diff --git a/doc/user_guide/eds.rst b/doc/user_guide/eds.rst index eee7ce488..6bf2b64c7 100644 --- a/doc/user_guide/eds.rst +++ b/doc/user_guide/eds.rst @@ -12,7 +12,7 @@ This chapter describes step-by-step the analysis of an EDS spectrum (SEM or TEM). .. NOTE:: - See also the `EDS tutorials `_. + See also the `EDS tutorials `_. Spectrum loading and parameters ------------------------------- diff --git a/exspy/components/eels_arctan.py b/exspy/components/eels_arctan.py index 5a52432bf..4faab579e 100644 --- a/exspy/components/eels_arctan.py +++ b/exspy/components/eels_arctan.py @@ -51,12 +51,12 @@ class EELSArctan(hs.model.components1D.Expression): """ - def __init__(self, A=1.0, k=1.0, x0=1.0, module=["numpy", "scipy"], **kwargs): + def __init__(self, A=1.0, k=1.0, x0=1.0, module=["numpy"], **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 * (pi /2 + arctan(k * (x - x0)))", + expression="A * (pi /2 + atan(k * (x - x0)))", name="EELSArctan", A=A, k=k, diff --git a/exspy/components/eels_cl_edge.py b/exspy/components/eels_cl_edge.py index 0a2b91854..3a2f9d8dd 100644 --- a/exspy/components/eels_cl_edge.py +++ b/exspy/components/eels_cl_edge.py @@ -75,16 +75,16 @@ class EELSCLEdge(Component): The preferred option is to use a database of cross sections in GOSH format. One such database can be freely downloaded from Zenodo at: - https://zenodo.org/record/6599071 while information on the GOSH format + https://doi.org/%s while information on the GOSH format are available at: https://gitlab.com/gguzzina/gosh . eXSpy also supports Peter Rez's Hartree Slater cross sections parametrised as distributed by Gatan in their Digital Micrograph (DM) - software. If Digital Micrograph is installed in the system eXSpy in the - standard location eXSpy should find the path to the HS GOS folder. - Otherwise, the location of the folder can be defined in eXSpy - preferences, which can be done through ~:func:`~.api.preferences.gui` or - the :attr:`~api.preferences.EELS.eels_gos_files_path` variable. + software. If Digital Micrograph is installed in the system in the + standard location, eXSpy should find the path to the HS GOS folder. + Otherwise, the location of the folder can be defined in the eXSpy + preferences, which can be done through :func:`hyperspy.api.preferences.gui` or + the :attr:`hyperspy.api.preferences.EELS.eels_gos_files_path` variable. Parameters ---------- @@ -96,8 +96,8 @@ class EELSCLEdge(Component): The GOS to use. Default is ``'gosh'``. If str, it must the path to gosh GOS file. gos_file_path : str, None - Only with GOS='gosh'. Specify the file path of the gosh file - to use. If None, use the file from doi:{} + Only with ``GOS='gosh'``. Specify the file path of the gosh file + to use. If None, use the file from https://doi.org/%s Attributes ---------- @@ -140,7 +140,7 @@ class EELSCLEdge(Component): fine_structure_components : set, default ``set()`` A set containing components to model the fine structure region of the EELS ionization edge. - """.format(_GOSH_DOI) + """ _fine_structure_smoothing = 0.3 _fine_structure_coeff_free = True @@ -290,12 +290,6 @@ def _set_active_fine_structure_components(self, active, **kwargs): @property def fine_structure_smoothing(self): - """Controls the level of the smoothing of the fine structure. - - It must a real number between 0 and 1. The higher close to 0 - the higher the smoothing. - - """ return self._fine_structure_smoothing @fine_structure_smoothing.setter @@ -539,3 +533,6 @@ def as_dictionary(self, fullcopy=True): ] dic["_whitelist"]["fine_structure_components"] = "" return dic + + +EELSCLEdge.__doc__ %= (_GOSH_DOI, _GOSH_DOI) diff --git a/exspy/components/pes_core_line_shape.py b/exspy/components/pes_core_line_shape.py index e0484c42d..4480b33c3 100644 --- a/exspy/components/pes_core_line_shape.py +++ b/exspy/components/pes_core_line_shape.py @@ -32,7 +32,10 @@ def _calculate_shirley_background(values): class PESCoreLineShape(Component): - """ """ + """ + Gaussian component with a Shirley background for photoemission + spectroscopy analysis. + """ def __init__(self, A=1.0, FWHM=1.0, origin=0.0, ab=0.0, shirley=0.0): Component.__init__(self, ["A", "FWHM", "origin", "ab", "shirley"]) diff --git a/upcoming_changes/55.bugfix.rst b/upcoming_changes/55.bugfix.rst new file mode 100644 index 000000000..2c5523ee9 --- /dev/null +++ b/upcoming_changes/55.bugfix.rst @@ -0,0 +1 @@ +Fix gradients of the :class:`~.components.EELSArctan` component. \ No newline at end of file diff --git a/upcoming_changes/55.doc.rst b/upcoming_changes/55.doc.rst new file mode 100644 index 000000000..38da8c411 --- /dev/null +++ b/upcoming_changes/55.doc.rst @@ -0,0 +1 @@ +Fix broken links in the documentation and missing docstring of the :class:`~.components.PESCoreLineShape` component in the API reference. \ No newline at end of file