def plot(axes, workspace, *args, **kwargs): ''' 3D plots - line plots :param axes: class:`matplotlib.axes.Axes3D` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param zdir: Which direction to use as z ('x', 'y' or 'z') when plotting a 2D set. :param indices: Specify which slice of an MDHistoWorkspace to use when plotting. Needs to be a tuple and will be interpreted as a list of indices. You need to use ``slice(None)`` to select which dimension to plot. *e.g.* to select the second axis to plot from a 3D volume use ``indices=(5, slice(None), 10)`` where the 5/10 are the bins selected for the other 2 axes. :param slicepoint: Specify which slice of an MDHistoWorkspace to use when plotting in the dimension units. You need to use ``None`` to select which dimension to plot. *e.g.* to select the second axis to plot from a 3D volume use ``slicepoint=(1.0, None, 2.0)`` where the 1.0/2.0 are the dimension selected for the other 2 axes. ''' if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) (x, y, z) = get_md_data1d(workspace, normalization, indices) else: (wksp_index, distribution, kwargs) = get_wksp_index_dist_and_label(workspace, **kwargs) (x, z, _, _) = get_spectrum(workspace, wksp_index, distribution, withDy=False, withDx=False) y_val = workspace.getAxis(1).extractValues()[wksp_index] y = [y_val for _ in range(len(x))] # fill x size array with y value _set_labels_3d(axes, workspace) return axes.plot(x, y, z, *args, **kwargs)
def _get_data_for_plot(axes, workspace, kwargs, with_dy=False, with_dx=False): if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) (x, y, dy) = get_md_data1d(workspace, normalization, indices) dx = None axis = None else: axis = MantidAxType(kwargs.pop("axis", MantidAxType.SPECTRUM)) normalize_by_bin_width, kwargs = get_normalize_by_bin_width( workspace, axes, **kwargs) workspace_index, distribution, kwargs = get_wksp_index_dist_and_label( workspace, axis, **kwargs) if axis == MantidAxType.BIN: # Overwrite any user specified xlabel axes.set_xlabel("Spectrum") x, y, dy, dx = get_bins(workspace, workspace_index, with_dy) elif axis == MantidAxType.SPECTRUM: x, y, dy, dx = get_spectrum(workspace, workspace_index, normalize_by_bin_width, with_dy, with_dx) else: raise ValueError( "Axis {} is not a valid axis number.".format(axis)) indices = None return x, y, dy, dx, indices, axis, kwargs
def _pcolormesh_nonortho(axes, workspace, to_display, *args, **kwargs): ''' Essentially the same as :meth:`matplotlib.axes.Axes.pcolormesh` and adds arguments related to plotting slices on nonorthogonal axes. It requires a non-standard Axes type. See https://matplotlib.org/examples/axes_grid/demo_curvelinear_grid.html. NOTE: Do NOT make this part of the public API until a discussion has been had about whether this api is sensible. It is placed here for testing purposes and is used in the sliceviewer. :param axes: :class:`matplotlib.axes.Axes` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param to_display: Callable accepting two numpy arrays to transfrom from nonorthogonal coordinates to orthogonal display :param transpose: ``bool`` to transpose the x and y axes of the plotted dimensions of an MDHistoWorkspace ''' transpose = kwargs.pop('transpose', False) (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) x, y, z = get_md_data2d_bin_bounds(workspace, indices=indices, normalization=normalization, transpose=transpose) X, Y = numpy.meshgrid(x, y) xx, yy = to_display(X, Y) _setLabels2D(axes, workspace, indices, transpose) return axes.pcolormesh(xx, yy, z, *args, **kwargs)
def imshow(axes, workspace, *args, **kwargs): ''' Essentially the same as :meth:`matplotlib.axes.Axes.imshow`. :param axes: :class:`matplotlib.axes.Axes` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param distribution: ``None`` (default) asks the workspace. ``False`` means divide by bin width. ``True`` means do not divide by bin width. Applies only when the the matrix workspace is a histogram. :param normalization: ``None`` (default) ask the workspace. Applies to MDHisto workspaces. It can override the value from displayNormalizationHisto. It checks only if the normalization is mantid.api.MDNormalization.NumEventsNormalization :param indices: Specify which slice of an MDHistoWorkspace to use when plotting. Needs to be a tuple and will be interpreted as a list of indices. You need to use ``slice(None)`` to select which dimensions to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``indices=(5, slice(None), slice(None))`` where the 5 is the bin selected for the first axis. :param slicepoint: Specify which slice of an MDHistoWorkspace to use when plotting in the dimension units. You need to use ``None`` to select which dimension to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``slicepoint=(1.0, None, None)`` where the 1.0 is the value of the dimension selected for the first axis. :param axisaligned: ``False`` (default). If ``True``, or if the workspace has a variable number of bins, the polygons will be aligned with the axes :param transpose: ``bool`` to transpose the x and y axes of the plotted dimensions of an MDHistoWorkspace ''' transpose = kwargs.pop('transpose', False) if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) x, y, z = get_md_data2d_bin_bounds(workspace, normalization, indices, transpose) _setLabels2D(axes, workspace, indices, transpose) else: (aligned, kwargs) = check_resample_to_regular_grid(workspace, **kwargs) (normalize_by_bin_width, kwargs) = get_normalize_by_bin_width(workspace, axes, **kwargs) (distribution, kwargs) = get_distribution(workspace, **kwargs) if aligned: (x, y, z) = get_matrix_2d_ragged(workspace, normalize_by_bin_width, histogram2D=True, transpose=transpose) else: (x, y, z) = get_matrix_2d_data(workspace, distribution=distribution, histogram2D=True, transpose=transpose) _setLabels2D(axes, workspace, transpose=transpose, normalize_by_bin_width=normalize_by_bin_width) if 'extent' not in kwargs: if x.ndim == 2 and y.ndim == 2: kwargs['extent'] = [x[0, 0], x[0, -1], y[0, 0], y[-1, 0]] else: kwargs['extent'] = [x[0], x[-1], y[0], y[-1]] return mantid.plots.modest_image.imshow(axes, z, *args, **kwargs)
def tricontourf(axes, workspace, *args, **kwargs): ''' Essentially the same as :meth:`mantid.plots.contourf`, but works for non-uniform grids. Currently this only works with workspaces that have a constant number of bins between spectra or with MDHistoWorkspaces. :param axes: :class:`matplotlib.axes.Axes` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param distribution: ``None`` (default) asks the workspace. ``False`` means divide by bin width. ``True`` means do not divide by bin width. Applies only when the the matrix workspace is a histogram. :param normalization: ``None`` (default) ask the workspace. Applies to MDHisto workspaces. It can override the value from displayNormalizationHisto. It checks only if the normalization is mantid.api.MDNormalization.NumEventsNormalization :param indices: Specify which slice of an MDHistoWorkspace to use when plotting. Needs to be a tuple and will be interpreted as a list of indices. You need to use ``slice(None)`` to select which dimensions to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``indices=(5, slice(None), slice(None))`` where the 5 is the bin selected for the first axis. :param slicepoint: Specify which slice of an MDHistoWorkspace to use when plotting in the dimension units. You need to use ``None`` to select which dimension to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``slicepoint=(1.0, None, None)`` where the 1.0 is the value of the dimension selected for the first axis. :param transpose: ``bool`` to transpose the x and y axes of the plotted dimensions of an MDHistoWorkspace See :meth:`matplotlib.axes.Axes.tricontourf` for more information. ''' transpose = kwargs.pop('transpose', False) if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) x_temp, y_temp, z = get_md_data2d_bin_centers(workspace, normalization, indices, transpose) x, y = numpy.meshgrid(x_temp, y_temp) _setLabels2D(axes, workspace, indices, transpose) else: (distribution, kwargs) = get_distribution(workspace, **kwargs) (x, y, z) = get_matrix_2d_data(workspace, distribution, histogram2D=False, transpose=transpose) _setLabels2D(axes, workspace, transpose=transpose) # tricontourf segfaults if many z values are not finite # https://github.com/matplotlib/matplotlib/issues/10167 x = x.ravel() y = y.ravel() z = z.ravel() condition = numpy.isfinite(z) x = x[condition] y = y[condition] z = z[condition] return axes.tricontourf(x, y, z, *args, **kwargs)
def _extract_3d_data(workspace, **kwargs): if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): normalization, kwargs = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) x_temp, y_temp, z = get_md_data2d_bin_centers(workspace, normalization, indices) x, y = numpy.meshgrid(x_temp, y_temp) else: distribution, kwargs = get_distribution(workspace, **kwargs) x, y, z = get_matrix_2d_data(workspace, distribution, histogram2D=False) indices = None return x, y, z, indices
def scatter(axes, workspace, *args, **kwargs): ''' Unpack mantid workspace and render it with matplotlib. ``args`` and ``kwargs`` are passed to :py:meth:`matplotlib.axes.Axes.scatter` after special keyword arguments are removed. This will automatically label the line according to the spectrum number unless specified otherwise. :param axes: :class:`matplotlib.axes.Axes` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param specNum: spectrum number to plot if MatrixWorkspace :param wkspIndex: workspace index to plot if MatrixWorkspace :param distribution: ``None`` (default) asks the workspace. ``False`` means divide by bin width. ``True`` means do not divide by bin width. Applies only when the the workspace is a MatrixWorkspace histogram. :param normalization: ``None`` (default) ask the workspace. Applies to MDHisto workspaces. It can override the value from displayNormalizationHisto. It checks only if the normalization is mantid.api.MDNormalization.NumEventsNormalization :param indices: Specify which slice of an MDHistoWorkspace to use when plotting. Needs to be a tuple and will be interpreted as a list of indices. You need to use ``slice(None)`` to select which dimension to plot. *e.g.* to select the second axis to plot from a 3D volume use ``indices=(5, slice(None), 10)`` where the 5/10 are the bins selected for the other 2 axes. :param slicepoint: Specify which slice of an MDHistoWorkspace to use when plotting in the dimension units. You need to use ``None`` to select which dimension to plot. *e.g.* to select the second axis to plot from a 3D volume use ``slicepoint=(1.0, None, 2.0)`` where the 1.0/2.0 are the dimension selected for the other 2 axes. For matrix workspaces with more than one spectra, either ``specNum`` or ``wkspIndex`` needs to be specified. Giving both will generate a :class:`RuntimeError`. There is no similar keyword for MDHistoWorkspaces. These type of workspaces have to have exactly one non integrated dimension ''' if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) (x, y, _) = get_md_data1d(workspace, normalization, indices) _setLabels1D(axes, workspace, indices) else: (wkspIndex, distribution, kwargs) = get_wksp_index_dist_and_label(workspace, **kwargs) (x, y, _, _) = get_spectrum(workspace, wkspIndex, distribution) _setLabels1D(axes, workspace) return axes.scatter(x, y, *args, **kwargs)
def contourf(axes, workspace, *args, **kwargs): ''' Essentially the same as :meth:`matplotlib.axes.Axes.contourf` but calculates the countour levels. Currently this only works with workspaces that have a constant number of bins between spectra. :param axes: :class:`matplotlib.axes.Axes` object that will do the plotting :param workspace: :class:`mantid.api.MatrixWorkspace` or :class:`mantid.api.IMDHistoWorkspace` to extract the data from :param distribution: ``None`` (default) asks the workspace. ``False`` means divide by bin width. ``True`` means do not divide by bin width. Applies only when the the matrix workspace is a histogram. :param normalization: ``None`` (default) ask the workspace. Applies to MDHisto workspaces. It can override the value from displayNormalizationHisto. It checks only if the normalization is mantid.api.MDNormalization.NumEventsNormalization :param indices: Specify which slice of an MDHistoWorkspace to use when plotting. Needs to be a tuple and will be interpreted as a list of indices. You need to use ``slice(None)`` to select which dimensions to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``indices=(5, slice(None), slice(None))`` where the 5 is the bin selected for the first axis. :param slicepoint: Specify which slice of an MDHistoWorkspace to use when plotting in the dimension units. You need to use ``None`` to select which dimension to plot. *e.g.* to select the last two axes to plot from a 3D volume use ``slicepoint=(1.0, None, None)`` where the 1.0 is the value of the dimension selected for the first axis. :param transpose: ``bool`` to transpose the x and y axes of the plotted dimensions of an MDHistoWorkspace ''' transpose = kwargs.pop('transpose', False) if isinstance(workspace, mantid.dataobjects.MDHistoWorkspace): (normalization, kwargs) = get_normalization(workspace, **kwargs) indices, kwargs = get_indices(workspace, **kwargs) x, y, z = get_md_data2d_bin_centers(workspace, normalization, indices, transpose) _setLabels2D(axes, workspace, indices, transpose) else: (distribution, kwargs) = get_distribution(workspace, **kwargs) (x, y, z) = get_matrix_2d_data(workspace, distribution, histogram2D=False, transpose=transpose) _setLabels2D(axes, workspace, transpose=transpose) return axes.contourf(x, y, z, *args, **kwargs)