arvi 0.1.10__py3-none-any.whl → 0.1.12__py3-none-any.whl

arvi/timeseries.py

@@ -11,16 +11,16 @@ import numpy as np
 from astropy import units
 
 from .setup_logger import logger
-from .config import return_self
+from .config import return_self, check_internet
 from .translations import translate
-from .dace_wrapper import get_observations, get_arrays
-from .dace_wrapper import do_download_ccf, do_download_s1d, do_download_s2d
+from .dace_wrapper import do_download_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
+from .utils import strtobool, there_is_internet
 
 
 @dataclass
@@ -50,7 +50,7 @@ class RV:
     do_sigma_clip: bool = field(init=True, repr=False, default=False)
     do_adjust_means: bool = field(init=True, repr=False, default=True)
     only_latest_pipeline: bool = field(init=True, repr=False, default=True)
-    load_extra_data: Union[bool, str] = field(init=True, repr=False, default=True)
+    load_extra_data: Union[bool, str] = field(init=True, repr=False, default=False)
     #
     _child: bool = field(init=True, repr=False, default=False)
     _did_secular_acceleration: bool = field(init=False, repr=False, default=False)
@@ -71,6 +71,9 @@ class RV:
         self.__star__ = translate(self.star)
 
         if not self._child:
+            if 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
             # fails, try after removing a trailing 'A'
             for target in (self.__star__, self.__star__.replace('A', '')):
@@ -83,11 +86,23 @@ class RV:
                 if self.verbose:
                     logger.error(f'simbad query for {self.__star__} failed')
 
+            # complicated way to query Gaia with self.__star__ or, if that
+            # fails, try after removing a trailing 'A'
+            for target in (self.__star__, self.__star__.replace('A', '')):
+                try:
+                    self.gaia = gaia(target)
+                    break
+                except ValueError:
+                    continue
+            else:
+                if self.verbose:
+                    logger.error(f'Gaia query for {self.__star__} failed')
+
             # query DACE
             if self.verbose:
                 logger.info(f'querying DACE for {self.__star__}...')
             try:
-                self.dace_result = get_observations(self.__star__, self.instrument, 
+                self.dace_result = get_observations(self.__star__, self.instrument,
                                                     verbose=self.verbose)
             except ValueError as e:
                 # querying DACE failed, should we raise an error?
@@ -226,6 +241,8 @@ class RV:
     @property
     def N_nights(self) -> int:
         """ Number of individual nights """
+        if self.mtime.size == 0:
+            return 0
         return binRV(self.mtime, None, None, binning_bins=True).size - 1
 
     @property
@@ -245,7 +262,7 @@ class RV:
         """ Masked array of times """
         return self.time[self.mask]
 
-    @property  
+    @property
     def mvrad(self) -> np.ndarray:
         """ Masked array of radial velocities """
         return self.vrad[self.mask]
@@ -371,7 +388,7 @@ class RV:
             star, timestamp = file.replace('.pkl', '').split('_')
         else:
             try:
-                file = sorted(glob(f'{star}_*.pkl'))[-1]
+                file = sorted(glob(f'{star}_*.*.pkl'))[-1]
             except IndexError:
                 raise ValueError(f'cannot find any file matching {star}_*.pkl')
             star, timestamp = file.replace('.pkl', '').split('_')
@@ -402,11 +419,11 @@ class RV:
             files = [files]
 
         if star is None:
-            star_ = np.unique([os.path.splitext(f)[0].split('_')[0] for f in files])
+            star_ = np.unique([os.path.splitext(os.path.basename(f))[0].split('_')[0] for f in files])
             if star_.size == 1:
                 logger.info(f'assuming star is {star_[0]}')
                 star = star_[0]
-        
+
         if instrument is None:
             instruments = np.array([os.path.splitext(f)[0].split('_')[1] for f in files])
             logger.info(f'assuming instruments: {instruments}')
@@ -439,12 +456,12 @@ class RV:
                     names = header.split()
 
             if len(names) > 3:
-                kw = dict(skip_header=2, dtype=None, encoding=None)
-                try:
-                    data = np.genfromtxt(f, **kw)
-                except ValueError:
+                kw = dict(skip_header=0, comments='--', names=True, dtype=None, encoding=None)
+                if '\t' in header:
                     data = np.genfromtxt(f, **kw, delimiter='\t')
-                data.dtype.names = names
+                else:
+                    data = np.genfromtxt(f, **kw)
+                # data.dtype.names = names
             else:
                 data = np.array([], dtype=np.dtype([]))
 
@@ -463,8 +480,10 @@ class RV:
 
             if 'rhk' in data.dtype.fields:
                 _s.rhk = data['rhk']
-                if 'srhk' in data.dtype.fields:
-                    _s.rhk_err = data['srhk']
+                _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]
             else:
                 _s.rhk = np.zeros_like(time)
                 _s.rhk_err = np.full_like(time, np.nan)
@@ -490,7 +509,7 @@ class RV:
             for q in ['drs_qc']:
                 setattr(_s, q, np.full(time.size, True))
                 _quantities.append(q)
-            
+
             #! end hack
 
             _s.mask = np.ones_like(time, dtype=bool)
@@ -517,10 +536,10 @@ class RV:
         except ImportError:
             logger.error('iCCF is not installed. Please install it with `pip install iCCF`')
             return
-        
+
         if isinstance(files, str):
             files = [files]
-    
+
         I = iCCF.from_file(files)
 
         objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in I])
@@ -624,11 +643,12 @@ class RV:
                 setattr(self, q, arr)
 
 
-    def download_ccf(self, instrument=None, limit=None, directory=None):
+    def download_ccf(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
         """ Download CCFs from DACE
 
         Args:
             instrument (str): Specific instrument for which to download data
+            index (int): Specific index of point for which to download data (0-based)
             limit (int): Maximum number of files to download.
             directory (str): Directory where to store data.
         """
@@ -638,18 +658,27 @@ class RV:
         if instrument is None:
             files = [file for file in self.raw_file if file.endswith('.fits')]
         else:
-            instrument = self._check_instrument(instrument)
+            strict = kwargs.pop('strict', False)
+            instrument = self._check_instrument(instrument, strict=strict)
             files = []
             for inst in instrument:
                 files += list(getattr(self, inst).raw_file)
 
-        do_download_ccf(files[:limit], directory)
+        if index is not None:
+            index = np.atleast_1d(index)
+            files = list(np.array(files)[index])
+
+        # remove empty strings
+        files = list(filter(None, files))
+
+        do_download_filetype('CCF', files[:limit], directory, **kwargs)
 
-    def download_s1d(self, instrument=None, limit=None, directory=None):
+    def download_s1d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
         """ Download S1Ds from DACE
 
         Args:
             instrument (str): Specific instrument for which to download data
+            index (int): Specific index of point for which to download data (0-based)
             limit (int): Maximum number of files to download.
             directory (str): Directory where to store data.
         """
@@ -659,18 +688,27 @@ class RV:
         if instrument is None:
             files = [file for file in self.raw_file if file.endswith('.fits')]
         else:
-            instrument = self._check_instrument(instrument)
+            strict = kwargs.pop('strict', False)
+            instrument = self._check_instrument(instrument, strict=strict)
             files = []
             for inst in instrument:
                 files += list(getattr(self, inst).raw_file)
 
-        do_download_s1d(files[:limit], directory)
+        if index is not None:
+            index = np.atleast_1d(index)
+            files = list(np.array(files)[index])
 
-    def download_s2d(self, instrument=None, limit=None, directory=None):
+        # remove empty strings
+        files = list(filter(None, files))
+
+        do_download_filetype('S1D', files[:limit], directory, **kwargs)
+
+    def download_s2d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
         """ Download S2Ds from DACE
 
         Args:
             instrument (str): Specific instrument for which to download data
+            index (int): Specific index of point for which to download data (0-based)
             limit (int): Maximum number of files to download.
             directory (str): Directory where to store data.
         """
@@ -680,12 +718,20 @@ class RV:
         if instrument is None:
             files = [file for file in self.raw_file if file.endswith('.fits')]
         else:
-            instrument = self._check_instrument(instrument)
+            strict = kwargs.pop('strict', False)
+            instrument = self._check_instrument(instrument, strict=strict)
             files = []
             for inst in instrument:
                 files += list(getattr(self, inst).raw_file)
 
-        extracted_files = do_download_s2d(files[:limit], directory)
+        if index is not None:
+            index = np.atleast_1d(index)
+            files = list(np.array(files)[index])
+
+        # remove empty strings
+        files = list(filter(None, files))
+
+        do_download_filetype('S2D', files[:limit], directory, **kwargs)
 
 
     from .plots import plot, plot_fwhm, plot_bis, plot_rhk, plot_quantity
@@ -697,13 +743,13 @@ class RV:
 
     def remove_instrument(self, instrument, strict=False):
         """ Remove all observations from one instrument
-        
+
         Args:
             instrument (str or list):
                 The instrument(s) for which to remove observations.
             strict (bool):
                 Whether to match (each) `instrument` exactly
-        
+
         Note:
             A common name can be used to remove observations for several subsets
             of a given instrument. For example
@@ -756,9 +802,24 @@ class RV:
         if return_self:
             return self
 
+    def remove_condition(self, condition):
+        """ Remove all observations that satisfy a condition
+
+        Args:
+            condition (np.ndarray):
+                Boolean array of the same length as the observations
+        """
+        if self.verbose:
+            inst = np.unique(self.instrument_array[condition])
+            logger.info(f"Removing {condition.sum()} points from instruments {inst}")
+        self.mask = self.mask & ~condition
+        self._propagate_mask_changes()
+
     def remove_point(self, index):
-        """ Remove individual observations at a given index (or indices)
-        
+        """
+        Remove individual observations at a given index (or indices).
+        NOTE: Like Python, the index is 0-based.
+
         Args:
             index (int, list, ndarray):
                 Single index, list, or array of indices to remove.
@@ -865,45 +926,76 @@ class RV:
             n_before = (self.obs < self.obs[m]).sum()
             getattr(self, inst).mask[m - n_before] = False
 
-    def secular_acceleration(self, epoch=55500, plot=False):
+    def secular_acceleration(self, epoch=None, just_compute=False, force_simbad=False):
         """
         Remove secular acceleration from RVs
 
         Args:
-            epoch (float):
+            epoch (float, optional):
                 The reference epoch (DACE uses 55500, 31/10/2010)
             instruments (bool or collection of str):
-                Only remove secular acceleration for some instruments, or for all 
+                Only remove secular acceleration for some instruments, or for all
                 if `instruments=True`
-            plot (bool):
-                Show a plot of the RVs with the secular acceleration
         """
-        if self._did_secular_acceleration:  # don't do it twice
+        if self._did_secular_acceleration and not just_compute:  # don't do it twice
             return
-        
+
+        #as_yr = units.arcsec / units.year
+        mas_yr = units.milliarcsecond / units.year
+        mas = units.milliarcsecond
+
         try:
-            self.simbad
-        except AttributeError:
+            if force_simbad:
+                raise AttributeError
+
+            self.gaia
+            self.gaia.plx
+
             if self.verbose:
-                logger.error('no information from simbad, cannot remove secular acceleration')
-            return
+                logger.info('using Gaia information to remove secular acceleration')
+
+            if epoch is None:
+                # Gaia DR3 epoch (astropy.time.Time('J2016.0', format='jyear_str').jd)
+                epoch = 57389.0
+
+            π = self.gaia.plx * mas
+            d = π.to(units.pc, equivalencies=units.parallax())
+            μα = self.gaia.pmra * mas_yr
+            μδ = self.gaia.pmdec * mas_yr
+            μ = μα**2 + μδ**2
+            sa = (μ * d).to(units.m / units.second / units.year,
+                            equivalencies=units.dimensionless_angles())
+
+        except AttributeError:
+            try:
+                self.simbad
+            except AttributeError:
+                if self.verbose:
+                    logger.error('no information from simbad, cannot remove secular acceleration')
+                return
+
+            if self.simbad.plx is None:
+                if self.verbose:
+                    logger.error('no parallax from simbad, cannot remove secular acceleration')
+                return
 
-        if self.simbad.plx_value is None:
             if self.verbose:
-                logger.error('no parallax from simbad, cannot remove secular acceleration')
-            return
+                logger.info('using Simbad information to remove secular acceleration')
 
-        #as_yr = units.arcsec / units.year
-        mas_yr = units.milliarcsecond / units.year
-        mas = units.milliarcsecond
+            if epoch is None:
+                epoch = 55500
+
+            π = self.simbad.plx * mas
+            d = π.to(units.pc, equivalencies=units.parallax())
+            μα = self.simbad.pmra * mas_yr
+            μδ = self.simbad.pmdec * mas_yr
+            μ = μα**2 + μδ**2
+            sa = (μ * d).to(units.m / units.second / units.year,
+                            equivalencies=units.dimensionless_angles())
+
+        if just_compute:
+            return sa
 
-        π = self.simbad.plx_value * mas
-        d = π.to(units.pc, equivalencies=units.parallax())
-        μα = self.simbad.pmra * mas_yr
-        μδ = self.simbad.pmdec * mas_yr
-        μ = μα**2 + μδ**2
-        sa = (μ * d).to(units.m / units.second / units.year,
-                        equivalencies=units.dimensionless_angles())
         sa = sa.value
 
         if self.verbose:
@@ -927,7 +1019,7 @@ class RV:
                     continue
 
                 s.vrad = s.vrad - sa * (s.time - epoch) / 365.25
-            
+
             self._build_arrays()
 
         self._did_secular_acceleration = True
@@ -978,7 +1070,7 @@ class RV:
 
     def clip_maxerror(self, maxerror:float):
         """ Mask out points with RV error larger than a given value
-        
+
         Args:
             maxerror (float): Maximum error to keep.
         """
@@ -1004,10 +1096,10 @@ class RV:
 
         WARNING: This creates and returns a new object and does not modify self.
         """
-        
+
         # create copy of self to be returned
         snew = deepcopy(self)
-        
+
         all_bad_quantities = []
 
         for inst in snew.instruments:
@@ -1016,7 +1108,7 @@ class RV:
             # only one observation?
             if s.N == 1:
                 continue
-        
+
             # are all observations masked?
             if s.mtime.size == 0:
                 continue
@@ -1067,7 +1159,7 @@ class RV:
                     with warnings.catch_warnings():
                         warnings.filterwarnings('ignore', category=RuntimeWarning)
                         try:
-                            _, yb = binRV(s.mtime, Q[s.mask], 
+                            _, yb = binRV(s.mtime, Q[s.mask],
                                         stat=np.nanmean, tstat=np.nanmean)
                             setattr(s, q, yb)
                         except TypeError:
@@ -1082,7 +1174,7 @@ class RV:
 
             s.time = tb
             s.mask = np.full(tb.shape, True)
-        
+
         if snew.verbose and len(all_bad_quantities) > 0:
             logger.warning('\nnew object will not have these non-float quantities')
 
@@ -1152,7 +1244,7 @@ class RV:
                 # log_msg += other
                 # if i < len(others) - 1:
                 #     log_msg += ', '
-            
+
             # if self.verbose:
             #     logger.info(log_msg)
 
@@ -1203,7 +1295,8 @@ class RV:
             self._build_arrays()
 
 
-    def save(self, directory=None, instrument=None, full=False, save_nans=True):
+    def save(self, directory=None, instrument=None, full=False, postfix=None,
+             save_masked=False, save_nans=True):
         """ Save the observations in .rdb files.
 
         Args:
@@ -1211,9 +1304,10 @@ class RV:
                 Directory where to save the .rdb files.
             instrument (str, optional):
                 Instrument for which to save observations.
-            full (bool, optional): 
-                Whether to save just RVs and errors (False) or more indicators
-                (True).
+            full (bool, optional):
+                Save just RVs and errors (False) or more indicators (True).
+            postfix (str, optional):
+                Postfix to add to the filenames ([star]_[instrument]_[postfix].rdb).
             save_nans (bool, optional)
                 Whether to save NaN values in the indicators, if they exist. If
                 False, the full observation is not saved.
@@ -1238,11 +1332,18 @@ class RV:
                 continue
 
             if full:
-                d = np.c_[
-                    _s.mtime, _s.mvrad, _s.msvrad,
-                    _s.fwhm[_s.mask], _s.fwhm_err[_s.mask],
-                    _s.rhk[_s.mask], _s.rhk_err[_s.mask],
-                ]
+                if save_masked:
+                    d = np.c_[
+                        _s.time, _s.vrad, _s.svrad,
+                        _s.fwhm, _s.fwhm_err,
+                        _s.rhk, _s.rhk_err,
+                    ]
+                else:
+                    d = np.c_[
+                        _s.mtime, _s.mvrad, _s.msvrad,
+                        _s.fwhm[_s.mask], _s.fwhm_err[_s.mask],
+                        _s.rhk[_s.mask], _s.rhk_err[_s.mask],
+                    ]
                 if not save_nans:
                     if np.isnan(d).any():
                         # remove observations where any of the indicators are # NaN
@@ -1254,10 +1355,16 @@ class RV:
                 header =  'bjd\tvrad\tsvrad\tfwhm\tsfwhm\trhk\tsrhk\n'
                 header += '---\t----\t-----\t----\t-----\t---\t----'
             else:
-                d = np.c_[_s.mtime, _s.mvrad, _s.msvrad]
+                if save_masked:
+                    d = np.c_[_s.time, _s.vrad, _s.svrad]
+                else:
+                    d = np.c_[_s.mtime, _s.mvrad, _s.msvrad]
                 header = 'bjd\tvrad\tsvrad\n---\t----\t-----'
-            
+
             file = f'{star_name}_{inst}.rdb'
+            if postfix is not None:
+                file = f'{star_name}_{inst}_{postfix}.rdb'
+
             files.append(file)
             file = os.path.join(directory, file)
 
@@ -1265,7 +1372,7 @@ class RV:
 
             if self.verbose:
                 logger.info(f'saving to {file}')
-        
+
         return files
 
     def checksum(self, write_to=None):
@@ -1280,7 +1387,7 @@ class RV:
 
 
     #
-    def run_lbl(self, instrument=None, data_dir=None, 
+    def run_lbl(self, instrument=None, data_dir=None,
                 skysub=False, tell=False, limit=None, **kwargs):
         from .lbl_wrapper import run_lbl, NIRPS_create_telluric_corrected_S2D
 
@@ -1294,7 +1401,7 @@ class RV:
                     logger.error(f"No data from instrument '{instrument}'")
                     logger.info(f'available: {self.instruments}')
                     return
-            
+
             if isinstance(instrument, str):
                 instruments = [instrument]
             else:
@@ -1349,7 +1456,7 @@ class RV:
                     logger.error(f"No data from instrument '{instrument}'")
                     logger.info(f'available: {self.instruments}')
                     return
-            
+
             if isinstance(instrument, str):
                 instruments = [instrument]
             else:
@@ -1403,4 +1510,4 @@ def fit_sine(t, y, yerr, period='gls', fix_period=False):
     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))
-    return xbest, partial(sine, p=xbest)
+    return xbest, partial(sine, p=xbest)

arvi/translations.py

@@ -1,3 +1,5 @@
+import re
+
 STARS = {
     'Barnard': 'GJ699',
     "Barnard's": 'GJ699',
@@ -5,6 +7,15 @@ STARS = {
 
 
 def translate(star):
+    # known translations
     if star in STARS:
         return STARS[star]
+
+    # regex translations
+    NGC_match = re.match(r'NGC([\s\d]+)No([\s\d]+)', star)
+    if NGC_match:
+        cluster = NGC_match.group(1).replace(' ', '')
+        target = NGC_match.group(2).replace(' ', '')
+        return f'Cl* NGC {cluster} MMU {target}'
+
     return star

arvi/utils.py

@@ -13,6 +13,12 @@ import logging
 from glob import glob
 import numpy as np
 
+try:
+    from tqdm import tqdm, trange
+except ImportError:
+    tqdm = lambda x, *args, **kwargs: x
+    trange = lambda *args, **kwargs: range(*args, **kwargs)
+
 
 def create_directory(directory):
     """ Create a directory if it does not exist """
@@ -70,6 +76,14 @@ def strtobool(val):
     else:
         raise ValueError("invalid truth value {!r}".format(val))
 
+def there_is_internet(timeout=1):
+    from socket import create_connection
+    try:
+        create_connection(('8.8.8.8', 53), timeout=timeout)
+        return True
+    except OSError:
+        pass
+    return False
 
 def find_data_file(file):
     here = os.path.dirname(os.path.abspath(__file__))

{arvi-0.1.10.dist-info → arvi-0.1.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.10
+Version: 0.1.12
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.12.dist-info/RECORD

@@ -0,0 +1,31 @@
+arvi/HZ.py,sha256=btqDFTxHeQlmvXOQKrjOpP8YFtmFjGhSZwsYYehLOaM,2885
+arvi/__init__.py,sha256=cECMjLbPiolmft2lsnNoszU6_1a-dKOVY8cb2D1CBfg,366
+arvi/ariadne_wrapper.py,sha256=jv8Wl35LfHl1UH1EklbvxHcQHqaEDhRGNogSYjFt7Y4,2141
+arvi/binning.py,sha256=G1nZvH2ev02quDPZCReygLkH7tX6B3hFAOoOYTfhLec,15249
+arvi/config.py,sha256=7ZoKzTwhIrlueYV1OF3q_iirAdZC0WheFUmXhl9wR4s,232
+arvi/dace_wrapper.py,sha256=CSq21VDt5n_Ln_A6jvxLVwo2TS25C_M00MfvH38uA8I,10621
+arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
+arvi/gaia_wrapper.py,sha256=dv-uKWIsHbW-CPI14Fn1xIngsZrV7YBROVamgH0SULc,3418
+arvi/instrument_specific.py,sha256=gDNu6xM0nL3AItAxipTdg3dIGaGGi7tNWE5nnad5MxM,2873
+arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
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