Plotting Tools: Display models and data¶
The plot
module provides mechanisms for plotting models, observations, and model fits.
The ModelPlot
class can be used plotting models and observations without any \(\chi^2\) fitting.
An example notebook for using ModelPlot is
PDRT_Example_ModelPlotting.ipynb .
Some classes are paired with analysis tools in the tool
module. LineRatioPlot
which is used to plot the results of LineRatioFit
, and H2ExcitationPlot
that is used in H2Excitation
. All plot classes are derived from PlotBase
.
Plot Keywords¶
To manage the plots, the methods in Plot
classes take keywords (**kwargs) that turn on or off various options, specify plot units, or map to matplotlib’s plot()
, imshow()
, contour()
keywords. The methods have reasonable defaults, so try them with no keywords to see what they do before modifying keywords.
units (
str
orastropy.units.Unit
) image data units to use in the plot. This can be either a string such as, ‘cm^-3’ or ‘Habing’, or it can be anastropy.units.Unit
. Data will be converted to the desired unit. Note these are not the axis units, but the image data units. Modifying axis units is implemented via the xaxis_unit and yaxis_unit keywords.image (
bool
) whether or not to display the image map (imshow).show (
str
) which quantity to display in the Measurement, one of ‘data’, ‘error’, ‘mask’. For example, this can be used to plot the errors in observed ratios. Default: ‘data’cmap (
str
) colormap name, Default: ‘plasma’colorbar (
str
) whether or not to display colorbarcolors (
str
) color of the contours. Default: ‘whitecolor of the contours. Default: ‘white’contours (
bool
), whether or not to plot contourslabel (
bool
), whether or not to label contourslinewidths (
float or sequence of float
), the line width in points, Default: 1.0legend (
bool
) Draw a legend on the plot. If False, a title is drawn above the plot with the value of the title keywordlevels (
int
or array-like) Determines the number and positions of the contour lines / regions. If an int n, use n data intervals; i.e. draw n+1 contour lines. The level heights are automatically chosen. If array-like, draw contour lines at the specified levels. The values must be in increasing order.measurements (array-like) A list of single pixel Measurements that can be contoured over a model ratio or intensity map.
meas_color (array of str) A list of colors to use when overlaying Measurement contours. There should be one color for each Measurement in the measurement keyword. The Default of None will use a color-blind friendly color cycle.
norm (
str
orastropy.visualization
normalization object) The normalization to use in the image. The string ‘simple’ will normalize withsimple_norm()
and ‘zscale’ will normalize with IRAF’s zscale algorithm. SeeZScaleInterval
.stretch (
str
) {‘linear’, ‘sqrt’, ‘power’, log’, ‘asinh’}. The stretch function to apply to the image for simple_norm. The Default is ‘linear’.aspect (
str
) aspect ratio, ‘equal’ or ‘auto’ are typical defaults.origin (
str
) Origin of the image. Default: ‘lower’title (
str
) A title for the plot. LaTeX allowed.vmin (
float
) Minimum value for colormap normalizationvmax (
float
) Maximum value for colormap normalizationxaxis_unit (
str
orastropy.units.Unit
) X axis (density) units to use when plotting models, such as inoverlay_all_ratios()
ormodelratio()
. If None, the native model axis units are used.yaxis_unit (
str
orastropy.units.Unit
) Y axis (FUV radiation field flux) units to use when plotting models, such as inoverlay_all_ratios()
ormodelratio()
. If None, the native model axis units are used.
The following keywords are available, but you probably won’t touch.
nrows (
int
) Number of rows in the subplotncols (
int
) Number of columns in the subplotindex (
int
) Index of the subplotreset (
bool
) Whether or not to reset the figure.
Providing keywords other than these has undefined results, but may just work!
PlotBase¶
- class pdrtpy.plot.plotbase.PlotBase(tool)[source]¶
Bases:
object
Base class for plotting.
- Parameters
tool (Any class derived from
ToolBase
) – Reference to atool
object or None. This is used for classes that inherit from PlotBase and are coupled to a specific tool, e.g.LineRatioPlot
andLineRatioFit
.- Attributes
Methods
savefig
(fname, **kwargs)Save the current figure to a file.
usetex
(use)Control whether plots use LaTeX formatting in axis labels and other text components.
- property axis¶
The last axis that was drawn.
- Return type
matplotlib.axes._subplots.AxesSubplot
- property figure¶
The last figure that was drawn.
- Return type
H2ExcitationPlot¶
- class pdrtpy.plot.h2excitationplot.H2ExcitationPlot(tool, **kwargs)[source]¶
Bases:
pdrtpy.plot.plotbase.PlotBase
Class to plot various results from H2 Excitation diagram fitting.
- Attributes
axis
The last axis that was drawn.
figure
The last figure that was drawn.
Methods
plot_diagram
(x, y, xsize, ysize[, norm])Plot the excitation diagram
savefig
(fname, **kwargs)Save the current figure to a file.
usetex
(use)Control whether plots use LaTeX formatting in axis labels and other text components.
- plot_diagram(x, y, xsize, ysize, norm=True)[source]¶
Plot the excitation diagram
- Parameters
norm (bool) – if True, normalize the column densities by the statistical weight of the upper state, \(g_u\).
x (int) – bottom left corner x
y (int) – bottom left corner y
xsize (int) – box width, pixels
ysize (int) – box height, pixels
line (bool) – if True, the returned dictionary index is the Line name, otherwise it is the upper state \(J\) number.
LineRatioPlot¶
- class pdrtpy.plot.lineratioplot.LineRatioPlot(tool)[source]¶
Bases:
pdrtpy.plot.plotbase.PlotBase
Class to plot various results from PDR Toolbox model fitting.
- Keyword Arguments
The methods of this class can take a variety of optional keywords. See the general Plot Keywords documentation
- Attributes
axis
The last axis that was drawn.
figure
The last figure that was drawn.
Methods
chisq
(**kwargs)Plot the \(\chi^2\) map that was computed by the
LineRatioFit
tool.confidence_intervals
(**kwargs)Plot the confidence intervals from the \(\chi^2\) map computed by the
LineRatioFit
tool.density
(**kwargs)Plot the hydrogen nucleus volume density map that was computed by
LineRatioFit
tool.modelintensity
(id, **kwargs)Plot one of the model intensities
modelratio
(id, **kwargs)Plot one of the model ratios
observedratio
(id, **kwargs)Plot one of the observed ratios
overlay_all_ratios
(**kwargs)Overlay all the measured ratios and their errors on the \((n,G_0)\) space.
radiation_field
(**kwargs)Plot the radiation field map that was computed by
LineRatioFit
tool.ratios_on_models
(**kwargs)Overlay all the measured ratios and their errors on the individual models for those ratios.
reduced_chisq
(**kwargs)Plot the reduced \(\chi^2\) map that was computed by the
LineRatioFit
tool.savefig
(fname, **kwargs)Save the current figure to a file.
show_both
([units])Plot both radiation field and volume density maps computed by the
LineRatioFit
tool in a 1x2 panel subplot.usetex
(use)Control whether plots use LaTeX formatting in axis labels and other text components.
- chisq(**kwargs)[source]¶
Plot the \(\chi^2\) map that was computed by the
LineRatioFit
tool.
- confidence_intervals(**kwargs)[source]¶
Plot the confidence intervals from the \(\chi^2\) map computed by the
LineRatioFit
tool. Default levels: [50., 68., 80., 95., 99.]Currently only works for single-pixel Measurements
- density(**kwargs)[source]¶
Plot the hydrogen nucleus volume density map that was computed by
LineRatioFit
tool. Default units: cm \(^{-3}\)
- observedratio(id, **kwargs)[source]¶
Plot one of the observed ratios
- Parameters
id – the ratio identifier, such as
CII_158/CO_32
.- Raises
KeyError – if id is not in existing observed ratios
- overlay_all_ratios(**kwargs)[source]¶
Overlay all the measured ratios and their errors on the \((n,G_0)\) space.
Currently only works for single-pixel Measurements
- radiation_field(**kwargs)[source]¶
Plot the radiation field map that was computed by
LineRatioFit
tool. Default units: Habing.
- ratios_on_models(**kwargs)[source]¶
Overlay all the measured ratios and their errors on the individual models for those ratios. Plots are displayed in multi-column format, controlled the ncols keyword. Default: ncols=2
Currently only works for single-pixel Measurements
- reduced_chisq(**kwargs)[source]¶
Plot the reduced \(\chi^2\) map that was computed by the
LineRatioFit
tool.
- show_both(units=['Habing', 'cm^-3'], **kwargs)[source]¶
Plot both radiation field and volume density maps computed by the
LineRatioFit
tool in a 1x2 panel subplot. Default units: [‘Habing’,’cm^-3’]
ModelPlot¶
- class pdrtpy.plot.modelplot.ModelPlot(modelset, figure=None, axis=None)[source]¶
Bases:
pdrtpy.plot.plotbase.PlotBase
Class to plot models and optionally Measurements. It does not require
LineRatioFit
first.- Keyword Arguments
The methods of this class can take a variety of optional keywords. See the general Plot Keywords documentation
- Attributes
axis
The last axis that was drawn.
figure
The last figure that was drawn.
Methods
intensity
(identifier, **kwargs)Plot a model ratio
overlay
(measurements, **kwargs)Overlay one or more single-pixel measurements in the model space ($n,G_0).
phasespace
(identifiers[, nax1_clip, …])Plot lines of constant density and radiation field on a ratio-ratio, ratio-intensity, or intensity-intensity map
plot
(identifier, **kwargs)Plot a model intensity or ratio
ratio
(identifier, **kwargs)Plot a model ratio
savefig
(fname, **kwargs)Save the current figure to a file.
usetex
(use)Control whether plots use LaTeX formatting in axis labels and other text components.
- intensity(identifier, **kwargs)[source]¶
Plot a model ratio
- Parameters
identifier (str) – Identifier tag for the model to plot, e.g., “OI_63”, “CII_158”, “CO_10”]
See also
supported_intensities()
for a list of available identifer tags
- overlay(measurements, **kwargs)[source]¶
Overlay one or more single-pixel measurements in the model space ($n,G_0).
- Parameters
measurements (list) – a list of one or more
pdrtpy.measurement.Measurement
to overlay.shading (float) – Controls how measurements and errors are drawn. If shading is zero, Measurements will be drawn in solid contour for the value and dashed for the +/- errors. If shading is between 0 and 1, Measurements are drawn with as filled contours representing the size of the errors (see
contourf()
) with alpha set to the shading value. Default value: 0.4
- phasespace(identifiers, nax1_clip=<Quantity [1.e+01, 1.e+07] 1 / cm3>, nax2_clip=<Quantity [1.e+01, 1.e+06] Habing>, reciprocal=[False, False])[source]¶
Plot lines of constant density and radiation field on a ratio-ratio, ratio-intensity, or intensity-intensity map
- Parameters
identifiers (list of str) – list of two identifier tags for the model to plot, e.g., [“OI_63/CO_21”, “CII_158”]
nax1_clip (array like, must contain Quantity) – The range of model densities on NAXIS1 to show in the plot. For most model NAXIS1 is hydrogen number density $n_H$ in cm$^{-3}$. For ionized gas models, it is electron temperature $T_e$ in K. Must be given as a range of astropy quanitities. Default: [10,1E7]*Unit(“cm-3”)
nax2_clip (array like, must contain Quantity) – The range of model parameters on NAXIS2 to show in the plot. For most models NAXIS2 is radiation field intensities in Habing or cgs units. For ionized gas models, it is electron volume density $n_e$. Must be given as a range of astropy quantities. Default: nax1_clip=[10,1E6]*utils.habing_unit.
reciprocal (list of bool) – Whether or not the plot the reciprocal of the model on each axis. Given as a pair of booleans. e.g. [False,True] means don’t flip the quantity X axis, but flip quantity the Y axis. i.e. if the model is “CII/OI”, and reciprocal=True then the axis will be “OI/CII”. Default: [False, False]
- plot(identifier, **kwargs)[source]¶
Plot a model intensity or ratio
- Parameters
identifier (str) – Identifier tag for the model to plot, e.g., “CII_158”,”OI_145”,”CO_43/CO_21’]
See also
supported_lines()
for a list of available identifer tags
- ratio(identifier, **kwargs)[source]¶
Plot a model ratio
- Parameters
identifier (str) – Identifier tag for the model to plot, e.g., “OI_63+CII_158/FIR”, “CO_43/CO_21’]
See also
supported_ratios()
for a list of available identifer tags