roman-snpit-snappl 0.2.2__tar.gz → 0.2.3__tar.gz

{roman_snpit_snappl-0.2.2/roman_snpit_snappl.egg-info → roman_snpit_snappl-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roman_snpit_snappl
-Version: 0.2.2
+Version: 0.2.3
 Summary: Photometry utilities for the Roman SNPIT
 Author: Roman Supernove Project Infrastructure Team
 Maintainer-email: Roman SN PIT <raknop@lbl.gov>

roman_snpit_snappl-0.2.3/changes/9.snappl.rst

@@ -0,0 +1 @@
+Added ability to set data from outside of the Image object for sky mean subtraction.

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/pyproject.toml

@@ -167,7 +167,7 @@ select = [ 'F', 'E101', 'E111', 'E112', 'E113', 'E115', 'E117',
 # This can be .rst or .md, towncrier's default template works with both.
 filename = "CHANGES.rst"
 directory = "changes"
-package = "roman_snpit_snappl"
+package = "snappl"
 package_dir = "snappl"
 title_format = "{version} ({project_date})"
 ignore = [".gitkeep"]

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3/roman_snpit_snappl.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roman_snpit_snappl
-Version: 0.2.2
+Version: 0.2.3
 Summary: Photometry utilities for the Roman SNPIT
 Author: Roman Supernove Project Infrastructure Team
 Maintainer-email: Roman SN PIT <raknop@lbl.gov>

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/roman_snpit_snappl.egg-info/SOURCES.txt

@@ -29,6 +29,7 @@ changes/13.bugfix.rst
 changes/3.snappl.rst
 changes/5.snappl.rst
 changes/8.snappl.rst
+changes/9.snappl.rst
 docs/Makefile
 docs/changes.rst
 docs/conf.py
@@ -37,8 +38,6 @@ docs/installation.rst
 docs/make.bat
 docs/usage.rst
 docs/_static/logo_black_filled.png
-examples/config_example.py
-examples/config_example.yaml
 licenses/.DS_Store
 licenses/LICENSE.rst
 licenses/README.rst

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/__init__.py

@@ -4,7 +4,7 @@ __all__ = []
 
 
 try:
-    __version__ = version("snappl")
+    __version__ = version("roman_snpit_snappl")
 except PackageNotFoundError:
     # package is not installed
     pass

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/_dev/__init__.py

@@ -1,4 +1,5 @@
-"""
+"""Dev files
+
 This package contains utilities that are only used when developing drms in a
 copy of the source repository.
 These files are not installed, and should not be assumed to exist at

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.2'
-__version_tuple__ = version_tuple = (0, 2, 2)
+__version__ = version = '0.2.3'
+__version_tuple__ = version_tuple = (0, 2, 3)

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/image.py

@@ -6,39 +6,22 @@ from astropy.nddata.utils import Cutout2D
 from snpit_utils.logger import SNLogger
 
 from astropy.wcs import WCS as AstropyWCS
-from astropy.coordinates import SkyCoord
-from astropy import units as u
+# from astropy.coordinates import SkyCoord
+
+import numpy as np
 
 
 class Exposure:
     pass
 
+
 class OpenUniverse2024Exposure:
     def __init__( self, pointing ):
         self.pointing = pointing
 
+
 class Image:
-    """Cole did this (with software):
-                    ___
-                   / _ \___  __ _  ___ ____
-                  / , _/ _ \/  ' \/ _ `/ _ \
-                 /_/|_|\___/_/_/_/\_,_/_//_/
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⣔⣴⣦⣔⣠⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣼⣿⣭⣿⣟⣿⣿⣿⣅⢀⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣾⣷⣾⣿⣿⣿⣿⣿⣿⣿⡶⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣄⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⡇⠄⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣀⣠⠤⢤⣄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣠⣾⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⣿⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⠀⡠⢒⣿⣿⣿⣠⠋⠀⠀⠀⠀⠀⠀⣀⣀⠤⠶⠿⠿⠛⠿⠿⠿⢻⢿⣿⣿⣿⠿⠟⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠀⡞⢀⣿⣿⣿⡟⠃⠀⠀⠀⣀⡰⠶⠛⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠘⠀⠃⠘⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
-⠀⠀⠀⠀⠀⠀⠀⠘⢧⣤⣈⣡⣤⠤⠴⠒⠊⠉⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
-
-
-                 _____  __     ___  __________
-                / __/ |/ /    / _ \/  _/_  __/
-               _\ \/    /    / ___// /  / /
-              /___/_/|_/    /_/  /___/ /_/
-
-       """
+    """Encapsulates a single 2d image."""
 
     data_array_list = [ 'all', 'data', 'noise', 'flags' ]
 
@@ -70,6 +53,10 @@ class Image:
         """The image data, a 2d numpy array."""
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement data" )
 
+    @data.setter
+    def data( self, new_value ):
+        raise NotImplementedError( f"{self.__class__.__name__} needs to implement data setter" )
+
     @property
     def noise( self ):
         """The 1σ pixel noise, a 2d numpy array."""
@@ -162,27 +149,20 @@ class Image:
 
     @property
     def coord_center(self):
-        '''
-        Get the RA and DEC at the center of the image.
+        """Get the RA and DEC at the center of the image.
+
         Note: By fetching the center from the WCS and not the header,
               this means that this works for cutouts too.
 
         Returns:
         coord_center: array of floats, shape (2,) [RA, DEC] in degrees.
-        '''
+        """
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement coord_center" )
 
     def get_image_shape(self):
         """Get the shape of the image."""
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement get_image_shape" )
 
-    @property
-    def band( self ):
-        """Band (str)"""
-        raise NotImplementedError( f"{self.__class__.__name__} needs to implement band" )
-
-
-
 
     #     # THE REST OF THIS MAY GO AWAY
 
@@ -235,7 +215,8 @@ class Image:
     #     psf_path = self.pipeline.temp_dir / f"psf_{self.image_name}"
     #     get_imsim_psf( self.image_path, self.pipeline.ra, self.pipeline.dec, self.pipeline.band,
     #                    self.pointing, self.sca,
-    #                    size=201, psf_path=psf_path, config_yaml_file=self.pipeline.galsim_config_file, include_photonOps=True )
+    #                    size=201, psf_path=psf_path, config_yaml_file=self.pipeline.galsim_config_file,
+    #                    include_photonOps=True )
     #     return psf_path
 
     # def save_psf_path( self, psf_path ):
@@ -267,18 +248,27 @@ class OpenUniverse2024FITSImage( Image ):
             self._load_data()
         return self._data
 
+    @data.setter
+    def data(self, new_value):
+        if isinstance(new_value, np.ndarray) and np.issubdtype(new_value.dtype, np.floating):
+            self._data = new_value
+        else:
+            raise ValueError("Data must be a numpy array of floats.")
+
     def _load_data( self ):
         """Loads the data from disk."""
         raise NotImplementedError( "Do." )
 
     def get_data( self, which='all' ):
         if self._is_cutout:
-            raise RuntimeError( "get_data called on a cutout image, this will return the ORIGINAL UNCUT image. Currently not supported.")
+            raise RuntimeError( "get_data called on a cutout image, this will return the ORIGINAL UNCUT image. "
+                                "Currently not supported.")
         if which not in Image.data_array_list:
             raise ValueError( f"Unknown which {which}, must be all, data, noise, or flags" )
         SNLogger.info( f"Reading FITS file {self.inputs.path}" )
         with fits.open( self.inputs.path ) as hdul:
             self._wcs = AstropyWCS( hdul[1].header )
+
             if which == 'all':
                 return [ hdul[1].data, hdul[2].data, hdul[3].data ]
             elif which == 'data':
@@ -303,6 +293,7 @@ class OpenUniverse2024FITSImage( Image ):
                 self._header = hdul[1].header
         return self._header
 
+
     @property
     def image_shape(self):
         """Get the shape of the image."""
@@ -318,13 +309,14 @@ class OpenUniverse2024FITSImage( Image ):
 
     @property
     def coord_center(self):
-        '''
+        """The RA and Dec at the cnter of the image (
         Get the RA and DEC at the center of the image.
         Works for cutouts too.
         Returns:
         coord_center: array of floats, shape (2,) [RA, DEC] in degrees.
-        '''
+        """
         wcs = self.get_wcs()
+        # ...this next method isn't defined for our WCS objects.  Something is broken.
         coord_center = wcs.wcs_pix2world(
             self.get_image_shape()[0] // 2,
             self.get_image_shape()[1] // 2,
@@ -333,19 +325,12 @@ class OpenUniverse2024FITSImage( Image ):
 
     @property
     def band(self):
-        '''
-        Return the band the image is taken in.
-
-        Returns:
-        band: str
-        '''
+        """The band the image is taken in (str)."""
         header = self.get_header()
         return header['FILTER'].strip()
 
     def get_cutout(self, x, y, xsize, ysize=None):
-        '''
-        Creates a new snappl image object that is a cutout of the original
-        image, at a location in pixel-space.
+        """Creates a new snappl image object that is a cutout of the original image, at a location in pixel-space.
 
         Parameters
         ----------
@@ -361,7 +346,8 @@ class OpenUniverse2024FITSImage( Image ):
         -------
         cutout : snappl.image.Image
             A new snappl image object that is a cutout of the original image.
-        '''
+
+        """
         if ysize is None:
             ysize = xsize
         if xsize % 2 != 1 or ysize % 2 != 1:
@@ -369,7 +355,7 @@ class OpenUniverse2024FITSImage( Image ):
                 pixel, you tried to pass a size of {xsize, ysize}.")
         loc = (x, y)
         SNLogger.debug(f'Cutting out at {x , y}')
-        data, noise, flags = self.get_data('all')
+        data, noise, _flags = self.get_data('all')
         astropy_cutout = Cutout2D(data, loc, size=(ysize, xsize), # Astropy asks for this order. Beats me. -Cole
                                    mode='strict', wcs=self.get_wcs())
         astropy_noise = Cutout2D(noise, loc, size=(ysize, xsize),
@@ -384,9 +370,8 @@ class OpenUniverse2024FITSImage( Image ):
         return snappl_cutout
 
     def get_ra_dec_cutout(self, ra, dec, xsize, ysize=None):
-        '''
-        Creates a new snappl image object that is a cutout of the original
-        image, at a location in pixel-space.
+        """Creates a new snappl image object that is a cutout of the original image, at a location in pixel-space.
+
         Parameters
         ----------
         ra : float
@@ -402,11 +387,10 @@ class OpenUniverse2024FITSImage( Image ):
         -------
         cutout : snappl.image.Image
             A new snappl image object that is a cutout of the original image.
-        '''
+        """
 
         wcs = self.get_wcs()
         x, y = wcs.wcs_world2pix(ra, dec, 0)  # <--- I DO NOT UNDERSTAND WHY THIS
         # NEEDS TO BE ZERO, BUT THAT MADE THIS NEW FUNCTION AGREE WITH THE
         # OUTPUT OF THE OLD FUNCTION. COLE IS CONFUSED!!!!!
         return self.get_cutout(x, y, xsize, ysize)
-

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/psf.py

@@ -3,6 +3,7 @@ import base64
 
 import numpy as np
 
+
 class PSF:
     def __init__( self, *args, **kwargs ):
         # Will define a PSF with a nominal position
@@ -34,7 +35,7 @@ class PSF:
         """
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement get_stamp" )
 
-        
+
 
 class OversampledImagePSF( PSF ):
     @classmethod
@@ -62,7 +63,7 @@ class OversampledImagePSF( PSF ):
         """
         # TODO : implement enforce_odd
         # TODO : enforce square
-        
+
         psf = cls()
         psf._data = data
         if normalize:
@@ -75,7 +76,7 @@ class OversampledImagePSF( PSF ):
     @property
     def x0( self ):
         return self._x0
-    
+
     @property
     def y0( self ):
         return self._x0
@@ -92,7 +93,7 @@ class OversampledImagePSF( PSF ):
     def clip_size( self ):
         """The size of the PSF image clip at image resolution."""
         return int( np.floor( self._data.shape[0] / self._oversamp ) )
-        
+
     def __init__( self, *args, **kwargs ):
         super().__init__( *args, **kwargs )
         self._data = None
@@ -103,7 +104,7 @@ class OversampledImagePSF( PSF ):
     def get_stamp( self, x=None, y=None, normalize=True ):
         x = float(x) if x is not None else self._x0
         y = float(y) if y is not None else self._y0
-        
+
         # round() isn't the right thing to use here, because it will
         #   behave differently when x - round(x) = 0.5 based on whether
         #   floor(x) is even or odd.  What we *want* is for the psf to
@@ -174,12 +175,10 @@ class OversampledImagePSF( PSF ):
             clip /= clip.sum()
 
         return clip
-        
 
 
-        
 class YamlSerialized_OversampledImagePSF( OversampledImagePSF ):
-    
+
     def __init__( self, *args, **kwargs ):
         super().__init__( *args, **kwargs )
 
@@ -190,7 +189,7 @@ class YamlSerialized_OversampledImagePSF( OversampledImagePSF ):
         self._oversamp = y['oversamp']
         self._data = np.frombuffer( base64.b64decode( y['data'] ), dtype=y['dtype'] )
         self._data = self._data.reshape( ( y['shape0'], y['shape1'] ) )
-        
+
     def write( self, filepath ):
         out = { 'x0': float( self._x0 ),
                 'y0': float( self._y0 ),

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/tests/conftest.py

@@ -3,4 +3,3 @@ import pytest # noqa: F401
 
 import tox # noqa: F401
 from tox.pytest import init_fixture # noqa: F401
-

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/tests/test_opensim2024fitsimage.py

@@ -12,6 +12,7 @@ import numpy as np
 from snappl.image import OpenUniverse2024FITSImage
 import astropy
 import pytest
+from snpit_utils.logger import SNLogger
 
 
 def test_get_cutout():
@@ -39,3 +40,17 @@ def test_get_cutout():
         cutout = image.get_ra_dec_cutout(ra, dec, 55)
         message = f"This should have caused a PartialOverlapError but was actually {str(excinfo.value)}"
         assert 'partial' in str(excinfo.value), message
+
+
+def test_set_data():
+    imagepath = str(pathlib.Path(__file__).parent/'image_test_data/Roman_TDS_simple_model_F184_662_11.fits.gz')
+    image = OpenUniverse2024FITSImage(imagepath, None, 11)
+
+    with pytest.raises(ValueError) as excinfo:
+        image.data = 'cheese'
+        SNLogger.debug(image.data)
+    message = f"This should have caused a ValueError but was actually {str(excinfo.value)}"
+    assert 'must be a' in str(excinfo.value), message
+    old_data = image.get_data()[0]
+    image._data = old_data + 1
+    assert np.array_equal(image._data, old_data + 1), "The data was not set correctly"

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/tests/test_oversampled_image_psf.py

@@ -1,5 +1,3 @@
-import yaml
-import random
 import pytest
 
 import numpy as np
@@ -7,6 +5,7 @@ from astropy.io import fits
 
 from snappl.psf import OversampledImagePSF
 
+
 @pytest.fixture
 def testpsf():
     loaded = np.load('psf_test_data/testpsfarray.npz')
@@ -14,6 +13,7 @@ def testpsf():
     mypsf = OversampledImagePSF.create( arr, 3832., 255., oversample_factor=3. )
     return mypsf
 
+
 def test_create( testpsf ):
     assert testpsf._data.sum() == pytest.approx( 1., rel=1e-9 )
 
@@ -22,4 +22,3 @@ def test_create( testpsf ):
 def test_interactive_write_stamp_to_fits_for_visual_inspection( testpsf ):
     fits.writeto( 'test_deleteme_orig.fits', testpsf._data, overwrite=True )
     fits.writeto( 'test_deleteme_resamp.fits', testpsf.get_stamp(), overwrite=True )
-

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/tests/test_yaml_serialized_oversampled_image_psf.py

@@ -5,7 +5,8 @@ import pytest
 
 import numpy as np
 
-from snappl.psf import OversampledImagePSF, YamlSerialized_OversampledImagePSF
+from snappl.psf import YamlSerialized_OversampledImagePSF
+
 
 @pytest.fixture
 def testpsf():
@@ -14,6 +15,7 @@ def testpsf():
     mypsf = YamlSerialized_OversampledImagePSF.create( arr, 3832., 255., oversample_factor=3. )
     return mypsf
 
+
 def test_write( testpsf ):
     barf = pathlib.Path( ''.join( random.choices( 'abcdefghijklmnopqrstuvwxyz', k=10 ) ) )
     try:
@@ -30,6 +32,7 @@ def test_write( testpsf ):
     finally:
         barf.unlink( missing_ok=True )
 
+
 def test_read( testpsf ):
     barf = pathlib.Path( ''.join( random.choices( 'abcdefghijklmnopqrstuvwxyz', k=10 ) ) )
     try:

{roman_snpit_snappl-0.2.2 → roman_snpit_snappl-0.2.3}/snappl/wcs.py

@@ -1,5 +1,6 @@
 import astropy.wcs
 
+
 class BaseWCS:
     def __init__( self ):
         pass
@@ -7,18 +8,21 @@ class BaseWCS:
     def pixel_to_world( self, *args, **kwargs ):
         """TODO DOCUMENT THIS"""
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement pixel_to_world" )
-    
+
     def world_to_pixel( self, *args, **kwargs ):
         """TODO DOCUMENT THIS"""
         raise NotImplementedError( f"{self.__class__.__name__} needs to implement world_to_pixel" )
-    
+
+
 class AstropyWCS(BaseWCS):
     def __init__( self ):
         self._wcs = None
-    
+
     @classmethod
     def from_header( cls, header ):
-        self._wcs = astropy.wcs.WCS( header )
+        wcs = AstropyWCS()
+        wcs._wcs = astropy.wcs.WCS( header )
+        return wcs
 
     def pixel_to_world( self, *args, **kwargs ):
         return self._wcs.pixel_to_world( *args, **kwargs )
@@ -27,6 +31,7 @@ class AstropyWCS(BaseWCS):
         return self._wcs.world_to_pixel( *args, **kwargs )
 
     ## More?
-    
+
+
 class TotalDisasterASDFWCS(BaseWCS):
     pass

roman_snpit_snappl-0.2.2/examples/config_example.py

@@ -1,48 +0,0 @@
-# Run this example in this directory with 
-#    SNAPPL_CONFIG=config_example.yaml python config_example.py
-#
-# then try
-#    SNAPPL_CONFIG=config_example.yaml python config_example.py --help
-#
-# then try
-#    SNAPPL_CONFIG=config.example.yaml python config_example.py --swallow-african_or_european European
-
-import sys
-import pathlib
-import argparse
-
-# This is a little bit ugly, but so that this example will work "in place"
-# we make sure that the directory where config.py is found is in our
-# PYTHONPATH.  Do NOT do this in your own code.  Make sure that things
-# are installed right, and that the PYTHONPATH includes all the snappl
-# path
-sys.path.insert( 0, str( pathlib.Path(__file__).parent.parent ) )
-from snappl.config import Config
-
-
-def main():
-    cfg = Config.get()
-
-    parser = argparse.ArgumentParser( 'config_example.py', description='Demonstrate config' )
-    parser.add_argument( '-g', '--gratuitous', default='not_given', help="Your own argument" )
-    cfg.augment_argparse( parser )
-    args = parser.parse_args()
-    cfg.parse_args( args )
-
-    print( f"Gratuitous is {args.gratuitous}" )
-
-    # Examples of extracting config values
-    
-    print( f"cfg.value('cat') is {cfg.value('cat')}" )
-    print( f"cfg.value('swallow.unladen.airspeed') is {cfg.value('swallow.unladen.airspeed')} "
-           f"with units {cfg.value('swallow.unladen.airspeed_units')}" )
-    birdtype = cfg.value( 'swallow.african_or_european' )
-    qt = "'"
-    print( f"cfg.value('swallow.african_or_european') is "
-           f"{f'I don{qt}t know that!.... AAAAAAAA!' if birdtype is None else birdtype}" )
-    print( f"cfg.value('list') is {cfg.value('list')}" )
-
-
-if __name__ == "__main__":
-    main()
-           

roman_snpit_snappl-0.2.2/examples/config_example.yaml

@@ -1,12 +0,0 @@
-cat: fluffy
-
-swallow:
-  unladen:
-    airspeed: 11
-    airspeed_units: miles per hour
-  african_or_european: null
-
-list:
-  - a
-  - b
-  - c