arvi 0.1.22__tar.gz → 0.1.23__tar.gz

{arvi-0.1.22 → arvi-0.1.23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.22
+Version: 0.1.23
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.22 → arvi-0.1.23}/arvi/dace_wrapper.py

@@ -34,10 +34,10 @@ def get_dace_id(star):
 
 def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='HE', verbose=True):
     arrays = []
-    instruments = list(result.keys())
+    instruments = [str(i) for i in result.keys()]
 
     for inst in instruments:
-        pipelines = list(result[inst].keys())
+        pipelines = [str(p) for p in result[inst].keys()]
 
         # select ESPRESSO mode, which is defined at the level of the pipeline
         if 'ESPRESSO' in inst:
@@ -55,20 +55,23 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
                 pipelines = [pipelines[i]]
 
         if latest_pipeline:
+            if 'NIRPS' in inst and any(['LBL' in p for p in pipelines]):
+                # TODO: correctly load both CCF and LBL
+                pipelines = [pipelines[1]]
+            else:
+                pipelines = [pipelines[0]]
+
             if verbose and len(pipelines) > 1:
                 logger.info(f'selecting latest pipeline ({pipelines[0]}) for {inst}')
 
-            pipelines = [pipelines[0]]
-
         for pipe in pipelines:
-            modes = list(result[inst][pipe].keys())
+            modes = [m for m in result[inst][pipe].keys()]
 
-                
             # select NIRPS mode, which is defined at the level of the mode
-            if 'NIRPS' in inst:
+            if 'NIRPS' in inst and len(modes) > 1:
                 if NIRPS_mode in modes:
                     if verbose:
-                        logger.info(f'selecting mode {NIRPS_mode} for NIRPS')
+                        logger.info(f'selecting mode {NIRPS_mode} for NIRPS - {pipe}')
                     i = modes.index(NIRPS_mode)
                     modes = [modes[i]]
                 else:

{arvi-0.1.22 → arvi-0.1.23}/arvi/timeseries.py

@@ -18,7 +18,7 @@ from .extra_data import get_extra_data
 from .stats import wmean, wrms
 from .binning import bin_ccf_mask, binRV
 from .HZ import getHZ_period
-from .utils import strtobool, there_is_internet, timer, chdir
+from .utils import sanitize_path, strtobool, there_is_internet, timer, chdir
 from .utils import lazy_import
 
 units = lazy_import('astropy.units')
@@ -240,7 +240,8 @@ class RV:
                 else:
                     path = None
                 try:
-                    self.__add__(get_extra_data(self.star, instrument=self.instrument, path=path),
+                    self.__add__(get_extra_data(self.star, instrument=self.instrument,
+                                                path=path, verbose=self.verbose),
                                  inplace=True)
 
                 except FileNotFoundError:
@@ -263,7 +264,9 @@ class RV:
             if self.do_adjust_means:
                 self.adjust_means()
         
-        self._download_directory = f'{self.star.replace(" ", "")}_downloads'
+        _star_no_space = self.star.replace(' ', '')
+        _directory = sanitize_path(_star_no_space)
+        self._download_directory = f'{_directory}_downloads'
 
     def __add__(self, other, inplace=False):
         # if not isinstance(other, self.__class__):
@@ -1243,6 +1246,9 @@ class RV:
         mas_yr = units.milliarcsecond / units.year
         mas = units.milliarcsecond
 
+        # store the source of coordinates and parallax, either Gaia or Simbad
+        using = ''
+
         try:
             if force_simbad:
                 raise AttributeError
@@ -1255,8 +1261,7 @@ class RV:
                     logger.error('negative Gaia parallax, falling back to Simbad')
                 raise AttributeError
 
-            if self.verbose:
-                logger.info('using Gaia information to remove secular acceleration')
+            using = 'Gaia'
 
             if epoch is None:
                 # Gaia DR3 epoch (astropy.time.Time('J2016.0', format='jyear_str').jd)
@@ -1284,8 +1289,7 @@ class RV:
                     logger.error('no parallax from simbad, cannot remove secular acceleration')
                 return
 
-            if self.verbose:
-                logger.info('using Simbad information to remove secular acceleration')
+            using = 'Simbad'
 
             if epoch is None:
                 epoch = 55500
@@ -1303,14 +1307,14 @@ class RV:
 
         sa = sa.value
 
-        if self.verbose:
-            logger.info('removing secular acceleration from RVs')
-
         if self.units == 'km/s':
             sa /= 1000
 
+        actually_removed_sa = False
+
         if self._child:
             self.vrad = self.vrad - sa * (self.time - epoch) / 365.25
+            actually_removed_sa = True
         else:
             for inst in self.instruments:
                 s = getattr(self, inst)
@@ -1320,9 +1324,7 @@ class RV:
                 if np.all(s.pub_reference != ''):
                     continue
 
-                if 'HIRES' in inst:  # never remove it from HIRES...
-                    continue
-                if 'NIRPS' in inst:  # never remove it from NIRPS...
+                if 'HIRES' in inst or 'HAMILTON' in inst:
                     continue
 
                 if hasattr(s, '_did_secular_acceleration') and s._did_secular_acceleration:
@@ -1330,8 +1332,14 @@ class RV:
 
                 s.vrad = s.vrad - sa * (s.time - epoch) / 365.25
 
+                actually_removed_sa = True
+
             self._build_arrays()
 
+        if actually_removed_sa and self.verbose:
+            logger.info(f'using {using} information to remove secular acceleration')
+            logger.info('removing secular acceleration from RVs')
+
         self._did_secular_acceleration = True
         self._did_secular_acceleration_epoch = epoch
         self._did_secular_acceleration_simbad = force_simbad
@@ -1710,11 +1718,11 @@ class RV:
         for inst in self.instruments:
             s = getattr(self, inst)
             if s.mask.any():
-                if np.abs(s.mvrad.mean()) < s.mvrad.ptp():
+                if np.abs(s.mvrad.mean()) < np.ptp(s.mvrad):
                     s.vrad += self.simbad.rvz_radvel * 1e3
                     changed = True
             else:  # all observations are masked, use non-masked arrays
-                if np.abs(s.vrad.mean()) < s.vrad.ptp():
+                if np.abs(s.vrad.mean()) < np.ptp(s.vrad):
                     s.vrad += self.simbad.rvz_radvel * 1e3
                     changed = True
         if changed:
@@ -1991,15 +1999,14 @@ def fit_sine(t, y, yerr=None, period='gls', fix_period=False):
     if fix_period:
         def sine(t, p):
             return p[0] * np.sin(2 * np.pi * t / period + p[1]) + p[2]
-        f = lambda p, t, y, ye: (sine(t, p) - y) / ye
-        p0 = [y.ptp(), 0.0, 0.0]
+        p0 = [np.ptp(y), 0.0, 0.0]
     else:
         def sine(t, p):
             return p[0] * np.sin(2 * np.pi * t / p[1] + p[2]) + p[3]
-        f = lambda p, t, y, ye: (sine(t, p) - y) / ye
-        p0 = [y.ptp(), period, 0.0, 0.0]
+        p0 = [np.ptp(y), period, 0.0, 0.0]
 
-    xbest, _ = leastsq(f, p0, args=(t, y, yerr))
+    xbest, _ = leastsq(lambda p, t, y, ye: (sine(t, p) - y) / ye, p0,
+                       args=(t, y, yerr))
     return xbest, partial(sine, p=xbest)
 
 

{arvi-0.1.22 → arvi-0.1.23}/arvi/utils.py

@@ -90,6 +90,7 @@ def timer(name=None):
 def sanitize_path(path):
     if os.name == 'nt':  # on Windows, be careful with ':' in filename
         path = path.replace(':', '_')
+    path = path.replace('*', '_')
     return path
 
 def pretty_print_table(rows, line_between_rows=True, logger=None):

{arvi-0.1.22 → arvi-0.1.23}/arvi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.22
+Version: 0.1.23
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT