Merge branch 'coordinates'

Author: temuller

README.md

@@ -1,6 +1,4 @@
-<p align="center">
-	<img src="docs/hostphot_logo.png" alt="drawing" width="300"/>
-</p>
+<p align="center"><img src="docs/hostphot_logo.png" alt="drawing" width="300"/></p>
 
 Global and local photometry of galaxies hosting supernovae or other transients
 
@@ -14,9 +12,9 @@ Global and local photometry of galaxies hosting supernovae or other transients
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6992139.svg)](https://doi.org/10.5281/zenodo.6992139)
 [![Coverage](https://raw.githubusercontent.com/temuller/hostphot/main/coverage.svg)](https://raw.githubusercontent.com/temuller/hostphot/main/coverage.svg)
 
-
 Read the full documentation at [hostphot.readthedocs.io](https://hostphot.readthedocs.io/en/latest/). It is recommended to read the **Further Information** section to understand how HostPhot works.
 ___
+
 ## Conda environment
 
 It is recommended to create an environment before installing HostPhot:
@@ -85,7 +83,6 @@ If the user is not happy with the result of the masking, there are a few paramet
 
 Local photometry can be obtained for multiple circular apertures:
 
-
 ```python
 import hostphot.photometry.local_photometry as lp
 
@@ -122,31 +119,30 @@ by Schlafly & Finkbeiner (2011) and the extinction law from Fitzpatrick (1999).
 
 This is the list of surveys in HostPhot:
 
-  * DES
-  * PS1
-  * SDSS
-  * GALEX
-  * 2MASS
-  * WISE
-  * unWISE
-  * Legacy Survey
-  * Spitzer (SEIP)
-  * VISTA (VHS, VIDEO, VIKING)
-  * HST (WFC3 only)
-  * SkyMapper (not well calibrated for extended sources)
-  * SPLUS
-  * UKIDSS
-  * JWST (NIRCam only)
+* DES
+* PS1
+* SDSS
+* GALEX
+* 2MASS
+* WISE
+* unWISE
+* Legacy Survey
+* Spitzer (SEIP)
+* VISTA (VHS, VIDEO, VIKING)
+* HST (WFC3 only)
+* SkyMapper (not well calibrated for extended sources)
+* SPLUS
+* UKIDSS
+* JWST (NIRCam only)
 
 ## Contributing
 
-To contribute, either open an issue or send a pull request (prefered option). You can also contact me directly (check my profile: https://github.com/temuller).
+To contribute, either open an issue or send a pull request (prefered option). You can also contact me directly (check my profile: [https://github.com/temuller](https://github.com/temuller)).
 
 ### Adding other surveys
 
 If you wish a survey to be added to HostPhot, there are a couple of ways of doing it. 1) You can do a pull request, following the same structure as used for the surveys that are already implemented, or 2) open an issue asking for a survey to be added. Either way, there are a fews things needed to add a survey: where to download the images from (e.g., using `astroquery`), zero-points to convert the images's flux/counts values into magnitudes, the magnitude system (e.g. AB, Vega), the pixel scaling of the images (in units of arcsec/pixel), the filters transmission functions and any other piece of information necessary to properly estimate magnitudes, errors, etc. If you open an issue asking for a survey to be added, please include all this information. For more information, please check the [Adding New Surveys](https://hostphot.readthedocs.io/en/latest/further_information/adding_surveys.html) section of the documentation.
 
-
 ## Citing HostPhot
 
 If you make use of HostPhot, please cite the following [paper](https://joss.theoj.org/papers/10.21105/joss.04508):
@@ -168,6 +164,11 @@ If you make use of HostPhot, please cite the following [paper](https://joss.theo
 
 ## What's new
 
+v3.1.2
+
+* Fixing download of GALEX images (issue introduced in v3.1.0 when trying to avoid timeout error - [#13](https://github.com/temuller/hostphot/issues/13)).
+* Also storing the coordinates of detected objects in RA,DEC and the ellipse parameters a/b in degrees.
+
 v3.1.1
 
 * Fixing minor bug when calculating dust extinction for Legacy Survey (Issue [#12](https://github.com/temuller/hostphot/issues/12))
@@ -176,7 +177,7 @@ v3.1.1
 v3.1.0
 
 * Using DES DR2 instead of DR1
-* Downloading images, for some surveys, trying to avoid timeout errors.
+* Avoid timeout errors when downloading image cutouts for some surveys.
 * Adapting global aperture even if the survey is the same as the reference (mainly to avoid issues with JWST).
 * Fixing/adding features from different issues, mainly for HST/JWST ([#8](https://github.com/temuller/hostphot/issues/8), [#9](https://github.com/temuller/hostphot/issues/9), [#10](https://github.com/temuller/hostphot/issues/10), [#11](https://github.com/temuller/hostphot/issues/11) - thanks Lisa!).
 

src/hostphot/_version.py

@@ -1,3 +1,3 @@
 # -*- coding: utf-8 -*-
 
-__version__ = "3.1.1"
+__version__ = "3.1.2"

src/hostphot/cutouts/galex.py

@@ -8,7 +8,6 @@
 from astropy.coordinates import SkyCoord
 from astroquery.mast import Observations
 
-from hostphot.utils import open_fits_from_url
 from hostphot.surveys_utils import get_survey_filters, check_filters_validity, survey_pixel_scale
 
 import warnings
@@ -93,9 +92,9 @@ def get_GALEX_images(ra: float, dec: float, size: float | u.Quantity = 3,
             hdu_list = []
             for file in files:
                 try:
-                    hdu = open_fits_from_url(file)
+                    hdu = fits.open(file)
                     hdu_list.append(hdu)
-                except:
+                except Exception:
                     pass
 
             # calculate the separation of the galaxy to the image center

src/hostphot/processing/masking.py

@@ -213,7 +213,6 @@ def create_mask(
         )
         sigma /= conv_factor
 
-    #masked_data = mask_image(data_sub, nongal_objs, r=r, sigma=sigma)
     if len(nongal_objs) > 0:
         masked_data = mask_image(data_sub, nongal_objs, r=r, sigma=sigma)
     else:

src/hostphot/processing/objects_detection.py

@@ -7,12 +7,14 @@
 from astropy.io import fits
 from astropy import units as u
 from astropy.coordinates import SkyCoord
+from astropy.wcs.utils import proj_plane_pixel_scales
+
 from astroquery.gaia import Gaia
 from astroquery.mast import Catalogs
 
 import sep
 from hostphot._constants import font_family
-from hostphot.utils import suppress_stdout
+from hostphot.utils import suppress_stdout, add_fields
 
 import warnings
 from astropy.utils.exceptions import AstropyWarning
@@ -68,6 +70,19 @@ def extract_objects(
         ra=host_ra, dec=host_dec, unit=(u.degree, u.degree), frame="icrs"
     )
     objs_coords = img_wcs.pixel_to_world(objects["x"], objects["y"])
+    # add coordinates and ellipse a/b in degrees
+    sx, sy = proj_plane_pixel_scales(img_wcs)  # degrees per pixel
+    a_deg, b_deg = objects["a"] * sx, objects["b"] * sy
+    objects = add_fields(objects, 
+                         names=["ra", "dec", "a_deg", "b_deg"], 
+                         dtypes=["f8", "f8", "f8", "f8"], 
+                         data=[objs_coords.ra.value, 
+                               objs_coords.dec.value,
+                               a_deg, 
+                               b_deg
+                               ]
+                         )
+    
     distances = host_coords.separation(objs_coords).to(u.arcsec)
     dist_arcsec = distances.value
 

src/hostphot/utils.py

@@ -1,13 +1,15 @@
 import os
 import sys
 import requests
+import numpy as np
 import pandas as pd
 from io import BytesIO
 from pathlib import Path
 import matplotlib.image as img
 import matplotlib.pyplot as plt
 from contextlib import contextmanager
 from datetime import datetime, timezone
+from numpy.lib import recfunctions as rfn
 
 import aplpy
 from astropy.io import fits
@@ -46,6 +48,31 @@ def open_fits_from_url(url: str) -> fits.hdu:
     hdu = fits.open(BytesIO(r.content))
     return hdu
 
+def add_fields(arr: np.ndarray, names: str | list, dtypes: str | list, data: np.ndarray) -> np.ndarray:
+    """Add new fields to a NumPy structured array.
+
+    Parameters
+    ----------
+    arr: Original structured array.
+    names: Name(s) of the new fields.
+    dtype: Dtype(s) of the new fields (e.g. 'f8', 'i4').
+    data: Data for the new fields.
+
+    Returns
+    -------
+    new_arr: New structured array with added fields.
+    """
+    if isinstance(names, str):
+        names = [names]
+    if isinstance(dtypes, (str, np.dtype)):
+        dtypes = [dtypes]
+    if not isinstance(data, (list, tuple)):
+        data = [data]
+        
+    new_arr = rfn.append_fields(arr, names, data, dtypes=dtypes, usemask=False)
+
+    return new_arr
+
 @contextmanager
 def suppress_stdout():
     """Suppresses annoying outputs.