roman-snpit-snappl 0.5.0__tar.gz → 0.7.0__tar.gz

{roman_snpit_snappl-0.5.0/roman_snpit_snappl.egg-info → roman_snpit_snappl-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roman_snpit_snappl
-Version: 0.5.0
+Version: 0.7.0
 Summary: Photometry utilities for the Roman SNPIT
 Author: Roman Supernove Project Infrastructure Team
 Maintainer-email: Roman SN PIT <raknop@lbl.gov>

roman_snpit_snappl-0.7.0/changes/31.feature.rst

@@ -0,0 +1 @@
+Offcenter PSFs in get_stamp(); test for ou24PSF; photutilsImagePSF

roman_snpit_snappl-0.7.0/changes/35.snappl.rst

@@ -0,0 +1 @@
+photon ops now actually turns off 

roman_snpit_snappl-0.7.0/changes/36.snappl.rst

@@ -0,0 +1 @@
+created OU24 SED Collection object 

roman_snpit_snappl-0.7.0/changes/37.snappl.rst

@@ -0,0 +1 @@
+Added the non-slow ou24PSF class

roman_snpit_snappl-0.7.0/changes/40.snappl.rst

@@ -0,0 +1 @@
+Added manual fits image and test

roman_snpit_snappl-0.7.0/experimentation/README.md

@@ -0,0 +1 @@
+This directory is for test scripts and such that aren't really part of the snappl package, but that might be useful to archive for future reference.

roman_snpit_snappl-0.7.0/experimentation/play_with_photutils.py

@@ -0,0 +1,118 @@
+import numpy as np
+
+import astropy.table
+import photutils.psf
+
+
+# You probably want stampsize = 2 * 5 * 2√(2ln2) * max(sigmax,sigmay)
+def make_gaussian_psf( oversamp=3, sigmax=1.2, sigmay=None, stampsize=None, x0=511, y0=511 ):
+    if oversamp % 2 != 1:
+        raise ValueError( "Please use an odd oversampling factor." )
+
+    sigmay = sigmax if sigmay is None else sigmay
+
+    # Default to a stamp size of 2 * 5 FHWMs (so "radius" 5 FWHM)
+    if stampsize is None:
+        stampsize = int( np.ceil( 10 * 2.35482 * max( sigmax, sigmay ) ) )
+        stampsize += 1 if stampsize % 2 ==0 else 0
+    if stampsize % 2 != 1:
+        raise ValueError( "stampsize must be odd" )
+
+    oversampsize = oversamp * stampsize
+    ctr = oversampsize // 2
+    xvals = np.arange( -ctr, ctr+1 )
+    yvals = np.arange( -ctr, ctr+1 )
+    ovsigmax = oversamp * sigmax
+    ovsigmay = oversamp * sigmay
+    data = np.exp( -( xvals[np.newaxis,:]**2 / ( 2. * ovsigmax**2 ) +
+                      yvals[:,np.newaxis]**2 / ( 2. * ovsigmay**2 ) ) )
+    # photutils expects an oversampled PSF to be normalized like this:
+    data /= data.sum() / ( oversamp**2 )
+
+    psf = photutils.psf.ImagePSF( data, flux=1, x_0=x0, y_0=y0, oversampling=oversamp )
+
+    return psf
+
+
+def make_fake_image( skynoise=10., starflux=100000., nx=1024, ny=1024, x=511, y=511,
+                     oversamp=3, sigmax=1.2, sigmay=None, stampsize=None ):
+    rng = np.random.default_rng()
+    image = rng.normal( scale=skynoise, size=(ny, nx) )
+
+    xc = int( np.floor( x + 0.5 ) )
+    yc = int( np.floor( y + 0.5 ) )
+
+    psf = make_gaussian_psf( oversamp=oversamp, sigmax=sigmax, sigmay=sigmay, stampsize=stampsize, x0=x, y0=y )
+    xmin = -( stampsize // 2 ) + xc
+    xmax = xmin + stampsize
+    ymin = -( stampsize // 2 ) + yc
+    ymax = ymin + stampsize
+    # WORRY : did I get the x, y order right?
+    xvals, yvals = np.meshgrid( np.arange( xmin, xmax ), np.arange( ymin, ymax ) )
+    # Not adding poisson noise to our PSF; deal
+    image[ ymin:ymax, xmin:xmax ] += psf( xvals, yvals ) * starflux
+
+    return image, psf
+
+
+# **********************************************************************
+# Actual experiments
+
+# Have a plenty-sampled PSF with a sigma of 1.2, stampsize 29, oversampling by 3)
+psf = make_gaussian_psf( oversamp=3, sigmax=1.2, stampsize=29, x0=511, y0=511 )
+xvals = np.arange( 511 - (29//2), 511 + (29//2) + 1 )
+yvals = np.arange( 511 - (29//2), 511 + (29//2) + 1 )
+xvals, yvals = np.meshgrid( xvals, yvals )
+print( f"1.2-sigma PSF clip sums to {psf( xvals, yvals ).sum()}" )
+
+# Have a PSF with a 1-pixel FWHM (so σ = 1/(2√(2ln2)) = 0.42 ), stampsize 11, oversamped 5x
+psf = make_gaussian_psf( oversamp=5, sigmax=0.42, stampsize=11, x0=511, y0=511 )
+xvals = np.arange( 511 - (29//2), 511 + (29//2) + 1 )
+yvals = np.arange( 511 - (29//2), 511 + (29//2) + 1 )
+xvals, yvals = np.meshgrid( xvals, yvals )
+print( f"0.42-sigma PSF clip sums to {psf( xvals, yvals ).sum()}" )
+
+
+# Now let's try some PSF photometry and see how it does
+# We are always going to use sky noise 10, and just not bother
+#  with star poisson noise for now (because we're naughty)
+
+# First with the happy big star
+image, psf = make_fake_image( oversamp=3, sigmax=1.2, stampsize=29 )
+noiseim = np.full_like( image, 10. )
+fit_shape = ( 15, 15 )
+photor = photutils.psf.PSFPhotometry( psf, fit_shape )
+phot = photor( image, error=noiseim,
+               init_params=astropy.table.Table( { 'x_init': [510.5], 'y_init': [513.], 'flux_init': [95000] } ) )
+print( f"Fit flux of 100000-flux star for sigma = 1.2: {phot['flux_fit'][0]}; "
+       f"(x,y)=({phot['x_fit'][0]}, {phot['y_fit'][0]}" )
+
+# Now with a little star
+image, psf = make_fake_image( oversamp=5, sigmax=0.42, stampsize=11 )
+fit_shape = ( 7, 7 )
+photor = photutils.psf.PSFPhotometry( psf, fit_shape )
+phot = photor( image, error=noiseim,
+               init_params=astropy.table.Table( { 'x_init': [511.2], 'y_init': [510.9], 'flux_init': [120000] } ) )
+print( f"Fit flux of 100000-flux star for sigma = 0.42: {phot['flux_fit'][0]}; "
+       f"(x,y)=({phot['x_fit'][0]}, {phot['y_fit'][0]}" )
+
+
+# RESULTS OF A RUN:
+#    root@655734bb3457:/snappl/experimentation# python play_with_photutils.py
+#    1.2-sigma PSF clip sums to 1.0000000000018092
+#    0.42-sigma PSF clip sums to 1.1267689222010988
+#    Fit flux of 100000-flux star for sigma = 1.2: 99833.32184334665; (x,y)=(511.00130567398907, 510.99895105013127
+#    Fit flux of 100000-flux star for sigma = 0.42: 100005.90585339173; (x,y)=(511.0002593061244, 511.0001099684552
+#
+# CONCLUSION:
+#
+# For PSFs whose FWHM is less than ~2 pixels on the original
+# image, the stamps you get from the __call__ method of a photutils
+# ImagePSF are not properly normalize.  (Interestingly, they are too big
+# by the same factor that lanczos4 interpolation gives....)  However,
+# photutils PSFPhotometry works in such a way that it takes this into
+# account (...or just doesn't use __call__) and produces reliable results.
+#
+# Which is all well and good if you just want to use PSFPhotometry, but
+# if you need thumbnails for other purposes (e.g. schene modelling),
+# that is very sad.

{roman_snpit_snappl-0.5.0 → roman_snpit_snappl-0.7.0/roman_snpit_snappl.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: roman_snpit_snappl
-Version: 0.5.0
+Version: 0.7.0
 Summary: Photometry utilities for the Roman SNPIT
 Author: Roman Supernove Project Infrastructure Team
 Maintainer-email: Roman SN PIT <raknop@lbl.gov>

{roman_snpit_snappl-0.5.0 → roman_snpit_snappl-0.7.0}/roman_snpit_snappl.egg-info/SOURCES.txt

@@ -34,6 +34,11 @@ changes/20.bugfix.rst
 changes/23.snappl.rst
 changes/26.feature.rst
 changes/3.snappl.rst
+changes/31.feature.rst
+changes/35.snappl.rst
+changes/36.snappl.rst
+changes/37.snappl.rst
+changes/40.snappl.rst
 changes/5.snappl.rst
 changes/8.snappl.rst
 changes/9.snappl.rst
@@ -45,6 +50,8 @@ docs/installation.rst
 docs/make.bat
 docs/usage.rst
 docs/_static/logo_black_filled.png
+experimentation/README.md
+experimentation/play_with_photutils.py
 licenses/.DS_Store
 licenses/LICENSE.rst
 licenses/README.rst
@@ -59,6 +66,7 @@ snappl/__init__.py
 snappl/_version.py
 snappl/image.py
 snappl/psf.py
+snappl/sed.py
 snappl/wcs.py
 snappl/_dev/__init__.py
 snappl/_dev/scm_version.py

{roman_snpit_snappl-0.5.0 → roman_snpit_snappl-0.7.0}/snappl/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.5.0'
-__version_tuple__ = version_tuple = (0, 5, 0)
+__version__ = version = '0.7.0'
+__version_tuple__ = version_tuple = (0, 7, 0)

{roman_snpit_snappl-0.5.0 → roman_snpit_snappl-0.7.0}/snappl/image.py

@@ -386,6 +386,42 @@ class FITSImage( Numpy2DImage ):
                 self._wcs = GalsimWCS.from_header( hdr )
         return self._wcs
 
+    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."
+            )
+        if which not in Image.data_array_list:
+            raise ValueError(f"Unknown which {which}, must be all, data, noise, or flags")
+
+        if (which == "all"):
+            if (self._data is not None) and (self._noise is not None) and (self._flags is not None):
+                return [self._data, self._noise, self._flags]
+            else:
+                raise RuntimeError(
+                    f"get_data called with which='all', but not all data arrays are set. "
+                    f"Data: {self._data is not None}, Noise: {self._noise is not None},"
+                    f" Flags: {self._flags is not None}"
+                )
+
+        if (which == "data"):
+            if (self._data is not None):
+                return [self._data]
+            else:
+                raise RuntimeError("get_data called with which='data', but data is not set.")
+
+        if (which == "noise"):
+            if (self._noise is not None):
+                return [self._noise]
+            else:
+                raise RuntimeError("get_data called with which='noise', but noise is not set.")
+
+        if (which == "flags"):
+            if (self._flags is not None):
+                return [self._flags]
+            else:
+                raise RuntimeError("get_data called with which='flags', but flags are not set.")
+
     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.
 
@@ -554,3 +590,27 @@ class OpenUniverse2024FITSImage( FITSImage ):
     def _get_zeropoint( self ):
         header = self._get_header()
         return galsim.roman.getBandpasses()[self.band].zeropoint + header['ZPTMAG']
+
+
+class ManualFITSImage(FITSImage):
+    def __init__(self, header, data, noise=None, flags=None, path = None, exposure = None, sca = None, *args, **kwargs):
+
+        self._data = data
+        self._noise = noise
+        self._flags = flags
+        self._header = header
+        self._wcs = None
+        self._is_cutout = False
+        self._image_shape = None
+
+        self.inputs = types.SimpleNamespace()
+        self.inputs.path = None
+        self.inputs.exposure = None
+        self.inputs.sca = None
+
+    def _get_header(self):
+        """Get the header of the image."""
+        if self._header is None:
+            raise RuntimeError("Header is not set for ManualFITSImage.")
+        return self._header
+