arvi 0.1.12__py3-none-any.whl → 0.1.14__py3-none-any.whl

arvi/timeseries.py

@@ -11,18 +11,21 @@ import numpy as np
 from astropy import units
 
 from .setup_logger import logger
-from .config import return_self, check_internet
+from . import config
 from .translations import translate
-from .dace_wrapper import do_download_filetype, get_observations, get_arrays
+from .dace_wrapper import do_download_filetype, do_symlink_filetype, get_observations, get_arrays
 from .simbad_wrapper import simbad
 from .gaia_wrapper import gaia
 from .extra_data import get_extra_data
 from .stats import wmean, wrms
 from .binning import bin_ccf_mask, binRV
 from .HZ import getHZ_period
-from .utils import strtobool, there_is_internet
+from .utils import strtobool, there_is_internet, timer
 
 
+class ExtraFields:
+    pass
+
 @dataclass
 class RV:
     """
@@ -71,7 +74,7 @@ class RV:
         self.__star__ = translate(self.star)
 
         if not self._child:
-            if check_internet and not there_is_internet():
+            if config.check_internet and not there_is_internet():
                 raise ConnectionError('There is no internet connection?')
 
             # complicated way to query Simbad with self.__star__ or, if that
@@ -102,8 +105,10 @@ class RV:
             if self.verbose:
                 logger.info(f'querying DACE for {self.__star__}...')
             try:
-                self.dace_result = get_observations(self.__star__, self.instrument,
-                                                    verbose=self.verbose)
+                with timer():
+                    mid = self.simbad.main_id if hasattr(self, 'simbad') else None
+                    self.dace_result = get_observations(self.__star__, self.instrument,
+                                                        main_id=mid, verbose=self.verbose)
             except ValueError as e:
                 # querying DACE failed, should we raise an error?
                 if self._raise_on_error:
@@ -216,6 +221,7 @@ class RV:
         self._did_secular_acceleration = False
         self._did_sigma_clip = False
         self._did_adjust_means = False
+        self._did_correct_berv = False
         self.__post_init__()
 
     def snapshot(self):
@@ -257,6 +263,10 @@ class RV:
         table += ' | '.join(map(str, self.NN.values())) + '\n'
         return table
 
+    @property
+    def point(self):
+        return [(t.round(4), v.round(4), sv.round(4)) for t, v, sv in zip(self.time, self.vrad, self.svrad)]
+
     @property
     def mtime(self) -> np.ndarray:
         """ Masked array of times """
@@ -376,6 +386,7 @@ class RV:
         s.mask = kwargs.get('mask', np.full_like(s.time, True, dtype=bool))
 
         s.instruments = [inst]
+        s._quantities = np.array([])
 
         return s
 
@@ -437,6 +448,13 @@ class RV:
 
         s = cls(star, _child=True, **kwargs)
 
+        def find_column(data, names):
+            has_col = np.array([name in data.dtype.fields for name in names])
+            if any(has_col):
+                col = np.where(has_col)[0][0]
+                return data[names[col]]
+            return False
+
         for i, (f, instrument) in enumerate(zip(files, instruments)):
             data = np.loadtxt(f, skiprows=2, usecols=range(3), unpack=True)
             _s = cls(star, _child=True, **kwargs)
@@ -465,10 +483,11 @@ class RV:
             else:
                 data = np.array([], dtype=np.dtype([]))
 
-            if 'fwhm' in data.dtype.fields:
-                _s.fwhm = data['fwhm']
-                if 'sfwhm' in data.dtype.fields:
-                    _s.fwhm_err = data['sfwhm']
+            # try to find FWHM and uncertainty
+            if (v := find_column(data, ['fwhm'])) is not False:  # walrus !!
+                _s.fwhm = v
+                if (sv := find_column(data, ['sfwhm', 'fwhm_err', 'sig_fwhm'])) is not False:
+                    _s.fwhm_err = sv
                 else:
                     _s.fwhm_err = 2 * _s.svrad
             else:
@@ -478,12 +497,11 @@ class RV:
             _quantities.append('fwhm')
             _quantities.append('fwhm_err')
 
-            if 'rhk' in data.dtype.fields:
-                _s.rhk = data['rhk']
+            if (v := find_column(data, ['rhk'])) is not False:
+                _s.rhk = v
                 _s.rhk_err = np.full_like(time, np.nan)
-                for possible_name in ['srhk', 'rhk_err']:
-                    if possible_name in data.dtype.fields:
-                        _s.rhk_err = data[possible_name]
+                if (sv := find_column(data, ['srhk', 'rhk_err', 'sig_rhk'])) is not False:
+                    _s.rhk_err = sv
             else:
                 _s.rhk = np.zeros_like(time)
                 _s.rhk_err = np.full_like(time, np.nan)
@@ -510,6 +528,12 @@ class RV:
                 setattr(_s, q, np.full(time.size, True))
                 _quantities.append(q)
 
+            _s.extra_fields = ExtraFields()
+            for field in data.dtype.names:
+                if field not in _quantities:
+                    setattr(_s.extra_fields, field, data[field])
+                    # _quantities.append(field)
+
             #! end hack
 
             _s.mask = np.ones_like(time, dtype=bool)
@@ -537,36 +561,80 @@ class RV:
             logger.error('iCCF is not installed. Please install it with `pip install iCCF`')
             return
 
+        verbose = kwargs.get('verbose', True)
+
         if isinstance(files, str):
             files = [files]
 
-        I = iCCF.from_file(files)
+        CCFs = iCCF.from_file(files)
+
+        if not isinstance(CCFs, list):
+            CCFs = [CCFs]
 
-        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in I])
+        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
         if objects.size != 1:
             logger.warning(f'found {objects.size} different stars in the CCF files, '
                            'choosing the first one')
         star = objects[0]
 
         s = cls(star, _child=True)
+        instruments = list(np.unique([i.instrument for i in CCFs]))
 
-        # time, RVs, uncertainties
-        s.time = np.array([i.bjd for i in I])
-        s.vrad = np.array([i.RV*1e3 for i in I])
-        s.svrad = np.array([i.RVerror*1e3 for i in I])
+        for instrument in instruments:
+            # time, RVs, uncertainties
+            time = np.array([i.bjd for i in CCFs])
+            vrad = np.array([i.RV*1e3 for i in CCFs])
+            svrad = np.array([i.RVerror*1e3 for i in CCFs])
+            _s = RV.from_arrays(star, time, vrad, svrad, inst=instrument)
 
-        s.fwhm = np.array([i.FWHM*1e3 for i in I])
-        s.fwhm_err = np.array([i.FWHMerror*1e3 for i in I])
+            _quantities = []
 
-        # mask
-        s.mask = np.full_like(s.time, True, dtype=bool)
+            _s.fwhm = np.array([i.FWHM*1e3 for i in CCFs])
+            _s.fwhm_err = np.array([i.FWHMerror*1e3 for i in CCFs])
+
+            _quantities.append('fwhm')
+            _quantities.append('fwhm_err')
+
+            _s.contrast = np.array([i.contrast for i in CCFs])
+            _s.contrast_err = np.array([i.contrast_error for i in CCFs])
+
+            _quantities.append('contrast')
+            _quantities.append('contrast_err')
 
-        s.instruments = list(np.unique([i.instrument for i in I]))
+            _s.texp = np.array([i.HDU[0].header['EXPTIME'] for i in CCFs])
+            _quantities.append('texp')
+
+            _s.date_night = np.array([
+                i.HDU[0].header['DATE-OBS'].split('T')[0] for i in CCFs
+            ])
+            _quantities.append('date_night')
+
+            _s.mask = np.full_like(_s.time, True, dtype=bool)
+
+            _s.drs_qc = np.array([i.HDU[0].header['HIERARCH ESO QC SCIRED CHECK'] for i in CCFs], dtype=bool)
+            # mask out drs_qc = False
+            if not _s.drs_qc.all():
+                n = (~ _s.drs_qc).sum()
+                if verbose:
+                    logger.warning(f'masking {n} points where DRS QC failed for {instrument}')
+                _s.mask &= _s.drs_qc
+            print(_s.mask)
+
+            _s._quantities = np.array(_quantities)
+            setattr(s, instrument, _s)
+
+        s._child = False
+        s.instruments = instruments
+        s._build_arrays()
+
+        if instruments == ['ESPRESSO']:
+            from .instrument_specific import divide_ESPRESSO
+            divide_ESPRESSO(s)
 
         return s
 
 
-    def _check_instrument(self, instrument, strict=False):# -> list | None:
+    def _check_instrument(self, instrument, strict=False, log=False):# -> list | None:
         """
         Check if there are observations from `instrument`.
 
@@ -599,6 +667,10 @@ class RV:
                 if any([instrument in inst for inst in self.instruments]):
                     return [inst for inst in self.instruments if instrument in inst]
 
+        if log:
+            logger.error(f"No data from instrument '{instrument}'")
+            logger.info(f'available: {self.instruments}')
+            return
 
     def _build_arrays(self):
         """ build all concatenated arrays of `self` from each of the `.inst`s """
@@ -642,8 +714,8 @@ class RV:
                 )
                 setattr(self, q, arr)
 
-
-    def download_ccf(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_ccf(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download CCFs from DACE
 
         Args:
@@ -671,9 +743,15 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('CCF', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                logger.warning('may need to provide `top_level` in kwargs to find file')
+            do_symlink_filetype('CCF', files[:limit], directory, **kwargs)
+        else:
+            do_download_filetype('CCF', files[:limit], directory, verbose=self.verbose, **kwargs)
 
-    def download_s1d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_s1d(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download S1Ds from DACE
 
         Args:
@@ -701,9 +779,15 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('S1D', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                logger.warning('may need to provide `top_level` in kwargs to find file')
+            do_symlink_filetype('S1D', files[:limit], directory, **kwargs)
+        else:
+            do_download_filetype('S1D', files[:limit], directory, verbose=self.verbose, **kwargs)
 
-    def download_s2d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_s2d(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download S2Ds from DACE
 
         Args:
@@ -731,11 +815,16 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('S2D', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                logger.warning('may need to provide `top_level` in kwargs to find file')
+            do_symlink_filetype('S2D', files[:limit], directory, **kwargs)
+        else:
+            do_download_filetype('S2D', files[:limit], directory, verbose=self.verbose, **kwargs)
 
 
-    from .plots import plot, plot_fwhm, plot_bis, plot_rhk, plot_quantity
-    from .plots import gls, gls_fwhm, gls_bis, gls_rhk
+    from .plots import plot, plot_fwhm, plot_bis, plot_rhk, plot_berv, plot_quantity
+    from .plots import gls, gls_fwhm, gls_bis, gls_rhk, window_function
     from .reports import report
 
     from .instrument_specific import known_issues
@@ -799,7 +888,7 @@ class RV:
             if self.verbose:
                 logger.info(f"Removed observations from '{instrument}'")
 
-        if return_self:
+        if config.return_self:
             return self
 
     def remove_condition(self, condition):
@@ -827,7 +916,7 @@ class RV:
         index = np.atleast_1d(index)
         try:
             instrument_index = self.obs[index]
-            instrument = np.array(self.instruments)[instrument_index - 1]
+            np.array(self.instruments)[instrument_index - 1]
         except IndexError:
             logger.errors(f'index {index} is out of bounds for N={self.N}')
             return
@@ -840,7 +929,7 @@ class RV:
         # for i, inst in zip(index, instrument):
         #     index_in_instrument = i - (self.obs < instrument_index).sum()
         #     getattr(self, inst).mask[index_in_instrument] = False
-        if return_self:
+        if config.return_self:
             return self
 
     def remove_non_public(self):
@@ -903,7 +992,7 @@ class RV:
         instruments = self._check_instrument(instrument)
         rng = np.random.default_rng(seed=seed)
         for inst in instruments:
-            s = getattr(self, inst)
+            # s = getattr(self, inst)
             mask_for_this_inst = self.obs == self.instruments.index(inst) + 1
             # only choose if there are more than n points
             if self.mask[mask_for_this_inst].sum() > n:
@@ -1008,13 +1097,18 @@ class RV:
             self.vrad = self.vrad - sa * (self.time - epoch) / 365.25
         else:
             for inst in self.instruments:
+                s = getattr(self, inst)
+
+                # if RVs come from a publication, don't remove the secular
+                # acceleration
+                if np.all(s.pub_reference != ''):
+                    continue
+
                 if 'HIRES' in inst:  # never remove it from HIRES...
                     continue
                 if 'NIRPS' in inst:  # never remove it from NIRPS...
                     continue
 
-                s = getattr(self, inst)
-
                 if hasattr(s, '_did_secular_acceleration') and s._did_secular_acceleration:
                     continue
 
@@ -1023,8 +1117,37 @@ class RV:
             self._build_arrays()
 
         self._did_secular_acceleration = True
-        if return_self:
+        self._did_secular_acceleration_epoch = epoch
+        self._did_secular_acceleration_simbad = force_simbad
+
+        if config.return_self:
             return self
+    
+    def _undo_secular_acceleration(self):
+        if self._did_secular_acceleration:
+            _old_verbose = self.verbose
+            self.verbose = False
+            sa = self.secular_acceleration(just_compute=True,
+                                           force_simbad=self._did_secular_acceleration_simbad)
+            self.verbose = _old_verbose
+            sa = sa.value
+
+            if self._child:
+                self.vrad = self.vrad + sa * (self.time - self._did_secular_acceleration_epoch) / 365.25
+            else:
+                for inst in self.instruments:
+                    if 'HIRES' in inst:  # never remove it from HIRES...
+                        continue
+                    if 'NIRPS' in inst:  # never remove it from NIRPS...
+                        continue
+
+                    s = getattr(self, inst)
+
+                    s.vrad = s.vrad + sa * (s.time - self._did_secular_acceleration_epoch) / 365.25
+
+                self._build_arrays()
+
+            self._did_secular_acceleration = False
 
     def sigmaclip(self, sigma=5, instrument=None, strict=True):
         """ Sigma-clip RVs (per instrument!) """
@@ -1053,7 +1176,7 @@ class RV:
             #     # if insts.size == 1: # of the same instrument?
             #     if self.verbose:
             #         logger.warning(f'would remove all observations from {insts[0]}, skipping')
-            #     if return_self:
+            #     if config.return_self:
             #         return self
             #     continue
 
@@ -1065,7 +1188,7 @@ class RV:
             self._did_adjust_means = False
             self.adjust_means()
 
-        if return_self:
+        if config.return_self:
             return self
 
     def clip_maxerror(self, maxerror:float):
@@ -1087,7 +1210,7 @@ class RV:
             logger.warning(f'clip_maxerror ({maxerror} {self.units}) removed {n} point' + s)
 
         self._propagate_mask_changes()
-        if return_self:
+        if config.return_self:
             return self
 
     def bin(self):
@@ -1220,6 +1343,11 @@ class RV:
         for inst in self.instruments:
             s = getattr(self, inst)
 
+            if s.mtime.size == 0:
+                if self.verbose:
+                    logger.info(f'all observations of {inst} are masked')
+                continue
+
             if s.N == 1:
                 if self.verbose:
                     msg = (f'only 1 observation for {inst}, '
@@ -1231,28 +1359,37 @@ class RV:
 
             s.rv_mean = wmean(s.mvrad, s.msvrad)
             s.vrad -= s.rv_mean
+
             if self.verbose:
                 logger.info(f'subtracted weighted average from {inst:10s}: ({s.rv_mean:.3f} {self.units})')
+
             if just_rv:
                 continue
-            # log_msg = 'same for '
+
             for i, other in enumerate(others):
                 y, ye = getattr(s, other), getattr(s, other + '_err')
                 m = wmean(y[s.mask], ye[s.mask])
                 setattr(s, f'{other}_mean', m)
                 setattr(s, other, getattr(s, other) - m)
-                # log_msg += other
-                # if i < len(others) - 1:
-                #     log_msg += ', '
-
-            # if self.verbose:
-            #     logger.info(log_msg)
 
         self._build_arrays()
         self._did_adjust_means = True
-        if return_self:
+        if config.return_self:
             return self
 
+    def add_to_vrad(self, values):
+        """ Add an array of values to the RVs of all instruments """
+        if values.size != self.vrad.size:
+            raise ValueError(f"incompatible sizes: len(values) must equal self.N, got {values.size} != {self.vrad.size}")
+
+        for inst in self.instruments:
+            s = getattr(self, inst)
+            mask = self.instrument_array == inst
+            s.vrad += values[mask]
+
+        self._build_arrays()
+
+
     def put_at_systemic_velocity(self):
         """
         For instruments in which mean(RV) < ptp(RV), "move" RVs to the systemic
@@ -1474,6 +1611,8 @@ class RV:
 
 
     #
+    from .stellar import calc_prot_age
+
     @property
     def HZ(self):
         if not hasattr(self, 'star_mass'):
@@ -1492,22 +1631,50 @@ class RV:
         return self._planets
 
 
-def fit_sine(t, y, yerr, period='gls', fix_period=False):
+def fit_sine(t, y, yerr=None, period='gls', fix_period=False):
+    """ Fit a sine curve of the form y = A * sin(2π * t / P + φ) + c
+
+    Args:
+        t (ndarray):
+            Time array
+        y (ndarray):
+            Array of observed values
+        yerr (ndarray, optional):
+            Array of uncertainties. Defaults to None.
+        period (str or float, optional):
+            Initial guess for period or 'gls' to get it from Lomb-Scargle
+            periodogram. Defaults to 'gls'.
+        fix_period (bool, optional):
+            Whether to fix the period. Defaults to False.
+
+    Returns:
+        p (ndarray):
+            Best-fit parameters [A, P, φ, c] or [A, φ, c]
+        f (callable):
+            Function that returns the best-fit sine curve for input times
+    """
     from scipy.optimize import leastsq
     if period == 'gls':
         from astropy.timeseries import LombScargle
         gls = LombScargle(t, y, yerr)
         freq, power = gls.autopower()
         period = 1 / freq[power.argmax()]
-
-    if fix_period and period is None:
-        logger.error('period is fixed but no value provided')
-        return
-
-    def sine(t, p):
-        return p[0] * np.sin(2 * np.pi * t / p[1] + p[2]) + p[3]
-
-    p0 = [y.ptp(), period, 0.0, 0.0]
-    xbest, _ = leastsq(lambda p, t, y, ye: (sine(t, p) - y) / ye,
-                       p0, args=(t, y, yerr))
+    else:
+        period = float(period)
+
+    if yerr is None:
+        yerr = np.ones_like(y)
+
+    if fix_period:
+        def sine(t, p):
+            return p[0] * np.sin(2 * np.pi * t / period + p[1]) + p[2]
+        f = lambda p, t, y, ye: (sine(t, p) - y) / ye
+        p0 = [y.ptp(), 0.0, 0.0]
+    else:
+        def sine(t, p):
+            return p[0] * np.sin(2 * np.pi * t / p[1] + p[2]) + p[3]
+        f = lambda p, t, y, ye: (sine(t, p) - y) / ye
+        p0 = [y.ptp(), period, 0.0, 0.0]
+
+    xbest, _ = leastsq(f, p0, args=(t, y, yerr))
     return xbest, partial(sine, p=xbest)

arvi/translations.py

@@ -1,8 +1,10 @@
 import re
 
 STARS = {
+    '_51Peg': '51 Peg',
     'Barnard': 'GJ699',
     "Barnard's": 'GJ699',
+    'Ross128': 'Ross  128',
 }
 
 

arvi/utils.py

@@ -1,4 +1,5 @@
 import os
+import time
 from contextlib import contextmanager
 try:
     from unittest.mock import patch
@@ -19,6 +20,9 @@ except ImportError:
     tqdm = lambda x, *args, **kwargs: x
     trange = lambda *args, **kwargs: range(*args, **kwargs)
 
+from .setup_logger import logger
+from . import config
+
 
 def create_directory(directory):
     """ Create a directory if it does not exist """
@@ -61,6 +65,23 @@ def all_logging_disabled():
     finally:
         logging.disable(previous_level)
 
+
+@contextmanager
+def timer():
+    """ A simple context manager to time a block of code """
+    if not config.debug:
+        yield
+        return
+
+    logger.debug(f'starting timer')
+    start = time.time()
+    try:
+        yield
+    finally:
+        end = time.time()
+        logger.debug(f'elapsed time: {end - start:.2f} seconds')
+
+
 def strtobool(val):
     """Convert a string representation of truth to true (1) or false (0).
 

{arvi-0.1.12.dist-info → arvi-0.1.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.12
+Version: 0.1.14
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.14.dist-info/RECORD

@@ -0,0 +1,35 @@
+arvi/HZ.py,sha256=u7rguhlILRBW-LOczlY3dkIB4LM8p8W7Xfg4FnNaYG0,2850
+arvi/__init__.py,sha256=stLL3UtXmR1jpNEoMyVohjvkCatunz1w5ZK0ApmWuYQ,814
+arvi/ariadne_wrapper.py,sha256=jv8Wl35LfHl1UH1EklbvxHcQHqaEDhRGNogSYjFt7Y4,2141
+arvi/berv.py,sha256=5avwcmc2nkYH1KDo-z4eMPsS1ElNvold2DWkziV13gE,17633
+arvi/binning.py,sha256=jJ_resqSvfI-2BT0cnGPFckTIei_k2Mk95oZyE5b5zQ,15250
+arvi/config.py,sha256=wyj6FTxN7QOZj8LaHAe_ZdPKVfrNfobNNOHRNLH-S7Q,339
+arvi/dace_wrapper.py,sha256=HmsyThieljcjorSSZgmGTZPGBqNrm9QoPwjoR_GpVKo,17025
+arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
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{arvi-0.1.12.dist-info → arvi-0.1.14.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (71.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any