type fixes/spelling

flint/bandpass.py

@@ -10,7 +10,7 @@
 from flint.calibrate.aocalibrate import AOSolutions, calibrate_apply_ms
 from flint.flagging import flag_ms_aoflagger
 from flint.logging import logger
-from flint.ms import MS, describe_ms, preprocess_askap_ms
+from flint.ms import MS, describe_ms, preprocess_askap_ms, get_field_id_for_field
 from flint.naming import create_ms_name
 from flint.sky_model import KNOWN_1934_FILES, get_1934_model
 
@@ -145,10 +145,10 @@ def extract_correct_bandpass_pointing(
             return ms.with_options(beam=ms_summary.beam)
 
     good_field_name = f"{source_name_prefix}_beam{ms_summary.beam}"
-    field_id = ms.get_field_id_for_field(field_name=good_field_name)
+    field_id = get_field_id_for_field(ms=ms, field_name=good_field_name)
 
     out_name = create_ms_name(ms_path=ms.path, field=f"{source_name_prefix}")
-
+    out_path = Path("./")
     # Handle writing out to elected output directory.
     # TODO: Move this to a helper utility.
     if ms_out_dir:
@@ -185,7 +185,7 @@ def calibrate_bandpass(
     set will be created container just the appropriate field to calibrate.
 
     Args:
-        ms_path (Path): Path the the measurement set containing bandpass obervations of B1934-638
+        ms_path (Path): Path the the measurement set containing bandpass observations of B1934-638
         data_column (str): The column that will be calibrated.
         mode (str): The calibration approach to use. Currently only `calibrate` is supported.
         calibrate_container (Path): The path to the singularity container that holds the appropriate software.
@@ -196,7 +196,7 @@ def calibrate_bandpass(
     Returns:
         MS: The calibrated measurement set with nominated column
     """
-    logger.info(f"Will calibrate {str(ms_path)}, colum {data_column}")
+    logger.info(f"Will calibrate {str(ms_path)}, column {data_column}")
 
     # TODO: Check to make sure only 1934-638
     model_path: Path = get_1934_model(mode=mode)

flint/imager/wsclean.py

@@ -25,7 +25,7 @@
 
 
 class ImageSet(NamedTuple):
-    """A structure to represent the images and auxillary products produced by
+    """A structure to represent the images and auxiliary products produced by
     wsclean"""
 
     prefix: str
@@ -48,7 +48,7 @@ class WSCleanOptions(NamedTuple):
 
     Basic support for environment variables is available. Should a value start
     with `$` it is assumed to be a environment variable, it is will be looked up.
-    Some basic attempts to deterimine if it is a path is made.
+    Some basic attempts to determine if it is a path is made.
 
     Should the `temp_dir` options be specified then all images will be
     created in this location, and then moved over to the same parent directory
@@ -78,7 +78,7 @@ class WSCleanOptions(NamedTuple):
     nmiter: int = 15
     """Maximum number of major cycles to perform"""
     niter: int = 750000
-    """Maximum numer of minor cycles"""
+    """Maximum number of minor cycles"""
     multiscale: bool = True
     """Enable multiscale deconvolution"""
     multiscale_scale_bias: float = 0.75
@@ -95,7 +95,7 @@ class WSCleanOptions(NamedTuple):
     )
     """Scales used for multi-scale deconvolution"""
     fit_spectral_pol: int = 2
-    """Number of spectral terms to include during sub-band subtractin"""
+    """Number of spectral terms to include during sub-band subtraction"""
     weight: str = "briggs -0.5"
     """Robustness of the weighting used"""
     data_column: str = "CORRECTED_DATA"
@@ -280,7 +280,7 @@ def delete_wsclean_outputs(
     Args:
         prefix (str): The prefix of the files to remove. This would correspond to the -name of wsclean.
         output_type (str, optional): What type of wsclean output to try to remove. Defaults to 'image'.
-        ignore_mfs (bool, optional): If True, do not remove MFS outputs (attempt to, atleast). Defaults to True.
+        ignore_mfs (bool, optional): If True, do not remove MFS outputs (attempt to, at least). Defaults to True.
 
     Returns:
         Collection[Path]: The paths that were removed (or at least attempted to be removed)/
@@ -330,12 +330,13 @@ def create_wsclean_name_argument(wsclean_options: WSCleanOptions, ms: MS) -> Pat
     temp_dir = wsclean_options_dict.get("temp_dir", None)
     if temp_dir:
         # Resolve if environment variable
-        name_dir = (
+        name_dir: Union[Path, str, None] = (
             get_environment_variable(variable=temp_dir)
             if isinstance(temp_dir, str) and temp_dir[0] == "$"
             else Path(temp_dir)
         )
         assert name_dir is not None, f"{name_dir=} is None, which is bad"
+        name_dir = Path(name_dir)
 
     name_argument_path = Path(name_dir) / name_prefix_str
     logger.info(f"Constructed -name {name_argument_path}")
@@ -359,7 +360,7 @@ def _resolve_wsclean_key_value_to_cli_str(key: str, value: Any) -> ResolvedCLIRe
     the appropriate form to pass to a CLI call into wsclean.
 
     Args:
-        key (str): The wsclean argument name to consider. Underscores will be converted to hypens, as expected by wsclean
+        key (str): The wsclean argument name to consider. Underscores will be converted to hyphens, as expected by wsclean
         value (Any): The value of the argument that should be converted to the appropriately formatted string
 
     Returns:
@@ -424,14 +425,14 @@ def create_wsclean_cmd(
     #. the `-name` argument will be generated and supplied to the CLI string and will default to the parent directory and name of the supplied measurement set
     #. If `wsclean_options.temp_dir` is specified this directory is used in place of the measurement sets parent directory
 
-    If `container` is supplied to immediatedly execute this command then the
+    If `container` is supplied to immediately execute this command then the
     output wsclean image products will be moved from the `temp-dir` to the
     same directory as the measurement set.
 
     Args:
         ms (MS): The measurement set to be imaged
         wsclean_options (WSCleanOptions): WSClean options to image with
-        container (Optional[Path], optional): If a path to a container is provided the command is executed immediatedly. Defaults to None.
+        container (Optional[Path], optional): If a path to a container is provided the command is executed immediately. Defaults to None.
 
     Raises:
         ValueError: Raised when a option has not been successfully processed
@@ -562,7 +563,7 @@ def combine_subbands_to_cube(
 def run_wsclean_imager(
     wsclean_cmd: WSCleanCommand,
     container: Path,
-    bind_dirs: Optional[Tuple[Path]] = None,
+    bind_dirs: Optional[Tuple[Path, ...]] = None,
     move_hold_directories: Optional[Tuple[Path, Optional[Path]]] = None,
     make_cube_from_subbands: bool = True,
     image_prefix_str: Optional[str] = None,
@@ -578,8 +579,8 @@ def run_wsclean_imager(
     Args:
         wsclean_cmd (WSCleanCommand): The command to run, and other properties (cleanup.)
         container (Path): Path to the container with wsclean available in it
-        bind_dirs (Optional[Tuple[Path]], optional): Additional directories to include when binding to the wsclean container. Defaults to None.
-        move_hold_directories (Optional[Tuple[Path,Optional[Path]]], optional): The `move_directory` and `hold_directory` passed to the temporary context manger. If None no `hold_then_move_into` manager is used. Defaults to None.
+        bind_dirs (Optional[Tuple[Path, ...]], optional): Additional directories to include when binding to the wsclean container. Defaults to None.
+        move_hold_directories (Optional[Tuple[Path,Optional[Path]]], optional): The `move_directory` and `hold_directory` passed to the temporary context manager. If None no `hold_then_move_into` manager is used. Defaults to None.
         make_cube_from_subbands (bool, optional): Form a single FITS cube from the set of sub-band images wsclean produces. Defaults to False.
         image_prefix_str (Optional[str], optional): The name used to search for wsclean outputs. If None, it is guessed from the name and location of the MS. Defaults to None.
 
@@ -665,7 +666,7 @@ def wsclean_imager(
     Args:
         ms (Union[Path,MS]): Path to the measurement set that will be imaged
         wsclean_container (Path): Path to the container with wsclean installed
-        update_wsclean_options (Optional[Dict[str, Any]], optional): Additional options to update the generated WscleanOptions with. Keys should be attributes of WscleanOptions. Defaults ot None.
+        update_wsclean_options (Optional[Dict[str, Any]], optional): Additional options to update the generated WscleanOptions with. Keys should be attributes of WscleanOptions. Defaults to None.
 
     Returns:
         WSCleanCommand: _description_
@@ -694,7 +695,7 @@ def get_parser() -> ArgumentParser:
     subparser = parser.add_subparsers(dest="mode")
 
     wsclean_parser = subparser.add_parser(
-        "image", help="Attempt to run a wsclean commmand. "
+        "image", help="Attempt to run a wsclean command. "
     )
     wsclean_parser.add_argument(
         "ms", type=Path, help="Path to a measurement set to image"

flint/masking.py

@@ -5,7 +5,6 @@
 from __future__ import annotations
 
 from argparse import ArgumentParser
-from collections import Iterable
 from pathlib import Path
 from typing import Collection, NamedTuple, Optional, Union
 
@@ -45,17 +44,17 @@ class MaskingOptions(NamedTuple):
     flood_fill_use_mbc_box_size: int = 75
     """The size of the mbc box size should mbc be used"""
     suppress_artefacts: bool = True
-    """Whether to attempt artefacts based on the presence of sigificant negatives"""
+    """Whether to attempt artefacts based on the presence of significant negatives"""
     suppress_artefacts_negative_seed_clip: float = 5
-    """The significance level of a negative island for the sidelobe suppresion to be activated. This should be a positive number (the signal map is internally inverted)"""
+    """The significance level of a negative island for the sidelobe suppression to be activated. This should be a positive number (the signal map is internally inverted)"""
     suppress_artefacts_guard_negative_dilation: float = 40
-    """The minimum positive signifance pixels should have to be guarded when attempting to suppress artefacts around bright sources"""
+    """The minimum positive significance pixels should have to be guarded when attempting to suppress artefacts around bright sources"""
     suppress_artefacts_large_island_threshold: float = 1.0
     """Threshold in units of beams for an island of negative pixels to be considered large"""
     grow_low_snr_island: bool = False
     """Whether to attempt to grow a mask to capture islands of low SNR (e.g. diffuse emission)"""
     grow_low_snr_island_clip: float = 1.75
-    """The minimum signifance levels of pixels to be to seed low SNR islands for consideration"""
+    """The minimum significance levels of pixels to be to seed low SNR islands for consideration"""
     grow_low_snr_island_size: int = 768
     """The number of pixels an island has to be for it to be accepted"""
     minimum_boxcar: bool = True
@@ -103,8 +102,9 @@ def consider_beam_mask_round(
     return mask_rounds is not None and (
         (isinstance(mask_rounds, str) and mask_rounds.lower() == "all")
         or (isinstance(mask_rounds, int) and current_round >= mask_rounds)
-        or (isinstance(mask_rounds, Iterable) and current_round in mask_rounds)  # type: ignore
-    )
+        or (isinstance(mask_rounds, (list, tuple)))
+        and current_round in mask_rounds
+    )  # type: ignore
 
 
 def extract_beam_mask_from_mosaic(
@@ -126,7 +126,7 @@ def extract_beam_mask_from_mosaic(
     Returns:
         FITSMaskNames: _description_
     """
-    # TODO: Ideally we can accept an arbitary WCS, or read the wsclean docs to
+    # TODO: Ideally we can accept an arbitrary WCS, or read the wsclean docs to
     # try to construct it ourselves. The last thing that this pirate wants is
     # to run the imager in a dry-run type mode n cleaning type mode purely for
     # the WCS.
@@ -198,7 +198,7 @@ def grow_low_snr_mask(
     a mask through to the imagery of choice the islands may be larger than the features at their
     native resolution, unless some other more sophisticated filtering is performed.
 
-    This function attempts to grow masks to capture islands of contigous pixels above a low
+    This function attempts to grow masks to capture islands of contiguous pixels above a low
     SNR cut that would otherwise go uncleaned.
 
     Args:
@@ -255,13 +255,13 @@ def minimum_boxcar_artefact_mask(
     increase_factor: float = 2.0,
 ) -> np.ndarray:
     """Attempt to remove islands from a potential clean mask by
-    examining surronding pixels. A boxcar is applied to find the
+    examining surrounding pixels. A boxcar is applied to find the
     minimum signal to noise in a small localised region. For each
     island the maximum signal is considered.
 
     If the absolute minimum signal increased by a factor in an
     island region is larger to the maximum signal then that island
-    is ommited.
+    is omitted.
 
 
     Args:
@@ -334,12 +334,12 @@ def suppress_artefact_mask(
     - negative islands are around bright sources with deconvolution/calibration errors
     - if there are brightish negative islands there is also positive brightish arteefact islands nearby
 
-    For this reason the guard mask should be sufficently high to protect the main source but nuke the fask positive islands
+    For this reason the guard mask should be sufficiently high to protect the main source but nuke the fask positive islands
 
 
     Args:
         signal (np.ndarray): The signal mask,
-        negative_seed_clip (float): The minimum signficance level to seed. This is a positive number (as it is applied to the inverted signal).
+        negative_seed_clip (float): The minimum significance level to seed. This is a positive number (as it is applied to the inverted signal).
         guard_negative_dilation (float): Regions of positive emission above this are protected. This is positive.
         pixels_per_beam (Optional[float], optional): The number of pixels per beam. If not None, seed islands larger than this many pixels are removed. Defaults to None.
         large_island_threshold (float, optional): The number of beams required for a large island of negative pixels to be dropped as an artefact seed. Only used if `pixels_per_beam` is set. Defaults to 1.0.
@@ -433,12 +433,12 @@ def reverse_negative_flood_fill(
     """Attempt to:
 
     * seed masks around bright regions of an image and grow them to lower significance thresholds
-    * remove regions of negative and positive islands that surrond bright sources.
+    * remove regions of negative and positive islands that surround bright sources.
 
     An initial set of islands (and masks) are constructed by first
     using the `positive_seed_clip` to create an initial SNR based
     mask. These islands then are binary dilated to grow the islands
-    to adjacent pixels at a lower signifcance level (see `scipy.ndimage.binary_dilation`).
+    to adjacent pixels at a lower significance level (see `scipy.ndimage.binary_dilation`).
 
     Next an attempt is made to remove artefacts around bright sources,  where
     there are likely to be positive and negative artefacts