"""
Module for managing the history of PypeIt output files.
.. include common links, assuming primary doc root is up one directory
.. include:: ../include/links.rst
"""
import os.path
import numpy as np
from IPython import embed
from astropy.time import Time
from astropy.io import fits
from pypeit.core.framematch import FrameTypeBitMask
[docs]class History:
"""
Holds and creates history entries for FITS files.
Args:
header (`astropy.io.fits.Header`_, optional):
Header from a fits file. The
history keyword entries in this header will be used to populate this
History object. Defaults to None.
Attributes:
history (:obj:`list` of `str`): List of history entries.
"""
def __init__(self, header=None):
"""
Initializes history.
"""
self.history = []
if header is not None and 'HISTORY' in header:
for card in header['HISTORY']:
self.history.append(str(card))
[docs] def add_reduce(self, calib_id, metadata, frames, bg_frames):
"""
Add history entries for reducing a frame. For example::
HISTORY 2021-03-05T23:56 PypeIt Reducing target HIP15339
HISTORY Combining frames:
HISTORY "S20161108S0087.fits.gz"
HISTORY "S20161108S0090.fits.gz"
HISTORY Subtracted background from frames:
HISTORY "S20161108S0088.fits.gz"
HISTORY "S20161108S0089.fits.gz"
HISTORY Calibration frames:
HISTORY arc,science,tilt "S20161108S0069.fits.gz"
HISTORY arc,science,tilt "S20161108S0070.fits.gz"
HISTORY arc,science,tilt "S20161108S0071.fits.gz"
HISTORY arc,science,tilt "S20161108S0072.fits.gz"
HISTORY pixelflat,trace "S20161108S0078.fits.gz"
Args:
calib_id (int): The calibration id being reduced.
metadata (:class:`pypeit.metadata.PypeItMetaData`): The metadata for all
the fits files PypeIt knows of.
frames (`numpy.ndarray`_): Array of indexes into metadata of the
frames being combined in the reduction.
bg_frames (`numpy.ndarray`_): Array of indexes into metadata of the
frames being subtracted in the reduction.
"""
self.append(f'PypeIt Reducing target {metadata["target"][frames[0]]}')
self.append('Combining frames:', add_date=False)
for frame in frames:
self.append(f'"{metadata["filename"][frame]}"', add_date=False)
if len(bg_frames) > 0:
self.append('Subtracted background from frames:', add_date=False)
for frame in bg_frames:
self.append(f'"{metadata["filename"][frame]}"', add_date=False)
frametype_bitmask = FrameTypeBitMask()
calibration_types = [x for x in frametype_bitmask.keys() if x not in ['science', 'standard']]
calib_frames = metadata[metadata.find_frames(calibration_types, calib_id)]
if len(calib_frames) > 0:
self.append('Calibration frames:', add_date=False)
for frame in calib_frames:
self.append(f'{frame["frametype"]} "{frame["filename"]}"', add_date=False)
[docs] def add_coadd1d(self, spec1d_files, objids, gpm_exp=None):
"""
Add history entries for 1D coadding.
The history shows what files and objects were used for coadding.
For example::
HISTORY 2021-01-23T02:12 PypeIt Coadded 4 objects from 3 spec1d files
HISTORY File 0 "spec1d_DE.20170425.53065-dra11_DEIMOS_2017Apr25T144418.240.fits"
HISTORY File 1 "spec1d_DE.20170425.51771-dra11_DEIMOS_2017Apr25T142245.350.fits"
HISTORY File 2 "spec1d_DE.20170425.50487-dra11_DEIMOS_2017Apr25T140121.014.fits"
HISTORY Object ID SPAT0692-SLIT0704-DET08 from file 0
HISTORY Object ID SPAT0695-SLIT0706-DET04 from file 2
HISTORY Object ID SPAT0691-SLIT0704-DET08 from file 2
HISTORY Object ID SPAT0695-SLIT0706-DET04 from file 1
Args:
spec1d_files (:obj:`list`): List of the spec1d files used for coadding.
objids (:obj:`list`): List of the PypeIt object ids used in coadding.
gpm_exp (:obj:`list`, optional): List of boolean indicating which exposures were coadded.
"""
if gpm_exp is not None:
# Not coadded files and objids
notcoadded_spec1d_files = [spec1d_file for (spec1d_file, gpm_exp) in zip(spec1d_files, gpm_exp) if not gpm_exp]
notcoadded_objids = [objid for (objid, gpm_exp) in zip(objids, gpm_exp) if not gpm_exp]
combined_notcoadd_files_objids = list(zip(notcoadded_spec1d_files, notcoadded_objids))
# Coadded files and objids
coadded_spec1d_files = [spec1d_file for (spec1d_file, gpm_exp) in zip(spec1d_files, gpm_exp) if gpm_exp]
coadded_objids = [objid for (objid, gpm_exp) in zip(objids, gpm_exp) if gpm_exp]
combined_files_objids = list(zip(coadded_spec1d_files, coadded_objids))
else:
combined_files_objids = list(zip(spec1d_files, objids))
combined_notcoadd_files_objids = None
files_objids = [combined_files_objids, combined_notcoadd_files_objids]
# add history
for file_objid in files_objids:
if file_objid is None:
continue
elif file_objid == combined_files_objids:
self.append(f'PypeIt Coadded {len(file_objid)} objects '
f'from {np.unique([f[0] for f in file_objid]).size} spec1d files')
elif file_objid == combined_notcoadd_files_objids and len(file_objid) > 0:
self.append(f'PypeIt DID NOT COADD {len(file_objid)} objects '
f'from {np.unique([f[0] for f in file_objid]).size} spec1d files', add_date=False)
current_spec1d = ""
for (spec1d, objid) in file_objid:
if spec1d != current_spec1d:
current_spec1d = spec1d
self.append(f'From "{os.path.basename(spec1d)}"', add_date=False)
header = fits.getheader(spec1d)
additional_info = None
if 'SEMESTER' in header:
additional_info = f"Semester: {header['SEMESTER']}"
if 'PROGID' in header:
additional_info += f" Program ID: {header['PROGID']}"
if additional_info is not None:
self.append(additional_info, add_date=False)
obj_info = objid
# get extension names
hnames = [h.name for h in fits.open(spec1d)]
# find the extension name that include objid
ind_ext = np.where([objid in h for h in hnames])[0]
if ind_ext.size > 0:
# get the header for this extension
this_ext_header = fits.getheader(spec1d, ext=ind_ext[0])
if 'MASKDEF_ID' in this_ext_header:
obj_info += f" {this_ext_header['MASKDEF_ID']}"
if 'MASKDEF_OBJNAME' in this_ext_header:
obj_info += f" {this_ext_header['MASKDEF_OBJNAME']}"
self.append(obj_info, add_date=False)
[docs] def append(self, history, add_date=True):
"""Append a new history entry.
Args:
history (str): The history text to add.
add_date (bool): If true a isot formatted date willbe prepended
to the history entry. Defaults to True.
"""
if add_date:
self.history.append(f'{Time.now().to_value("isot", subfmt="date_hm")} {history}')
else:
self.history.append(history)