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tools.py

Functions and classes related to VAST that have no specific category and can be used generically.

WiseClass (Enum)

WISE object classes defined in the WISE color-color plot.

Source code in vasttools/tools.py
class WiseClass(enum.Enum):
    """WISE object classes defined in the WISE color-color plot."""

    COOL_T_DWARFS = "CoolTDwarfs"
    STARS = "Stars"
    ELLIPTICALS = "Ellipticals"
    SPIRALS = "Spirals"
    LIRGS = "LIRGs"
    STARBURSTS = "Starbursts"
    SEYFERTS = "Seyferts"
    QSOS = "QSOs"
    OBSCURED_AGN = "ObscuredAGN"

WisePatchConfig dataclass

Style and annotation configurations for the patch drawn to represent a WISE object class in the WISE color-color plot.

Attributes:

Name Type Description
style Dict[str, Any]

Any style keyword arguments and values supported by matplotlib.patches.PathPatch.

annotation_text str

Text to annotate the patch.

annotation_position Tuple[float, float]

Position in data coordinates

Source code in vasttools/tools.py
@dataclass
class WisePatchConfig:
    """Style and annotation configurations for the patch drawn to represent a
    WISE object class in the WISE color-color plot.

    Attributes:
        style (Dict[str, Any]): Any style keyword arguments and values
            supported by `matplotlib.patches.PathPatch`.
        annotation_text (str): Text to annotate the patch.
        annotation_position (Tuple[float, float]): Position in data coordinates
        for the annotation text.
    """

    style: Dict[str, Any]
    annotation_text: str
    annotation_position: Tuple[float, float]

    def copy(self):
        return deepcopy(self)

add_credible_levels(filename, df, pipe=True)

Calculate the minimum credible region containing each source and add to the dataframe in-place.

Parameters:

Name Type Description Default
filename str

Path to the healpix skymap file.

required
df DataFrame

Dataframe of sources.

required
pipe bool

Whether the dataframe is from the pipeline. Defaults to True.

True

Returns:

Type Description
None

None

Exceptions:

Type Description
Exception

Path does not exist.

Source code in vasttools/tools.py
def add_credible_levels(
    filename: str,
    df: pd.DataFrame,
    pipe: bool = True
) -> None:
    """
    Calculate the minimum credible region containing each source
    and add to the dataframe in-place.

    Args:
        filename: Path to the healpix skymap file.
        df: Dataframe of sources.
        pipe: Whether the dataframe is from the pipeline. Defaults to True.

    Returns:
        None

    Raises:
        Exception: Path does not exist.
    """

    skymap = Path(filename)
    if not skymap.is_file():
        raise Exception("{} does not exist".format(filename))

    if pipe:
        ra_col = 'wavg_ra'
        dec_col = 'wavg_dec'
    else:
        ra_col = 'ra'
        dec_col = 'dec'

    hpx = hp.read_map(filename)
    nside = hp.get_nside(hpx)

    i = np.flipud(np.argsort(hpx))
    sorted_credible_levels = np.cumsum(hpx[i])
    credible_levels = np.empty_like(sorted_credible_levels)
    credible_levels[i] = sorted_credible_levels
    theta = 0.5 * np.pi - np.deg2rad(df[dec_col].values)
    phi = np.deg2rad(df[ra_col].values)

    ipix = hp.ang2pix(nside, theta, phi)

    df.loc[:, 'credible_level'] = credible_levels[ipix]

add_obs_date(epoch, image_type, image_dir, epoch_path=None)

Add datetime information to all fits files in a single epoch.

Parameters:

Name Type Description Default
epoch str

The epoch of interest.

required
image_type str

COMBINED or TILES.

required
image_dir str

The name of the folder containing the images to be updated. E.g. STOKESI_IMAGES.

required
epoch_path str

Full path to the folder containing the epoch. Defaults to None, which will set the value based on the VAST_DATA_DIR environment variable and epoch.

None

Returns:

Type Description
None

None

Exceptions:

Type Description
ValueError

When image_type is not 'TILES' or 'COMBINED'.

Source code in vasttools/tools.py
def add_obs_date(epoch: str,
                 image_type: str,
                 image_dir: str,
                 epoch_path: str = None
                 ) -> None:
    """
    Add datetime information to all fits files in a single epoch.

    Args:
        epoch: The epoch of interest.
        image_type: `COMBINED` or `TILES`.
        image_dir: The name of the folder containing the images to be updated.
            E.g. `STOKESI_IMAGES`.
        epoch_path: Full path to the folder containing the epoch.
            Defaults to None, which will set the value based on the
            `VAST_DATA_DIR` environment variable and `epoch`.

    Returns:
        None

    Raises:
        ValueError: When image_type is not 'TILES' or 'COMBINED'.
    """
    epoch_info = load_fields_file(epoch)

    if epoch_path is None:
        epoch_path = _set_epoch_path(epoch)

    raw_images = _get_epoch_images(epoch_path, image_type, image_dir)

    for filename in raw_images:
        split_name = filename.split("/")[-1].split(".")
        if image_type == 'TILES':
            field = split_name[4]
        elif image_type == 'COMBINED':
            field = split_name[0]
        else:
            raise ValueError(
                "Image type not recognised, "
                "must be either 'TILES' or 'COMBINED'."
            )

        field_info = epoch_info[epoch_info.FIELD_NAME == field].iloc[0]
        field_start = Time(field_info.DATEOBS)
        field_end = Time(field_info.DATEEND)
        duration = field_end - field_start

        hdu = fits.open(filename, mode="update")
        hdu_index = 0
        if filename.endswith('.fits.fz'):
            hdu_index = 1
        hdu[hdu_index].header["DATE-OBS"] = field_start.fits
        hdu[hdu_index].header["MJD-OBS"] = field_start.mjd
        hdu[hdu_index].header["DATE-BEG"] = field_start.fits
        hdu[hdu_index].header["DATE-END"] = field_end.fits
        hdu[hdu_index].header["MJD-BEG"] = field_start.mjd
        hdu[hdu_index].header["MJD-END"] = field_end.mjd
        hdu[hdu_index].header["TELAPSE"] = duration.sec
        hdu[hdu_index].header["TIMEUNIT"] = "s"
        hdu.close()

create_fields_metadata(epoch_num, db_path, outdir='.')

Create and write the fields csv and skycoord pickle for a single epoch.

Parameters:

Name Type Description Default
epoch_num str

Epoch number of interest.

required
db_path str

Path to the askap_surveys database.

required
outdir Union[str, pathlib.Path]

Path to the output directory. Defaults to the current directory.

'.'

Returns:

Type Description
None

None

Exceptions:

Type Description
Exception

Path does not exist.

Source code in vasttools/tools.py
def create_fields_metadata(epoch_num: str,
                           db_path: str,
                           outdir: Union[str, Path] = '.'
                           ) -> None:
    """
    Create and write the fields csv and skycoord pickle for a single epoch.

    Args:
        epoch_num: Epoch number of interest.
        db_path: Path to the askap_surveys database.
        outdir: Path to the output directory.
            Defaults to the current directory.

    Returns:
        None

    Raises:
        Exception: Path does not exist.
    """

    if isinstance(outdir, str):
        outdir = Path(outdir)

    if not outdir.exists():
        raise Exception("{} does not exist!".format(outdir))

    fields_df = _create_fields_df(epoch_num, db_path)
    fields_sc = _create_fields_sc(fields_df)

    if len(epoch_num.rstrip('x')) == 1:
        epoch_num = f'0{epoch_num}'
    fields_outfile = f'vast_epoch{epoch_num}_info.csv'
    sc_outfile = f'vast_epoch{epoch_num}_fields_sc.pickle'

    fields_df.to_csv(outdir / fields_outfile, index=False)

    with open(outdir / sc_outfile, 'wb') as picklefile:
        pickle.dump(fields_sc, picklefile)

find_in_moc(moc, df, pipe=True)

Find the sources that are contained within a MOC

Parameters:

Name Type Description Default
moc MOC

The MOC of interest.

required
df DataFrame

Dataframe of sources.

required
pipe bool

Whether the dataframe is from the pipeline. Defaults to True.

True

Returns:

Type Description
ndarray

Indices of all sources contained within the MOC.

Source code in vasttools/tools.py
def find_in_moc(
    moc: MOC,
    df: pd.DataFrame,
    pipe: bool = True
) -> np.ndarray:
    """
    Find the sources that are contained within a MOC

    Args:
        moc: The MOC of interest.
        df: Dataframe of sources.
        pipe: Whether the dataframe is from the pipeline. Defaults to True.

    Returns:
        Indices of all sources contained within the MOC.
    """

    if pipe:
        ra_col = 'wavg_ra'
        dec_col = 'wavg_dec'
    else:
        ra_col = 'ra'
        dec_col = 'dec'

    ra = Angle(df[ra_col], unit='deg')
    dec = Angle(df[dec_col], unit='deg')

    return np.where(moc.contains(ra, dec))[0]

gen_mocs_epoch(epoch, image_type, image_dir, epoch_path=None, outdir='.', base_stmoc=None)

Generate MOCs and STMOCs for all images in a single epoch, and create a new full pilot STMOC.

Parameters:

Name Type Description Default
epoch str

The epoch of interest.

required
image_type str

COMBINED or TILES.

required
image_dir str

The name of the folder containing the images to be updated. E.g. STOKESI_IMAGES.

required
epoch_path str

Full path to the folder containing the epoch. Defaults to None, which will set the value based on the VAST_DATA_DIR environment variable and epoch.

None
outdir Union[str, pathlib.Path]

Path to the output directory. Defaults to the current directory.

'.'
base_stmoc Union[str, pathlib.Path]

Path to the STMOC to use as the base. Defaults to None, in which case the VAST STMOC installed with vast-tools will be used.

None

Returns:

Type Description
None

None

Exceptions:

Type Description
Exception

Path does not exist.

Source code in vasttools/tools.py
def gen_mocs_epoch(epoch: str,
                   image_type: str,
                   image_dir: str,
                   epoch_path: str = None,
                   outdir: Union[str, Path] = '.',
                   base_stmoc: Union[str, Path] = None
                   ) -> None:
    """
    Generate MOCs and STMOCs for all images in a single epoch, and create a new
    full pilot STMOC.

    Args:
        epoch: The epoch of interest.
        image_type: `COMBINED` or `TILES`.
        image_dir: The name of the folder containing the images to be updated.
            E.g. `STOKESI_IMAGES`.
        epoch_path: Full path to the folder containing the epoch.
            Defaults to None, which will set the value based on the
            `VAST_DATA_DIR` environment variable and `epoch`.
        outdir: Path to the output directory.
            Defaults to the current directory.
        base_stmoc: Path to the STMOC to use as the base. Defaults to `None`,
            in which case the VAST STMOC installed with vast-tools will
            be used.

    Returns:
        None

    Raises:
        Exception: Path does not exist.
    """

    if isinstance(outdir, str):
        outdir = Path(outdir)

    if not outdir.exists():
        raise Exception("{} does not exist".format(outdir))

    if base_stmoc is None:
        vtm = VASTMOCS()
        full_STMOC = vtm.load_pilot_stmoc()
    else:
        if isinstance(base_stmoc, str):
            base_stmoc = Path(base_stmoc)

        if not base_stmoc.exists():
            raise Exception("{} does not exist".format(base_stmoc))

        full_STMOC = STMOC.from_fits(base_stmoc)

    if epoch_path is None:
        epoch_path = _set_epoch_path(epoch)

    raw_images = _get_epoch_images(epoch_path, image_type, image_dir)

    for i, f in enumerate(raw_images):
        themoc, thestmoc = gen_mocs_image(f)

        if i == 0:
            mastermoc = themoc
            masterstemoc = thestmoc
        else:
            mastermoc = mastermoc.union(themoc)
            masterstemoc = masterstemoc.union(thestmoc)

    master_name = "VAST_PILOT_EPOCH{}.moc.fits".format(epoch)
    master_stmoc_name = master_name.replace("moc", "stmoc")

    mastermoc.write(outdir / master_name, overwrite=True)
    masterstemoc.write(outdir / master_stmoc_name, overwrite=True)

    full_STMOC = full_STMOC.union(masterstemoc)
    full_STMOC.write(outdir / 'VAST_PILOT.stmoc.fits', overwrite=True)

gen_mocs_image(fits_file, outdir='.', write=False)

Generate a MOC and STMOC for a single fits file.

Parameters:

Name Type Description Default
fits_file str

path to the fits file.

required
outdir Union[str, pathlib.Path]

Path to the output directory. Defaults to the current directory.

'.'
write bool

Write the MOC/STMOC to file.

False

Returns:

Type Description
Union[mocpy.moc.moc.MOC, mocpy.stmoc.stmoc.STMOC]

The MOC and STMOC.

Exceptions:

Type Description
Exception

Path does not exist.

Source code in vasttools/tools.py
def gen_mocs_image(fits_file: str,
                   outdir: Union[str, Path] = '.',
                   write: bool = False
                   ) -> Union[MOC, STMOC]:
    """
    Generate a MOC and STMOC for a single fits file.

    Args:
        fits_file: path to the fits file.
        outdir: Path to the output directory.
            Defaults to the current directory.
        write: Write the MOC/STMOC to file.

    Returns:
        The MOC and STMOC.

    Raises:
        Exception: Path does not exist.
    """

    if isinstance(outdir, str):
        outdir = Path(outdir)

    if not outdir.exists():
        raise Exception("{} does not exist".format(outdir))

    if not Path(fits_file).exists():
        raise Exception("{} does not exist".format(fits_file))

    moc = create_moc_from_fits(fits_file)

    header = fits.getheader(fits_file, 0)
    start = Time([header['DATE-BEG']])
    end = Time([header['DATE-END']])
    stmoc = STMOC.from_spatial_coverages(
        start, end, [moc]
    )

    if write:
        filename = os.path.split(fits_file)[1]
        moc_name = filename.replace(".fits", ".moc.fits")
        stmoc_name = filename.replace(".fits", ".stmoc.fits")

        moc.write(outdir / moc_name, overwrite=True)
        stmoc.write(outdir / stmoc_name, overwrite=True)

    return moc, stmoc

offset_postagestamp_axes(ax, centre_sc, ra_units=Unit("arcsec"), dec_units=Unit("arcsec"), ra_label='R.A. Offset', dec_label='Dec. Offset', major_tick_length=6, minor_tick_length=3)

Display axis ticks and labels as offsets from a given coordinate, rather than in absolute coordinates.

Parameters:

Name Type Description Default
ax Axes

The axis of interest

required
centre_sc SkyCoord

SkyCoord to calculate offsets from

required
ra_units Unit

Right Ascension axis ticklabel units

Unit("arcsec")
dec_units Unit

Declination axis ticklabel units

Unit("arcsec")
ra_label str

Right Ascension axis label

'R.A. Offset'
dec_label str

Declination axis label

'Dec. Offset'
major_tick_length Union[int, float]

Major tick length in points

6
minor_tick_length Union[int, float]

Minor tick length in points

3

Returns:

Type Description
None

None

Exceptions:

Type Description
Exception

R.A. and Dec. units must be angles.

Source code in vasttools/tools.py
def offset_postagestamp_axes(ax: plt.Axes,
                             centre_sc: SkyCoord,
                             ra_units: u.core.Unit = u.arcsec,
                             dec_units: u.core.Unit = u.arcsec,
                             ra_label: str = 'R.A. Offset',
                             dec_label: str = 'Dec. Offset',
                             major_tick_length: Union[int, float] = 6,
                             minor_tick_length: Union[int, float] = 3,
                             ) -> None:
    """
    Display axis ticks and labels as offsets from a given coordinate,
    rather than in absolute coordinates.

    Args:
        ax: The axis of interest
        centre_sc: SkyCoord to calculate offsets from
        ra_units: Right Ascension axis ticklabel units
        dec_units: Declination axis ticklabel units
        ra_label: Right Ascension axis label
        dec_label: Declination axis label
        major_tick_length: Major tick length in points
        minor_tick_length: Minor tick length in points

    Returns:
        None

    Raises:
        Exception: R.A. and Dec. units must be angles.
    """

    if ra_units.physical_type != 'angle' or dec_units.physical_type != 'angle':
        raise Exception("R.A. and Dec. units must be angles.")

    ra_offs, dec_offs = ax.get_coords_overlay(centre_sc.skyoffset_frame())
    plt.minorticks_on()
    ra_offs.set_coord_type('longitude', 180)
    ra_offs.set_format_unit(ra_units, decimal=True)
    dec_offs.set_format_unit(dec_units, decimal=True)
    ra_offs.tick_params(direction='in', color='black')
    ra_offs.tick_params(which='major', length=major_tick_length)
    ra_offs.tick_params(which='minor', length=minor_tick_length)

    dec_offs.tick_params(direction='in', color='black')
    dec_offs.tick_params(which='major', length=major_tick_length)
    dec_offs.tick_params(which='minor', length=minor_tick_length)

    ra, dec = ax.coords

    ra.set_ticks_visible(False)
    ra.set_ticklabel_visible(False)
    dec.set_ticks_visible(False)
    dec.set_ticklabel_visible(False)
    ra_offs.display_minor_ticks(True)
    dec_offs.display_minor_ticks(True)

    dec_offs.set_ticks_position('lr')
    dec_offs.set_ticklabel_position('l')
    dec_offs.set_axislabel_position('l')
    dec_offs.set_axislabel(dec_label)

    ra_offs.set_ticks_position('tb')
    ra_offs.set_ticklabel_position('b')
    ra_offs.set_axislabel_position('b')
    ra_offs.set_axislabel(ra_label)

    return

skymap2moc(filename, cutoff)

Creates a MOC of the specified credible region of a given skymap.

Parameters:

Name Type Description Default
filename str

Path to the healpix skymap file.

required
cutoff float

Credible level cutoff.

required

Returns:

Type Description
MOC

A MOC containing the credible region.

Exceptions:

Type Description
ValueError

Credible level cutoff must be between 0 and 1.

Exception

Path does not exist.

Source code in vasttools/tools.py
def skymap2moc(filename: str, cutoff: float) -> MOC:
    """
    Creates a MOC of the specified credible region of a given skymap.

    Args:
        filename: Path to the healpix skymap file.
        cutoff: Credible level cutoff.

    Returns:
        A MOC containing the credible region.

    Raises:
        ValueError: Credible level cutoff must be between 0 and 1.
        Exception: Path does not exist.
    """
    skymap = Path(filename)

    if not 0.0 <= cutoff <= 1.0:
        raise Exception("Credible level cutoff must be between 0 and 1")

    if not skymap.is_file():
        raise Exception("{} does not exist".format(skymap))

    hpx = hp.read_map(filename, nest=True)
    nside = hp.get_nside(hpx)
    level = np.log2(nside)

    i = np.flipud(np.argsort(hpx))
    sorted_credible_levels = np.cumsum(hpx[i])
    credible_levels = np.empty_like(sorted_credible_levels)
    credible_levels[i] = sorted_credible_levels

    idx = np.where(credible_levels < cutoff)[0]
    levels = np.ones(len(idx)) * level

    moc = MOC.from_healpix_cells(idx, depth=levels)

    return moc

wise_color_color_plot(patch_style_overrides=None, annotation_text_size='x-small')

Make an empty WISE color-color plot with common object classes drawn as patches. The patches have default styles that may be overridden. To override a patch style, pass in a dict containing the desired style and annotation settings. The overrides must be complete, i.e. a complete WisePatchConfig object must be provided for each WiseClass you wish to modify. Partial updates to the style or annotation of individual patches is not supported.

For example, to change the color of the stars patch to blue:

fig = wise_color_color_plot({
    WiseClass.STARS: WisePatchConfig(
        style=dict(fc="blue", ec="none"),
        annotation_text="Stars",
        annotation_position=(0.5, 0.4),
    )
})

Parameters:

Name Type Description Default
patch_style_overrides Optional[Dict[WiseClass, WisePatchConfig]], optional

Override the default patch styles for the given WISE object class. If None, use defaults for each patch. Defaults to None.

None
annotation_text_size Union[float, str]

Font size for the patch annotations. Accepts a font size (float) or a matplotlib font scale string (e.g. "xx-small", "medium", "xx-large"). Defaults to "x-small".

'x-small'

Returns:

Type Description
`matplotlib.figure.Figure`

the WISE color-color figure. Access the axes with the .axes attribute.

Source code in vasttools/tools.py
def wise_color_color_plot(
    patch_style_overrides: Optional[Dict[WiseClass, WisePatchConfig]] = None,
    annotation_text_size: Union[float, str] = "x-small",
) -> matplotlib.figure.Figure:
    """Make an empty WISE color-color plot with common object classes drawn as
    patches. The patches have default styles that may be overridden. To
    override a patch style, pass in a dict containing the desired style and
    annotation settings. The overrides must be complete, i.e. a complete
    `WisePatchConfig` object must be provided for each `WiseClass` you wish to
    modify. Partial updates to the style or annotation of individual patches is
    not supported.

    For example, to change the color of the stars patch to blue:
    ```python
    fig = wise_color_color_plot({
        WiseClass.STARS: WisePatchConfig(
            style=dict(fc="blue", ec="none"),
            annotation_text="Stars",
            annotation_position=(0.5, 0.4),
        )
    })
    ```

    Args:
        patch_style_overrides (Optional[Dict[WiseClass, WisePatchConfig]],
            optional): Override the default patch styles for the given WISE
            object class. If None, use defaults for each patch. Defaults to
            None.
        annotation_text_size (Union[float, str]): Font size for the patch
            annotations. Accepts a font size (float) or a matplotlib font scale
            string (e.g. "xx-small", "medium", "xx-large"). Defaults to
            "x-small".
    Returns:
        `matplotlib.figure.Figure`: the WISE color-color figure. Access the
            axes with the `.axes` attribute.
    """
    # set the WISE object classification patch styles
    if patch_style_overrides is not None:
        patch_styles = WISE_DEFAULT_PATCH_CONFIGS.copy()
        patch_styles.update(patch_style_overrides)
    else:
        patch_styles = WISE_DEFAULT_PATCH_CONFIGS

    # parse the WISE color-color SVG that contains the object class patches
    with importlib.resources.path(
        "vasttools.data", "WISE-color-color.svg"
    ) as svg_path:
        doc = minidom.parse(str(svg_path))
    # define the transform from the SVG frame to the plotting frame
    transform = (
        matplotlib.transforms.Affine2D().scale(sx=1, sy=-1).translate(-1, 4)
    )

    fig, ax = plt.subplots()
    # add WISE object classification patches
    for svg_path in doc.getElementsByTagName("path"):
        name = svg_path.getAttribute("id")
        patch_style = patch_styles[getattr(WiseClass, name)]
        path_mpl = parse_path(svg_path.getAttribute("d")).transformed(
            transform
        )
        patch = matplotlib.patches.PathPatch(path_mpl, **patch_style.style)
        ax.add_patch(patch)
        ax.annotate(
            patch_style.annotation_text,
            patch_style.annotation_position,
            ha="center",
            fontsize=annotation_text_size,
        )
    ax.set_xlim(-1, 6)
    ax.set_ylim(-0.5, 4)
    ax.set_aspect(1)
    ax.set_xlabel("[4.6] - [12] (mag)")
    ax.set_ylabel("[3.4] - [4.6] (mag)")
    ax.xaxis.set_major_locator(matplotlib.ticker.MultipleLocator(1))
    ax.yaxis.set_major_locator(matplotlib.ticker.MultipleLocator(1))
    return fig

Last update: July 30, 2024
Created: July 30, 2024