merge pipeline control flow changes from sourcefinder testing into main

Author: m-stclair

gPhoton/lightcurve/core.py

@@ -1,16 +1,16 @@
 from pathlib import Path
 from typing import Mapping, Collection
 
-import numpy as np
 
 import gPhoton.constants as c
 from gPhoton.lightcurve._steps import (
     find_sources,
     count_full_depth_image,
     extract_photometry,
-    write_exptime_file, load_source_catalog,
+    write_exptime_file,
+    load_source_catalog
 )
-from gPhoton.reference import FakeStopwatch, eclipse_to_paths
+from gPhoton.reference import FakeStopwatch
 from gPhoton.types import GalexBand
 
 
@@ -19,28 +19,23 @@ def make_lightcurves(
     eclipse: int,
     band: GalexBand,
     aperture_sizes: Collection[float],
-    photonlist_path,
+    output_filenames,
     source_catalog_file=None,
     threads=None,
-    output_filenames=None,
     stopwatch: FakeStopwatch = FakeStopwatch(),
 ):
     """
     make lightcurves from preprocessed structures generated from FITS images
     and movies, especially ones produced by the gPhoton.moviemaker pipeline.
     """
-    if output_filenames is None:
-        output_filenames = eclipse_to_paths(
-            eclipse, Path(photonlist_path).parent, None
-        )[band]
     if source_catalog_file is not None:
         sources = load_source_catalog(source_catalog_file, eclipse)
     else:
         sources = None
     source_table = find_sources(
         eclipse,
         band,
-        str(photonlist_path.parent),
+        str(Path(output_filenames['photomfile']).parent),
         sky_arrays["image_dict"],
         sky_arrays["wcs"],
         source_table=sources,
@@ -60,15 +55,19 @@ def make_lightcurves(
             sky_arrays["wcs"],
         )
         stopwatch.click()
-        photometry_table = extract_photometry(
-            sky_arrays["movie_dict"], photometry_table, apertures, threads
-        )
+        if len(sky_arrays['movie_dict']) > 0:
+            photometry_table = extract_photometry(
+                sky_arrays["movie_dict"], photometry_table, apertures, threads
+            )
+            write_exptime_file(
+                output_filenames["expfile"], sky_arrays["movie_dict"]
+            )
         photomfile = (
             f"{output_filenames['photomfile']}"
             f"{str(aperture_size).replace('.', '_')}.csv"
         )
         print(f"writing source table to {photomfile}")
         photometry_table.to_csv(photomfile, index=False)
         stopwatch.click()
-    write_exptime_file(output_filenames["expfile"], sky_arrays["movie_dict"])
+
     return "successful"