arvi 0.1.12__tar.gz → 0.1.14__tar.gz

{arvi-0.1.12 → arvi-0.1.14}/.github/workflows/install.yml

@@ -19,9 +19,9 @@ jobs:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
 

{arvi-0.1.12 → arvi-0.1.14}/.github/workflows/python-publish.yml

@@ -9,6 +9,7 @@
 name: Upload Python Package
 
 on:
+  workflow_dispatch:
   release:
     types: [published]
 

{arvi-0.1.12 → arvi-0.1.14}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.12
+Version: 0.1.14
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT

{arvi-0.1.12 → arvi-0.1.14}/arvi/HZ.py

@@ -1,4 +1,3 @@
-from collections import namedtuple
 import numpy as np
 from astropy.constants import G
 from astropy import units

arvi-0.1.14/arvi/__init__.py

@@ -0,0 +1,34 @@
+__all__ = ['RV']
+
+from .timeseries import RV
+
+## OLD
+# # the __getattr__ function is always called twice, so we need this
+# # to only build and return the RV object on the second time
+# _ran_once = False
+
+def __getattr__(name: str):
+    if name in (
+        '_ipython_canary_method_should_not_exist_',
+        '_ipython_display_',
+        '_repr_mimebundle_',
+        '__wrapped__'
+    ):
+        return
+
+    try:
+        globals()[name] = RV(name)
+        return globals()[name]
+    except ValueError as e:
+        raise ImportError(e) from None
+        # raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+
+    ## OLD
+    # # can't do it any other way :(
+    # global _ran_once
+
+    # if _ran_once:
+    #     _ran_once = False
+    #     return RV(name)
+    # else:
+    #     _ran_once = True

arvi-0.1.14/arvi/berv.py

@@ -0,0 +1,437 @@
+import os
+import numpy as np
+import matplotlib.pyplot as plt
+
+from arvi.headers import get_headers
+from barycorrpy import get_BC_vel
+from astropy.coordinates import SkyCoord
+from astropy.time import Time
+from astropy import units as u
+from astropy import constants as const
+from astropy.timeseries import LombScargle
+from tqdm import tqdm
+
+from .setup_logger import logger
+from . import config
+
+
+def correct_rvs(self, simple=False, H=None, save_files=False, plot=True):
+    """
+    """
+    import pickle
+
+    if hasattr(self, '_did_correct_berv') and self._did_correct_berv:
+        logger.info('Already corrected for the BERV! Not doing anything.')
+        return
+
+    path = os.path.dirname(__file__)
+    path = os.path.join(path, 'data')
+    pkl = os.path.join(path, 'berv_espresso_sine.pkl')
+    berv_espresso = pickle.load(open(pkl, 'rb'))
+    
+    if simple:
+        logger.info('Correcting RVs with a previously-fitted sinusoid function')
+        _f = berv_espresso['func'].replace('lambda t: ', '')
+        logger.info(f': {_f}')
+        f = eval(berv_espresso['func'])
+        if plot:
+            _, ax = self.plot()
+            ax.plot(self._tt, f(self._tt) + self.vrad.mean(), 'k')
+            _, axgls = self.gls(label='before')
+        
+        self.vrad = self.vrad + f(self.time)
+
+        if plot:
+            self.gls(ax=axgls, label='after')
+
+        return f(self.time)
+
+    else:
+        logger.info('Correcting RVs with actual difference between BERVs')
+        logger.info('(basically, use BERV_barycorrpy for BERV correction)')
+
+        old_vrad = self.vrad.copy()
+
+        _, berv = BERV(self, H=H, use_gaia_meassurements=True, plx=self.gaia.plx, 
+                       plot=False, ignore_mask=True)
+
+        if plot:
+            fig, axs = plt.subplots(2, 1, constrained_layout=True, height_ratios=(3, 1), sharex=True)
+            _, ax = self.plot(ax=axs[0])
+            _, axgls = self.gls(label='before')
+
+        # undo secular acceleration, if it was done
+        _did_secular_acceleration = self._did_secular_acceleration
+        self._undo_secular_acceleration()
+
+        # transform RVs: RV --> RV - BERVpipe + BERVbarycorrpy
+
+        diff = berv[self.star]['berv_barycorrpy'] - berv[self.star]['berv_pipeline']
+
+        if save_files:
+            i_inst = np.hstack([np.arange(n) for n in self.NN.values()])
+            with open(f'{self.star}_berv_correction.rdb', 'w') as rdb:
+                rdb.write('# time\n')
+                rdb.write('# vrad\n')
+                rdb.write('# svrad\n')
+                rdb.write('# berv - BERV value from header\n')
+                rdb.write('# berv_pipe - BERV from header corrected for 1.55e-8 factor\n')
+                rdb.write('# berv_barycorrpy - BERV value from barycorrpy\n')
+                rdb.write('# diff - difference between berv_barycorrpy and berv_pipe\n')
+                rdb.write('# vrad_berv_corrected = vrad + diff\n')
+                rdb.write('# instrument\n')
+                rdb.write('# i - index\n')
+                rdb.write('# i_inst - index within the instrument\n')
+                rdb.write('#\n')
+                rdb.write('# --> TO CORRECT vrad, we ** add the diff column **\n')
+                rdb.write('# --> the result of this operation is in column vrad_berv_corrected\n')
+                rdb.write('# --> vrad_berv_corrected is already corrected for the secular acceleration, vrad is not\n')
+                rdb.write('#\n')
+                # 
+                cols = [
+                    'time', 'vrad', 'svrad', 
+                    'berv', 'berv_pipe', 'berv_barycorrpy', 'diff', 'vrad_berv_corrected',
+                    'instrument', 'i', 'i_inst'
+                ]
+                rdb.write('# ' + '\t'.join(cols) + '\n')
+                for i, t in enumerate(self.time):
+                    rdb.write(f'{t:11.5f}\t')
+                    # if _did_secular_acceleration:
+                    #     rdb.write(f'{old_vrad[i]:13.5f}\t')
+                    # else:
+                    rdb.write(f'{self.vrad[i]:13.7f}\t')
+                    rdb.write(f'{self.svrad[i]:13.7f}\t')
+                    rdb.write(f'{self.berv[i]:15.7f}\t')
+                    rdb.write(f'{berv[self.star]["berv_pipeline"][i]/1e3:15.7f}\t')
+                    rdb.write(f'{berv[self.star]["berv_barycorrpy"][i]/1e3:15.7f}\t')
+                    rdb.write(f'{diff[i]:15.7f}\t')
+                    rdb.write(f'{self.vrad[i] + diff[i]:13.7f}\t')
+                    rdb.write(f'{self.instrument_array[i]}\t')
+                    rdb.write(f'{i}\t')
+                    rdb.write(f'{i_inst[i]}\t')
+                    rdb.write('\n')
+
+        self.add_to_vrad(diff)
+        self._did_correct_berv = True
+        self._did_secular_acceleration = True # "automatically", by using BERV_barycorrpy
+        self._did_secular_acceleration_simbad = False
+        self._did_secular_acceleration_epoch = Time('J2016').jd - 24e5
+
+        # the secular acceleration hadn't been done, but it was introduced by
+        # BERV_barycorrpy, so we need to undo it
+        if not _did_secular_acceleration:
+            self._undo_secular_acceleration()
+
+        if plot:
+            self.plot(ax=axs[0], marker='+', ms=5)
+            axs[1].plot(self.time, old_vrad - self.vrad, '.k', label='old RV - new RV')
+            ma = np.abs(axs[1].get_ylim()).max()
+            axs[1].set(ylim=(-ma, ma), xlabel=axs[0].get_xlabel(), ylabel='RV difference [m/s]')
+            self.gls(ax=axgls, label='after')
+
+        return diff
+
+def get_A_and_V_from_lesta(self, username=config.username):
+    try:
+        import paramiko
+    except ImportError:
+        raise ImportError("paramiko is not installed. Please install it with 'pip install paramiko'")
+
+    logs = []
+    for f in self.raw_file:
+        f = f.replace('espresso/', '/projects/astro/ESPRESSODRS/')
+        f = f.replace('nirps/', '/projects/astro/NIRPSDRS/')
+        f = f.replace('.fits', '_SCIENCE_FP.log')
+        f = f.replace('reduced', 'log')
+        f = f.replace('r.ESPRE', 'ESPRESSO')
+        logs.append(f)
+
+    A, V = [], []
+
+    try:
+        ssh = paramiko.SSHClient()
+        ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+        ssh.connect("lesta02.astro.unige.ch", username=username, timeout=5)
+    except Exception as e:
+        if 'getaddrinfo failed' in str(e):
+            jump = paramiko.SSHClient()
+            jump.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+            jump.connect('login01.astro.unige.ch', username=username, timeout=5)
+            jump_transport = jump.get_transport()
+            jump_channel = jump_transport.open_channel('direct-tcpip', ('10.194.64.162', 22), ('129.194.64.20', 22))
+            ssh = paramiko.SSHClient()
+            ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
+            ssh.connect('lesta02.astro.unige.ch', username=username, sock=jump_channel)
+        else:
+            raise e
+
+    with ssh.open_sftp() as sftp:
+        pbar = tqdm(logs, total=len(logs), unit='file', desc='Reading logs')
+        for f in pbar:
+            with sftp.open(f) as fp:
+                pattern1 = 'Sun-Earth'
+                pattern2 = "Barycentric Observer's Velocity"
+                for line in fp:
+                    if pattern1 in line:
+                        value = line.strip().split(':')[-1].replace('\x1b[32m', '').replace('\x1b[0m', '').replace(' ', '')
+                        A.append(float(value))
+                    if pattern2 in line:
+                        value = line.strip().split(':')[-1].replace('\x1b[32m', '').replace('\x1b[0m', '').replace(' ', '')
+                        V.append(float(value))
+
+    ssh.close()
+
+    return np.array(A), np.array(V)
+
+
+def BERV(self, H=None, use_gaia_meassurements=False, plx=None,
+         A=None, V=None, plot=True, ignore_mask=False, verbose=False, dpi=None):
+    """ Calculate Barycentric Radial Velocity with barycorr and compare with pipeline
+
+    Args:
+        H (list, optional):
+            List of (CCF/S1D/etc) headers for the target. If None, try to
+            download the CCF files to get the headers.
+        use_gaia_meassurements (bool, optional):
+            Use Gaia coordinates and proper motions instead of those in the headers.
+        plx (float, optional):
+            Value of stellar parallax [mas] to use in barycorr.
+        A (array, optional):
+            Earth-Sun distance [AU] for each BJD (found in the pipeline logs).
+        V (array, optional):
+            Earth's orbital velocity [km/s] for each BJD (found in the pipeline logs).
+        plot (bool, optional):
+            Plot the results.
+    """
+    if H is None:
+        H = get_headers(self, check_lesta=False, check_exo2=False, instrument='ESPRE')
+
+    if len(H) != self.N:
+        raise ValueError(f'Expected {self.N} headers (in `H`), got {len(H)}')
+
+    if 'HARPS' in H[0]['INSTRUME'] or 'NIRPS' in H[0]['INSTRUME']:
+        obsname = 'lasilla'
+    elif 'ESPRESSO' in H[0]['INSTRUME']:
+        obsname = 'paranal'
+    else:
+        raise ValueError('unknown instrument')
+
+    bjd = np.array([h['HIERARCH ESO QC BJD'] for h in H])
+    bjd -= 24e5
+    berv_pipeline = np.array([h['HIERARCH ESO QC BERV'] for h in H])
+
+    # in the pipeline, the BERV is used to shift wavelenghts with this formula
+    # berv_factor = (1 + 1.55e-8) * (1 + BERV/c)
+    # The 1.55e-8 factor is an average of some relativistic effects, which are
+    # probably already included in the BERV calculated from barycorrpy.
+    # Therefore, we compute an "effective" BERV from the pipeline doing
+    # (1 + 1.55e-8) * (1 + BERV/c) = 1 + effBERV/c 
+    # => effBERV = ((1 + 1.55e-8) * (1 + BERV/c) - 1) * c
+
+    if A is None and V is None:
+        if verbose:
+            logger.info("Using mean value for Earth-Sun distance and Earth's orbital velocity")
+
+    if A is None:
+        Φobs = const.G * const.M_sun / const.au + const.G * const.M_earth / const.R_earth
+    else:
+        A = np.atleast_1d(A) * u.km
+        Φobs = const.G * const.M_sun / A + const.G * const.M_earth / const.R_earth
+
+    if V is None:
+        V = 29785 *u.m / u.second
+    else:
+        V = np.atleast_1d(V) * u.km / u.second
+
+    f = 1 / (1 - Φobs / const.c**2 - V**2 / (2*const.c**2))
+    c = const.c.to(u.km / u.second).value
+    berv_pipeline = (f * (1 + berv_pipeline/c) - 1) * c
+
+
+    tmmean = np.array([h['HIERARCH ESO QC TMMEAN USED'] for h in H])
+    mjdobs = np.array([h['MJD-OBS'] for h in H])
+    texp = np.array([h['EXPTIME'] for h in H])
+    jd = mjdobs + 24e5 + 0.5 + (texp * tmmean)/60/60/24
+
+    if verbose:
+        logger.info(f"Unique exposure times: {np.unique(texp)}")
+
+    berv = []
+    if verbose:
+        pbar = enumerate(jd)
+    else:
+        pbar = tqdm(enumerate(jd), total=len(jd),
+                    unit='observation', desc='Computing BERV')
+
+    for i, _jd in pbar:
+        if use_gaia_meassurements:
+            if not hasattr(self, 'gaia'):
+                raise ValueError('No Gaia data available')
+            
+            target = self.gaia.coords
+            pmra = self.gaia.pmra
+            pmdec = self.gaia.pmdec
+            epoch = Time('J2016').jd
+        else:
+            ra = H[i]['* TARG ALPHA'][0]
+            ra = f'{ra:09.2f}'
+            ra = ra[:2] + 'h' + ra[2:4] + 'm' + ra[4:] + 's'
+
+            dec = H[i]['* TARG DELTA'][0]
+            if dec < 0:
+                dec = f'{dec:010.2f}'
+            else:
+                dec = f'{dec:09.2f}'
+            if dec.startswith('-'):
+                dec = dec[:3] + 'd' + dec[3:5] + 'm' + dec[5:] + 's'
+            else:
+                dec = dec[:2] + 'd' + dec[2:4] + 'm' + dec[4:] + 's'
+
+            target = SkyCoord(ra, dec)
+            pmra = H[i]['* TARG PMA'][0] * 1e3
+            pmdec = H[i]['* TARG PMD'][0] * 1e3
+            epoch = Time('J2000').jd
+
+        if verbose:
+            logger.info(f'jd: {_jd}')
+            logger.info(f'\t ra: {target.ra}')
+            logger.info(f'\t dec: {target.dec}')
+            logger.info(f'\t pmra: {pmra}')
+            logger.info(f'\t pmdec: {pmdec}')
+                        
+
+        px = plx or 0.0
+        out = get_BC_vel(_jd, obsname=obsname, rv=0.0, px=px, zmeas=0.0, epoch=epoch,
+                         ra=target.ra.value, dec=target.dec.value, pmra=pmra, pmdec=pmdec)
+        # print(out[1][3])
+        berv.append(out[0])
+    
+    berv = np.array(berv).flatten()
+
+    if ignore_mask: # ignore the system's masked points
+        pass
+    else: # mask points in the BERV output as well
+        bjd = bjd[self.mask]
+        berv = berv[self.mask]
+        berv_pipeline = berv_pipeline[self.mask]
+
+    fig = None
+    if plot:
+        fig, axs = plt.subplots(2, 1, figsize=(8, 6), dpi=dpi, sharex=True,
+                                constrained_layout=True)
+    
+        axs[0].set_title(f'{self.star}', loc='right')
+        axs[0].plot(bjd, berv_pipeline*1e3, '.', label='pipeline', alpha=0.5)
+        axs[0].plot(bjd, berv, '.', label='barycorrpy', alpha=0.5)
+        axs[0].legend(bbox_to_anchor=(0.0, 1.15), loc=2, borderaxespad=0., ncol=2)
+        axs[0].set(xlabel='BJD - 2450000', ylabel='BERV [m/s]')
+
+
+        if plx is not None:
+            epoch = 55500
+            sa = self.secular_acceleration(just_compute=True)
+            print('sa:', sa)
+            sec_acc = sa.value * (bjd - epoch) / 365.25
+
+            axs[0].plot(bjd, sec_acc)
+
+            # fitp = np.polyfit(bjd - epoch, diff, 1)
+            # axs[1].plot(bjd, np.polyval(fitp, bjd - epoch))
+            # axs[1].plot(bjd, np.mean(diff) + diff - np.polyval(fitp, bjd - epoch), '.')
+
+        if plx is None:
+            diff = berv - berv_pipeline*1e3
+            label=r'BERV$_{\rm barycorrpy}$ - BERV$_{\rm pipeline}$'
+        else:
+            diff = berv + sec_acc - berv_pipeline*1e3
+            label=r'BERV$_{\rm barycorrpy}$ (+SA) - BERV$_{\rm pipeline}$'
+
+        axs[1].plot(bjd, diff, 'k.', label=label)
+        axs[1].axhline(np.mean(diff), ls='--', c='k', alpha=0.1)
+
+        from adjustText import adjust_text
+        text = axs[1].text(bjd.max(), diff.min() + 0.1*diff.ptp(), 
+                           f'ptp: {diff.ptp()*1e2:.2f} cm/s',
+                           ha='right', va='bottom', color='g', alpha=0.8)
+        axs[1].plot([bjd[np.argmax(diff)], bjd.max() + 0.05 * bjd.ptp()], 
+                    [np.max(diff), np.max(diff)], 'g--', alpha=0.3)
+        axs[1].plot([bjd[np.argmin(diff)], bjd.max() + 0.05 * bjd.ptp()], 
+                    [np.min(diff), np.min(diff)], 'g--', alpha=0.3)
+
+        ax = axs[1].twinx()
+        diff_cms = 1e2*(diff - np.mean(diff))
+        ax.plot(bjd, diff_cms, alpha=0)
+        ma = np.max(np.abs(ax.get_ylim()))
+        ax.set_ylim(-1 - 5*round(ma/5), 1 + 5*round(ma/5))
+        ax.set(ylabel='diff - mean(diff) [cm/s]')
+        axs[1].set_ylim(np.mean(diff)-ma/100, np.mean(diff)+ma/100)
+
+        axs[1].legend(bbox_to_anchor=(0.0, 1.15), loc=2, borderaxespad=0.)
+        axs[1].set(xlabel='BJD - 2450000', ylabel='diff [m/s]')
+    
+        # adjust_text([text], va='bottom')
+
+    return fig, {
+        self.star: {
+            'bjd': bjd,
+            'berv_pipeline': berv_pipeline*1e3,
+            'berv_barycorrpy': berv
+        }
+    }
+
+
+def plot_BERV_correction(self, H, A, V, berv2=None, berv6=None,
+                         inset=False, inset_range=(3, 5)):
+    fig, axs = plt.subplot_mosaic('ab\ncc\ndd\nee', constrained_layout=True, figsize=(2*3.57, 10))
+
+    if berv2 is None:
+        _, berv2 = BERV(self, H, plot=False)
+    if berv6 is None:
+        _, berv6 = BERV(self, H, A=A, V=V, plot=False)
+
+    self.plot(ax=axs['a'], ms=2)
+    axs['a'].set_title('original', loc='right')
+    self.gls(ax=axs['e'], label='original', color='r', alpha=0.5,
+             fill_between=True, samples_per_peak=20)
+
+    temp_vrad = self.vrad.copy()
+    self.vrad[self.mask] = self.vrad[self.mask] - berv2[self.star]['berv_pipeline'].value + berv6[self.star]['berv_pipeline'].value
+
+    self.plot(ax=axs['b'], ms=2)
+    axs['b'].set_title('after correction', loc='right')
+
+    diff = temp_vrad[self.mask] - self.vrad[self.mask]
+
+    axs['c'].plot(self.mtime, diff, 'k.')
+    axs['c'].set_title('RV difference', loc='right')
+    axs['c'].set(xlabel='BJD - 2450000', ylabel='RV diff [m/s]')
+
+    text = axs['c'].text(self.mtime.max(), diff.min() + 0.1*diff.ptp(), 
+                         f'ptp: {diff.ptp()*1e2:.2f} cm/s',
+                         ha='right', va='bottom', color='g', alpha=0.8)
+    axs['c'].plot([self.mtime[np.argmax(diff)], self.mtime.max() + 0.05 * self.mtime.ptp()], 
+                [np.max(diff), np.max(diff)], 'g--', alpha=0.3)
+    axs['c'].plot([self.mtime[np.argmin(diff)], self.mtime.max() + 0.05 * self.mtime.ptp()], 
+                [np.min(diff), np.min(diff)], 'g--', alpha=0.3)
+
+
+    f, p = LombScargle(self.mtime, diff).autopower(maximum_frequency=1.0, samples_per_peak=10)
+    axs['d'].semilogx(1/f, p, color='k', alpha=0.8)
+    axs['d'].vlines([365.25, 365.25/2], 0, 1, color='k', ls='--', alpha=0.3)
+    axs['d'].set(xlabel='Period [days]', ylabel='normalized power', ylim=(0, 1))
+    axs['d'].set_title('GLS of RV difference', loc='right')
+
+    if inset:
+        inset = axs['d'].inset_axes(bounds=[0.15, 0.3, 0.3, 0.6])
+        m = (1/f > inset_range[0]) & (1/f < inset_range[1])
+        inset.plot(1/f[m], p[m], color='k', alpha=0.8)
+        inset.set(xlim=inset_range, yticks=[])
+        inset.minorticks_on()
+
+    self.gls(ax=axs['e'], label='after correction', color='g', alpha=1,
+             lw=0.8, samples_per_peak=20)
+    axs['e'].set(xlabel='Period [days]', ylabel='normalized power')
+    axs['e'].sharex(axs['d'])
+
+    self.vrad = temp_vrad
+    return fig

{arvi-0.1.12 → arvi-0.1.14}/arvi/binning.py

@@ -1,6 +1,9 @@
 import numpy as np
 from numpy.testing import suppress_warnings
 
+from scipy.stats import binned_statistic as old_binned_statistic,\
+                        binned_statistic_dd as old_binned_statistic_dd
+
 from .setup_logger import logger
 
 ###############################################################################
@@ -212,8 +215,6 @@ def binned_statistic_dd(sample, values, statistic='mean', bins=10, range=None,
 
 
 # put back the documentation
-from scipy.stats import binned_statistic as old_binned_statistic,\
-                        binned_statistic_dd as old_binned_statistic_dd
 doc1 = old_binned_statistic.__doc__
 doc2 = old_binned_statistic_dd.__doc__
 binned_statistic.__doc__ = doc1

{arvi-0.1.12 → arvi-0.1.14}/arvi/config.py

@@ -5,4 +5,10 @@ return_self = False
 check_internet = False
 
 # make all DACE requests without using a .dacerc file
-request_as_public = False
+request_as_public = False
+
+# whether to adjust instrument means before gls by default
+adjust_means_gls = True
+
+# debug
+debug = False