Spectrum Analysis¶
grizli.utils Module¶
Dumping ground for general utilities
Functions¶
RGBtoHex(vals[, rgbtype]) |
Converts RGB values in a variety of formats to Hex values. |
apply_flt_dq(filename[, replace, verbose, …]) |
Read and apply the compact exposure information file |
argv_to_dict(argv[, defaults, dot_dict]) |
Convert a list of (simple) command-line arguments to a dictionary. |
array_templates(templates[, wave, max_R, z, …]) |
Return an array version of the templates that have all been interpolated to the same grid. |
blot_nearest_exact(in_data, in_wcs, out_wcs) |
Own blot function for blotting exact pixels without rescaling for input and output pixel size |
bspline_templates(wave[, degree, df, …]) |
B-spline basis functions, modeled after splines |
calc_header_zeropoint(im[, ext]) |
Determine AB zeropoint from image header |
catalog_area([ra, dec, make_plot, NMAX, …]) |
Compute the surface area of a list of RA/DEC coordinates |
catalog_mask(cat[, ecol, …]) |
Compute a catalog mask for |
cheb_templates(wave[, order, get_matrix, …]) |
Chebyshev polynomial basis functions |
column_string_operation(col, test[, method, …]) |
Analogous to str.contains but for table column. |
column_values_in_list(col, test_list) |
Test if column elements “in” an iterable (e.g., a list of strings) |
combine_phot_dict(phots[, templates, MW_EBV]) |
Combine photmetry dictionaries |
compute_equivalent_widths(templates, coeffs, …) |
Compute template-fit emission line equivalent widths |
compute_output_wcs(wcs_list[, pixel_scale, …]) |
Compute output WCS that contains the full list of input WCS |
convex_hull_wrapper(x, y) |
Generate a convex hull from a list of points |
ctime_to_iso(mtime[, format, strip_decimal, …]) |
Convert time.ctime strings to ISO dates |
detect_with_photutils(sci[, err, dq, seg, …]) |
Use photutils to detect objects and make segmentation map |
dot_templates(coeffs, templates[, z, max_R, …]) |
Compute template sum analogous to np.dot(coeffs, templates). |
drizzle_array_groups(sci_list, wht_list, …) |
Drizzle array data with associated wcs |
drizzle_from_visit(visit, output[, pixfrac, …]) |
Make drizzle mosaic from exposures in a visit dictionary |
dump_flt_dq(filename[, replace, verbose]) |
Dump FLT/FLC header & DQ extensions to a compact file |
emission_line_templates() |
Testing FSPS line templates |
eval_bspline_templates(wave, bspl, coefs) |
|
fetch_acs_wcs_files(beams_file[, bucket_name]) |
Fetch wcs files for a given beams.fits files |
fetch_config_files([ACS, get_sky, …]) |
Config files needed for Grizli |
fetch_default_calibs([ACS]) |
Fetch a set of default HST calibration files |
fetch_hst_calib([file, ftpdir, verbose, …]) |
TBD |
fetch_hst_calibs(flt_file[, ftpdir, …]) |
TBD Fetch necessary calibration files needed for running calwf3 from STScI FTP |
fetch_s3_url([url, file_func, …]) |
Fetch file from an S3 bucket |
fetch_wfpc2_calib([file, path, use_mast, …]) |
Fetch static WFPC2 calibration file and run stsci.tools.convertwaiveredfits on it. |
fill_between_steps(x, y0, y1[, ax]) |
Make fill_between work like linestyle=’steps-mid’. |
fill_masked_covar(covar, mask) |
Fill a covariance matrix in a larger array that had masked values |
fix_flt_nan(flt_file[, bad_bit, verbose]) |
Fix NaN values in FLT files |
flt_to_dict(fobj[, primary_keys, …]) |
Parse basic elements from a FLT/FLC header to a dictionary |
full_spectrum_wcsheader([center_wave, dlam, …]) |
Make a WCS header for a 2D spectrum |
generate_tempfilt(templates, filters[, …]) |
|
get_Vizier_photometry(ra, dec[, templates, …]) |
Fetch photometry from a Vizier catalog |
get_common_slices(a_origin, a_shape, …) |
Get slices of overlaps between two rectangular grids |
get_filter_obsmode([filter, acs_chip, …]) |
Derive pysynphot obsmode keyword from a filter name, where UVIS filters end in ‘u’ |
get_flt_footprint(flt_file[, extensions, …]) |
Compute footprint of all SCI extensions of an HST exposure |
get_flt_info([files, columns]) |
Extract header information from a list of FLT files |
get_hst_filter(header[, filter_only]) |
Get simple filter name out of an HST image header. |
get_line_wavelengths() |
Get a dictionary of common emission line wavelengths and line ratios |
get_set_bits(value) |
Compute which binary bits are set for an integer |
get_spectrum_AB_mags(spectrum[, bandpasses]) |
Integrate a pysynphot spectrum through filter bandpasses |
get_visit_footprints(visits) |
Add Polygon ‘footprint’ attributes to visit dict. |
get_wcs_pscale(wcs[, set_attribute]) |
Get correct pscale from a WCS object |
get_wcs_slice_header(wcs, slx, sly) |
TBD |
half_pixel_scale(wcs) |
Create a new WCS with half the pixel scale of another that can be block-averaged 2x2 |
header_keys_from_filelist(fits_files[, …]) |
Dump header keywords to a Table |
hull_area(x, y) |
Return the area of a convex hull of a list of points |
hull_edge_mask(x, y[, pad, pad_is_absolute, …]) |
Compute geometrical edge mask for points within a convex hull |
load_beta_templates([wave, betas]) |
Step-function templates with f_lambda ~ (wave/1216.)**beta |
load_phoenix_stars([logg_list, teff_list, …]) |
Load Phoenix stellar templates |
load_quasar_templates([broad_fwhm, …]) |
Make templates suitable for fitting broad-line quasars |
load_sdss_pca_templates([file, smooth]) |
Load SDSS eigen templates |
load_templates([fwhm, line_complexes, …]) |
Generate a list of templates for fitting to the grism spectra |
log_comment(LOGFILE, comment[, verbose, …]) |
Log a message to a file, optionally including a date tag |
log_exception(LOGFILE, traceback[, verbose, …]) |
Log exception information to a file, or print to screen |
log_function_arguments(LOGFILE, frame[, …]) |
Log local variables, e.g., parameter arguements to a file |
log_scale_ds9(im[, lexp, cmap, scale]) |
Scale an array like ds9 log scaling |
log_zgrid([zr, dz]) |
Make a logarithmically spaced redshift grid |
make_alf_template() |
Make Alf + FSPS template |
make_maximal_wcs(files[, pixel_scale, …]) |
Compute an ImageHDU with a footprint that contains all of files |
make_spectrum_wcsheader([center_wave, dlam, …]) |
Make a WCS header for a 2D spectrum |
make_wcsheader([ra, dec, size, pixscale, …]) |
Make a celestial WCS header |
mast_query_from_file_list([files, os_open]) |
Generate a MAST query on datasets in a list. |
mode_statistic(data[, percentiles]) |
Get modal value of a distribution of data following Connor et al. |
multiprocessing_ndfilter(data, filter_func) |
Cut up a large array and send slices to scipy.ndimage filters |
nmad(data) |
Normalized NMAD=1.4826022 * median_absolute_deviation |
nowtime([iso]) |
Wrapper for astropy.time.now |
parse_flt_files([files, info, uniquename, …]) |
Read header information from a list of exposures and parse out groups based on filter/target/orientation. |
parse_grism_associations(exposure_groups[, …]) |
Get associated lists of grism and direct exposures |
parse_s3_url([url]) |
Parse s3 path string |
parse_visit_overlaps(visits[, buffer]) |
Find overlapping visits/filters to make combined mosaics |
patch_photutils() |
Patch to fix inconsistency with drizzlepac=3.2.1 and photutils>1.0, where The latter is needed for jwst=1.3.2 |
polynomial_templates(wave[, ref_wave, …]) |
|
radec_to_targname([ra, dec, round_arcsec, …]) |
Turn decimal degree coordinates into a string with rounding. |
read_catalog(file[, sextractor, format]) |
Wrapper around gread. |
read_gzipped_header([file, BLOCK, NMAX, …]) |
Read primary header from a (potentially large) zipped FITS file |
remove_text_labels(fig) |
Remove all Text annotations from fig.axes. |
reproject_faster(input_hdu, output[, pad]) |
Speed up reproject module with array slices of the input image |
safe_invert(arr) |
version-safe matrix inversion using np.linalg or np.matrix.I |
set_warnings([numpy_level, astropy_level]) |
Set global numpy and astropy warnings |
simple_LCDM([Om0, Ode0, H0, Ob0, Tcmb0, name]) |
Simple LambdaCDM cosmology |
split_poly_template(templ[, ref_wave, order]) |
Multiply a single template by polynomial bases to effectively generate a polynomial multiplicative correction that can be fit with linear least squares. |
split_spline_template(templ[, …]) |
Multiply a single template by spline bases to effectively generate a spline multiplicative correction that can be fit with linear least squares. |
split_visit(visit[, visit_split_shift, …]) |
Check if files in a visit have large shifts and split them otherwise |
step_templates([wlim, bin_steps, R, round, …]) |
Step-function templates for easy binning |
strip_header_keys(header[, comment, …]) |
Strip header keywords |
symlink_templates([force]) |
Symlink templates from module to $GRIZLI/templates as part of the initial setup |
synphot_encircled_energy([obsmode, sp, …]) |
Compute encircled energy curves with pysynphot |
synphot_zeropoint([obsmode, radius]) |
Compute synphot for a specific aperture |
tabulate_encircled_energy([aper_radii, …]) |
|
to_header(wcs[, add_naxis, relax, key]) |
Modify astropy.wcs.WCS.to_header to produce more keywords |
transform_wcs(in_wcs[, translation, …]) |
Update WCS with shift, rotation, & scale |
trapz_dx(x) |
Return trapezoid rule coefficients, useful for numerical integration using a dot product |
unset_dq_bits(value[, okbits, verbose]) |
Unset bit flags from a DQ array |
Classes¶
EffectivePSF() |
Tools for handling WFC3/IR Effective PSF |
GTable([data, masked, names, dtype, meta, …]) |
Extend Table class with more automatic IO and other helper methods. |
HubbleXYZ([spt_file, param_dict]) |
Helper to compute HST geocentric coordinates from orbital parameters |
MW_F99(a_v[, r_v]) |
Wrapper around the specutils.extinction / extinction modules, which are called differently |
SRegion(inp[, label]) |
Helper class for parsing an S_REGION strings and general polygon tools |
SpectrumTemplate([wave, flux, central_wave, …]) |
Container for template spectra. |
Unique(array[, verbose]) |
Helper for unique items in an array |
WCSFootprint(wcs[, ext, label]) |
Helper functions for dealing with WCS footprints |
WCSMapAll(input, output[, origin]) |
Sample class to demonstrate how to define a coordinate transformation |
grizli.grismconf Module¶
Demonstrate aXe trace polynomials.
Initial code taken from (Brammer, Pirzkal, & Ryan 2014), which contains a detailed explanation how the grism configuration parameters and coefficients are defined and evaluated.
Functions¶
get_config_filename([instrume, filter, …]) |
Generate a config filename based on the instrument, filter & grism combination. |
load_grism_config(conf_file) |
Load parameters from an aXe configuration file |
Classes¶
JwstDispersionTransform([instrument, …]) |
Rotate NIRISS and NIRCam coordinates such that slitless dispersion has wavelength increasing towards +x. |
OrderedDict |
Dictionary that remembers insertion order |
TransformGrismconf([conf_file]) |
Transform GRISMCONF-format configuration files to grizli convention of wavelength increasing towards +x |
aXeConf([conf_file]) |
Read an aXe-compatible configuration file |
grizli.model Module¶
Model grism spectra in individual FLTs
Classes¶
BeamCutout([flt, beam, conf, …]) |
Cutout spectral object from the full frame. |
GrismDisperser([id, direct, segmentation, …]) |
Object for computing dispersed model spectra |
GrismFLT([grism_file, sci_extn, …]) |
Scripts for modeling of individual grism FLT images |
ImageData([sci, err, dq, header, wcs, …]) |
Container for image data with WCS, etc. |
grizli.multifit Module¶
Functionality for manipulating multiple grism exposures simultaneously
Functions¶
drizzle_2d_spectrum(beams[, data, wlimit, …]) |
Drizzle 2D spectrum from a list of beams |
drizzle_2d_spectrum_wcs(beams[, data, …]) |
Drizzle 2D spectrum from a list of beams |
drizzle_to_wavelength(beams[, wcs, ra, dec, …]) |
Drizzle a cutout at a specific wavelength from a list of BeamCutout objects |
get_redshift_fit_defaults() |
TBD |
show_drizzle_HDU(hdu[, diff, …]) |
Make a figure from the multiple extensions in the drizzled grism file. |
Classes¶
GroupFLT([grism_files, sci_extn, …]) |
Main container for handling multiple grism exposures together |
MultiBeam(beams[, group_name, fcontam, psf, …]) |
Tools for dealing with multiple BeamCutout instances |
grizli.fitting Module¶
Tools for fitting spectra with templates.
Functions¶
compute_cdf_percentiles(fit[, cdf_sigmas]) |
Compute tabulated percentiles of the CDF for a (lossy) compressed version of the redshift PDF. |
compute_sps_params([full, cosmology, H0, …]) |
|
full_sed_plot(mb, tfit[, zfit, bin, minor, …]) |
Make a separate plot showing photometry and the spectrum |
make_summary_catalog([target, sextractor, …]) |
|
refit_beams([root, append, id, keep_dict, …]) |
Regenerate a MultiBeam object selecting only certiain PAs |
run_all(id[, t0, t1, fwhm, zr, dz, fitter, …]) |
Run the full template-fitting procedure |
run_all_parallel(id[, get_output_data, …]) |
Wrapper function for grizli.fitting.run_all that preloads all keyword options from a stored file. |
show_drizzled_lines(line_hdu[, …]) |
Make a figure with the drizzled line maps |
Classes¶
GroupFitter |
Base class for StackFitter and MultiBeam spectrum fitting objects |
Catalog tools¶
grizli.catalog Module¶
Catalog table tools
Functions¶
table_to_radec(table[, output]) |
Make a “radec” ascii file with ra, dec columns from a table object |
table_to_regions(table[, output, comment, …]) |
Make a DS9 region file from a table object |
randomize_segmentation_labels(seg[, …]) |
Randomize labels on a segmentation image for easier visualization |
get_ukidss_catalog([ra, dec, radius, …]) |
Query for objects in the UKIDSS catalogs |
get_sdss_catalog([ra, dec, radius]) |
Query for objects in the SDSS photometric catalog |
get_twomass_catalog([ra, dec, radius, catalog]) |
|
get_irsa_catalog([ra, dec, tab, radius, …]) |
Query for objects in the AllWISE source catalog |
get_gaia_radec_at_time(gaia_tbl[, date, format]) |
Use apply_space_motion to compute GAIA positions at a specific observation date |
get_gaia_DR2_vizier_columns() |
Get translation of Vizier GAIA DR2 columns. |
get_gaia_DR2_vizier([ra, dec, radius, max, …]) |
Query GAIA catalog from Vizier |
gaia_dr2_conesearch_query([ra, dec, radius, max]) |
Generate a query string for the TAP servers TBD |
get_gaia_DR2_catalog([ra, dec, radius, …]) |
Query GAIA DR2 astrometric catalog |
gen_tap_box_query([ra, dec, radius, …]) |
Generate a query string for the NOAO Legacy Survey TAP server |
query_tap_catalog([ra, dec, radius, …]) |
Query NOAO Catalog holdings |
get_hubble_source_catalog([ra, dec, radius, …]) |
Query NOAO Source Catalog, which is aligned to GAIA DR1. |
get_nsc_catalog([ra, dec, radius, corners, …]) |
Query NOAO Source Catalog, which is aligned to GAIA DR1. |
get_desdr1_catalog([ra, dec, radius, …]) |
Query DES DR1 Catalog from Vizier |
get_skymapper_catalog([ra, dec, radius, …]) |
Get Skymapper DR1 from Vizier |
get_vexas_catalog([ra, dec, radius, …]) |
VEXAS DR2 from vizier |
get_panstarrs_catalog([ra, dec, radius, …]) |
Get PS1 from Vizier |
get_radec_catalog([ra, dec, radius, …]) |
Decide what reference astrometric catalog to use |
Pipeline tools¶
grizli.pipeline.default_params Module¶
Parameter handling with YAML
Functions¶
compare_args() |
|
get_yml_parameters([local_file, …]) |
Read default parameters from the YAML file in grizli/data |
safe_yaml_loader(yamlfile[, loaders]) |
Try different YAML loaders |
test_aws_availability() |
Test if aws s3 is available |
write_params_to_yml(kwargs[, output_file, …]) |
Write grizli parameters to a file |
grizli.pipeline.auto_script Module¶
Automatic processing scripts for grizli
Functions¶
clean_prep([field_root]) |
Clean unneeded files after the field preparation |
convert_visits_npy_to_yaml(npy_file) |
|
count_grism_exposures(phot, groups[, …]) |
Count number of grism exposures that contain objects in a catalog |
create_path_dict([root, home, raw, prep, …]) |
Generate path dict. |
drizzle_overlaps(field_root[, filters, …]) |
Drizzle filter groups based on precomputed image associations |
exposure_report(root[, log]) |
Save exposure info to webpage & json file |
extract([field_root, maglim, prior, MW_EBV, …]) |
|
fetch_files([field_root, HOME_PATH, paths, …]) |
Fully automatic script |
field_psf([root, PREP_PATH, RAW_PATH, …]) |
Generate PSFs for the available filters in a given field |
field_rgb([root, xsize, output_dpi, …]) |
RGB image of the field mosaics |
fill_filter_mosaics(field_root) |
Fill field mosaics with the average value taken from other filters so that all images have the same coverage |
find_visit_file([root, path]) |
Find the yaml or npy visits file, return None if neither found |
fine_alignment([field_root, HOME_PATH, …]) |
Try fine alignment from visit-based SExtractor catalogs |
generate_fit_params([field_root, fitter, …]) |
Generate a parameter dictionary for passing to the fitting script |
get_extra_data([root, HOME_PATH, …]) |
|
get_rgb_filters(filter_list[, force_ir, …]) |
Compute which filters to use to make an RGB cutout |
get_visit_exposure_footprints([root, …]) |
Add exposure-level footprints to the visit dictionary |
go([root, HOME_PATH, RAW_PATH, PREP_PATH, …]) |
Run the full pipeline for a given target |
grism_prep([field_root, PREP_PATH, …]) |
Contamination model for grism exposures |
load_GroupFLT([field_root, PREP_PATH, …]) |
Initialize a GroupFLT object |
load_fine_yaml([yaml_file]) |
Load fine_alignment result |
load_visit_info([root, path, verbose]) |
Load visit info from a visits.npy or visits.yaml file |
load_visits_yaml(file) |
Load a {root}_visits.yaml file |
make_combined_mosaics(root[, fix_stars, …]) |
Drizzle combined mosaics |
make_directories([root, HOME_PATH, paths]) |
Make RAW, Prep, Persistence, Extractions directories |
make_filter_combinations(root[, weight_fnu, …]) |
Combine ir/opt mosaics manually scaling a specific zeropoint |
make_mosaic_footprints(field_root) |
Make region files where wht images nonzero |
make_reference_wcs(info[, files, output, …]) |
Make a reference image WCS based on the grism exposures |
make_report(root[, gzipped_links, xsize, …]) |
Make HTML report of the imaging and grism data products |
make_rgb_thumbnails([root, ids, maglim, …]) |
Make RGB thumbnails in working directory |
manual_alignment([field_root, HOME_PATH, …]) |
|
mask_IR_psf_spikes([visit, mag_lim, cat, …]) |
Mask 45-degree diffraction spikes around bright stars |
multiband_catalog([field_root, threshold, …]) |
Make a detection catalog and run aperture photometry with the SExtractor clone sep. |
parse_visits([field_root, RAW_PATH, …]) |
Organize exposures into “visits” by filter / position / PA / epoch |
photutils_catalog([field_root, threshold, …]) |
Make a detection catalog with SExtractor and then measure photometry with photutils. |
preprocess([field_root, HOME_PATH, …]) |
master_radec: force use this radec file |
refine_model_with_fits([field_root, grp, …]) |
Refine the full-field grism models with the best fit spectra from individual extractions. |
remove_bad_expflag([field_root, HOME_PATH, …]) |
Remove FLT files in RAW directory with bad EXPFLAG values, which usually corresponds to failed guide stars. |
save_fine_yaml(visits, fit[, yaml_file]) |
Save results from fine_alignment |
summary_catalog(**kwargs) |
|
update_wcs_headers_with_fine(field_root[, …]) |
Update grism headers with the fine shifts |
visit_dict_from_strings(v) |
Make visit dictionary cleaner for writing to YAML |
visit_dict_to_strings(v) |
Make visit dictionary cleaner for writing to YAML |
write_visit_info(visits, groups, info[, …]) |
Write visit association files |
grizli.pipeline.photoz Module¶
Helpers for working with eazy-py.
Functions¶
apply_catalog_corrections(root[, …]) |
Aperture and background corrections to photometric catalog |
eazy_photoz(root[, force, object_only, …]) |
|
fix_aperture_corrections(tab[, verbose, …]) |
June 2020: Reapply total corrections using fixed bug for the kron total corrections where the necessary pixel scale wasn’t used. |
get_external_catalog(phot[, filter_file, …]) |
Fetch photometry from vizier |
show_all_thumbnails([label, filters, …]) |
Show individual filter and RGB thumbnails |
show_from_ds9(ds9, self, zout[, use_sky]) |
Simulations¶
Some basic tools for simulating HST/JWST/Roman grism data. See multimission_simulaation.ipynb for some examples.
grizli.fake_image Module¶
Tools for generating very basic fake images for HST/JWST/Roman simulations
Functions¶
make_fake_image(header[, output, …]) |
Use the header from NIRISS, WFC3/IR or WFIRST/Roman and make an FLT-like image that grizli can read as a reference. |
make_roman_config([save_to_conf]) |
Use pandeia to calculate a Roman/G150 configuration file and sensitivity curve for grizli |
nircam_header([ra, dec, pa_aper, filter, …]) |
Make JWST/NIRCAM image header |
niriss_header([ra, dec, pa_aper, filter, grism]) |
Make JWST/NIRISS image header |
roman_header([ra, dec, pa_aper, naxis]) |
Make WFIRST/Roman WFI header |
roman_hls_image([exptime, nexp, background, …]) |
Make a simple FITS file for a Roman High Latitude Survey Image |
rotate_CD_matrix(cd, pa_aper) |
Rotate CD matrix |
wfc3ir_header([ra, dec, pa_aper, flt, filter]) |
Make HST/WFC3-IR image header |
wfirst_header(**kwargs) |
Alias to roman_header |