diff --git a/.buildinfo b/.buildinfo old mode 100644 new mode 100755 diff --git a/.nojekyll b/.nojekyll old mode 100644 new mode 100755 diff --git a/.prospector.yaml b/.prospector.yaml old mode 100644 new mode 100755 diff --git a/COPYING b/COPYING old mode 100644 new mode 100755 diff --git a/MANIFEST.in b/MANIFEST.in old mode 100644 new mode 100755 diff --git a/Stoner/Image/folders.py b/Stoner/Image/folders.py index 32ba64acc..3dd24f757 100755 --- a/Stoner/Image/folders.py +++ b/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"): diff --git a/Stoner/Image/tessdata/eng.traineddata b/Stoner/Image/tessdata/eng.traineddata old mode 100644 new mode 100755 diff --git a/Stoner/Image/tessdata/equ.traineddata b/Stoner/Image/tessdata/equ.traineddata old mode 100644 new mode 100755 diff --git a/Stoner/Image/tessdata/kerr-patterns.txt b/Stoner/Image/tessdata/kerr-patterns.txt old mode 100644 new mode 100755 diff --git a/Stoner/analysis/filtering.py b/Stoner/analysis/filtering.py index bcee26010..150d0338c 100755 --- a/Stoner/analysis/filtering.py +++ b/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}") diff --git a/Stoner/analysis/fitting/models/magnetism.py b/Stoner/analysis/fitting/models/magnetism.py index d4bf183f5..5333899d5 100755 --- a/Stoner/analysis/fitting/models/magnetism.py +++ b/Stoner/analysis/fitting/models/magnetism.py @@ -267,7 +267,7 @@ 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) @@ -275,7 +275,7 @@ def __init__(self, *args, **kwargs): 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))) diff --git a/Stoner/compat.py b/Stoner/compat.py index ddeb1b526..2a246f788 100755 --- a/Stoner/compat.py +++ b/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) diff --git a/Stoner/folders/mixins.py b/Stoner/folders/mixins.py index 66f8b3600..b81d170ce 100755 --- a/Stoner/folders/mixins.py +++ b/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 diff --git a/Stoner/formats/generic.py b/Stoner/formats/generic.py index 572f4588f..21a02eb32 100755 --- a/Stoner/formats/generic.py +++ b/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. diff --git a/Stoner/plot/__init__.py b/Stoner/plot/__init__.py old mode 100644 new mode 100755 diff --git a/Stoner/plot/core.py b/Stoner/plot/core.py index 9a0954654..6fb23ce6a 100755 --- a/Stoner/plot/core.py +++ b/Stoner/plot/core.py @@ -1,4 +1,4 @@ -"""Provides the a class to facilitate easier plotting of Stoner Data. +"""Provides the a class to facilitte easier plotting of Stoner Data. Classes: PlotMixin: @@ -12,6 +12,7 @@ from collections.abc import Mapping from functools import wraps import copy +from inspect import getfullargspec import numpy as np from scipy.interpolate import griddata @@ -20,7 +21,7 @@ from matplotlib import figure as mplfig from matplotlib import cm, colors, colormaps -from Stoner.compat import string_types, index_types, int_types, getargspec +from Stoner.compat import string_types, index_types, int_types, get_func_params from Stoner.tools import AttributeStore, isnone, isanynone, all_type, isiterable, typedList, get_option, fix_signature from .formats import DefaultPlotStyle from .utils import errorfill @@ -37,6 +38,24 @@ _3D = False +def _getargspec(*args, **kargs): + """Get the function signature spec.""" + ret = getfullargspec(*args, **kargs) + if ret.args and ret.args[0] == "self": # remove self for bound methods + del ret.args[0] + deflen = len(ret.defaults) if ret.defaults else 0 + kwargs = ret.args[-deflen:] + kwargs.extend(ret.kwonlyargs) + args = ret.args[: len(ret.args) - deflen] + defaults = list(ret.defaults) if ret.defaults else [] + if ret.kwonlydefaults: + defaults.extend(list(ret.kwonlydefaults.values())) + return args, kwargs, defaults, len(kwargs) - len(ret.kwonlyargs) + + +FIG_KARGS = _getargspec(plt.figure)[1] + ["ax"] + + def __mpl3DQuiver(x_coord, y_coord, z_coord, u_comp, v_comp, w_comp, **kargs): """Plot vector fields using mpltoolkit.quiver. @@ -308,7 +327,8 @@ def _surface_plotter(self, x_coord, y_coord, z_coord, **kargs): This function attempts to work the same as the 2D surface plotter pcolor, but draws a 3D axes set""" if not _3D: raise RuntimeError("3D plotting Not available. Install matplotlib toolkits") - ax = plt.axes(projection="3d") + if not isinstance(ax := self.__figure.gca(), Axes3D): + ax = plt.axes(projection="3d") z_coord = np.nan_to_num(z_coord) surf = ax.plot_surface(x_coord, y_coord, z_coord, **kargs) self.fig.colorbar(surf, shrink=0.5, aspect=5, extend="both") @@ -328,7 +348,7 @@ def _vector_color(self, xcol=None, ycol=None, ucol=None, vcol=None, wcol=None, * qdata = 0.5 + (np.arctan2(self.column(c.ucol), self.column(c.vcol)) / (2 * np.pi)) rdata = np.sqrt(self.column(c.ucol) ** 2 + self.column(c.vcol) ** 2 + wdata**2) rdata = rdata / rdata.max() - Z = hsl2rgb(qdata, rdata, phidata).astype("f") / 255.0 + Z = hsl2rgb(qdata, rdata, phidata).astype("f") / 255.0001 + 1e-7 return Z def _span_slice(self, col, num): @@ -436,6 +456,7 @@ def _fix_fig(self, figure, **kargs): else: figure, ax = self.template.new_figure(None, **kargs) self.__figure = figure + figure.sca(ax) # Esur4e we're set for plotting on the correct axes return figure, ax def _fix_kargs(self, function=None, defaults=None, otherkargs=None, **kargs): @@ -448,10 +469,8 @@ def _fix_kargs(self, function=None, defaults=None, otherkargs=None, **kargs): defaults = dict() defaults.update(kargs) - fig_kargs = ["num", "figsize", "dpi", "facecolor", "edgecolor", "frameon", "FigureClass", "clear", "ax"] - pass_fig_kargs = {} - for k in set(fig_kargs) & set(kargs.keys()): + for k in set(FIG_KARGS) & set(kargs.keys()): pass_fig_kargs[k] = kargs[k] if k not in otherkargs and k not in defaults: del kargs[k] @@ -469,16 +488,18 @@ def _fix_kargs(self, function=None, defaults=None, otherkargs=None, **kargs): if self.__figure is not plt.gcf(): plt.close(plt.gcf()) - (args, _, kwargs) = getargspec(function)[:3] + (args, kwargs) = _getargspec(function)[:2] # Manually override the list of arguments that the plotting function takes if it takes keyword dictionary - if isinstance(otherkargs, (list, tuple)) and kwargs is not None: - args.extend(otherkargs) - nonkargs = dict() - for k in list(defaults.keys()): - nonkargs[k] = defaults[k] - if k not in args: - del defaults[k] - return defaults, nonkargs, pass_fig_kargs + if isinstance(otherkargs, (list, tuple)): + kwargs.extend(otherkargs) + nonkargs = {} + func_kwargs = {} + for key, value in defaults.items(): + if key in kwargs: + func_kwargs[key] = value + else: + nonkargs[key] = value + return func_kwargs, nonkargs, pass_fig_kargs def _fix_titles(self, ix, multiple, **kargs): """Do the titling and labelling for a matplotlib plot.""" @@ -736,7 +757,6 @@ def colormap_xyz(self, xcol=None, ycol=None, zcol=None, **kargs): ax = self.plot_xyz(xcol, ycol, zcol, shape, xlim, ylim, **kargs) if colorbar: plt.colorbar() - plt.tight_layout() return ax def contour_xyz(self, xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim=None, plotter=None, **kargs): @@ -1306,6 +1326,7 @@ def plot_xy(self, xcol=None, ycol=None, fmt=None, xerr=None, yerr=None, **kargs) title = kargs.pop("title", self.basename) defaults = { + "capsize": 4, "plotter": plt.plot, "show_plot": True, "figure": self.__figure, @@ -1456,11 +1477,13 @@ def plot_xy(self, xcol=None, ycol=None, fmt=None, xerr=None, yerr=None, **kargs) c.ycol = [c.ycol] if len(c.ycol) > 1: if multiple == "panels": - self.__figure, _ = plt.subplots(nrows=len(c.ycol), sharex=True, gridspec_kw={"hspace": 0}) + self.__figure, _ = plt.subplots( + nrows=len(c.ycol), sharex=True, gridspec_kw={"hspace": 0}, layout="constrained", **fig_kargs + ) elif multiple == "subplots": m = int(np.floor(np.sqrt(len(c.ycol)))) n = int(np.ceil(len(c.ycol) / m)) - self.__figure, _ = plt.subplots(nrows=m, ncols=n) + self.__figure, _ = plt.subplots(nrows=m, ncols=n, layout="constrained", **fig_kargs) else: self.__figure, _ = self._fix_fig(nonkargs["figure"], **fig_kargs) else: @@ -1602,16 +1625,15 @@ def plot_xyz(self, xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim= "shade", "linewidth", "ax", + "alpha", ] else: otherkargs = ["vmin", "vmax", "shade", "color", "linewidth", "marker"] - kargs, nonkargs, _ = self._fix_kargs( - kargs.get("plotter", None), defaults, otherkargs=otherkargs, projection=projection, **kargs - ) - plotter = nonkargs["plotter"] - self.__figure, ax = self._fix_fig(nonkargs["figure"], projection=projection) + plotter = kargs.get("plotter", defaults["plotter"]) + self.__figure, ax = self._fix_fig(kargs.get("figure", defaults["figure"]), projection=projection) if isinstance(plotter, string_types): plotter = ax.__getattribute__(plotter) + kargs, nonkargs, _ = self._fix_kargs(plotter, defaults, otherkargs=otherkargs, projection=projection, **kargs) self.plot3d = plotter(xdata, ydata, zdata, **kargs) if plotter is not self._surface_plotter: del nonkargs["zlabel"] @@ -1621,38 +1643,38 @@ def plot_xyz(self, xcol=None, ycol=None, zcol=None, shape=None, xlim=None, ylim= def plot_xyuv(self, xcol=None, ycol=None, ucol=None, vcol=None, wcol=None, **kargs): """Make an overlaid image and quiver plot. - Args: - xcol (index): - Xcolumn index or label - ycol (index): - Y column index or label - zcol (index): - Z column index or label - ucol (index): - U column index or label - vcol (index): - V column index or label - wcol (index): - W column index or label - - Keyword Arguments: - show_plot (bool): - True Turns on interactive plot control - title (string): - Optional parameter that specifies the plot title - otherwise the current DataFile filename is used - save_filename (string): - Filename used to save the plot - figure (matplotlib figure): - Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False - then a new figure is always used, otherwise it will default to using the last figure used by this - DataFile object. - no_quiver (bool): - Do not overlay quiver plot (in cases of dense meshes of points) - plotter (callable): - Optional argument that passes a plotting function into the routine. Default is a 3d surface plotter, - but contour plot and pcolormesh also work. - **kargs (dict): - A dictionary of other keyword arguments to pass into the plot function. + Args: + !c xcol (index): + Xcolumn index or label + ycol (index): + Y column index or label + zcol (index): + Z column index or label + ucol (index): + U column index or label + vcol (index): + V column index or label + wcol (index): + W column index or label + + Keyword Arguments: + show_plot (bool): + True Turns on interactive plot control + title (string): + Optional parameter that specifies the plot title - otherwise the current DataFile filename is used + save_filename (string): + Filename used to save the plot + figure (matplotlib figure): + Controls what matplotlib figure to use. Can be an integer, or a matplotlib.figure or False. If False + then a new figure is always used, otherwise it will default to using the last figure used by this + DataFile object. + no_quiver (bool): + Do not overlay quiver plot (in cases of dense meshes of points) + plotter (callable): + Optional argument that passes a plotting function into the routine. Default is a 3d surface plotter, + but contour plot and pcolormesh also work. + **kargs (dict): + A dictionary of other keyword arguments to pass into the plot function. """ c = self._fix_cols(xcol=xcol, ycol=ycol, ucol=ucol, vcol=vcol, wcol=wcol, **kargs) Z = self._vector_color(xcol=xcol, ycol=ycol, ucol=ucol, vcol=vcol, wcol=wcol) @@ -2042,7 +2064,7 @@ def subplot(self, *args, **kargs): def subplot2grid(self, *args, **kargs): """Provide a pass through to :py:func:`matplotlib.pyplot.subplot2grid`.""" if self.__figure is None: - self.figure() + self.figure(no_axes=True) figure = self.template.new_figure(self.__figure.number, no_axes=True)[0] @@ -2069,6 +2091,6 @@ def y2(self): """ ax = self.fig.gca() ax2 = ax.twinx() - plt.subplots_adjust(right=self.__figure.subplotpars.right - 0.05) + # plt.subplots_adjust(right=self.__figure.subplotpars.right - 0.05) plt.sca(ax2) return ax2 diff --git a/Stoner/plot/formats.py b/Stoner/plot/formats.py index 74cedc135..e8fc7cc62 100755 --- a/Stoner/plot/formats.py +++ b/Stoner/plot/formats.py @@ -19,6 +19,7 @@ import matplotlib.pyplot as plt from matplotlib.ticker import EngFormatter, Formatter from matplotlib.ticker import AutoLocator +from mpl_toolkits.mplot3d import Axes3D import numpy as np from numpy.random import normal @@ -418,14 +419,13 @@ def new_figure(self, figure=False, **kargs): params[attrname] = value projection = kargs.pop("projection", "rectilinear") self.template_figure__figsize = kargs.pop("figsize", self.template_figure__figsize) # pylint: disable=W0201 - if "ax" in kargs: # Giving an axis instance in kargs means we can use that as our figure - ax = kargs.get("ax") - plt.sca(ax) - figure = plt.gcf().number + if "ax" in kargs and isinstance(kargs["ax"], (Axes3D, plt.Axes)): + # Giving an axis instance in kargs means we can use that as our figure + figure = kargs["ax"].figure.number if isinstance(figure, bool) and not figure: return None, None elif figure is not None: - fig = plt.figure(figure, figsize=self.template_figure__figsize) + fig = plt.figure(figure, figsize=self.template_figure__figsize, layout="constrained") if len(fig.axes) == 0: rect = [plt.rcParams[f"figure.subplot.{i}"] for i in ["left", "bottom", "right", "top"]] rect[2] = rect[2] - rect[0] @@ -446,7 +446,7 @@ def new_figure(self, figure=False, **kargs): ax = kargs.pop("ax") else: for ax in plt.gcf().axes: - if "zaxis" in ax.properties(): + if isinstance(ax, Axes3D): break else: ax = plt.axes(projection="3d") @@ -457,6 +457,7 @@ def new_figure(self, figure=False, **kargs): else: no_axes = kargs.pop("no_axes", False) if projection == "3d": + kargs.setdefault("layout", "constrained") ret = plt.figure(figsize=self.template_figure__figsize, **kargs) if not no_axes: ax = ret.add_subplot(111, projection="3d") @@ -466,6 +467,7 @@ def new_figure(self, figure=False, **kargs): ax.remove() return ret, None else: + kargs.setdefault("layout", "constrained") if not no_axes: return plt.subplots(figsize=self.template_figure__figsize, **kargs) else: @@ -541,7 +543,7 @@ def annotate(self, ix, multiple, plot, **kargs): if multiple in self.subplot_settings: if ix == 0: i = 0 - elif 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b/doc/samples/Fitting/BDR.py index 493b34326..96ed16758 100755 --- a/doc/samples/Fitting/BDR.py +++ b/doc/samples/Fitting/BDR.py @@ -50,4 +50,3 @@ d.ylabel = "Current" d.title = "BDR Model test" -d.tight_layout() diff --git a/doc/samples/Fitting/FowlerNordheim.py b/doc/samples/Fitting/FowlerNordheim.py index 29c57f328..26483ad44 100755 --- a/doc/samples/Fitting/FowlerNordheim.py +++ b/doc/samples/Fitting/FowlerNordheim.py @@ -51,4 +51,3 @@ d.ylabel = "Current" d.title = "Fowler-Nordheim Model test" -d.tight_layout() diff --git a/doc/samples/Fitting/Simmons.py b/doc/samples/Fitting/Simmons.py index 48ea51de1..8c6919066 100755 --- a/doc/samples/Fitting/Simmons.py +++ b/doc/samples/Fitting/Simmons.py @@ -43,4 +43,3 @@ d.xlabel = "Bias (V)" d.title = "Simmons Model test" d.yscale("symlog", linthresh=1e-5) -d.tight_layout() diff --git a/doc/samples/Fitting/__init__.py b/doc/samples/Fitting/__init__.py old mode 100644 new mode 100755 diff --git a/doc/samples/Fitting/b_g.py b/doc/samples/Fitting/b_g.py index 8fa131d26..e64d70649 100755 --- a/doc/samples/Fitting/b_g.py +++ b/doc/samples/Fitting/b_g.py @@ -41,4 +41,3 @@ prefix="BlochGrueneisen", ) d.title = "Bloch-Grueneisen Fit" -d.tight_layout() diff --git a/doc/samples/Fitting/data/IV.txt b/doc/samples/Fitting/data/IV.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Fitting/data/Ic_B.txt b/doc/samples/Fitting/data/Ic_B.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Fitting/f_s.py b/doc/samples/Fitting/f_s.py index d2760d88e..0101298fb 100755 --- a/doc/samples/Fitting/f_s.py +++ b/doc/samples/Fitting/f_s.py @@ -43,4 +43,3 @@ prefix="FluchsSondheimer", ) d.title = "Fluchs-Sondheimer Fit" -d.tight_layout() diff --git a/doc/samples/Fitting/kittel.py b/doc/samples/Fitting/kittel.py index 06a2324d0..73eee1f47 100755 --- a/doc/samples/Fitting/kittel.py +++ b/doc/samples/Fitting/kittel.py @@ -53,4 +53,3 @@ d.title = "Kittel Fit" d.fig.gca().xaxis.set_major_formatter(TexEngFormatter()) d.fig.gca().yaxis.set_major_formatter(TexEngFormatter()) -d.tight_layout() diff --git a/doc/samples/Fitting/weak_localisation.py b/doc/samples/Fitting/weak_localisation.py old mode 100644 new mode 100755 index fada3ba19..af5c02b1b --- a/doc/samples/Fitting/weak_localisation.py +++ b/doc/samples/Fitting/weak_localisation.py @@ -39,4 +39,3 @@ prefix="WLfit", ) d.title = "Weak Localisation Fit" -d.tight_layout() diff --git a/doc/samples/L2_2 5mm length limiting slit Offspec RSM 0p05 2t step_0SecsAnneal.ras b/doc/samples/L2_2 5mm length limiting slit Offspec RSM 0p05 2t step_0SecsAnneal.ras old mode 100644 new mode 100755 diff --git a/doc/samples/Noisy_Data.txt b/doc/samples/Noisy_Data.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Nosiy_Data.txt b/doc/samples/Nosiy_Data.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Stitch-scan1.txt b/doc/samples/Stitch-scan1.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Stitch-scan2.txt b/doc/samples/Stitch-scan2.txt old mode 100644 new mode 100755 diff --git a/doc/samples/Vectorfield.py b/doc/samples/Vectorfield.py index fb4cf1ddf..665b8ff6a 100755 --- a/doc/samples/Vectorfield.py +++ b/doc/samples/Vectorfield.py @@ -23,5 +23,3 @@ e.setas = "xy.uvw" e.plot() e.title = "3D Vector, 3D Field" - -e.tight_layout() diff --git a/doc/samples/__init__.py b/doc/samples/__init__.py old mode 100644 new mode 100755 diff --git a/doc/samples/bins.py b/doc/samples/bins.py index 3767a1bfd..8cfa55e38 100755 --- a/doc/samples/bins.py +++ b/doc/samples/bins.py @@ -27,4 +27,3 @@ d.xlim = (1, 6) d.ylim(-100.0, 400) d.title = "Bin demo" if i == 0 else "" -d.tight_layout() diff --git a/doc/samples/channel_math.py b/doc/samples/channel_math.py index f05223492..584f0feb1 100755 --- a/doc/samples/channel_math.py +++ b/doc/samples/channel_math.py @@ -7,7 +7,7 @@ from Stoner.plot.utils import errorfill seed(12345) # Ensure consistent random numbers! -x = linspace(0, 10 * pi, 101) +x = linspace(0, 10 * pi, 101) + 1e-9 e = 0.01 * ones_like(x) y = 0.1 * sin(x) + normal(size=len(x), scale=0.01) + 0.1 e2 = 0.01 * cos(x) @@ -31,4 +31,10 @@ d.divide(a, b, replace=False) d.diffsum(a, b, replace=False) d.setas = "xyeyeyeyeyeyeye" -d.plot(multiple="panels", plotter=errorfill, color="red", alpha_fill=0.2) +d.plot( + multiple="panels", + plotter=errorfill, + color="red", + alpha_fill=0.2, + figsize=(5, 8), +) diff --git a/doc/samples/common_y_plot.py b/doc/samples/common_y_plot.py old mode 100644 new mode 100755 diff --git a/doc/samples/curve_fit_data.dat b/doc/samples/curve_fit_data.dat old mode 100644 new mode 100755 diff --git a/doc/samples/curve_fit_line.py b/doc/samples/curve_fit_line.py old mode 100644 new mode 100755 diff --git a/doc/samples/curve_fit_plane.py b/doc/samples/curve_fit_plane.py index 45d369d52..fe2c72103 100755 --- a/doc/samples/curve_fit_plane.py +++ b/doc/samples/curve_fit_plane.py @@ -26,13 +26,20 @@ def plane(coord, a, b, c): ) d.column_headers = ["X", "Y", "Z"] -d.figure(projection="3d") -d.plot_xyz(plotter="scatter") +d.plot_xyz(plotter="scatter", title=None, griddata=False, color="k") popt, pcov = d.curve_fit(plane, [0, 1], 2, result=True) -d.setas = "xy.z" +col = linspace(-10, 10, 128) +X, Y = meshgrid(col, col) +Z = plane(array([X, Y]).T, *popt) +e = Data( + column_stack((X.ravel(), Y.ravel(), Z.ravel())), + filename="Fitting a Plane", + setas="xyz", +) +e.column_headers = d.column_headers -d.plot_xyz(linewidth=0, cmap=cmap.jet) +e.plot_xyz(linewidth=0, cmap=cmap.jet, alpha=0.5, figure=d.fig) txt = "$z=c-ax+by$\n" txt += "\n".join( @@ -40,4 +47,4 @@ def plane(coord, a, b, c): ) ax = d.axes[0] -ax.text(15, 5, -50, txt) +ax.text(-30, -10, 10, txt) diff --git a/doc/samples/curvefit_models.py b/doc/samples/curvefit_models.py index b3c04aaae..1ca81c202 100755 --- a/doc/samples/curvefit_models.py +++ b/doc/samples/curvefit_models.py @@ -33,8 +33,8 @@ ) # Reset labels d.labels = [] - # Make nice two panel plot layout +d.figure(figsize=(7, 5), no_axes=True) ax = d.subplot2grid((3, 1), (2, 0)) d.setas = "x..y" d.plot(fmt="g+", label="Fit residuals") diff --git a/doc/samples/decompose.py b/doc/samples/decompose.py index 602ce3731..e5f428fb2 100755 --- a/doc/samples/decompose.py +++ b/doc/samples/decompose.py @@ -22,4 +22,3 @@ ) d.ylabel = "Data" d.title = "Decompose Example" -d.tight_layout() diff --git a/doc/samples/differential_evolution_simple.py b/doc/samples/differential_evolution_simple.py index 1ca8871a4..cf415509c 100755 --- a/doc/samples/differential_evolution_simple.py +++ b/doc/samples/differential_evolution_simple.py @@ -11,8 +11,6 @@ d = Data(x, y, column_headers=["Time", "Signal"], setas="xy") -d.plot(fmt="ro") # plot our data - func = lambda x, A, B, C: A + B * exp(-x / C) diff --git a/doc/samples/double_y_plot.py b/doc/samples/double_y_plot.py old mode 100644 new mode 100755 index 5fe4da17e..51209fb8e --- a/doc/samples/double_y_plot.py +++ b/doc/samples/double_y_plot.py @@ -3,7 +3,6 @@ from Stoner import Data p = Data("sample.txt", setas="xyy") - p.plot_xy(0, 1, "k-") p.y2() p.plot_xy(0, 2, "r-") diff --git a/doc/samples/image/STXMIMage_Demo.py b/doc/samples/image/STXMIMage_Demo.py index 08b03951b..936a1fe0a 100755 --- a/doc/samples/image/STXMIMage_Demo.py +++ b/doc/samples/image/STXMIMage_Demo.py @@ -53,7 +53,7 @@ # Create a profile and plot it profile = xmcd.profile_line((0, 0), (100, 100)) -profile.figure(figsize=(7, 5), no_axes=True) +profile.figure(figsize=(7, 6), no_axes=True) profile.subplot(222) profile.plot() profile.title = "XMCD Cross Section" @@ -120,6 +120,3 @@ def guess(self, data, **kwargs): profile.subplot(224) hist.plot(fmt=["b+", "b--", "r-"]) hist.title = "Intensity histogram" - -# Tidy up -plt.tight_layout() diff --git a/doc/samples/image/__init__.py b/doc/samples/image/__init__.py old mode 100644 new mode 100755 diff --git a/doc/samples/inset_plot.py b/doc/samples/inset_plot.py old mode 100644 new mode 100755 diff --git a/doc/samples/lmfit_chi^2_demo.py b/doc/samples/lmfit_chi^2_demo.py index f3755c224..e570fdf66 100755 --- a/doc/samples/lmfit_chi^2_demo.py +++ b/doc/samples/lmfit_chi^2_demo.py @@ -12,7 +12,5 @@ model, p0 = cfg_model_from_ini(config, data=d) fit = d.lmfit(model, p0=p0, result=True, header="Fit", output="data") - fit.plot(multiple="panels", capsize=3) fit.yscale = "log" # Adjust y scale for chi^2 -fit.tight_layout() diff --git a/doc/samples/lmfit_data.txt b/doc/samples/lmfit_data.txt old mode 100644 new mode 100755 diff --git a/doc/samples/lmfit_example.py b/doc/samples/lmfit_example.py old mode 100644 new mode 100755 diff --git a/doc/samples/multiple_panels_plot.py b/doc/samples/multiple_panels_plot.py old mode 100644 new mode 100755 index ebd1294a2..7392baada --- a/doc/samples/multiple_panels_plot.py +++ b/doc/samples/multiple_panels_plot.py @@ -6,4 +6,5 @@ # Quick plot p.plot(multiple="panels") # Helps to fix layout ! -p.tight_layout() +p.set_layout_engine("tight") +p.draw() diff --git a/doc/samples/multiple_y2_plot.py b/doc/samples/multiple_y2_plot.py old mode 100644 new mode 100755 diff --git a/doc/samples/panel_plot.py b/doc/samples/panel_plot.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/GBStyle.py b/doc/samples/plotstyles/GBStyle.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/JTBStyle.py b/doc/samples/plotstyles/JTBStyle.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/PRBStyle.py b/doc/samples/plotstyles/PRBStyle.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/SeabornStyle.py b/doc/samples/plotstyles/SeabornStyle.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/__init__.py b/doc/samples/plotstyles/__init__.py old mode 100644 new mode 100755 diff --git a/doc/samples/plotstyles/default.py b/doc/samples/plotstyles/default.py old mode 100644 new mode 100755 diff --git a/doc/samples/scale_curves.py b/doc/samples/scale_curves.py index ba4a48f81..162229312 100755 --- a/doc/samples/scale_curves.py +++ b/doc/samples/scale_curves.py @@ -1,14 +1,16 @@ """Example of using scale to overlap data.""" # pylint: disable=invalid-name, no-member from numpy import linspace, sin, exp, pi, column_stack -from numpy.random import normal +from numpy.random import normal, seed import matplotlib as mpl from tabulate import tabulate from Stoner import Data +seed(3) # Just fix the random numbers to stop optimizer warnings mpl.rc("text", usetex=True) + x = linspace(0, 10 * pi, 201) x2 = x * 1.5 + 0.23 y = 10 * exp(-x / (2 * pi)) * sin(x) + normal(size=len(x), scale=0.1) diff --git a/doc/samples/select_example.py b/doc/samples/select_example.py old mode 100644 new mode 100755 diff --git a/doc/samples/single_plot.py b/doc/samples/single_plot.py old mode 100644 new mode 100755 diff --git a/doc/samples/sphere_fit.py b/doc/samples/sphere_fit.py index 01de9abac..a7ed9df45 100755 --- a/doc/samples/sphere_fit.py +++ b/doc/samples/sphere_fit.py @@ -54,6 +54,7 @@ def sphere(coords, a, b, c, r): d.template.fig_width = 5.2 d.template.fig_height = 5.0 # Square aspect ratio d.plot_xyz(plotter="scatter", marker=",", griddata=False) +d.set_box_aspect((1, 1, 1.0)) # Passing through to the current axes # curve_fit does the hard work popt, pcov = d.curve_fit(sphere, (0, 1, 2), zeros_like(d.x)) diff --git a/doc/samples/subplot_plot.py b/doc/samples/subplot_plot.py old mode 100644 new mode 100755 index a756cae36..25ec5b452 --- a/doc/samples/subplot_plot.py +++ b/doc/samples/subplot_plot.py @@ -5,5 +5,3 @@ p = Data("sample.txt", setas="xyy") # Quick plot p.plot(multiple="subplots") -# Helps to fix layout ! -p.tight_layout() diff --git a/doc/samples/template2.py b/doc/samples/template2.py old mode 100644 new mode 100755 diff --git a/doc/samples/voxel_plot.py b/doc/samples/voxel_plot.py index a6a37d8b4..0b5210a5d 100755 --- a/doc/samples/voxel_plot.py +++ b/doc/samples/voxel_plot.py @@ -16,4 +16,5 @@ p = Data(x, y, z, u, setas="xyzu", column_headers=["X", "Y", "Z"]) p.plot_voxels(cmap=matplotlib.cm.jet, visible=lambda x, y, z: x - y + z < 2.0) +p.set_box_aspect((1, 1, 1.0)) # Passing through to the current axes p.title = "Voxel plot" diff --git a/prospector-report.txt b/prospector-report.txt old mode 100644 new mode 100755 diff --git a/sample-data/6221-Lockin-DAQ Temperature Control -30.0Deg 0.004T.txt b/sample-data/6221-Lockin-DAQ Temperature Control -30.0Deg 0.004T.txt old mode 100644 new mode 100755 diff --git a/sample-data/APS_Data.txt b/sample-data/APS_Data.txt old mode 100644 new mode 100755 diff --git a/sample-data/ASF008_01_ref.ras b/sample-data/ASF008_01_ref.ras old mode 100644 new mode 100755 diff --git a/sample-data/BNL-data.txt b/sample-data/BNL-data.txt old mode 100644 new mode 100755 diff --git a/sample-data/Bad_Data.txt b/sample-data/Bad_Data.txt old mode 100644 new mode 100755 diff --git a/sample-data/Birge_Group_IV.dat b/sample-data/Birge_Group_IV.dat old mode 100644 new mode 100755 diff --git a/sample-data/Cu_resistivity_vs_T.txt b/sample-data/Cu_resistivity_vs_T.txt old mode 100644 new mode 100755 diff --git a/sample-data/Example Data.txt b/sample-data/Example Data.txt old mode 100644 new mode 100755 diff --git a/sample-data/FMR-data.txt b/sample-data/FMR-data.txt old mode 100644 new mode 100755 diff --git a/sample-data/Fit_200919_000.dat b/sample-data/Fit_200919_000.dat old mode 100644 new mode 100755 diff --git a/sample-data/FmokeFile.dat b/sample-data/FmokeFile.dat old mode 100644 new mode 100755 diff --git a/sample-data/GenX.hgx b/sample-data/GenX.hgx old mode 100644 new mode 100755 diff --git a/sample-data/Harribo_map.spc b/sample-data/Harribo_map.spc old mode 100644 new mode 100755 diff --git a/sample-data/IV_t2_703 _5.46K.txt b/sample-data/IV_t2_703 _5.46K.txt old mode 100644 new mode 100755 diff --git a/sample-data/May2.hgx b/sample-data/May2.hgx old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.010000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.010000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.020000!0000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.020000!0000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.020000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.020000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.030000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.030000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.040000!0000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.040000!0000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.040000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.040000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.050000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.050000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.060000!0000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at -0.060000!0000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0001.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0001.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0002.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000!0002.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.000000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.020000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.020000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.030000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.030000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.040000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.040000.txt old mode 100644 new mode 100755 diff --git a/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.060000!0000.txt b/sample-data/NLIV/6221-2182 DC IV Multi-Parameter NLIV at 0.060000!0000.txt old mode 100644 new mode 100755 diff --git a/sample-data/PCAR Chi^2.txt b/sample-data/PCAR Chi^2.txt old mode 100644 new mode 100755 diff --git a/sample-data/PCAR Co Data.csv b/sample-data/PCAR Co Data.csv old mode 100644 new mode 100755 diff --git a/sample-data/PCAR TDI.txt b/sample-data/PCAR TDI.txt old mode 100644 new mode 100755 diff --git a/sample-data/Pd3Fe01_02_2.dat b/sample-data/Pd3Fe01_02_2.dat old mode 100644 new mode 100755 diff --git a/sample-data/PinkLib_test.dat b/sample-data/PinkLib_test.dat old mode 100644 new mode 100755 diff --git a/sample-data/Pollux-STXM Image.hdf5 b/sample-data/Pollux-STXM Image.hdf5 old mode 100644 new mode 100755 diff --git a/sample-data/QD-MH.dat b/sample-data/QD-MH.dat old mode 100644 new mode 100755 diff --git a/sample-data/QD-PPMS.dat b/sample-data/QD-PPMS.dat old mode 100644 new mode 100755 diff --git a/sample-data/QD-PPMS2.dat b/sample-data/QD-PPMS2.dat old mode 100644 new mode 100755 diff --git a/sample-data/QD-SQUID-VSM.dat b/sample-data/QD-SQUID-VSM.dat old mode 100644 new mode 100755 diff --git a/sample-data/RASOR.dat b/sample-data/RASOR.dat old mode 100644 new mode 100755 diff --git a/sample-data/Raman-graphene.spc b/sample-data/Raman-graphene.spc old mode 100644 new mode 100755 diff --git a/sample-data/Raman.spc b/sample-data/Raman.spc old mode 100644 new mode 100755 diff --git a/sample-data/SLD_200919.dat b/sample-data/SLD_200919.dat old mode 100644 new mode 100755 diff --git a/sample-data/Sample_Image_2017-10-15_100.hdf5 b/sample-data/Sample_Image_2017-10-15_100.hdf5 old mode 100644 new mode 100755 diff --git a/sample-data/Sample_Image_2017-10-15_101.hdf5 b/sample-data/Sample_Image_2017-10-15_101.hdf5 old mode 100644 new mode 100755 diff --git a/sample-data/TDMS_File.tdms b/sample-data/TDMS_File.tdms old mode 100644 new mode 100755 diff --git a/sample-data/TDMS_File.tdms_index b/sample-data/TDMS_File.tdms_index old mode 100644 new mode 100755 diff --git a/sample-data/ZipFile_Example.zip b/sample-data/ZipFile_Example.zip old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-Parameters.txt b/sample-data/attocube_scan/SC_085-Parameters.txt old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_Amp-AFM-LeftFrame-bwd.asc b/sample-data/attocube_scan/SC_085-sc_Amp-AFM-LeftFrame-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_Amp-AFM-LeftFrame-fwd.asc b/sample-data/attocube_scan/SC_085-sc_Amp-AFM-LeftFrame-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_Amp-bwd.asc b/sample-data/attocube_scan/SC_085-sc_Amp-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_Amp-fwd.asc b/sample-data/attocube_scan/SC_085-sc_Amp-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_PosX-bwd.asc b/sample-data/attocube_scan/SC_085-sc_PosX-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_PosX-fwd.asc b/sample-data/attocube_scan/SC_085-sc_PosX-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_PosY-bwd.asc b/sample-data/attocube_scan/SC_085-sc_PosY-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_PosY-fwd.asc b/sample-data/attocube_scan/SC_085-sc_PosY-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_dF-bwd.asc b/sample-data/attocube_scan/SC_085-sc_dF-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_dF-fwd.asc b/sample-data/attocube_scan/SC_085-sc_dF-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_phase-bwd.asc b/sample-data/attocube_scan/SC_085-sc_phase-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_phase-fwd.asc b/sample-data/attocube_scan/SC_085-sc_phase-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_topo-bwd.asc b/sample-data/attocube_scan/SC_085-sc_topo-bwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/attocube_scan/SC_085-sc_topo-fwd.asc b/sample-data/attocube_scan/SC_085-sc_topo-fwd.asc old mode 100644 new mode 100755 diff --git a/sample-data/hairboRaman.spc b/sample-data/hairboRaman.spc old mode 100644 new mode 100755 diff --git a/sample-data/harribo.spc b/sample-data/harribo.spc old mode 100644 new mode 100755 diff --git a/sample-data/kermit2.png b/sample-data/kermit2.png old mode 100644 new mode 100755 diff --git a/sample-data/recursivefoldertest/Cu_resistivity_vs_T.txt b/sample-data/recursivefoldertest/Cu_resistivity_vs_T.txt old mode 100644 new mode 100755 diff --git a/sample-data/skyrmion_bin4.ovf b/sample-data/skyrmion_bin4.ovf old mode 100644 new mode 100755 diff --git a/sample-data/skyrmion_bin8.ovf b/sample-data/skyrmion_bin8.ovf old mode 100644 new mode 100755 diff --git a/sample-data/skyrmion_txt.ovf b/sample-data/skyrmion_txt.ovf old mode 100644 new mode 100755 diff --git a/sample-data/working/CSVFile_test.dat b/sample-data/working/CSVFile_test.dat old mode 100644 new mode 100755 diff --git a/sample-data/working/Sample_Image_2017-06-03_035.hdf5 b/sample-data/working/Sample_Image_2017-06-03_035.hdf5 old mode 100644 new mode 100755 diff --git a/sample-data/working/Sample_Image_2017-06-03_036.hdf5 b/sample-data/working/Sample_Image_2017-06-03_036.hdf5 old mode 100644 new mode 100755 diff --git a/sample-data/working/hydra_0017.edf b/sample-data/working/hydra_0017.edf old mode 100644 new mode 100755 diff --git a/scripts/B-G Fit.py b/scripts/B-G Fit.py old mode 100644 new mode 100755 diff --git a/scripts/PCAR-New.ini b/scripts/PCAR-New.ini old mode 100644 new mode 100755 diff --git a/scripts/PCAR-chi^2.ini b/scripts/PCAR-chi^2.ini old mode 100644 new mode 100755 diff --git a/scripts/VSManalysis_v3.py b/scripts/VSManalysis_v3.py old mode 100644 new mode 100755 diff --git a/setup.cfg b/setup.cfg old mode 100644 new mode 100755 diff --git a/tests/Stoner/CoreTest.dat b/tests/Stoner/CoreTest.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/CoreTest.txt b/tests/Stoner/CoreTest.txt old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/__init__.py b/tests/Stoner/Image/__init__.py old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/im1_annotated.png b/tests/Stoner/Image/coretestdata/im1_annotated.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/im2_noannotations.png b/tests/Stoner/Image/coretestdata/im2_noannotations.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field235_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field235_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field240_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field240_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field245_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field245_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field250_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field250_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field255_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field255_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field260_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field260_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field265_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field265_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testims/000_field270_run0_unproccessed.png b/tests/Stoner/Image/coretestdata/testims/000_field270_run0_unproccessed.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/coretestdata/testsave.tiff b/tests/Stoner/Image/coretestdata/testsave.tiff old mode 100644 new mode 100755 diff --git a/tests/Stoner/Image/kerr_testdata/kermit3.png b/tests/Stoner/Image/kerr_testdata/kermit3.png old mode 100644 new mode 100755 diff --git a/tests/Stoner/__init__.py b/tests/Stoner/__init__.py old mode 100644 new mode 100755 diff --git a/tests/Stoner/analysis/test_filtering.py b/tests/Stoner/analysis/test_filtering.py index 0eb577157..d76939fd7 100755 --- a/tests/Stoner/analysis/test_filtering.py +++ b/tests/Stoner/analysis/test_filtering.py @@ -4,6 +4,9 @@ import pytest import numpy as np from Stoner import Data +import warnings + +warnings.filterwarnings("error") testd = None np.random.seed(12345) diff --git a/tests/Stoner/folder_data/CoreTest!0000.dat b/tests/Stoner/folder_data/CoreTest!0000.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/folder_data/CoreTest!0001.dat b/tests/Stoner/folder_data/CoreTest!0001.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/folder_data/CoreTest!0002.dat b/tests/Stoner/folder_data/CoreTest!0002.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/folder_data/CoreTest!0003.dat b/tests/Stoner/folder_data/CoreTest!0003.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/folder_data/CoreTest.dat b/tests/Stoner/folder_data/CoreTest.dat old mode 100644 new mode 100755 diff --git a/tests/Stoner/plot/test_plot.py b/tests/Stoner/plot/test_plot.py index 5fda1e7dc..80774475a 100755 --- a/tests/Stoner/plot/test_plot.py +++ b/tests/Stoner/plot/test_plot.py @@ -31,6 +31,8 @@ selfd = Data(path.join(__home__, "..", "sample-data", "New-XRay-Data.dql")) +warnings.filterwarnings("error") + def test_set_no_figs(): global selfd assert Options.no_figs, "Default setting for no_figs option is incorrect." @@ -146,7 +148,6 @@ def test_misc_funcs(): selfd.x2() selfd.setas = ".yx" selfd.plot() - selfd.tight_layout() assert len(selfd.fig_axes) == 2, "Creating a second X axis failed" plt.close("all") for i in range(4): diff --git a/tests/Stoner/tools/dump.txt b/tests/Stoner/tools/dump.txt old mode 100644 new mode 100755