Fix bug that arose when users would supply --fixed-posns in the cli

sourcefinder/utility/cli.py

@@ -160,10 +160,10 @@ def construct_argument_parser():
         "--structuring-element",
         type=ast.literal_eval,
         help="""
-        Structuring element for morphological operations, provided as a 
-        Python-style nested list, e.g. '[[1,1,1], [1,1,1], [1,1,1]]' for 
+        Structuring element for morphological operations, provided as a
+        Python-style nested list, e.g. '[[1,1,1], [1,1,1], [1,1,1]]' for
         8-connectivity and '[[0,1,0], [1,1,1], [0,1,0]]' for 4-connectivity.
-        This is used for defining the connectivity in connected-component 
+        This is used for defining the connectivity in connected-component
         labelling.
         """,
     )
@@ -575,9 +575,8 @@ def run_sourcefinder(files, conf, mode):
         imagedata = sourcefinder_image_from_accessor(ff, conf=conf)
 
         if mode == "fixed":
-            # FIXME: conf.image.fixed_coords does not exist
             sr = imagedata.fit_fixed_positions(
-                conf.image.fixed_coords,
+                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_scripts/test_pyse.py

@@ -1,5 +1,6 @@
 import subprocess
 from pathlib import Path
+import pandas as pd
 
 
 def run_pyse(files, extra_args, out_dir):
@@ -10,20 +11,7 @@ def run_pyse(files, extra_args, out_dir):
     test = subprocess.Popen(cli_args, stdout=subprocess.PIPE)
     raw_output = test.communicate()[0]
     output = raw_output.decode("utf8").split("\n")
-
-    nr_sources_per_image = []
-    for line in output:
-        if "Number of detected sources" in line:
-            nr_sources = int(line.split(" = ")[-1].strip())
-            nr_sources_per_image.append(nr_sources)
-
-    if len(nr_sources_per_image) != len(files):
-        raise ValueError(
-            f"Not all images finished correctly. Found {len(nr_sources_per_image)} sets of sources with {len(files)} input images. "
-        )
-
-    return nr_sources_per_image
-
+    return output
 
 def test_pyse_export(tmpdir):
     files = ["test/data/GRB120422A-120429.fits"]
@@ -37,13 +25,12 @@ def test_pyse_export(tmpdir):
         "--islands",
     ]
     extra_args = ["--detection-thr", "6", "--analysis-thr", "5", *export_args]
-    nr_sources_per_image = run_pyse(files, extra_args, tmpdir)
-
-    for n in nr_sources_per_image:
-        assert n == 1
+    output = run_pyse(files, extra_args, tmpdir)
 
     # Check CSV
     assert Path(f"{tmpdir}/GRB120422A-120429.csv").exists()
+    df = pd.read_csv(f"{tmpdir}/GRB120422A-120429.csv")
+    assert len(df) == 1
 
     # Check skymodel
     assert Path(f"{tmpdir}/GRB120422A-120429.skymodel").exists()
@@ -62,3 +49,16 @@ def test_pyse_export(tmpdir):
 
     # Check islands
     assert Path(f"{tmpdir}/GRB120422A-120429.islands.fits").exists()
+
+def test_pyse_fixed_posns(tmpdir):
+    files = ["test/data/GRB120422A-120429.fits"]
+    export_args = [
+        "--csv",
+    ]
+    extra_args = ["--detection-thr", "6", "--analysis-thr", "5", "--fixed-posns", "[[136.896, 14.0222]]", *export_args]
+    nr_sources_per_image = run_pyse(files, extra_args, tmpdir)
+
+    # Check CSV
+    assert Path(f"{tmpdir}/GRB120422A-120429.csv").exists()
+    df = pd.read_csv(f"{tmpdir}/GRB120422A-120429.csv")
+    assert len(df) == 1