placeholder while I wait for Rob's snappl PR. also, some ruff

Author: laldoroty

phrosty/pipeline.py

@@ -94,8 +94,7 @@ def __init__( self, image, pipeline ):
         self.psf_data = None
 
     def run_sky_subtract( self, mp=True ):
-        """
-        Run sky subtraction using Source Extractor.
+        """Run sky subtraction using Source Extractor.
 
         Parameters
         ----------
@@ -108,24 +107,23 @@ def run_sky_subtract( self, mp=True ):
             Tuple containing sky subtracted image, detection
             mask array, and sky RMS value. 
             Output of phrosty.imagesubtraction.sky_subtract().
-        """        
+        """
         try:
             return sky_subtract( self.image )
         except Exception as ex:
             SNLogger.exception( ex )
             raise
 
     def save_sky_subtract_info( self, info ):
-        """
-        Saves the sky-subtracted image, detection mask array,
+        """Saves the sky-subtracted image, detection mask array,
         and sky RMS values to attributes. 
 
         Parameters
         ----------
         info : tuple
             Output of self.run_sky_subtract(). See documentation
             for phrosty.imagesubtraction.sky_subtract().
-        """        
+        """
         try:
             SNLogger.debug( f"Saving sky_subtract info for path {info[0]}" )
             self.skysub_img = info[0]
@@ -177,8 +175,7 @@ def get_psf( self, ra, dec ):
             return None
 
     def keep_psf_data( self, psf_data ):
-        """
-        Save PSF data to attribute. If self.get_psf() failed,
+        """Save PSF data to attribute. If self.get_psf() failed,
         then the image is recorded as a failure.
 
         Parameters
@@ -298,8 +295,7 @@ def __init__( self, diaobj, imgcol, band,
 
 
     def _read_csv( self, csvfile ):
-        """
-        Reads input csv files with columns:
+        """Reads input csv files with columns:
         'path pointing sca mjd band'.
 
         Parameters
@@ -332,21 +328,20 @@ def _read_csv( self, csvfile ):
 
 
     def sky_sub_all_images( self ):
-        """
-        Sky subtracts all snappl.image.Image objects in 
+        """Sky subtracts all snappl.image.Image objects in 
         self.science_images and self.template_images using
         Source Extractor.
 
         Contains its own error logging function, log_error().
 
-        """        
+        """
 
         # Currently, this writes out a bunch of FITS files.  Further refactoring needed
         #   to support more general image types.
         all_imgs = self.science_images.copy()     # shallow copy
         all_imgs.extend( self.template_images )
 
-        def log_error( img, x ):   
+        def log_error( img, x ):
 
             SNLogger.error( f"Sky subtraction failure on {img.image.path}: {x}" )
             self.failures['skysub'].append( f'{img.image.band} {img.image.pointing} {img.image.sca}' )
@@ -364,8 +359,7 @@ def log_error( img, x ):
                 img.save_sky_subtract_info( img.run_sky_subtract( mp=False ) )
 
     def get_psfs( self ):
-        """
-        Retrieve PSFs for all snappl.image.Image objects in
+        """Retrieve PSFs for all snappl.image.Image objects in
         self.science_images and self.template_images.
 
         Contains its own error logging function, log_error().
@@ -385,7 +379,7 @@ def log_error( img, x ):
                     # callback_partial = partial( img.save_psf_path, all_imgs )
                     pool.apply_async( img.get_psf, (self.diaobj.ra, self.diaobj.dec), {},
                                       callback=img.keep_psf_data,
-                                      error_callback=partial(log_error,img) )
+                                      error_callback=partial(log_error, img) )
                 pool.close()
                 pool.join()
         else:
@@ -598,8 +592,7 @@ def make_phot_info_dict( self, sci_image, templ_image, ap_r=4 ):
         return results_dict
 
     def add_to_results_dict( self, one_pair ):
-        """
-        Record results from self.make_phot_info_dict() to the
+        """Record results from self.make_phot_info_dict() to the
         aggregate dictionary for the entire light curve.
 
         Parameters
@@ -619,9 +612,7 @@ def add_to_results_dict( self, one_pair ):
         SNLogger.debug( "Done adding to results dict" )
 
     def save_stamp_paths( self, sci_image, templ_image, paths ):
-        """
-
-        Helper function for recording the stamp paths returned in
+        """Helper function for recording the stamp paths returned in
         self.do_stamps.
 
         Parameters
@@ -641,8 +632,7 @@ def save_stamp_paths( self, sci_image, templ_image, paths ):
         sci_image.diff_var_stamp_path[ templ_image.image.name ] = paths[2]
 
     def do_stamps( self, sci_image, templ_image ):
-        """
-        Make stamps from the zero point image, decorrelated
+        """Make stamps from the zero point image, decorrelated
         difference image, and variance image centered at the
         location of the supernova.
 
@@ -659,7 +649,7 @@ def do_stamps( self, sci_image, templ_image ):
             Paths to the stamps corresponding to the zero point image,
             decorrelated difference image, and variance image centered
             at the location of the supernova.
-        """        
+        """
 
         try:
             zptim = FITSImageOnDisk( sci_image.decorr_zptimg_path[ templ_image.image.name ] )
@@ -694,9 +684,9 @@ def do_stamps( self, sci_image, templ_image ):
             self.failures['make_stamps'].append({'science': f'{sci_image.image.band} {sci_image.image.pointing} {sci_image.image.sca}',
                                                  'template': f'{templ_image.image.band} {templ_image.image.pointing} {templ_image.image.sca}'
                                                 })
+
     def make_lightcurve( self ):
-        """
-        Collect all results from photometry in one dictionary.
+        """Collect all results from photometry in one dictionary.
         Write the output to a csv as a table.
 
         Contains its own error logging function, log_error().
@@ -705,7 +695,7 @@ def make_lightcurve( self ):
         -------
         pathlib.Path
             Path to output csv file that contains a light curve.
-        """        
+        """
         SNLogger.info( "Making lightcurve." )
 
         self.results_dict = {
@@ -760,8 +750,7 @@ def log_error( sci_image, templ_image, x ):
         return results_savepath
 
     def write_fits_file( self, data, header, savepath ):
-        """
-        Helper function for writing fits files.
+        """Helper function for writing fits files.
 
         Parameters
         ----------
@@ -784,15 +773,14 @@ def write_fits_file( self, data, header, savepath ):
             raise
 
     def clear_contents( self, directory ):
-        """
-        Delete contents of a directory. Used to clear temporary
+        """Delete contents of a directory. Used to clear temporary
         files.
 
         Parameters
         ----------
         directory : pathlib.Path
             Path to directory to empty.
-        """        
+        """
         for f in directory.iterdir():
             try:
                 if f.is_dir():

phrosty/tests/conftest.py

@@ -1,11 +1,12 @@
+import numpy as np
 import pytest # noqa: F401
 import pathlib
 
 import tox # noqa: F401
 from tox.pytest import init_fixture # noqa: F401
 
 from snpit_utils.config import Config
-from snappl.image import FITSImageOnDisk
+from snappl.image import FITSImageOnDisk, ManualFITSImage
 from snappl.diaobject import DiaObject
 from snappl.imagecollection import ImageCollection
 
@@ -174,3 +175,14 @@ def two_ou2024_science_images( ou2024_image_collection ):
     img1 = ou2024_image_collection.get_image( pointing=35198, sca=2, band='Y106' )
     img2 = ou2024_image_collection.get_image( pointing=39790, sca=15, band='Y106' )
     return img1, img2
+
+@pytest.fixture
+def nan_image( ou2024_image_collection ):
+    ou_img = ou2024_image_collection.get_image( pointing=35198, sca=2, band='Y106' )
+    ou_header = ou_img.get_fits_header()
+
+    nan_arr = np.empty((4088,4088))
+    nan_arr[:] = np.nan
+
+    nan_img = ManualFITSImage(header=ou_header, data=nan_arr, pointing=35198, sca=2)
+    return nan_img

phrosty/tests/test_pipeline.py

@@ -1,4 +1,5 @@
 import os
+import numpy as np
 import pytest
 from phrosty.pipeline import Pipeline
 
@@ -70,16 +71,27 @@ def test_pipeline_run( object_for_tests, ou2024_image_collection,
     #   directories for tests and for running... so don't do that... but the
     #   way we're set up right now, you probably are.
 
+
 @pytest.mark.skipif( os.getenv("SKIP_GPU_TESTS", 0 ), reason="SKIP_GPU_TESTS is set" )
 def test_pipeline_failures( object_for_tests, ou2024_image_collection,
-                            one_ou2024_template_image, two_ou2024_science_images ):
+                            one_ou2024_template_image, two_ou2024_science_images,
+                            nan_image ):
     pip = Pipeline( object_for_tests, ou2024_image_collection, 'Y106',
                     science_images=two_ou2024_science_images,
                     template_images=[one_ou2024_template_image],
                     nprocs=2, nwrite=3 )
-    
+
     # First, check the images as-is. Make sure there are no failures.
     for key in pip.failures:
         assert len(pip.failures[key]) == 0
+    
+    new_test_imgs = [nan_image, two_ou2024_science_images[1]]
 
-    
+    pip = Pipeline( object_for_tests, ou2024_image_collection, 'Y106',
+                science_images=new_test_imgs,
+                template_images=[one_ou2024_template_image],
+                nprocs=2, nwrite=3 )
+
+    for key in pip.failures:
+        print(key)
+        print(len(pip.failures[key]))