arvi 0.1.29__py3-none-any.whl → 0.2.0__py3-none-any.whl

arvi/dace_wrapper.py

@@ -15,6 +15,7 @@ def load_spectroscopy(user=None) -> SpectroscopyClass:
     from .config import config
     # requesting as public
     if config.request_as_public:
+        logger.warning('requesting DACE data as public')
         with all_logging_disabled():
             dace = DaceClass(dace_rc_config_path='none')
         return SpectroscopyClass(dace_instance=dace)
@@ -300,26 +301,53 @@ def get_observations(star, instrument=None, user=None, main_id=None, verbose=Tru
             msg = f'no {instrument} observations for {star}'
         raise ValueError(msg)
 
-    # sort pipelines, being extra careful with HARPS pipeline names
-    # (i.e. ensure that 3.x.x > 3.5)
+    # # sort pipelines, being extra careful with HARPS pipeline names
+    # # (i.e. ensure that 3.x.x > 3.5)
+    # from re import match
+    # def cmp(a, b):
+    #     if a[0] in ('3.5', '3.5 EGGS') or 'EGGS' in a[0] and match(r'3.\d.\d', b[0]):
+    #         return -1
+    #     if b[0] in ('3.5', '3.5 EGGS') or 'EGGS' in b[0] and match(r'3.\d.\d', a[0]):
+    #         return 1
+
+    #     if a[0] == b[0]:
+    #         return 0
+    #     elif a[0] > b[0]:
+    #         return 1
+    #     else:
+    #         return -1
+
+    # sort pipelines, must be extra careful with HARPS/HARPN pipeline version numbers
+    # got here with the help of DeepSeek
     from re import match
-    def cmp(a, b):
-        if a[0] in ('3.5', '3.5 EGGS') or 'EGGS' in a[0] and match(r'3.\d.\d', b[0]):
-            return -1
-        if b[0] in ('3.5', '3.5 EGGS') or 'EGGS' in b[0] and match(r'3.\d.\d', a[0]):
-            return 1
-
-        if a[0] == b[0]:
-            return 0
-        elif a[0] > b[0]:
-            return 1
-        else:
-            return -1
-
-    from functools import cmp_to_key
+    def custom_sort_key(s):
+        s = s[0]
+        # Check for version number pattern (e.g., 3.2.5 or 3.2.5-EGGS)
+        version_match = match(r'^(\d+(?:\.\d+)*)(?:-(.*))?$', s)
+        if version_match:
+            version_parts = tuple(map(int, version_match.group(1).split('.')))
+            suffix = version_match.group(2)
+            
+            if suffix is not None:
+                # Suffixed versions: sort in ascending order (3.2.5-HR11 < 3.3.1-HR11)
+                return (0, 0, version_parts, suffix)
+            else:
+                # Unsuffixed versions: sort in descending order (3.5 > 3.2.5)
+                return (0, 1, tuple(-x for x in version_parts))
+        
+        # Check for scientific reference pattern (e.g., 2004A&A...)
+        year_match = match(r'^(\d{4})', s)
+        if year_match:
+            year = int(year_match.group(1))
+            return (1, year)
+        
+        # For all other strings, sort alphabetically
+        return (2, s)
+
+    # from functools import cmp_to_key
     new_result = {}
     for inst in instruments:
-        new_result[inst] = dict(sorted(result[inst].items(), key=cmp_to_key(cmp), reverse=True))
+        new_result[inst] = dict(sorted(result[inst].items(), key=custom_sort_key, reverse=True))
 
     if verbose:
         logger.info('RVs available from')

arvi/instrument_specific.py

@@ -2,12 +2,25 @@ import os, sys
 import numpy as np
 
 from .setup_logger import logger
+from .utils import ESPRESSO_ADC_issues, ESPRESSO_cryostat_issues
 
 
+# HARPS started operations in October 1st, 2003
+# https://www.eso.org/sci/facilities/lasilla/instruments/harps/news.html
+HARPS_start = 52913
+
 # HARPS fiber upgrade (28 May 2015)
 # https://www.eso.org/sci/facilities/lasilla/instruments/harps/news/harps_upgrade_2015.html
 HARPS_technical_intervention = 57170
 
+# From Lo Curto et al. (2015), The Messenger, vol. 162, p. 9-15  
+# On **19 May 2015** HARPS stopped operations and the instrument was opened.
+# Installation and alignment of the fibre link lasted roughly one week. On 29
+# May, the vacuum vessel was closed and evacuated for the last time. Finally, a
+# formal commissioning of the new fibre took place, finishing on **3 June**,
+# when the instrument was handed back to Science Operations.
+HARPS_technical_intervention_range = (57161, 57176)
+
 # ESPRESSO fiber link upgrade (1 July 2019)
 ESPRESSO_technical_intervention = 58665
 
@@ -86,10 +99,78 @@ def divide_HARPS(self):
         logger.info(f'divided HARPS into {self.instruments}')
     
 
+def check(self, instrument):
+    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
+
+
+# HARPS commissioning
+def HARPS_commissioning(self, mask=True, plot=True):
+    """ Identify and optionally mask points during HARPS commissioning (HARPS).
+
+    Args:
+        mask (bool, optional):
+            Whether to mask out the points.
+        plot (bool, optional):
+            Whether to plot the masked points.
+    """
+    if check(self, 'HARPS') is None:
+        return
+
+    affected = self.time < HARPS_start
+    total_affected = affected.sum()
+
+    if self.verbose:
+        n = total_affected
+        logger.info(f"there {'are'[:n^1]}{'is'[n^1:]} {n} frame{'s'[:n^1]} "
+                     "during HARPS commissioning")
+
+    if mask:
+        self.mask[affected] = False
+        self._propagate_mask_changes()
+
+        if plot:
+            self.plot(show_masked=True)
+
+    return affected
 
-# ESPRESSO ADC issues
-from .utils import ESPRESSO_ADC_issues
 
+# HARPS fiber commissioning
+def HARPS_fiber_commissioning(self, mask=True, plot=True):
+    """ Identify and optionally mask points affected by fiber commissioning (HARPS).
+
+    Args:
+        mask (bool, optional):
+            Whether to mask out the points.
+        plot (bool, optional):
+            Whether to plot the masked points.
+    """
+    if check(self, 'HARPS') is None:
+        return
+
+    affected = (self.time >= HARPS_technical_intervention_range[0]) & (self.time <= HARPS_technical_intervention_range[1])
+    total_affected = affected.sum()
+
+    if self.verbose:
+        n = total_affected
+        logger.info(f"there {'are'[:n^1]}{'is'[n^1:]} {n} frame{'s'[:n^1]} "
+                     "during the HARPS fiber commissioning period")
+
+    if mask:
+        self.mask[affected] = False
+        self._propagate_mask_changes()
+
+        if plot:
+            self.plot(show_masked=True)
+
+    return affected
+
+
+# ESPRESSO ADC issues
 def ADC_issues(self, mask=True, plot=True, check_headers=False):
     """ Identify and optionally mask points affected by ADC issues (ESPRESSO).
 
@@ -137,8 +218,6 @@ def ADC_issues(self, mask=True, plot=True, check_headers=False):
     return intersect
 
 # ESPRESSO cryostat issues
-from .utils import ESPRESSO_cryostat_issues
-
 def blue_cryostat_issues(self, mask=True, plot=True):
     """ Identify and mask points affected by blue cryostat issues (ESPRESSO).
 
@@ -221,7 +300,7 @@ def qc_scired_issues(self, plot=False, **kwargs):
 
 
 def known_issues(self, mask=True, plot=False, **kwargs):
-    """ Identify and optionally mask known instrumental issues (ADC and blue cryostat for ESPRESSO)
+    """ Identify and optionally mask known instrumental issues.
 
     Args:
         mask (bool, optional): Whether to mask out the points.
@@ -230,18 +309,28 @@ def known_issues(self, mask=True, plot=False, **kwargs):
     try:
         adc = ADC_issues(self, mask, plot, **kwargs)
     except IndexError:
-        # logger.error(e)
         logger.error('are the data binned? cannot proceed to mask these points...')
 
     try:
         cryostat = blue_cryostat_issues(self, mask, plot)
     except IndexError:
-        # logger.error(e)
         logger.error('are the data binned? cannot proceed to mask these points...')
 
-    if adc is None and cryostat is None:
-        return
     try:
-        return adc | cryostat
+        harps_comm = HARPS_commissioning(self, mask, plot)
+    except IndexError:
+        logger.error('are the data binned? cannot proceed to mask these points...')
+
+    try:
+        harps_fibers = HARPS_fiber_commissioning(self, mask, plot)
+    except IndexError:
+        logger.error('are the data binned? cannot proceed to mask these points...')
+
+    # if None in (adc, cryostat, harps_comm, harps_fibers):
+    #     return
+
+    try:
+        # return adc | cryostat
+        return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
     except UnboundLocalError:
         return

arvi/plots.py

@@ -137,8 +137,8 @@ def clickable_legend(fig, ax, leg):
 
 # @plot_fast
 def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
-         remove_50000=False, tooltips=False, show_legend=True, label=None,
-         N_in_label=False, versus_n=False, show_histogram=False, bw=False, **kwargs):
+         remove_50000=False, tooltips=True, show_title=False, show_legend=True, label=None, 
+         jitter=None, N_in_label=False, versus_n=False, show_histogram=False, bw=False, **kwargs):
     """ Plot the RVs
 
     Args:
@@ -154,6 +154,8 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
             Whether to subtract 50000 from time. Defaults to False.
         tooltips (bool, optional):
             Show information upon clicking a point. Defaults to True.
+        show_title (bool, optional):
+            Show the star name in the plot title. Defaults to False.
         show_legend (bool, optional):
             Show legend. Defaults to True.
         N_in_label (bool, optional):
@@ -371,6 +373,9 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
         else:
             ax.set_xlabel('BJD - 2400000 [days]')
 
+    if show_title:
+        ax.set_title(self.star, loc='right')
+
     # from matplotlib.backend_tools import ToolBase, ToolToggleBase
     # tm = fig.canvas.manager.toolmanager
     # class InfoTool(ToolToggleBase):

arvi/simbad_wrapper.py

@@ -10,7 +10,9 @@ try:
 except ImportError:
     ufloat = lambda x, y: x
 
+from .stellar import EFFECTIVE_TEMPERATURES, teff_to_sptype
 from .translations import translate
+from .setup_logger import logger
 
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
@@ -71,15 +73,15 @@ class Measurements:
     bibcode: list
 
 
-def run_query(query):
-    url = 'http://simbad.u-strasbg.fr/simbad/sim-tap/sync'
+def run_query(query, SIMBAD_URL='http://simbad.u-strasbg.fr'):
+    url = f'{SIMBAD_URL}/simbad/sim-tap/sync'
     data = dict(query=query, request='doQuery', lang='ADQL', format='text/plain', phase='run')
     try:
         response = requests.post(url, data=data, timeout=2)
     except requests.ReadTimeout as err:
-        raise IndexError(err)
+        raise IndexError(err) from None
     except requests.ConnectionError as err:
-        raise IndexError(err)
+        raise IndexError(err) from None
     return response.content.decode()
 
 def parse_table1(table, cols=None, values=None):
@@ -120,14 +122,6 @@ def parse_value(value, err=None, prec=None):
     return v
 
 
-effective_temperatures = {
-    'F0': 7350, 'F2': 7050, 'F3': 6850, 'F5': 6700, 'F6': 6550, 'F7': 6400, 'F8': 6300, 
-    'G0': 6050, 'G1': 5930, 'G2': 5800, 'G5': 5660, 'G8': 5440,
-    'K0': 5240, 'K1': 5110, 'K2': 4960, 'K3': 4800, 'K4': 4600, 'K5': 4400, 'K7': 4000,
-    'M0': 3750, 'M1': 3700, 'M2': 3600, 'M3': 3500, 'M4': 3400, 'M5': 3200, 'M6': 3100, 'M7': 2900, 'M8': 2700,
-}
-
-
 class simbad:
     """
     A very simple wrapper around a TAP query to simbad for a given target. This
@@ -146,7 +140,7 @@ class simbad:
         V (float): V magnitude
         ids (list): list of identifiers
     """
-    def __init__(self, star:str):
+    def __init__(self, star:str, _debug=False):
         """
         Args:
             star (str): The name of the star to query simbad
@@ -173,12 +167,18 @@ class simbad:
 
         try:
             table1 = run_query(query=QUERY.format(star=self.star))
+            if _debug:
+                print('table1:', table1)
             cols, values = parse_table1(table1)
 
             table2 = run_query(query=BV_QUERY.format(star=self.star))
+            if _debug:
+                print('table2:', table2)
             cols, values = parse_table1(table2, cols, values)
 
             table3 = run_query(query=IDS_QUERY.format(star=self.star))
+            if _debug:
+                print('table3:', table3)
             line = table3.splitlines()[2]
             self.ids = line.replace('"', '').replace('    ', ' ').replace('   ', ' ').replace('  ', ' ').split('|')
 
@@ -203,9 +203,8 @@ class simbad:
 
             self.measurements = Measurements(_teff, _logg, _feh, _bibcode)
 
-
         except IndexError:
-            raise ValueError(f'simbad query for {star} failed')
+            raise ValueError(f'simbad query for {star} failed') from None
 
         try:
             self.gaia_id = int([i for i in self.ids if 'Gaia DR3' in i][0]
@@ -242,10 +241,14 @@ class simbad:
                 raise IndexError
             else:
                 self.teff = data['teff']
+                self.sweetcat = data
 
         except IndexError:
-            if self.sp_type[:2] in effective_temperatures:
-                self.teff = effective_temperatures[self.sp_type[:2]]
+            if self.sp_type == '':
+                self.teff = int(np.mean(self.measurements.teff))
+                self.sp_type = teff_to_sptype(self.teff)
+            elif self.sp_type[:2] in EFFECTIVE_TEMPERATURES:
+                self.teff = EFFECTIVE_TEMPERATURES[self.sp_type[:2]]
 
     def __repr__(self):
         V = self.V

arvi/stellar.py

@@ -1,6 +1,31 @@
-
 import numpy as np
 
+# from Table 5 of Pecaut & Mamajek (2013, ApJS, 208, 9; http://adsabs.harvard.edu/abs/2013ApJS..208....9P)
+# https://www.pas.rochester.edu/~emamajek/EEM_dwarf_UBVIJHK_colors_Teff.txt
+EFFECTIVE_TEMPERATURES = {
+    'F0': 7220, 'F1': 7020, 'F2': 6820, 'F3': 6750, 'F4': 6670, 'F5': 6550, 'F6': 6350, 'F7': 6280, 'F8': 6180, 'F9': 6050,
+    'G0': 5930, 'G1': 5860, 'G2': 5770, 'G3': 5720, 'G4': 5680, 'G5': 5660, 'G6': 5600, 'G7': 5550, 'G8': 5480, 'G9': 5380,
+    'K0': 5270, 'K1': 5170, 'K2': 5100, 'K3': 4830, 'K4': 4600, 'K5': 4440, 'K6': 4300, 'K7': 4100, 'K8': 3990, 'K9': 3930,
+    'M0': 3850, 'M1': 3660, 'M2': 3560, 'M3': 3430, 'M4': 3210, 'M5': 3060, 'M6': 2810, 'M7': 2680, 'M8': 2570, 'M9': 2380,
+}
+
+def teff_to_sptype(teff):
+    """
+    Estimate the spectral type from the effective temperature, using the
+    Pecaut & Mamajek (2013) table.
+
+    Args:
+        teff (float): Effective temperature
+
+    Returns:
+        str: Spectral type
+    """
+    teffs = list(EFFECTIVE_TEMPERATURES.values())
+    sptypes = list(EFFECTIVE_TEMPERATURES.keys())
+    i = np.argmin(np.abs(np.array(teffs) - teff))
+    return sptypes[i]
+
+
 class prot_age_result:
     prot_n84 = None #: float | np.ndarray
     prot_n84_err = None #: float | np.ndarray

arvi/timeseries.py

@@ -414,9 +414,9 @@ class RV:
         ind = np.where(self.instrument_array == instrument)[0]
         return ind[getattr(self, instrument).mask][index]
 
-    @property
-    def _tt(self) -> np.ndarray:
-        return np.linspace(self.mtime.min(), self.mtime.max(), 20*self.N)
+    # @property
+    def _tt(self, f=20) -> np.ndarray:
+        return np.linspace(self.mtime.min(), self.mtime.max(), f*self.N)
 
     @classmethod
     def from_dace_data(cls, star, inst, pipe, mode, data, **kwargs):
@@ -765,13 +765,19 @@ class RV:
         if isinstance(files, str):
             files = [files]
 
-        CCFs = iCCF.from_file(files)
+        hdu_number = kwargs.pop('hdu_number', 1)
+        data_index = kwargs.pop('data_index', -1)
+        CCFs = iCCF.from_file(files, hdu_number=hdu_number, data_index=data_index)
 
         if not isinstance(CCFs, list):
             CCFs = [CCFs]
 
-        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
-        if objects.size != 1:
+        try:
+            objects = np.unique([i.OBJECT for i in CCFs])
+        except AttributeError:
+            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, '
                            'choosing the first one')
         star = objects[0]
@@ -808,7 +814,7 @@ class RV:
 
             _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)
+            _s.drs_qc = np.array([i.HDU[0].header['*QC SCIRED CHECK'][0] for i in CCFs], dtype=bool)
             # mask out drs_qc = False
             if not _s.drs_qc.all():
                 n = (~ _s.drs_qc).sum()
@@ -859,7 +865,7 @@ class RV:
         fits_file = f'{star}_RVs.fits'
 
         local_exists = os.path.exists(local_targz_file)
-        local_recent = os.path.getmtime(local_targz_file) > pytime() - 60*60*2
+        local_recent = local_exists and os.path.getmtime(local_targz_file) > pytime() - 60*60*2
 
         if os.path.exists(os.path.join(directory, fits_file)):
             logger.info(f'found file "{fits_file}" in "{directory}"')
@@ -877,7 +883,6 @@ class RV:
         else:
             resp = requests.get(f'https://kobe.caha.es/internal/fitsfiles/{fits_file}',
                                 auth=HTTPBasicAuth('kobeteam', config.kobe_password))
-            logger.info(f'found file "{fits_file}" on server')
             
             if resp.status_code != 200:
                 # something went wrong, try to extract the file by downloading the
@@ -904,6 +909,7 @@ class RV:
                 hdul = fits.open(tar.extractfile(fits_file))
 
             else:
+                logger.info(f'found file "{fits_file}" on server')
                 # found the file on the server, read it directly
                 hdul = fits.open(BytesIO(resp.content))
 
@@ -1050,7 +1056,7 @@ class RV:
         self._download_directory = value
 
     def download_ccf(self, instrument=None, index=None, limit=None,
-                     directory=None, symlink=False, load=True, **kwargs):
+                     directory=None, clobber=False, symlink=False, load=True, **kwargs):
         """ Download CCFs from DACE
 
         Args:
@@ -1058,6 +1064,7 @@ class RV:
             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.
+            clobber (bool): Whether to overwrite existing files.
         """
         directory = directory or self.download_directory
 
@@ -1079,7 +1086,7 @@ class RV:
                 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, 
+            do_download_filetype('CCF', files[:limit], directory, clobber=clobber,
                                  verbose=self.verbose, user=self.user, **kwargs)
 
         if load:
@@ -1105,7 +1112,7 @@ class RV:
                 pass
 
     def download_s1d(self, instrument=None, index=None, limit=None,
-                     directory=None, symlink=False, **kwargs):
+                     directory=None, clobber=False, apply_mask=True, symlink=False, **kwargs):
         """ Download S1Ds from DACE
 
         Args:
@@ -1113,6 +1120,8 @@ class RV:
             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.
+            clobber (bool): Whether to overwrite existing files.
+            apply_mask (bool): Apply mask to the observations before downloading.
         """
         directory = directory or self.download_directory
 
@@ -1120,7 +1129,11 @@ class RV:
         instrument = self._check_instrument(instrument, strict=strict)
         files = []
         for inst in instrument:
-            files += list(getattr(self, inst).raw_file)
+            _s = getattr(self, inst)
+            if apply_mask:
+                files += list(_s.raw_file[_s.mask])
+            else:
+                files += list(_s.raw_file)
 
         if index is not None:
             index = np.atleast_1d(index)
@@ -1134,11 +1147,11 @@ class RV:
                 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, 
+            do_download_filetype('S1D', files[:limit], directory, clobber=clobber,
                                  verbose=self.verbose, user=self.user, **kwargs)
 
     def download_s2d(self, instrument=None, index=None, limit=None,
-                     directory=None, symlink=False, **kwargs):
+                     directory=None, clobber=False, symlink=False, **kwargs):
         """ Download S2Ds from DACE
 
         Args:
@@ -1146,6 +1159,7 @@ class RV:
             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.
+            clobber (bool): Whether to overwrite existing files.
         """
         directory = directory or self.download_directory
 
@@ -1722,7 +1736,7 @@ class RV:
 
             if snew.verbose and len(bad_quantities) > 0:
                 logger.warning(f"{inst}, skipping non-float quantities in binning:")
-                logger.warning(' ' + str(bad_quantities))
+                logger.warning(' ' + str(list(map(str, bad_quantities))))
                 for bq in bad_quantities:
                     s._quantities = np.delete(s._quantities, s._quantities==bq)
                     delattr(s, bq)  #! careful here
@@ -1731,7 +1745,7 @@ class RV:
             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')
+            logger.warning('\nnew object will not have these quantities')
 
         for q in np.unique(all_bad_quantities):
             delattr(snew, q)
@@ -1771,14 +1785,18 @@ class RV:
             s.vrad += self._meanRV
         self._build_arrays()
 
-    def adjust_means(self, just_rv=False, instrument=None, **kwargs):
+    def adjust_means(self, just_rv=False, exclude_rv=False, instrument=None, **kwargs):
         """
-        Subtract individual mean RVs from each instrument or from specific
-        instruments
+        Subtract individual weighted mean RV from each instrument or from
+        specific instruments
         """
         if self._child or self._did_adjust_means:
             return
 
+        if just_rv and exclude_rv:
+            logger.error('cannot use `just_rv` and `exclude_rv` at the same time')
+            return
+
         # if self.verbose:
         #     print_as_table = len(self.instruments) > 2 and len(self.instruments) < 7
         #     rows = [self.instruments]
@@ -1807,14 +1825,12 @@ class RV:
                 s.vrad = np.zeros_like(s.time)
                 continue
 
-            s.rv_mean = wmean(s.mvrad, s.msvrad)
-            s.vrad -= s.rv_mean
+            if not exclude_rv:
+                s.rv_mean = wmean(s.mvrad, s.msvrad)
+                s.vrad -= s.rv_mean
 
-            if self.verbose:
-                # if print_as_table:
-                #     row.append(f'{s.rv_mean:.3f}')
-                # else:
-                logger.info(f'subtracted weighted average from {inst:10s}: ({s.rv_mean:.3f} {self.units})')
+                if self.verbose:
+                    logger.info(f'subtracted weighted average from {inst:10s}: ({s.rv_mean:.3f} {self.units})')
 
             if just_rv:
                 continue
@@ -1828,6 +1844,9 @@ class RV:
                 setattr(s, f'{other}_mean', m)
                 setattr(s, other, getattr(s, other) - m)
 
+        if self.verbose:
+            logger.info(f'subtracted weighted averages from {others}')
+
         # if print_as_table:
         #     from .utils import pretty_print_table
         #     rows.append(row)
@@ -2142,13 +2161,13 @@ class RV:
                     #     if self.verbose:
                     #         logger.warning(f'masking {nan_mask.sum()} observations with NaN in indicators')
 
-                header = '\t'.join(['bjd', 'vrad', 'svrad', 
+                header = '\t'.join(['rjd', 'vrad', 'svrad', 
                                     'fwhm', 'sig_fwhm',
                                     'bispan', 'sig_bispan',
                                     'contrast', 'sig_contrast',
                                     'rhk', 'sig_rhk',
                                     'berv',
-                                    ]) 
+                                    ])
                 header += '\n'
                 header += '\t'.join(['-' * len(c) for c in header.strip().split('\t')])
 
@@ -2159,7 +2178,7 @@ class RV:
                     arrays = [_s.mtime, _s.mvrad, _s.msvrad]
 
                 # d = np.stack(arrays, axis=1)
-                header = 'bjd\tvrad\tsvrad\n---\t----\t-----'
+                header = 'rjd\tvrad\tsvrad\n---\t----\t-----'
 
             file = f'{star_name}_{inst}.rdb'
             if postfix is not None:
@@ -2292,7 +2311,11 @@ class RV:
             self.star_mass = float(input('stellar mass (Msun): '))
         if not hasattr(self, 'lum'):
             self.lum = float(input('luminosity (Lsun): '))
-        return getHZ_period(self.simbad.teff, self.star_mass, 1.0, self.lum)
+        if hasattr(self, 'teff'):
+            teff = self.teff
+        else:
+            teff = self.simbad.teff
+        return getHZ_period(teff, self.star_mass, 1.0, self.lum)
 
 
     @property

arvi/utils.py

@@ -197,6 +197,18 @@ def ESPRESSO_cryostat_issues():
     return np.array(file_roots)
 
 
+def get_ra_sexagesimal(ra):
+    """ Convert RA in degrees to sexagesimal string representation. """
+    from astropy.coordinates import Angle
+    from astropy import units as u
+    return Angle(ra, unit=u.deg).to(u.hourangle).to_string(sep=':', pad=True)
+
+def get_dec_sexagesimal(dec):
+    """ Convert DEC in degrees to sexagesimal string representation. """
+    from astropy.coordinates import Angle
+    from astropy import units as u
+    return Angle(dec, unit=u.deg).to_string(sep=':', pad=True)
+
 def get_max_berv_span(self, n=None):
     """
     Return the indices of the n observations which maximize the BERV span.

{arvi-0.1.29.dist-info → arvi-0.2.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.2
+Metadata-Version: 2.4
 Name: arvi
-Version: 0.1.29
+Version: 0.2.0
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -20,6 +20,7 @@ Requires-Dist: loguru
 Requires-Dist: tqdm
 Requires-Dist: pySWEETCat
 Requires-Dist: kepmodel
+Dynamic: license-file
 
 <p align="center">
   <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>
@@ -58,7 +59,7 @@ s = RV('HD1234', instrument='ESPRESSO')
 
 #### Current version
 
-![PyPI - Version](https://img.shields.io/pypi/v/arvi)
+[![PyPI - Version](https://img.shields.io/pypi/v/arvi?color=32c854)](https://pypi.org/project/arvi/)
 
 #### Actions
 

{arvi-0.1.29.dist-info → arvi-0.2.0.dist-info}/RECORD

@@ -4,33 +4,33 @@ arvi/ariadne_wrapper.py,sha256=YvilopJa9T4NwPcj3Nah_U8smSeSAU5-HYZMb_GJ-BQ,2232
 arvi/berv.py,sha256=eKnpuPC1w45UrUEyFRbs9F9j3bXz3kxYzNXbnRgvFQM,17596
 arvi/binning.py,sha256=jbemJ-bM3aqoOsqMo_OhWt_co-JAQ0nhdG_GpTsrRsw,15403
 arvi/config.py,sha256=W-v8NNhRd_PROu0wCMilXmOhYcju4xbUalugd5u7SRU,1881
-arvi/dace_wrapper.py,sha256=dwGj_XuN8J5An9I8ioeK7saj2TNLwwcobOu6oRo_HmM,22228
+arvi/dace_wrapper.py,sha256=G1b2O7JNhYbfSXorRqqs8oZJ6rtJ1t3KMCE4wjjgJmQ,23446
 arvi/extra_data.py,sha256=cpJGMle0ZqY_dtrmbbMQcyU48PkNjfzUgQ-qY-2XTj8,3249
 arvi/gaia_wrapper.py,sha256=2q_7bm6MGvTLlegfNUCY_EhnMKYv1CZmcbanOm_ot-k,4197
 arvi/headers.py,sha256=uvdJebw1M5YkGjE3vJJwYBOnLikib75uuZE9FXB5JJM,1673
-arvi/instrument_specific.py,sha256=-pbm2Vk3iK_1K7nDa1avlJOKHBcXllwILI4lQn-Ze-A,7761
+arvi/instrument_specific.py,sha256=ORjlw79EumEiGugmGn_2WBOuEPhsfgDNryEMBDe9RgM,10733
 arvi/kima_wrapper.py,sha256=BvNTVqzM4lMNhLCyBFVh3T84hHfGKAFpgiYiOi4lh0g,2731
 arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
 arvi/nasaexo_wrapper.py,sha256=mWt7eHgSZe4MBKCmUvMPTyUPGuiwGTqKugNBvmjOg9s,7306
-arvi/plots.py,sha256=gZzwv1VbWMml3tF0ET8Z56ekA-VHd0nZw11XR-Qo0GA,31950
+arvi/plots.py,sha256=Ut9_AOhhlp-fsYaOacZoYnKBVnbpgxKw1BXlEgTphOo,32152
 arvi/programs.py,sha256=BW7xBNKLei7NVLLW3_lsVskwzkaIoNRiHK2jn9Tn2ZM,8879
 arvi/reports.py,sha256=ayPdZ4HZO9iCDdnADQ18gQPJh79o-1UYG7TYkvm9Lrc,4051
 arvi/setup_logger.py,sha256=pBzaRTn0hntozjbaRVx0JIbWGuENkvYUApa6uB-FsRo,279
-arvi/simbad_wrapper.py,sha256=hyMnTeZ4DpnTzyEopkdUfNtJ_roSgdvYPXwYcmXVX2U,8238
+arvi/simbad_wrapper.py,sha256=9hH7VczHAjLnOiqkrd1a6mTd-3Y-o_3d3SYJ7uyF_1Y,8406
 arvi/spectra.py,sha256=ebF1ocodTastLx0CyqLSpE8EZNDXBF8riyfxMr3L6H0,7491
 arvi/stats.py,sha256=ilzzGL9ew-SyVa9eEdrYCpD3DliOAwhoNUg9LIlHjzU,2583
-arvi/stellar.py,sha256=veuL_y9kJvvApU_jqYQqP3EkcRnQffTc8Us6iT5UrFI,3790
-arvi/timeseries.py,sha256=ZHk0SgkzlWELyklcnVi586qAGvHIH7PwTqIE-ScX6u0,87830
+arvi/stellar.py,sha256=GQ7yweuBRnfkJ0M5eWjvLd8uvGq_by81PbXfidBvWis,4918
+arvi/timeseries.py,sha256=jZXO_dW0hzE0EmeUwZclMMywFSeBvMYZktNi7h-_kpc,88893
 arvi/translations.py,sha256=PUSrn4zvYO2MqGzUxlFGwev_tBkgJaJrIYs6NKHzbWo,951
-arvi/utils.py,sha256=LImV8iPjG8ZKjPCT9lp25_pDb-51ZZk42Hc8bzZt7M0,6568
+arvi/utils.py,sha256=V4uSpr75YVjE0NP3T5PxnfVQQ06nd-O8X679BfVyD30,7068
 arvi/data/info.svg,sha256=0IMI6W-eFoTD8acnury79WJJakpBwLa4qKS4JWpsXiI,489
 arvi/data/obs_affected_ADC_issues.dat,sha256=tn93uOL0eCTYhireqp1wG-_c3CbxPA7C-Rf-pejVY8M,10853
 arvi/data/obs_affected_blue_cryostat_issues.dat,sha256=z4AK17xfz8tGTDv1FjRvQFnio4XA6PNNfDXuicewHk4,1771
 arvi/data/extra/HD86226_PFS1.rdb,sha256=vfAozbrKHM_j8dYkCBJsuHyD01KEM1asghe2KInwVao,3475
 arvi/data/extra/HD86226_PFS2.rdb,sha256=F2P7dB6gVyzCglUjNheB0hIHVClC5RmARrGwbrY1cfo,4114
 arvi/data/extra/metadata.json,sha256=C69hIw6CohyES6BI9vDWjxwSz7N4VOYX0PCgjXtYFmU,178
-arvi-0.1.29.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.1.29.dist-info/METADATA,sha256=aRUdDo4XitNY1xqg7OpHKw1nDGT_mGIyNl4FoEJquYg,1852
-arvi-0.1.29.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-arvi-0.1.29.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.1.29.dist-info/RECORD,,
+arvi-0.2.0.dist-info/licenses/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.2.0.dist-info/METADATA,sha256=ZBpnSY92f4u9TgpzpM1PxIqPY8u191X2HKhUq8ILEzw,1920
+arvi-0.2.0.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+arvi-0.2.0.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.2.0.dist-info/RECORD,,

{arvi-0.1.29.dist-info → arvi-0.2.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.8.0)
+Generator: setuptools (78.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any