arvi 0.2.5__tar.gz → 0.2.7__tar.gz

{arvi-0.2.5/arvi.egg-info → arvi-0.2.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.5
+Version: 0.2.7
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.5 → arvi-0.2.7}/arvi/dace_wrapper.py

@@ -2,7 +2,7 @@ import os
 import sys
 import tarfile
 import collections
-from functools import lru_cache
+from functools import lru_cache, partial
 from itertools import islice
 import numpy as np
 
@@ -170,7 +170,7 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
     """
     Spectroscopy = load_spectroscopy(user)
     found_dace_id = False
-    with timer('simbad query'):
+    with timer('dace_id query'):
         try:
             dace_id = get_dace_id(star, verbose=verbose, raise_error=True)
             found_dace_id = True
@@ -212,17 +212,22 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
 
     for inst in np.unique(result['ins_name']):
         mask1 = result['ins_name'] == inst
-        r[inst] = {}
+        r[str(inst)] = {}
 
-        for pipe in np.unique(result['ins_drs_version'][mask1]):
-            mask2 = mask1 & (result['ins_drs_version'] == pipe)
-            r[inst][pipe] = {}
+        key2 = 'ins_drs_version'
+        n_key2 = len(np.unique(result[key2][mask1]))
+        if len(np.unique(result['pub_bibcode'][mask1])) >= n_key2:
+            key2 = 'pub_bibcode'
+
+        for pipe in np.unique(result[key2][mask1]):
+            mask2 = mask1 & (result[key2] == pipe)
+            r[str(inst)][str(pipe)] = {}
 
             for ins_mode in np.unique(result['ins_mode'][mask2]):
                 mask3 = mask2 & (result['ins_mode'] == ins_mode)
                 _nan = np.full(mask3.sum(), np.nan)
 
-                r[inst][pipe][ins_mode] = {
+                r[str(inst)][str(pipe)][str(ins_mode)] = {
                     'texp': result['texp'][mask3],
                     'bispan': result['spectro_ccf_bispan'][mask3],
                     'bispan_err': result['spectro_ccf_bispan_err'][mask3],
@@ -372,9 +377,11 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
     #     # For all other strings, sort alphabetically
     #     return (2, s)
 
-    def custom_key(val):
+    def custom_key(val, strip_EGGS=False):
+        if strip_EGGS:
+            val = val.replace('-EGGS', '').replace(' EGGS', '')
         key = 0
-        key -= 2 if val == '3.5' else 0
+        key -= 1 if '3.5' in val else 0
         key -= 1 if 'EGGS' in val else 0
         key -= 1 if ('UHR' in val or 'MR' in val) else 0
         key -= 1 if 'LBL' in val else 0
@@ -385,6 +392,8 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
         # new_result[inst] = dict(
         #     sorted(result[inst].items(), key=custom_sort_key, reverse=True)
         # )
+        if all(['EGGS' in k for k in result[inst].keys()]):
+            custom_key = partial(custom_key, strip_EGGS=True)
         # WARNING: not the same as reverse=True (not sure why)
         sorted_keys = sorted(result[inst].keys(), key=custom_key)[::-1]
         new_result[inst] = {}

{arvi-0.2.5 → arvi-0.2.7}/arvi/gaia_wrapper.py

@@ -3,8 +3,6 @@ from io import StringIO
 from csv import DictReader
 import requests
 
-from astropy.coordinates import SkyCoord
-
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
 
@@ -78,6 +76,8 @@ class gaia:
         Args:
             star (str): The name of the star to query simbad
         """
+        from astropy.coordinates import SkyCoord
+
         self.star = star
 
         if simbad is None:

{arvi-0.2.5 → arvi-0.2.7}/arvi/instrument_specific.py

@@ -107,14 +107,7 @@ def divide_HARPS(self):
     
 
 def check(self, instrument):
-    logger = setup_logger()
-    instruments = self._check_instrument(instrument)
-    if instruments is None:
-        if self.verbose:
-            logger.error(f"HARPS_fiber_commissioning: no data from {instrument}")
-        return None
-    return instruments
-
+    return self._check_instrument(instrument)
 
 # HARPS commissioning
 def HARPS_commissioning(self, mask=True, plot=True):

{arvi-0.2.5 → arvi-0.2.7}/arvi/simbad_wrapper.py

@@ -1,6 +1,7 @@
 import os
 import requests
 from dataclasses import dataclass
+from functools import partial
 
 import numpy as np
 
@@ -63,6 +64,23 @@ JOIN ident ON oidref = oid
 WHERE id = '{star}';
 """
 
+HD_GJ_HIP_QUERY = """
+SELECT id2.id
+FROM ident AS id1 JOIN ident AS id2 USING(oidref)
+WHERE id1.id = '{star}' AND id2.id LIKE '{name}%';
+"""
+
+def find_identifier(identifier, star):
+    response = run_query(HD_GJ_HIP_QUERY.format(name=identifier, star=star))
+    if identifier in response:
+        return response.split('"')[1]
+    raise ValueError(f'no {identifier} identifier found for "{star}"')
+
+find_HD = partial(find_identifier, 'HD')
+find_GJ = partial(find_identifier, 'GJ')
+find_HIP = partial(find_identifier, 'HIP')
+
+
 @dataclass
 class Measurements:
     teff: list

arvi-0.2.7/arvi/sophie_wrapper.py

@@ -0,0 +1,111 @@
+from multiprocessing.pool import ThreadPool
+import re
+import requests
+from io import StringIO
+
+import numpy as np
+
+from .setup_logger import setup_logger
+
+URL_CCF = "http://atlas.obs-hp.fr/sophie/sophie.cgi?n=sophiecc&ob=date&a=t&o={target}"
+URL_HEADER = "http://atlas.obs-hp.fr/sophie/sophie.cgi?n=sophiecc&c=i&z=fd&a=t&o=sophie:[ccf,{seq},{mask},0]"
+
+def extract_keyword(keyword, text, raise_error=True):
+    for line in text.splitlines():
+        if keyword in line:
+            value = re.findall(fr'{keyword}\s+([\'\w\d.]+)', line)[0]
+            value = value.replace("'", "")
+            try:
+                return float(value)
+            except ValueError:
+                return value
+    if raise_error:
+        raise KeyError(f'Keyword {keyword} not found')
+
+def query_sophie_archive(star: str, verbose=True):
+    from .timeseries import RV
+    logger = setup_logger()
+
+    resp = requests.get(URL_CCF.format(target=star))
+    if 'leda did not return a position for the name' in resp.text:
+        raise ValueError(f'no SOPHIE observations for {star}')
+
+    data = np.genfromtxt(StringIO(resp.text), dtype=None, usecols=(0, 4),
+                         names=("seq", "mask"))
+    
+    if verbose:
+        logger.info(f'found {len(data)} SOPHIE observations for {star}')
+
+    urls = [URL_HEADER.format(seq=seq, mask=mask) for seq, mask in data]
+    with ThreadPool(8) as pool:
+        responses = pool.map(requests.get, urls)
+
+    bjd, vrad, svrad = [], [], []
+    fwhm, contrast = [], []
+    ccf_mask = []
+    _quantities = []
+    errors = []
+
+    for i, resp in enumerate(responses):
+        if resp.text == '':
+            errors.append(i)
+            continue
+        
+        try:
+            t, v = map(lambda k: extract_keyword(k, resp.text), 
+                       ("OHP DRS BJD", "OHP DRS CCF RV"))
+        except KeyError:
+            errors.append(i)
+            continue
+        else:
+            bjd.append(t)
+            vrad.append(v)
+        
+        try:
+            svrad.append(extract_keyword("OHP DRS CCF ERR", resp.text))
+        except KeyError:
+            try:
+                svrad.append(1e-3 * extract_keyword("OHP DRS DVRMS", resp.text))
+            except KeyError:
+                bjd.pop(-1)
+                vrad.pop(-1)
+                errors.append(i)
+                continue
+
+        fwhm.append(extract_keyword('OHP DRS CCF FWHM', resp.text))
+        _quantities.append('fwhm')
+
+        contrast.append(extract_keyword('OHP DRS CCF CONTRAST', resp.text))
+        _quantities.append('contrast')
+
+        ccf_mask.append(extract_keyword('OHP DRS CCF MASK', resp.text))
+        _quantities.append('ccf_mask')
+
+    if len(errors) > 0:
+        logger.warning(f'Could not retrieve {len(errors)} observation'
+                       f'{"s" if len(errors) > 1 else ""}')
+
+    bjd = np.array(bjd) - 2400000.5
+
+    s = RV.from_arrays(star, bjd, vrad, svrad, 'SOPHIE',
+                       fwhm=fwhm, fwhm_err=2*np.array(svrad),
+                       contrast=contrast, 
+                       ccf_mask=ccf_mask)
+    s.units = 'km/s'
+
+    # strings
+    for q in ['date_night', 'prog_id', 'raw_file', 'pub_reference']:
+        setattr(s, q, np.full(bjd.size, ''))
+        _quantities.append(q)
+
+    s._quantities = np.array(_quantities)
+
+    setattr(s, 'SOPHIE', s)
+    s._child = False
+    s.verbose = False
+    s._build_arrays()
+    s.change_units('m/s')
+    s.verbose = verbose
+
+    return s
+    

{arvi-0.2.5 → arvi-0.2.7}/arvi/timeseries.py

@@ -40,43 +40,74 @@ class RV(ISSUES, REPORTS):
     """
     A class holding RV observations
 
+    Args:
+        star (str):
+            Name of the star
+        instrument (str, list):
+            Name of the instrument or list of instruments
+        verbose (bool):
+            Print logging messages
+        do_maxerror:
+            Mask points based on a maximum RV uncertainty
+        do_secular_acceleration:
+            Apply secular acceleration correction. This only applies
+            to certain instruments.
+        do_sigma_clip (bool):
+            Apply sigma clipping on the RVs
+        do_adjust_means (bool):
+            Subtract individual weighted mean RV from each instrument
+        only_latest_pipeline (bool):
+            Select only the latest pipeline from each instrument
+        load_extra_data (bool):
+        check_drs_qc (bool):
+            Mask points based on DRS quality control flags
+        user (str):
+            User name for DACE queries (should be a section in `~/.dacerc` file)
+
     Examples:
         >>> s = RV('Proxima')
+        >>> s = RV('HD10180', instrument='HARPS')
 
-    Attributes:
-        star (str):
-            The name of the star
-        N (int):
-            Total number of observations
-        instruments (list):
-            List of instruments for which there are RVs. Each instrument is also
-            stored as an attribute (e.g. `self.CORALIE98` or `self.HARPS`)
-        simbad (simbad):
-            Information on the target from Simbad
     """
+    # Attributes:
+    #     star (str):
+    #         The name of the star
+    #     N (int):
+    #         Total number of observations
+    #     NN (dict):
+    #         Number of observations per instrument
+    #     instruments (list):
+    #         List of instruments for which there are RVs. Each instrument is also
+    #         stored as an attribute (e.g. `self.CORALIE98` or `self.HARPS`)
+    #     simbad (simbad):
+    #         Information on the target from Simbad
+    #     gaia (gaia):
+    #         Information on the target from Gaia DR3
     star: str
     instrument: Union[str, list] = field(init=True, repr=False, default=None)
     verbose: bool = field(init=True, repr=False, default=True)
-    do_maxerror: Union[bool, float] = field(init=True, repr=False, default=False)
+    do_maxerror: float = field(init=True, repr=False, default=None)
     do_secular_acceleration: bool = field(init=True, repr=False, default=True)
     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=False)
     check_drs_qc: bool = field(init=True, repr=False, default=True)
-    user: bool = field(init=True, repr=False, default=None)
+    check_sophie_archive: bool = field(init=True, repr=False, default=False)
+    user: Union[str, None] = field(init=True, repr=False, default=None)
     #
     units = 'm/s'
     _child: bool = field(init=True, repr=False, default=False)
-    _did_secular_acceleration: bool = field(init=False, repr=False, default=False)
-    _did_sigma_clip: bool = field(init=False, repr=False, default=False)
-    _did_adjust_means: bool = field(init=False, repr=False, default=False)
-    _did_simbad_query: bool = field(init=False, repr=False, default=False)
-    _did_gaia_query: bool = field(init=False, repr=False, default=False)
-    _did_toi_query: bool = field(init=False, repr=False, default=False)
-    _raise_on_error: bool = field(init=True, repr=False, default=True)
-    __masked_numbers: bool = field(init=False, repr=False, default=False)
-    # 
+    #
+    _did_secular_acceleration : bool = field(init=False, repr=False, default=False)
+    _did_sigma_clip           : bool = field(init=False, repr=False, default=False)
+    _did_adjust_means         : bool = field(init=False, repr=False, default=False)
+    _did_simbad_query         : bool = field(init=False, repr=False, default=False)
+    _did_gaia_query           : bool = field(init=False, repr=False, default=False)
+    _did_toi_query            : bool = field(init=False, repr=False, default=False)
+    _raise_on_error  : bool = field(init=True, repr=False, default=True)
+    __masked_numbers : bool = field(init=False, repr=False, default=False)
+    #
     _simbad = None
     _gaia = None
     _toi = None
@@ -104,7 +135,7 @@ class RV(ISSUES, REPORTS):
 
         if self._child:
             return None
-    
+
         if self._did_simbad_query:
             return None
 
@@ -215,7 +246,7 @@ class RV(ISSUES, REPORTS):
                     else:
                         mid = None
 
-                    with timer():
+                    with timer('dace query'):
                         self.dace_result = get_observations(self.__star__, self.instrument,
                                                             user=self.user, main_id=mid, verbose=self.verbose)
                 except ValueError as e:
@@ -288,6 +319,21 @@ class RV(ISSUES, REPORTS):
                 # all other quantities
                 self._build_arrays()
 
+                # self.actin = get_actin_data(self, verbose=self.verbose)
+
+
+        # check for SOPHIE observations
+        cond = not self._child
+        cond = cond and self.instrument is None
+        cond = cond and self.check_sophie_archive
+        if cond:
+            try:
+                from arvi.sophie_wrapper import query_sophie_archive
+                self.__add__(query_sophie_archive(self.star, verbose=self.verbose),
+                             inplace=True)
+            except Exception as e:
+                print(e)
+
         # do clip_maxerror, secular_acceleration, sigmaclip, adjust_means
         if not self._child:
             if self.do_maxerror:
@@ -301,7 +347,7 @@ class RV(ISSUES, REPORTS):
 
             if self.do_adjust_means:
                 self.adjust_means()
-        
+
         _star_no_space = self.star.replace(' ', '')
         _directory = sanitize_path(_star_no_space)
         self._download_directory = f'{_directory}_downloads'
@@ -526,7 +572,7 @@ class RV(ISSUES, REPORTS):
         return s
 
     @classmethod
-    def from_arrays(cls, star, time, vrad, svrad, inst, *args, **kwargs):
+    def from_arrays(cls, star, time, vrad, svrad, inst, **kwargs):
         s = cls(star, _child=True)
         time, vrad, svrad = map(np.atleast_1d, (time, vrad, svrad))
 
@@ -541,11 +587,15 @@ class RV(ISSUES, REPORTS):
         s.time = time
         s.vrad = vrad
         s.svrad = svrad
-        # mask
-        s.mask = kwargs.get('mask', np.full_like(s.time, True, dtype=bool))
+
+        s.mask = kwargs.pop('mask', np.full_like(s.time, True, dtype=bool))
+        s.units = kwargs.pop('units', 'm/s')
+
+        for k, v in kwargs.items():
+            setattr(s, k, np.atleast_1d(v))
 
         s.instruments = [inst]
-        s._quantities = np.array([])
+        s._quantities = np.array(list(kwargs.keys()))
 
         return s
 
@@ -566,7 +616,7 @@ class RV(ISSUES, REPORTS):
         dt = datetime.fromtimestamp(float(timestamp))
         if verbose:
             logger.info(f'reading snapshot of {star} from {dt}')
-        
+
         s = pickle.load(open(file, 'rb'))
         s._snapshot = file
         return s
@@ -578,7 +628,7 @@ class RV(ISSUES, REPORTS):
 
         Args:
             files (str, list):
-                File name or list of file names
+                File name, file object, or list of file names
             star (str, optional):
                 Name of the star. If None, try to infer it from file name
             instrument (str, list, optional):
@@ -589,37 +639,68 @@ class RV(ISSUES, REPORTS):
                 Number of lines to skip in the header. Defaults to 2.
 
         Examples:
-            s = RV.from_rdb('star_HARPS.rdb')
+            >>> s = RV.from_rdb('star_HARPS.rdb')
         """
         from glob import glob
         from os.path import splitext, basename
 
         verbose = kwargs.pop('verbose', True)
 
+        file_object = False
+
         if isinstance(files, str):
             if '*' in files:
                 files = glob(files)
             else:
                 files = [files]
+        elif isinstance(files, list):
+            pass
+        else:
+            file_object = hasattr(files, 'read')
+            files = [files]
 
-        if len(files) == 0:
-            if verbose:
-                logger.error('no files found')
-            return
+        # if len(files) == 0:
+        #     if verbose:
+        #         logger.error('no files found')
+        #     return
+        def get_star_name(file):
+            return splitext(basename(file))[0].split('_')[0].replace('-', '_')
+        
+        def get_instrument(file):
+            return splitext(basename(file))[0].split('_')[1]
 
-        if star is None:
-            star_ = np.unique([splitext(basename(f))[0].split('_')[0] for f in files])
-            if star_.size == 1:
-                star = star_[0].replace('-', '_')
+        if file_object:
+            if star is None:
+                try:
+                    star = get_star_name(files[0].name)
+                except Exception:
+                    star ='unknown'
                 if verbose:
                     logger.info(f'assuming star is {star}')
 
-        if instrument is None:
-            instruments = np.array([splitext(basename(f))[0].split('_')[1] for f in files])
-            if verbose:
-                logger.info(f'assuming instruments: {instruments}')
+            if instrument is None:
+                try:
+                    instrument = get_instrument(files[0].name)
+                except Exception:
+                    instrument = 'unknown'
+                if verbose:
+                    logger.info(f'assuming instrument is {instrument}')
+
+            instruments = np.array([instrument])
         else:
-            instruments = np.atleast_1d(instrument)
+            if star is None:
+                star = np.unique([get_star_name(f) for f in files])[0]
+                if verbose:
+                    logger.info(f'assuming star is {star}')
+            else:
+                star = 'unknown'
+
+            if instrument is None:
+                instruments = np.array([splitext(basename(f))[0].split('_')[1] for f in files])
+                if verbose:
+                    logger.info(f'assuming instruments: {instruments}')
+            else:
+                instruments = np.atleast_1d(instrument)
 
         if instruments.size == 1 and len(files) > 1:
             instruments = np.repeat(instruments, len(files))
@@ -652,12 +733,16 @@ class RV(ISSUES, REPORTS):
             _quantities = []
 
             #! hack
-            with open(f) as ff:
-                header = ff.readline().strip()
-                if '\t' in header:
-                    names = header.split('\t')
-                else:
-                    names = header.split()
+            if file_object:
+                header = f.readline().strip()
+            else:
+                with open(f) as ff:
+                    header = ff.readline().strip()
+
+            if '\t' in header:
+                names = header.split('\t')
+            else:
+                names = header.split()
 
             if len(names) > 3:
                 # if f.endswith('.rdb'):
@@ -670,7 +755,7 @@ class RV(ISSUES, REPORTS):
                     data = np.genfromtxt(f, **kw, delimiter='\t')
                 else:
                     data = np.genfromtxt(f, **kw)
-                
+
                 # if data.ndim in (0, 1):
                 #     data = data.reshape(-1, 1)
 
@@ -814,7 +899,22 @@ class RV(ISSUES, REPORTS):
 
     @classmethod
     def from_ccf(cls, files, star=None, instrument=None, **kwargs):
-        """ Create an RV object from a CCF file or a list of CCF files """
+        """ Create an RV object from a CCF file or a list of CCF files
+
+        !!! Note
+            This function relies on the `iCCF` package
+
+        Args:
+            files (str or list):
+                CCF file or list of CCF files
+            star (str):
+                Star name. If not provided, it will be inferred from the header
+                of the CCF file
+            instrument (str):
+                Instrument name. If not provided, it will be inferred from the
+                header of the CCF file
+        
+        """
         try:
             import iCCF
         except ImportError:
@@ -839,7 +939,7 @@ class RV(ISSUES, REPORTS):
             objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
 
         if len(objects) != 1:
-            logger.warning(f'found {objects.size} different stars in the CCF files, '
+            logger.warning(f'found {objects.size} different stars in the CCF files ({objects}), '
                            'choosing the first one')
         star = objects[0]
 
@@ -865,9 +965,22 @@ class RV(ISSUES, REPORTS):
             _quantities.append('contrast')
             _quantities.append('contrast_err')
 
+            _s.bispan = np.array([i.BIS*1e3 for i in CCFs])
+            _s.bispan_err = np.array([i.BISerror*1e3 for i in CCFs])
+            _quantities.append('bispan')
+            _quantities.append('bispan_err')
+
+            _s.rhk = np.full_like(time, np.nan)
+            _s.rhk_err = np.full_like(time, np.nan)
+            _quantities.append('rhk')
+            _quantities.append('rhk_err')
+
             _s.texp = np.array([i.HDU[0].header['EXPTIME'] for i in CCFs])
             _quantities.append('texp')
 
+            _s.berv = np.array([i.HDU[0].header['HIERARCH ESO QC BERV'] for i in CCFs])
+            _quantities.append('berv')
+
             _s.date_night = np.array([
                 i.HDU[0].header['DATE-OBS'].split('T')[0] for i in CCFs
             ])
@@ -938,17 +1051,17 @@ class RV(ISSUES, REPORTS):
             if fits_file not in tar.getnames():
                 logger.error(f'KOBE file not found for {star}')
                 return
-            
+
             hdul = fits.open(tar.extractfile(fits_file))
 
         else:
             resp = requests.get(f'https://kobe.caha.es/internal/fitsfiles/{fits_file}',
                                 auth=HTTPBasicAuth('kobeteam', config.kobe_password))
-            
+
             if resp.status_code != 200:
                 # something went wrong, try to extract the file by downloading the
                 # full tar.gz archive
-                
+
                 logger.warning(f'could not find "{fits_file}" on server, trying to download full archive')
                 resp = requests.get('https://kobe.caha.es/internal/fitsfiles.tar.gz',
                                     auth=HTTPBasicAuth('kobeteam', config.kobe_password))
@@ -966,7 +1079,7 @@ class RV(ISSUES, REPORTS):
                 if fits_file not in tar.getnames():
                     logger.error(f'KOBE file not found for {star}')
                     return
-                
+
                 hdul = fits.open(tar.extractfile(fits_file))
 
             else:
@@ -1365,7 +1478,9 @@ class RV(ISSUES, REPORTS):
     def remove_point(self, index):
         """
         Remove individual observations at a given index (or indices).
-        NOTE: Like Python, the index is 0-based.
+        
+        !!! Note
+            Like Python, the index is 0-based.
 
         Args:
             index (int, list, ndarray):
@@ -1376,7 +1491,7 @@ class RV(ISSUES, REPORTS):
             instrument_index = self.obs[index]
             np.array(self.instruments)[instrument_index - 1]
         except IndexError:
-            logger.errors(f'index {index} is out of bounds for N={self.N}')
+            logger.error(f'index {index} is out of bounds for N={self.N}')
             return
 
         if self.verbose:
@@ -1397,18 +1512,21 @@ class RV(ISSUES, REPORTS):
     def restore_point(self, index):
         """
         Restore previously deleted individual observations at a given index (or
-        indices). NOTE: Like Python, the index is 0-based.
+        indices). 
+        
+        !!! Note
+            Like Python, the index is 0-based
 
         Args:
             index (int, list, ndarray):
-                Single index, list, or array of indices to restore.
+                Single index, list, or array of indices to restore
         """
         index = np.atleast_1d(index)
         try:
             instrument_index = self.obs[index]
             np.array(self.instruments)[instrument_index - 1]
         except IndexError:
-            logger.errors(f'index {index} is out of bounds for N={self.N}')
+            logger.error(f'index {index} is out of bounds for N={self.N}')
             return
 
         if self.verbose:
@@ -1427,6 +1545,14 @@ class RV(ISSUES, REPORTS):
         self.mask = self.mask & self.public
         self._propagate_mask_changes()
 
+    def remove_public(self):
+        """ Remove public observations """
+        if self.verbose:
+            n = self.public.sum()
+            logger.info(f'masking public observations ({n})')
+        self.mask = self.mask & (~self.public)
+        self._propagate_mask_changes()
+
     def remove_single_observations(self):
         """ Remove instruments for which there is a single observation """
         singles = [i for i in self.instruments if getattr(self, i).mtime.size == 1]
@@ -1452,26 +1578,26 @@ class RV(ISSUES, REPORTS):
                 if self.verbose:
                     logger.warning(f'no observations for prog_id "{prog_id}"')
 
-    def remove_after_bjd(self, bjd):
+    def remove_after_bjd(self, bjd: float):
         """ Remove observations after a given BJD """
         if (self.time > bjd).any():
             ind = np.where(self.time > bjd)[0]
             self.remove_point(ind)
 
-    def remove_before_bjd(self, bjd):
+    def remove_before_bjd(self, bjd: float):
         """ Remove observations before a given BJD """
         if (self.time < bjd).any():
             ind = np.where(self.time < bjd)[0]
             self.remove_point(ind)
-    
-    def remove_between_bjds(self, bjd1, bjd2):
+
+    def remove_between_bjds(self, bjd1: float, bjd2: float):
         """ Remove observations between two BJDs """
         to_remove = (self.time > bjd1) & (self.time < bjd2)
         if to_remove.any():
             ind = np.where(to_remove)[0]
             self.remove_point(ind)
 
-    def choose_n_points(self, n, seed=None, instrument=None):
+    def choose_n_points(self, n: int, seed=None, instrument=None):
         """ Randomly choose `n` observations and mask out the remaining ones
 
         Args:
@@ -1509,15 +1635,20 @@ class RV(ISSUES, REPORTS):
             getattr(self, inst).mask[m - n_before] = False
 
     def secular_acceleration(self, epoch=None, just_compute=False, force_simbad=False):
-        """
-        Remove secular acceleration from RVs
+        """ 
+        Remove secular acceleration from RVs. This uses the proper motions from
+        Gaia (in `self.gaia`) if available, otherwise from Simbad (in
+        `self.simbad`), unless `force_simbad=True`.
+
 
         Args:
             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
-                if `instruments=True`
+            just_compute (bool, optional):
+                Just compute the secular acceleration and return, without
+                changing the RVs
+            force_simbad (bool, optional):
+                Use Simbad proper motions even if Gaia is available
         """
         if self._did_secular_acceleration and not just_compute:  # don't do it twice
             return
@@ -1626,7 +1757,7 @@ class RV(ISSUES, REPORTS):
 
         if config.return_self:
             return self
-    
+
     def _undo_secular_acceleration(self):
         if self._did_secular_acceleration:
             _old_verbose = self.verbose
@@ -1654,7 +1785,15 @@ class RV(ISSUES, REPORTS):
             self._did_secular_acceleration = False
 
     def sigmaclip(self, sigma=5, instrument=None, strict=True):
-        """ Sigma-clip RVs (per instrument!) """
+        """
+        Sigma-clip RVs (per instrument!), by MAD away from the median.
+
+        Args:
+            sigma (float):
+                Number of MADs to clip
+            instrument (str, list):
+                Instrument(s) to sigma-clip
+        """
         #from scipy.stats import sigmaclip as dosigmaclip
         from .stats import sigmaclip_median as dosigmaclip
 
@@ -1691,7 +1830,7 @@ class RV(ISSUES, REPORTS):
 
         self._propagate_mask_changes()
 
-        if self._did_adjust_means:
+        if len(changed_instruments) > 0 and self._did_adjust_means:
             self._did_adjust_means = False
             self.adjust_means(instrument=changed_instruments)
 
@@ -1724,7 +1863,8 @@ class RV(ISSUES, REPORTS):
         """
         Nightly bin the observations.
 
-        WARNING: This creates and returns a new object and does not modify self.
+        !!! Warning
+            This creates and returns a new object and does not modify self.
         """
 
         # create copy of self to be returned
@@ -1828,7 +1968,7 @@ class RV(ISSUES, REPORTS):
         return np.nanmean(z, axis=0)
 
     def subtract_mean(self):
-        """ Subtract (single) mean RV from all instruments """
+        """ Subtract (a single) non-weighted mean RV from all instruments """
         self._meanRV = meanRV = self.mvrad.mean()
         for inst in self.instruments:
             s = getattr(self, inst)
@@ -1864,7 +2004,7 @@ class RV(ISSUES, REPORTS):
         #     row = []
         #     if print_as_table:
         #         logger.info('subtracted weighted average from each instrument:')
-    
+
         others = ('fwhm', 'bispan', )
 
         instruments = self._check_instrument(instrument, strict=kwargs.get('strict', False))
@@ -2143,10 +2283,10 @@ class RV(ISSUES, REPORTS):
         """ Sort instruments by first or last observation date.
 
         Args:
-            by_first_observation (bool, optional, default=True):
-                Sort by first observation date.
-            by_last_observation (bool, optional, default=False):
-                Sort by last observation date.
+            by_first_observation (bool, optional):
+                Sort by first observation date
+            by_last_observation (bool, optional):
+                Sort by last observation date
         """
         if by_last_observation:
             by_first_observation = False
@@ -2222,7 +2362,7 @@ class RV(ISSUES, REPORTS):
                     #     if self.verbose:
                     #         logger.warning(f'masking {nan_mask.sum()} observations with NaN in indicators')
 
-                header = '\t'.join(['rjd', 'vrad', 'svrad', 
+                header = '\t'.join(['rjd', 'vrad', 'svrad',
                                     'fwhm', 'sig_fwhm',
                                     'bispan', 'sig_bispan',
                                     'contrast', 'sig_contrast',

{arvi-0.2.5 → arvi-0.2.7}/arvi/utils.py

@@ -79,14 +79,17 @@ def timer(name=None):
     if name is None:
         logger.debug('starting timer')
     else:
-        logger.debug(f'starting timer: {name}')
+        logger.debug(f'{name}: starting timer')
 
     start = time.time()
     try:
         yield
     finally:
         end = time.time()
-        logger.debug(f'elapsed time: {end - start:.2f} seconds')
+        if name is None:
+            logger.debug(f'elapsed time {end - start:.2f} seconds')
+        else:
+            logger.debug(f'{name}: elapsed time {end - start:.2f} seconds')
 
 
 def sanitize_path(path):

{arvi-0.2.5 → arvi-0.2.7/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.5
+Version: 0.2.7
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.5 → arvi-0.2.7}/arvi.egg-info/SOURCES.txt

@@ -28,6 +28,7 @@ arvi/programs.py
 arvi/reports.py
 arvi/setup_logger.py
 arvi/simbad_wrapper.py
+arvi/sophie_wrapper.py
 arvi/spectra.py
 arvi/stats.py
 arvi/stellar.py