai = sg.geometry_refinement
if label is None:
label = sg.label
ax.imshow(numpy.arcsinh(img).astype(numpy.float32), origin="lower", cmap="inferno")
ax.set_title(label)
if cp is not None:
for lbl in cp.get_labels():
pt = numpy.array(cp.get(lbl=lbl).points)
if len(pt) > 0:
ax.scatter(pt[:, 1], pt[:, 0], label=lbl)
if ai is not None and cp.calibrant is not None:
tth = cp.calibrant.get_2th()
ttha = ai.twoThetaArray()
ax.contour(ttha, levels=tth, cmap="autumn", linewidths=2, linestyles="dashed")
legend()
return ax
def plot1d(result, calibrant=None, label=None, ax=None):
"""Display the powder diffraction pattern in the jupyter notebook
:param result: instance of Integrate1dResult
:param calibrant: Calibrant instance to overlay diffraction lines
:param label: (str) name of the curve
:param ax: subplot object to display in, if None, a new one is created.
:return: Matplotlib subplot
"""
if ax is None:
_fig, ax = subplots()
unit = result.unit
if result.sigma is not None:
ax.errorbar(result.radial, result.intensity, result.sigma, label=label)
else:
ax.plot(result.radial, result.intensity, label=label)
if label:
ax.legend()
if calibrant:
x_values = calibrant.get_peaks(unit)
if x_values is not None:
for x in x_values:
line = lines.Line2D([x, x], ax.axis()[2:4],
color='red', linestyle='--')
ax.add_line(line)
ax.set_title("1D integration")
ax.set_xlabel(unit.label)
ax.set_ylabel("Intensity")
return ax
def plot2d(result, calibrant=None, label=None, ax=None):
"""Display the caked image in the jupyter notebook
:param result: instance of Integrate2dResult
:param calibrant: Calibrant instance to overlay diffraction lines
:param label: (str) name of the curve
:param ax: subplot object to display in, if None, a new one is created.
:return: Matplotlib subplot
"""
img = result.intensity
pos_rad = result.radial
pos_azim = result.azimuthal
if ax is None:
_fig, ax = subplots()
ax.imshow(numpy.arcsinh(img),
origin="lower",
extent=[pos_rad.min(), pos_rad.max(), pos_azim.min(), pos_azim.max()],
aspect="auto",
cmap="inferno")
if label:
ax.set_title("2D regrouping")
else:
ax.set_title(label)
ax.set_xlabel(result.unit.label)
ax.set_ylabel(r"Azimuthal angle $\chi$ ($^{o}$)")
if calibrant:
from pyFAI import units
x_values = None
twotheta = numpy.array([i for i in calibrant.get_2th() if i]) # in radian
unit = result.unit
if unit == units.TTH_DEG:
x_values = numpy.rad2deg(twotheta)
elif unit == units.TTH_RAD:
x_values = twotheta
elif unit == units.Q_A:
x_values = (4.e-10 * numpy.pi / calibrant.wavelength) * numpy.sin(.5 * twotheta)
elif unit == units.Q_NM:
x_values = (4.e-9 * numpy.pi / calibrant.wavelength) * numpy.sin(.5 * twotheta)
if x_values is not None:
for x in x_values:
line = lines.Line2D([x, x], [pos_azim.min(), pos_azim.max()],
color='red', linestyle='--')
ax.add_line(line)
return ax
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