arvi 0.1.25__tar.gz → 0.1.26__tar.gz

{arvi-0.1.25 → arvi-0.1.26}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.25
+Version: 0.1.26
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.25 → arvi-0.1.26}/arvi/dace_wrapper.py

@@ -70,7 +70,6 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
             if verbose and npipe > 1:
                 logger.info(f'selecting latest pipeline ({pipelines[0]}) for {inst}')
 
-
         for pipe in pipelines:
             modes = [m for m in result[inst][pipe].keys()]
 
@@ -85,24 +84,19 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
                     if verbose:
                         logger.warning(f'no observations for requested NIRPS mode ({NIRPS_mode})')
 
-            # HARPS15 observations should not be separated by 'mode' if some are
-            # done together with NIRPS
-            if 'HARPS15' in inst:
+            # HARPS observations should not be separated by 'mode' if some are
+            # done together with NIRPS, but should be separated by 'EGGS' mode
+            if 'HARPS' in inst:
+                m0 = modes[0]
+                data = {
+                    k: np.concatenate([result[inst][pipe][m][k] for m in modes])
+                    for k in result[inst][pipe][m0].keys()
+                }
                 if 'HARPS+NIRPS' in modes:
-                    m0 = modes[0]
-                    data = {
-                        k: np.concatenate([result[inst][pipe][m][k] for m in modes])
-                        for k in result[inst][pipe][m0].keys()
-                    }
                     arrays.append( ((str(inst), str(pipe), str(m0)), data) )
                     continue
 
-                if 'EGGS+NIRPS' in modes:
-                    m0 = modes[0]
-                    data = {
-                        k: np.concatenate([result[inst][pipe][m][k] for m in modes])
-                        for k in result[inst][pipe][m0].keys()
-                    }
+                if 'EGGS+NIRPS' in modes or 'EGGS' in modes:
                     arrays.append( ((str(inst + '_EGGS'), str(pipe), str(m0)), data) )
                     continue
 

{arvi-0.1.25 → arvi-0.1.26}/arvi/extra_data.py

@@ -10,7 +10,8 @@ refs = {
     'HD86226': 'Teske et al. 2020 (AJ, 160, 2)'
 }
 
-def get_extra_data(star, instrument=None, path=None, verbose=True):
+def get_extra_data(star, instrument=None, path=None, verbose=True,
+                   check_for_kms=True):
     if path is None:
         path = os.path.dirname(__file__)
         path = os.path.join(path, 'data', 'extra')
@@ -18,7 +19,7 @@ def get_extra_data(star, instrument=None, path=None, verbose=True):
     metadata = json.load(open(os.path.join(path, 'metadata.json'), 'r'))
     # print(metadata)
 
-    files = glob(os.path.join(path, star + '*'))
+    files = glob(os.path.join(path, star.replace(' ', '') + '*.rdb'))
     files = [f for f in files if os.path.isfile(f)]
     files = [f for f in files if not os.path.basename(f).endswith('.zip')]
 
@@ -57,9 +58,24 @@ def get_extra_data(star, instrument=None, path=None, verbose=True):
             if 'corrected_for_secular_acceleration' in metadata[file_basename]:
                 did_sa[i] = metadata[file_basename]['corrected_for_secular_acceleration']
 
-    s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
-    for file, instrument, unit in zip(files[1:], instruments[1:], units[1:]):
-        s = s + timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+    with logger.contextualize(indent='  '):
+        s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
+        if check_for_kms and s.svrad.min() < 0.01:
+            units[0] = 'kms'
+            s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
+        if verbose:
+            logger.info(f'{instruments[0]:>12s} ├ ({s.N} observations)')
+
+        for file, instrument, unit in zip(files[1:], instruments[1:], units[1:]):
+            _s = timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+            if check_for_kms and _s.svrad.min() < 0.01:
+                unit = 'kms'
+                _s = timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+            if verbose:
+                logger.info(f'{instrument:>12s} ├ ({_s.N} observations)')
+
+            s = s + _s
+
 
     for i, (inst, ref, inst_did_sa) in enumerate(zip(s.instruments, reference, did_sa)):
         _s = getattr(s, inst)

{arvi-0.1.25 → arvi-0.1.26}/arvi/gaia_wrapper.py

@@ -31,6 +31,7 @@ gaia_source.source_id = {id}
 
 translate = {
     'Proxima': '5853498713190525696',
+    'GJ699': '4472832130942575872',
     'LS II +14 13': '4318465066420528000',
 }
 
@@ -81,7 +82,7 @@ class gaia:
         pmra = simbad.pmra
         pmdec = simbad.pmdec
         rv = simbad.rvz_radvel
-        args = dict(ra=ra, dec=dec, plx=plx, pmra=pmra, pmdec=pmdec, rv=rv)          
+        args = dict(ra=ra, dec=dec, plx=plx, pmra=pmra, pmdec=pmdec, rv=rv) 
 
         try:
             if star in translate:

{arvi-0.1.25 → arvi-0.1.26}/arvi/plots.py

@@ -6,7 +6,7 @@ import numpy as np
 from astropy.timeseries import LombScargle
 
 from .setup_logger import logger
-from . import config
+from .config import config
 from .stats import wmean
 
 from .utils import lazy_import
@@ -123,8 +123,12 @@ def clickable_legend(fig, ax, leg):
                 h = handles[labels.index(artist.get_text())]
                 alpha_text = {None:0.2, 1.0: 0.2, 0.2:1.0}[artist.get_alpha()]
                 alpha_point = {None: 0.0, 1.0: 0.0, 0.2: 1.0}[artist.get_alpha()]
-                h[0].set_alpha(alpha_point)
-                h[2][0].set_alpha(alpha_point)
+                try:
+                    h[0].set_alpha(alpha_point)
+                    h[2][0].set_alpha(alpha_point)
+                except TypeError:
+                    h.set_alpha(alpha_point)
+
                 artist.set_alpha(alpha_text)
                 fig.canvas.draw()
             except ValueError:
@@ -488,14 +492,15 @@ def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
 
 
 plot_fwhm = partialmethod(plot_quantity, quantity='fwhm')
-plot_bis = partialmethod(plot_quantity, quantity='bispan')
+plot_bispan = partialmethod(plot_quantity, quantity='bispan')
 plot_contrast = partialmethod(plot_quantity, quantity='contrast')
 plot_rhk = partialmethod(plot_quantity, quantity='rhk')
 plot_berv = partialmethod(plot_quantity, quantity='berv')
 
 
 @plot_fast
-def gls(self, ax=None, label=None, fap=True, instrument=None, adjust_means=config.adjust_means_gls,
+def gls(self, ax=None, label=None, fap=True, instrument=None, 
+        adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):
     """
     Calculate and plot the Generalised Lomb-Scargle periodogram of the radial
@@ -711,7 +716,7 @@ def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
 
 
 gls_fwhm = partialmethod(gls_quantity, quantity='fwhm')
-gls_bis = partialmethod(gls_quantity, quantity='bispan')
+gls_bispan = partialmethod(gls_quantity, quantity='bispan')
 gls_rhk = partialmethod(gls_quantity, quantity='rhk')
 
 

{arvi-0.1.25 → arvi-0.1.26}/arvi/timeseries.py

@@ -25,7 +25,10 @@ units = lazy_import('astropy.units')
 # from astropy import units
 
 class ExtraFields:
-    pass
+    @property
+    def fields(self):
+        return list(self.__dict__.keys())
+
 
 @dataclass
 class RV:
@@ -70,13 +73,17 @@ class RV:
     _gaia = None
 
     def __repr__(self):
+        ni = len(self.instruments)
         if self.N == 0:
             return f"RV(star='{self.star}', N=0)"
+
+        i = f'{ni} instrument' + ('s' if ni > 1 else '')
+
         if self.time.size == self.mtime.size:
-            return f"RV(star='{self.star}', N={self.N})"
+            return f"RV(star='{self.star}', N={self.N}, {i})"
         else:
             nmasked = self.N - self.mtime.size
-            return f"RV(star='{self.star}', N={self.N}, masked={nmasked})"
+            return f"RV(star='{self.star}', N={self.N}, masked={nmasked}, {i})"
 
     @property
     def simbad(self):
@@ -272,11 +279,20 @@ class RV:
         # if not isinstance(other, self.__class__):
         #     raise TypeError('unsupported operand type(s) for +: '
         #                     f"'{self.__class__.__name__}' and '{other.__class__.__name__}'")
+        if other is None:
+            if inplace:
+                return
+            else:
+                return deepcopy(self)
 
         if np.isin(self.instruments, other.instruments).any():
             logger.error('the two objects share instrument(s), cannot add them')
             return
 
+        if self._did_adjust_means or other._did_adjust_means:
+            self.adjust_means()
+            other.adjust_means()
+
         if inplace:
             #? could it be as simple as this?
             for i in other.instruments:
@@ -511,18 +527,33 @@ class RV:
         Examples:
             s = RV.from_rdb('star_HARPS.rdb')
         """
+        from glob import glob
+        from os.path import splitext, basename
+
+        verbose = kwargs.pop('verbose', True)
+
         if isinstance(files, str):
-            files = [files]
+            if '*' in files:
+                files = glob(files)
+            else:
+                files = [files]
+
+        if len(files) == 0:
+            if verbose:
+                logger.error('no files found')
+            return
 
         if star is None:
-            star_ = np.unique([os.path.splitext(os.path.basename(f))[0].split('_')[0] for f in files])
+            star_ = np.unique([splitext(basename(f))[0].split('_')[0] for f in files])
             if star_.size == 1:
-                logger.info(f'assuming star is {star_[0]}')
-                star = star_[0]
+                star = star_[0].replace('-', '_')
+                if verbose:
+                    logger.info(f'assuming star is {star}')
 
         if instrument is None:
-            instruments = np.array([os.path.splitext(f)[0].split('_')[1] for f in files])
-            logger.info(f'assuming instruments: {instruments}')
+            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)
 
@@ -537,11 +568,14 @@ class RV:
             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 np.atleast_1d(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)
+            if data.ndim == 1:
+                data = data.reshape(-1, 1)
+
             _s = cls(star, _child=True, **kwargs)
             time = data[0]
             _s.time = time
@@ -559,14 +593,20 @@ class RV:
                     names = header.split()
 
             if len(names) > 3:
-                if f.endswith('.rdb'):
-                    kw = dict(skip_header=2, dtype=None, encoding=None)
-                else:
-                    kw = dict(skip_header=0, comments='--', names=True, dtype=None, encoding=None)
+                # if f.endswith('.rdb'):
+                #     kw = dict(skip_header=2, dtype=None, encoding=None)
+                # else:
+                comments = '#'
+                kw = dict(skip_header=2, comments=comments,
+                          names=names, dtype=None, encoding=None)
                 if '\t' in header:
                     data = np.genfromtxt(f, **kw, delimiter='\t')
                 else:
                     data = np.genfromtxt(f, **kw)
+                
+                # if data.ndim in (0, 1):
+                #     data = data.reshape(-1, 1)
+
                 if len(names) == len(data.dtype.names):
                     data.dtype.names = names
             else:
@@ -580,19 +620,20 @@ class RV:
                 else:
                     _s.fwhm_err = 2 * _s.svrad
             else:
-                _s.fwhm = np.zeros_like(time)
+                _s.fwhm = np.full_like(time, np.nan)
                 _s.fwhm_err = np.full_like(time, np.nan)
 
             _quantities.append('fwhm')
             _quantities.append('fwhm_err')
 
+            # try to find R'HK and uncertainty
             if (v := find_column(data, ['rhk'])) is not False:
                 _s.rhk = v
                 _s.rhk_err = np.full_like(time, np.nan)
                 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 = np.full_like(time, np.nan)
                 _s.rhk_err = np.full_like(time, np.nan)
 
             _quantities.append('rhk')
@@ -636,8 +677,9 @@ class RV:
 
             _s.extra_fields = ExtraFields()
             for name in data.dtype.names:
-                if name not in _quantities:
-                    name_ = name.replace(' ', '_')
+                # don't repeat some quantities
+                if name not in _quantities + ['bjd', 'rjd', 'vrad', 'svrad']:
+                    name_ = name.replace(' ', '_').replace('-', '_')
                     setattr(_s.extra_fields, name_, data[name])
                     # _quantities.append(field)
 
@@ -744,8 +786,8 @@ class RV:
         return s
 
     @classmethod
-    @lru_cache(maxsize=60)
-    def from_KOBE_file(cls, star, **kwargs):
+    # @lru_cache(maxsize=60)
+    def from_KOBE_file(cls, star, directory='.', force_download=False, **kwargs):
         assert 'KOBE' in star, f'{star} is not a KOBE star?'
         import requests
         from requests.auth import HTTPBasicAuth
@@ -766,7 +808,14 @@ class RV:
         local_targz_file = os.path.join(get_data_path(), 'KOBE_fitsfiles.tar.gz')
         fits_file = f'{star}_RVs.fits'
 
-        if os.path.exists(local_targz_file) and os.path.getmtime(local_targz_file) > pytime() - 60*60*2:
+        local_exists = os.path.exists(local_targz_file)
+        local_recent = 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}"')
+            hdul = fits.open(fits_file)
+
+        elif local_exists and local_recent and not force_download:
             tar = tarfile.open(local_targz_file)
 
             if fits_file not in tar.getnames():
@@ -778,6 +827,7 @@ 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
@@ -983,13 +1033,18 @@ class RV:
 
         if load:
             try:
-                from os.path import basename, join
+                from os.path import basename, join, exists
                 from .utils import sanitize_path
                 import iCCF
                 downloaded = [
                     sanitize_path(join(directory, basename(f).replace('.fits', '_CCF_A.fits')))
                     for f in files[:limit]
                 ]
+                downloaded = [
+                    skysub 
+                    if exists(skysub := f.replace('CCF_A.fits', 'CCF_SKYSUB_A.fits')) else f
+                    for f in downloaded
+                ]
                 if self.verbose:
                     logger.info('loading the CCF(s) into `.CCF` attribute')
 
@@ -1063,12 +1118,45 @@ class RV:
             do_download_filetype('S2D', files[:limit], directory, verbose=self.verbose, **kwargs)
 
 
-    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 .plots import plot, plot_fwhm, plot_bispan, plot_contrast, plot_rhk, plot_berv, plot_quantity
+    from .plots import gls, gls_fwhm, gls_bispan, gls_rhk, gls_quantity, window_function
     from .reports import report
 
     from .instrument_specific import known_issues
 
+    def change_instrument_name(self, old_name, new_name, strict=False):
+        """ Change the name of an instrument
+
+        Args:
+            old_name (str):
+                The old name of the instrument
+            new_name (str):
+                The new name of the instrument, or postfix if `strict` is False
+            strict (bool):
+                Whether to match (each) `instrument` exactly
+        """
+        if new_name == '':
+            if self.verbose:
+                logger.error('new name cannot be empty string')
+            return
+
+        instruments = self._check_instrument(old_name, strict, log=True)
+        if instruments is not None:
+            several = len(instruments) >= 2
+            for instrument in instruments:
+                if several:
+                    new_name_instrument = f'{instrument}_{new_name}'
+                else:
+                    new_name_instrument = new_name
+                if self.verbose:
+                    logger.info(f'Renaming {instrument} to {new_name_instrument}')
+
+                setattr(self, new_name_instrument, getattr(self, instrument))
+                delattr(self, instrument)
+                self.instruments[self.instruments.index(instrument)] = new_name_instrument
+
+            self._build_arrays()
+
 
     def remove_instrument(self, instrument, strict=False):
         """ Remove all observations from one instrument
@@ -1697,8 +1785,52 @@ class RV:
         if config.return_self:
             return self
 
+    def detrend(self, degree=1):
+        """ Detrend the RVs of all instruments """
+        instrument_indices = np.unique_inverse(self.instrument_array).inverse_indices
+        def fun(p, t, degree, ninstruments, just_model=False, index=None):
+            polyp, offsets = p[:degree], p[-ninstruments:]
+            polyp = np.r_[polyp, 0.0]
+            if index is None:
+                model = offsets[instrument_indices] + np.polyval(polyp, t)
+            else:
+                model = offsets[index] + np.polyval(polyp, t)
+            if just_model:
+                return model
+            return self.mvrad - model
+        coef = np.polyfit(self.mtime, self.mvrad, degree)
+        x0 = np.append(coef, [0.0] * (len(self.instruments) - 1))
+        print(x0)
+        fun(x0, self.mtime, degree, len(self.instruments))
+        from scipy.optimize import leastsq
+        xbest, _ = leastsq(fun, x0, args=(self.mtime, degree, len(self.instruments)))
+
+        fig, ax = self.plot()
+        ax.remove()
+        ax = fig.add_subplot(2, 1, 1)
+        self.plot(ax=ax)
+        for i, inst in enumerate(self.instruments):
+            s = getattr(self, inst)
+            ax.plot(s.time, fun(xbest, s.time, degree, len(self.instruments), just_model=True, index=i),
+                    color=f'C{i}')
+        ax.set_title('original', loc='left', fontsize=10)
+        ax.set_title(f'coefficients: {xbest[:degree]}', loc='right', fontsize=10)
+
+        self.add_to_vrad(-fun(xbest, self.time, degree, len(self.instruments), just_model=True))
+        ax = fig.add_subplot(2, 1, 2)
+        self.plot(ax=ax)
+        ax.set_title('detrended', loc='left', fontsize=10)
+
+        # axs[0].plot(self.time, fun(xbest, self.time, degree, len(self.instruments), just_model=True))
+        # axs[1].errorbar(self.mtime, fun(xbest, self.mtime, degree, len(self.instruments)), self.msvrad, fmt='o')
+
+        return
+        
+
+
+
     def add_to_vrad(self, values):
-        """ Add a value of array of values to the RVs of all instruments """
+        """ Add a value or array of values to the RVs of all instruments """
         values = np.atleast_1d(values)
         if values.size == 1:
             values = np.full_like(self.vrad, values)
@@ -1723,7 +1855,7 @@ class RV:
 
     def add_to_quantity(self, quantity, values):
         """
-        Add a value of array of values to the given quantity of all instruments
+        Add a value or array of values to the given quantity of all instruments
         """
         if not hasattr(self, quantity):
             logger.error(f"cannot find '{quantity}' attribute")
@@ -1742,6 +1874,75 @@ class RV:
             setattr(s, quantity, getattr(s, quantity) + values[mask])
         self._build_arrays()
 
+    def replace_vrad(self, values):
+        """ Replace the RVs of all instruments with a value or array of values """
+        values = np.atleast_1d(values)
+        if values.size == 1:
+            values = np.full_like(self.vrad, values)
+
+        masked = False
+        if values.size != self.vrad.size:
+            if values.size == self.mvrad.size:
+                logger.warning('adding to masked RVs only')
+                masked = True
+            else:
+                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)
+            if masked:
+                mask = self.instrument_array[self.mask] == inst
+                s.vrad[s.mask] = values[mask]
+            else:
+                mask = self.instrument_array == inst
+                s.vrad = values[mask]
+        self._build_arrays()
+
+    def replace_svrad(self, values):
+        """ Replace the RV uncertainties of all instruments with a value or array of values """
+        values = np.atleast_1d(values)
+        if values.size == 1:
+            values = np.full_like(self.svrad, values)
+
+        masked = False
+        if values.size != self.svrad.size:
+            if values.size == self.msvrad.size:
+                logger.warning('adding to masked RV uncertainties only')
+                masked = True
+            else:
+                raise ValueError(f"incompatible sizes: len(values) must equal self.N, got {values.size} != {self.svrad.size}")
+
+        for inst in self.instruments:
+            s = getattr(self, inst)
+            if masked:
+                mask = self.instrument_array[self.mask] == inst
+                s.svrad[s.mask] = values[mask]
+            else:
+                mask = self.instrument_array == inst
+                s.svrad = values[mask]
+        self._build_arrays()
+
+    def replace_quantity(self, quantity, values):
+        """ Replace the given quantity of all instruments by a value or array of values """
+        if not hasattr(self, quantity):
+            logger.error(f"cannot find '{quantity}' attribute")
+            return
+        q = getattr(self, quantity)
+
+        values = np.atleast_1d(values)
+        if values.size == 1:
+            values = np.full_like(q, values)
+        if values.size != q.size:
+            raise ValueError(f"incompatible sizes: len(values) must equal self.N, got {values.size} != {q.size}")
+
+        for inst in self.instruments:
+            s = getattr(self, inst)
+            mask = self.instrument_array == inst
+            setattr(s, quantity, values[mask])
+        self._build_arrays()
+
+
+
     def change_units(self, new_units):
         possible = {'m/s': 'm/s', 'km/s': 'km/s', 'ms': 'm/s', 'kms': 'km/s'}
         if new_units not in possible:
@@ -1809,20 +2010,18 @@ class RV:
         """ Sort instruments by first or last observation date.
 
         Args:
-            by_first_observation (bool, optional):
+            by_first_observation (bool, optional, default=True):
                 Sort by first observation date.
-            by_last_observation (bool, optional):
-                Sort by last observation data.
+            by_last_observation (bool, optional, default=False):
+                Sort by last observation date.
         """
         if by_last_observation:
             by_first_observation = False
         if by_first_observation:
-            fun = lambda i: getattr(self, i).time.min()
-            self.instruments = sorted(self.instruments, key=fun)
+            self.instruments = sorted(self.instruments, key=lambda i: getattr(self, i).time.min())
             self._build_arrays()
         if by_last_observation:
-            fun = lambda i: getattr(self, i).time.max()
-            self.instruments = sorted(self.instruments, key=fun)
+            self.instruments = sorted(self.instruments, key=lambda i: getattr(self, i).time.max())
             self._build_arrays()
 
 
@@ -1841,7 +2040,7 @@ class RV:
                 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.
+                False, the full observation which contains NaN values is not saved.
         """
         star_name = self.star.replace(' ', '')
 
@@ -1864,7 +2063,7 @@ class RV:
 
             if full:
                 if save_masked:
-                    d = np.c_[
+                    arrays = [
                         _s.time, _s.vrad, _s.svrad,
                         _s.fwhm, _s.fwhm_err,
                         _s.bispan, _s.bispan_err,
@@ -1873,7 +2072,7 @@ class RV:
                         _s.berv,
                     ]
                 else:
-                    d = np.c_[
+                    arrays = [
                         _s.mtime, _s.mvrad, _s.msvrad,
                         _s.fwhm[_s.mask], _s.fwhm_err[_s.mask],
                         _s.bispan[_s.mask], _s.bispan_err[_s.mask],
@@ -1882,12 +2081,13 @@ class RV:
                         _s.berv[_s.mask],
                     ]
                 if not save_nans:
-                    if np.isnan(d).any():
-                        # remove observations where any of the indicators are # NaN
-                        nan_mask = np.isnan(d[:, 3:]).any(axis=1)
-                        d = d[~nan_mask]
-                        if self.verbose:
-                            logger.warning(f'masking {nan_mask.sum()} observations with NaN in indicators')
+                    raise NotImplementedError
+                    # if np.isnan(d).any():
+                    #     # remove observations where any of the indicators are # NaN
+                    #     nan_mask = np.isnan(d[:, 3:]).any(axis=1)
+                    #     d = d[~nan_mask]
+                    #     if self.verbose:
+                    #         logger.warning(f'masking {nan_mask.sum()} observations with NaN in indicators')
 
                 header = '\t'.join(['bjd', 'vrad', 'svrad', 
                                     'fwhm', 'sig_fwhm',
@@ -1901,9 +2101,11 @@ class RV:
 
             else:
                 if save_masked:
-                    d = np.c_[_s.time, _s.vrad, _s.svrad]
+                    arrays = [_s.time, _s.vrad, _s.svrad]
                 else:
-                    d = np.c_[_s.mtime, _s.mvrad, _s.msvrad]
+                    arrays = [_s.mtime, _s.mvrad, _s.msvrad]
+
+                # d = np.stack(arrays, axis=1)
                 header = 'bjd\tvrad\tsvrad\n---\t----\t-----'
 
             file = f'{star_name}_{inst}.rdb'
@@ -1913,7 +2115,17 @@ class RV:
             files.append(file)
             file = os.path.join(directory, file)
 
-            np.savetxt(file, d, fmt='%9.5f', header=header, delimiter='\t', comments='')
+            N = len(arrays[0])
+            with open(file, 'w') as f:
+                f.write(header + '\n')
+                for i in range(N):
+                    for j, a in enumerate(arrays):
+                        f.write(str(a[i]))
+                        if j < len(arrays) - 1:
+                            f.write('\t')
+                    f.write('\n')
+
+            # np.savetxt(file, d, header=header, delimiter='\t', comments='', fmt='%f')
 
             if self.verbose:
                 logger.info(f'saving to {file}')

{arvi-0.1.25 → arvi-0.1.26}/arvi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.25
+Version: 0.1.26
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.25 → arvi-0.1.26}/arvi.egg-info/SOURCES.txt

@@ -48,7 +48,9 @@ docs/detailed.md
 docs/index.md
 docs/logo/detective.png
 docs/logo/logo.png
+tests/HD10700-Bcor_ESPRESSO18.rdb
 tests/test_binning.py
+tests/test_create_RV.py
 tests/test_import_object.py
 tests/test_simbad.py
 tests/test_stats.py

arvi-0.1.26/tests/HD10700-Bcor_ESPRESSO18.rdb

@@ -0,0 +1,3 @@
+bjd	vrad	svrad	fwhm	fwhm_err	bispan	bispan_err
+---	----	-----	----	--------	------	----------
+58412.58101	-16666.0713512	0.1684819	0.0000000	0.0000000	0.0000000	0.0000000

arvi-0.1.26/tests/test_create_RV.py

@@ -0,0 +1,21 @@
+import pytest
+import os
+from numpy import isnan
+
+@pytest.fixture
+def change_test_dir(request):
+    os.chdir(request.fspath.dirname)
+    yield
+    os.chdir(request.config.invocation_params.dir)
+
+def test_from_rdb(change_test_dir):
+    from arvi import RV
+    s = RV.from_rdb('./HD10700-Bcor_ESPRESSO18.rdb', verbose=False)
+    assert s.star == 'HD10700_Bcor'
+    assert s.instruments == ['ESPRESSO18']
+    assert s.N == 1
+    assert s.fwhm.shape == (1,)
+    assert (s.fwhm == 0).all()
+    assert (s.bispan == 0).all()
+    assert isnan(s.rhk).all()
+