Works on new updated library versions: run_photometry.py --targetid 5…

…06 --fileid 2966 --filter all

flows/catalogs.py

@@ -469,10 +469,10 @@ def query_all(coo_centre, radius=24 * u.arcmin, dist_cutoff=2 * u.arcsec):
 
     # REFCAT results table does not have uBV
     N = len(AT_results)
-    d = np.full(N, np.NaN)
-    AT_results.add_column(MaskedColumn(name='B_mag', unit='mag', dtype='float32', fill_value=np.NaN, data=d))
-    AT_results.add_column(MaskedColumn(name='V_mag', unit='mag', dtype='float32', fill_value=np.NaN, data=d))
-    AT_results.add_column(MaskedColumn(name='u_mag', unit='mag', dtype='float32', fill_value=np.NaN, data=d))
+    d = np.full(N, np.nan)
+    AT_results.add_column(MaskedColumn(name='B_mag', unit='mag', dtype='float32', fill_value=np.nan, data=d))
+    AT_results.add_column(MaskedColumn(name='V_mag', unit='mag', dtype='float32', fill_value=np.nan, data=d))
+    AT_results.add_column(MaskedColumn(name='u_mag', unit='mag', dtype='float32', fill_value=np.nan, data=d))
 
     # Query APASS around the target position:
     results_apass = query_apass(coo_centre, radius=radius)

flows/image.py

@@ -80,7 +80,7 @@ def create_wcs(self) -> WCS:
 
     def create_masked_image(self) -> None:
         """Warning: this is destructive and will overwrite image data setting masked values to NaN"""
-        self.image[self.mask] = np.NaN
+        self.image[self.mask] = np.nan
         self.clean = np.ma.masked_array(data=self.image, mask=self.mask, copy=False)
 
     def set_edge_rows_to_value(self, y: Tuple[float] = None, value: Union[int, float, np.float64] = 0) -> None:

flows/magnitudes.py

@@ -60,7 +60,7 @@ def instrumental_mag(tab: Table, target: Target, make_fig: bool = False) -> Tupl
     if n_weights > 1:
         zp_error = np.sqrt(n_weights * nansum(weights * (y - best_fit(x)) ** 2) / nansum(weights) / (n_weights - 1))
     else:
-        zp_error = np.NaN
+        zp_error = np.nan
     logger.info('Leastsquare ZP = %.3f, ZP_error = %.3f', zp, zp_error)
 
     # Determine sigma clipping sigma according to Chauvenet method

flows/photometry.py

@@ -117,10 +117,15 @@ def make_epsf(self, stars):
         """
         # Build ePSF
         logger.info("Building ePSF...")
+
+        # from photutils docs: recentering_boxsize must have odd values and be greater than or equal to 3
+        discrete_width = int(np.round(2 * self.fwhm))
+        rcb = discrete_width if discrete_width % 2 else discrete_width + 1
+
         builder = self.epsf_builder(
             oversampling=1, shape=1 * self.star_size,
             fitter=EPSFFitter(fit_boxsize=max(int(np.round(1.5 * self.fwhm)), 5)),
-            recentering_boxsize=max(int(np.round(2 * self.fwhm)), 5),
+            recentering_boxsize=max(rcb, 5),
             norm_radius=max(self.fwhm, 5), maxiters=100,
             progress_bar=multiprocessing.parent_process() is None and logger.getEffectiveLevel() <= 20
         )
@@ -161,16 +166,32 @@ def apphot(self, coordinates: ArrayLike, image: FlowsImage, fwhm: float, use_raw
     def create_photometry_object(self, fwhm: Union[float, u.Quantity], psf_model: photutils.psf.EPSFModel,
                                  fitsize: Union[int, Tuple[int]], fitter: Callable = fitting.LevMarLSQFitter(),
                                  bkg: PhotutilsBackground = MedianBackground()):
-        self.photometry_obj = PSFPhotometry(group_maker=SourceGrouper(fwhm), bkg_estimator=bkg, psf_model=psf_model,
-                                                 fitter=fitter, fitshape=fitsize, aperture_radius=fwhm)
+        # 2024-09 erik:
+        # photutils version 1.1.0 (or possibly lower?):
+        # self.photometry_obj = PSFPhotometry(group_maker=SourceGrouper(fwhm), bkg_estimator=bkg, psf_model=psf_model,
+        #                                          fitter=fitter, fitshape=fitsize, aperture_radius=fwhm)
+        # It seems that 'group_maker' -> 'grouper', 'bkg_estimator' -> 'localbkg_estimator', 'fitshape' -> 'fit_shape'
+        # in newer photutils versions.
+        # In addition, localbkg_estimator requires a LocalBackground object which in turn requires us to specify an
+        # inner and an outer radius, which we have not been doing previously... Comments/suggestions, anyone?
+        self.photometry_obj = PSFPhotometry(psf_model=psf_model, fit_shape=fitsize, grouper=SourceGrouper(fwhm),
+                                            fitter=fitter,
+                                            localbkg_estimator=photutils.background.LocalBackground(inner_radius=5,
+                                                                                                    outer_radius=10,
+                                                                                                    bkg_estimator=bkg),
+                                            aperture_radius=fwhm)
 
     def psfphot(self, image: ArrayLike, init_table: Table) -> Tuple[PSFPhotometry, Table]:
         """PSF photometry on init guesses table/row.
         """
         if self.photometry_obj is None:
             raise ValueError('Photometry object not initialized.')
         # logger.info(f"{init_table}")
-        output: Table = self.photometry_obj(image=image, init_guesses=init_table)
+        # 2024-09 erik:
+        # 'image' and 'init_guesses' not recognised.
+        # Trying to supply image as implicit 'data' and doing 'init_guesses' -> 'init_params'.
+        # output: Table = self.photometry_obj(image=image, init_guesses=init_table)
+        output: Table = self.photometry_obj(image, init_params=init_table)
         return self.photometry_obj, output
 
     @staticmethod
@@ -182,7 +203,9 @@ def rescale_flux_error(phot_tables: Dict[int, Table],
 
         for fit_shape, row in phot_tables.items():
             row = row[0] if select_first_row else row
-            new_err = row['flux_unc'] / exptime
+            # 'flux_unc' -> 'flux_err' at some version transition of photutils (not documented in changelog,
+            # found with debugger).
+            new_err = row['flux_err'] / exptime
             new_flux = row['flux_fit'] / exptime
             if new_flux <= flux + flux_err:
                 return fit_shape, new_err
@@ -355,7 +378,7 @@ def rescale_uncertainty(self, psfphot_tbl: Table, dynamic: bool = True,
                 if self.diff_im_exists:
                     _table = self.diff_psf_phot()
                 _table = self.raw_psf_phot(self.init_guesses.init_guess_target)
-                if "flux_unc" in _table.colnames:
+                if "flux_err" in _table.colnames:
                     _phot_tables_dict[fitshape] = _table
 
             if len(_phot_tables_dict) == 0:
@@ -364,7 +387,7 @@ def rescale_uncertainty(self, psfphot_tbl: Table, dynamic: bool = True,
             else:
                 # Find the fit shape elbow:
                 flux = psfphot_tbl[0]['flux_fit']
-                flux_err = psfphot_tbl[0]['flux_unc']
+                flux_err = psfphot_tbl[0]['flux_err']
                 exptime = self.image.exptime
                 dynamic_fit_shape, new_err = self.photometry.rescale_flux_error(_phot_tables_dict, flux, flux_err,
                                                                                 exptime)
@@ -374,13 +397,13 @@ def rescale_uncertainty(self, psfphot_tbl: Table, dynamic: bool = True,
         logger.info(f"Recalculating all reference uncertainties using new fitsize:"
                     f" {fit_shape} pixels, ({fit_shape/self.fwhm if dynamic else static_fwhm :.2} * FWHM).")
         psfphot_tbl_rescaled = self.psfphot(fit_shape)
-        if psfphot_tbl['flux_unc'][0] > psfphot_tbl_rescaled['flux_unc'][0] + epsilon_mag and ensure_greater:
+        if psfphot_tbl['flux_err'][0] > psfphot_tbl_rescaled['flux_err'][0] + epsilon_mag and ensure_greater:
             logger.info("Recalculated uncertainties were smaller than original and ``ensure_greater`` was True:"
                         "Not using rescaled uncertainties for the SN.")
-            psfphot_tbl['flux_unc'][1:] = psfphot_tbl_rescaled['flux_unc'][1:]
+            psfphot_tbl['flux_err'][1:] = psfphot_tbl_rescaled['flux_err'][1:]
             return psfphot_tbl
 
-        psfphot_tbl['flux_unc'] = psfphot_tbl_rescaled['flux_unc']
+        psfphot_tbl['flux_err'] = psfphot_tbl_rescaled['flux_err']
         return psfphot_tbl
 
     def make_result_table(self, psfphot_tbl: Table, apphot_tbl: Table):

flows/reference_cleaning.py

@@ -54,8 +54,8 @@ class References:
     xy: Optional[RefTable] = None
 
     def replace_nans_pm(self) -> None:
-        replace(self.table['pm_ra'], np.NaN, 0.)
-        replace(self.table['pm_dec'], np.NaN, 0.)
+        replace(self.table['pm_ra'], np.nan, 0.)
+        replace(self.table['pm_dec'], np.nan, 0.)
 
     def make_sky_coords(self, reference_time: float = 2015.5) -> None:
         self.replace_nans_pm()
@@ -105,9 +105,9 @@ def add_target(self, target: Target, starid: int = 0) -> None:
 def use_sep(image: FlowsImage, tries: int = 5, thresh: float = 5.):
 
     # Use sep to for soure extraction
-    sep_background = sep.Background(image.image, mask=image.mask)
+    sep_background = sep_pjw.Background(image.image, mask=image.mask)
     try:
-        objects = sep.extract(image.image - sep_background, thresh=thresh, err=sep_background.globalrms,
+        objects = sep_pjw.extract(image.image - sep_background, thresh=thresh, err=sep_background.globalrms,
                               mask=image.mask, deblend_cont=0.1, minarea=9, clean_param=2.0)
     except KeyboardInterrupt as e:
         raise e
@@ -161,9 +161,9 @@ def force_reject_g2d(xarray: ArrayLike, yarray: ArrayLike, image: Union[NDArray,
 
     # Stars reject
     N = len(xarray)
-    fwhms = np.full((N, 2), np.NaN)
-    xys = np.full((N, 2), np.NaN)
-    rsqs = np.full(N, np.NaN)
+    fwhms = np.full((N, 2), np.nan)
+    xys = np.full((N, 2), np.nan)
+    rsqs = np.full(N, np.nan)
     for i, (x, y) in enumerate(zip(xarray, yarray)):
         x = int(np.round(x))
         y = int(np.round(y))
@@ -185,8 +185,8 @@ def force_reject_g2d(xarray: ArrayLike, yarray: ArrayLike, image: Union[NDArray,
         nan_filter = nan_filter & np.isfinite(curr_star)
         if len(curr_star[nan_filter]) < 3:  # Not enough pixels to fit
             logger.debug(f"Not enough pixels to fit star, curr_star[nan_filter]:{curr_star[nan_filter]}")
-            rsqs[i] = np.NaN
-            fwhms[i] = np.NaN
+            rsqs[i] = np.nan
+            fwhms[i] = np.nan
             continue
 
         gfit = gfitter(g2d, x=xpos[nan_filter], y=ypos[nan_filter], z=curr_star[nan_filter])

flows/result_model.py

@@ -68,17 +68,19 @@ def make_results_table(cls, ref_table: Table, apphot_tbl: Table, psfphot_tbl: Ta
         results_table['flux_aperture'] = apphot_tbl['flux_aperture'] / image.exptime
         results_table['flux_aperture_error'] = apphot_tbl['flux_aperture_error'] / image.exptime
         results_table['flux_psf'] = psfphot_tbl['flux_fit'] / image.exptime
-        results_table['flux_psf_error'] = psfphot_tbl['flux_unc'] / image.exptime
+        results_table['flux_psf_error'] = psfphot_tbl['flux_err'] / image.exptime
         results_table['pixel_column_psf_fit'] = psfphot_tbl['x_fit']
         results_table['pixel_row_psf_fit'] = psfphot_tbl['y_fit']
-        results_table['pixel_column_psf_fit_error'] = psfphot_tbl['x_0_unc']
-        results_table['pixel_row_psf_fit_error'] = psfphot_tbl['y_0_unc']
+        # 'x_0_unc' -> 'x_err' and 'y_0_unc' -> 'y_err' at some version transition of photutils (not documented in
+        # changelog, found with debugger).
+        results_table['pixel_column_psf_fit_error'] = psfphot_tbl['x_err']
+        results_table['pixel_row_psf_fit_error'] = psfphot_tbl['y_err']
 
         return results_table
 
     @staticmethod
     def verify_uncertainty_column(tab):
-        if "flux_unc" in tab.colnames:
+        if "flux_err" in tab.colnames:
             return tab
-        tab['flux_unc'] = tab['flux_fit'] * 0.04  # Assume 4% errors
+        tab['flux_err'] = tab['flux_fit'] * 0.04  # Assume 4% errors
         logger.warning("Flux uncertainty not found from PSF fit, assuming 4% error.")

notes/LCOGT_Reduce_SingleStandards.ipynb

@@ -562,7 +562,7 @@
     "            dict(x_0=coordinates.centered_x[i], y_0=coordinates.centered_y[i])\n",
     "        ])\n",
     "    )\n",
-    "    coordinates.psf.append((res['flux_fit'].data[0], res['flux_unc'].data[0]))\n",
+    "    coordinates.psf.append((res['flux_fit'].data[0], res['flux_err'].data[0]))\n",
     "\n",
     "if verbose:       \n",
     "    print('Psf Phot Success')\n",

requirements.txt.erik

@@ -0,0 +1,21 @@
+numpy-2.1.1
+scipy-1.14.1
+astropy-6.1.3
+photutils-1.13.0
+bottleneck-1.4.0
+matplotlib-3.9.2
+mplcursors-0.5.3
+seaborn-0.13.2
+pandas-2.2.2
+requests-2.32.3
+pyyaml-6.0.2
+psycopg2-binary-2.9.9
+jplephem-2.22
+scikit_image-0.24.0
+tqdm-4.66.5
+pytz-2024.2
+sep_pjw-1.3.5
+astroalign-2.5.1
+networkx-3.3
+astroquery-0.4.7
+tendrils-0.3.2