arrakis.imager

Arrkis imager

Attributes

TQDM_OUT

Classes

`ImageSet`	Container to organise files related to t he imaging of a measurement set.
`MFSImage`	Representation of a multi-frequency synthesis image.

Functions

`cleanup`(→ None)	Utility to remove all images described by an collection of ImageSets. Internally
`cleanup_imageset`(→ None)	Delete images associated with an input ImageSet
`cli`()	Command-line interface
`fix_ms`(→ pathlib.Path)	Apply the corrections to the FEED table of a measurement set that
`fix_ms_askap_corrs`(→ pathlib.Path)	Applies a correction to raw telescope polarisation products to rotate them
`get_beam`(→ pathlib.Path)	Derive a common resolution across all images within a set of ImageSet
`get_mfs_image`() → MFSImage)	Get the MFS image from the image set.
`get_pol_axis_task`(→ float)
`get_prefix`(→ pathlib.Path)	Derive a consistent prefix style from a input MS name.
`get_wsclean`(→ pathlib.Path)	Pull wsclean image from dockerhub (or wherver).
`image_beam`(→ ImageSet)	Image a single beam
`imager_parser`(→ argparse.ArgumentParser)	Return the argument parser for the imager routine.
`main`(msdir, out_dir[, num_beams, temp_dir_images, ...])	Arrakis imager flow
`make_cube`(→ Tuple[pathlib.Path, pathlib.Path])	Make a cube from the images
`make_validation_plots`(→ None)	Make validation plots for the images.
`merge_imagesets`(→ ImageSet)	Merge a collection of ImageSets into a single ImageSet.
`run_wsclean_singuarlity`(→ None)
`smooth_imageset`(→ ImageSet)	Smooth all images described within an ImageSet to a desired resolution

Module Contents

class arrakis.imager.ImageSet[source]

Bases: NamedTuple

Container to organise files related to t he imaging of a measurement set.

aux_lists: Dict[Tuple[str, str], List[str]] | None = None[source]: Dictionary of lists of auxillary images. The keys are a tuple of the polarisation and the image type, and the values are the list of images for that polarisation and image type.

image_lists: Dict[str, List[str]][source]: Dictionary of lists of images. The keys are the polarisations and the values are the list of images for that polarisation.

ms: pathlib.Path[source]: Path to the measurement set that was imaged.

prefix: str[source]: Prefix used for the wsclean output files.

class arrakis.imager.MFSImage[source]

Bases: NamedTuple

Representation of a multi-frequency synthesis image.

image: numpy.ndarray[source]: The image data.

model: numpy.ndarray[source]: The model data.

residual: numpy.ndarray[source]: The residual data.

arrakis.imager.cleanup(purge: bool, image_sets: List[ImageSet], ignore_files: List[Any] | None = None) → None[source]

Utility to remove all images described by an collection of ImageSets. Internally called cleanup_imageset.

Parameters:

purge (bool) – Whether files are actually removed or skipped.
image_sets (List[ImageSet]) – Collection of ImageSets that would be deleted
ignore_files (Optional, List[Any]) – Collection of items to ignore. Nothing is done with this
and is purely used to exploit the dask dependency tracking.

arrakis.imager.cleanup_imageset(purge: bool, image_set: ImageSet) → None[source]

Delete images associated with an input ImageSet

Parameters:

purge (bool) – Whether files will be deleted or skipped.
image_set (ImageSet) – Collection of files that will be removed.

arrakis.imager.cli()[source]: Command-line interface

arrakis.imager.fix_ms(ms: pathlib.Path) → pathlib.Path[source]

Apply the corrections to the FEED table of a measurement set that is required for the ASKAP measurement sets.

Parameters:: ms (Path) – Path to the measurement set to fix.
Returns:: Path to the corrected measurement set.
Return type:: Path

arrakis.imager.fix_ms_askap_corrs(ms: pathlib.Path, *args, **kwargs) → pathlib.Path[source]

Applies a correction to raw telescope polarisation products to rotate them to the wsclean espected form. This is essentially related to the third-axis of ASKAP and reorientating its ‘X’ and ‘Y’s.

Parameters:: ms (Path) – Path to the measurement set to be corrected.
Returns:: Path of the measurementt set containing the corrections.
Return type:: Path

arrakis.imager.get_beam(image_set: ImageSet, cutoff: float | None) → pathlib.Path[source]

Derive a common resolution across all images within a set of ImageSet

Parameters:

image_set (ImageSet) – ImageSet that a common resolution will be derived for
cuttoff (float, optional) – The maximum major axis of the restoring beam that is allowed when
searching for the lowest common beam. Images whose restoring beam’s major acis is larger than
this are ignored. Defaults to None.

Returns:

Path to the pickled beam object

Return type:

Path

arrakis.imager.get_mfs_image(prefix_str: str, pol: str, small_size: Tuple[int, int] = (512, 512)) → MFSImage[source]

Get the MFS image from the image set.

Returns:: The MFS image.
Return type:: MFSImage

arrakis.imager.get_pol_axis_task(ms: pathlib.Path, feed_idx: int | None = None, col: str = 'RECEPTOR_ANGLE') → float[source]

arrakis.imager.get_prefix(ms: pathlib.Path, out_dir: pathlib.Path) → pathlib.Path[source]

Derive a consistent prefix style from a input MS name.

Parameters:

ms (Path) – Path to a Measurement Set that a prefix will be derived from
out_dir (Path) – The final location that wsclean output data will be written to

Returns:

The prefix, including the output directory name.

Return type:

Path

arrakis.imager.get_wsclean(wsclean: pathlib.Path | str) → pathlib.Path[source]

Pull wsclean image from dockerhub (or wherver).

Parameters:: version (str, optional) – wsclean image tag. Defaults to “3.1”.
Returns:: Path to wsclean image.
Return type:: Path

arrakis.imager.image_beam(ms: pathlib.Path, field_idx: int, out_dir: pathlib.Path, prefix: pathlib.Path, simage: pathlib.Path, temp_dir_wsclean: pathlib.Path, temp_dir_images: pathlib.Path, pols: str = 'IQU', nchan: int = 36, scale: float = 2.5, npix: int = 4096, join_polarizations: bool = True, join_channels: bool = True, squared_channel_joining: bool = True, mgain: float = 0.7, niter: int = 100000, auto_mask: float = 3, force_mask_rounds: int | None = None, auto_threshold: float = 1, gridder: str | None = None, robust: float = -0.5, mem: float = 90, absmem: float | None = None, taper: float | None = None, minuv_l: float = 0.0, parallel_deconvolution: int | None = None, nmiter: int | None = None, local_rms: bool = False, local_rms_window: float | None = None, multiscale: bool = False, multiscale_scale_bias: float | None = None, multiscale_scales: str | None = '0,2,4,8,16,32,64,128', data_column: str = 'CORRECTED_DATA', no_mf_weighting: bool = False, no_update_model_required: bool = True, beam_fitting_size: float | None = 1.25, disable_pol_local_rms: bool = False, disable_pol_force_mask_rounds: bool = False) → ImageSet[source]: Image a single beam

arrakis.imager.imager_parser(parent_parser: bool = False) → argparse.ArgumentParser[source]

Return the argument parser for the imager routine.

Parameters:: parent_parser (bool, optional) – Ensure the parser is configured so it can be added as a parent to a new parser. This will disables the -h/–help action from being generated. Defaults to False.
Returns:: Arguments required for the imager routine
Return type:: argparse.ArgumentParser

arrakis.imager.main(msdir: pathlib.Path, out_dir: pathlib.Path, num_beams: int = 36, temp_dir_images: pathlib.Path | None = None, temp_dir_wsclean: pathlib.Path | None = None, cutoff: float | None = None, robust: float = -0.5, pols: str = 'IQU', nchan: int = 36, size: int = 6074, scale: float = 2.5, mgain: float = 0.8, niter: int = 100000, auto_mask: float = 3, force_mask_rounds: int | None = None, auto_threshold: float = 1, taper: float | None = None, purge: bool = False, minuv: float = 0.0, parallel_deconvolution: int | None = None, gridder: str | None = None, nmiter: int | None = None, local_rms: bool = False, local_rms_window: float | None = None, wsclean_path: pathlib.Path | str = 'docker://alecthomson/wsclean:latest', multiscale: bool | None = None, multiscale_scale_bias: float | None = None, multiscale_scales: str | None = '0,2,4,8,16,32,64,128', absmem: float | None = None, make_residual_cubes: bool | None = False, ms_glob_pattern: str = 'scienceData*_averaged_cal.leakage.ms', data_column: str = 'CORRECTED_DATA', skip_fix_ms: bool = False, no_mf_weighting: bool = False, disable_pol_local_rms: bool = False, disable_pol_force_mask_rounds: bool = False)[source]

Arrakis imager flow

Parameters:

msdir (Path) – Path to the directory containing the MS files.
out_dir (Path) – Path to the directory where the images will be written.
num_beams (int, optional) – Number of beams to image. Defaults to 36.
temp_dir_images (Optional[Path], optional) – Path for temporary files to be written. Defaults to None.
temp_dir_wsclean (Optional[Path], optional) – Path for temporary files to be written by WSClean. Defaults to None.
cutoff (Optional[float], optional) – WSClean cutoff. Defaults to None.
robust (float, optional) – WSClean Briggs robust parameter. Defaults to -0.5.
pols (str, optional) – WSClean polarisations. Defaults to “IQU”.
nchan (int, optional) – WSClean number of output channels. Defaults to 36.
size (int, optional) – WSClean image size. Defaults to 6074.
scale (float, optional) – WSClean pixel size (arcseconds). Defaults to 2.5.
mgain (float, optional) – WSClean mgain. Defaults to 0.8.
niter (int, optional) – WSClean niter. Defaults to 100_000.
auto_mask (float, optional) – WSClean automatic masking (in SNR). Defaults to 3.
force_mask_rounds (Union[int, None], optional) – WSClean force mask rounds (requires modified WSClean). Defaults to None.
auto_threshold (float, optional) – WSClean auto threshold (in SNR). Defaults to 1.
taper (Union[float, None], optional) – WSClean taper (in arcsec). Defaults to None.
purge (bool, optional) – Purge auxillary files after imaging. Defaults to False.
minuv (float, optional) – WSClean minuv-l. Defaults to 0.0.
parallel_deconvolution (Optional[int], optional) – WSClean parallel deconvolution. Defaults to None.
gridder (Optional[str], optional) – WSClean gridder. Defaults to None.
nmiter (Optional[int], optional) – WSClean nmiter. Defaults to None.
local_rms (bool, optional) – WSClean local_rms. Defaults to False.
local_rms_window (Optional[float], optional) – WSClean local_rms_window. Defaults to None.
wsclean_path (Path | str, optional) – Path or URL for WSClean container. Defaults to “docker://alecthomson/wsclean:latest”.
multiscale (Optional[bool], optional) – WSClean multiscale. Defaults to None.
multiscale_scale_bias (Optional[float], optional) – WSClean multiscale bias. Defaults to None.
multiscale_scales (Optional[str], optional) – WSClean scales. Defaults to “0,2,4,8,16,32,64,128”.
absmem (Optional[float], optional) – WSClean absmem usage. Defaults to None.
make_residual_cubes (Optional[bool], optional) – Make resiudal image cubes. Defaults to False.
ms_glob_pattern (str, optional) – Globe pattern for MS files. Defaults to “scienceData*_averaged_cal.leakage.ms”.
data_column (str, optional) – Data column to image. Defaults to “CORRECTED_DATA”.
skip_fix_ms (bool, optional) – Apply FixMS. Defaults to False.
no_mf_weighting (bool, optional) – WSClean no_mf_weighting. Defaults to False.
disable_pol_local_rms (bool, optional) – Disable local RMS for polarisation images. Defaults to False.
disable_pol_force_mask_rounds (bool, optional) – Disable force mask rounds for polarisation images. Defaults to False.

arrakis.imager.make_cube(pol: str, image_set: ImageSet, common_beam_pkl: pathlib.Path, pol_angle_deg: float, aux_mode: str | None = None) → Tuple[pathlib.Path, pathlib.Path][source]: Make a cube from the images

arrakis.imager.make_validation_plots(prefix: pathlib.Path, pols: str) → None[source]

Make validation plots for the images.

Parameters:

prefix (Path) – Prefix of the images.
pols (str) – Polarisation to make the plots for.

arrakis.imager.merge_imagesets(image_sets: List[ImageSet | None]) → ImageSet[source]

Merge a collection of ImageSets into a single ImageSet.

Parameters:: image_sets (List[ImageSet]) – Collection of ImageSets to merge.
Returns:: A single ImageSet containing all the images from the input ImageSets.
Return type:: ImageSet

arrakis.imager.run_wsclean_singuarlity(command: str, simage: pathlib.Path, out_dir: pathlib.Path, root_dir: pathlib.Path) → None[source]

arrakis.imager.smooth_imageset(image_set: ImageSet, common_beam_pkl: pathlib.Path, cutoff: float | None = None, aux_mode: str | None = None) → ImageSet[source]

Smooth all images described within an ImageSet to a desired resolution

Parameters:

image_set (ImageSet) – Container whose image_list will be convolved to common resolution
common_beam_pkl (Path) – Location of pickle file with beam description
cutoff (Optional[float], optional) – PSF cutoff passed to the beamcon_2D worker. Defaults to None.
aux_model (Optional[str], optional) – The image type in the aux_lists property of image_set that contains the images to smooth. If
not set then the `image_lists` property of `image_set` is used. Defaults to None.

Returns:

A copy of image_set pointing to the smoothed images. Note the aux_images property is not carried forward.

Return type:

ImageSet

arrakis.imager.TQDM_OUT[source]