hyperspy 2.0rc0__py3-none-any.whl

hyperspy/Release.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy 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.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+name = 'hyperspy'
+
+# The commit following to a release must update the version number
+# to the version number of the release followed by ".dev", e.g.
+# if the version of the last release is 0.4.1 the version of the
+# next development version afterwards must be 0.4.1.dev.
+# When running setup.py the ".dev" string will be replaced (if possible)
+# by the output of "git describe" if git is available or the git
+# hash if .git is present.
+version = "2.0rc0"
+__version__ = version
+description = "Multidimensional data analysis toolbox"
+license = 'GPL v3'
+
+authors = {
+    'all': ('The HyperSpy developers',), }
+
+url = 'https://hyperspy.org'
+
+download_url = 'https://www.hyperspy.org'
+documentation_url = 'https://hyperspy.org/hyperspy-doc/current/index.html'
+
+PROJECT_URLS = {
+    'Bug Tracker': 'https://github.com/hyperspy/hyperspy/issues',
+    'Documentation': 'https://hyperspy.org/hyperspy-doc/current/index.html',
+    'Source Code': 'https://github.com/hyperspy/hyperspy',
+    'Support' : 'https://gitter.im/hyperspy/hyperspy'
+}
+
+platforms = ['Linux', 'Mac OSX', 'Windows XP/2000/NT', 'Windows 95/98/ME']
+
+keywords = ['EDX',
+            'EELS',
+            'EFTEM',
+            'EMSA',
+            'FEI',
+            'ICA',
+            'PCA',
+            'PES',
+            'STEM',
+            'TEM',
+            'curve fitting',
+            'data analysis',
+            'dm3',
+            'electron energy loss spectroscopy',
+            'electron microscopy',
+            'emi',
+            'energy dispersive x-rays',
+            'hyperspectral',
+            'hyperspectrum',
+            'multidimensional',
+            'hyperspy',
+            'machine learning',
+            'microscopy',
+            'model',
+            'msa',
+            'numpy',
+            'python',
+            'quantification',
+            'scipy',
+            'ser',
+            'spectroscopy',
+            'spectrum image']
+
+info = """
+    H y p e r S p y
+    Version %s
+
+    https://www.hyperspy.org
+
+    """ % version.replace('_', ' ')

hyperspy/__init__.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy 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.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+import importlib
+import logging
+from hyperspy import docstrings
+
+_logger = logging.getLogger(__name__)
+
+
+__doc__ = """
+HyperSpy: a multi-dimensional data analysis package for Python
+==============================================================
+
+Documentation is available in the docstrings and online at
+https://hyperspy.org/hyperspy-doc/current/index.html.
+
+All public packages, functions and classes are in :mod:`~hyperspy.api`. All
+other packages and modules are for internal consumption and should not be
+needed for data analysis.
+
+%s
+
+More details in the :mod:`~hyperspy.api` docstring.
+
+""" % docstrings.START_HSPY
+
+
+__all__ = [
+    "api",
+    "__version__"
+    ]
+
+
+def __dir__():
+    return sorted(__all__)
+
+
+_import_mapping = {
+    '__version__':'.Release',
+    }
+
+
+def __getattr__(name):
+    if name in __all__:
+        if name in _import_mapping.keys():
+            import_path = 'hyperspy' + _import_mapping.get(name)
+            return getattr(importlib.import_module(import_path), name)
+        else:  # pragma: no cover
+            # We can't get this block covered in the test suite because it is
+            # already imported, when running the test suite.
+            # If this is broken, a lot of things will be broken!
+            return importlib.import_module("." + name, 'hyperspy')
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")

hyperspy/_components/arctan.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy 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.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+
+from hyperspy._components.expression import Expression
+
+
+class Arctan(Expression):
+
+    r"""Arctan function component.
+
+    .. math::
+
+        f(x) = A \cdot \arctan \left[ k \left( x-x_0 \right) \right]
+
+
+    ============ =============
+    Variable      Parameter
+    ============ =============
+    :math:`A`     A
+    :math:`k`     k
+    :math:`x_0`   x0
+    ============ =============
+
+
+    Parameters
+    -----------
+    A : float
+        Amplitude parameter. :math:`\lim_{x\to -\infty}f(x)=-A` and
+        :math:`\lim_{x\to\infty}f(x)=A`
+    k : float
+        Slope (steepness of the step). The larger :math:`k`, the sharper the
+        step.
+    x0 : float
+        Center parameter (position of zero crossing :math:`f(x_0)=0`).
+
+    """
+
+    def __init__(self, A=1., k=1., x0=1., module=["numpy", "scipy"], **kwargs):
+        # To be able to still read old file versions that contain this argument
+        if "minimum_at_zero" in kwargs:
+            del kwargs["minimum_at_zero"]
+        super().__init__(
+            expression="A * arctan(k * (x - x0))",
+            name="Arctan",
+            A=A,
+            k=k,
+            x0=x0,
+            position="x0",
+            module=module,
+            autodoc=False,
+            **kwargs,
+        )

hyperspy/_components/bleasdale.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy 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.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+import numpy as np
+
+from hyperspy._components.expression import Expression
+
+class Bleasdale(Expression):
+
+    r"""Bleasdale function component.
+
+    Also called the Bleasdale-Nelder function. Originates from
+    the description of the yield-density relationship in crop growth.
+
+    .. math::
+
+        f(x) = \left(a+b\cdot x\right)^{-1/c}
+
+    Parameters
+    ----------
+    a : float, default=1.0
+        The value of Parameter a.
+    b : float, default=1.0
+        The value of Parameter b.
+    c : float, default=1.0
+        The value of Parameter c.        
+    **kwargs
+        Extra keyword arguments are passed to
+        :py:class:`~.api.model.components1D.Expression`.
+
+    Note
+    ----
+    For :math:`(a+b\cdot x)\leq0`, the component will be set to 0.
+
+    """
+
+    def __init__(self, a=1., b=1., c=1., module=None, **kwargs):
+        super().__init__(
+            expression="where((a + b * x) > 0, pow(a + b * x, -1 / c), 0)",
+            name="Bleasdale",
+            a=a,
+            b=b,
+            c=c,
+            module=module,
+            autodoc=False,
+            compute_gradients=False,
+            linear_parameter_list=['b'],
+            check_parameter_linearity=False,
+            **kwargs)
+        module = self._whitelist['module'][1]
+        if module in ("numpy", "scipy"):
+            # Issue with calculating component at 0...
+            raise ValueError(
+                f"{module} is not supported for this component, use numexpr instead."
+                )
+
+    def grad_a(self, x):
+        """
+        Returns d(function)/d(parameter_1)
+        """
+        a = self.a.value
+        b = self.b.value
+        c = self.c.value
+
+        return np.where((a + b * x) > 0, -(a + b * x) ** (-1 / c - 1) / c, 0)
+
+    def grad_b(self, x):
+        """
+        Returns d(function)/d(parameter_1)
+        """
+        a = self.a.value
+        b = self.b.value
+        c = self.c.value
+
+        return np.where((a + b * x) > 0, -x * (a + b * x) ** (-1 / c - 1) / c
+               , 0)
+
+    def grad_c(self, x):
+        """
+        Returns d(function)/d(parameter_1)
+        """
+        a = self.a.value
+        b = self.b.value
+        c = self.c.value
+        return np.where((a + b * x) > 0, np.log(a + b * x) / (c ** 2. *
+               (b * x + a) ** (1. / c)), 0)

hyperspy/_components/doniach.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy is free software: you can redistribute it and/or modify
+# it under the terms of  GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+import math
+import numpy as np
+
+from hyperspy.component import _get_scaling_factor
+from hyperspy._components.expression import Expression
+from hyperspy._components.gaussian import _estimate_gaussian_parameters
+
+sqrt2pi = math.sqrt(2 * math.pi)
+
+
+tiny = np.finfo(float).eps
+
+
+class Doniach(Expression):
+
+    r""" Doniach Sunjic lineshape component.
+
+    .. math::
+        :nowrap:
+
+        \[
+        f(x) = \frac{A \cos[ \frac{{\pi\alpha}}{2}+
+        (1-\alpha)\tan^{-1}(\frac{x-centre+dx}{\sigma})]}
+        {(\sigma^2 + (x-centre+dx)^2)^{\frac{(1-\alpha)}{2}}}
+        \]
+
+
+        \[
+        dx = \frac{2.354820\sigma}{2 tan[\frac{\pi}{2-\alpha}]}
+        \]
+
+
+    =============== ===========
+    Variable         Parameter
+    =============== ===========
+    :math:`A`        A
+    :math:`\sigma`   sigma
+    :math:`\alpha`   alpha
+    :math:`centre`   centre
+    =============== ===========
+
+    Parameters
+    -----------
+    A : float
+        Height
+    sigma : float
+        Variance parameter of the distribution
+    alpha : float
+        Tail or asymmetry parameter
+    centre : float
+        Location of the maximum (peak position).
+    **kwargs
+        Extra keyword arguments are passed to the
+        :py:class:`~._components.expression.Expression` component.
+
+    Note
+    -----
+    This is an asymmetric lineshape, originially design for xps but generally
+    useful for fitting peaks with low side tails
+    See Doniach S. and Sunjic M., J. Phys. 4C31, 285 (1970)
+    or http://www.casaxps.com/help_manual/line_shapes.htm for a more detailed
+    description
+
+    """
+
+    def __init__(self, centre=0., A=1., sigma=1., alpha=0.5,
+                 module=["numpy", "scipy"], **kwargs):
+        super().__init__(
+            expression="A*cos(0.5*pi*alpha+\
+            ((1.0 - alpha) * arctan( (x-centre+offset)/sigma) ) )\
+            /(sigma**2 + (x-centre+offset)**2)**(0.5 * (1.0 - alpha));\
+            offset = 2.354820*sigma / (2 * tan(pi / (2 - alpha)))",
+            name="Doniach",
+            centre=centre,
+            A=A,
+            sigma=sigma,
+            alpha=alpha,
+            module=module,
+            autodoc=False,
+            **kwargs,
+        )
+        #
+        self.sigma.bmin = 1.0e-8
+        self.alpha.bmin = 1.0e-8
+        self.isbackground = False
+        self.convolved = True
+
+    def estimate_parameters(self, signal, x1, x2, only_current=False):
+        """Estimate the Donach by calculating the median (centre) and the
+        variance parameter (sigma).
+
+        Note that an insufficient range will affect the accuracy of this
+        method and that this method doesn't estimate the asymmetry parameter
+        (alpha).
+
+        Parameters
+        ----------
+        signal : Signal1D instance
+        x1 : float
+            Defines the left limit of the spectral range to use for the
+            estimation.
+        x2 : float
+            Defines the right limit of the spectral range to use for the
+            estimation.
+
+        only_current : bool
+            If False estimates the parameters for the full dataset.
+
+        Returns
+        -------
+        bool
+            Returns True when the parameters estimation is successful
+
+        Examples
+        --------
+
+        >>> g = hs.model.components1D.Lorentzian()
+        >>> x = np.arange(-10, 10, 0.01)
+        >>> data = np.zeros((32, 32, 2000))
+        >>> data[:] = g.function(x).reshape((1, 1, 2000))
+        >>> s = hs.signals.Signal1D(data)
+        >>> s.axes_manager[-1].offset = -10
+        >>> s.axes_manager[-1].scale = 0.01
+        >>> g.estimate_parameters(s, -10, 10, False)
+        """
+
+        super()._estimate_parameters(signal)
+        axis = signal.axes_manager.signal_axes[0]
+        centre, height, sigma = _estimate_gaussian_parameters(signal, x1, x2,
+                                                              only_current)
+        scaling_factor = _get_scaling_factor(signal, axis, centre)
+
+        if only_current is True:
+            self.centre.value = centre
+            self.sigma.value = sigma
+            self.A.value = height * 1.3
+            if axis.is_binned:
+                self.A.value /= scaling_factor
+            return True
+        else:
+            if self.A.map is None:
+                self._create_arrays()
+            self.A.map['values'][:] = height * 1.3
+            if axis.is_binned:
+                self.A.map['values'][:] /= scaling_factor
+            self.A.map['is_set'][:] = True
+            self.sigma.map['values'][:] = sigma
+            self.sigma.map['is_set'][:] = True
+            self.centre.map['values'][:] = centre
+            self.centre.map['is_set'][:] = True
+            self.fetch_stored_values()
+            return True

hyperspy/_components/error_function.py

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+# -*- coding: utf-8 -*-
+# Copyright 2007-2023 The HyperSpy developers
+#
+# This file is part of HyperSpy.
+#
+# HyperSpy 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.
+#
+# HyperSpy 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 HyperSpy. If not, see <https://www.gnu.org/licenses/#GPL>.
+
+from hyperspy._components.expression import Expression
+
+
+class Erf(Expression):
+
+    r"""Error function component.
+
+    .. math::
+
+        f(x) = \frac{A}{2}~\mathrm{erf}\left[\frac{(x - x_0)}{\sqrt{2}
+            \sigma}\right]
+
+
+    ============== =============
+    Variable        Parameter
+    ============== =============
+    :math:`A`       A
+    :math:`\sigma`  sigma
+    :math:`x_0`     origin
+    ============== =============
+
+    Parameters
+    ----------
+    A : float
+        The min/max values of the distribution are -A/2 and A/2.
+    sigma : float
+        Width of the distribution.
+    origin : float
+        Position of the zero crossing.
+    **kwargs
+        Extra keyword arguments are passed to the
+        :py:class:`~._components.expression.Expression` component.
+    """
+
+    def __init__(self, A=1., sigma=1., origin=0., module=["numpy", "scipy"],
+                 **kwargs):
+        super().__init__(
+            expression="A * erf((x - origin) / sqrt(2) / sigma) / 2",
+            name="Erf",
+            A=A,
+            sigma=sigma,
+            origin=origin,
+            module=module,
+            autodoc=False,
+            **kwargs,
+        )
+
+        # Boundaries
+        self.A.bmin = 0.
+
+        self.isbackground = False
+        self.convolved = True