arvi 0.1.8__tar.gz → 0.1.11__tar.gz

{arvi-0.1.8 → arvi-0.1.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.8
+Version: 0.1.11
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

arvi-0.1.11/arvi/HZ.py

@@ -0,0 +1,95 @@
+from collections import namedtuple
+import numpy as np
+from astropy.constants import G
+from astropy import units
+
+# Coeffcients to be used in the analytical expression to calculate habitable
+# zone flux boundaries
+seffsun = [1.776, 1.107, 0.356, 0.320, 1.188, 0.99]
+a = [2.136e-4, 1.332e-4, 6.171e-5, 5.547e-5, 1.433e-4, 1.209e-4]
+b = [2.533e-8, 1.580e-8, 1.698e-9, 1.526e-9, 1.707e-8, 1.404e-8]
+c = [-1.332e-11, -8.308e-12, -3.198e-12, -2.874e-12, -8.968e-12, -7.418e-12]
+d = [-3.097e-15, -1.931e-15, -5.575e-16, -5.011e-16, -2.084e-15, -1.713e-15]
+seffsun = np.array(seffsun)
+a, b, c, d = np.array([a, b, c, d])
+
+
+def getHZ(teff, lum, which='conservative'):
+    """ 
+    Calculate the limits of the HZ, according to Kopparapu et al.(2013).
+
+    Parameters
+    ----------
+    teff : float
+        Stellar effective temperature
+    lum : float
+        Stellar luminosity (in units of the solar luminosity)
+    which : str
+        Either 'conservative' or 'optimistic' habitable zone
+
+    Returns
+    -------
+    innerHZf, outerHZf : floats
+        Inner and outer limits of the HZ [in stellar flux compared to the Sun].
+    innerHZd, outerHZd : floats
+        Inner and outer limits of the HZ [in AU].
+    """
+    tstar = teff - 5780
+    seff = seffsun + a * tstar + b * tstar**2 + c * tstar**3 + d * tstar**4
+    dist = np.sqrt(lum / seff)
+
+    # the order of the coefficients is
+    # recentVenus
+    # runawayGreenhouse
+    # maxGreenhouse
+    # earlyMars
+    # runaway5Me
+    # runaway10Me
+
+    if which in ('conservative', 'con'):
+        return (seff[1], seff[2]), (dist[1], dist[2])
+    elif which in ('optimistic', 'opt'):
+        return (seff[0], seff[3]), (dist[0], dist[3])
+    else:
+        raise ValueError(f'Could not recognise `which={which}`')
+
+
+def getHZ_period(teff, Mstar, Mplanet, lum=1, Mplanet_units='earth',
+                 which='conservative'):
+    """
+    Calculate the period limits of the HZ.
+
+    Parameters
+    ----------
+    teff : float
+        Stellar effective temperature
+    Mstar : float
+        Mass of the star
+    Mplanet : float
+        Mass of the planet
+    lum : float
+        Stellar luminosity (in units of the solar luminosity)
+    Mplanet_units : str
+        Units of the planet mass, 'earth' or 'jupiter'
+    which : str
+        Either 'conservative' or 'optimistic' habitable zone
+    
+    Returns
+    -------
+    innerHZd, outerHZd : floats
+        Inner and outer limits of the HZ [in days].
+    """
+    # this function is nothing more than Kepler's 3rd law
+
+    f = 4 * np.pi**2 / G
+    
+    HZa = np.array(getHZ(teff, lum, which)[1]) * units.AU
+
+    Mstar = Mstar * units.solMass
+
+    if Mplanet_units.lower() == 'earth':
+        Mplanet = Mplanet * units.earthMass
+    elif Mplanet_units.lower() in ('jupiter', 'jup'):
+        Mplanet = Mplanet * units.jupiterMass
+
+    return np.sqrt(f * HZa**3 / (Mstar + Mplanet)).to(units.day)

{arvi-0.1.8 → arvi-0.1.11}/arvi/__init__.py

@@ -5,6 +5,12 @@ from .timeseries import RV
 _ran_once = False
 
 def __getattr__(name: str):
+    if name in (
+        '_ipython_canary_method_should_not_exist_',
+        '_repr_mimebundle_',
+    ):
+        return
+
     global _ran_once  # can't do it any other way :(
     if _ran_once:
         return RV(name)

{arvi-0.1.8 → arvi-0.1.11}/arvi/binning.py

@@ -1,6 +1,8 @@
 import numpy as np
 from numpy.testing import suppress_warnings
 
+from .setup_logger import logger
+
 ###############################################################################
 # the following is mostly a copy of the scipy implementation of
 # binned_statistic and binned_statistic_dd
@@ -379,3 +381,18 @@ def binRV(time, rv, err=None, stat='wmean', tstat='wmean', estat='addquad',
         if n_consecutive and consecutive_step:
             return btime, brv, random_choices
         return btime, brv
+
+
+def bin_ccf_mask(time, ccf_mask):
+    indices = binRV(time, None, binning_indices=True)
+    indices = np.r_[indices, time.size]
+    bmask = []
+    for i1, i2 in zip(indices, indices[1:]):
+        um = np.unique(ccf_mask[i1:i2]).squeeze()
+        if um.size > 1:
+            logger.error(f'Non-unique CCF mask within one night (t={time[i1]:.1f}). '
+                         'Setting to NaN, but RV should be discarded')
+            bmask.append('nan')
+        else:
+            bmask.append(um)
+    return np.array(bmask)

arvi-0.1.11/arvi/config.py

@@ -0,0 +1,2 @@
+return_self = False
+check_internet = False

{arvi-0.1.8 → arvi-0.1.11}/arvi/dace_wrapper.py

@@ -5,10 +5,10 @@ import numpy as np
 from dace_query import DaceClass
 from dace_query.spectroscopy import SpectroscopyClass, Spectroscopy as default_Spectroscopy
 from .setup_logger import logger
-from .utils import create_directory, all_logging_disabled, stdout_disabled
+from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
 
 
-def load_spectroscopy():
+def load_spectroscopy() -> SpectroscopyClass:
     if 'DACERC' in os.environ:
         dace = DaceClass(dace_rc_config_path=os.environ['DACERC'])
         return SpectroscopyClass(dace_instance=dace)
@@ -151,10 +151,18 @@ def get_observations(star, instrument=None, verbose=True):
 
 
 def check_existing(output_directory, files, type):
+    """ Check how many of `files` exist in `output_directory` """
     existing = [
         f.partition('.fits')[0] for f in os.listdir(output_directory)
         if type in f
     ]
+
+    # also check for lowercase type
+    existing += [
+        f.partition('.fits')[0] for f in os.listdir(output_directory)
+        if type.lower() in f
+    ]
+
     if os.name == 'nt':  # on Windows, be careful with ':' in filename
         import re
         existing = [re.sub(r'T(\d+)_(\d+)_(\d+)', r'T\1:\2:\3', f) for f in existing]
@@ -171,13 +179,14 @@ def check_existing(output_directory, files, type):
     return np.array(missing)
 
 def download(files, type, output_directory):
-    
+    """ Download files from DACE """
     Spectroscopy = load_spectroscopy()
     # with stdout_disabled(), all_logging_disabled():
-    Spectroscopy.download_files(files, file_type=type,
+    Spectroscopy.download_files(files, file_type=type.lower(),
                                 output_directory=output_directory)
 
 def extract_fits(output_directory):
+    """ Extract fits files from tar.gz file """
     file = os.path.join(output_directory, 'spectroscopy_download.tar.gz')
     with tarfile.open(file, "r") as tar:
         files = []
@@ -192,14 +201,16 @@ def extract_fits(output_directory):
     return files
 
 
-def do_download_ccf(raw_files, output_directory, clobber=False, verbose=True):
+def do_download_filetype(type, raw_files, output_directory, clobber=False,
+                         verbose=True, chunk_size=20):
+    """ Download CCFs / S1Ds / S2Ds from DACE """
     raw_files = np.atleast_1d(raw_files)
 
     create_directory(output_directory)
 
     # check existing files to avoid re-downloading
     if not clobber:
-        raw_files = check_existing(output_directory, raw_files, 'CCF')
+        raw_files = check_existing(output_directory, raw_files, type)
 
     # any file left to download?
     if raw_files.size == 0:
@@ -209,66 +220,71 @@ def do_download_ccf(raw_files, output_directory, clobber=False, verbose=True):
 
     if verbose:
         n = raw_files.size
-        logger.info(f"Downloading {n} CCFs into '{output_directory}'...")
+        logger.info(f"Downloading {n} {type}s into '{output_directory}'...")
 
-    download(raw_files, 'ccf', output_directory)
+    # avoid an empty chunk
+    if chunk_size > n:
+        chunk_size = n
 
-    if verbose:
-        logger.info('Extracting .fits files')
+    for files in tqdm(zip(*(iter(raw_files),) * chunk_size), total=n // chunk_size):
+        download(files, type, output_directory)
+        extract_fits(output_directory)
 
-    extract_fits(output_directory)
+    logger.info('Extracted .fits files')
 
 
-def do_download_s1d(raw_files, output_directory, clobber=False, verbose=True):
-    raw_files = np.atleast_1d(raw_files)
+# def do_download_s1d(raw_files, output_directory, clobber=False, verbose=True):
+#     """ Download S1Ds from DACE """
+#     raw_files = np.atleast_1d(raw_files)
 
-    create_directory(output_directory)
+#     create_directory(output_directory)
 
-    # check existing files to avoid re-downloading
-    if not clobber:
-        raw_files = check_existing(output_directory, raw_files, 'S1D')
+#     # check existing files to avoid re-downloading
+#     if not clobber:
+#         raw_files = check_existing(output_directory, raw_files, 'S1D')
 
-    # any file left to download?
-    if raw_files.size == 0:
-        if verbose:
-            logger.info('no files to download')
-        return
+#     # any file left to download?
+#     if raw_files.size == 0:
+#         if verbose:
+#             logger.info('no files to download')
+#         return
 
-    if verbose:
-        n = raw_files.size
-        logger.info(f"Downloading {n} S1Ds into '{output_directory}'...")
+#     if verbose:
+#         n = raw_files.size
+#         logger.info(f"Downloading {n} S1Ds into '{output_directory}'...")
 
-    download(raw_files, 's1d', output_directory)
+#     download(raw_files, 's1d', output_directory)
 
-    if verbose:
-        logger.info('Extracting .fits files')
+#     if verbose:
+#         logger.info('Extracting .fits files')
 
-    extract_fits(output_directory)
+#     extract_fits(output_directory)
 
 
-def do_download_s2d(raw_files, output_directory, clobber=False, verbose=True):
-    raw_files = np.atleast_1d(raw_files)
+# def do_download_s2d(raw_files, output_directory, clobber=False, verbose=True):
+#     """ Download S2Ds from DACE """
+#     raw_files = np.atleast_1d(raw_files)
 
-    create_directory(output_directory)
+#     create_directory(output_directory)
 
-    # check existing files to avoid re-downloading
-    if not clobber:
-        raw_files = check_existing(output_directory, raw_files, 'S2D')
+#     # check existing files to avoid re-downloading
+#     if not clobber:
+#         raw_files = check_existing(output_directory, raw_files, 'S2D')
 
-    # any file left to download?
-    if raw_files.size == 0:
-        if verbose:
-            logger.info('no files to download')
-        return
+#     # any file left to download?
+#     if raw_files.size == 0:
+#         if verbose:
+#             logger.info('no files to download')
+#         return
 
-    if verbose:
-        n = raw_files.size
-        logger.info(f"Downloading {n} S2Ds into '{output_directory}'...")
+#     if verbose:
+#         n = raw_files.size
+#         logger.info(f"Downloading {n} S2Ds into '{output_directory}'...")
 
-    download(raw_files, 's2d', output_directory)
+#     download(raw_files, 's2d', output_directory)
 
-    if verbose:
-        logger.info('Extracting .fits files')
+#     if verbose:
+#         logger.info('Extracting .fits files')
 
-    extracted_files = extract_fits(output_directory)
-    return extracted_files
+#     extracted_files = extract_fits(output_directory)
+#     return extracted_files

arvi-0.1.11/arvi/data/extra/HD86226_PFS1.rdb

@@ -0,0 +1,50 @@
+bjd vrad    svrad   sindex   note
+--- ----    -----   ------   ----
+55198.80046232133736339165     1.69      1.8200            0.1647 pfs1
+55198.80272248463552386966     7.35      1.9800            0.1714 pfs1
+55252.70830374259912787238     3.79      1.6000            0.1575 pfs1
+55256.67966442795204784488     1.40      1.5900            0.1930 pfs1
+55339.53760546142984821927    10.71      1.1200            0.1590 pfs1
+55339.54366497264436475234    12.31      1.0300            0.1615 pfs1
+55581.81336310460210370366     2.01      1.5400            0.1653 pfs1
+55588.75747179496465832926     5.36      1.9400            0.1741 pfs1
+55588.76391210197834880091     0.96      1.7700            0.1600 pfs1
+55664.60144363600556971505    -2.50      1.8300            0.1605 pfs1
+55953.81271478361486515496   -12.68      1.7600            0.1664 pfs1
+55955.78313663220797025133    -4.83      1.6300            0.1595 pfs1
+55958.78249719663108407985   -13.95      1.7300            0.1607 pfs1
+56087.49751283174737181980    -6.21      1.2200            0.1629 pfs1
+56087.50102254691228154115   -12.52      1.3100            0.2072 pfs1
+56092.49371338664695940679    -7.55      1.2100            0.1588 pfs1
+56281.80971364229299069848   -15.15      1.7200            0.1536 pfs1
+56343.71369983421755023301   -10.69      1.6500            0.1544 pfs1
+56356.73510193424954195507   -10.83      1.4400            0.1498 pfs1
+56428.52030044805815123254   -12.86      1.2900            0.1494 pfs1
+56432.51966593080487655243   -10.69      1.4100            0.1511 pfs1
+56438.50234741292752005393    -2.34      1.3000            0.1669 pfs1
+56694.70676536645714804763    -5.71      1.6900            0.1556 pfs1
+56697.69280276263998530339     1.81      1.6900            0.1470 pfs1
+56701.70015445011449628510    -5.08      1.5100            0.1458 pfs1
+56732.69609971049703744939     3.97      1.6800            0.1544 pfs1
+56734.71282864823933778098     7.00      1.4800            0.1484 pfs1
+56817.47683799520291358931     3.61      1.1700            0.1499 pfs1
+57021.77403655086800426943    -8.31      1.5600            0.1447 pfs1
+57025.76921799563115200726    -4.49      1.6300            0.1464 pfs1
+57055.75204189672695065383     3.03      1.6100            0.1466 pfs1
+57062.66716833305508771446    -4.02      1.6400            0.1457 pfs1
+57067.62944563883502269164     4.15      1.8400            0.1501 pfs1
+57117.62039468254715757212    -3.21      1.6900            0.1510 pfs1
+57388.78167686419419624144    -9.75      1.6500            0.1547 pfs1
+57395.73140734456137579400    -4.64      1.8100            0.1537 pfs1
+57452.68808872029239864787   -12.29      1.3100            0.1525 pfs1
+57468.64404368715167947812    -6.42      1.6400            0.1560 pfs1
+57474.66793088545728096506    -9.87      1.6600            0.1543 pfs1
+57478.63241514035780710401    -6.08      1.6700            0.1506 pfs1
+57498.58900430634002987063    -7.94      1.7100            0.1614 pfs1
+57555.47357154744440776994    -7.63      1.3000            0.1634 pfs1
+57737.83878056255798583152     6.39      1.9200            0.1745 pfs1
+57759.78635257452424411895   -15.35      1.5700            0.1561 pfs1
+57763.76870947524730581790   -18.94      1.6700            0.1560 pfs1
+57769.73997213117309001973    -9.05      1.5000            0.1547 pfs1
+57825.71407201319289015373   -10.32      1.5300            0.1576 pfs1
+57851.57088638147524761735    -3.14      1.9100            0.1611 pfs1

arvi-0.1.11/arvi/data/extra/HD86226_PFS2.rdb

@@ -0,0 +1,59 @@
+bjd vrad    svrad   sindex   note
+--- ----    -----   ------   ----
+58271.48476701452273118775    -0.39      1.0600            0.1576 pfs2
+58469.85188790411484660581     7.66      1.6000            0.1709 pfs2
+58469.85452811854338506237     6.11      1.5400            0.1746 pfs2
+58469.85708832627824449446     4.70      1.7900            0.1747 pfs2
+58507.82192559534996689763    -4.30      1.6100            0.1669 pfs2
+58527.71946652651968179271    -1.36      1.6400            0.1672 pfs2
+58527.72314662046119337901    -3.06      1.6800            0.1668 pfs2
+58530.71117664554913062602     3.42      1.6600            0.1611 pfs2
+58530.71417670958180679008     2.70      1.7200            0.1620 pfs2
+58530.71736677762783074286     3.57      1.5200            0.1626 pfs2
+58618.45879877419247350190     3.71      1.8200            0.2130 pfs2
+58618.46154856201974325813     0.66      1.1200            0.1625 pfs2
+58618.46607821243924263399     1.14      1.1400            0.1643 pfs2
+58618.54730191529779403936     0.75      1.1900            0.1762 pfs2
+58618.55266149781709827948     0.92      1.1300            0.1661 pfs2
+58619.45689150650832743850    -4.38      1.3000            0.1732 pfs2
+58619.45968128995627921540    -2.79      1.0900            0.1678 pfs2
+58619.46247107380804663990    -1.45      1.1800            0.1728 pfs2
+58619.57906197325974062551    -1.01      1.2900            0.1806 pfs2
+58619.58182175672118319198    -1.77      1.2900            0.1821 pfs2
+58619.58463153612683527172     2.15      1.4300            0.1823 pfs2
+58620.52444841803662711754     1.78      1.2200            0.1705 pfs2
+58620.52726819673625868745    -1.67      1.2300            0.1709 pfs2
+58620.53005797750483907294    -2.07      1.2900            0.1790 pfs2
+58620.61090160662024572957     0.50      1.0600            0.1666 pfs2
+58620.61716111190617084503     1.46      1.1300            0.1679 pfs2
+58621.45879538112058071420     0.23      1.1200            0.1766 pfs2
+58621.46448493526622769423     2.79      1.1000            0.1600 pfs2
+58621.46914457000093534589     5.11      1.2500            0.1656 pfs2
+58621.57597614719270495698     4.89      1.1200            0.1713 pfs2
+58621.58011581905338971410     1.91      1.1900            0.1766 pfs2
+58621.58434548389777773991     0.95      1.2300            0.1836 pfs2
+58622.45716698968499258626     1.05      1.1800            0.1692 pfs2
+58622.45998676735325716436    -1.59      1.2500            0.1749 pfs2
+58622.46285654186794999987     0.63      1.1300            0.1686 pfs2
+58622.57642754959124431480     1.66      1.0900            0.1664 pfs2
+58622.58053722261684015393    -0.68      1.1300            0.1661 pfs2
+58623.55484038770191546064     0.32      1.1300            0.1672 pfs2
+58623.56155985150689957663    -4.31      1.0400            0.1722 pfs2
+58624.46357848408115387429    -1.26      1.0900            0.1632 pfs2
+58624.46821811556947068311    -3.43      1.0900            0.1657 pfs2
+58624.55298135494194866624    -0.65      1.2400            0.1724 pfs2
+58624.55781096817190700676     0.00      1.2200            0.1611 pfs2
+58625.46538890280135092326     1.06      1.1800            0.1641 pfs2
+58625.47024851558853697497     1.90      1.0500            0.1586 pfs2
+58625.56686077608901541680     3.21      1.1600            0.1648 pfs2
+58625.57112043322740646545     6.55      1.2300            0.1657 pfs2
+58626.52836415075398690533     3.57      1.2200            0.1717 pfs2
+58626.53363372676540166140     6.35      1.1600            0.1674 pfs2
+58626.58020997056337364484     0.33      1.1900            0.1673 pfs2
+58626.58559953517396934330     5.12      1.0800            0.1661 pfs2
+58627.45867979986178397667     0.10      0.9600            0.1577 pfs2
+58627.46152957162485108711    -0.50      1.0200            0.1585 pfs2
+58627.46432934695258154534    -1.31      1.0600            0.1591 pfs2
+58627.59090913418367563281     1.08      1.2000            0.1770 pfs2
+58627.59374890412800596096    -0.50      1.2000            0.1760 pfs2
+58627.59652867844306456391     4.50      1.1100            0.1766 pfs2

arvi-0.1.11/arvi/data/extra/metadata.json

@@ -0,0 +1,10 @@
+{
+
+    "HD86226_PFS1.rdb": {
+        "reference": "Teske et al. 2020 (AJ, 160, 2)"
+    },
+    "HD86226_PFS2.rdb": {
+        "reference": "Teske et al. 2020 (AJ, 160, 2)"
+    }
+
+}

arvi-0.1.11/arvi/extra_data.py

@@ -0,0 +1,71 @@
+import os
+from glob import glob
+import json
+
+from numpy import full
+from .setup_logger import logger
+from . import timeseries
+
+refs = {
+    'HD86226': 'Teske et al. 2020 (AJ, 160, 2)'
+}
+
+def get_extra_data(star, instrument=None, path=None, verbose=True):
+    if path is None:
+        path = os.path.dirname(__file__)
+        path = os.path.join(path, 'data', 'extra')
+
+    metadata = json.load(open(os.path.join(path, 'metadata.json'), 'r'))
+    # print(metadata)
+
+    files = glob(os.path.join(path, star + '*'))
+    files = [f for f in files if os.path.isfile(f)]
+    files = [f for f in files if not os.path.basename(f).endswith('.zip')]
+
+    if len(files) == 0:
+        raise FileNotFoundError
+
+    def get_instruments(files):
+        instruments = [os.path.basename(f).split('.')[0] for f in files]
+        instruments = [i.split('_', maxsplit=1)[1] for i in instruments]
+        return instruments
+    
+    instruments = get_instruments(files)
+
+    if instrument is not None:
+        if not any([instrument in i for i in instruments]):
+            raise FileNotFoundError
+        files = [f for f in files if instrument in f]
+        instruments = get_instruments(files)
+
+    if verbose:
+        logger.info(f'loading extra data for {star}')
+
+    units = len(files) * ['ms']
+    reference = len(files) * [None]
+    did_sa = len(files) * [False]
+
+    for i, file in enumerate(files):
+        file_basename = os.path.basename(file)
+        if file_basename in metadata:
+            if 'instrument' in metadata[file_basename]:
+                instruments[i] = metadata[file_basename]['instrument']
+            if 'units' in metadata[file_basename]:
+                units[i] = metadata[file_basename]['units']
+            if 'reference' in metadata[file_basename]:
+                reference[i] = metadata[file_basename]['reference']
+            if 'corrected_for_secular_acceleration' in metadata[file_basename]:
+                did_sa[i] = metadata[file_basename]['corrected_for_secular_acceleration']
+
+    s = timeseries.RV.from_rdb(files[0], star=star, instrument=instruments[0], units=units[0])
+    for file, instrument, unit in zip(files[1:], instruments[1:], units[1:]):
+        s = s + timeseries.RV.from_rdb(file, star=star, instrument=instrument, units=unit)
+
+    for i, (inst, ref, inst_did_sa) in enumerate(zip(s.instruments, reference, did_sa)):
+        _s = getattr(s, inst)
+        if ref is not None:
+            _s.pub_reference = full(_s.N, ref)
+        if inst_did_sa:
+            _s._did_secular_acceleration = True
+
+    return s