arvi 0.1.13__py3-none-any.whl → 0.1.15__py3-none-any.whl

arvi/timeseries.py

@@ -11,7 +11,7 @@ import numpy as np
 from astropy import units
 
 from .setup_logger import logger
-from .config import return_self, check_internet, debug
+from . import config
 from .translations import translate
 from .dace_wrapper import do_download_filetype, do_symlink_filetype, get_observations, get_arrays
 from .simbad_wrapper import simbad
@@ -23,6 +23,9 @@ from .HZ import getHZ_period
 from .utils import strtobool, there_is_internet, timer
 
 
+class ExtraFields:
+    pass
+
 @dataclass
 class RV:
     """
@@ -71,7 +74,7 @@ class RV:
         self.__star__ = translate(self.star)
 
         if not self._child:
-            if check_internet and not there_is_internet():
+            if config.check_internet and not there_is_internet():
                 raise ConnectionError('There is no internet connection?')
 
             # complicated way to query Simbad with self.__star__ or, if that
@@ -103,9 +106,9 @@ class RV:
                 logger.info(f'querying DACE for {self.__star__}...')
             try:
                 with timer():
+                    mid = self.simbad.main_id if hasattr(self, 'simbad') else None
                     self.dace_result = get_observations(self.__star__, self.instrument,
-                                                        main_id=self.simbad.main_id,
-                                                        verbose=self.verbose)
+                                                        main_id=mid, verbose=self.verbose)
             except ValueError as e:
                 # querying DACE failed, should we raise an error?
                 if self._raise_on_error:
@@ -218,6 +221,7 @@ class RV:
         self._did_secular_acceleration = False
         self._did_sigma_clip = False
         self._did_adjust_means = False
+        self._did_correct_berv = False
         self.__post_init__()
 
     def snapshot(self):
@@ -382,6 +386,7 @@ class RV:
         s.mask = kwargs.get('mask', np.full_like(s.time, True, dtype=bool))
 
         s.instruments = [inst]
+        s._quantities = np.array([])
 
         return s
 
@@ -443,6 +448,13 @@ 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])
+            if any(has_col):
+                col = np.where(has_col)[0][0]
+                return 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)
             _s = cls(star, _child=True, **kwargs)
@@ -471,10 +483,11 @@ class RV:
             else:
                 data = np.array([], dtype=np.dtype([]))
 
-            if 'fwhm' in data.dtype.fields:
-                _s.fwhm = data['fwhm']
-                if 'sfwhm' in data.dtype.fields:
-                    _s.fwhm_err = data['sfwhm']
+            # try to find FWHM and uncertainty
+            if (v := find_column(data, ['fwhm'])) is not False:  # walrus !!
+                _s.fwhm = v
+                if (sv := find_column(data, ['sfwhm', 'fwhm_err', 'sig_fwhm'])) is not False:
+                    _s.fwhm_err = sv
                 else:
                     _s.fwhm_err = 2 * _s.svrad
             else:
@@ -484,12 +497,11 @@ class RV:
             _quantities.append('fwhm')
             _quantities.append('fwhm_err')
 
-            if 'rhk' in data.dtype.fields:
-                _s.rhk = data['rhk']
+            if (v := find_column(data, ['rhk'])) is not False:
+                _s.rhk = v
                 _s.rhk_err = np.full_like(time, np.nan)
-                for possible_name in ['srhk', 'rhk_err']:
-                    if possible_name in data.dtype.fields:
-                        _s.rhk_err = data[possible_name]
+                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_err = np.full_like(time, np.nan)
@@ -516,6 +528,12 @@ class RV:
                 setattr(_s, q, np.full(time.size, True))
                 _quantities.append(q)
 
+            _s.extra_fields = ExtraFields()
+            for field in data.dtype.names:
+                if field not in _quantities:
+                    setattr(_s.extra_fields, field, data[field])
+                    # _quantities.append(field)
+
             #! end hack
 
             _s.mask = np.ones_like(time, dtype=bool)
@@ -543,31 +561,75 @@ class RV:
             logger.error('iCCF is not installed. Please install it with `pip install iCCF`')
             return
 
+        verbose = kwargs.get('verbose', True)
+
         if isinstance(files, str):
             files = [files]
 
-        I = iCCF.from_file(files)
+        CCFs = iCCF.from_file(files)
+
+        if not isinstance(CCFs, list):
+            CCFs = [CCFs]
 
-        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in I])
+        objects = np.unique([i.HDU[0].header['OBJECT'].replace(' ', '') for i in CCFs])
         if objects.size != 1:
             logger.warning(f'found {objects.size} different stars in the CCF files, '
                            'choosing the first one')
         star = objects[0]
 
         s = cls(star, _child=True)
+        instruments = list(np.unique([i.instrument for i in CCFs]))
 
-        # time, RVs, uncertainties
-        s.time = np.array([i.bjd for i in I])
-        s.vrad = np.array([i.RV*1e3 for i in I])
-        s.svrad = np.array([i.RVerror*1e3 for i in I])
+        for instrument in instruments:
+            # time, RVs, uncertainties
+            time = np.array([i.bjd for i in CCFs])
+            vrad = np.array([i.RV*1e3 for i in CCFs])
+            svrad = np.array([i.RVerror*1e3 for i in CCFs])
+            _s = RV.from_arrays(star, time, vrad, svrad, inst=instrument)
 
-        s.fwhm = np.array([i.FWHM*1e3 for i in I])
-        s.fwhm_err = np.array([i.FWHMerror*1e3 for i in I])
+            _quantities = []
 
-        # mask
-        s.mask = np.full_like(s.time, True, dtype=bool)
+            _s.fwhm = np.array([i.FWHM*1e3 for i in CCFs])
+            _s.fwhm_err = np.array([i.FWHMerror*1e3 for i in CCFs])
+
+            _quantities.append('fwhm')
+            _quantities.append('fwhm_err')
+
+            _s.contrast = np.array([i.contrast for i in CCFs])
+            _s.contrast_err = np.array([i.contrast_error for i in CCFs])
+
+            _quantities.append('contrast')
+            _quantities.append('contrast_err')
+
+            _s.texp = np.array([i.HDU[0].header['EXPTIME'] for i in CCFs])
+            _quantities.append('texp')
+
+            _s.date_night = np.array([
+                i.HDU[0].header['DATE-OBS'].split('T')[0] for i in CCFs
+            ])
+            _quantities.append('date_night')
+
+            _s.mask = np.full_like(_s.time, True, dtype=bool)
 
-        s.instruments = list(np.unique([i.instrument for i in I]))
+            _s.drs_qc = np.array([i.HDU[0].header['HIERARCH ESO QC SCIRED CHECK'] for i in CCFs], dtype=bool)
+            # mask out drs_qc = False
+            if not _s.drs_qc.all():
+                n = (~ _s.drs_qc).sum()
+                if verbose:
+                    logger.warning(f'masking {n} points where DRS QC failed for {instrument}')
+                _s.mask &= _s.drs_qc
+            print(_s.mask)
+
+            _s._quantities = np.array(_quantities)
+            setattr(s, instrument, _s)
+
+        s._child = False
+        s.instruments = instruments
+        s._build_arrays()
+
+        if instruments == ['ESPRESSO']:
+            from .instrument_specific import divide_ESPRESSO
+            divide_ESPRESSO(s)
 
         return s
 
@@ -610,7 +672,6 @@ class RV:
             logger.info(f'available: {self.instruments}')
             return
 
-
     def _build_arrays(self):
         """ build all concatenated arrays of `self` from each of the `.inst`s """
         if self._child:
@@ -653,7 +714,6 @@ class RV:
                 )
                 setattr(self, q, arr)
 
-
     def download_ccf(self, instrument=None, index=None, limit=None,
                      directory=None, symlink=False, **kwargs):
         """ Download CCFs from DACE
@@ -828,7 +888,7 @@ class RV:
             if self.verbose:
                 logger.info(f"Removed observations from '{instrument}'")
 
-        if return_self:
+        if config.return_self:
             return self
 
     def remove_condition(self, condition):
@@ -856,7 +916,7 @@ class RV:
         index = np.atleast_1d(index)
         try:
             instrument_index = self.obs[index]
-            instrument = np.array(self.instruments)[instrument_index - 1]
+            np.array(self.instruments)[instrument_index - 1]
         except IndexError:
             logger.errors(f'index {index} is out of bounds for N={self.N}')
             return
@@ -869,7 +929,7 @@ class RV:
         # for i, inst in zip(index, instrument):
         #     index_in_instrument = i - (self.obs < instrument_index).sum()
         #     getattr(self, inst).mask[index_in_instrument] = False
-        if return_self:
+        if config.return_self:
             return self
 
     def remove_non_public(self):
@@ -932,7 +992,7 @@ class RV:
         instruments = self._check_instrument(instrument)
         rng = np.random.default_rng(seed=seed)
         for inst in instruments:
-            s = getattr(self, inst)
+            # s = getattr(self, inst)
             mask_for_this_inst = self.obs == self.instruments.index(inst) + 1
             # only choose if there are more than n points
             if self.mask[mask_for_this_inst].sum() > n:
@@ -1037,13 +1097,18 @@ class RV:
             self.vrad = self.vrad - sa * (self.time - epoch) / 365.25
         else:
             for inst in self.instruments:
+                s = getattr(self, inst)
+
+                # if RVs come from a publication, don't remove the secular
+                # acceleration
+                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...
                     continue
 
-                s = getattr(self, inst)
-
                 if hasattr(s, '_did_secular_acceleration') and s._did_secular_acceleration:
                     continue
 
@@ -1055,7 +1120,7 @@ class RV:
         self._did_secular_acceleration_epoch = epoch
         self._did_secular_acceleration_simbad = force_simbad
 
-        if return_self:
+        if config.return_self:
             return self
     
     def _undo_secular_acceleration(self):
@@ -1111,7 +1176,7 @@ class RV:
             #     # if insts.size == 1: # of the same instrument?
             #     if self.verbose:
             #         logger.warning(f'would remove all observations from {insts[0]}, skipping')
-            #     if return_self:
+            #     if config.return_self:
             #         return self
             #     continue
 
@@ -1123,7 +1188,7 @@ class RV:
             self._did_adjust_means = False
             self.adjust_means()
 
-        if return_self:
+        if config.return_self:
             return self
 
     def clip_maxerror(self, maxerror:float):
@@ -1145,7 +1210,7 @@ class RV:
             logger.warning(f'clip_maxerror ({maxerror} {self.units}) removed {n} point' + s)
 
         self._propagate_mask_changes()
-        if return_self:
+        if config.return_self:
             return self
 
     def bin(self):
@@ -1309,7 +1374,7 @@ class RV:
 
         self._build_arrays()
         self._did_adjust_means = True
-        if return_self:
+        if config.return_self:
             return self
 
     def add_to_vrad(self, values):
@@ -1546,6 +1611,8 @@ class RV:
 
 
     #
+    from .stellar import calc_prot_age
+
     @property
     def HZ(self):
         if not hasattr(self, 'star_mass'):

arvi/translations.py

@@ -1,8 +1,10 @@
 import re
 
 STARS = {
+    '_51Peg': '51 Peg',
     'Barnard': 'GJ699',
     "Barnard's": 'GJ699',
+    'Ross128': 'Ross  128',
 }
 
 

arvi/utils.py

@@ -122,6 +122,19 @@ def find_data_file(file):
 
     return data_file
 
+
+import importlib.util
+import sys
+def lazy_import(name):
+    spec = importlib.util.find_spec(name)
+    loader = importlib.util.LazyLoader(spec.loader)
+    spec.loader = loader
+    module = importlib.util.module_from_spec(spec)
+    sys.modules[name] = module
+    loader.exec_module(module)
+    return module
+
+
 def ESPRESSO_ADC_issues():
     adc_file = find_data_file('obs_affected_ADC_issues.dat')
     lines = [line.strip() for line in open(adc_file).readlines()]

{arvi-0.1.13.dist-info → arvi-0.1.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.13
+Version: 0.1.15
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -13,15 +13,13 @@ License-File: LICENSE
 Requires-Dist: numpy
 Requires-Dist: scipy
 Requires-Dist: matplotlib
-Requires-Dist: mplcursors
 Requires-Dist: astropy
 Requires-Dist: dace-query
 Requires-Dist: loguru
-Requires-Dist: mpldatacursor
 Requires-Dist: tqdm
 Requires-Dist: pySWEETCat
 Requires-Dist: kepmodel
-Requires-Dist: mock ; python_version < "3.3"
+Requires-Dist: mock; python_version < "3.3"
 
 <p align="center">
   <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>

arvi-0.1.15.dist-info/RECORD

@@ -0,0 +1,35 @@
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+arvi/__init__.py,sha256=stLL3UtXmR1jpNEoMyVohjvkCatunz1w5ZK0ApmWuYQ,814
+arvi/ariadne_wrapper.py,sha256=jv8Wl35LfHl1UH1EklbvxHcQHqaEDhRGNogSYjFt7Y4,2141
+arvi/berv.py,sha256=5avwcmc2nkYH1KDo-z4eMPsS1ElNvold2DWkziV13gE,17633
+arvi/binning.py,sha256=jbemJ-bM3aqoOsqMo_OhWt_co-JAQ0nhdG_GpTsrRsw,15403
+arvi/config.py,sha256=wyj6FTxN7QOZj8LaHAe_ZdPKVfrNfobNNOHRNLH-S7Q,339
+arvi/dace_wrapper.py,sha256=Ng7uBwULoX5hxF5pF9feZIAYYsCn3do5fYB2B6rBvtc,17022
+arvi/extra_data.py,sha256=WEEaYeLh52Zdv0uyHO72Ys5MWS3naTAP4wJV2BJ1mbk,2551
+arvi/gaia_wrapper.py,sha256=sapurDBceHbj-pj9t9hcPUrg-3NZEoQouo__lXFD6p8,3554
+arvi/headers.py,sha256=uvdJebw1M5YkGjE3vJJwYBOnLikib75uuZE9FXB5JJM,1673
+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=92z0A46cnVdGv840oZZ7PP_fssZECYe5Zyl5OZl1p3k,27996
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+arvi/reports.py,sha256=8HiwWdaOh_P2V4-F6PV4TjasZLeZ8kC5dUYB1tQam1o,3368
+arvi/setup_logger.py,sha256=pBzaRTn0hntozjbaRVx0JIbWGuENkvYUApa6uB-FsRo,279
+arvi/simbad_wrapper.py,sha256=d8svoEUF6in2M3WrqSXfJ_drwnXD1NGPUnxP94qUOI0,5579
+arvi/spectra.py,sha256=pTAWSW4vk96DWRQ-6l5mNJHUhiAyaPR-QDjZdOT6Ak0,7489
+arvi/stats.py,sha256=ilzzGL9ew-SyVa9eEdrYCpD3DliOAwhoNUg9LIlHjzU,2583
+arvi/stellar.py,sha256=MdO1_-ZXHnMHbkG-a5LvrnYeULy6MCAnWMKPvR4NZxQ,2954
+arvi/timeseries.py,sha256=sdm9l_LHItZHDAVI6r_wsQwkrfbuMX46q3Wqs0y-KGA,60787
+arvi/translations.py,sha256=SUIrJHt3JZdL_GQh3OJyg2Gm3X5ut86w5zW8hZpxHe0,498
+arvi/utils.py,sha256=2TEj6t_6gW6dPQTPn5AFyg_F5SdI7P6IUGkecOkzoV4,4387
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+arvi/data/obs_affected_ADC_issues.dat,sha256=tn93uOL0eCTYhireqp1wG-_c3CbxPA7C-Rf-pejVY8M,10853
+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-0.1.15.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.1.15.dist-info/METADATA,sha256=nA_TpNY5eTcx8DZ3Jzmno-Rt0kKqOlq2v0o5AmojFZc,1250
+arvi-0.1.15.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
+arvi-0.1.15.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.1.15.dist-info/RECORD,,

{arvi-0.1.13.dist-info → arvi-0.1.15.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.1.0)
+Generator: setuptools (75.1.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

arvi-0.1.13.dist-info/RECORD

@@ -1,32 +0,0 @@
-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
-arvi/utils.py,sha256=nuIOuUdysMesWF9ute4v-kbeo6DylWjWW-SJhCsHn9I,4078
-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
-arvi/data/extra/HD86226_PFS1.rdb,sha256=vfAozbrKHM_j8dYkCBJsuHyD01KEM1asghe2KInwVao,3475
-arvi/data/extra/HD86226_PFS2.rdb,sha256=F2P7dB6gVyzCglUjNheB0hIHVClC5RmARrGwbrY1cfo,4114
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