Source code for synphot.utils

# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""Synthetic photometry utility functions."""

import os
from shutil import copyfile

import numpy as np

from astropy import units as u
from astropy.config import ConfigItem
from import download_file

from . import exceptions, units

__all__ = ['overlap_status', 'validate_totalflux', 'validate_wavelengths',
           'generate_wavelengths', 'merge_wavelengths', 'download_data']

[docs]def overlap_status(a, b): """Check overlap between two arrays. Parameters ---------- a, b : array-like Arrays to check. Assumed to be in the same unit. Returns ------- result : {'full', 'partial', 'none'} * 'full' - ``a`` is within or same as ``b`` * 'partial' - ``a`` partially overlaps with ``b`` * 'none' - ``a`` does not overlap ``b`` """ # Get the endpoints a1, a2 = a.min(), a.max() b1, b2 = b.min(), b.max() # Do the comparison if a1 >= b1 and a2 <= b2: result = 'full' elif a2 < b1 or b2 < a1: result = 'none' else: result = 'partial' return result
[docs]def validate_totalflux(totalflux): """Check integrated flux for invalid values. Parameters ---------- totalflux : float Integrated flux. Raises ------ synphot.exceptions.SynphotError Input is zero, negative, or not a number. """ if totalflux <= 0.0: raise exceptions.SynphotError('Integrated flux is <= 0') elif np.isnan(totalflux): raise exceptions.SynphotError('Integrated flux is NaN') elif np.isinf(totalflux): raise exceptions.SynphotError('Integrated flux is infinite')
[docs]def validate_wavelengths(wavelengths): """Check wavelengths for ``synphot`` compatibility. Wavelengths must satisfy these conditions: * valid unit type, if given * no zeroes * monotonic ascending or descending * no duplicate values Parameters ---------- wavelengths : array-like or `~astropy.units.quantity.Quantity` Wavelength values. Raises ------ synphot.exceptions.SynphotError Wavelengths unit type is invalid. synphot.exceptions.DuplicateWavelength Wavelength array contains duplicate entries. synphot.exceptions.UnsortedWavelength Wavelength array is not monotonic. synphot.exceptions.ZeroWavelength Negative or zero wavelength occurs in wavelength array. """ if isinstance(wavelengths, u.Quantity): units.validate_wave_unit(wavelengths.unit) wave = wavelengths.value else: wave = wavelengths if np.isscalar(wave): wave = [wave] wave = np.asarray(wave) # Check for zeroes if np.any(wave <= 0): raise exceptions.ZeroWavelength( 'Negative or zero wavelength occurs in wavelength array', rows=np.where(wave <= 0)[0]) # Check for monotonicity sorted_wave = np.sort(wave) if not np.alltrue(sorted_wave == wave): if np.alltrue(sorted_wave[::-1] == wave): pass # Monotonic descending is allowed else: raise exceptions.UnsortedWavelength( 'Wavelength array is not monotonic', rows=np.where(sorted_wave != wave)[0]) # Check for duplicate values if wave.size > 1: dw = sorted_wave[1:] - sorted_wave[:-1] if np.any(dw == 0): raise exceptions.DuplicateWavelength( 'Wavelength array contains duplicate entries', rows=np.where(dw == 0)[0])
[docs]def generate_wavelengths(minwave=500, maxwave=26000, num=10000, delta=None, log=True, wave_unit=u.AA): """Generate wavelength array to be used for spectrum sampling. .. math:: minwave \\le \\lambda < maxwave Parameters ---------- minwave, maxwave : float Lower and upper limits of the wavelengths. These must be values in linear space regardless of ``log``. num : int The number of wavelength values. This is only used when ``delta=None``. delta : float or `None` Delta between wavelength values. When ``log=True``, this is the spacing in log space. log : bool If `True`, the wavelength values are evenly spaced in log scale. Otherwise, spacing is linear. wave_unit : str or `~astropy.units.core.Unit` Wavelength unit. Default is Angstrom. Returns ------- waveset : `~astropy.units.quantity.Quantity` Generated wavelength set. waveset_str : str Info string associated with the result. """ wave_unit = units.validate_unit(wave_unit) if delta is not None: num = None waveset_str = 'Min: {0}, Max: {1}, Num: {2}, Delta: {3}, Log: {4}'.format( minwave, maxwave, num, delta, log) # Log space if log: logmin = np.log10(minwave) logmax = np.log10(maxwave) if delta is None: waveset = np.logspace(logmin, logmax, num, endpoint=False) else: waveset = 10 ** np.arange(logmin, logmax, delta) # Linear space else: if delta is None: waveset = np.linspace(minwave, maxwave, num, endpoint=False) else: waveset = np.arange(minwave, maxwave, delta) return waveset.astype(np.float64) * wave_unit, waveset_str
[docs]def merge_wavelengths(waveset1, waveset2, threshold=1e-12): """Return the union of the two sets of wavelengths using :func:`numpy.union1d`. The merged wavelengths may sometimes contain numbers which are nearly equal but differ at levels as small as 1e-14. Having values this close together can cause problems down the line. So, here we test whether any such small differences are present, with a small difference defined as less than ``threshold``. If a small difference is present, the lower of the too-close pair is removed. Parameters ---------- waveset1, waveset2 : array-like or `None` Wavelength values, assumed to be in the same unit already. Also see :func:`~synphot.models.get_waveset`. threshold : float, optional Merged wavelength values are considered "too close together" when the difference is smaller than this number. The default is 1e-12. Returns ------- out_wavelengths : array-like or `None` Merged wavelengths. `None` if undefined. """ if waveset1 is None and waveset2 is None: out_wavelengths = None elif waveset1 is not None and waveset2 is None: out_wavelengths = waveset1 elif waveset1 is None and waveset2 is not None: out_wavelengths = waveset2 else: out_wavelengths = np.union1d(waveset1, waveset2) delta = out_wavelengths[1:] - out_wavelengths[:-1] i_good = np.where(delta > threshold) # Remove "too close together" duplicates if len(i_good[0]) < delta.size: out_wavelengths = np.append( out_wavelengths[i_good], out_wavelengths[-1]) return out_wavelengths
[docs]def download_data(path_root, verbose=True, dry_run=False): """Download ``synphot`` data files to given root directory or the ``astropy`` cache. Download is skipped if a data file already exists. .. warning:: Downloading data to ``astropy`` cache only is not recommended if you plan to provide a custom ``synphot.cfg``. Parameters ---------- path_root : str or `None` Root directory for data files. If `None`, download to the ``astropy`` cache location instead of a specific directory. verbose : bool Print extra information to screen. dry_run : bool Go through the logic but skip the actual download. This would return a list of files that *would have been* downloaded without network calls. The sub-directories would still be created regardless. Use this option for debugging or testing. Raises ------ OSError Problem with directory. Returns ------- file_list : list of str A list of downloaded files. """ from .config import conf # Avoid potential circular import BASE_HOST = '' if path_root is not None: if not os.path.exists(path_root): os.makedirs(path_root, exist_ok=True) if verbose: # pragma: no cover print('Created {}'.format(path_root)) elif not os.path.isdir(path_root): raise OSError('{} must be a directory'.format(path_root)) if not path_root.endswith(os.sep): path_root += os.sep file_list = [] # See for cfgitem in conf.__class__.__dict__.values(): if (not isinstance(cfgitem, ConfigItem) or not'file')): continue url = cfgitem.defaultvalue if not url.startswith(BASE_HOST): if verbose: # pragma: no cover print('{} is not from {}, skipping download'.format( url, BASE_HOST)) continue if path_root is not None: dst = url.replace(BASE_HOST, path_root).replace('/', os.sep) if os.path.exists(dst): if verbose: # pragma: no cover print('{} already exists, skipping download'.format(dst)) continue # Create sub-directories, if needed. subdirs = os.path.dirname(dst) os.makedirs(subdirs, exist_ok=True) if not dry_run: # pragma: no cover try: src = download_file(url, cache=True) if path_root is not None: copyfile(src, dst) except Exception as exc: print('Download failed - {}'.format(str(exc))) continue if path_root is None: if dry_run: file_list.append(url) else: # pragma: no cover file_list.append(src) else: file_list.append(dst) if verbose: # pragma: no cover print('{} downloaded to {}'.format(url, file_list[-1])) return file_list