Fix 186 and 173

sourcefinder/config.py

@@ -203,18 +203,25 @@ class ImgConf(_Validate):
 
     """
 
-    back_size_x: int | None = 32
+    back_size_x: int | None = None
     """Subimage size for estimation of background node values (X
     direction). The nodes are centred on the subimages.
 
     """
 
-    back_size_y: int | None = 32
+    back_size_y: int | None = None
     """Subimage size for estimation of background node values (Y
     direction). The nodes are centred on the subimages.
 
     """
 
+    grid: int | None = 64
+    """Background subimage size used as fallback for back_size_x and
+    back_size_y. If both are not set, this implies
+    back_size_x=backsize_y=grid, i.e. the subimages are squares.
+
+    """
+
     eps_ra: float = 0.0
     """Calibration uncertainty in right ascension (degrees), see
     equation 27a of the NVSS paper.
@@ -326,13 +333,6 @@ class ImgConf(_Validate):
     deblend_nthresh: int = 0
     """Number of deblending subthresholds; 0 to disable."""
 
-    grid: int | None = None
-    """Background subimage size used as fallback for back_size_x and
-    back_size_y. If both are not set, this implies
-    back_size_x=backsize_y=grid, i.e. the subimages are squares.
-
-    """
-
     bmaj: float | None = None
     """Set beam: Major axis of restoring beam (degrees)."""
 

sourcefinder/image.py

@@ -10,9 +10,7 @@
 from numba import guvectorize, float32, int32
 import pandas as pd
 
-from sourcefinder import extract
-from sourcefinder import stats
-from sourcefinder import utils
+from sourcefinder import extract, stats, utils
 from sourcefinder.config import Conf, ImgConf, ExportSettings
 from sourcefinder.utility import containers
 from sourcefinder.utility.uncertain import Uncertain

sourcefinder/utility/cli.py

@@ -34,6 +34,7 @@
 import astropy.io.fits as pyfits
 import numpy
 
+import sourcefinder
 from sourcefinder.accessors import open as open_accessor
 from sourcefinder.accessors import sourcefinder_image_from_accessor
 from sourcefinder.accessors import writefits as tkp_writefits
@@ -124,6 +125,13 @@ def construct_argument_parser():
     """,
     )
 
+    general_group.add_argument(
+        "-v",
+        "--version",
+        action="version",
+        version=f"PySE {sourcefinder.__version__} (Python {sys.version.split()[0]})",
+    )
+
     image_group = parser.add_argument_group("Image parameters")
 
     image_group.add_argument(
@@ -456,11 +464,21 @@ def excepthook(type, value, traceback):
                 # command line we get a None value, ignore these
                 cli_args[section_name][arg_name] = cli_value
 
+    image_args = cli_args["Image parameters"]
+    # Handle grid vs back-size-x/y precedence
+    if image_args.get("grid") is not None:
+        if image_args.get("back_size_x") is None:
+            image_args["back_size_x"] = image_args["grid"]
+        if image_args.get("back_size_y") is None:
+            image_args["back_size_y"] = image_args["grid"]
+
     # Note: Dataclass replace is not recursive for stacked dataclasses.
     #       Replace one by one to avoid arguments being reset to their
     #       defaults.
-    conf_image = replace(conf.image, **cli_args["Image parameters"])
+    conf_image = replace(conf.image, **image_args)
     conf_export = replace(conf.export, **cli_args["Export parameters"])
+    # The functions skymodel, csv, summary and regions are currently not able
+    # to handle Pandas DataFrames.
     no_pandas_df_dict = {"pandas_df": False}
     conf_export = replace(conf_export, **no_pandas_df_dict)
     conf = replace(conf, image=conf_image, export=conf_export)
@@ -581,7 +599,9 @@ def run_sourcefinder(files, conf, mode):
 
         if mode == "fixed":
             sr = imagedata.fit_fixed_positions(
-                eval(conf.image.fixed_posns), # fixed_posns is a string, use eval to obtain it's contents
+                eval(
+                    conf.image.fixed_posns
+                ),  # fixed_posns is a string, use eval to obtain it's contents
                 conf.image.ffbox * max(imagedata.beam[0:2]),
             )
 

test/test_image.py

@@ -79,7 +79,8 @@ def setUp(self):
         eye in DS9
         """
         self.image = accessors.sourcefinder_image_from_accessor(
-            accessors.open(os.path.join(DATAPATH, "NCP_sample_image_1.fits"))
+            accessors.open(os.path.join(DATAPATH, "NCP_sample_image_1.fits")),
+            conf=Conf(ImgConf(grid=32), export=ExportSettings()),
         )
         self.assertListEqual(list(self.image.data.shape), [1024, 1024])
         self.boxsize = BOX_IN_BEAMPIX * max(
@@ -389,7 +390,7 @@ def testSingleSourceExtraction(self):
         # Start with comparing results from fitting with ground truth results
         # from fitting. This implies "vectorized==False".
         conf_fitting = Conf(
-            image=ImgConf(detection_thr=5, vectorized=False),
+            image=ImgConf(detection_thr=5, grid=32, vectorized=False),
             export=ExportSettings(
                 source_params=source_params, pandas_df=False
             ),
@@ -417,7 +418,7 @@ def testSingleSourceExtraction(self):
         # Next, compare results from "tweaked moments" with ground truth results
         # from "tweaked moments". This implies "vectorized==True".
         conf_moments = Conf(
-            image=ImgConf(detection_thr=5, vectorized=True),
+            image=ImgConf(detection_thr=5, grid=32, vectorized=True),
             export=ExportSettings(
                 source_params=source_params, pandas_df=False
             ),
@@ -451,7 +452,7 @@ def testForceSourceShape(self):
         major/minor axes to be held constant when fitting.
         """
         conf = Conf(
-            image=ImgConf(detection_thr=5, force_beam=True),
+            image=ImgConf(detection_thr=5, grid=32, force_beam=True),
             export=ExportSettings(pandas_df=False),
         )
         image = accessors.sourcefinder_image_from_accessor(
@@ -470,7 +471,7 @@ def testWcsConversionConsistency(self):
         """
 
         conf = Conf(
-            image=ImgConf(detection_thr=5),
+            image=ImgConf(detection_thr=5, grid=32),
             export=ExportSettings(pandas_df=False),
         )
         fits_image = accessors.sourcefinder_image_from_accessor(
@@ -514,7 +515,7 @@ def testNoLabelledIslandsCase(self):
         image = accessors.sourcefinder_image_from_accessor(
             FitsImage(GRB120422A),
             conf=Conf(
-                ImgConf(detection_thr=5e10, analysis_thr=5e10),
+                ImgConf(detection_thr=5e10, grid=32, analysis_thr=5e10),
                 export=ExportSettings(pandas_df=False),
             ),
         )