Imexamine

class imexam.imexamine.Imexamine

Bases: object

The imexamine class controls plotting and analysis functions.

do imexamine like routines on the current frame.

read the returned cursor key value to decide what to do

region_size is the default radius or side of the square for stat info

Methods Summary

aper_phot(x, y[, data, fig])	Perform aperture photometry.
close()	For use with the Imexamine object standalone.
column_fit(x, y[, data, form, genplot, fig])	Compute the 1d fit to the column of data.
contour(x, y[, data, fig])	plot contours in a region around the specified location.
curve_of_growth(x, y[, data, genplot, fig])	Display a curve of growth plot.
cutout(x, y[, data, size, fig])	Make a fits cutout around the pointer location without wcs.
do_option(x, y, key)	Run the imexam option.
gauss_center(x, y[, data, delta, sigma_factor])	Return the 2d gaussian fit center of the data.
get_options()	Return the imexam options as a key list.
get_plot_name()	return the default plot name.
histogram(x, y[, data, genplot, fig])	Calulate a histogram of the data values.
line_fit(x, y[, data, form, genplot, fig, col])	compute the 1D fit to the line of data using the specified form.
new_plot_window(x, y[, data])	make the next plot in a new plot window.
option_descrip(key[, field])	Return the looked up dictionary of options.
plot_column(x, y[, data, fig])	column plot of data at point y.
plot_line(x, y[, data, fig])	line plot of data at point x.
print_options()	Print the imexam options to screen.
radial_profile(x, y[, data, form, genplot, fig])	Display the radial profile plot (intensity vs radius) for the object.
register(user_funcs)	register a new imexamine function made by the user as an option.
report_stat(x, y[, data])	report the statisic of values in a box with side region_size.
reset_defpars()	set all pars to their defaults.
save([filename, fig])	Save to file the figure that’s currently displayed.
save_figure(x, y[, data, fig])	Save to file the figure that’s currently displayed.
set_aper_phot_pars([user_dict])	the user may supply a dictionary of par settings.
set_colplot_pars()	set parameters for column plots.
set_column_fit_pars()	set parameters for 1D line fit plots.
set_contour_pars()	set parameters for contour plots.
set_curve_pars()	set parameters for curve of growth plots.
set_cutout_pars()	set parameters for cutout images.
set_data([data, dtype])	initialize the data that imexamine uses.
set_histogram_pars()	set parameters for histogram plots.
set_line_fit_pars()	set parameters for 1D line fit plots.
set_lineplot_pars()	set parameters for line plots.
set_option_funcs()	Define the dictionary which maps imexam keys to their functions.
set_plot_name([filename])	set the default plot name for the “s” key.
set_radial_pars()	set parameters for radial profile plots.
set_surface_pars()	set parameters for surface plots.
setlog([filename, on, level])	Turn on and off logging to a logfile or the screen.
show_fit_models()	Print the available astropy models for plot fits.
show_xy_coords(x, y[, data])	print the x,y,value to the screen.
surface(x, y[, data, fig])	plot a surface around the specified location.
unlearn_all()	reset the default parameters for all functions.

Methods Documentation

aper_phot(x, y, data=None, fig=None)

Perform aperture photometry.

uses photutils functions, photutils must be available

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure object for redirect

Used for interaction with the ginga GUI

close()

For use with the Imexamine object standalone.

column_fit(x, y, data=None, form=None, genplot=True, fig=None)

Compute the 1d fit to the column of data.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

form: string

This is the functional form specified in the column fit parameters

genplot: int

produce the plot or return the fit model

fig: figure name for redirect

Used for interaction with the ginga GUI

Notes

delta is the range of data values to use around the x,y location

The background is currently ignored

if centering is True, then the center is fit with a 2d gaussian, but this is currently not done for Polynomial1D

contour(x, y, data=None, fig=None)

plot contours in a region around the specified location.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure for redirect

Used for interaction with the ginga GUI

curve_of_growth(x, y, data=None, genplot=True, fig=None)

Display a curve of growth plot.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure name for redirect

Used for interaction with the ginga GUI

Notes

the object photometry is taken from photutils

cutout(x, y, data=None, size=None, fig=None)

Make a fits cutout around the pointer location without wcs.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

size: int

The radius of the cutout region

fig: figure for redirect

Used for interaction with the ginga GUI

do_option(x, y, key)

Run the imexam option.

Parameters:

x: int

The x location of the cursor or data point

y: int

The y location of the cursor or data point

key: string

The key which was pressed

gauss_center(x, y, data=None, delta=10, sigma_factor=0)

Return the 2d gaussian fit center of the data.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

delta: int

The range of data values (bounding box) to use around the x,y location for calculating the center

sigma_factor: float, optional

The sigma clipping factor to use on the data fit

get_options()

Return the imexam options as a key list.

get_plot_name()

return the default plot name.

histogram(x, y, data=None, genplot=True, fig=None)

Calulate a histogram of the data values.

Parameters:

x: int, required

The x location of the object

y: int, required

The y location of the object

data: numpy array, optional

The data array to work on

genplot: boolean, optional

If false, returns the hist, bin_edges tuple

fig: figure name for redirect

Used for interaction with the ginga GUI

Notes

This functional originally used the pylab histogram routine for plotting. In order to accomodate returning just the histogram data, this was changed to the numpy histogram, with a subsequent plot if genplot is True.

Does not yet support numpy v1.11 strings for bin estimation.

line_fit(x, y, data=None, form=None, genplot=True, fig=None, col=False)

compute the 1D fit to the line of data using the specified form.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

form: string

This is the functional form specified in the line fit parameters see show_fit_models()

genplot: bool

produce the plot or return the fit

fig: figure for redirect

Used for interaction with the ginga GUI

col: bool (False)

Plot column instead of line

Notes

The background is currently ignored

If centering is True in the parameter set, then the center is fit with a 2d gaussian, not performed for Polynomial1D

new_plot_window(x, y, data=None)

make the next plot in a new plot window.

Notes

x,y, data, are not used here, but the calls are setup to take them for all imexam options. Is there a better way to do the calls in general? Once the new plotting window is open all plots will be directed towards it. The old window cannot be used again.

option_descrip(key, field=1)

Return the looked up dictionary of options.

Parameters:

key: string

The key which was pressed, it relates to the function to call

field: int

This tells where in the option dictionary the function name can be found

plot_column(x, y, data=None, fig=None)

column plot of data at point y.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure name for redirect

Used for interaction with the ginga GUI

plot_line(x, y, data=None, fig=None)

line plot of data at point x.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure object for redirect

Used for interaction with the ginga GUI

print_options()

Print the imexam options to screen.

radial_profile(x, y, data=None, form=None, genplot=True, fig=None)

Display the radial profile plot (intensity vs radius) for the object.

From the parameters Dictionary: If pixel is True, then every pixel at each radius is plotted. If pixel is False, then the sum of all pixels in integer bins is plotted

Background may be subtracted and centering can be done with a 2D Gaussian fit. These options are read from the plot parameters dict.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

form: string

The string name of the form of the fit to use

genplot: bool

Generate the plot if True, else retfurn the fit data

register(user_funcs)

register a new imexamine function made by the user as an option.

Parameters:

user_funcs: dict

Contains a dictionary where each key is the binding for the (function,description) tuple

Notes

The new binding will be added to the dictionary of imexamine functions as long as the key is unique. The new functions do not have to have default dictionaries associated with them.

report_stat(x, y, data=None)

report the statisic of values in a box with side region_size.

The statistic can be any numpy function

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

reset_defpars()

set all pars to their defaults.

save(filename=None, fig=None)

Save to file the figure that’s currently displayed.

this is used for the standalone plotting

Parameters:

filename: string

Name of the file the plot will be saved to. The extension on the filename determines the filetype

fig: figure name for redirect

Used for interaction with the ginga GUI

save_figure(x, y, data=None, fig=None)

Save to file the figure that’s currently displayed.

this is used for the imexam loop, because there is a standard api for the loop

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure for redirect

Used for interaction with the ginga GUI

set_aper_phot_pars(user_dict=None)

the user may supply a dictionary of par settings.

set_colplot_pars()

set parameters for column plots.

set_column_fit_pars()

set parameters for 1D line fit plots.

set_contour_pars()

set parameters for contour plots.

set_curve_pars()

set parameters for curve of growth plots.

set_cutout_pars()

set parameters for cutout images.

set_data(data=array([], dtype=float64))

initialize the data that imexamine uses.

set_histogram_pars()

set parameters for histogram plots.

set_line_fit_pars()

set parameters for 1D line fit plots.

set_lineplot_pars()

set parameters for line plots.

set_option_funcs()

Define the dictionary which maps imexam keys to their functions.

Notes

The user can modify this dictionary to add or change options, the first item in the tuple is the associated function the second item in the tuple is the description of what the function does when that key is pressed

set_plot_name(filename=None)

set the default plot name for the “s” key.

Parameters:

filename: string

The name which is used to save the current plotting window to a file The extension on the name decides which file type is used

set_radial_pars()

set parameters for radial profile plots.

set_surface_pars()

set parameters for surface plots.

setlog(filename=None, on=True, level=20)

Turn on and off logging to a logfile or the screen.

Parameters:

filename: str, optional

Name of the output file to record log information

on: bool, optional

True by default, turn the logging on or off

level: logging class, optional

set the level for logging messages, turn off screen messages by setting to logging.CRITICAL

show_fit_models()

Print the available astropy models for plot fits.

show_xy_coords(x, y, data=None)

print the x,y,value to the screen.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

surface(x, y, data=None, fig=None)

plot a surface around the specified location.

Parameters:

x: int

The x location of the object

y: int

The y location of the object

data: numpy array

The data array to work on

fig: figure for redirect

Used for interaction with the ginga GUI

unlearn_all()

reset the default parameters for all functions.