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Show the pyse inputs, similar to -h #192

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Merged
HannoSpreeuw merged 2 commits into from
Jan 13, 2026
Merged

Show the pyse inputs, similar to -h #192

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ff44793
Show the inputs in terminal when --show_input is passed, similar to -h
tmillenaar Jan 12, 2026
7dba72a
Rename show-input to show-args
tmillenaar Jan 13, 2026
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72 changes: 42 additions & 30 deletions sourcefinder/utility/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
See chapters 2 & 3 of Spreeuw, PhD Thesis, University of Amsterdam, 2010,
<http://dare.uva.nl/en/record/340633> for details.
"""

import argparse
import ast
import json
Expand All @@ -27,7 +28,7 @@
import os.path
import pdb
import sys
from dataclasses import replace
from dataclasses import asdict, replace
from io import StringIO
from pathlib import Path

Expand Down Expand Up @@ -89,8 +90,7 @@ def parse_monitoringlist_positions(
monitor_coords.extend(mon_list)
except json.JSONDecodeError:
logging.error(
"Could not parse monitor-coords from file: "
+ getattr(args, list_name)
"Could not parse monitor-coords from file: " + getattr(args, list_name)
)
raise
return monitor_coords
Expand Down Expand Up @@ -123,6 +123,14 @@ def construct_argument_parser():
Enter debug mode when the application crashes. Meant to be used for more comprehensive debugging.
""",
)
general_group.add_argument(
"--show-args",
action="store_true",
help="""
View all arguments pyse will run with in the current configuration after aggregating the command-line
arguments, config-file parameters and pyse defaults.
""",
)

image_group = parser.add_argument_group("Image parameters")

Expand Down Expand Up @@ -215,12 +223,8 @@ def construct_argument_parser():
image_group.add_argument(
"--eps-dec", type=float, help="Dec matching tolerance in arcseconds."
)
image_group.add_argument(
"--detection-thr", type=float, help="Detection threshold"
)
image_group.add_argument(
"--analysis-thr", type=float, help="Analysis threshold"
)
image_group.add_argument("--detection-thr", type=float, help="Detection threshold")
image_group.add_argument("--analysis-thr", type=float, help="Analysis threshold")
image_group.add_argument(
"--fdr", action="store_true", help="Use False Detection Rate algorithm"
)
Expand All @@ -230,9 +234,7 @@ def construct_argument_parser():
type=int,
help="Number of deblending subthresholds; 0 to disable",
)
image_group.add_argument(
"--grid", type=int, help="Background grid segment size"
)
image_group.add_argument("--grid", type=int, help="Background grid segment size")
image_group.add_argument(
"--bmaj", type=float, help="Set beam: Major axis of beam (deg)"
)
Expand Down Expand Up @@ -296,9 +298,7 @@ def construct_argument_parser():
export_group.add_argument(
"--regions", action="store_true", help="Generate DS9 region file(s)"
)
export_group.add_argument(
"--rmsmap", action="store_true", help="Generate RMS map"
)
export_group.add_argument("--rmsmap", action="store_true", help="Generate RMS map")
export_group.add_argument(
"--sigmap", action="store_true", help="Generate significance map"
)
Expand All @@ -310,7 +310,7 @@ def construct_argument_parser():
)

# Finally, as positional arguments, the file list:
parser.add_argument("files", nargs="+", help="Image files for processing")
parser.add_argument("files", nargs="*", help="Image files for processing")
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@tmillenaar tmillenaar Jan 12, 2026

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Ik heb dit aangepast zodat ik ook --show-input aan kan roepen zonder een file mee te geven. De nargs="+" zorgde ervoor dat er een error werd gegooid als er geen file werd meegegeven. Dit doe ik nu zelf verderop in de code als de logia voor --show-input voorbij is en het tijd is voor echte processing doe ik zelf een check dat er in elk geval een file is meegegeven

return parser


Expand Down Expand Up @@ -392,9 +392,7 @@ def summary(filename, sourcelist):
output = StringIO()
print("** %s **\n" % filename, file=output)
for source in sourcelist:
print(
"RA: %s, dec: %s" % (str(source.ra), str(source.dec)), file=output
)
print("RA: %s, dec: %s" % (str(source.ra), str(source.dec)), file=output)
print(
"Error radius (arcsec): %s" % (str(source.error_radius)),
file=output,
Expand Down Expand Up @@ -436,6 +434,8 @@ def excepthook(type, value, traceback):

sys.excepthook = excepthook

show_args = unstructured_args.pop("show_args")

# Merge the CLI arguments with the config file parameters
config_file = unstructured_args.pop("config_file")
conf = read_conf(config_file)
Expand Down Expand Up @@ -470,6 +470,23 @@ def excepthook(type, value, traceback):
fixed_coords = parse_monitoringlist_positions(
conf.image, str_name="fixed_posns", list_name="fixed_posns_file"
)

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@HannoSpreeuw HannoSpreeuw Jan 12, 2026 •
edited
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This is the implementation of the new feature and almost all of the rest is reformatting from Black?

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@tmillenaar tmillenaar Jan 13, 2026

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Mostly, though there is the added argument to the parser around line 126

if show_args:

def print_dict_content_recursively(dict_, current_depth):
for key, value in dict_.items():
if isinstance(value, dict):
print(current_depth * " ", f"=== {key} ===")
print_dict_content_recursively(value, current_depth + 1)
else:
print(current_depth * " ", f"{key}: {value}")

print_dict_content_recursively(asdict(conf), current_depth=0)
sys.exit(0)

if len(files) == 0:
raise ValueError("At least one input file must be supplied")

# Quick & dirty check that the position list looks plausible
if fixed_coords:
mlist = numpy.array(fixed_coords)
Expand All @@ -489,9 +506,7 @@ def excepthook(type, value, traceback):
if conf.image.fdr:
parser.error("--fdr not supported with fixed positions")
elif conf.image.detection_image:
parser.error(
"--detection-image not supported with fixed positions"
)
parser.error("--detection-image not supported with fixed positions")
elif conf.export.residuals:
parser.error("--residuals not supported with fixed positions")
elif conf.export.islands:
Expand Down Expand Up @@ -571,17 +586,16 @@ def run_sourcefinder(files, conf, mode):
labels, labelled_data = [], None

for counter, filename in enumerate(files):
print(
"Processing %s (file %d of %d)."
% (filename, counter + 1, len(files))
)
print("Processing %s (file %d of %d)." % (filename, counter + 1, len(files)))
imagename = os.path.splitext(os.path.basename(filename))[0]
ff = open_accessor(filename, beam=beam, plane=0)
imagedata = sourcefinder_image_from_accessor(ff, conf=conf)

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]),
)

Expand Down Expand Up @@ -653,9 +667,7 @@ def run_sourcefinder(files, conf, mode):
pyfits.getheader(filename),
)
if conf.export.skymodel:
with open(
export_dir / (imagename + ".skymodel"), "w"
) as skymodelfile:
with open(export_dir / (imagename + ".skymodel"), "w") as skymodelfile:
if ff.freq_eff:
skymodelfile.write(skymodel(sr, ff.freq_eff))
else:
Expand Down