arvi 0.1.16__py3-none-any.whl → 0.1.19__py3-none-any.whl

arvi/plots.py

@@ -431,12 +431,16 @@ def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
             p = p.replace('_', '.')
             label = f'{i}-{p}'
 
-        y = getattr(s, quantity)
+        y = getattr(s, quantity).copy()
         try:
-            ye = getattr(s, quantity + '_err')
+            ye = getattr(s, quantity + '_err').copy()
         except AttributeError:
             ye = np.zeros_like(y)
 
+        if (nans := np.isnan(y)).any():
+            if self.verbose:
+                logger.warning(f'{nans.sum()} NaN values for {inst}')
+            ye[nans] = np.nan
 
         if np.isnan(y).all() or np.isnan(ye).all():
             lines, *_ = ax.errorbar([], [], [],
@@ -464,7 +468,7 @@ def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
     ax.minorticks_on()
 
     ylabel = {
-        quantity: quantity,
+        quantity.lower(): quantity,
         'fwhm': f'FWHM [{self.units}]',
         'bispan': f'BIS [{self.units}]',
         'rhk': r"$\log$ R'$_{HK}$",
@@ -485,6 +489,7 @@ 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_contrast = partialmethod(plot_quantity, quantity='contrast')
 plot_rhk = partialmethod(plot_quantity, quantity='rhk')
 plot_berv = partialmethod(plot_quantity, quantity='berv')
 
@@ -518,7 +523,7 @@ def gls(self, ax=None, label=None, fap=True, instrument=None, adjust_means=confi
 
     if not self._did_adjust_means and not adjust_means:
         logger.warning('gls() called before adjusting instrument means, '
-                       'consider using `adjust_means` argument')
+                       'consider using the `adjust_means` argument')
 
     if instrument is not None:
         strict = kwargs.pop('strict', False)
@@ -536,11 +541,11 @@ def gls(self, ax=None, label=None, fap=True, instrument=None, adjust_means=confi
         if adjust_means and not self._child:
             if self.verbose:
                 logger.info('adjusting instrument means before gls')
-            means = np.empty_like(y)
+            means = np.zeros_like(y)
             for i in instrument:
                 mask = self.instrument_array[instrument_mask & self.mask] == i
                 if len(y[mask]) > 0:
-                    means += wmean(y[mask], e[mask]) * mask
+                    means = means + wmean(y[mask], e[mask]) * mask
             y = y - means
 
     else:
@@ -551,11 +556,11 @@ def gls(self, ax=None, label=None, fap=True, instrument=None, adjust_means=confi
         if adjust_means and not self._child:
             if self.verbose:
                 logger.info('adjusting instrument means before gls')
-            means = np.empty_like(y)
+            means = np.zeros_like(y)
             for i in self.instruments:
                 mask = self.instrument_array[self.mask] == i
                 if len(y[mask]) > 0:
-                    means += wmean(y[mask], e[mask]) * mask
+                    means = means + wmean(y[mask], e[mask]) * mask
             y = y - means
 
     self._gls = gls = LombScargle(t, y, e)
@@ -623,31 +628,70 @@ def gls(self, ax=None, label=None, fap=True, instrument=None, adjust_means=confi
         return fig, ax
 
 
-@plot_fast
-def gls_quantity(self, quantity, ax=None, fap=True, picker=True):
+# @plot_fast
+def gls_quantity(self, quantity, ax=None, fap=True, instrument=None,
+                 adjust_means=True, picker=True, **kwargs):
+
     if not hasattr(self, quantity):
-        logger.error(f"cannot find '{quantity}' attribute")
+        if self.verbose:
+            logger.error(f"cannot find '{quantity}' attribute")
         return
 
-    if ax is None:
-        fig, ax = plt.subplots(1, 1, constrained_layout=True)
-    else:
-        fig = ax.figure
+    if self.N == 0:
+        if self.verbose:
+            logger.error('no data to compute gls')
+        return
+
+    if not self._did_adjust_means and not adjust_means:
+        logger.warning('gls() called before adjusting instrument means, '
+                       'consider using the `adjust_means` argument')
+
+    strict = kwargs.pop('strict', False)
+    instrument = self._check_instrument(instrument, strict=strict, log=True)
+    if instrument is None:
+        return
+
+    instrument_mask = np.isin(self.instrument_array, instrument)
+    final_mask = instrument_mask & self.mask
 
-    t = self.mtime
-    y = getattr(self, quantity)[self.mask]
+    t = self.time[final_mask].copy()
+    y = getattr(self, quantity)[final_mask].copy()
     try:
-        ye = getattr(self, quantity + '_err')[self.mask]
+        ye = getattr(self, quantity + '_err')[final_mask].copy()
     except AttributeError:
         ye = None
 
-    if np.isnan(y).any():
+    if self.verbose:
+        logger.info(f'calculating periodogram for instrument {instrument}')
+
+    nan_mask = np.isnan(y)
+    if nan_mask.any():
         if self.verbose:
             logger.warning(f'{quantity} contains NaNs, ignoring them')
-        m = np.isnan(y)
-        t = t[~m]
-        y = y[~m]
-        ye = ye[~m]
+
+    if adjust_means and not self._child:
+        if self.verbose:
+            logger.info('adjusting instrument means before gls')
+        means = np.zeros_like(y)
+        for i in instrument:
+            mask = (self.instrument_array[final_mask] == i) & ~nan_mask
+            if len(y[mask]) > 0:
+                # print(wmean(y[mask], ye[mask]))
+                means += wmean(y[mask], ye[mask]) * mask
+        y = y - means
+
+    t = t[~nan_mask]
+    y = y[~nan_mask]
+    ye = ye[~nan_mask]
+
+    if len(y) == 0:
+        logger.error('no data left to compute gls after removing NaNs')
+        return
+
+    if ax is None:
+        fig, ax = plt.subplots(1, 1, constrained_layout=True)
+    else:
+        fig = ax.figure
 
     gls = LombScargle(t, y, ye)
     freq, power = gls.autopower(maximum_frequency=1.0)

arvi/reports.py

@@ -27,6 +27,29 @@ def sine_picker(event, self, fig, ax, ax1):
     fig.canvas.draw_idle()
 
 
+def summary(self, add_ccf_mask=True, add_prog_id=False):
+    from .utils import pretty_print_table
+    rows = []
+    rows.append([self.star] + [''] * len(self.instruments))
+    rows.append([''] + self.instruments)
+    rows.append(['N'] + list(self.NN.values()))
+
+    if add_ccf_mask:
+        row = ['CCF mask']
+        for inst in self.instruments:
+            row.append(', '.join(np.unique(getattr(self, inst).ccf_mask)))
+        rows.append(row)
+
+    if add_prog_id:
+        row = ['prog ID']
+        for inst in self.instruments:
+            p = ', '.join(np.unique(getattr(self, inst).prog_id))
+            row.append(p)
+        rows.append(row)
+
+    pretty_print_table(rows)
+
+
 def report(self, save=None):
     import matplotlib.pyplot as plt
     import matplotlib.gridspec as gridspec

arvi/simbad_wrapper.py

@@ -3,6 +3,8 @@ import requests
 
 import pysweetcat
 
+from .translations import translate
+
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
 
@@ -98,7 +100,7 @@ class simbad:
         """
         from astropy.coordinates import SkyCoord
 
-        self.star = star
+        self.star = translate(star, ngc=True, ic=True)
 
         if 'kobe' in self.star.lower():
             fname = os.path.join(DATA_PATH, 'KOBE-translate.csv')
@@ -108,19 +110,22 @@ class simbad:
                     for line in f.readlines():
                         kobe_id, catname = line.strip().split(',')
                         kobe_translate[kobe_id] = catname
-                self.star = star = kobe_translate[self.star]
+                try:
+                    self.star = star = kobe_translate[self.star]
+                except KeyError:
+                    raise ValueError(f'simbad query for {star} failed')
 
         # oid = run_query(query=OID_QUERY.format(star=star))
         # self.oid = str(oid.split()[-1])
 
         try:
-            table1 = run_query(query=QUERY.format(star=star))
+            table1 = run_query(query=QUERY.format(star=self.star))
             cols, values = parse_table(table1)
 
-            table2 = run_query(query=BV_QUERY.format(star=star))
+            table2 = run_query(query=BV_QUERY.format(star=self.star))
             cols, values = parse_table(table2, cols, values)
 
-            table3 = run_query(query=IDS_QUERY.format(star=star))
+            table3 = run_query(query=IDS_QUERY.format(star=self.star))
             line = table3.splitlines()[2]
             self.ids = line.replace('"', '').replace('    ', ' ').replace('   ', ' ').replace('  ', ' ').split('|')
         except IndexError:

arvi/stellar.py

@@ -1,22 +1,32 @@
+
 import numpy as np
 
 class prot_age_result:
-    prot_n84: float
-    prot_n84_err: float
-    prot_m08: float
-    prot_m08_err: float
-    age_m08: float
-    age_m08_err: float
+    prot_n84 = None #: float | np.ndarray
+    prot_n84_err = None #: float | np.ndarray
+    prot_m08 = None #: float | np.ndarray
+    prot_m08_err = None #: float | np.ndarray
+    age_m08 = None #: float | np.ndarray
+    age_m08_err = None #: float | np.ndarray
     def __init__(self):
         pass
     def __repr__(self):
-        s = f'{self.prot_n84=:.2f} ± {self.prot_n84_err:.2f}, '
-        s += f'{self.prot_m08=:.2f} ± {self.prot_m08_err:.2f}, '
-        s += f'{self.age_m08=:.2f} ± {self.age_m08_err:.2f}'
+        if isinstance(self.prot_n84, np.ndarray):
+            s = f'{self.prot_n84.mean()=:.2f} ± {self.prot_n84_err.mean():.2f}, '
+        else:
+            s = f'{self.prot_n84=:.2f} ± {self.prot_n84_err:.2f}, '
+        if isinstance(self.prot_m08, np.ndarray):
+            s += f'{self.prot_m08.mean()=:.2f} ± {self.prot_m08_err.mean():.2f}, '
+        else:
+            s += f'{self.prot_m08=:.2f} ± {self.prot_m08_err:.2f}, '
+        if isinstance(self.age_m08, np.ndarray):
+            s += f'{self.age_m08.mean()=:.2f} ± {self.age_m08_err.mean():.2f}'
+        else:
+            s += f'{self.age_m08=:.2f} ± {self.age_m08_err:.2f}'
         return s.replace('self.', '')
 
 
-def calc_prot_age(self, bv=None):
+def calc_prot_age(self, bv=None, array=False):
     """
     Calculate rotation period and age from logR'HK activity level, based on the
     empirical relations of Noyes et al. (1984) and Mamajek & Hillenbrand (2008).
@@ -46,7 +56,12 @@ def calc_prot_age(self, bv=None):
     Range of logR'HK-Prot relation: -5.5 < logR'HK < -4.3
     Range of Mamajek & Hillenbrand (2008) relation for ages: 0.5 < B-V < 0.9
     """
-    log_rhk = np.nanmean(self.rhk[self.mask])
+
+    if array:
+        log_rhk = self.rhk[~np.isnan(self.rhk)]
+    else:
+        log_rhk = np.nanmean(self.rhk[self.mask])
+
     if bv is None:
         bv = self.simbad.B - self.simbad.V
 
@@ -60,9 +75,13 @@ def calc_prot_age(self, bv=None):
         prot_n84 = 0.324 - 0.400*(5 + log_rhk) - 0.283*(5 + log_rhk)**2 - 1.325*(5 + log_rhk)**3 + tau
         prot_n84 = 10**prot_n84
         prot_n84_err = np.log(10)*0.08*prot_n84
+        if array:
+            prot_n84_err = np.full_like(log_rhk, prot_n84_err)
 
         prot_m08 = (0.808 - 2.966*(log_rhk + 4.52))*10**tau
         prot_m08_err = 4.4*bv*1.7 - 1.7
+        if array:
+            prot_m08_err = np.full_like(log_rhk, prot_m08_err)
     else:
         prot_n84 = np.nan
         prot_n84_err = np.nan