arvi 0.2.5__tar.gz → 0.2.6__tar.gz

{arvi-0.2.5/arvi.egg-info → arvi-0.2.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.5
+Version: 0.2.6
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.5 → arvi-0.2.6}/arvi/gaia_wrapper.py

@@ -3,8 +3,6 @@ from io import StringIO
 from csv import DictReader
 import requests
 
-from astropy.coordinates import SkyCoord
-
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
 
@@ -78,6 +76,8 @@ class gaia:
         Args:
             star (str): The name of the star to query simbad
         """
+        from astropy.coordinates import SkyCoord
+
         self.star = star
 
         if simbad is None:

{arvi-0.2.5 → arvi-0.2.6}/arvi/instrument_specific.py

@@ -107,14 +107,7 @@ def divide_HARPS(self):
     
 
 def check(self, instrument):
-    logger = setup_logger()
-    instruments = self._check_instrument(instrument)
-    if instruments is None:
-        if self.verbose:
-            logger.error(f"HARPS_fiber_commissioning: no data from {instrument}")
-        return None
-    return instruments
-
+    return self._check_instrument(instrument)
 
 # HARPS commissioning
 def HARPS_commissioning(self, mask=True, plot=True):

{arvi-0.2.5 → arvi-0.2.6}/arvi/simbad_wrapper.py

@@ -1,6 +1,7 @@
 import os
 import requests
 from dataclasses import dataclass
+from functools import partial
 
 import numpy as np
 
@@ -63,6 +64,23 @@ JOIN ident ON oidref = oid
 WHERE id = '{star}';
 """
 
+HD_GJ_HIP_QUERY = """
+SELECT id2.id
+FROM ident AS id1 JOIN ident AS id2 USING(oidref)
+WHERE id1.id = '{star}' AND id2.id LIKE '{name}%';
+"""
+
+def find_identifier(identifier, star):
+    response = run_query(HD_GJ_HIP_QUERY.format(name=identifier, star=star))
+    if identifier in response:
+        return response.split('"')[1]
+    raise ValueError(f'no {identifier} identifier found for "{star}"')
+
+find_HD = partial(find_identifier, 'HD')
+find_GJ = partial(find_identifier, 'GJ')
+find_HIP = partial(find_identifier, 'HIP')
+
+
 @dataclass
 class Measurements:
     teff: list

arvi-0.2.6/arvi/sophie_wrapper.py

@@ -0,0 +1,111 @@
+from multiprocessing.pool import ThreadPool
+import re
+import requests
+from io import StringIO
+
+import numpy as np
+
+from .setup_logger import setup_logger
+
+URL_CCF = "http://atlas.obs-hp.fr/sophie/sophie.cgi?n=sophiecc&ob=date&a=t&o={target}"
+URL_HEADER = "http://atlas.obs-hp.fr/sophie/sophie.cgi?n=sophiecc&c=i&z=fd&a=t&o=sophie:[ccf,{seq},{mask},0]"
+
+def extract_keyword(keyword, text, raise_error=True):
+    for line in text.splitlines():
+        if keyword in line:
+            value = re.findall(fr'{keyword}\s+([\'\w\d.]+)', line)[0]
+            value = value.replace("'", "")
+            try:
+                return float(value)
+            except ValueError:
+                return value
+    if raise_error:
+        raise KeyError(f'Keyword {keyword} not found')
+
+def query_sophie_archive(star: str, verbose=True):
+    from .timeseries import RV
+    logger = setup_logger()
+
+    resp = requests.get(URL_CCF.format(target=star))
+    if 'leda did not return a position for the name' in resp.text:
+        raise ValueError(f'no SOPHIE observations for {star}')
+
+    data = np.genfromtxt(StringIO(resp.text), dtype=None, usecols=(0, 4),
+                         names=("seq", "mask"))
+    
+    if verbose:
+        logger.info(f'found {len(data)} SOPHIE observations for {star}')
+
+    urls = [URL_HEADER.format(seq=seq, mask=mask) for seq, mask in data]
+    with ThreadPool(8) as pool:
+        responses = pool.map(requests.get, urls)
+
+    bjd, vrad, svrad = [], [], []
+    fwhm, contrast = [], []
+    ccf_mask = []
+    _quantities = []
+    errors = []
+
+    for i, resp in enumerate(responses):
+        if resp.text == '':
+            errors.append(i)
+            continue
+        
+        try:
+            t, v = map(lambda k: extract_keyword(k, resp.text), 
+                       ("OHP DRS BJD", "OHP DRS CCF RV"))
+        except KeyError:
+            errors.append(i)
+            continue
+        else:
+            bjd.append(t)
+            vrad.append(v)
+        
+        try:
+            svrad.append(extract_keyword("OHP DRS CCF ERR", resp.text))
+        except KeyError:
+            try:
+                svrad.append(1e-3 * extract_keyword("OHP DRS DVRMS", resp.text))
+            except KeyError:
+                bjd.pop(-1)
+                vrad.pop(-1)
+                errors.append(i)
+                continue
+
+        fwhm.append(extract_keyword('OHP DRS CCF FWHM', resp.text))
+        _quantities.append('fwhm')
+
+        contrast.append(extract_keyword('OHP DRS CCF CONTRAST', resp.text))
+        _quantities.append('contrast')
+
+        ccf_mask.append(extract_keyword('OHP DRS CCF MASK', resp.text))
+        _quantities.append('ccf_mask')
+
+    if len(errors) > 0:
+        logger.warning(f'Could not retrieve {len(errors)} observation'
+                       f'{"s" if len(errors) > 1 else ""}')
+
+    bjd = np.array(bjd) - 2400000.5
+
+    s = RV.from_arrays(star, bjd, vrad, svrad, 'SOPHIE',
+                       fwhm=fwhm, fwhm_err=2*np.array(svrad),
+                       contrast=contrast, 
+                       ccf_mask=ccf_mask)
+    s.units = 'km/s'
+
+    # strings
+    for q in ['date_night', 'prog_id', 'raw_file', 'pub_reference']:
+        setattr(s, q, np.full(bjd.size, ''))
+        _quantities.append(q)
+
+    s._quantities = np.array(_quantities)
+
+    setattr(s, 'SOPHIE', s)
+    s._child = False
+    s.verbose = False
+    s._build_arrays()
+    s.change_units('m/s')
+    s.verbose = verbose
+
+    return s
+    

{arvi-0.2.5 → arvi-0.2.6}/arvi/timeseries.py

@@ -64,19 +64,21 @@ class RV(ISSUES, REPORTS):
     only_latest_pipeline: bool = field(init=True, repr=False, default=True)
     load_extra_data: Union[bool, str] = field(init=True, repr=False, default=False)
     check_drs_qc: bool = field(init=True, repr=False, default=True)
-    user: bool = field(init=True, repr=False, default=None)
+    check_sophie_archive: bool = field(init=True, repr=False, default=False)
+    user: Union[str, None] = field(init=True, repr=False, default=None)
     #
     units = 'm/s'
     _child: bool = field(init=True, repr=False, default=False)
-    _did_secular_acceleration: bool = field(init=False, repr=False, default=False)
-    _did_sigma_clip: bool = field(init=False, repr=False, default=False)
-    _did_adjust_means: bool = field(init=False, repr=False, default=False)
-    _did_simbad_query: bool = field(init=False, repr=False, default=False)
-    _did_gaia_query: bool = field(init=False, repr=False, default=False)
-    _did_toi_query: bool = field(init=False, repr=False, default=False)
-    _raise_on_error: bool = field(init=True, repr=False, default=True)
-    __masked_numbers: bool = field(init=False, repr=False, default=False)
-    # 
+    #
+    _did_secular_acceleration : bool = field(init=False, repr=False, default=False)
+    _did_sigma_clip           : bool = field(init=False, repr=False, default=False)
+    _did_adjust_means         : bool = field(init=False, repr=False, default=False)
+    _did_simbad_query         : bool = field(init=False, repr=False, default=False)
+    _did_gaia_query           : bool = field(init=False, repr=False, default=False)
+    _did_toi_query            : bool = field(init=False, repr=False, default=False)
+    _raise_on_error  : bool = field(init=True, repr=False, default=True)
+    __masked_numbers : bool = field(init=False, repr=False, default=False)
+    #
     _simbad = None
     _gaia = None
     _toi = None
@@ -104,7 +106,7 @@ class RV(ISSUES, REPORTS):
 
         if self._child:
             return None
-    
+
         if self._did_simbad_query:
             return None
 
@@ -288,6 +290,21 @@ class RV(ISSUES, REPORTS):
                 # all other quantities
                 self._build_arrays()
 
+                # self.actin = get_actin_data(self, verbose=self.verbose)
+
+
+        # check for SOPHIE observations
+        cond = not self._child
+        cond = cond and self.instrument is None
+        cond = cond and self.check_sophie_archive
+        if cond:
+            try:
+                from arvi.sophie_wrapper import query_sophie_archive
+                self.__add__(query_sophie_archive(self.star, verbose=self.verbose),
+                             inplace=True)
+            except Exception as e:
+                print(e)
+
         # do clip_maxerror, secular_acceleration, sigmaclip, adjust_means
         if not self._child:
             if self.do_maxerror:
@@ -1376,7 +1393,7 @@ class RV(ISSUES, REPORTS):
             instrument_index = self.obs[index]
             np.array(self.instruments)[instrument_index - 1]
         except IndexError:
-            logger.errors(f'index {index} is out of bounds for N={self.N}')
+            logger.error(f'index {index} is out of bounds for N={self.N}')
             return
 
         if self.verbose:
@@ -1408,7 +1425,7 @@ class RV(ISSUES, REPORTS):
             instrument_index = self.obs[index]
             np.array(self.instruments)[instrument_index - 1]
         except IndexError:
-            logger.errors(f'index {index} is out of bounds for N={self.N}')
+            logger.error(f'index {index} is out of bounds for N={self.N}')
             return
 
         if self.verbose:

{arvi-0.2.5 → arvi-0.2.6}/arvi/utils.py

@@ -79,14 +79,17 @@ def timer(name=None):
     if name is None:
         logger.debug('starting timer')
     else:
-        logger.debug(f'starting timer: {name}')
+        logger.debug(f'{name}: starting timer')
 
     start = time.time()
     try:
         yield
     finally:
         end = time.time()
-        logger.debug(f'elapsed time: {end - start:.2f} seconds')
+        if name is None:
+            logger.debug(f'elapsed time {end - start:.2f} seconds')
+        else:
+            logger.debug(f'{name}: elapsed time {end - start:.2f} seconds')
 
 
 def sanitize_path(path):

{arvi-0.2.5 → arvi-0.2.6/arvi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.5
+Version: 0.2.6
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.2.5 → arvi-0.2.6}/arvi.egg-info/SOURCES.txt

@@ -28,6 +28,7 @@ arvi/programs.py
 arvi/reports.py
 arvi/setup_logger.py
 arvi/simbad_wrapper.py
+arvi/sophie_wrapper.py
 arvi/spectra.py
 arvi/stats.py
 arvi/stellar.py