Detailed StraKLIP API

straklip.config module

straklip.dataframe module

This module implements the DataFrame class, which manages the storage and manipulation of the data tables (multivisits detections, average visits detections, stamps, photometry, psf subtraction, false positives, etc) through all the pipeline

class straklip.dataframe.DataFrame(path2data='', path2out='', path2database='', path2pam='', target='', inst='', pixscale=1, gain=1, PAMdict={}, tilebase=15, radec=[], filters=[], xyaxis=[], fitsext='_flt', skipphot=False, dq2mask=[], zpt={}, Av={}, dist=0, kmodes=[], type='type', maxsep=2, minsep=0, df_ext_in='.h5', df_ext_out='.h5', steps=[])

Bases: object

list_of_HDF5_keys(path, ext=None)

generate list of keys in dataframe

Parameters

verbosebool, optional

choose to show prints. The default is False.

Returns

None.

load_dataframe()

Load DataFrame from file

Returns

None.

remove_HDF5_key()

remove keys from dataframe

Returns

None.

save_dataframes(step)

Save DataFrame to file

Parameters

Returns

None.

straklip.fake_star module

Fake star class to create singles and binaries for false positives analysis

class straklip.fake_star.Fake_Star(psf, flux, shift=None, Sky=0, eSky=0, PNoise=True)

Bases: object

combine(companion, shift)

Combine the fake star with onother one to create a binary Parameters ———- companion: another fake_star sigmaclip: coordinate position in the tile where to place the companion Output —— None

straklip.input_tables module

class straklip.input_tables.Tables(data_cfg, pipe_cfg, skip_originals=False)

Bases: object

ancillary_info()

canonize(label_list=['vis'])

Enforce cannonicity of df str values lowercase

check_fits_file_existence()

load_table_into_df(table_name)

rename_df(table, table_labels='mvs_table', default_labels='default_mvs_table', new_labels_dict={})

select_tables()

straklip.photometry module

This module implements the Detection class, which defines the Detection object fundamental to perform photomerty, as well ass the photometry classes (aperture,PSF and matched filter) and lux2counts (and viceversa) transofrmations

class straklip.photometry.Detection(data, x, y, edata=None, psf=None, fwhm=None, Sky=0, eSky=0, nSky=1, thrpt=1, ethrpt=0, Ei=1, grow_corr=0)

Bases: object

This class define the master Detection object for photometry

find_peaks(threshold, box_size)

find_sources(fwhm=2.5, sigma=5.0, std=0)

class straklip.photometry.flux_converter

Bases: object

This class handle transnformation that can be applyed to the output of each photometry

counts_and_errors()

evaluate counts and uncertainties following DAOPHOT formula for aperture/MF photometry or the equivalent noise area for PSF photometry

flux2mag(zpt=0.0, ezpt=0.0, exptime=1.0)

Convert flux to magnitudes and uncertanties

Parameters

zptfloat, optional

zeropoint for the observation. The default is 0.

zptfloat, optional

error on the zeropoint. The default is 1.

ezptfloat, optional

exposure time for this detection. The default is 1.

exptimefloat, optional

exposure time for this detection. The default is 1.

Returns

None.

mag2flux()

radial_profile(max_rad=5, initial_guess=[1, 0, 1, 0], showplot=False)

Evaluate the radial profile of the fistribution of counts in the tile

Parameters

max_radint, optional

maximum distance from the target in pixels where to evaluate the profile. The default is 5.

initial_guesslist, optional

initial guess for the gaussian fit. The default is [1,0,1,0].

showplotbool, optional

choose to show pltos. The default is False.

Returns

None.

class straklip.photometry.photometry_AP

Bases: object

This class handle the aperture photometry

aperture_mask(aptype='circular', method='exact', radius1=1, radius2=None, ap_x=2, ap_y=2)

Create an aperture based on aptype selection

Parameters

aptype(circular,square,4pixels), optional

defin the aperture type to use during aperture photometry. The default is ‘cirular’.

methodInt or None, optional

The method used to determine the overlap of the aperture on the pixel grid. With center they are either 0 or 1, while exact produces partial-pixel masks (i.e., values between 0 and 1). With subpixel, a pixel is divided into subpixels, each of which are considered to be entirely in or out of the aperture depending on whether its center is in or out of the aperture. If subpixels=1, this method is equivalent to ‘center’. The aperture weights will contain values between 0 and 1. The default is ‘exact’.

radius1Int, optional

radius of circula aperture in pixels or inner radius for annulus aperture. The default is 1.

radius2Int or None, optional

outer radius for annulus aperture. if None use circular aperture. The default is None.

ap_xInt, optional

widht of the square aperture. The default is 2.

ap_y: Int or None, optional

hight of the square aperture. The default is 2.

Returns

None.

aperture_stats(aperture=None, sigmaclip=False, sigma=2.5, fill=0, r=3, sat_thr=inf)

Provide usefull stats about the aperture

Parameters

apertureTYPE, optional

type of aperture performed. Can be either a list of positions in the tile or an aperture object. The default is None.

sigmaclipbool, optional

choose perform sigma clip on data. The default is False.

sigmafloat, optional

number of sigma clip. The default is 3.

fillfloat, optional

fill the data outside the mask with this value. The default is 0.

rint, optional

number of decimals to round to. The default is 3.

sat_thrfloat, optional

threshold (in counts) above which the source is considered saturatated. The default is inf.

Returns

None.

grow_curves(fig=None, ax=None, gstep=0.25, sigma=4.5, p=2, showplot=False, r_in=1, r_min=3, r_max=15)

Evaluate grow curves for aperture photometry

Parameters

figmatplotlib.pyplot

plot figure.

axmatplotlib.pyplot

plot axis.

gstepfloat, optional

step to create different growcurves. The default is 0.25.

sigmafloat, optional

value of the sigma cut. The default is 3.

pfloat, optional

create different growcurves in range -p, +p. The default is 2.

showplotbool, optional

choose to show plots. The default is False.

r_inint, optional

starting distance from the center of the tile to consider when evaluate the for growcurves. The default is 1.

r_minint, optional

minimum distance from the center of the tile to consider when evaluate the flatness of the for growcurves. The default is 3.

r_maxint, optional

maximum distance from the center of the tile to consider when evaluate the flatness of the for growcurves. The default is 15.

Returns

None.

mask_aperture_data(mask_shape=(2, 2))

Mask the data inside the aperture. Results depending on the selected type of aperture through ‘aperture’

Parameters

mask_shapetuple, optional

shape dimension for the new data mask . The default is (2,2).

Returns

None

class straklip.photometry.photometry_MF

Bases: object

This class handle the match filter photometry

mf_stats(aperture=False, aptype='circular', method='exact', radius1=1, radius2=None, ap_x=1, ap_y=1)

Provide usefull stats about the MF

Parameters

aptype(circular,square,4pixels), optional

defin the aperture type to use during aperture photometry. The default is ‘cirular’.

methodInt or None, optional

The method used to determine the overlap of the aperture on the pixel grid. With center they are either 0 or 1, while exact produces partial-pixel masks (i.e., values between 0 and 1). With subpixel, a pixel is divided into subpixels, each of which are considered to be entirely in or out of the aperture depending on whether its center is in or out of the aperture. If subpixels=1, this method is equivalent to ‘center’. The aperture weights will contain values between 0 and 1. The default is ‘exact’.

radius1Int, optional

radius of circula aperture in pixels or inner radius for annulus aperture. The default is 1.

radius2Int or None, optional

outer radius for annulus aperture. if None use circular aperture. The default is None.

ap_xInt, optional

widht of the square aperture. The default is 1.

ap_y: Int or None, optional

hight of the square aperture. The default is None.

Output

None

class straklip.photometry.photometry_PSF

Bases: object

This class handle the psf photometry

equivalent_noise_area(weavelenght, pixelscale, telescope_aperture=2.3774)

evaluate equivalent noise area for psf photometry noise estimation

Parameters

weavelenghtfloat

filter wavelenght.

pixelscalefloat

instrument pixelscale

telescope_aperturefloat, optional

telescope aperture. The default is 2.3774.

Output

None

psf_stats(fitshape, aperture_radius=5, flux=None, method='subpixel')

Perform PSF photometry and provide usefull stats about the PSF photometry

Parameters

fitshapeint,list

Rectangular shape around the center of a star which will be used to collect the data to do the fitting. Can be an integer to be the same along both axes. For example, 5 is the same as (5, 5), which means to fit only at the following relative pixel positions: [-2, -1, 0, 1, 2]. Each element of fitshape must be an odd number..

aperture_radiusint, optional

The radius (in units of pixels) used to compute initial estimates for the fluxes of sources. aperture_radius must be set if initial flux guesses are not input to the photometry. The default is None.

fluxfloat, optional

Estimated flux of the target for a better fit. The default is None.

methodInt or None, optional

The method used to determine the overlap of the aperture on the pixel grid. With center they are either 0 or 1, while exact produces partial-pixel masks (i.e., values between 0 and 1). With subpixel, a pixel is divided into subpixels, each of which are considered to be entirely in or out of the aperture depending on whether its center is in or out of the aperture. If subpixels=1, this method is equivalent to ‘center’. The aperture weights will contain values between 0 and 1. The default is ‘subpixel’.

Returns

None.

straklip.showroom module

straklip.stralog module

class straklip.stralog.MakeFileHandler(filename, mode='a', encoding=None, delay=0)

Bases: FileHandler

straklip.stralog.getLogger(args, **kwargs)

straklip.stralog.mkdir_p(path)

http://stackoverflow.com/a/600612/190597 (tzot)

straklip.stralog.setupLogger(configfile, logfile)

straklip.tiles module

This module implements the Tile class, which help create/load/save tiles cubes centered around each target (data, error, dq, modles, residuals)

class straklip.tiles.Tile(data=[], delta=0, x=nan, y=nan, tile_base=1, inst=None, dqdata=[], Python_origin=True, raise_errors=False)

Bases: object

append_tile(path2tile, Datacube=None, verbose=False, name='SCI', header=None, return_Datacube=False, write=True)

load_tile(path2tile, hdul_max=None, ext=None, verbose=False, return_Datacube=False, mode='readonly', raise_errors=True)

mk_tile(fig=None, ax=None, step=2, title='', cmap='viridis', xy_tile=False, xy_m=False, xy_cen=False, xy_dmax=3, box_size=3, fwhm=2.5, sigma=4, background=0, std=0, showplot=True, cbar=False, lpad=0.5, fx=5, fy=5, legend=False, mk_arrow=False, xa=None, ya=None, theta=0, PAV3=None, L=None, dtx=0.3, dty=0.15, head_width=0.5, head_length=0.5, width=0.15, fc='k', ec='k', tc='k', north=True, east=False, roll=True, simplenorm=None, min_percent=0, max_percent=100, power=1, log=1000, cr_remove=False, la_cr_remove=False, cr_radius=3, verbose=False, kill=False, close=True, vmin=None, vmax=None, pad_data=False, pad=None, keep_size=False, return_tile=False, kill_plots=False, path2savefig=None)

Select a smaller portion of an imput image and create a new tile from it.

Parameters

figmatplotlib, optional

outside figure. The default is None

axmatplotlib, optional

outside axis. The default is None.

stepint, optional

step of the axis ticks. The default is 1.

titlestr, optional

title for the plot. The default is ‘’.

cmapstr, optional

color map. The default is ‘Greys_r’.

xy_tilebool, optional

choose to show the original coordinates on the tile frame. The default is False.

xy_cenbool, optional

choose to evaluate and show the coordinate of the centroids on the tile frame. The default is False.

xy_mbool, optional

choose to evaluate and show the coordinate of the maximum on the tile frame. The default is False.

xy_dmax: int, optional

distance from the center to look for maximum. The default is 2

showplotbool, optional

choose to show the plot. The default is True.

cbarbool, optional

choose to show the colorbar. The default is False.

lpadfloat, optional

legend border pad. The default is 0.5.

fxint, optional

figure x dimemsion. The default is 5.

fyint, optional

figure y dimension. The default is 5.

legendbool, optional

choose to show the legend. The default is False.

mk_arrowbool, optional

choose to show arrows on tile. The default is False.

xafloat, optional

x arrow anchoring point. The default is None.

yafloat, optional

y arrow anchoring point. The default is None.

thetafloat, optional

arrow angle. The default is 0.

PAV3float, optional

PAV3 of the telescope. The default is None.

Lfloat, optional

length of the arrow. The default is None.

dtxfloat, optional

add x space between arrow and text. The default is 0.3.

dtyfloat, optional

add y space between arrow and text. The default is 0.3.

head_widthgloat, optional

arrow head width. The default is 0.5.

head_lengthfloat, optional

arrow head lenght. The default is 0.5.

widthfloat, optional

arrow body width. The default is 0.15.

fcstr, optional

arrow face color. The default is ‘k’.

ecstr, optional

arrow edge color. The default is ‘k’.

tcstr, optional

arrow text color. The default is ‘k’.

northbool, optional

choose to show the north arrow. The default is True.

eastbool, optional

choose to show the east arrow. The default is False.

rollbool, optional

choose to show the PA arrow. The default is True.

simplenormTYPE, optional

use simplenorm normalization. The default is None.

min_percent: float, optional

The percentile value used to determine the pixel value of minimum cut level. The default is 0.0. min_percent overrides percent.

max_percent: float, optional

The percentile value used to determine the pixel value of maximum cut level. The default is 100.0. max_percent overrides percent.

power: float, optional

The power index for stretch=’power’. The default is 1.0.

log: float, optional

The log index for stretch=’log’. The default is 1000.

cr_removebool, optional

choose to apply cosmic ray removal. The default is False.

la_cr_removebool, optional

choose to apply L.A. cosmic ray removal. The default is False.

cr_radiusint, optional

minimum distance from center where to not apply the cosmic ray filter. The default is 3.

closebool, optional

choose to close plot istances. The default is True.

killbool, optional

choose to kill bad pixels instead of using the median of the neighbouring pixels. The default is False.

verbosebool, optional

choose to show prints. The default is False.

vminfloat, optional

define the data range that the colormap covers. The default is None.

vmaxfloat, optional

define the data range that the colormap covers. The default is None.

pad_databool, optional

choose to pad the input data. The default is False.

padint, optional

number of pixels to pad the data. If None use the base of the tile. The default is None.

return_tile: bool, optional

choose to return the newly created tile as output of the fuction.

kill_plots:

choose to kill all plots created. The default is False.

Returns

im: numpy array. optional

new created tile.

plot_tile(fig, ax, title=None, cmap='viridis', xy_tile=True, xy_cen=True, xy_m=True, cbar=False, bad_pixel_c='r', lpad=0.5, legend=False, tight=False, mk_arrow=False, xa=None, ya=None, theta=0, PAV3=None, L=None, dtx=0.3, dty=0.15, head_width=0.5, head_length=0.5, width=0.15, fc='k', ec='k', tc='k', north=True, east=False, roll=True, showplot=True, step=2, simplenorm=None, verbose=False, close=True, kill=False, vmin=None, vmax=None, min_percent=0, max_percent=100.0, power=1, log=1000, savename=None, extent=None, kill_plots=False)

plot the input tile

Parameters

figmatplotlib.pyplot

plot figure.

axmatplotlib.pyplot

plot axis.

titlestr, optional

title for the plot. The default is ‘’.

cmapstr, optional

color map. The default is ‘Greys_r’.

xy_tilebool, optional

choose to show the original coordinates on the tile frame. The default is False.

xy_cenbool, optional (deprecated)

choose to evaluate and show the coordinate of the centroids on the tile frame. The default is False.

xy_mbool, optional

choose to evaluate and show the coordinate of the maximum on the tile frame. The default is False.

cbarbool, optional

choose to show the colorbar. The default is False.

bad_pixel_cstr, optional

NaN pixel color for colorbar. The default is ‘r’.

lpadfloat, optional

legend border pad. The default is 0.5.

legendbool, optional

choose to show the legend. The default is False.

tightbool, optional

choose to apply tight layout to plot. The default is False.

mk_arrowbool, optional

choose to show arrows on tile. The default is False.

xafloat, optional

x arrow anchoring point. The default is None.

yafloat, optional

y arrow anchoring point. The default is None.

thetafloat, optional

arrow angle. The default is 0.

PAV3float, optional

PAV3 of the telescope. The default is None.

Lfloat, optional

length of the arrow. The default is None.

dtxfloat, optional

add x space between arrow and text. The default is 0.3.

dtyfloat, optional

add y space between arrow and text. The default is 0.3.

head_widthgloat, optional

arrow head width. The default is 0.5.

head_lengthfloat, optional

arrow head lenght. The default is 0.5.

widthfloat, optional

arrow body width. The default is 0.15.

fcstr, optional

arrow face color. The default is ‘k’.

ecstr, optional

arrow edge color. The default is ‘k’.

tcstr, optional

arrow text color. The default is ‘k’.

northbool, optional

choose to show the north arrow. The default is True.

eastbool, optional

choose to show the east arrow. The default is False.

rollbool, optional

choose to show the PA arrow. The default is True.

showplotTYPE, optional

DESCRIPTION. The default is True.

stepTYPE, optional

DESCRIPTION. The default is 1.

simplenormTYPE, optional

use simplenorm normalization. The default is None.

verbosebool, optional

choose to show prints. The default is False.

closebool, optional

choose to close plot istances. The default is True.

killbool, optional

choose to kill bad pixels instead of using the median of the neighbouring pixels. The default is False.

vminfloat, optional

define the data range that the colormap covers. The default is None.

vmaxfloat, optional

define the data range that the colormap covers. The default is None.

min_percent: float, optional

The percentile value used to determine the pixel value of minimum cut level. The default is 0.0. min_percent overrides percent.

max_percent: float, optional

The percentile value used to determine the pixel value of maximum cut level. The default is 100.0. max_percent overrides percent.

power: float, optional

The power index for stretch=’power’. The default is 1.0.

log: float, optional

The log index for stretch=’log’. The default is 1000.

savenamestr, optional

path and file name to save the plot. The default is None.

kill_plots:

choose to kill all plots created. The default is False.

Returns

im: numpy array.

new created tle.