Update GenXFile for version 3

Stoner/Analysis.py

@@ -17,7 +17,6 @@
 
 
 class AnalysisMixin:
-
     """A mixin calss designed to work with :py:class:`Stoner.Core.DataFile` to provide additional analysis methods."""
 
     def __dir__(self):

Stoner/Core.py

@@ -1,4 +1,5 @@
 """Stoner.Core provides the core classes for the Stoner package."""
+
 __all__ = [
     "StonerLoadError",
     "StonerSetasError",
@@ -64,7 +65,6 @@ class DataFile(
     metadataObject,
     MutableSequence,
 ):
-
     """Base class object that represents a matrix of data, associated metadata and column headers.
 
     Attributes:

Stoner/Folders.py

@@ -2,6 +2,7 @@
 
 The core classes provides a means to access them as an ordered collection or as a mapping.
 """
+
 __all__ = ["DataFolder", "PlotFolder"]
 
 from Stoner.tools import make_Data
@@ -11,7 +12,6 @@
 
 
 class DataFolder(DataMethodsMixin, DiskBasedFolderMixin, baseFolder):
-
     """Provide an interface to manipulating lots of data files stored within a directory structure on disc.
 
     By default, the members of the DataFolder are instances of :class:`Stoner.Data`. The DataFolder emplys a lazy
@@ -28,5 +28,4 @@ def __init__(self, *args, **kargs):
 
 
 class PlotFolder(PlotMethodsMixin, DataFolder):
-
     """A :py:class:`Stoner.folders.baseFolder` that knows how to ploth its underlying data files."""

Stoner/HDF5.py

@@ -9,6 +9,7 @@
 to :py:class:`Stoner.Core.Data`.
 
 """
+
 __all__ = ["HDF5File", "HDF5Folder", "HGXFile", "SLS_STXMFile", "STXMImage", "HDFFileManager"]
 import importlib
 import os.path as path
@@ -52,7 +53,6 @@ def get_hdf_loader(f, default_loader=lambda *args, **kargs: None):
 
 
 class HDFFileManager:
-
     """Context manager for HDF5 files."""
 
     def __init__(self, filename, mode="r"):
@@ -115,7 +115,6 @@ def __exit__(self, _type, _value, _traceback):
 
 
 class HDF5File(DataFile):
-
     """A sub class of DataFile that sores itself in a HDF5File or group.
 
     Args:
@@ -287,7 +286,6 @@ def to_hdf(self, filename=None, **kargs):  # pylint: disable=unused-argument
 
 
 class HGXFile(DataFile):
-
     """A subclass of DataFile for reading GenX HDF Files.
 
     These files typically have an extension .hgx. This class has been based on a limited sample
@@ -372,7 +370,6 @@ def main_data(self, data_grp):
 
 
 class HDF5FolderMixin:
-
     """Provides a method to load and save data from a single HDF5 file with groups.
 
     See :py:class:`Stoner.Folders.DataFolder` for documentation on constructor.
@@ -568,7 +565,6 @@ def save(self, root=None):
 
 
 class HDF5Folder(HDF5FolderMixin, DataFolder):
-
     """Just enforces the loader attriobute to be an HDF5File."""
 
     def __init__(self, *args, **kargs):
@@ -578,7 +574,6 @@ def __init__(self, *args, **kargs):
 
 
 class SLS_STXMFile(DataFile):
-
     """Load images from the Swiss Light Source Pollux beamline."""
 
     priority = 16
@@ -671,7 +666,6 @@ def scan_meta(self, group):
 
 
 class STXMImage(ImageFile):
-
     """An instance of KerrArray that will load itself from a Swiss Light Source STXM image."""
 
     # pylint: disable=no-member

Stoner/Image/attrs.py

@@ -47,7 +47,6 @@ def _proxy(self, *args, **kargs):
 
 @class_modifier(draw, adaptor=_draw_apaptor, RTD_restrictions=False, no_long_names=True)
 class DrawProxy:
-
     """Provides a wrapper around :py:mod:`skimage.draw` to allow easy drawing of objects onto images.
 
     This class allows access the user to draw simply shapes on an image (or its mask) by specifying the desired shape
@@ -205,7 +204,6 @@ def square(self, r, c, w, angle=0.0, shape=None, value=1.0):
 
 
 class MaskProxy:
-
     """Provides a wrapper to support manipulating the image mask easily.
 
     The actual mask of a :py:class:`Stonmer.ImageFile` is held by the mask attribute of the underlying

Stoner/Image/core.py

@@ -151,7 +151,6 @@ def copy_into(source: "ImageFile", dest: "ImageFile") -> "ImageFile":
 @class_modifier([ndi], transpose=True)
 @class_modifier(imagefuncs, overload=True)
 class ImageArray(np.ma.MaskedArray, metadataObject):
-
     """A numpy array like class with a metadata parameter and pass through to skimage methods.
 
     ImageArray is for manipulating images stored as a 2d numpy array.
@@ -701,7 +700,6 @@ def save(self, filename=None, **kargs):
 @class_modifier(imagefuncs, overload=True, adaptor=image_file_adaptor)
 @class_wrapper(target=ImageArray, exclude_below=metadataObject)
 class ImageFile(metadataObject):
-
     """An Image file type that is analogous to :py:class:`Stoner.Data`.
 
     This contains metadata and an image attribute which

Stoner/Image/folders.py

@@ -19,7 +19,6 @@
 
 
 class ImageFolderMixin:
-
     """Mixin to provide a folder object for images.
 
     ImageFolderMixin is designed to behave pretty much like DataFolder but with
@@ -474,7 +473,6 @@ def to_tiff(self, filename):
 
 
 class ImageFolder(ImageFolderMixin, DiskBasedFolderMixin, baseFolder):
-
     """Folder object for images.
 
     ImageFolder is designed to behave pretty much like DataFolder but with

Stoner/Image/kerr.py

@@ -33,7 +33,6 @@
 
 @class_modifier(kerrfuncs)
 class KerrArray(ImageArray):
-
     """A subclass for Kerr microscopy specific image functions."""
 
     # useful_keys are metadata keys that we'd usually like to keep from a
@@ -90,7 +89,6 @@ def save(self, filename=None, **kargs):
 
 @class_modifier(kerrfuncs, adaptor=image_file_adaptor)
 class KerrImageFile(ImageFile):
-
     """Subclass of ImageFile that keeps the data as a KerrArray so that extra functions are available."""
 
     priority = 16
@@ -127,7 +125,6 @@ def image(self, v):  # pylint: disable=function-redefined
 
 
 class KerrStackMixin:
-
     """A mixin for :py:class:`ImageStack` that adds some functionality particular to Kerr images.
 
     Attributes:
@@ -331,7 +328,6 @@ def average_Hcmap(self, weights=None, ignore_zeros=False):
 
 
 class MaskStackMixin:
-
     """A Mixin for :py:class:`Stoner.Image.ImageStack` but made for stacks of boolean or binary images."""
 
     def __init__(self, *args, **kargs):
@@ -398,10 +394,8 @@ def switch_index(self, saturation_end=True, saturation_value=True):
 
 
 class KerrStack(KerrStackMixin, ImageStack):
-
     """Represent a stack of Kerr images."""
 
 
 class MaskStack(MaskStackMixin, KerrStackMixin, ImageStack):
-
     """Represent a set of masks for Kerr images."""

Stoner/Image/stack.py

@@ -25,7 +25,6 @@ def _load_ImageArray(f, **kargs):
 
 
 class ImageStackMixin:
-
     """Implement an interface for a baseFolder to store images in a 3D numpy array for faster access."""
 
     _defaults = {"type": ImageFile}
@@ -481,7 +480,6 @@ def show(self):
 
 
 class StackAnalysisMixin:
-
     """Add some analysis capability to ImageStack.
 
     These functions may override :py:class:`Stoner,Image.ImageFile` functions but do them efficiently for a numpy
@@ -520,5 +518,4 @@ def subtract(self, background):
 
 
 class ImageStack(StackAnalysisMixin, ImageStackMixin, ImageFolderMixin, DiskBasedFolderMixin, baseFolder):
-
     """An alternative implementation of an image stack based on baseFolder."""

Stoner/Image/widgets.py

@@ -45,7 +45,6 @@ def _rotated_ellipse(p, data):
 
 
 class LineSelect:
-
     """Show an Image and slow the user to draw a line on it using cursors."""
 
     def __init__(self):
@@ -171,7 +170,6 @@ def draw_line(self, event):
 
 
 class RegionSelect:
-
     """Show an Image and slow the user to select a rectangular section."""
 
     def __init__(self):
@@ -257,7 +255,6 @@ def finish(self, key_event):
 
 
 class ShapeSelect:
-
     """Show an Image and slow the user to draw a line on it using cursors."""
 
     def __init__(self):

Stoner/Zip.py

@@ -54,7 +54,6 @@ def test_is_zip(filename, member=""):
 
 
 class ZippedFile(DataFile):
-
     """A sub class of DataFile that sores itself in a zip file.
 
     If the first non-keyword argument is not an :py:class:`zipfile:ZipFile` then
@@ -228,7 +227,6 @@ def save(self, filename=None, **kargs):
 
 
 class ZipFolderMixin:
-
     """Provides methods to load and save data from a single Zip file.
 
     See :py:class:`Stoner.Folders.DataFolder` for documentation on constructor.
@@ -511,7 +509,6 @@ def _save(self, f, trail):
 
 
 class ZipFolder(ZipFolderMixin, DiskBasedFolderMixin, baseFolder):
-
     """A sub class of DataFile that sores itself in a zip file.
 
     If the first non-keyword argument is not an :py:class:`zipfile:ZipFile` then

Stoner/__init__.py

@@ -3,6 +3,7 @@
 It has been developed by members of the `Condensed Matter Group<http://www.stoner.leeds.ac.uk/>` at the
 `University  of Leeds<http://www.leeds.ac.uk>`.
 """
+
 # pylint: disable=import-error
 __all__ = [
     "core",

Stoner/analysis/__init__.py

@@ -1,4 +1,5 @@
 """Subpaclage to support the data analysis functions."""
+
 from . import fitting, utils, columns
 
 __all__ = ["fitting", "utils", "columns", "filtering", "features"]

Stoner/analysis/columns.py

@@ -11,7 +11,6 @@
 
 
 class ColumnOpsMixin:
-
     """A mixin calss designed to work with :py:class:`Stoner.Core.DataFile` to provide additional stats methods."""
 
     def _do_error_calc(self, col_a, col_b, error_type="relative"):

Stoner/analysis/features.py

@@ -14,7 +14,6 @@
 
 
 class FeatureOpsMixin:
-
     """Mixin to provide additional functions to support finding features in a dataset."""
 
     def peaks(self, **kargs):

Stoner/analysis/filtering.py

@@ -19,7 +19,6 @@
 
 
 class FilteringOpsMixin:
-
     """Provide additional filtering sndsmoothing methods to :py:class:`Stoner.Data`."""
 
     def SG_Filter(

Stoner/analysis/fitting/__init__.py

@@ -1,4 +1,5 @@
 """Provides additional functionality for doing curve fitting to data."""
+
 __all__ = ["odr_Model", "FittingMixin", "models"]
 from .mixins import odr_Model, FittingMixin
 from . import models

Stoner/analysis/fitting/mixins.py

@@ -24,7 +24,6 @@
 
 
 class odr_Model(odrModel):
-
     """A wrapper for converting lmfit models to odr models."""
 
     def __init__(self, *args, **kargs):
@@ -109,7 +108,6 @@ def param_names(self):
 
 
 class MimizerAdaptor:
-
     """Work with an lmfit.Model or generic callable to use with scipy.optimize global minimization functions.
 
     The :pymod:`scipy.optimize` module's minimizers generally expect functions  which take an array like parameter
@@ -171,7 +169,6 @@ def wrapper(beta, x, y, sigma, *args):
 
 
 class _curve_fit_result:
-
     """Represent a result from fitting using :py:func:`scipy.optimize.curve_fit`
     as a class to make handling easier.
     """
@@ -471,7 +468,6 @@ def _prep_lmfit_p0(model, ydata, xdata, p0, kargs):
 
 
 class FittingMixin:
-
     """A mixin calss for :py:class:`Stoner.Core.DataFile` to provide additional curve_fiotting methods."""
 
     def annotate_fit(self, model, x=None, y=None, z=None, text_only=False, **kargs):

Stoner/analysis/fitting/models/__init__.py

@@ -1,4 +1,5 @@
 """Sub package of various built-in models for the Stoner package."""
+
 __all__ = [
     "generic",
     "thermal",

Stoner/analysis/fitting/models/e_transport.py

@@ -131,7 +131,6 @@ def blochGrueneisen(T, thetaD, rho0, A, n):
 
 
 class WLfit(Model):
-
     """Weak localisation model class.
 
     Args:
@@ -175,7 +174,6 @@ def guess(self, data, x=None, **kwargs):
 
 
 class FluchsSondheimer(Model):
-
     """Evaluate a Fluchs-Sondheumer model function for conductivity.
 
     Args:
@@ -210,7 +208,6 @@ def guess(self, data, t=None, **kwargs):  # pylint: disable=unused-argument
 
 
 class BlochGrueneisen(Model):
-
     """BlochGrueneiseen Function for fitting R(T).
 
     Args:

Stoner/analysis/fitting/models/generic.py

@@ -112,7 +112,6 @@ def lorentzian_diff(x, A, sigma, mu):
 
 
 class Linear(_Linear):
-
     """Simple linear fit class."""
 
 

Stoner/analysis/fitting/models/magnetism.py

@@ -125,11 +125,7 @@ def inverse_kittel(f, g, M_s, H_k):
        \gamma^{2} \mu_{0}^{2} + 16 \pi^{2} f^{2}}`
     """
     gamma = g * cnst.e / (2 * cnst.m_e)
-    return (
-        -H_k
-        - M_s / 2
-        + np.sqrt(M_s**2 * gamma**2 * cnst.mu_0**2 + 16 * np.pi**2 * f**2) / (2 * gamma * cnst.mu_0)
-    )
+    return -H_k - M_s / 2 + np.sqrt(M_s**2 * gamma**2 * cnst.mu_0**2 + 16 * np.pi**2 * f**2) / (2 * gamma * cnst.mu_0)
 
 
 def fmr_power(H, H_res, Delta_H, K_1, K_2):