JWSTNirspec_cal
- class breads.instruments.JWSTNirspec_cal(filename=None, utils_dir=None, save_utils=True, load_utils=True, preproc_task_list=None, verbose=True)[source]
Bases:
JWST_IFUsJWST NIRSpec 2D calibrated data class.
- Parameters:
- utils_dir: str or None
Path to the folder saving the intermediate products of each preprocessing step.
- save_utils: bool (default=True)
Whether to save intermediate products.
- load_utils: bool (default=True)
Whether to load intermediate products.
- preproc_task_list: list or None
List of preprocessing tasks to run.
- verbose: bool (default=True)
If True, the code is returning more printing.
- wv_reffloat
Reference wavelength. If not set, the shortest wavelength will be used by default.
- About the “preproc_task_list” parameter. Each task should be a list containing:
task[0] = the name of the class method task[1] = a dictionary with any relevant method arguments (but not including save_utils, see task[2])
If not defined, it assumes no parameters are needed (task[1] = {}).
- task[2] = a boolean saying if the outputs should be saved in the utils folder.
Default to class save_utils if not defined for the task. If it is a string instead, it will be saved with the string as the filename.
- task[3] = a boolean saying if we should attempt to load the data from the utils folder.
Default to class load_utils if not defined for the task.
Methods Summary
compute_charge_bleeding_mask([save_utils, ...])Compute charge bleeding bar mask
compute_med_filt_badpix([save_utils, ...])Quick bad pixel identification.
Compute star spectrum continuum normalized by 2d spline
Compute Star Subtraction with 2D Spline
Mask interpolated elements too far from the edge bins
reload_charge_bleeding_mask([load_filename])Reload charge bleeding bar mask
Reload star spectrum continuum normalized by 2d spline
reload_starsubtraction_2dspline([load_filename])Reload Star Subtraction with 2D spline
save_charge_bleeding_mask(save_utils, bar_mask)Save charge bleeding bar mask
Methods Documentation
- compute_charge_bleeding_mask(save_utils=False, threshold2mask=0.15)[source]
Compute charge bleeding bar mask
- Parameters:
- save_utils: bool (default is False)
if True, save the computed charge bleeding mask.
- threshold2mask: float (default is 0.15) in arcsec
Separation threshold to mask the traces sitting in the charge bleeding region.
- Returns:
- compute_med_filt_badpix(save_utils=False, window_size=50, mad_threshold=50, crop_Npix_from_trace_edges=0)[source]
Quick bad pixel identification.
The data is first high-pass filtered row by row with a median filter with a window size of 50 (window_size) pixels. The median absolute deviation (MAP) is then calculated row by row, and any pixel deviating by more than 50x the MAP are identified as bad.
Only returns (or save) the newly identified bad pixels, the ones already included in self.bad_pixels won’t be in new_badpix. But this map is automatically applied to self.bad_pixels: self.bad_pixels *= new_badpix
- Parameters:
- crop_Npix_from_trace_edges
- mad_threshold
- window_size
- save_utilsbool or string
Save the computed bad pixel map (nans=bad) into the utils directory Default filename (set save_utils as a string instead of bool to override filename): os.path.join(self.utils_dir, os.path.basename(self.filename).replace(“.fits”, “_med_filt_badpix.fits”))
- Returns:
- new_badpixnp.array
nans = bad.
- compute_starspectrum_contnorm_2dspline(save_utils=False, im=None, im_wvs=None, err=None, mppool=None, spec_R_sampling=None, threshold_badpix=10, wv_nodes=None, N_wvs_nodes=20, ifuy_nodes=None, delta_ifuy=0.05, apply_new_bad_pixels=False, iterative=True, independent_trace=True)[source]
Compute star spectrum continuum normalized by 2d spline
- Parameters:
- save_utils
- im
- im_wvs
- err
- mppool
- spec_R_sampling
- threshold_badpix
- wv_nodes
- N_wvs_nodes
- ifuy_nodes
- delta_ifuy
- apply_new_bad_pixels
- iterative
- independent_trace
- Returns:
- compute_starsubtraction_2dspline(save_utils=False, im=None, im_wvs=None, err=None, threshold_badpix=10, mppool=None, starsub_dir='starsub2d', iterative=True, independent_trace=True)[source]
Compute Star Subtraction with 2D Spline
- Parameters:
- save_utils
- im
- im_wvs
- err
- threshold_badpix
- mppool
- starsub_dir
- iterative
- independent_trace
- Returns:
- subtracted_im, star_model, spline_paras0, self.wv_nodes, self.ifuy_nodes
- mask_interp_elements_too_far_from_bin_edges(dwv_threshold)[source]
Mask interpolated elements too far from the edge bins
- Parameters:
- dwv_threshold
- Returns:
- maskndarray
Mask of which pixels are masked
- Also modifies self.bad_pixels
- reload_charge_bleeding_mask(load_filename=None)[source]
Reload charge bleeding bar mask
- Parameters:
- load_filenamestr or None
Filename to load mask data from, or leave None to use default filename
- Returns:
- bar_maskndarray
- Also modifies self.badpixels, by multiplying that times the bar_mask
- reload_starspectrum_contnorm_2dspline(load_filename=None, apply_new_bad_pixels=False)[source]
Reload star spectrum continuum normalized by 2d spline
- Parameters:
- load_filenamestr or None
Filename to load spectrum data from, or leave None to use default filename
- apply_new_bad_pixelsbool
If set, multiply self.badpixels times the NEW_BADPIX extension of the spectrum
- Returns:
- new_wavelengths,combined_fluxes,combined_errors,spline_cont0,spline_paras0,wv_nodes,ifuy_nodes