arvi 0.1.5__tar.gz → 0.1.6__tar.gz

{arvi-0.1.5 → arvi-0.1.6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.5
+Version: 0.1.6
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -29,18 +29,6 @@ Requires-Dist: kepmodel
 
 
 
-## Goals
-
-- _Fast_:
-  all `arvi` operations must be completed in under **1 second**
-
-- _Reproducible_:
-  **everyone** must be able to use `arvi`
-
-- _Accurate_:
-  `arvi` must always provide the **correct result**
-
-
 #### Actions
 
 [![Deploy docs](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml)

{arvi-0.1.5 → arvi-0.1.6}/README.md

@@ -4,20 +4,8 @@
 
 
 
-## Goals
-
-- _Fast_:
-  all `arvi` operations must be completed in under **1 second**
-
-- _Reproducible_:
-  **everyone** must be able to use `arvi`
-
-- _Accurate_:
-  `arvi` must always provide the **correct result**
-
-
 #### Actions
 
 [![Deploy docs](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml)
 [![Install-Test](https://github.com/j-faria/arvi/actions/workflows/install.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/install.yml)
-[![Upload Python Package](https://github.com/j-faria/arvi/actions/workflows/python-publish.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/python-publish.yml)
+[![Upload Python Package](https://github.com/j-faria/arvi/actions/workflows/python-publish.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/python-publish.yml)

{arvi-0.1.5 → arvi-0.1.6}/arvi/dace_wrapper.py

@@ -152,14 +152,22 @@ def get_observations(star, instrument=None, save_rdb=False, verbose=True):
 
 def check_existing(output_directory, files, type):
     existing = [
-        f.partition('_')[0] for f in os.listdir(output_directory)
+        f.partition('.fits')[0] for f in os.listdir(output_directory)
         if type 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]
+    
+    # remove type of file (e.g. _CCF_A)
+    existing = [f.partition('_')[0] for f in existing]
+    
     missing = []
     for file in files:
         if any(other in file for other in existing):
             continue
         missing.append(file)
+
     return np.array(missing)
 
 def download(files, type, output_directory):

{arvi-0.1.5 → arvi-0.1.6}/arvi/plots.py

@@ -272,7 +272,7 @@ def gls(self, ax=None, label=None, fap=True, picker=True, instrument=None, **kwa
         y = self.vrad[self.mask]
         e = self.svrad[self.mask]
 
-    gls = LombScargle(t, y, e)
+    self._gls = gls = LombScargle(t, y, e)
     freq, power = gls.autopower(maximum_frequency=1.0, samples_per_peak=10)
     ax.semilogx(1/freq, power, picker=picker, label=label, **kwargs)
 

{arvi-0.1.5 → arvi-0.1.6}/arvi/timeseries.py

@@ -294,9 +294,9 @@ class RV:
             star, timestamp = file.replace('.pkl', '').split('_')
         else:
             try:
-                file = sorted(glob(f'{star}*.pkl'))[-1]
+                file = sorted(glob(f'{star}_*.pkl'))[-1]
             except IndexError:
-                raise ValueError(f'cannot find any file matching {star}*.pkl')
+                raise ValueError(f'cannot find any file matching {star}_*.pkl')
             star, timestamp = file.replace('.pkl', '').split('_')
 
         dt = datetime.fromtimestamp(float(timestamp))
@@ -314,7 +314,7 @@ class RV:
                 logger.info(f'assuming star is {star_[0]}')
                 star = star_[0]
         
-        instruments = np.unique([os.path.splitext(f)[0].split('_')[1] for f in files])
+        instruments = np.array([os.path.splitext(f)[0].split('_')[1] for f in files])
         logger.info(f'assuming instruments: {instruments}')
 
         if instruments.size == 1 and len(files) > 1:
@@ -508,18 +508,19 @@ class RV:
         extracted_files = do_download_s2d(files[:limit], directory)
 
 
-    from .plots import plot, plot_fwhm, plot_bis, plot_rhk
+    from .plots import plot, plot_fwhm, plot_bis, plot_rhk, plot_quantity
     from .plots import gls, gls_fwhm, gls_bis, gls_rhk
     from .reports import report
 
     from .instrument_specific import known_issues
 
 
-    def remove_instrument(self, instrument):
+    def remove_instrument(self, instrument, strict=False):
         """ Remove all observations from one instrument
         
         Args:
             instrument (str): The instrument for which to remove observations.
+            strict (bool): Whether to match `instrument` exactly
         
         Note:
             A common name can be used to remove observations for several subsets
@@ -538,34 +539,37 @@ class RV:
 
             will remove observations from the specific subset.
         """
-        if instrument not in self.instruments:
+        instruments = self._check_instrument(instrument, strict)
+
+        if instruments is None:
             logger.error(f"No data from instrument '{instrument}'")
             logger.info(f'available: {self.instruments}')
             return
 
-        ind = self.instruments.index(instrument) + 1
-        remove = np.where(self.obs == ind)
-        self.obs = np.delete(self.obs, remove)
-        self.obs[self.obs > ind] -= 1
-        #
-        self.time = np.delete(self.time, remove)
-        self.vrad = np.delete(self.vrad, remove)
-        self.svrad = np.delete(self.svrad, remove)
-        #
-        self.mask = np.delete(self.mask, remove)
-        #
-        # all other quantities
-        for q in self._quantities:
-            if q not in ('rjd', 'rv', 'rv_err'):
-                new = np.delete(getattr(self, q), remove)
-                setattr(self, q, new)
-        #
-        self.instruments.remove(instrument)
-        #
-        delattr(self, instrument)
+        for instrument in instruments:
+            ind = self.instruments.index(instrument) + 1
+            remove = np.where(self.obs == ind)
+            self.obs = np.delete(self.obs, remove)
+            self.obs[self.obs > ind] -= 1
+            #
+            self.time = np.delete(self.time, remove)
+            self.vrad = np.delete(self.vrad, remove)
+            self.svrad = np.delete(self.svrad, remove)
+            #
+            self.mask = np.delete(self.mask, remove)
+            #
+            # all other quantities
+            for q in self._quantities:
+                if q not in ('rjd', 'rv', 'rv_err'):
+                    new = np.delete(getattr(self, q), remove)
+                    setattr(self, q, new)
+            #
+            self.instruments.remove(instrument)
+            #
+            delattr(self, instrument)
 
-        if self.verbose:
-            logger.info(f"Removed observations from '{instrument}'")
+            if self.verbose:
+                logger.info(f"Removed observations from '{instrument}'")
 
         if return_self:
             return self
@@ -610,6 +614,30 @@ class RV:
             if getattr(self, inst).mtime.size == 1:
                 self.remove_instrument(inst)
 
+    def remove_prog_id(self, prog_id):
+        from glob import has_magic
+        if has_magic(prog_id):
+            from fnmatch import filter
+            matching = np.unique(filter(self.prog_id, prog_id))
+            mask = np.full_like(self.time, False, dtype=bool)
+            for m in matching:
+                mask |= np.isin(self.prog_id, m)
+            ind = np.where(mask)[0]
+            self.remove_point(ind)
+        else:
+            if prog_id in self.prog_id:
+                ind = np.where(self.prog_id == prog_id)[0]
+                self.remove_point(ind)
+            else:
+                if self.verbose:
+                    logger.warning(f'no observations for prog_id "{prog_id}"')
+
+
+    def remove_after_bjd(self, bjd):
+        if (self.time > bjd).any():
+            ind = np.where(self.time > bjd)[0]
+            self.remove_point(ind)
+
 
     def _propagate_mask_changes(self):
         """ link self.mask with each self.`instrument`.mask """
@@ -763,31 +791,38 @@ class RV:
             bad_quantities = []
 
             for q in s._quantities:
+                Q = getattr(s, q)
+
                 # treat date_night specially, basically doing a group-by
                 if q == 'date_night':
                     inds = binRV(s.mtime, None, None, binning_indices=True)
-                    setattr(s, q, getattr(s, q)[s.mask][inds])
+                    setattr(s, q, Q[s.mask][inds])
                     continue
 
-                if getattr(s, q).dtype != np.float64:
+                if Q.dtype != np.float64:
                     bad_quantities.append(q)
                     all_bad_quantities.append(q)
                     continue
 
-                if np.isnan(getattr(s, q)).all():
+                if np.isnan(Q).all():
                     yb = np.full_like(tb, np.nan)
                     setattr(s, q, yb)
+
                 elif q + '_err' in s._quantities:
-                    _, yb, eb = binRV(s.mtime, 
-                                      getattr(s, q)[s.mask], 
-                                      getattr(s, q + '_err')[s.mask])
+                    Qerr = getattr(s, q + '_err')
+                    if (Qerr == 0.0).all():
+                        _, yb = binRV(s.mtime, Q[s.mask], stat='mean', tstat='mean')
+                    else:
+                        _, yb, eb = binRV(s.mtime, Q[s.mask], Qerr[s.mask])
+                        setattr(s, q + '_err', eb)
+
                     setattr(s, q, yb)
-                    setattr(s, q + '_err', eb)
+
                 elif not q.endswith('_err'):
                     with warnings.catch_warnings():
                         warnings.filterwarnings('ignore', category=RuntimeWarning)
                         try:
-                            _, yb = binRV(s.mtime, getattr(s, q)[s.mask], 
+                            _, yb = binRV(s.mtime, Q[s.mask], 
                                         stat=np.nanmean, tstat=np.nanmean)
                             setattr(s, q, yb)
                         except TypeError:
@@ -820,13 +855,26 @@ class RV:
         return np.nanmean(z, axis=0)
 
     def subtract_mean(self):
-        meanRV = self.mvrad.mean()
+        """ Subtract (single) mean RV from all instruments """
+        self._meanRV = meanRV = self.mvrad.mean()
         for inst in self.instruments:
             s = getattr(self, inst)
             s.vrad -= meanRV
         self._build_arrays()
 
+    def _add_back_mean(self):
+        """ Add the (single) mean RV removed by self.subtract_mean() """
+        if not hasattr(self, '_meanRV'):
+            logger.warning("no mean RV stored, run 'self.subtract_mean()'")
+            return
+
+        for inst in self.instruments:
+            s = getattr(self, inst)
+            s.vrad += self._meanRV
+        self._build_arrays()
+
     def adjust_means(self, just_rv=False):
+        """ Subtract individual mean RVs from each instrument """
         if self._child or self._did_adjust_means:
             return
 
@@ -877,9 +925,14 @@ class RV:
         changed = False
         for inst in self.instruments:
             s = getattr(self, inst)
-            if np.abs(s.mvrad.mean()) < s.mvrad.ptp():
-                s.vrad += self.simbad.rvz_radvel * 1e3
-                changed = True
+            if s.mask.any():
+                if np.abs(s.mvrad.mean()) < s.mvrad.ptp():
+                    s.vrad += self.simbad.rvz_radvel * 1e3
+                    changed = True
+            else:  # all observations are masked, use non-masked arrays
+                if np.abs(s.vrad.mean()) < s.vrad.ptp():
+                    s.vrad += self.simbad.rvz_radvel * 1e3
+                    changed = True
         if changed:
             self._build_arrays()
 
@@ -913,6 +966,11 @@ class RV:
         """
         star_name = self.star.replace(' ', '')
 
+        if directory is None:
+            directory = '.'
+        else:
+            os.makedirs(directory, exist_ok=True)
+
         files = []
 
         for inst in self.instruments:
@@ -920,15 +978,11 @@ class RV:
                 if instrument not in inst:
                     continue
 
-            file = f'{star_name}_{inst}.rdb'
-            files.append(file)
-
-            if directory is not None:
-                os.makedirs(directory, exist_ok=True)
-                file = os.path.join(directory, file)
-
             _s = getattr(self, inst)
 
+            if not _s.mask.any():  # all observations are masked, don't save
+                continue
+
             if full:
                 d = np.c_[
                     _s.mtime, _s.mvrad, _s.msvrad,
@@ -941,6 +995,10 @@ class RV:
                 d = np.c_[_s.mtime, _s.mvrad, _s.msvrad]
                 header = 'bjd\tvrad\tsvrad\n---\t----\t-----'
             
+            file = f'{star_name}_{inst}.rdb'
+            files.append(file)
+            file = os.path.join(directory, file)
+
             np.savetxt(file, d, fmt='%9.5f', header=header, delimiter='\t', comments='')
 
             if self.verbose:

{arvi-0.1.5 → arvi-0.1.6}/arvi.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: arvi
-Version: 0.1.5
+Version: 0.1.6
 Summary: The Automated RV Inspector
 Author-email: João Faria <joao.faria@unige.ch>
 License: MIT
@@ -29,18 +29,6 @@ Requires-Dist: kepmodel
 
 
 
-## Goals
-
-- _Fast_:
-  all `arvi` operations must be completed in under **1 second**
-
-- _Reproducible_:
-  **everyone** must be able to use `arvi`
-
-- _Accurate_:
-  `arvi` must always provide the **correct result**
-
-
 #### Actions
 
 [![Deploy docs](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml/badge.svg)](https://github.com/j-faria/arvi/actions/workflows/docs-gh-pages.yml)

{arvi-0.1.5 → arvi-0.1.6}/pyproject.toml

@@ -8,7 +8,7 @@ authors = [
     {name = "João Faria", email = "joao.faria@unige.ch"},
 ]
 description = "The Automated RV Inspector"
-version = "0.1.5"
+version = "0.1.6"
 readme = {file = "README.md", content-type = "text/markdown"}
 requires-python = ">=3.8"
 keywords = ["RV", "exoplanets"]