arvi 0.0.2__py3-none-any.whl → 0.0.3__py3-none-any.whl

arvi/__init__.py

@@ -1,30 +1,13 @@
-__version__ = '0.0.2'
+__version__ = '0.0.3'
 __all__ = []
 
 from .timeseries import RV
 
 _ran_once = False
+
 def __getattr__(name: str):
-    global _ran_once
+    global _ran_once  # can't do it any other way :(
     if _ran_once:
         return RV(name)
     else:
         _ran_once = True
-
-
-# from importlib import import_module
-
-# HACK_IMPORTS = True
-
-# if HACK_IMPORTS:
-#     timeseries = import_module('.timeseries', 'arvi')
-#     class FakeModule(object):
-#         def __getattribute__(self, name):
-#             print(name)
-#             r = RV(name)
-#             return r
-#     # first, load (some) subpackages
-#     # then, replace the 'arvi' module to allow for dynamic imports
-#     # of the type "from arvi import HD1"
-#     import sys
-#     sys.modules['arvi'] = FakeModule()

arvi/dace_wrapper.py

@@ -1,7 +1,17 @@
+import os
+import tarfile
 import numpy as np
-from dace_query.spectroscopy import Spectroscopy
+from dace_query import DaceClass
+from dace_query.spectroscopy import SpectroscopyClass, Spectroscopy as default_Spectroscopy
 from .setup_logger import logger
 
+def load_spectroscopy():
+    if 'DACERC' in os.environ:
+         dace = DaceClass(dace_rc_config_path=os.environ['DACERC'])
+         return SpectroscopyClass(dace_instance=dace)
+    # elif os.path.exists(os.path.expanduser('~/.dacerc')):
+    return default_Spectroscopy
+
 
 def get_arrays(result, latest_pipeline=True):
     arrays = []
@@ -25,11 +35,22 @@ def get_arrays(result, latest_pipeline=True):
 
 
 def get_observations(star, save_rdb=False, verbose=True):
+    Spectroscopy = load_spectroscopy()
     result = Spectroscopy.get_timeseries(target=star,
                                          sorted_by_instrument=True,
                                          output_format='numpy')
     instruments = list(result.keys())
 
+    # sort pipelines, being extra careful with HARPS pipeline names
+    # (i.e. ensure that 3.0.0 > 3.5)
+    class sorter:
+        def __call__(self, x):
+            return '0.3.5' if x == '3.5' else x
+
+    for inst in instruments:
+        result[inst] = dict(sorted(result[inst].items(), 
+                                   key=sorter(), reverse=True))
+
     if verbose:
         logger.info('RVs available from')
         with logger.contextualize(indent='   '):
@@ -44,5 +65,28 @@ def get_observations(star, save_rdb=False, verbose=True):
     return result
 
 
-def save_rdb(data, columns):
-    pass
+def do_download_ccf(raw_files, output_directory, verbose=True):
+    raw_files = np.atleast_1d(raw_files)
+    if not os.path.isdir(output_directory):
+        os.makedirs(output_directory)
+    if verbose:
+        logger.info(f"Downloading {len(raw_files)} CCFs into '{output_directory}'...")
+
+    Spectroscopy = load_spectroscopy()
+    
+    from .utils import all_logging_disabled, stdout_disabled
+    with stdout_disabled(), all_logging_disabled():
+        Spectroscopy.download_files(raw_files[:2],
+                                    file_type='ccf',
+                                    output_directory=output_directory)
+
+    if verbose:
+        logger.info('Extracting .fits files')
+    
+    file = os.path.join(output_directory, 'spectroscopy_download.tar.gz')
+    tar = tarfile.open(file, "r")
+    for member in tar.getmembers():
+        if member.isreg():  # skip if the TarInfo is not a file
+            member.name = os.path.basename(member.name)  # remove the path
+            tar.extract(member, output_directory)
+    os.remove(file)

arvi/simbad_wrapper.py

@@ -1,6 +1,8 @@
 from dataclasses import dataclass, field
 import requests
 
+from astropy.coordinates import SkyCoord
+
 QUERY = """
 SELECT basic.OID,
        RA,
@@ -58,6 +60,7 @@ class simbad:
     Attributes:
         ra (float): right ascension
         dec (float): declination
+        coords (SkyCoord): coordinates as a SkyCoord object
         main_id (str): main identifier
         plx_value (float): parallax
         rvz_radvel (float): radial velocity
@@ -72,15 +75,18 @@ class simbad:
             star (str): The name of the star to query simbad
         """
         self.star = star
-        table1 = run_query(query=QUERY.format(star=star))
-        cols, values = parse_table(table1)
+        try:
+            table1 = run_query(query=QUERY.format(star=star))
+            cols, values = parse_table(table1)
 
-        table2 = run_query(query=BV_QUERY.format(star=star))
-        cols, values = parse_table(table2, cols, values)
+            table2 = run_query(query=BV_QUERY.format(star=star))
+            cols, values = parse_table(table2, cols, values)
 
-        table3 = run_query(query=IDS_QUERY.format(star=star))
-        line = table3.splitlines()[2]
-        self.ids = line.replace('"', '').replace('    ', ' ').split('|')
+            table3 = run_query(query=IDS_QUERY.format(star=star))
+            line = table3.splitlines()[2]
+            self.ids = line.replace('"', '').replace('    ', ' ').split('|')
+        except IndexError:
+            raise ValueError(f'simbad query for {star} failed')
 
         for col, val in zip(cols, values):
             try:
@@ -88,6 +94,9 @@ class simbad:
             except ValueError:
                 setattr(self, col, val)
 
+        self.coords = SkyCoord(self.ra, self.dec, unit='deg')
+
+
     def __repr__(self):
         V = self.V
         sp_type = self.sp_type

arvi/timeseries.py

@@ -1,11 +1,12 @@
 from dataclasses import dataclass, field
+from typing import Union
 from functools import partial
 from datetime import datetime, timezone
 import numpy as np
 
 from .setup_logger import logger
 from .translations import translate
-from .dace_wrapper import get_observations, get_arrays
+from .dace_wrapper import get_observations, get_arrays, do_download_ccf
 from .simbad_wrapper import simbad
 from .stats import wmean, wrms
 
@@ -29,6 +30,7 @@ class RV:
     N: int = field(init=False, repr=True)
     verbose: bool = field(init=True, repr=False, default=True)
     do_sigma_clip: bool = field(init=True, repr=False, default=True)
+    do_maxerror: Union[bool, float] = field(init=True, repr=False, default=100)
     do_adjust_means: bool = field(init=True, repr=False, default=True)
     #
     _child: bool = field(init=True, repr=False, default=False)
@@ -37,7 +39,10 @@ class RV:
 
     def __post_init__(self):
         self.__star__ = translate(self.star)
-        self.simbad = simbad(self.__star__)
+        try:
+            self.simbad = simbad(self.__star__)
+        except ValueError as e:
+            logger.error(e.msg)
 
         if not self._child:
             if self.verbose:
@@ -71,11 +76,16 @@ class RV:
             # all other quantities
             self._build_arrays()
 
-        if self.do_sigma_clip:
-            self.sigmaclip()
+        # do clip_maxerror, sigmaclip, adjust_means
+        if not self._child:
+            if self.do_maxerror:
+                self.clip_maxerror(self.do_maxerror)
+
+            if self.do_sigma_clip:
+                self.sigmaclip()
 
-        if self.do_adjust_means:
-            self.adjust_means()
+            if self.do_adjust_means:
+                self.adjust_means()
 
 
     def reload(self):
@@ -171,6 +181,21 @@ class RV:
                 )
                 setattr(self, q, arr)
 
+
+    def download_ccf(self, instrument=None):
+        directory = f'{self.star}_downloads'
+        if instrument is None:
+            files = [file for file in self.raw_file if file.endswith('.fits')]
+        else:
+            if instrument not in self.instruments:
+                logger.error(f"No data from instrument '{instrument}'")
+                logger.info(f'available: {self.instruments}')
+                return
+            files = getattr(self, instrument).raw_file
+
+        do_download_ccf(files, directory)
+
+
     from .plots import plot, plot_fwhm, plot_bis
     from .plots import gls, gls_fwhm, gls_bis
     from .reports import report
@@ -237,12 +262,19 @@ class RV:
         self.mask[~ind] = False
         self._propagate_mask_changes()
 
-    def sigmaclip_errors(self, maxerror:float, plot=False):
+    def clip_maxerror(self, maxerror:float, plot=False):
         """ Mask out points with RV error larger than `maxerror` """
         if self._child:
             return
         self.maxerror = maxerror
-        self.mask[self.svrad > maxerror] = False
+        above = self.svrad > maxerror
+        n = above.sum()
+        self.mask[above] = False
+
+        if self.verbose and above.sum() > 0:
+            s = 's' if (n == 0 or n > 1) else ''
+            logger.warning(f'clip_maxerror removed {n} point' + s)
+
         self._propagate_mask_changes()
 
     def adjust_means(self, just_rv=False):
@@ -258,13 +290,19 @@ class RV:
                 logger.info(f'subtracted weighted average from {inst:10s}: ({s.rv_mean:.3f} {self.units})')
             if just_rv:
                 continue
-            for other in others:
+            log_msg = 'same for '
+            for i, other in enumerate(others):
                 y, ye = getattr(s, other), getattr(s, other + '_err')
                 m = wmean(y, ye)
                 setattr(s, f'{other}_mean', m)
                 setattr(s, other, getattr(s, other) - m)
-                if self.verbose:
-                    logger.info(f'same for {other}')
+                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
 

arvi/utils.py

@@ -0,0 +1,32 @@
+import os
+from contextlib import contextmanager
+from mock import patch
+import logging
+
+
+@contextmanager
+def stdout_disabled():
+    devnull = open(os.devnull, 'w')
+    with patch('sys.stdout', devnull):
+        yield
+
+
+@contextmanager
+def all_logging_disabled():
+    """
+    A context manager that will prevent any logging messages triggered during
+    the body from being processed.
+    """
+    # two kind-of hacks here:
+    #    * can't get the highest logging level in effect => delegate to the user
+    #    * can't get the current module-level override => use an undocumented
+    #       (but non-private!) interface
+
+    previous_level = logging.root.manager.disable
+
+    logging.disable(logging.CRITICAL)
+
+    try:
+        yield
+    finally:
+        logging.disable(previous_level)

{arvi-0.0.2.dist-info → arvi-0.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.0.2
+Version: 0.0.3
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@astro.up.pt>
 License: MIT

arvi-0.0.3.dist-info/RECORD

@@ -0,0 +1,15 @@
+arvi/__init__.py,sha256=d4UTdSj3oRwFvO1a_m5uz_fqEVFR9U-afio38MNuESU,241
+arvi/dace_wrapper.py,sha256=0zId_2uti-_UOkCZHJnRvajO5EMNgwNfc5AgV-LjSPQ,3340
+arvi/plots.py,sha256=uOruz1xhlx7nNjIEtLTX6gs_iya2Yds71eIYoYt2LVw,6925
+arvi/reports.py,sha256=FtalLbmBHOSHQ3RldImUZTHPc3cc3Z3W5r3d-31FIo8,3261
+arvi/setup_logger.py,sha256=nvnd2PtXYnpYMGleTeqAKFe-TnC6SjNlTZ-EmiewLyY,278
+arvi/simbad_wrapper.py,sha256=7XnuM7Kq5kK4EchHjh-uyRoTWm6kCx0sx7Ak0eDaALo,3023
+arvi/stats.py,sha256=OIlXisf_kuUhfDRhvCirmJ2e-YSIJnoBjdFOXaYd0bQ,868
+arvi/timeseries.py,sha256=tWKAn5tCQpI1YaCE_breyQ_dXAsj0X06jox4nH9ES5E,11159
+arvi/translations.py,sha256=eyUJei8wlsyBecTz8E_ntpP35-Mre2Tzm_mUMMGaZWY,150
+arvi/utils.py,sha256=OPb6rXafv7b8vRRTEg9zQAQnhi3lRLICF62R8Fhy43A,788
+arvi-0.0.3.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.0.3.dist-info/METADATA,sha256=01PYughU6O-f6cwMA_6elKUMallpnN5uaxN6k8xgeys,827
+arvi-0.0.3.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+arvi-0.0.3.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.0.3.dist-info/RECORD,,

arvi-0.0.2.dist-info/RECORD

@@ -1,14 +0,0 @@
-arvi/__init__.py,sha256=rEegmfeT2Xy3gBLpx7_MZOHUcbo_Mg_4aPlD_QsGzaI,708
-arvi/dace_wrapper.py,sha256=N3-cdj8YrryZFA4Tztrb3cJ-2MKgWjLV0rJ6bue8bQQ,1567
-arvi/plots.py,sha256=uOruz1xhlx7nNjIEtLTX6gs_iya2Yds71eIYoYt2LVw,6925
-arvi/reports.py,sha256=FtalLbmBHOSHQ3RldImUZTHPc3cc3Z3W5r3d-31FIo8,3261
-arvi/setup_logger.py,sha256=nvnd2PtXYnpYMGleTeqAKFe-TnC6SjNlTZ-EmiewLyY,278
-arvi/simbad_wrapper.py,sha256=oCcyoWPtkP2RntUNZ3Y0pPFk1hK2nawRlYHCpTRETaE,2725
-arvi/stats.py,sha256=OIlXisf_kuUhfDRhvCirmJ2e-YSIJnoBjdFOXaYd0bQ,868
-arvi/timeseries.py,sha256=KHTUHEgp7m_ZQYGufntn-pHwFqzVhAlqFWuFolsWUEM,9893
-arvi/translations.py,sha256=eyUJei8wlsyBecTz8E_ntpP35-Mre2Tzm_mUMMGaZWY,150
-arvi-0.0.2.dist-info/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.0.2.dist-info/METADATA,sha256=U7NMIBTxucQP3aY7siFcaR04dXGfxthu3HEI40bi7xI,827
-arvi-0.0.2.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-arvi-0.0.2.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.0.2.dist-info/RECORD,,