Remove tight_layout and use constrained layout instead.

Fix several issues with not passing figure kwargs in plot routines
Rebuild docs

Stoner/Image/folders.py

@@ -8,7 +8,7 @@
 from copy import deepcopy, copy
 
 import numpy as np
-from matplotlib.pyplot import figure, Figure, subplot, tight_layout
+from matplotlib.pyplot import figure, Figure, subplot
 from PIL.TiffImagePlugin import ImageFileDirectory_v2
 from PIL import Image
 
@@ -314,8 +314,6 @@ def montage(self, *args, **kargs):
                 Passed to matplotlib figure call.
             plots_per_page(int):
                 maximum number of plots per figure.
-            tight_layout(dict or False):
-                If not False, arguments to pass to a call of :py:func:`matplotlib.pyplot.tight_layout`. Defaults to {}
 
         Returns:
             A list of :py:class:`matplotlib.pyplot.Axes` instances.
@@ -332,7 +330,6 @@ def montage(self, *args, **kargs):
         plts = min(plts, len(self))
 
         extra = kargs.pop("extra", lambda i, j, d: None)
-        tight = kargs.pop("tight_layout", {})
 
         fig_num = kargs.pop("figure", getattr(self, "_figure", None))
         if isinstance(fig_num, Figure):
@@ -344,7 +341,7 @@ def montage(self, *args, **kargs):
             fig_num = fig_num.number
 
         fig_args = getattr(self, "_fig_args", [])
-        fig_kargs = getattr(self, "_fig_kargs", {})
+        fig_kargs = getattr(self, "_fig_kargs", {"layout": "constrained"})
         for arg in ("figsize", "dpi", "facecolor", "edgecolor", "frameon", "FigureClass"):
             if arg in kargs:
                 fig_kargs[arg] = kargs.pop(arg)
@@ -363,8 +360,6 @@ def montage(self, *args, **kargs):
         for i, d in enumerate(self):
             plt_kargs = copy(kargs)
             if i % plts == 0 and i != 0:
-                if isinstance(tight, dict):
-                    tight_layout(**tight)
                 fig = figure(*fig_args, **fig_kargs)
                 fignum = fig.number
                 j = 1
@@ -381,8 +376,6 @@ def montage(self, *args, **kargs):
                     plt_kargs["title"] = kargs["title"](d)
             ret.append(d.imshow(*args, **plt_kargs))
             extra(i, j, d)
-            if isinstance(tight, dict):
-                tight_layout(**tight)
         return ret
 
     def stddev(self, weights=None, _box=False, _metadata="first"):

Stoner/analysis/filtering.py

@@ -85,7 +85,7 @@ def SG_Filter(
 
         ddata = savgol_filter(data, window_length=points, polyorder=poly, deriv=order, mode="interp")
         if isinstance(pad, bool) and pad:
-            offset = int(np.ceil(points * order**2 / 8))
+            offset = int(np.ceil(points * (order + 1) ** 2 / 8))
             padv = np.mean(ddata[:, offset:-offset], axis=1)
             pad = np.ones((ddata.shape[0], offset))
             for ix, v in enumerate(padv):
@@ -478,6 +478,7 @@ def make_bins(self, xcol, bins, mode="lin", **kargs):
             if mode.lower().startswith("lin"):
                 bin_centres = (bin_start + bin_stop) / 2.0
             elif mode.lower().startswith("log"):
+                bin_start = np.where(bin_start <= 0, 1e-9, bin_start)
                 bin_centres = np.exp(np.log(bin_start) + np.log(bin_stop) / 2.0)
             else:
                 raise ValueError(f"mode should be either lin(ear) or log(arthimitc) not {mode}")

Stoner/analysis/fitting/models/magnetism.py

@@ -267,15 +267,15 @@ class BlochLawThin(Model):
     """
 
     def __init__(self, *args, **kwargs):
-        """Setup the model."""
+        """Initialise the model."""
         super().__init__(self.blochs_law_thinfilm, *args, **kwargs)
         self.set_param_hint("g", vary=False, value=2.0)
         self.set_param_hint("A", vary=True, min=0)
         self.set_param_hint("Ms", vary=True, min=0)
         self.prefactor = gamma(1.5) * zeta(1.5) / (4 * np.pi**2)
 
     def blochs_law_thinfilm(self, T, D, Bz, S, v_ws, a, nz):
-        """Thin film version of Blopch's Law.
+        r"""Thin film version of Blopch's Law.
 
         Parameters:
             T (array):
@@ -310,7 +310,6 @@ def blochs_law_thinfilm(self, T, D, Bz, S, v_ws, a, nz):
                         ln\left[1-\exp\left( -\frac{1}{k_B T}\left(g\mu_B B_z+D\left(\frac{m \pi}{a(n_z-1)}\right)^2
                                                                    \right)\right) \right]`
         """
-
         kz_sum = sum(
             np.log(1.0 - np.exp(-(D * (m * np.pi / ((nz - 1) * a)) ** 2 + Bz) / (k * T))) for m in range(0, nz - 1)
         )
@@ -346,7 +345,8 @@ def guess(self, data, x=None, **kwargs):
         r"""Guess some starting values.
 
         M_s is taken as half the difference of the range of thew M data,
-        we can find m/T from the susceptibility :math:`chi= M_s \mu_o m / kT`,"""
+        we can find m/T from the susceptibility :math:`chi= M_s \mu_o m / kT`
+        """
         M_s = (np.max(data) - np.min(data)) / 2.0
         if x is not None:
             d = np.sort(np.row_stack((x, data)))

Stoner/compat.py

@@ -4,7 +4,6 @@
     "str2bytes",
     "bytes2str",
     "get_filedialog",
-    "getargspec",
     "string_types",
     "path_types",
     "int_types",
@@ -68,11 +67,6 @@
     from re import Pattern as _pattern_type  # pylint: disable = E0611
 
 
-def getargspec(*args, **kargs):
-    """Wrap for getargspec for Python V3."""
-    return getfullargspec(*args, **kargs)[:4]
-
-
 def get_func_params(func):
     """Get the parameters for a function."""
     sig = signature(func)

Stoner/folders/mixins.py

@@ -13,7 +13,7 @@
 
 from numpy import mean, std, array, append, any as np_any, floor, sqrt, ceil
 from numpy.ma import masked_invalid
-from matplotlib.pyplot import figure, tight_layout, subplots
+from matplotlib.pyplot import figure, subplots
 
 from Stoner.tools import isiterable, make_Data
 from ..compat import string_types, get_filedialog, _pattern_type, makedirs, path_types
@@ -683,8 +683,6 @@ def plot(self, *args, **kargs):
                 Passed to matplotlib figure call.
             plots_per_page(int):
                 maximum number of plots per figure.
-            tight_layout(dict or False):
-                If not False, arguments to pass to a call of :py:func:`matplotlib.pyplot.tight_layout`. Defaults to {}
 
         Returns:
             A list of :py:class:`matplotlib.pyplot.Axes` instances.
@@ -705,7 +703,6 @@ def plot(self, *args, **kargs):
                 self[i] = make_Data(d)
 
         extra = kargs.pop("extra", lambda i, j, d: None)
-        tight = kargs.pop("tight_layout", {})
 
         fig_args = getattr(self, "_fig_args", [])
         fig_kargs = getattr(self, "_fig_kargs", {})
@@ -721,21 +718,18 @@ def plot(self, *args, **kargs):
         fignum = fig.number
         for i, d in enumerate(self):
             if i % plts == 0 and i != 0:
-                if isinstance(tight, dict):
-                    tight_layout(**tight)
                 fig, axs = subplots(plt_x, plt_y, *fig_args, **fig_kargs)
                 fignum = fig.number
                 j = 0
             else:
                 j += 1
             fig = figure(fignum)
-            kargs["fig"] = fig
+            kargs["figure"] = fig
             kargs["ax"] = axs.ravel()[j]
             ret.append(d.plot(*args, **kargs))
             extra(i, j, d)
         for n in range(j + 1, plt_x * plt_y):
             axs.ravel()[n].remove()
-        tight_layout()
         return ret
 
 

Stoner/formats/generic.py

@@ -8,6 +8,24 @@
 import re
 from collections.abc import Mapping
 import sys
+import logging
+
+import PIL
+import numpy as np
+
+from ..Core import DataFile
+from ..compat import str2bytes, Hyperspy_ok, hs, hsload
+from ..core.exceptions import StonerLoadError
+from ..tools.file import FileManager
+
+
+class _refuse_log(logging.Filter):
+
+    """Refuse to log all records."""
+
+    def filter(self, record):
+        """Do not log anything."""
+        return False
 
 
 @contextlib.contextmanager
@@ -16,20 +34,14 @@ def catch_sysout(*args):
     stdout, stderr = sys.stdout, sys.stderr
     out = io.StringIO()
     sys.stdout, sys.stderr = out, out
+    logger = logging.getLogger("hyperspy.io")
+    logger.addFilter(_refuse_log)
     yield None
+    logger.removeFilter(_refuse_log)
     sys.stdout, sys.stderr = stdout, stderr
     return
 
 
-import PIL
-import numpy as np
-
-from ..Core import DataFile
-from ..compat import str2bytes, Hyperspy_ok, hs, hsload
-from ..core.exceptions import StonerLoadError
-from ..tools.file import FileManager
-
-
 def _delim_detect(line):
     """Detect a delimiter in a line.