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scan_plot_manager

Plot Manager for the Scan object

ScanPlotManager

ScanPlotManager scan.plot = ScanPlotManager(scan) scan.plot() # plot default axes scan.plot.plot(xaxis, yaxis) # creates figure scan.plot.plotline(xaxis, yaxis) # plots line on current figure scan.plot.image() # create figure and display detector image

Parameters:

Name Type Description Default
scan NexusScan

NexusScan object

 required
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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class ScanPlotManager:
    """
    ScanPlotManager
        scan.plot = ScanPlotManager(scan)
        scan.plot() # plot default axes
        scan.plot.plot(xaxis, yaxis)  # creates figure
        scan.plot.plotline(xaxis, yaxis)  # plots line on current figure
        scan.plot.image()  # create figure and display detector image

    :param scan: NexusScan object
    """
    set_plot_defaults = set_plot_defaults

    def __init__(self, scan: NexusScan):
        self.scan = scan
        self.show = plt.show

    def __call__(self, *args, **kwargs) -> plt.Axes:
        return self.plot(*args, **kwargs)

    def plotline(self, xaxis: str = 'axes', yaxis: str = 'signal', *args, **kwargs) -> list[plt.Line2D]:
        """
        Plot scanned datasets on matplotlib axes subplot

        :param xaxis: str name or address of array to plot on x axis
        :param yaxis: str name or address of array to plot on y axis
        :param args: given directly to plt.plot(..., *args, **kwars)
        :param axes: matplotlib.axes subplot, or None to use plt.gca()
        :param kwargs: given directly to plt.plot(..., *args, **kwars)
        :return: list lines object, output of plot
        """
        data = self.scan.get_plot_data(xaxis, yaxis)

        if 'label' not in kwargs:
            kwargs['label'] = self.scan.label()
        axes = kwargs.pop('axes') if 'axes' in kwargs else new_plot()
        lines = plot_line(axes, data['x'], data['y'], None, *args, **kwargs)
        return lines

    def plot(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal', *args,
             axes: plt.Axes | None = None, **kwargs) -> plt.Axes:
        """
        Create matplotlib figure with 1D lineplot of the scan

        :param xaxis: str name or address of array to plot on x axis
        :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple lines
        :param args: given directly to plt.plot(..., *args, **kwars)
        :param axes: matplotlib.axes subplot, or None to create a figure
        :param kwargs: given directly to plt.plot(..., *args, **kwars)
        :return: axes object
        """
        axes = new_plot() if axes is None else axes

        yaxis = [yaxis] if isinstance(yaxis, str) else yaxis
        data = self.scan.get_plot_data(xaxis, *yaxis)
        plot_line(axes, data['xdata'], data['ydata'], None, *args, **kwargs)

        # Add labels
        axes.set_xlabel(data['xlabel'])
        axes.set_title(data['title'])
        if len(yaxis) == 1:
            axes.set_ylabel(data['ylabel'])
        else:
            axes.legend(data['legend'])
        return axes

    def map2d(self, xaxis: str = 'axes0', yaxis: str = 'axes1', zaxis: str = 'signal',
              axes: plt.Axes | None = None, clim: tuple[float, float] | None = None,
              cmap: str = DEFAULT_CMAP, colorbar: bool = True, **kwargs) -> plt.Axes:
        """
        Create matplotlib figure with 2D colormap of the scan, for 2D grid scans

        :param xaxis: str name or address of array to plot on x-axis
        :param yaxis: str name or address of array to plot on y-axis
        :param zaxis: str name or address of array to plot on colour axis
        :param axes: matplotlib axes to plot on (None to create figure)
        :param clim: [min, max] colormap cut-offs (None for auto)
        :param cmap: str colormap name (None for auto)
        :param colorbar: False/ True add colorbar to plot
        :param axes: matplotlib.axes subplot, or None to create a figure
        :param kwargs: given directly to plt.pcolormesh(..., *args, **kwars)
        :return: axes object
        """
        if len(self.scan.map.scannables_shape()) != 2:
            raise ValueError(f"Scan {repr(self.scan)} has shape {self.scan.map.scannables_shape()} inconsistent with map2d")
        data = self.scan.get_plot_data(xaxis, yaxis, z_axis=zaxis)

        axes = new_plot() if axes is None else axes
        mesh = plot_2d_surface(
            axes=axes,
            xdata=data['grid_xdata'],
            ydata=data['grid_ydata'],
            image=data['grid_data'],
            clim=clim,
            cmap=cmap,
            **kwargs
        )
        axes.set_xlabel(data['grid_xlabel'])
        axes.set_ylabel(data['grid_ylabel'])
        axes.set_title(data['title'])
        if colorbar:
            plt.colorbar(mesh, ax=axes, label=data['grid_label'])
        return axes

    def image(self, index: int | tuple | slice | None = None, xaxis: str = 'axes',
              axes: plt.Axes | None = None, clim: tuple[float, float] | None = None,
              cmap: str = DEFAULT_CMAP, colorbar: bool = False, **kwargs) -> plt.Axes:
        """
        Plot image in matplotlib figure (if available)
        :param index: int, detector image index, 0-length of scan, if None, use centre index
        :param xaxis: name or address of xaxis dataset
        :param axes: matplotlib axes to plot on (None to create figure)
        :param clim: [min, max] colormap cut-offs (None for auto)
        :param cmap: str colormap name (None for auto)
        :param colorbar: False/ True add colorbar to plot
        :param kwargs: additional arguments for plot_detector_image
        :return: axes object
        """
        # x axis data
        xdata, xname = self.scan.get_plot_axis(xaxis, reduce_shape=True, flatten=True)

        # image data
        im = self.scan.image(index)
        if im is None:
            im = np.zeros((101, 101))
        if index is None or index == 'sum':
            xvalue = xdata[np.size(xdata) // 2]
        else:
            xvalue = xdata[index]

        # plot
        axes = new_plot() if axes is None else axes
        plot_image(axes, im, clim=clim, cmap=cmap, **kwargs)
        if not self.scan.map.image_data:
            axes.text(0.5, 0.5, 'No Detector Image', c='w',
                      horizontalalignment='center',
                      verticalalignment='center',
                      transform=axes.transAxes)
        if colorbar:
            plt.colorbar(ax=axes)
        ttl = '%s\n%s [%s] = %s' % (self.scan.title(), xname, index, xvalue)
        axes.set_title(ttl)
        return axes

    def detail(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal',
               index: int | tuple | slice | None = None, clim: tuple[float, float] | None = None,
               cmap: str = DEFAULT_CMAP, **kwargs) -> plt.Figure:
        """
        Create matplotlib figure with plot of the scan and detector image
        :param xaxis: str name or address of array to plot on x axis
        :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple plots
        :param index: int, detector image index, 0-length of scan, if None, use centre index
        :param clim: [min, max] colormap cut-offs (None for auto)
        :param cmap: str colormap name (None for auto)
        :param kwargs: given directly to plt.plot(..., *args, **kwars)
        :return: figure object
        """

        # Create figure
        fig, ((lt, rt), (lb, rb)) = plt.subplots(2, 2, figsize=[FIG_SIZE[0] * 1.2, FIG_SIZE[1] * 1.2], dpi=FIG_DPI)
        fig.subplots_adjust(hspace=0.35, left=0.1, right=0.95)

        # Top left - line plot
        self.plot(xaxis, yaxis, axes=lt, **kwargs)

        # Top right - image plot
        try:
            self.image(index, xaxis, cmap=cmap, clim=clim, axes=rt)
        except (FileNotFoundError, KeyError, TypeError):
            rt.text(0.5, 0.5, 'No Image')
            rt.set_axis_off()

        # Bottom-Left - details
        details = str(self.scan)
        lb.text(-0.2, 1, details, ha='left', va='top', multialignment="left", fontsize=12, wrap=True)
        lb.set_axis_off()

        # Bottom-Right - fit results
        rb.set_axis_off()
        if 'fit' in yaxis:
            fit_report = str(self.scan.fit)
            rb.text(-0.2, 1, fit_report, ha='left', va='top',  multialignment="left", fontsize=12, wrap=True)
        return fig

    def scananddetector(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal',
                        index: int | tuple | slice | None = None, clim: tuple[float, float] | None = None,
                        cmap: str = DEFAULT_CMAP, **kwargs) -> plt.Figure:
        """
        Create matplotlib figure with plot of the scan and detector image
        :param xaxis: str name or address of array to plot on x axis
        :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple plots
        :param index: int, detector image index, 0-length of scan, if None, use centre index
        :param clim: [min, max] colormap cut-offs (None for auto)
        :param cmap: str colormap name (None for auto)
        :param kwargs: given directly to plt.plot(..., *args, **kwars)
        :return: Figure object
        """

        # Create figure
        fig, (lt, rt) = plt.subplots(1, 2, figsize=[FIG_SIZE[0] * 1.5, FIG_SIZE[1]], dpi=FIG_DPI)
        fig.subplots_adjust(hspace=0.35, left=0.1, right=0.95)

        # left - line plot
        self.plot(xaxis, yaxis, axes=lt, **kwargs)

        # right - image plot
        self.image(index, xaxis, cmap=cmap, clim=clim, axes=rt)
        return fig

    def image_histogram(self, index: int | tuple | slice | None = None,
                        axes: plt.Axes | None = None, **kwargs) -> plt.Axes:
        """
        Plot image in matplotlib figure (if available)
        :param index: int, detector image index, 0-length of scan, if None, use centre index
        :param axes: matplotlib axes to plot on (None to create figure)
        :param kwargs: additional arguments for plot_detector_image
        :param cut_ratios: list of cut-ratios, each cut has a different colour and given as ratio of max intensity
        :return: axes object
        """
        if index is None:
            index = ()
        vol = self.scan.get_image(index=index)

        axes.hist(np.log10(vol[vol > 0].flatten()), 100)

        axes.set_xlabel('Log$_{10}$ Pixel Intensity')
        axes.set_ylabel('N')
        axes.set_title(self.scan.title())
        return axes

detail(xaxis='axes', yaxis='signal', index=None, clim=None, cmap=DEFAULT_CMAP, **kwargs)

Create matplotlib figure with plot of the scan and detector image

Parameters:

Name Type Description Default
xaxis str

str name or address of array to plot on x axis

 'axes'
yaxis str | list[str]

str name or address of array to plot on y axis, also accepts list of names for multiple plots

 'signal'
index int | tuple | slice | None

int, detector image index, 0-length of scan, if None, use centre index

 None
clim tuple[float, float] | None

[min, max] colormap cut-offs (None for auto)

 None
cmap str

str colormap name (None for auto)

 DEFAULT_CMAP
kwargs

given directly to plt.plot(..., args, *kwars)

 {}

Returns:

Type Description
Figure

figure object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def detail(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal',
           index: int | tuple | slice | None = None, clim: tuple[float, float] | None = None,
           cmap: str = DEFAULT_CMAP, **kwargs) -> plt.Figure:
    """
    Create matplotlib figure with plot of the scan and detector image
    :param xaxis: str name or address of array to plot on x axis
    :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple plots
    :param index: int, detector image index, 0-length of scan, if None, use centre index
    :param clim: [min, max] colormap cut-offs (None for auto)
    :param cmap: str colormap name (None for auto)
    :param kwargs: given directly to plt.plot(..., *args, **kwars)
    :return: figure object
    """

    # Create figure
    fig, ((lt, rt), (lb, rb)) = plt.subplots(2, 2, figsize=[FIG_SIZE[0] * 1.2, FIG_SIZE[1] * 1.2], dpi=FIG_DPI)
    fig.subplots_adjust(hspace=0.35, left=0.1, right=0.95)

    # Top left - line plot
    self.plot(xaxis, yaxis, axes=lt, **kwargs)

    # Top right - image plot
    try:
        self.image(index, xaxis, cmap=cmap, clim=clim, axes=rt)
    except (FileNotFoundError, KeyError, TypeError):
        rt.text(0.5, 0.5, 'No Image')
        rt.set_axis_off()

    # Bottom-Left - details
    details = str(self.scan)
    lb.text(-0.2, 1, details, ha='left', va='top', multialignment="left", fontsize=12, wrap=True)
    lb.set_axis_off()

    # Bottom-Right - fit results
    rb.set_axis_off()
    if 'fit' in yaxis:
        fit_report = str(self.scan.fit)
        rb.text(-0.2, 1, fit_report, ha='left', va='top',  multialignment="left", fontsize=12, wrap=True)
    return fig

image(index=None, xaxis='axes', axes=None, clim=None, cmap=DEFAULT_CMAP, colorbar=False, **kwargs)

Plot image in matplotlib figure (if available)

Parameters:

Name Type Description Default
index int | tuple | slice | None

int, detector image index, 0-length of scan, if None, use centre index

 None
xaxis str

name or address of xaxis dataset

 'axes'
axes Axes | None

matplotlib axes to plot on (None to create figure)

 None
clim tuple[float, float] | None

[min, max] colormap cut-offs (None for auto)

 None
cmap str

str colormap name (None for auto)

 DEFAULT_CMAP
colorbar bool

False/ True add colorbar to plot

 False
kwargs

additional arguments for plot_detector_image

 {}

Returns:

Type Description
Axes

axes object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def image(self, index: int | tuple | slice | None = None, xaxis: str = 'axes',
          axes: plt.Axes | None = None, clim: tuple[float, float] | None = None,
          cmap: str = DEFAULT_CMAP, colorbar: bool = False, **kwargs) -> plt.Axes:
    """
    Plot image in matplotlib figure (if available)
    :param index: int, detector image index, 0-length of scan, if None, use centre index
    :param xaxis: name or address of xaxis dataset
    :param axes: matplotlib axes to plot on (None to create figure)
    :param clim: [min, max] colormap cut-offs (None for auto)
    :param cmap: str colormap name (None for auto)
    :param colorbar: False/ True add colorbar to plot
    :param kwargs: additional arguments for plot_detector_image
    :return: axes object
    """
    # x axis data
    xdata, xname = self.scan.get_plot_axis(xaxis, reduce_shape=True, flatten=True)

    # image data
    im = self.scan.image(index)
    if im is None:
        im = np.zeros((101, 101))
    if index is None or index == 'sum':
        xvalue = xdata[np.size(xdata) // 2]
    else:
        xvalue = xdata[index]

    # plot
    axes = new_plot() if axes is None else axes
    plot_image(axes, im, clim=clim, cmap=cmap, **kwargs)
    if not self.scan.map.image_data:
        axes.text(0.5, 0.5, 'No Detector Image', c='w',
                  horizontalalignment='center',
                  verticalalignment='center',
                  transform=axes.transAxes)
    if colorbar:
        plt.colorbar(ax=axes)
    ttl = '%s\n%s [%s] = %s' % (self.scan.title(), xname, index, xvalue)
    axes.set_title(ttl)
    return axes

image_histogram(index=None, axes=None, **kwargs)

Plot image in matplotlib figure (if available)

Parameters:

Name Type Description Default
index int | tuple | slice | None

int, detector image index, 0-length of scan, if None, use centre index

 None
axes Axes | None

matplotlib axes to plot on (None to create figure)

 None
kwargs

additional arguments for plot_detector_image

 {}
cut_ratios

list of cut-ratios, each cut has a different colour and given as ratio of max intensity

 required

Returns:

Type Description
Axes

axes object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def image_histogram(self, index: int | tuple | slice | None = None,
                    axes: plt.Axes | None = None, **kwargs) -> plt.Axes:
    """
    Plot image in matplotlib figure (if available)
    :param index: int, detector image index, 0-length of scan, if None, use centre index
    :param axes: matplotlib axes to plot on (None to create figure)
    :param kwargs: additional arguments for plot_detector_image
    :param cut_ratios: list of cut-ratios, each cut has a different colour and given as ratio of max intensity
    :return: axes object
    """
    if index is None:
        index = ()
    vol = self.scan.get_image(index=index)

    axes.hist(np.log10(vol[vol > 0].flatten()), 100)

    axes.set_xlabel('Log$_{10}$ Pixel Intensity')
    axes.set_ylabel('N')
    axes.set_title(self.scan.title())
    return axes

map2d(xaxis='axes0', yaxis='axes1', zaxis='signal', axes=None, clim=None, cmap=DEFAULT_CMAP, colorbar=True, **kwargs)

Create matplotlib figure with 2D colormap of the scan, for 2D grid scans

Parameters:

Name Type Description Default
xaxis str

str name or address of array to plot on x-axis

 'axes0'
yaxis str

str name or address of array to plot on y-axis

 'axes1'
zaxis str

str name or address of array to plot on colour axis

 'signal'
axes Axes | None

matplotlib axes to plot on (None to create figure)

 None
clim tuple[float, float] | None

[min, max] colormap cut-offs (None for auto)

 None
cmap str

str colormap name (None for auto)

 DEFAULT_CMAP
colorbar bool

False/ True add colorbar to plot

 True
kwargs

given directly to plt.pcolormesh(..., args, *kwars)

 {}

Returns:

Type Description
Axes

axes object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def map2d(self, xaxis: str = 'axes0', yaxis: str = 'axes1', zaxis: str = 'signal',
          axes: plt.Axes | None = None, clim: tuple[float, float] | None = None,
          cmap: str = DEFAULT_CMAP, colorbar: bool = True, **kwargs) -> plt.Axes:
    """
    Create matplotlib figure with 2D colormap of the scan, for 2D grid scans

    :param xaxis: str name or address of array to plot on x-axis
    :param yaxis: str name or address of array to plot on y-axis
    :param zaxis: str name or address of array to plot on colour axis
    :param axes: matplotlib axes to plot on (None to create figure)
    :param clim: [min, max] colormap cut-offs (None for auto)
    :param cmap: str colormap name (None for auto)
    :param colorbar: False/ True add colorbar to plot
    :param axes: matplotlib.axes subplot, or None to create a figure
    :param kwargs: given directly to plt.pcolormesh(..., *args, **kwars)
    :return: axes object
    """
    if len(self.scan.map.scannables_shape()) != 2:
        raise ValueError(f"Scan {repr(self.scan)} has shape {self.scan.map.scannables_shape()} inconsistent with map2d")
    data = self.scan.get_plot_data(xaxis, yaxis, z_axis=zaxis)

    axes = new_plot() if axes is None else axes
    mesh = plot_2d_surface(
        axes=axes,
        xdata=data['grid_xdata'],
        ydata=data['grid_ydata'],
        image=data['grid_data'],
        clim=clim,
        cmap=cmap,
        **kwargs
    )
    axes.set_xlabel(data['grid_xlabel'])
    axes.set_ylabel(data['grid_ylabel'])
    axes.set_title(data['title'])
    if colorbar:
        plt.colorbar(mesh, ax=axes, label=data['grid_label'])
    return axes

plot(xaxis='axes', yaxis='signal', *args, axes=None, **kwargs)

Create matplotlib figure with 1D lineplot of the scan

Parameters:

Name Type Description Default
xaxis str

str name or address of array to plot on x axis

 'axes'
yaxis str | list[str]

str name or address of array to plot on y axis, also accepts list of names for multiple lines

 'signal'
args

given directly to plt.plot(..., args, *kwars)

 ()
axes Axes | None

matplotlib.axes subplot, or None to create a figure

 None
kwargs

given directly to plt.plot(..., args, *kwars)

 {}

Returns:

Type Description
Axes

axes object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def plot(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal', *args,
         axes: plt.Axes | None = None, **kwargs) -> plt.Axes:
    """
    Create matplotlib figure with 1D lineplot of the scan

    :param xaxis: str name or address of array to plot on x axis
    :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple lines
    :param args: given directly to plt.plot(..., *args, **kwars)
    :param axes: matplotlib.axes subplot, or None to create a figure
    :param kwargs: given directly to plt.plot(..., *args, **kwars)
    :return: axes object
    """
    axes = new_plot() if axes is None else axes

    yaxis = [yaxis] if isinstance(yaxis, str) else yaxis
    data = self.scan.get_plot_data(xaxis, *yaxis)
    plot_line(axes, data['xdata'], data['ydata'], None, *args, **kwargs)

    # Add labels
    axes.set_xlabel(data['xlabel'])
    axes.set_title(data['title'])
    if len(yaxis) == 1:
        axes.set_ylabel(data['ylabel'])
    else:
        axes.legend(data['legend'])
    return axes

plotline(xaxis='axes', yaxis='signal', *args, **kwargs)

Plot scanned datasets on matplotlib axes subplot

Parameters:

Name Type Description Default
xaxis str

str name or address of array to plot on x axis

 'axes'
yaxis str

str name or address of array to plot on y axis

 'signal'
args

given directly to plt.plot(..., args, *kwars)

 ()
axes

matplotlib.axes subplot, or None to use plt.gca()

 required
kwargs

given directly to plt.plot(..., args, *kwars)

 {}

Returns:

Type Description
list[Line2D]

list lines object, output of plot
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def plotline(self, xaxis: str = 'axes', yaxis: str = 'signal', *args, **kwargs) -> list[plt.Line2D]:
    """
    Plot scanned datasets on matplotlib axes subplot

    :param xaxis: str name or address of array to plot on x axis
    :param yaxis: str name or address of array to plot on y axis
    :param args: given directly to plt.plot(..., *args, **kwars)
    :param axes: matplotlib.axes subplot, or None to use plt.gca()
    :param kwargs: given directly to plt.plot(..., *args, **kwars)
    :return: list lines object, output of plot
    """
    data = self.scan.get_plot_data(xaxis, yaxis)

    if 'label' not in kwargs:
        kwargs['label'] = self.scan.label()
    axes = kwargs.pop('axes') if 'axes' in kwargs else new_plot()
    lines = plot_line(axes, data['x'], data['y'], None, *args, **kwargs)
    return lines

scananddetector(xaxis='axes', yaxis='signal', index=None, clim=None, cmap=DEFAULT_CMAP, **kwargs)

Create matplotlib figure with plot of the scan and detector image

Parameters:

Name Type Description Default
xaxis str

str name or address of array to plot on x axis

 'axes'
yaxis str | list[str]

str name or address of array to plot on y axis, also accepts list of names for multiple plots

 'signal'
index int | tuple | slice | None

int, detector image index, 0-length of scan, if None, use centre index

 None
clim tuple[float, float] | None

[min, max] colormap cut-offs (None for auto)

 None
cmap str

str colormap name (None for auto)

 DEFAULT_CMAP
kwargs

given directly to plt.plot(..., args, *kwars)

 {}

Returns:

Type Description
Figure

Figure object
Source code in mmg_toolbox/plotting/scan_plot_manager.py 
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def scananddetector(self, xaxis: str = 'axes', yaxis: str | list[str] = 'signal',
                    index: int | tuple | slice | None = None, clim: tuple[float, float] | None = None,
                    cmap: str = DEFAULT_CMAP, **kwargs) -> plt.Figure:
    """
    Create matplotlib figure with plot of the scan and detector image
    :param xaxis: str name or address of array to plot on x axis
    :param yaxis: str name or address of array to plot on y axis, also accepts list of names for multiple plots
    :param index: int, detector image index, 0-length of scan, if None, use centre index
    :param clim: [min, max] colormap cut-offs (None for auto)
    :param cmap: str colormap name (None for auto)
    :param kwargs: given directly to plt.plot(..., *args, **kwars)
    :return: Figure object
    """

    # Create figure
    fig, (lt, rt) = plt.subplots(1, 2, figsize=[FIG_SIZE[0] * 1.5, FIG_SIZE[1]], dpi=FIG_DPI)
    fig.subplots_adjust(hspace=0.35, left=0.1, right=0.95)

    # left - line plot
    self.plot(xaxis, yaxis, axes=lt, **kwargs)

    # right - image plot
    self.image(index, xaxis, cmap=cmap, clim=clim, axes=rt)
    return fig