Skip to content

Bug fixes to make the legacy SD pipeline work again #410

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
thomaswilliamsastro merged 1 commit into from
Oct 7, 2026
Merged

Bug fixes to make the legacy SD pipeline work again #410

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Appropriately change spectral units from velocity to frequency when regridding (#398).
- Ensure fits import adds Stokes axis in feather routines (#407).
- Fixed regression in get_ghz_range_for_line (#409).
- Remove obsolete keywords so legacy singledish pipeline works again (#410).

### Dependencies
- Bump actions/upload-artifact from 6 to 7 (#313).
Expand Down
38 changes: 16 additions & 22 deletions phangsPipeline/handlerSingleDish.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -240,7 +240,7 @@ def task_execute_single_dish_pipeline(

for ird in input_raw_data:

ms_dir = str(os.path.basename(ird))
ms_dir = str(os.path.basename(os.path.normpath(ird)))
ms_dirs.append(ms_dir)

path_galaxy = os.path.join(str(os.path.abspath(path_galaxy_root)), ms_dir) + os.sep
Expand All @@ -266,28 +266,28 @@ def task_execute_single_dish_pipeline(

product = product_list[0]

vlow2 = product_dict[product]['vel_cube'][0]
vhigh2 = product_dict[product]['vel_cube'][1]
vlow1 = product_dict[product]['vel_cube'][0]
vhigh1 = product_dict[product]['vel_cube'][1]

vlow1 = product_dict[product]['vel_line_mask'][0]
vhigh1 = product_dict[product]['vel_line_mask'][1]
vlow2 = product_dict[product]['vel_line_mask'][0]
vhigh2 = product_dict[product]['vel_line_mask'][1]

kwargs = {}
kwargs['path_galaxy'] = path_galaxy_root #
kwargs['ms_dirs'] = ms_dirs
kwargs['flag_file'] = '' #
kwargs['doplots'] = False # Do non-interactive. additional plots (plots will be saved in "calibration/plots" folder)
kwargs['doplots'] = False # Do non-interactive. additional plots (plots will be saved in "calibration/plots" folder)
kwargs['bl_order'] = 1 # Order for the baseline fitting
kwargs['max_flag_frac'] = 0.9 # Remove antennae with significant amounts of flagged data
kwargs['in_source'] = source # Source name. This comes from the field name in the MS file keys
kwargs['freq_rest'] = product_dict[product]['freq_rest_MHz'] # Rest frequency of requested line in MHz (ex: "freq_rest = 230538" for CO(2-1))
kwargs['vel_cube'] = vel_cube = '%.3f~%.3f'%(vlow2, vhigh2) # Range in velocity in km/s to extract the line cube.
kwargs['vel_line'] = vel_line = '%.3f~%.3f'%(vlow1, vhigh1) # Range in velocity in km/s to exclude the line emission from the baseline fit.
kwargs['in_sources'] = source # Source name. This comes from the field name in the MS file keys
kwargs['freq_rest'] = product_dict[product]['freq_rest_MHz'] # Rest frequency of requested line in MHz (ex: "freq_rest = 230538" for CO(2-1))
kwargs['vel_cube'] = '%.3f~%.3f'%(vlow2, vhigh2) # Range in velocity in km/s to extract the line cube.
kwargs['vel_line'] = '%.3f~%.3f'%(vlow1, vhigh1) # Range in velocity in km/s to exclude the line emission from the baseline fit.
kwargs['phase_center'] = phase_center # Provide coordinate of phase center, otherwise set to "False" and coordinates will be read from the data
kwargs['source_vel_kms'] = product_dict[product]['vsys'] # Provide velocity of the source, otherwise set to "False" and coordinates will be read from the data
kwargs['vwidth_kms'] = product_dict[product]['vwidth'] # width in velocity and velocity resolution in km/s
kwargs['chan_dv_kms'] = product_dict[product]['max_chanwidth_kms'] #
kwargs['freq_rest_im'] = product_dict[product]['freq_rest_GHz'] # rest frequency in GHz for imaging
kwargs['freq_rest_im'] = product_dict[product]['freq_rest_MHz'] / 1e3 # rest frequency in GHz for imaging
kwargs['name_line'] = product_dict[product]['line_name'] # Name of the line, to be used for naming the files -- will not be used anymore
kwargs['output_file'] = product_dict[product]['output_file'] # Output file path
#kwargs['joint_imaging_dirs'] = joint_imaging_dirs # Do a joint imaging by including *.cal.jy in joint_imaging_dir
Expand Down Expand Up @@ -351,17 +351,11 @@ def recipe_process_one_target(
logger.warning('Warning! Multiple single dish raw data entries are found in the ms_file_key! We will only process the first one! [TODO]')
#<TODO># We can only process one single dish raw data for now. Not sure how to combine those. Unless we specify line_product in the ms_file_key?

for idx in range(len(fname_dict['sd_raw_data_list'])):
self.task_execute_single_dish_pipeline(
target = target,
product = product,
source = fname_dict['source'],
input_raw_data = fname_dict['sd_raw_data_list'][idx],
output_file = fname_dict['sd_file'],
)
if idx > 0:
break
#<TODO># We can only process one single dish raw data for now. Not sure how to combine those. Unless we specify line_product in the ms_file_key?
self.task_execute_single_dish_pipeline(
target = target,
product = product,
source = fname_dict['source'],
)

return

Expand Down
Loading