arvi 0.2.2__py3-none-any.whl → 0.2.4__py3-none-any.whl

arvi/__init__.py

@@ -1,4 +1,4 @@
-__all__ = ['RV']
+__all__ = ['RV', 'config', 'simbad', 'gaia']
 
 from importlib.metadata import version, PackageNotFoundError
 try:
@@ -8,17 +8,15 @@ except PackageNotFoundError:
     pass
 
 from .config import config
-from .timeseries import RV
-
 from .simbad_wrapper import simbad
+from .gaia_wrapper import gaia
 
-
-## 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
+from .timeseries import RV
 
 def __getattr__(name: str):
+    if not config.fancy_import:
+        raise AttributeError
+    
     if name in (
         '_ipython_canary_method_should_not_exist_',
         '_ipython_display_',
@@ -31,15 +29,5 @@ def __getattr__(name: str):
         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
+        raise AttributeError(e)
 
-    # if _ran_once:
-    #     _ran_once = False
-    #     return RV(name)
-    # else:
-    #     _ran_once = True

arvi/binning.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 
 ###############################################################################
 # the following is mostly a copy of the scipy implementation of
@@ -390,6 +390,7 @@ def binRV(time, rv, err=None, stat='wmean', tstat='wmean', estat='addquad',
 
 
 def bin_ccf_mask(time, ccf_mask):
+    logger = setup_logger()
     indices = binRV(time, None, binning_indices=True)
     indices = np.r_[indices, time.size]
     bmask = []

arvi/config.py

@@ -8,6 +8,7 @@ def get_config_path():
 
 def get_config():
     config = configparser.ConfigParser()
+    config.add_section('config')
     if (path := get_config_path()).exists():
         config.read(path)
     return config
@@ -31,6 +32,10 @@ class config:
         'check_internet': False,
         # make all DACE requests without using a .dacerc file
         'request_as_public': False,
+        # enable from arvi import star_name
+        'fancy_import': True,
+        # use the 'dark_background' matplotlib theme
+        'dark_plots': False,
         # debug
         'debug': False,
     }
@@ -43,10 +48,16 @@ class config:
             # return {'return_self': 'help!'}
             return {}
 
-        if self.__user_config.has_option('config', name):
-            self.__conf[name] = self.__user_config.get('config', name)
+        try:
+            if self.__user_config.has_option('config', name):
+                value = self.__user_config.get('config', name)
+                value = True if value == 'True' else value
+                value = False if value == 'False' else value
+                self.__conf[name] = value
 
-        return self.__conf[name]
+            return self.__conf[name]
+        except KeyError:
+            raise KeyError(f"unknown config option '{name}'")
 
     def __setattr__(self, name, value):
         if name in config.__setters:
@@ -54,7 +65,7 @@ class config:
         else:
             if 'config' not in self.__user_config:
                 self.__user_config.add_section('config')
-            self.__user_config.set('config', name, value)
+            self.__user_config.set('config', name, str(value))
             save_config(self.__user_config)
             # raise NameError(f"unknown configuration name '{name}'")
 

arvi/dace_wrapper.py

@@ -5,11 +5,13 @@ import collections
 from functools import lru_cache
 from itertools import islice
 import numpy as np
-from .setup_logger import logger
+
+from .setup_logger import setup_logger
 from .utils import create_directory, all_logging_disabled, stdout_disabled, tqdm
 
 
 def load_spectroscopy(user=None):
+    logger = setup_logger()
     with all_logging_disabled():
         from dace_query.spectroscopy import SpectroscopyClass, Spectroscopy as default_Spectroscopy
         from dace_query import DaceClass
@@ -45,8 +47,10 @@ def load_spectroscopy(user=None):
         logger.warning('requesting DACE data as public (no .dacerc file found)')
     return default_Spectroscopy
 
-@lru_cache()
-def get_dace_id(star, verbose=True):
+
+@lru_cache(maxsize=1024)
+def get_dace_id(star, verbose=True, raise_error=False):
+    logger = setup_logger()
     filters = {"obj_id_catname": {"equal": [star]}}
     try:
         with all_logging_disabled():
@@ -55,9 +59,13 @@ def get_dace_id(star, verbose=True):
     except KeyError:
         if verbose:
             logger.error(f"Could not find DACE ID for {star}")
+        if not raise_error:
+            return None
         raise ValueError from None
 
+
 def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='HE', verbose=True):
+    logger = setup_logger()
     arrays = []
     instruments = [str(i) for i in result.keys()]
 
@@ -66,7 +74,6 @@ def get_arrays(result, latest_pipeline=True, ESPRESSO_mode='HR11', NIRPS_mode='H
 
         # select ESPRESSO mode, which is defined at the level of the pipeline
         if 'ESPRESSO' in inst:
-
             find_mode = [ESPRESSO_mode in pipe for pipe in pipelines]
             # the mode was not found
             if not any(find_mode):
@@ -160,12 +167,12 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
 
     found_dace_id = False
     try:
-        dace_id = get_dace_id(star, verbose=verbose)
+        dace_id = get_dace_id(star, verbose=verbose, raise_error=True)
         found_dace_id = True
     except ValueError as e:
         if main_id is not None:
             try:
-                dace_id = get_dace_id(main_id, verbose=verbose)
+                dace_id = get_dace_id(main_id, verbose=verbose, raise_error=True)
                 found_dace_id = True
             except ValueError:
                 pass
@@ -259,6 +266,7 @@ def get_observations_from_instrument(star, instrument, user=None, main_id=None,
     return r
 
 def get_observations(star, instrument=None, user=None, main_id=None, verbose=True):
+    logger = setup_logger()
     if instrument is None:
         Spectroscopy = load_spectroscopy(user)
 
@@ -444,6 +452,7 @@ def extract_fits(output_directory, filename=None):
 
 
 def do_symlink_filetype(type, raw_files, output_directory, clobber=False, top_level=None, verbose=True):
+    logger = setup_logger()
     terminations = {
         'CCF': '_CCF_A.fits',
         'S1D': '_S1D_A.fits',
@@ -489,6 +498,7 @@ def do_symlink_filetype(type, raw_files, output_directory, clobber=False, top_le
 def do_download_filetype(type, raw_files, output_directory, clobber=False, user=None,
                          verbose=True, chunk_size=20, parallel_limit=30):
     """ Download CCFs / S1Ds / S2Ds from DACE """
+    logger = setup_logger()
     raw_files = np.atleast_1d(raw_files)
 
     create_directory(output_directory)

arvi/exofop_wrapper.py

@@ -4,9 +4,10 @@ import time
 import importlib.resources as resources
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 
 def get_toi_list(verbose=True):
+    logger = setup_logger()
     toi_list = resources.files('arvi') / 'data' / 'exofop_toi_list.csv'
     now = time.time()
     download = not toi_list.exists() or toi_list.stat().st_mtime < now - 48 * 60 * 60

arvi/extra_data.py

@@ -3,8 +3,7 @@ from glob import glob
 import json
 
 from numpy import full
-from .setup_logger import logger
-from . import timeseries
+from .setup_logger import setup_logger
 
 refs = {
     'HD86226': 'Teske et al. 2020 (AJ, 160, 2)'
@@ -12,7 +11,8 @@ refs = {
 
 def get_extra_data(star, instrument=None, path=None, verbose=True,
                    check_for_kms=True):
-    
+    from . import timeseries
+    logger = setup_logger()
     if path is None:
         path = os.path.dirname(__file__)
         path = os.path.join(path, 'data', 'extra')

arvi/instrument_specific.py

@@ -1,7 +1,7 @@
 import os, sys
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .utils import ESPRESSO_ADC_issues, ESPRESSO_cryostat_issues
 
 
@@ -27,6 +27,7 @@ ESPRESSO_technical_intervention = 58665
 
 def divide_ESPRESSO(self):
     """ Split ESPRESSO data into separate sub ESP18 and ESP19 subsets """
+    logger = setup_logger()
     if self._check_instrument('ESPRESSO', strict=False) is None:
         return
     if 'ESPRESSO18' in self.instruments and 'ESPRESSO19' in self.instruments:
@@ -64,6 +65,7 @@ def divide_ESPRESSO(self):
 
 def divide_HARPS(self):
     """ Split HARPS data into separate sub HARPS03 and HARPS15 subsets """
+    logger = setup_logger()
     if self._check_instrument('HARPS', strict=False) is None:
         return
     if 'HARPS03' in self.instruments and 'HARPS15' in self.instruments:
@@ -100,6 +102,7 @@ def divide_HARPS(self):
     
 
 def check(self, instrument):
+    logger = setup_logger()
     instruments = self._check_instrument(instrument)
     if instruments is None:
         if self.verbose:
@@ -118,6 +121,7 @@ def HARPS_commissioning(self, mask=True, plot=True):
         plot (bool, optional):
             Whether to plot the masked points.
     """
+    logger = setup_logger()
     if check(self, 'HARPS') is None:
         return
 
@@ -149,6 +153,7 @@ def HARPS_fiber_commissioning(self, mask=True, plot=True):
         plot (bool, optional):
             Whether to plot the masked points.
     """
+    logger = setup_logger()
     if check(self, 'HARPS') is None:
         return
 
@@ -182,6 +187,7 @@ def ADC_issues(self, mask=True, plot=True, check_headers=False):
         check_headers (bool, optional):
             Whether to (double-)check the headers for missing/zero keywords.
     """
+    logger = setup_logger()
     instruments = self._check_instrument('ESPRESSO')
     
     if instruments is None:
@@ -225,6 +231,7 @@ def blue_cryostat_issues(self, mask=True, plot=True):
         mask (bool, optional): Whether to mask out the points.
         plot (bool, optional): Whether to plot the masked points.
     """
+    logger = setup_logger()
     instruments = self._check_instrument('ESPRESSO')
     
     if instruments is None:
@@ -259,6 +266,7 @@ def qc_scired_issues(self, plot=False, **kwargs):
     Args:
         plot (bool, optional): Whether to plot the masked points.
     """
+    logger = setup_logger()
     from .headers import get_headers
 
     instruments = self._check_instrument('ESPRESSO')
@@ -299,38 +307,40 @@ def qc_scired_issues(self, plot=False, **kwargs):
     return affected
 
 
-def known_issues(self, mask=True, plot=False, **kwargs):
-    """ Identify and optionally mask known instrumental issues.
-
-    Args:
-        mask (bool, optional): Whether to mask out the points.
-        plot (bool, optional): Whether to plot the masked points.
-    """
-    try:
-        adc = ADC_issues(self, mask, plot, **kwargs)
-    except IndexError:
-        logger.error('are the data binned? cannot proceed to mask these points...')
-
-    try:
-        cryostat = blue_cryostat_issues(self, mask, plot)
-    except IndexError:
-        logger.error('are the data binned? cannot proceed to mask these points...')
-
-    try:
-        harps_comm = HARPS_commissioning(self, mask, plot)
-    except IndexError:
-        logger.error('are the data binned? cannot proceed to mask these points...')
-
-    try:
-        harps_fibers = HARPS_fiber_commissioning(self, mask, plot)
-    except IndexError:
-        logger.error('are the data binned? cannot proceed to mask these points...')
-
-    # if None in (adc, cryostat, harps_comm, harps_fibers):
-    #     return
-
-    try:
-        # return adc | cryostat
-        return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
-    except UnboundLocalError:
-        return
+class ISSUES:
+    def known_issues(self, mask=True, plot=False, **kwargs):
+        """ Identify and optionally mask known instrumental issues.
+
+        Args:
+            mask (bool, optional): Whether to mask out the points.
+            plot (bool, optional): Whether to plot the masked points.
+        """
+        logger = setup_logger()
+        try:
+            adc = ADC_issues(self, mask, plot, **kwargs)
+        except IndexError:
+            logger.error('are the data binned? cannot proceed to mask these points...')
+
+        try:
+            cryostat = blue_cryostat_issues(self, mask, plot)
+        except IndexError:
+            logger.error('are the data binned? cannot proceed to mask these points...')
+
+        try:
+            harps_comm = HARPS_commissioning(self, mask, plot)
+        except IndexError:
+            logger.error('are the data binned? cannot proceed to mask these points...')
+
+        try:
+            harps_fibers = HARPS_fiber_commissioning(self, mask, plot)
+        except IndexError:
+            logger.error('are the data binned? cannot proceed to mask these points...')
+
+        # if None in (adc, cryostat, harps_comm, harps_fibers):
+        #     return
+
+        try:
+            # return adc | cryostat
+            return np.logical_or.reduce((adc, cryostat, harps_comm, harps_fibers))
+        except UnboundLocalError:
+            return

arvi/plots.py

@@ -5,7 +5,7 @@ import numpy as np
 
 from astropy.timeseries import LombScargle
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .config import config
 from .stats import wmean
 
@@ -13,10 +13,12 @@ from .utils import lazy_import
 plt = lazy_import('matplotlib.pyplot')
 
 
-def plot_fast(func):
+def plot_settings(func):
     @wraps(func)
     def wrapper(*args, **kwargs):
-        with plt.style.context('fast'):
+        # with plt.style.context('fast'):
+        theme = 'dark_background' if config.dark_plots else 'fast'
+        with plt.style.context(theme):
             return func(*args, **kwargs)
     return wrapper
 
@@ -135,7 +137,7 @@ def clickable_legend(fig, ax, leg):
                 pass
     return on_pick_legend
 
-# @plot_fast
+@plot_settings
 def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
          remove_50000=False, tooltips=True, show_title=False, show_legend=True, label=None, 
          jitter=None, N_in_label=False, versus_n=False, show_histogram=False, bw=False, **kwargs):
@@ -172,6 +174,7 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
         Figure: the figure
         Axes: the axis
     """
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to plot')
@@ -402,10 +405,11 @@ def plot(self, ax=None, show_masked=False, instrument=None, time_offset=0,
     return fig, ax
 
 
-@plot_fast
+# @plot_fast
 def plot_quantity(self, quantity, ax=None, show_masked=False, instrument=None,
                   time_offset=0, remove_50000=False, tooltips=False, show_legend=True,
                   N_in_label=False, **kwargs):
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to plot')
@@ -504,7 +508,88 @@ plot_rhk = partialmethod(plot_quantity, quantity='rhk')
 plot_berv = partialmethod(plot_quantity, quantity='berv')
 
 
-@plot_fast
+def plot_xy(self, x, y, ax=None, instrument=None, show_legend=True, **kwargs):
+    logger = setup_logger()
+    if self.N == 0:
+        if self.verbose:
+            logger.error('no data to plot')
+        return
+
+    if ax is None:
+        fig, ax = plt.subplots(1, 1, constrained_layout=True)
+    else:
+        fig = ax.figure
+
+    kwargs.setdefault('marker', 'o')
+    kwargs.setdefault('ls', '')
+    kwargs.setdefault('capsize', 0)
+    kwargs.setdefault('ms', 4)
+
+    instruments = self._check_instrument(instrument)
+
+    for inst in instruments:
+        s = self if self._child else getattr(self, inst)
+        label = inst
+
+        missing = False
+        try:
+            xdata = getattr(s, x).copy()
+        except AttributeError:
+            missing = True
+        try:
+            e_xdata = getattr(s, x + '_err').copy()
+        except AttributeError:
+            e_xdata = np.zeros_like(xdata)
+
+        try:
+            ydata = getattr(s, y).copy()
+        except AttributeError:
+            missing = True
+        try:
+            e_ydata = getattr(s, y + '_err').copy()
+        except AttributeError:
+            e_ydata = np.zeros_like(ydata)
+
+        if missing:
+            lines, *_ = ax.errorbar([], [], [],
+                                    label=label, picker=True, **kwargs)
+            continue
+
+        ax.errorbar(xdata[s.mask], ydata[s.mask], e_xdata[s.mask], e_ydata[s.mask],
+                    label=label, **kwargs)
+
+    # if show_masked:
+    #     ax.errorbar(self.time[~self.mask] - time_offset,
+    #                 getattr(self, quantity)[~self.mask],
+    #                 getattr(self, quantity + '_err')[~self.mask],
+    #                 label='masked', fmt='x', ms=10, color='k', zorder=-2)
+
+    if show_legend:
+        leg = ax.legend()
+        on_pick_legend = clickable_legend(fig, ax, leg)
+        plt.connect('pick_event', on_pick_legend)
+
+    ax.minorticks_on()
+
+    delta = 'Δ' if self._did_adjust_means else ''
+
+    # ylabel = {
+    #     quantity.lower(): quantity,
+    #     'fwhm': f'{delta}FWHM [{self.units}]',
+    #     'bispan': f'{delta}BIS [{self.units}]',
+    #     'rhk': r"$\log$ R'$_{HK}$",
+    #     'berv': 'BERV [km/s]',
+    # }
+
+    # ax.set_ylabel(ylabel[quantity.lower()])
+
+    if config.return_self:
+        return self
+    else:
+        return fig, ax
+
+
+# @plot_fast
 def gls(self, ax=None, label=None, instrument=None, 
         fap=True, fap_method='baluev', adjust_means=config.adjust_means_gls,
         picker=True, **kwargs):
@@ -531,6 +616,7 @@ def gls(self, ax=None, label=None, instrument=None,
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
     """
+    logger = setup_logger()
     if self.N == 0:
         if self.verbose:
             logger.error('no data to compute gls')
@@ -692,7 +778,7 @@ def gls_quantity(self, quantity, ax=None, instrument=None,
             Whether to adjust (subtract) the weighted means of each instrument.
             Default is `config.adjust_means_gls`.
     """
-
+    logger = setup_logger()
     if not hasattr(self, quantity):
         if self.verbose:
             logger.error(f"cannot find '{quantity}' attribute")
@@ -812,6 +898,8 @@ def window_function(self, ax1=None, ax2=None, instrument=None, crosshair=False,
         crosshair (bool):
             If True, a crosshair will be drawn on the plot.
     """
+    logger = setup_logger()
+
     if self.N == 0:
         if self.verbose:
             logger.error('no data to compute window function')

arvi/reports.py

@@ -2,7 +2,7 @@ from functools import partial
 import numpy as np
 from astropy.timeseries import LombScargle
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 
 
 sine_line = None
@@ -27,104 +27,178 @@ def sine_picker(event, self, fig, ax, ax1):
     fig.canvas.draw_idle()
 
 
-def summary(self, add_ccf_mask=True, add_prog_id=False):
-    from .utils import pretty_print_table
-    rows = []
-    rows.append([self.star] + [''] * len(self.instruments))
-    rows.append([''] + self.instruments)
-    rows.append(['N'] + list(self.NN.values()))
-
-    if add_ccf_mask:
-        row = ['CCF mask']
-        for inst in self.instruments:
-            row.append(', '.join(np.unique(getattr(self, inst).ccf_mask)))
-        rows.append(row)
-
-    if add_prog_id:
-        row = ['prog ID']
-        for inst in self.instruments:
-            p = ', '.join(np.unique(getattr(self, inst).prog_id))
-            row.append(p)
-        rows.append(row)
-
-    pretty_print_table(rows)
-
-
-def report(self, save=None):
-    import matplotlib.pyplot as plt
-    import matplotlib.gridspec as gridspec
-    from matplotlib.backends.backend_pdf import PdfPages
-
-    # size = A4
-    size = 8.27, 11.69
-    fig = plt.figure(figsize=size, constrained_layout=True)
-    gs = gridspec.GridSpec(5, 3, figure=fig, height_ratios=[2, 2, 1, 1, 0.1])
-
-    # first row, all columns
-    ax1 = plt.subplot(gs[0, :])
-
-    title = f'{self.star}'
-    ax1.set_title(title, loc='left', fontsize=14)
-    # ax1.set_title(r"\href{http://www.google.com}{link}", color='blue',
-    #               loc='center')
-
-    if self._did_adjust_means:
-        title = '(instrument means subtracted) '
-    else:
-        title = ''
-    title += f'V={self.simbad.V}, {self.simbad.sp_type}'
-    ax1.set_title(title, loc='right', fontsize=12)
-
-    self.plot(ax=ax1, N_in_label=True, tooltips=False, remove_50000=True)
-
-
-    ax1.legend().remove()
-    legend_ax = plt.subplot(gs[1, -1])
-    legend_ax.axis('off')
-    leg = plt.legend(*ax1.get_legend_handles_labels(),
-                     prop={'family': 'monospace'})
-    legend_ax.add_artist(leg)
-    second_legend = f'rms  : {self.rms:.2f} {self.units}\n'
-    second_legend += f'error: {self.error:.2f} {self.units}'
-    legend_ax.legend([],
-                     title=second_legend,
-                     loc='lower right', frameon=False,
-                     prop={'family': 'monospace'})
-
-    ax2 = plt.subplot(gs[1, :-1])
-    self.gls(ax=ax2, picker=True)
-
-    ax3 = plt.subplot(gs[2, :-1])
-    self.plot_fwhm(ax=ax3, tooltips=False, remove_50000=True)
-    ax3.legend().remove()
-    ax3p = plt.subplot(gs[2, -1])
-    self.gls_fwhm(ax=ax3p, picker=False)
-
-    ax4 = plt.subplot(gs[3, :-1])
-    self.plot_bis(ax=ax4, tooltips=False, remove_50000=True)
-    ax4.legend().remove()
-    ax4p = plt.subplot(gs[3, -1])
-    self.gls_bis(ax=ax4p, picker=False)
-
-
-    if save is None:
-        fig.canvas.mpl_connect(
-            'pick_event',
-            partial(sine_picker, self=self, fig=fig, ax=ax2, ax1=ax1))
-
-    if save is not None:
-        if save is True:
-            save = f'report_{"".join(self.star.split())}.pdf'
-
-        if save.endswith('.png'):
-            fig.savefig(save)
+class REPORTS:
+    def summary(self, add_ccf_mask=True, add_prog_id=False, **kwargs):
+        from .utils import pretty_print_table
+        if isinstance(self, list):
+            selfs = self
         else:
-            with PdfPages(save) as pdf:
-                #pdf.attach_note('hello', positionRect=[5, 15, 20, 30])
-
-                if self.verbose:
-                    logger.info(f'saving to {save}')
-                pdf.savefig(fig)
-            # os.system(f'evince {save} &')
-
-    return fig
+            selfs = [self]
+        
+        rows = []
+        for self in selfs:
+            rows.append([self.star] + [''] * len(self.instruments) + [''])
+            rows.append([''] + self.instruments + ['full'])
+            rows.append(['N'] + list(self.NN.values()) + [self.N])
+            rows.append(['RV span'] + [np.ptp(s.mvrad).round(3) for s in self] + [np.ptp(self.mvrad).round(3)])
+            rows.append(['RV std'] + [s.mvrad.std().round(3) for s in self] + [self.mvrad.std().round(3)])
+            rows.append(['eRV mean'] + [s.msvrad.mean().round(3) for s in self] + [self.msvrad.mean().round(3)])
+
+            if add_ccf_mask:
+                if hasattr(self, 'ccf_mask'):
+                    row = ['CCF mask']
+                    for inst in self.instruments:
+                        row.append(', '.join(np.unique(getattr(self, inst).ccf_mask)))
+                    row.append('')
+                    rows.append(row)
+
+            if add_prog_id:
+                row = ['prog ID']
+                for inst in self.instruments:
+                    p = ', '.join(np.unique(getattr(self, inst).prog_id))
+                    row.append(p)
+                rows.append(row)
+
+        return pretty_print_table(rows, **kwargs)
+
+
+    def summary_one_instrument(self):
+        from .utils import pretty_print_table
+        if isinstance(self, list):
+            selfs = self
+        else:
+            selfs = [self]
+
+        rows = []
+        rows.append(['', 'N', 'Δt', 'RV std', 'median σRV'])
+        for self in selfs:
+            rows.append([
+                self.star, 
+                self.N, 
+                int(np.ptp(self.mtime).round(0)),
+                np.std(self.mvrad).round(1),
+                np.median(self.msvrad).round(1),
+            ])
+
+        pretty_print_table(rows)
+
+
+    def summary_stellar(self, show_ra_dec=True, show_pm=True, **kwargs):
+        from .utils import pretty_print_table, get_ra_sexagesimal, get_dec_sexagesimal
+        if isinstance(self, list):
+            selfs = self
+        else:
+            selfs = [self]
+        
+
+
+        rows = []
+        rows.append(['star'] + [self.star for self in selfs])
+        if show_ra_dec:
+            rows.append(['RA'] + [get_ra_sexagesimal(self.simbad.ra) for self in selfs])
+            rows.append(['DEC'] + [get_dec_sexagesimal(self.simbad.dec) for self in selfs])
+        
+        if show_pm:
+            rows.append(['pm ra'] + [(self.gaia or self.simbad).pmra for self in selfs])
+            rows.append(['pm dec'] + [(self.gaia or self.simbad).pmdec for self in selfs])
+
+        rows.append(['π (mas)'] + [(self.gaia or self.simbad).plx for self in selfs])
+        # 
+        rows.append(['B (mag)'] + [self.simbad._B for self in selfs])
+        rows.append(['V (mag)'] + [self.simbad._V for self in selfs])
+        rows.append(['B-V'] + [self.simbad._B - self.simbad._V for self in selfs])
+        rows.append(["log R'HK"] + [np.nanmean(self.rhk).round(2) for self in selfs])
+            # rows.append([''] + self.instruments + ['full'])
+            # rows.append(['N'] + list(self.NN.values()) + [self.N])
+            # rows.append(['RV span'] + [np.ptp(s.mvrad).round(3) for s in self] + [np.ptp(self.mvrad).round(3)])
+            # rows.append(['RV std'] + [s.mvrad.std().round(3) for s in self] + [self.mvrad.std().round(3)])
+            # rows.append(['eRV mean'] + [s.msvrad.mean().round(3) for s in self] + [self.msvrad.mean().round(3)])
+
+        return pretty_print_table(rows, **kwargs)
+
+
+
+
+    def report(self, save=None):
+        import matplotlib.pyplot as plt
+        import matplotlib.gridspec as gridspec
+        from matplotlib.backends.backend_pdf import PdfPages
+        logger = setup_logger()
+
+        # size = A4
+        size = 8.27, 11.69
+        fig = plt.figure(figsize=size, constrained_layout=True)
+        gs = gridspec.GridSpec(5, 3, figure=fig, height_ratios=[2, 2, 1, 1, 0.1])
+
+        # first row, all columns
+        ax1 = plt.subplot(gs[0, :])
+
+        title = f'{self.star}'
+        ax1.set_title(title, loc='left', fontsize=14)
+        # ax1.set_title(r"\href{http://www.google.com}{link}", color='blue',
+        #               loc='center')
+
+        if self._did_adjust_means:
+            title = '(instrument means subtracted) '
+        else:
+            title = ''
+        title += f'V={self.simbad.V}, {self.simbad.sp_type}'
+        ax1.set_title(title, loc='right', fontsize=12)
+
+        self.plot(ax=ax1, N_in_label=True, tooltips=False, remove_50000=True)
+
+
+        ax1.legend().remove()
+        legend_ax = plt.subplot(gs[1, -1])
+        legend_ax.axis('off')
+        leg = plt.legend(*ax1.get_legend_handles_labels(),
+                        prop={'family': 'monospace'})
+        legend_ax.add_artist(leg)
+        
+        second_legend = f'rms  : {self.rms:.2f} {self.units}'
+        second_legend += f'\nerror: {self.error:.2f} {self.units}'
+
+        second_legend += f'\n\nCCF masks: {np.unique(self.ccf_mask)}'
+
+        legend_ax.legend([],
+                        title=second_legend,
+                        loc='lower right', frameon=False,
+                        prop={'family': 'monospace'})
+
+        ax2 = plt.subplot(gs[1, :-1])
+        self.gls(ax=ax2, picker=True)
+
+        ax3 = plt.subplot(gs[2, :-1])
+        self.plot_fwhm(ax=ax3, tooltips=False, remove_50000=True)
+        ax3.legend().remove()
+        ax3p = plt.subplot(gs[2, -1])
+        self.gls_fwhm(ax=ax3p, picker=False)
+
+        ax4 = plt.subplot(gs[3, :-1])
+        self.plot_rhk(ax=ax4, tooltips=False, remove_50000=True)
+        ax4.legend().remove()
+        ax4p = plt.subplot(gs[3, -1])
+        self.gls_rhk(ax=ax4p, picker=False)
+
+
+        if save is None:
+            fig.canvas.mpl_connect(
+                'pick_event',
+                partial(sine_picker, self=self, fig=fig, ax=ax2, ax1=ax1))
+
+        if save is not None:
+            if save is True:
+                save = f'report_{"".join(self.star.split())}.pdf'
+
+            if save.endswith('.png'):
+                fig.savefig(save)
+            else:
+                with PdfPages(save) as pdf:
+                    #pdf.attach_note('hello', positionRect=[5, 15, 20, 30])
+
+                    if self.verbose:
+                        logger.info(f'saving to {save}')
+                    pdf.savefig(fig)
+                # os.system(f'evince {save} &')
+
+        return fig

arvi/setup_logger.py

@@ -1,20 +1,24 @@
 import sys
-from loguru import logger
 
-try:
-    import marimo as mo
-    if mo.running_in_notebook():
-        raise ImportError
-except (ImportError, ModuleNotFoundError):
-    pass
-else:
-    logger.remove()
+def setup_logger():
+    from loguru import logger
+    try:
+        import marimo as mo
+        if mo.running_in_notebook():
+            raise NotImplementedError
+    except (NotImplementedError, AttributeError):
+        pass
+    except (ImportError, ModuleNotFoundError):
+        logger.remove()
+    else:
+        logger.remove()
 
+    logger.configure(extra={"indent": ""})
+    logger.add(
+        sys.stdout,
+        colorize=True,
+        # format="<green>{time:YYYY-MM-DDTHH:mm:ss}</green> <level>{message}</level>",
+        format="{extra[indent]}<level>{message}</level>",
+    )
 
-logger.configure(extra={"indent": ""})
-logger.add(
-    sys.stdout,
-    colorize=True,
-    # format="<green>{time:YYYY-MM-DDTHH:mm:ss}</green> <level>{message}</level>",
-    format="{extra[indent]}<level>{message}</level>",
-)
+    return logger

arvi/simbad_wrapper.py

@@ -1,9 +1,8 @@
 import os
-import numpy as np
 import requests
 from dataclasses import dataclass
 
-import pysweetcat
+import numpy as np
 
 try:
     from uncertainties import ufloat
@@ -12,7 +11,6 @@ except ImportError:
 
 from .stellar import EFFECTIVE_TEMPERATURES, teff_to_sptype
 from .translations import translate
-from .setup_logger import logger
 
 DATA_PATH = os.path.dirname(__file__)
 DATA_PATH = os.path.join(DATA_PATH, 'data')
@@ -146,6 +144,7 @@ class simbad:
             star (str): The name of the star to query simbad
         """
         from astropy.coordinates import SkyCoord
+        import pysweetcat
 
         self.star = translate(star, ngc=True, ic=True)
 

arvi/timeseries.py

@@ -1,14 +1,16 @@
 import os
 from dataclasses import dataclass, field
 from typing import Union
-from functools import lru_cache, partial, partialmethod
+from functools import partial, partialmethod
 from glob import glob
 import warnings
 from copy import deepcopy
 from datetime import datetime, timezone
 import numpy as np
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
+logger = setup_logger()
+
 from .config import config
 from .translations import translate
 from .dace_wrapper import do_download_filetype, do_symlink_filetype, get_observations, get_arrays
@@ -19,6 +21,8 @@ from .extra_data import get_extra_data
 from .stats import wmean, wrms
 from .binning import bin_ccf_mask, binRV
 from .HZ import getHZ_period
+from .instrument_specific import ISSUES
+from .reports import REPORTS
 from .utils import sanitize_path, strtobool, there_is_internet, timer, chdir
 from .utils import lazy_import
 
@@ -31,8 +35,8 @@ class ExtraFields:
         return list(self.__dict__.keys())
 
 
-@dataclass
-class RV:
+@dataclass(order=False)
+class RV(ISSUES, REPORTS):
     """
     A class holding RV observations
 
@@ -1245,9 +1249,9 @@ class RV:
 
     from .plots import plot, plot_fwhm, plot_bispan, plot_contrast, plot_rhk, plot_berv, plot_quantity
     from .plots import gls, gls_fwhm, gls_bispan, gls_rhk, gls_quantity, window_function
-    from .reports import report
 
-    from .instrument_specific import known_issues
+    # from .reports import report
+    # from .instrument_specific import known_issues
 
     def change_instrument_name(self, old_name, new_name, strict=False):
         """ Change the name of an instrument

arvi/utils.py

@@ -21,7 +21,7 @@ except ImportError:
     tqdm = lambda x, *args, **kwargs: x
     trange = lambda *args, **kwargs: range(*args, **kwargs)
 
-from .setup_logger import logger
+from .setup_logger import setup_logger
 from .config import config
 
 
@@ -70,6 +70,8 @@ def all_logging_disabled():
 @contextmanager
 def timer(name=None):
     """ A simple context manager to time a block of code """
+    logger = setup_logger()
+
     if not config.debug:
         yield
         return

{arvi-0.2.2.dist-info → arvi-0.2.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: arvi
-Version: 0.2.2
+Version: 0.2.4
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -23,7 +23,7 @@ Requires-Dist: kepmodel
 Dynamic: license-file
 
 <p align="center">
-  <img width = "140" src="https://github.com/j-faria/arvi/blob/main/docs/logo/logo.png?raw=true"/>
+  <img width = "140" src="https://raw.githubusercontent.com/j-faria/arvi/refs/heads/main/docs/logo/logo.png"/>
 </p>
 
 This package sits alongside [DACE](https://dace.unige.ch/) to help with the

{arvi-0.2.2.dist-info → arvi-0.2.4.dist-info}/RECORD

@@ -1,37 +1,37 @@
 arvi/HZ.py,sha256=u7rguhlILRBW-LOczlY3dkIB4LM8p8W7Xfg4FnNaYG0,2850
-arvi/__init__.py,sha256=sgl66ujggmM6wUh1Og65MAXfL0YqcrjY6o7E6iQOSsI,1048
+arvi/__init__.py,sha256=8IeHbu8LR1H3MxVi9aJHNpBU6SDbmzj9FZGKsiF0AKE,740
 arvi/ariadne_wrapper.py,sha256=YvilopJa9T4NwPcj3Nah_U8smSeSAU5-HYZMb_GJ-BQ,2232
 arvi/berv.py,sha256=eKnpuPC1w45UrUEyFRbs9F9j3bXz3kxYzNXbnRgvFQM,17596
-arvi/binning.py,sha256=jbemJ-bM3aqoOsqMo_OhWt_co-JAQ0nhdG_GpTsrRsw,15403
-arvi/config.py,sha256=W-v8NNhRd_PROu0wCMilXmOhYcju4xbUalugd5u7SRU,1881
-arvi/dace_wrapper.py,sha256=b0uBw2Or8ElsRky25iYP2uFkOb9I3BUo7lC-UwajcFg,23341
-arvi/exofop_wrapper.py,sha256=ceBLff_8TWqUKWsYMsTESI2dPGE4upAHAJjwWzmRj4o,2380
-arvi/extra_data.py,sha256=bInAgiZNuw5vkxcCYf1Ns4w72PoxpqwV48RFBIZ3rGE,3364
+arvi/binning.py,sha256=NK9y9bUrdyWCbh79LkcRABHG-n5MtlETMHMvLj1z-OM,15437
+arvi/config.py,sha256=JkHSwF-EEqwwbcc8thGgbFc9udDZPjQH-9XFjqDepBY,2337
+arvi/dace_wrapper.py,sha256=uUiHHqyU8T74cmgGtVVoJKbVnTGLjNYYIUkR2BeAtvk,23636
+arvi/exofop_wrapper.py,sha256=8S7UEcrBAgANIweMV0-CvaWaVTPgGVo8vQQk_KRa0nU,2414
+arvi/extra_data.py,sha256=Xi65pI5kkzqlMmHGl9xFoumtH699611pJJ5PV-a_IfU,3397
 arvi/gaia_wrapper.py,sha256=jfBdK9N9ZOqHIzE5MRFmXNyN3PAOT_uzXM23MIy0POY,4371
 arvi/headers.py,sha256=uvdJebw1M5YkGjE3vJJwYBOnLikib75uuZE9FXB5JJM,1673
-arvi/instrument_specific.py,sha256=ORjlw79EumEiGugmGn_2WBOuEPhsfgDNryEMBDe9RgM,10733
+arvi/instrument_specific.py,sha256=StRcHVDszm2a4yMWkO1pYYCsEWvXsS2ZtYTrSGD9JHM,11125
 arvi/kima_wrapper.py,sha256=BvNTVqzM4lMNhLCyBFVh3T84hHfGKAFpgiYiOi4lh0g,2731
 arvi/lbl_wrapper.py,sha256=_ViGVkpakvuBR_xhu9XJRV5EKHpj5Go6jBZGJZMIS2Y,11850
 arvi/nasaexo_wrapper.py,sha256=mWt7eHgSZe4MBKCmUvMPTyUPGuiwGTqKugNBvmjOg9s,7306
-arvi/plots.py,sha256=EheFTUldVaslO5GDpgCKl9jgyc_5ipluDTfmah05-5w,32693
+arvi/plots.py,sha256=fHc6ScATCzvM4KQ77TYfHYmY6HSZ4N4oMYsLEUvxJpU,35279
 arvi/programs.py,sha256=BW7xBNKLei7NVLLW3_lsVskwzkaIoNRiHK2jn9Tn2ZM,8879
-arvi/reports.py,sha256=ayPdZ4HZO9iCDdnADQ18gQPJh79o-1UYG7TYkvm9Lrc,4051
-arvi/setup_logger.py,sha256=26Z0uyzlOJCYOT_pJixJZWQfWEND_DZl5358RadMD8Y,431
-arvi/simbad_wrapper.py,sha256=vDSsxwCsqiasjxOPJRUw3lC870qbIixLGQOaQOM8tgI,8654
+arvi/reports.py,sha256=CKmtg5rewMyT26gbWeoZDYrL0z5Sbb6cTJry0HWk_rs,7445
+arvi/setup_logger.py,sha256=dHzO2gPjw6CaKWpYZd2f83z09tmxgi--qpp7k1jROjI,615
+arvi/simbad_wrapper.py,sha256=U1XmOR7bg_mq4KSutTgEsusjBph8BfEqHh-8YuHNMog,8629
 arvi/spectra.py,sha256=ebF1ocodTastLx0CyqLSpE8EZNDXBF8riyfxMr3L6H0,7491
 arvi/stats.py,sha256=ilzzGL9ew-SyVa9eEdrYCpD3DliOAwhoNUg9LIlHjzU,2583
 arvi/stellar.py,sha256=GQ7yweuBRnfkJ0M5eWjvLd8uvGq_by81PbXfidBvWis,4918
-arvi/timeseries.py,sha256=_p4Ovv_xGQkLxCCCyaU-KkdtcoK21RdBq58bBEpNPd0,90751
+arvi/timeseries.py,sha256=CCTcuA9vk3KUiXygsSgP9_pA0EeNdqh-tHHZUUuF4tA,90874
 arvi/translations.py,sha256=PUSrn4zvYO2MqGzUxlFGwev_tBkgJaJrIYs6NKHzbWo,951
-arvi/utils.py,sha256=V4uSpr75YVjE0NP3T5PxnfVQQ06nd-O8X679BfVyD30,7068
+arvi/utils.py,sha256=BZoafVF1TWCI44GSMi1o66kJ1wqihjaqpf3y1Q3XGlk,7103
 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
 arvi/data/extra/metadata.json,sha256=C69hIw6CohyES6BI9vDWjxwSz7N4VOYX0PCgjXtYFmU,178
-arvi-0.2.2.dist-info/licenses/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
-arvi-0.2.2.dist-info/METADATA,sha256=29i7G2YPkMftx3Mhk9UvitLbiWoiIqjWDPUshqrOK4Y,1920
-arvi-0.2.2.dist-info/WHEEL,sha256=SmOxYU7pzNKBqASvQJ7DjX3XGUF92lrGhMb3R6_iiqI,91
-arvi-0.2.2.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
-arvi-0.2.2.dist-info/RECORD,,
+arvi-0.2.4.dist-info/licenses/LICENSE,sha256=6JfQgl7SpM55t0EHMFNMnNh-AdkpGW25MwMiTnhdWQg,1068
+arvi-0.2.4.dist-info/METADATA,sha256=LCnkFQigSAvVBAB-5yy53uPgFSw13sdbGYX_qreIf9s,1932
+arvi-0.2.4.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
+arvi-0.2.4.dist-info/top_level.txt,sha256=4EeiKDVLD45ztuflTGfQ3TU8GVjJg5Y95xS5XjI-utU,5
+arvi-0.2.4.dist-info/RECORD,,

{arvi-0.2.2.dist-info → arvi-0.2.4.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (79.0.1)
+Generator: setuptools (80.7.1)
 Root-Is-Purelib: true
 Tag: py3-none-any