Merge pull request #95 from mstcyr2/fits-cut-cloud

Cloud functionality for astrocut.fits_cut()

Author: jaymedina

astrocut/cutouts.py

@@ -230,6 +230,9 @@ def fits_cut(input_files, coordinates, cutout_size, correct_wcs=False, extension
         set the number of returned `~astropy.io.fits.HDUList` objects.
     verbose : bool
         Default False. If true intermediate information is printed.
+    fsspec_kwargs : any
+        Default value {"anon": True}. This parameter should be used to provide cloud credentials to
+        access private data buckets (e.g. {"key": "YOUR-SECRET-KEY-ID", "secret": "YOUR-SECRET-KEY"}).
 
     Returns
     -------
@@ -267,12 +270,16 @@ def fits_cut(input_files, coordinates, cutout_size, correct_wcs=False, extension
     cutout_hdu_dict = {}
     num_empty = 0
     num_cutouts = 0
+    fsspec_kwargs = None
     for in_fle in input_files:
         if verbose:
             print("\nCutting out {}".format(in_fle))
 
+        if "s3://" in in_fle:
+            fsspec_kwargs = {"anon": True}
+
         warnings.filterwarnings("ignore", category=wcs.FITSFixedWarning)
-        with fits.open(in_fle, mode='denywrite', memmap=True) as hdulist:
+        with fits.open(in_fle, mode='denywrite', memmap=True, fsspec_kwargs=fsspec_kwargs) as hdulist:
 
             # Sorting out which extension(s) to cutout
             all_inds = np.where([x.is_image and (x.data is not None) for x in hdulist])[0]

astrocut/tests/test_cutouts.py

@@ -182,6 +182,17 @@ def test_fits_cut(tmpdir, capsys, ffi_type):
     assert "10-x-15" in cutout_file
     assert "x-20" not in cutout_file
 
+    # Test single cloud image
+    test_s3_uri = "s3://stpubdata/hst/public/j8pu/j8pu0y010/j8pu0y010_drc.fits"
+    center_coord = SkyCoord("150.4275416667 2.42155", unit='deg')
+    cutout_size = [10, 15]
+    cutout_file = cutouts.fits_cut(test_s3_uri, center_coord, cutout_size, output_dir=tmpdir)
+    assert isinstance(cutout_file, str)
+    assert "10-x-15" in cutout_file
+    
+    with fits.open(cutout_file) as cutout_hdulist:
+        assert cutout_hdulist[1].data.shape == (15, 10)
+
 
 def test_normalize_img():
 

docs/astrocut/index.rst

@@ -84,7 +84,29 @@ The cutout(s) can also be returned in memory as `~astropy.io.fits.HDUList` objec
                   2  CUTOUT        1 ImageHDU        44   (200, 300)   float32
 
                   
-                  
+`~astrocut.fits_cut` also has the ability to take FITS files from the cloud using S3 URIs. 
+
+.. code-block:: python
+
+                >>> from astrocut import fits_cut
+                >>> from astropy.io import fits
+                >>> from astropy.coordinates import SkyCoord
+
+                >>> s3_uri = "s3://stpubdata/hst/public/j8pu/j8pu0y010/j8pu0y010_drz.fits"
+
+                >>> center_coord = SkyCoord("150.42838	2.421421", unit='deg')
+                >>> cutout_size = [100,100]
+                
+                >>> cutout_file = fits_cut(input_files, center_coord, cutout_size,
+                ...                        single_outfile=True, memory_only=True)  #doctest: +SKIP
+                >>> cutout_hdulist = fits.open(cutout_file)  #doctest: +SKIP
+                >>> cutout_hdulist.info() #doctest: +SKIP
+                Filename: ./cutout_150.428380_2.421421_100-x-100_astrocut.fits
+                No.    Name      Ver    Type      Cards   Dimensions   Format
+                  0  PRIMARY       1 PrimaryHDU      11   ()      
+                  1  CUTOUT        1 ImageHDU        97   (100, 100)   float32
+                
+
 Creating image cutouts
 ----------------------