arvi 0.1.27__tar.gz → 0.1.29__tar.gz

{arvi-0.1.27/arvi.egg-info → arvi-0.1.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: arvi
-Version: 0.1.27
+Version: 0.1.29
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.27 → arvi-0.1.29}/arvi/plots.py

@@ -471,13 +471,16 @@ def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
 
     ax.minorticks_on()
 
+    delta = 'Δ' if self._did_adjust_means else ''
+
     ylabel = {
         quantity.lower(): quantity,
-        'fwhm': f'FWHM [{self.units}]',
-        'bispan': f'BIS [{self.units}]',
+        'fwhm': f'{delta}FWHM [{self.units}]',
+        'bispan': f'{delta}BIS [{self.units}]',
         'rhk': r"$\log$ R'$_{HK}$",
         'berv': 'BERV [km/s]',
     }
+
     ax.set_ylabel(ylabel[quantity.lower()])
 
     if remove_50000:
@@ -499,8 +502,8 @@ 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, instrument=None, 
+        fap=True, fap_method='baluev', adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):
     """
     Calculate and plot the Generalised Lomb-Scargle periodogram of the radial
@@ -512,11 +515,15 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
             created.
         label (str):
             The label to use for the plot.
-        fap (bool):
-            Whether to show the false alarm probability. Default is True.
         instrument (str or list):
             Which instruments' data to include in the periodogram. Default is
             all instruments.
+        fap (bool or float):
+            Whether to show the false alarm probability. A value (not a
+            percentage) can be provided to display a given FAP. Default is True.
+        fap_method (str):
+            Method used to estimate the FAP, passed directly to
+            `astropy.timeseries.LombScargle`. Default is 'baluev'.
         adjust_means (bool):
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
@@ -591,8 +598,17 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
         ax.semilogx(1/freq, power, picker=picker, label=label, **kwargs)
 
     if fap:
-        ax.axhline(gls.false_alarm_level(0.01),
-                   color='k', alpha=0.2, zorder=-1)
+        fap_level = 0.01
+        if isinstance(fap, float):
+            fap_level = fap
+
+        fap = gls.false_alarm_level(fap_level, method=fap_method)
+
+        if fap > 0.05 and fap_method == 'baluev':
+            logger.warning('FAP is high (>5%), the analytical estimate may be underestimated. Using the bootstrap method instead.')
+            fap = gls.false_alarm_level(fap_level, method='bootstrap')
+
+        ax.axhline(fap, color='k', alpha=0.2, zorder=-1)
 
     ax.set(xlabel='Period [days]', ylabel='Normalized power', ylim=(0, None))
     ax.minorticks_on()
@@ -634,8 +650,32 @@ def gls(self, ax=None, label=None, fap=True, instrument=None,
 
 
 # @plot_fast
-def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
+def gls_quantity(self, quantity, ax=None, instrument=None,
+                 fap=True, fap_method='baluev',
                  adjust_means=True, picker=True, **kwargs):
+    """
+    Calculate and plot the Generalised Lomb-Scargle periodogram of the given
+    quantity (e.g. fwhm, rhk, etc.)
+
+    Args:
+        quantity (str):
+            The quantity to calculate for which to compute the periodogram.
+        ax (matplotlib.axes.Axes):
+            The matplotlib axes to plot on. If None, a new figure will be
+            created.
+        instrument (str or list):
+            Which instruments' data to include in the periodogram. Default is
+            all instruments.
+        fap (bool or float):
+            Whether to show the false alarm probability. A value (not a
+            percentage) can be provided to display a given FAP. Default is True.
+        fap_method (str):
+            Method used to estimate the FAP, passed directly to
+            `astropy.timeseries.LombScargle`. Default is 'baluev'.
+        adjust_means (bool):
+            Whether to adjust (subtract) the weighted means of each instrument.
+            Default is `config.adjust_means_gls`.
+    """
 
     if not hasattr(self, quantity):
         if self.verbose:
@@ -698,13 +738,25 @@ def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
     else:
         fig = ax.figure
 
+    spp = kwargs.get('samples_per_peak', 5)
+
     gls = LombScargle(t, y, ye)
-    freq, power = gls.autopower(maximum_frequency=1.0)
-    ax.semilogx(1/freq, power, picker=picker)
+    freq, power = gls.autopower(maximum_frequency=1.0, samples_per_peak=spp)
+
+    ax.semilogx(1/freq, power, picker=picker, **kwargs)
 
     if fap:
-        ax.axhline(gls.false_alarm_level(0.01),
-                   color='k', alpha=0.2, zorder=-1)
+        fap_level = 0.01
+        if isinstance(fap, float):
+            fap_level = fap
+
+        fap = gls.false_alarm_level(fap_level, method=fap_method)
+
+        if fap > 0.05 and fap_method == 'baluev':
+            logger.warning('FAP is high (>5%), the analytical estimate may be underestimated. Using the bootstrap method instead.')
+            fap = gls.false_alarm_level(fap_level, method='bootstrap')
+
+        ax.axhline(fap, color='k', alpha=0.2, zorder=-1)
 
     ax.set(xlabel='Period [days]', ylabel='Normalized power', ylim=(0, None))
     ax.minorticks_on()

{arvi-0.1.27 → arvi-0.1.29}/arvi/timeseries.py

@@ -310,6 +310,10 @@ class RV:
             new_self._build_arrays()
             return new_self
 
+    def __iter__(self):
+        for inst in self.instruments:
+            yield getattr(self, inst)
+
 
     def reload(self):
         self._did_secular_acceleration = False
@@ -512,7 +516,8 @@ class RV:
         return s
 
     @classmethod
-    def from_rdb(cls, files, star=None, instrument=None, units='ms', **kwargs):
+    def from_rdb(cls, files, star=None, instrument=None, units='ms', 
+                 header_skip=2, **kwargs):
         """ Create an RV object from an rdb file or a list of rdb files
 
         Args:
@@ -524,6 +529,8 @@ class RV:
                 Name of the instrument(s). If None, try to infer it from file name
             units (str, optional):
                 Units of the radial velocities. Defaults to 'ms'.
+            header_skip (int, optional):
+                Number of lines to skip in the header. Defaults to 2.
 
         Examples:
             s = RV.from_rdb('star_HARPS.rdb')
@@ -566,14 +573,14 @@ class RV:
         s = cls(star, _child=True, **kwargs)
 
         def find_column(data, names):
-            has_col = np.array([name in data.dtype.fields for name in names])
+            has_col = np.array([name.casefold() in data.dtype.fields for name in names])
             if any(has_col):
                 col = np.where(has_col)[0][0]
                 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)
+            data = np.loadtxt(f, skiprows=header_skip, usecols=range(3), unpack=True)
             if data.ndim == 1:
                 data = data.reshape(-1, 1)
 
@@ -615,11 +622,13 @@ class RV:
 
             # try to find FWHM and uncertainty
             if (v := find_column(data, ['fwhm'])) is not False:  # walrus !!
-                _s.fwhm = v
+                _s.fwhm = v * factor
                 if (sv := find_column(data, ['sfwhm', 'fwhm_err', 'sig_fwhm'])) is not False:
-                    _s.fwhm_err = sv
+                    _s.fwhm_err = sv * factor
+                    logger.debug('found columns for FWHM and uncertainty') if verbose else None
                 else:
                     _s.fwhm_err = 2 * _s.svrad
+                    logger.debug('found column for FWHM') if verbose else None
             else:
                 _s.fwhm = np.full_like(time, np.nan)
                 _s.fwhm_err = np.full_like(time, np.nan)
@@ -633,6 +642,7 @@ class RV:
                 _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
+                    logger.debug('found columns for logRhk and uncertainty') if verbose else None
             else:
                 _s.rhk = np.full_like(time, np.nan)
                 _s.rhk_err = np.full_like(time, np.nan)
@@ -641,11 +651,11 @@ class RV:
             _quantities.append('rhk_err')
 
             # try to find BISPAN and uncertainty
-            if (v := find_column(data, ['bispan'])) is not False:
-                _s.bispan = v
+            if (v := find_column(data, ['bis', 'bispan'])) is not False:
+                _s.bispan = v * factor
                 _s.bispan_err = np.full_like(time, np.nan)
-                if (sv := find_column(data, ['sbispan'])) is not False:
-                    _s.bispan_err = sv
+                if (sv := find_column(data, ['sbispan', 'sig_bispan', 'bispan_err'])) is not False:
+                    _s.bispan_err = sv * factor
             else:
                 _s.bispan = np.full_like(time, np.nan)
                 _s.bispan_err = np.full_like(time, np.nan)
@@ -660,18 +670,57 @@ class RV:
                 _s.berv = np.full_like(time, np.nan)
             _quantities.append('berv')
 
-            # other quantities, but all NaNs
-            for q in ['caindex', 'ccf_asym', 'contrast', 'haindex', 'naindex', 'sindex']:
-                setattr(_s, q, np.full_like(time, np.nan))
-                setattr(_s, q + '_err', np.full_like(time, np.nan))
+            # other quantities
+            msg = ''
+
+            for q, possible in {
+                'caindex': ['caindex', 'ca', 'caII'],
+                'ccf_asym': ['ccf_asym'],
+                'contrast': ['contrast'],
+                'haindex': ['haindex', 'ha', 'halpha'],
+                'heindex': ['heindex', 'he', 'heII'],
+                'naindex': ['naindex', 'na'],
+                'sindex': ['sindex', 's_mw'],
+            }.items():
+                # try to find columns for each quantity
+                if (v := find_column(data, possible)) is not False:
+                    msg += f'{q}, '
+                    setattr(_s, q, v)
+                    # try to find uncertainty column for each quantity
+                    possible_errors = ['s' + p for p in possible] + ['sig_' + p for p in possible] + [p + '_err' for p in possible]
+                    if (sv := find_column(data, possible_errors)) is not False:
+                        setattr(_s, q + '_err', sv)
+                    else:
+                        setattr(_s, q + '_err', np.full_like(time, np.nan))
+                else:
+                    setattr(_s, q, np.full_like(time, np.nan))
+                    setattr(_s, q + '_err', np.full_like(time, np.nan))
                 _quantities.append(q)
                 _quantities.append(q + '_err')
+
+            if verbose and msg != '':
+                if msg.endswith(', '):
+                    msg = msg[:-2]
+                logger.debug('found columns for ' + msg)
+
+
+            # more values
             for q in ['texp', ]:
-                setattr(_s, q, np.full_like(time, np.nan))
+                if (v := find_column(data, q)) is not False:
+                    setattr(_s, q, v)
+                else:
+                    setattr(_s, q, np.full_like(time, np.nan))
                 _quantities.append(q)
+
+            # strings
             for q in ['ccf_mask', 'date_night', 'prog_id', 'raw_file', 'pub_reference']:
-                setattr(_s, q, np.full(time.size, ''))
+                if (v := find_column(data, q)) is not False:
+                    setattr(_s, q, v)
+                else:
+                    setattr(_s, q, np.full(time.size, ''))
                 _quantities.append(q)
+
+            # booleans
             for q in ['drs_qc', ]:
                 setattr(_s, q, np.full(time.size, True))
                 _quantities.append(q)

{arvi-0.1.27 → arvi-0.1.29/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: arvi
-Version: 0.1.27
+Version: 0.1.29
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT