Plotting classes and functions

Plotting classes and functions#

Classes and functions for plotting spectra and SDFITS data

Core Functions and Classes#

Core plotting functions.

dysh.plot.core.check_kwargs(known_kwargs, kwargs)[source]#: Check if kwargs are in known_kwargs

dysh.plot.core.parse_html(s)[source]#: Turn html-styled text from spectral line search to matplotlib mathtext

PlotBase#

Plot a spectrum using matplotlib

class dysh.plot.plotbase.PlotBase[source]#

Bases: object

This class describes describes the common interface to all Plot classes.

Attributes:

axis: The underlying Axes object.

Methods

`fmt_scans`([abbreviate])	Format the scan numbers.
`refresh`()	Refresh the plot
`savefig`(file[, hidebuttons])	Save the plot

has_axes
has_figure
has_selector
show

property axis#: The underlying Axes object.

fmt_scans(abbreviate=True)[source]#: Format the scan numbers.

has_axes()[source]#

has_figure()[source]#

has_selector()[source]#

refresh()[source]#: Refresh the plot

savefig(file, hidebuttons=True, **kwargs)[source]#

Save the plot

Parameters:

filestr: The output file name.
hidebuttonsbool: Hide the buttons in the output.
**kwargsdict or key=value pairs: Other arguments to pass to savefig

show()[source]#

SpecPlot#

Plot a spectrum using matplotlib

class dysh.plot.specplot.MultiSpanSelector(ax, minspan=1, xy0=(0, 0))[source]#

Bases: object

Methods

`clear`()	Clear all regions.
`clear_region`([event])	Clear a single region.
`clear_regions`([event])	Clear all regions and start a new empty region.
`disconnect`()	Disconnect all event handlers to prevent memory leaks and dangling references.
`get_selected_regions`([ignore_incomplete])
`init_first_span`()	Add the first span selector to this object.
`set_minspan`(minspan)	Set the minimum span in data units for the spans.
`set_xy0`(xy0)	Set the bottom left coordinates in data units for the spans and their handles.

close
init_span
on_press
on_select

clear()[source]#: Clear all regions.

clear_region(event=None)[source]#: Clear a single region.

clear_regions(event=None)[source]#: Clear all regions and start a new empty region.

close()[source]#

disconnect()[source]#: Disconnect all event handlers to prevent memory leaks and dangling references.

get_selected_regions(ignore_incomplete=True)[source]#

Parameters:

ignore_completebool: If True ignore spans that are smaller than self.minspan.

Returns:

regionslist of tuples: List with edges of the spans as tuples.

init_first_span()[source]#: Add the first span selector to this object.

init_span()[source]#

on_press(event)[source]#

on_select(vmin, vmax)[source]#

set_minspan(minspan: float) → None[source]#: Set the minimum span in data units for the spans.

set_xy0(xy0: tuple) → None[source]#: Set the bottom left coordinates in data units for the spans and their handles.

class dysh.plot.specplot.SpectrumPlot(spectrum, select=True, **kwargs)[source]#

Bases: PlotBase

The SpectrumPlot class is for simple plotting of a Spectrum using matplotlib functions. Plots attributes are modified using keywords (**kwargs) described below. SpectrumPlot will attempt to make smart default choices for the plot if no additional keywords are given.

Parameters:

spectrumSpectrum: The spectrum to plot

Attributes:

axis: The underlying Axes object.
spectrum: The underlying Spectrum

Methods

`annotate_vline`(xval[, text, rotation])	Add a single annotated vline to the plot.
`clear_overlays`([blines, oshows, catalog])	Clear Overlays from the plot.
`fmt_scans`([abbreviate])	Format the scan numbers.
`oshow`(spectra[, color, linestyle, label, alpha])	Add `spectra` to the current plot.
`plot`([show_header, select, oshow, oshow_kwargs])	Plot the spectrum.
`refresh`()	Refresh the plot
`reset`()	Reset the plot keyword arguments to their defaults.
`savefig`(file[, hidebuttons])	Save the plot
`set_xaxis_unit`(xunit)	Set the units of the abscissa axis of the plot.
`set_yaxis_unit`(yunit)	Set the units of the ordinate axis of the plot.
`set_ydata`(ydata[, keep_unit])	Set the ordinate data values for the plot line.
`show_baseline`(y, args, *kwargs)	Show a baseline model with values `y`.
`show_catalog_lines`([rotation])	Overlay spectral lines from various catalogs on the plot, with annotations.
`update_limits`()	Recompute the data limits based on the current artists (`relim`), and then autoscale the view limits using the data limits (`autoscale_view`).

clear_lines
default_plot_kwargs
get_selected_regions
has_axes
has_figure
has_selector
show

Other Parameters:

xaxis_unitstr or Unit: The units to use on the x-axis, e.g. “km/s” to plot velocity.
yaxis_unitstr or Unit: The units to use on the y-axis.
xminfloat: Minimum x-axis value, in xaxis_unit.
xmaxfloat: Maximum x-axis value, in yaxis_unit.
yminfloat: Minimum y-axis value, in xaxis_unit.
ymaxfloat: Maximum y-axis value, in yaxis_unit.
xlabelstr: x-axis label.
ylabelstr: y-axis label.
labelstr: Label for legend.
alphafloat: Alpha value for the plot. Between 0 and 1.
gridbool: Show a plot grid or not.
figsizetuple: Figure size (see matplotlib).
linewidthfloat: Line width, default: 2.0.
drawstylestr: Line style, default ‘default’.
colorstr: Line color, c also works.
titlestr: Plot title.
vel_framestr: The velocity frame (see VELDEF FITS Keyword).
doppler_convention: str: The velocity convention (see VELDEF FITS Keyword).

annotate_vline(xval, text='', rotation=0)[source]#

Add a single annotated vline to the plot. Can be cleared with the “catalog” gid.

Parameters:

xvalfloat: X value of the line, in the same units as the plot.
textstr: Associated text for the vline. Defaults to an empty string.
rotationfloat: Rotate the text CCW degrees. Default 0.

clear_lines(gid)[source]#

clear_overlays(blines=True, oshows=True, catalog=True)[source]#

Clear Overlays from the plot.

Parameters:

blinesbool: Remove baseline models overlaid on the plot. Default: True
oshowsbool: Remove other spectra overlaid on the plot. Default: True
catalogbool: Remove catalog spectral lines overlaid on the plot. Default: True

default_plot_kwargs()[source]#

get_selected_regions()[source]#

oshow(spectra, color=None, linestyle=None, label=None, alpha=None)[source]#

Add spectra to the current plot.

Parameters:

spectralist of dysh.spectra.spectrum.Spectrum or dysh.spectra.spectrum.Spectrum: Spectra to add to the plot.
colorlist of valid matplotlib colors or matplotlib color: Colors for the spectra. There must be one element per spectra.
linestylelist of valid matplotlib linestyles or matplotlib linestyle: Linestyles for the spectra. There must be one element per spectra.
labellist of str: Labels for the spectra. There must be one element per spectra.
alphalist of float: Alpha values for the spectra, between 0 and 1. There must be one element per spectra.

plot(show_header=True, select=True, oshow=None, oshow_kwargs=None, **kwargs)[source]#

Plot the spectrum.

Parameters:

show_headerbool: Show informational header.
selectbool: Allow selecting regions via click and drag.
oshowlist or Spectrum: Spectra to overlay in the plot.
oshow_kwargsdict: Dictionary with parameters for SpectrumPlot.oshow. These include color, linestyle, label, and alpha.

Other Parameters:

xaxis_unitstr or Unit: The units to use on the x-axis, e.g. “km/s” to plot velocity.
yaxis_unitstr or Unit: The units to use on the y-axis.
xminfloat: Minimum x-axis value, in xaxis_unit.
xmaxfloat: Maximum x-axis value, in yaxis_unit.
yminfloat: Minimum y-axis value, in xaxis_unit.
ymaxfloat: Maximum y-axis value, in yaxis_unit.
xlabelstr: x-axis label.
ylabelstr: y-axis label.
labelstr: Label for legend.
alphafloat: Alpha value for the plot. Between 0 and 1.
gridbool: Show a plot grid or not.
figsizetuple: Figure size (see matplotlib).
linewidthfloat: Line width, default: 2.0.
drawstylestr: Line style, default ‘default’.
colorstr: Line color, c also works.
titlestr: Plot title.
vel_framestr: The velocity frame (see VELDEF FITS Keyword).
doppler_convention: str: The velocity convention (see VELDEF FITS Keyword).

reset()[source]#: Reset the plot keyword arguments to their defaults.

set_xaxis_unit(xunit: str | Quantity) → None[source]#

Set the units of the abscissa axis of the plot.

Parameters:

xunitstr or Quantity: New units for the x-axis. It must be a valid unit for the data.

set_yaxis_unit(yunit: str | Quantity) → None[source]#

Set the units of the ordinate axis of the plot.

Parameters:

yunitstr or Quantity: New units for the y-axis. It must be a valid unit for the data.

set_ydata(ydata, keep_unit=False) → None[source]#

Set the ordinate data values for the plot line. That is the line that representes the underlying Spectrum.

Parameters:

ydataarray: Ordinate axes values to display. These can be floats or quantities.
keep_unitbool: Only used if ydata is a Quantity. If True, keep the units of ydata. If False, scale to the units of the current plot line.

show_baseline(y, *args, **kwargs) → None[source]#

Show a baseline model with values y.

Parameters:

yarray: Ordinate axes values of the baseline model.
argstuple: Arguments passed to plot.
kwargsLine2D properties, optional: Keyword arguments passed to plot.

show_catalog_lines(rotation=0, **kwargs)[source]#

Overlay spectral lines from various catalogs on the plot, with annotations.

Parameters:

rotationfloat, degrees: Rotate the annotation text CCW to aid in readability. Default 0.
**kwargs: All other kwargs get passed to dysh.line.query_lines.

property spectrum#: The underlying Spectrum

update_limits()[source]#: Recompute the data limits based on the current artists (relim), and then autoscale the view limits using the data limits (autoscale_view).

ScanPlot#

Plot a spectrum using matplotlib

class dysh.plot.scanplot.ScanPlot(scanblock_or_scan, **kwargs)[source]#

Bases: PlotBase

The ScanPlot class is for simple plotting of a Scan or ScanBlock using matplotlib functions. Plot attributes are modified using keywords (**kwargs) described below. SpectrumPlot will attempt to make smart default choices for the plot if no additional keywords are given.

Parameters:

scanblock_or_scanScan or ScanBlock: The scan or scanblock to plot.
**kwargsdict: Plot attribute keyword arguments, see below.

Attributes:

axis: The underlying Axes object.

Methods

`fmt_scans`([abbreviate])	Format the scan numbers.
`plot`([show_header, spectral_unit])	Plot the scan.
`refresh`()	Refresh the plot
`reset`()	Reset the plot keyword arguments to their defaults.
`savefig`(file[, hidebuttons])	Save the plot
`set_clim`([vmin, vmax])	Set the vmin and vmax parameters of the image.
`set_cmap`([cmap])	Set the cmap of the image.
`set_interpolation`([interpolation])	Set the interpolation of the image.
`set_norm`([norm])	Set the normalization of the image colormap.
`write`(filename[, avechan, chan, overwrite])	Write the current spectrogram as a FITS image.

has_axes
has_figure
has_selector
show

Other Parameters:

spectral_unitstr: The units to use on the frequency axis. Can be ‘MHz’ or ‘GHz’.

plot(show_header=True, spectral_unit=None, **kwargs)[source]#

Plot the scan.

Parameters:

spectral_unitUnit: The units to use on the frequency axis. Default: MHz if below 1 GHz, GHz if above. Otherwise, can be any valid frequency unit.
**kwargsvarious: keyword=value arguments drawn from imshow kwargs. Currently implemented kwargs include cmap, interpolation, vmin, vmax, and norm.

reset()[source]#: Reset the plot keyword arguments to their defaults.

set_clim(vmin=None, vmax=None)[source]#

Set the vmin and vmax parameters of the image.

Parameters:

vminfloat: The minimum value of the color scale. Default None; to autoscale.
vmaxfloat: The maximum value of the color scale. Default None; to autoscale.

set_cmap(cmap='inferno')[source]#

Set the cmap of the image.

Parameters:

cmapstr: cmap used for the color scale. Default: “inferno”.

set_interpolation(interpolation='nearest')[source]#

Set the interpolation of the image.

Parameters:

interpolationstr: Interpolation method. Default: “nearest”.

set_norm(norm=None)[source]#

Set the normalization of the image colormap. Can be any value supported by the imshow norm keyword, e.g. ‘linear’, ‘log’ etc or a Normalize object.

Parameters:

normstr | Normalize | None: norm used for the color scale. Default: “None”, for linear scaling.

write(filename, avechan=1, chan=None, overwrite=False)[source]#

Write the current spectrogram as a FITS image. No WCS is maintained yet. The integrations are in the first axis and the channels in the second.

Parameters:

filenamestr: Filename of FITS file to be saved. No default
avechanint: Averaging number of channels. Only supports averaging by a multiple of the number of channels. Default: 1
chan[int,int]: If given, it will select this channel range for output. Default: all channels will be selected
overwriteboolean: Overwrite existing file. Default: False

GUIs#

BaseGUI#

Base class for dysh GUIs

class dysh.plot.basegui.BaseGUI[source]#

Bases: object

Methods

`connect_buttons`(plotbase)	Connect the GUI button(s) callbacks.
`disconnect_buttons`()	Disconnect the GUI button(s) callbacks.
`is_window_alive`()	Is the GUI window alive.
`show`()	Show the GUI contents.

connect_buttons(plotbase)[source]#

Connect the GUI button(s) callbacks.

Parameters:

plotbasePlotBase: Plotting class that defines the functions to be used in the callbacks.

disconnect_buttons()[source]#: Disconnect the GUI button(s) callbacks.

is_window_alive()[source]#

Is the GUI window alive.

Returns:

True if the GUI window is still alive.

show()[source]#: Show the GUI contents.

ShellGUI#

Graphical User Interface for dysh shell.

class dysh.plot.shellgui.ShellGUI(plotbase)[source]#

Bases: BaseGUI

Tk based GUI. Used for plotting in the shell.

Methods

`connect_buttons`(plotbase)	Connect the GUI button(s) callbacks.
`disconnect_buttons`()	Disconnect the GUI button(s) callbacks.
`is_window_alive`()	Is the GUI window alive.
`show`()	Show the GUI contents.

connect_buttons(plotbase)[source]#

Connect the GUI button(s) callbacks.

Parameters:

plotbasePlotBase: Plotting class that defines the functions to be used in the callbacks.

disconnect_buttons()[source]#: Disconnect the GUI button(s) callbacks.

is_window_alive()[source]#

Is the GUI window alive.

Returns:

True if the GUI window is still alive.

show()[source]#: Show the GUI contents.

LabGUI#

dysh lab (Jupyter) plotting interface.

class dysh.plot.labgui.LabGUI(plotbase)[source]#

Bases: BaseGUI

NBAgg based GUI. Used for jupyter.

Methods

`connect_buttons`(plotbase)	Connect the GUI button(s) callbacks.
`disconnect_buttons`()	Disconnect the GUI button(s) callbacks.
`is_window_alive`()	Is the GUI window alive.
`show`()	Show the GUI contents.

connect_buttons(plotbase)[source]#

Connect the GUI button(s) callbacks.

Parameters:

plotbasePlotBase: Plotting class that defines the functions to be used in the callbacks.

disconnect_buttons()[source]#: Disconnect the GUI button(s) callbacks.

is_window_alive()[source]#

Is the GUI window alive.

Returns:

True if the GUI window is still alive.

show()[source]#: Show the GUI contents.

class dysh.plot.labgui.StaticLabGUI(plotbase)[source]#

Bases: BaseGUI

Agg based GUI, i.e., no GUI at all. Used for jupyter rendering in documentation.

Methods

`connect_buttons`(plotbase)	Connect the GUI button(s) callbacks.
`disconnect_buttons`()	Disconnect the GUI button(s) callbacks.
`is_window_alive`()	Is the GUI window alive.
`show`()	Show the GUI contents.

show()[source]#: Show the GUI contents.

StaticGUI#

dysh headless “GUI”.

class dysh.plot.staticgui.StaticGUI(plotbase)[source]#

Bases: BaseGUI

Agg based GUI, i.e., no GUI at all.

Methods

`connect_buttons`(plotbase)	Connect the GUI button(s) callbacks.
`disconnect_buttons`()	Disconnect the GUI button(s) callbacks.
`is_window_alive`()	Is the GUI window alive.
`show`()	Show the GUI contents.

Plotting classes and functions

Contents

Plotting classes and functions#

Core Functions and Classes#

PlotBase#

SpecPlot#

ScanPlot#

GUIs#

BaseGUI#

ShellGUI#

LabGUI#

StaticGUI#