arvi 0.1.12__py3-none-any.whl → 0.1.13__py3-none-any.whl

arvi/timeseries.py

@@ -11,16 +11,16 @@ import numpy as np
 from astropy import units
 
 from .setup_logger import logger
-from .config import return_self, check_internet
+from .config import return_self, check_internet, debug
 from .translations import translate
-from .dace_wrapper import do_download_filetype, get_observations, get_arrays
+from .dace_wrapper import do_download_filetype, do_symlink_filetype, get_observations, get_arrays
 from .simbad_wrapper import simbad
 from .gaia_wrapper import gaia
 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
+from .utils import strtobool, there_is_internet, timer
 
 
 @dataclass
@@ -102,8 +102,10 @@ class RV:
             if self.verbose:
                 logger.info(f'querying DACE for {self.__star__}...')
             try:
-                self.dace_result = get_observations(self.__star__, self.instrument,
-                                                    verbose=self.verbose)
+                with timer():
+                    self.dace_result = get_observations(self.__star__, self.instrument,
+                                                        main_id=self.simbad.main_id,
+                                                        verbose=self.verbose)
             except ValueError as e:
                 # querying DACE failed, should we raise an error?
                 if self._raise_on_error:
@@ -257,6 +259,10 @@ class RV:
         table += ' | '.join(map(str, self.NN.values())) + '\n'
         return table
 
+    @property
+    def point(self):
+        return [(t.round(4), v.round(4), sv.round(4)) for t, v, sv in zip(self.time, self.vrad, self.svrad)]
+
     @property
     def mtime(self) -> np.ndarray:
         """ Masked array of times """
@@ -566,7 +572,7 @@ class RV:
         return s
 
 
-    def _check_instrument(self, instrument, strict=False):# -> list | None:
+    def _check_instrument(self, instrument, strict=False, log=False):# -> list | None:
         """
         Check if there are observations from `instrument`.
 
@@ -599,6 +605,11 @@ class RV:
                 if any([instrument in inst for inst in self.instruments]):
                     return [inst for inst in self.instruments if instrument in inst]
 
+        if log:
+            logger.error(f"No data from instrument '{instrument}'")
+            logger.info(f'available: {self.instruments}')
+            return
+
 
     def _build_arrays(self):
         """ build all concatenated arrays of `self` from each of the `.inst`s """
@@ -643,7 +654,8 @@ class RV:
                 setattr(self, q, arr)
 
 
-    def download_ccf(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_ccf(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download CCFs from DACE
 
         Args:
@@ -671,9 +683,15 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('CCF', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                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, verbose=self.verbose, **kwargs)
 
-    def download_s1d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_s1d(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download S1Ds from DACE
 
         Args:
@@ -701,9 +719,15 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('S1D', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                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, verbose=self.verbose, **kwargs)
 
-    def download_s2d(self, instrument=None, index=None, limit=None, directory=None, **kwargs):
+    def download_s2d(self, instrument=None, index=None, limit=None,
+                     directory=None, symlink=False, **kwargs):
         """ Download S2Ds from DACE
 
         Args:
@@ -731,11 +755,16 @@ class RV:
         # remove empty strings
         files = list(filter(None, files))
 
-        do_download_filetype('S2D', files[:limit], directory, **kwargs)
+        if symlink:
+            if 'top_level' not in kwargs:
+                logger.warning('may need to provide `top_level` in kwargs to find file')
+            do_symlink_filetype('S2D', files[:limit], directory, **kwargs)
+        else:
+            do_download_filetype('S2D', files[:limit], directory, verbose=self.verbose, **kwargs)
 
 
-    from .plots import plot, plot_fwhm, plot_bis, plot_rhk, plot_quantity
-    from .plots import gls, gls_fwhm, gls_bis, gls_rhk
+    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 .reports import report
 
     from .instrument_specific import known_issues
@@ -1023,8 +1052,37 @@ class RV:
             self._build_arrays()
 
         self._did_secular_acceleration = True
+        self._did_secular_acceleration_epoch = epoch
+        self._did_secular_acceleration_simbad = force_simbad
+
         if return_self:
             return self
+    
+    def _undo_secular_acceleration(self):
+        if self._did_secular_acceleration:
+            _old_verbose = self.verbose
+            self.verbose = False
+            sa = self.secular_acceleration(just_compute=True,
+                                           force_simbad=self._did_secular_acceleration_simbad)
+            self.verbose = _old_verbose
+            sa = sa.value
+
+            if self._child:
+                self.vrad = self.vrad + sa * (self.time - self._did_secular_acceleration_epoch) / 365.25
+            else:
+                for inst in self.instruments:
+                    if 'HIRES' in inst:  # never remove it from HIRES...
+                        continue
+                    if 'NIRPS' in inst:  # never remove it from NIRPS...
+                        continue
+
+                    s = getattr(self, inst)
+
+                    s.vrad = s.vrad + sa * (s.time - self._did_secular_acceleration_epoch) / 365.25
+
+                self._build_arrays()
+
+            self._did_secular_acceleration = False
 
     def sigmaclip(self, sigma=5, instrument=None, strict=True):
         """ Sigma-clip RVs (per instrument!) """
@@ -1220,6 +1278,11 @@ class RV:
         for inst in self.instruments:
             s = getattr(self, inst)
 
+            if s.mtime.size == 0:
+                if self.verbose:
+                    logger.info(f'all observations of {inst} are masked')
+                continue
+
             if s.N == 1:
                 if self.verbose:
                     msg = (f'only 1 observation for {inst}, '
@@ -1231,28 +1294,37 @@ class RV:
 
             s.rv_mean = wmean(s.mvrad, s.msvrad)
             s.vrad -= s.rv_mean
+
             if self.verbose:
                 logger.info(f'subtracted weighted average from {inst:10s}: ({s.rv_mean:.3f} {self.units})')
+
             if just_rv:
                 continue
-            # log_msg = 'same for '
+
             for i, other in enumerate(others):
                 y, ye = getattr(s, other), getattr(s, other + '_err')
                 m = wmean(y[s.mask], ye[s.mask])
                 setattr(s, f'{other}_mean', m)
                 setattr(s, other, getattr(s, other) - m)
-                # log_msg += other
-                # if i < len(others) - 1:
-                #     log_msg += ', '
-
-            # if self.verbose:
-            #     logger.info(log_msg)
 
         self._build_arrays()
         self._did_adjust_means = True
         if return_self:
             return self
 
+    def add_to_vrad(self, values):
+        """ Add an array of values to the RVs of all instruments """
+        if values.size != self.vrad.size:
+            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)
+            mask = self.instrument_array == inst
+            s.vrad += values[mask]
+
+        self._build_arrays()
+
+
     def put_at_systemic_velocity(self):
         """
         For instruments in which mean(RV) < ptp(RV), "move" RVs to the systemic
@@ -1492,22 +1564,50 @@ class RV:
         return self._planets
 
 
-def fit_sine(t, y, yerr, period='gls', fix_period=False):
+def fit_sine(t, y, yerr=None, period='gls', fix_period=False):
+    """ Fit a sine curve of the form y = A * sin(2π * t / P + φ) + c
+
+    Args:
+        t (ndarray):
+            Time array
+        y (ndarray):
+            Array of observed values
+        yerr (ndarray, optional):
+            Array of uncertainties. Defaults to None.
+        period (str or float, optional):
+            Initial guess for period or 'gls' to get it from Lomb-Scargle
+            periodogram. Defaults to 'gls'.
+        fix_period (bool, optional):
+            Whether to fix the period. Defaults to False.
+
+    Returns:
+        p (ndarray):
+            Best-fit parameters [A, P, φ, c] or [A, φ, c]
+        f (callable):
+            Function that returns the best-fit sine curve for input times
+    """
     from scipy.optimize import leastsq
     if period == 'gls':
         from astropy.timeseries import LombScargle
         gls = LombScargle(t, y, yerr)
         freq, power = gls.autopower()
         period = 1 / freq[power.argmax()]
-
-    if fix_period and period is None:
-        logger.error('period is fixed but no value provided')
-        return
-
-    def sine(t, p):
-        return p[0] * np.sin(2 * np.pi * t / p[1] + p[2]) + p[3]
-
-    p0 = [y.ptp(), period, 0.0, 0.0]
-    xbest, _ = leastsq(lambda p, t, y, ye: (sine(t, p) - y) / ye,
-                       p0, args=(t, y, yerr))
+    else:
+        period = float(period)
+
+    if yerr is None:
+        yerr = np.ones_like(y)
+
+    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]
+    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]
+
+    xbest, _ = leastsq(f, p0, args=(t, y, yerr))
     return xbest, partial(sine, p=xbest)

arvi/utils.py

@@ -1,4 +1,5 @@
 import os
+import time
 from contextlib import contextmanager
 try:
     from unittest.mock import patch
@@ -19,6 +20,9 @@ except ImportError:
     tqdm = lambda x, *args, **kwargs: x
     trange = lambda *args, **kwargs: range(*args, **kwargs)
 
+from .setup_logger import logger
+from . import config
+
 
 def create_directory(directory):
     """ Create a directory if it does not exist """
@@ -61,6 +65,23 @@ def all_logging_disabled():
     finally:
         logging.disable(previous_level)
 
+
+@contextmanager
+def timer():
+    """ A simple context manager to time a block of code """
+    if not config.debug:
+        yield
+        return
+
+    logger.debug(f'starting timer')
+    start = time.time()
+    try:
+        yield
+    finally:
+        end = time.time()
+        logger.debug(f'elapsed time: {end - start:.2f} seconds')
+
+
 def strtobool(val):
     """Convert a string representation of truth to true (1) or false (0).
 

{arvi-0.1.12.dist-info → arvi-0.1.13.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.12
+Version: 0.1.13
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.13.dist-info/RECORD

@@ -0,0 +1,32 @@
+arvi/HZ.py,sha256=u7rguhlILRBW-LOczlY3dkIB4LM8p8W7Xfg4FnNaYG0,2850
+arvi/__init__.py,sha256=cECMjLbPiolmft2lsnNoszU6_1a-dKOVY8cb2D1CBfg,366
+arvi/ariadne_wrapper.py,sha256=jv8Wl35LfHl1UH1EklbvxHcQHqaEDhRGNogSYjFt7Y4,2141
+arvi/binning.py,sha256=jJ_resqSvfI-2BT0cnGPFckTIei_k2Mk95oZyE5b5zQ,15250
+arvi/config.py,sha256=wyj6FTxN7QOZj8LaHAe_ZdPKVfrNfobNNOHRNLH-S7Q,339
+arvi/dace_wrapper.py,sha256=VjC1YjZ7URkHkgRO7rUKjkxBtdMMjoEqcqTtZQ8M7NY,17034
+arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
+arvi/gaia_wrapper.py,sha256=YxqqlWkLAKBY7AGHfDpNbkOLYWK0lt0L5GZenn0FfxM,3555
+arvi/instrument_specific.py,sha256=fhkvR5jJzpJH7XbT8Fbzkaz6tGeoFYugkJCIAJgSR7o,4746
+arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
+arvi/nasaexo_wrapper.py,sha256=mWt7eHgSZe4MBKCmUvMPTyUPGuiwGTqKugNBvmjOg9s,7306
+arvi/plots.py,sha256=2W1IwUeMdNq5--l6nQXn3EFft0UQgEyPyudRxTCRM40,25566
+arvi/programs.py,sha256=WpFE2cXYG-4ax2xmih0fFhvQbcVhnOEofVcwjePNmKQ,4505
+arvi/reports.py,sha256=yrdajC-zz5_kH1Ucc6cU70DK-5dpG0Xyeru-EITKpNo,3355
+arvi/setup_logger.py,sha256=pBzaRTn0hntozjbaRVx0JIbWGuENkvYUApa6uB-FsRo,279
+arvi/simbad_wrapper.py,sha256=fwO0NbMvxAW3RyC58FPkLjXqLs9OkRyK0sYcb0ZVBQA,5571
+arvi/spectra.py,sha256=pTAWSW4vk96DWRQ-6l5mNJHUhiAyaPR-QDjZdOT6Ak0,7489
+arvi/stats.py,sha256=MQiyLvdiAFxIC29uajTy8kuxD-b2Y6mraL4AfWkRJkM,2576
+arvi/timeseries.py,sha256=PCQntiNK8MnlgKeyGOTd4BrQXm8NSjZRtGfLa4hfaE0,58257
+arvi/translations.py,sha256=AljjMsHRqzfcirdeavHsyVJFLvwKrM1wDLMv2RApG58,446
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+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
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+arvi-0.1.13.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.1.13.dist-info/METADATA,sha256=9wDBsoyGzFt-Eo186zVKLVJT_VdUlr_2C2uzrqQ5Fxs,1306
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+arvi-0.1.13.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.1.13.dist-info/RECORD,,

{arvi-0.1.12.dist-info → arvi-0.1.13.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (70.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

arvi-0.1.12.dist-info/RECORD

@@ -1,31 +0,0 @@
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-arvi/ariadne_wrapper.py,sha256=jv8Wl35LfHl1UH1EklbvxHcQHqaEDhRGNogSYjFt7Y4,2141
-arvi/binning.py,sha256=G1nZvH2ev02quDPZCReygLkH7tX6B3hFAOoOYTfhLec,15249
-arvi/config.py,sha256=7ZoKzTwhIrlueYV1OF3q_iirAdZC0WheFUmXhl9wR4s,232
-arvi/dace_wrapper.py,sha256=CSq21VDt5n_Ln_A6jvxLVwo2TS25C_M00MfvH38uA8I,10621
-arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
-arvi/gaia_wrapper.py,sha256=dv-uKWIsHbW-CPI14Fn1xIngsZrV7YBROVamgH0SULc,3418
-arvi/instrument_specific.py,sha256=gDNu6xM0nL3AItAxipTdg3dIGaGGi7tNWE5nnad5MxM,2873
-arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
-arvi/nasaexo_wrapper.py,sha256=xrdF4KKXmlZAqu4IQtdcqfOeUXJXoui5M-eZpnVXNlk,7311
-arvi/plots.py,sha256=J1FR-7NgWL0zdjtD0Sumj6ZHLXSRC_EtnpXkTguxQ-s,17549
-arvi/programs.py,sha256=WpFE2cXYG-4ax2xmih0fFhvQbcVhnOEofVcwjePNmKQ,4505
-arvi/reports.py,sha256=yrdajC-zz5_kH1Ucc6cU70DK-5dpG0Xyeru-EITKpNo,3355
-arvi/setup_logger.py,sha256=pBzaRTn0hntozjbaRVx0JIbWGuENkvYUApa6uB-FsRo,279
-arvi/simbad_wrapper.py,sha256=7sqaVHDKtqLDxhcTzoa0EUcOAPGLEtoqkZz_XQS9eKw,5504
-arvi/stats.py,sha256=MQiyLvdiAFxIC29uajTy8kuxD-b2Y6mraL4AfWkRJkM,2576
-arvi/timeseries.py,sha256=LjMiht2LVi17s40aBTrNznANKpKfBxQ7b8uoi_vdZ8A,54371
-arvi/translations.py,sha256=AljjMsHRqzfcirdeavHsyVJFLvwKrM1wDLMv2RApG58,446
-arvi/utils.py,sha256=ay3GouZYqn66zF43KgSs8Ngsfb4YInKZEmk70YqVDoA,3676
-arvi/data/info.svg,sha256=0IMI6W-eFoTD8acnury79WJJakpBwLa4qKS4JWpsXiI,489
-arvi/data/obs_affected_ADC_issues.dat,sha256=pbwzvRBjS8KsLrKi1Cdgfihvo3hK3FUN8Csdysw-vAw,10653
-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-0.1.12.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.1.12.dist-info/METADATA,sha256=ZYHmuqlbt45XyTKJO4_Jzwi4rM2-K_t0ty6dvnNJOBc,1306
-arvi-0.1.12.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-arvi-0.1.12.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.1.12.dist-info/RECORD,,