psimager 0.1__py3-none-any.whl

psimager/__init__.py

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+"""Fast dirty imaging of measurement sets for power spectrum analyses."""
+
+__version__ = '0.1'

psimager/cli.py

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+"""psimager command line, with WSClean's options."""
+
+import re
+import sys
+import time
+
+import click
+
+from psimager import __version__
+from psimager.imager import Imager, Settings
+
+SCALE_UNITS = {'mas': 1 / 3.6e6, 'asec': 1 / 3600, 'amin': 1 / 60, 'deg': 1.}
+# WSClean options without meaning here, accepted so that a WSClean command line runs unchanged:
+# name -> number of values
+IGNORED = {'oversampling': 1, 'kernel-size': 1, 'nwlayers': 1, 'nwlayers-factor': 1,
+           'grid-mode': 1, 'wstack-oversampling': 1, 'wstack-kernel-size': 1,
+           'wstack-nwlayers': 1, 'wstack-grid-mode': 1, 'gridder': 1, 'temp-dir': 1,
+           'parallel-reordering': 1, 'reorder': 0, 'no-reorder': 0, 'use-wgridder': 0,
+           'small-inversion': 0, 'no-small-inversion': 0, 'no-update-model-required': 0,
+           'quiet': 0}
+
+
+class WSCleanCommand(click.Command):
+    """Command reading WSClean's '-weight briggs ROBUST' (two values) as '-weight briggs:ROBUST'."""
+
+    def parse_args(self, ctx, args):
+        args = list(args)
+        for i, arg in enumerate(args[:-2]):
+            if arg == '-weight' and args[i + 1] == 'briggs' and re.fullmatch(r'[-+0-9.eE]+', args[i + 2]):
+                args[i + 1:i + 3] = [f'briggs:{args[i + 2]}']
+                break
+        return super().parse_args(ctx, args)
+
+
+def parse_scale(ctx, param, text):
+    """Pixel scale as WSClean's -scale: degrees, or a number followed by mas, asec, amin or deg."""
+    m = re.fullmatch(r'\s*([0-9.eE+-]+)\s*(mas|asec|amin|deg)?\s*', text)
+    try:
+        value = float(m.group(1)) * SCALE_UNITS[m.group(2) or 'deg']
+    except (AttributeError, ValueError):
+        value = -1
+    if not value > 0:
+        raise click.BadParameter(f'invalid scale {text!r}')
+    return value
+
+
+def ignored_options(f):
+    for name, nargs in IGNORED.items():
+        if nargs:
+            f = click.option(f'-{name}', multiple=True, hidden=True)(f)
+        else:
+            f = click.option(f'-{name}', is_flag=True, default=None, hidden=True)(f)
+    return f
+
+
+@click.command(cls=WSCleanCommand, context_settings={'show_default': True})
+@click.argument('ms', nargs=-1, required=True, type=click.Path(exists=True, file_okay=False))
+@click.option('-name', required=True, help='Prefix of the output files.')
+@click.option('-data-column', default='DATA', help='Visibility column.')
+@click.option('-pol', default='I', help='Stokes parameters among I, Q, U, V, e.g. IV or I,V.')
+@click.option('-size', nargs=2, type=int, default=(512, 512), help='Image WIDTH HEIGHT in pixels.')
+@click.option('-scale', default='1amin', callback=parse_scale, help='Pixel scale, e.g. 6amin.')
+@click.option('-channel-range', nargs=2, type=int, default=None,
+              help='Input channels START to END-1.  [default: all]')
+@click.option('-channels-out', default=1,
+              help='Output channels, each averaging its input channels gridded at their own frequency.')
+@click.option('-interval', nargs=2, type=int, default=None,
+              help='Time steps START to END-1; END <= START: until the end.  [default: all]')
+@click.option('-intervals-out', default=1, help='Images of equal time slices.')
+@click.option('-even-timesteps', is_flag=True, help='Only the even time steps.')
+@click.option('-odd-timesteps', is_flag=True, help='Only the odd time steps.')
+@click.option('-even-odd', is_flag=True,
+              help='Even and odd time steps in one pass, as NAME-even-* and NAME-odd-* (not in WSClean).')
+@click.option('-minuv-l', type=float, help='Minimum uv distance (lambda).')
+@click.option('-maxuv-l', type=float, help='Maximum uv distance (lambda).')
+@click.option('-minuvw-m', type=float, help='Minimum uvw distance (m).')
+@click.option('-maxuvw-m', type=float, help='Maximum uvw distance (m).')
+@click.option('-weight', default='natural', help='natural, uniform, or briggs ROBUST.')
+@click.option('-visibility-weighting-mode', type=click.Choice(['normal', 'squared', 'unit']),
+              default='normal', help='Visibility weights: as stored, squared, or all equal.')
+@click.option('-taper-edge', type=float, help='Tukey taper of this width (lambda) inside the uv edge.')
+@click.option('-padding', default=1.2, help='Padding of the weighting grid.')
+@click.option('-wgridder-accuracy', default=1e-6, help='ducc0 gridding accuracy.')
+@click.option('-j', 'threads', type=int, help='Threads.  [default: all available cores]')
+@click.option('-parallel-gridding', type=int, help='Output channels gridded at once.  [default: -j]')
+@click.option('-mem', default=50., help='Memory for the data, in % of the RAM.')
+@click.option('-abs-mem', type=float, help='Memory for the data, in GB (overrides -mem).')
+@click.option('-make-psf', is_flag=True, help='Also write the PSF.')
+@click.option('-no-dirty', is_flag=True, help='Write only the -image files.')
+@click.version_option(__version__, '-version')
+@ignored_options
+def main(ms, name, data_column, pol, size, scale, channel_range, channels_out, interval,
+         intervals_out, even_timesteps, odd_timesteps, even_odd, minuv_l, maxuv_l, minuvw_m,
+         maxuvw_m, weight, visibility_weighting_mode, taper_edge, padding, wgridder_accuracy,
+         threads, parallel_gridding, mem, abs_mem, make_psf, no_dirty, **wsclean_options):
+    """Dirty Stokes and PSF images of the measurement sets MS with the ducc0 w-gridder, with the
+    options, file names and FITS keywords of WSClean."""
+    if even_timesteps + odd_timesteps + even_odd > 1:
+        raise click.UsageError('Give only one of -even-timesteps, -odd-timesteps and -even-odd.')
+    ignored = [k for k, v in wsclean_options.items() if v]
+    if ignored:
+        click.echo('psimager: ignoring the WSClean options ' +
+                   ' '.join('-' + k.replace('_', '-') for k in ignored), err=True)
+    mode, _, robust = weight.partition(':')
+    parity = ('even' if even_timesteps else 'odd' if odd_timesteps else 'both' if even_odd else 'all')
+    try:
+        settings = Settings(
+            name=name, data_column=data_column, pols=pol.replace(',', ''), size=size, scale_deg=scale,
+            channel_range=channel_range, channels_out=channels_out, interval=interval,
+            intervals_out=intervals_out, parity=parity, minuv_l=minuv_l, maxuv_l=maxuv_l,
+            minuvw_m=minuvw_m, maxuvw_m=maxuvw_m, weight=mode, robust=float(robust or 0),
+            visibility_weighting=visibility_weighting_mode, taper_edge=taper_edge, padding=padding,
+            epsilon=wgridder_accuracy, threads=threads, parallel_gridding=parallel_gridding,
+            mem_percent=mem, abs_mem_gb=abs_mem, make_psf=make_psf, write_dirty=not no_dirty)
+        imager = Imager(ms, settings)
+        start = time.time()
+        paths = imager.run()
+    except (ValueError, OSError, RuntimeError) as error:
+        raise click.ClickException(str(error)) from error
+    click.echo(f'psimager: {len(ms)} MS(s), channels {imager.chans[0]}-{imager.chans[1] - 1} into '
+               f'{len(imager.blocks)} image(s), {imager.workers} channels x {imager.gridder_threads} '
+               f'threads: {len(paths)} files in {time.time() - start:.1f} s')
+
+
+if __name__ == '__main__':
+    sys.exit(main())

psimager/imager.py

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+"""Dirty Stokes and PSF images of measurement sets with the ducc0 w-gridder, in WSClean's format.
+
+The MSs are read once, in row chunks, and the output channels are gridded in parallel, each by
+one ducc0 call over its input channels. Images are in Jy/PSF, one FITS file per output channel
+and Stokes parameter, with WSClean's names and WSC* keywords.
+"""
+
+import math
+import os
+from concurrent.futures import ThreadPoolExecutor
+from dataclasses import dataclass
+from pathlib import Path
+
+import numpy as np
+from astropy.io import fits
+from astropy.time import Time
+from casacore.tables import table
+from ducc0.wgridder.experimental import vis2dirty
+
+from psimager import __version__
+
+SPEED_OF_LIGHT = 299792458.0
+# Stokes from linear feeds (XX, XY, YX, YY): XX = I + Q, YY = I - Q, XY = U + iV, YX = U - iV
+STOKES = {'I': ((0, 3), (.5, .5)), 'Q': ((0, 3), (.5, -.5)),
+          'U': ((1, 2), (.5, .5)), 'V': ((1, 2), (-.5j, .5j))}
+STOKES_CODE = {'I': 1, 'Q': 2, 'U': 3, 'V': 4, 'psf': 1}
+LINEAR_CORRELATIONS = [9, 10, 11, 12]
+
+
+@dataclass
+class Settings:
+    """Imaging settings, named after WSClean's options."""
+    name: str
+    data_column: str = 'DATA'
+    pols: str = 'I'
+    size: tuple = (512, 512)
+    scale_deg: float = 1 / 60
+    channel_range: tuple = None
+    channels_out: int = 1
+    interval: tuple = None
+    intervals_out: int = 1
+    parity: str = 'all'                 # all, even, odd, or both (even and odd in one pass)
+    minuv_l: float = None
+    maxuv_l: float = None
+    minuvw_m: float = None
+    maxuvw_m: float = None
+    weight: str = 'natural'             # natural, uniform or briggs
+    robust: float = 0.
+    visibility_weighting: str = 'normal'    # normal, squared or unit
+    taper_edge: float = None            # lambda
+    padding: float = 1.2                # of the weighting grid, as WSClean's -padding
+    epsilon: float = 1e-6
+    threads: int = None
+    parallel_gridding: int = None       # output channels gridded at once (default: threads)
+    mem_percent: float = 50.
+    abs_mem_gb: float = None
+    make_psf: bool = False
+    write_dirty: bool = True
+
+    def __post_init__(self):
+        self.pols = self.pols.upper()
+        if not self.pols or set(self.pols) - set(STOKES) or len(set(self.pols)) != len(self.pols):
+            raise ValueError(f'Invalid polarizations {self.pols!r}: distinct letters of IQUV')
+        if self.weight not in ('natural', 'uniform', 'briggs'):
+            raise ValueError(f'Invalid weighting {self.weight!r}')
+        if self.visibility_weighting not in ('normal', 'squared', 'unit'):
+            raise ValueError(f'Invalid visibility weighting mode {self.visibility_weighting!r}')
+        if self.parity not in ('all', 'even', 'odd', 'both'):
+            raise ValueError(f'Invalid time step parity {self.parity!r}')
+        if min(self.size) < 16 or any(s % 2 for s in self.size):
+            raise ValueError('Image sizes must be even and at least 16 pixels')
+        self.threads = self.threads or len(os.sched_getaffinity(0))
+        self.parallel_gridding = min(self.parallel_gridding or self.threads, self.threads)
+
+    @property
+    def products(self):
+        return list(self.pols) + (['psf'] if self.make_psf else [])
+
+    @property
+    def parities(self):
+        return ['even', 'odd'] if self.parity == 'both' else [self.parity]
+
+
+@dataclass
+class MSInfo:
+    path: Path
+    freqs: np.ndarray
+    widths: np.ndarray
+    phase_rad: np.ndarray
+    times: np.ndarray
+    telescope: str
+    observer: str
+    field_name: str
+    nrow: int
+
+
+def read_ms_info(path, data_column):
+    """Metadata of a single-field, single-SPW MS with linear correlations."""
+    path = Path(path)
+    with table(str(path), ack=False) as ms:
+        for column in ('FIELD_ID', 'DATA_DESC_ID'):
+            if len(np.unique(ms.getcol(column))) != 1:
+                raise ValueError(f'{path}: only single-field, single-SPW MSs are supported')
+        if data_column not in ms.colnames():
+            raise ValueError(f'{path}: no column {data_column}')
+        times, nrow = np.unique(ms.getcol('TIME')), ms.nrows()
+    with table(str(path / 'SPECTRAL_WINDOW'), ack=False) as spw:
+        freqs, widths = spw.getcell('CHAN_FREQ', 0), spw.getcell('CHAN_WIDTH', 0)
+    with table(str(path / 'POLARIZATION'), ack=False) as pol:
+        if list(pol.getcell('CORR_TYPE', 0)) != LINEAR_CORRELATIONS:
+            raise ValueError(f'{path}: expected XX, XY, YX, YY correlations')
+    with table(str(path / 'FIELD'), ack=False) as field:
+        phase = np.asarray(field.getcell('PHASE_DIR', 0)).reshape(-1, 2)[0]
+        field_name = field.getcell('NAME', 0)
+    with table(str(path / 'OBSERVATION'), ack=False) as obs:
+        telescope, observer = obs.getcell('TELESCOPE_NAME', 0), obs.getcell('OBSERVER', 0)
+    return MSInfo(path, freqs, widths, phase, times, telescope, observer, field_name, nrow)
+
+
+def channel_blocks(start, end, n):
+    """Input channels of each output channel: N blocks as equal as possible."""
+    return [(int(b[0]), int(b[-1]) + 1) for b in np.array_split(np.arange(start, end), n)]
+
+
+class WeightingGrid:
+    """WSClean's half-plane uv weighting grid, one per image (interval, parity, channel).
+
+    Its cells follow the padded image (size x padding, rounded up to a multiple of 4) over
+    |u|, |v| < 1 / (2 pixel): samples beyond get no weight. The uv range in lambda is tested at
+    each cell position and the uniform and Briggs densities are counted per cell.
+    """
+
+    def __init__(self, settings, nimages):
+        s = settings
+        self.nx, self.ny = (self.padded(n, s.padding) for n in s.size)
+        self.pixel = math.radians(s.scale_deg)
+        self.settings = s
+        u = (np.arange(self.nx) - self.nx // 2) / (self.nx * self.pixel)
+        v = np.arange(self.ny // 2) / (self.ny * self.pixel)
+        uv2 = (u[None, :] ** 2 + v[:, None] ** 2).ravel()
+        self.keep = np.ones(uv2.size, bool)
+        if s.minuv_l is not None:
+            self.keep &= uv2 >= s.minuv_l ** 2
+        if s.maxuv_l is not None:
+            self.keep &= uv2 <= s.maxuv_l ** 2
+        self.density = np.zeros((nimages, uv2.size)) if s.weight != 'natural' else None
+        self.factors = None
+
+    @staticmethod
+    def padded(size, padding):
+        n = math.ceil(size * padding)
+        return n + (4 - n % 4) % 4
+
+    def cells(self, uvw, freq):
+        """Cell index of each (row, channel) sample, -1 outside the grid."""
+        u, v = (uvw[:, k, None] * freq[None, :] / SPEED_OF_LIGHT for k in (0, 1))
+        u = np.where(v < 0, -u, u)
+        x = np.floor(u * self.nx * self.pixel + self.nx // 2).astype(np.int64)
+        y = np.floor(np.abs(v) * self.ny * self.pixel).astype(np.int64)
+        return np.where((x >= 0) & (x < self.nx) & (y < self.ny // 2), y * self.nx + x, -1)
+
+    def add(self, image, cells, weights):
+        keep = (weights > 0) & (cells >= 0)
+        self.density[image] += np.bincount(cells[keep], weights[keep], minlength=self.keep.size)
+
+    def finish(self):
+        if self.density is None:
+            return
+        d = self.density
+        if self.settings.weight == 'uniform':
+            f = np.divide(1, d, out=np.zeros_like(d), where=d > 0)
+        else:
+            total = d.sum(axis=1, keepdims=True)
+            mean = np.divide((d ** 2).sum(axis=1, keepdims=True), total, out=np.ones_like(total),
+                             where=total > 0)
+            f = 1 / (1 + d * (5 * 10 ** -self.settings.robust) ** 2 / mean)
+        self.factors = f * self.keep
+
+    def taper(self, image, cells, uvw, freq):
+        """Imaging weight factor of each sample."""
+        f = self.keep[cells] if self.factors is None else self.factors[image][cells]
+        f = np.where(cells >= 0, f, 0.)
+        if self.settings.taper_edge:
+            # Tukey transition of TAPER_EDGE lambda inside the edge of the uv plane of the image
+            edge = 1 / (2 * self.pixel)
+            u, v = (np.abs(uvw[:, k, None] * freq[None, :]) / SPEED_OF_LIGHT for k in (0, 1))
+            x = np.clip((edge - np.maximum(u, v)) / self.settings.taper_edge, 0, 1)
+            f = f * np.where(x < 1, .5 - .5 * np.cos(np.pi * x), 1)
+        return f
+
+
+class Chunk:
+    """Rows of one MS: UVW, image index of each row (-1: not imaged), flags, weights, data."""
+
+    def __init__(self, ms, start, count, info, settings, chans, data=True):
+        s = settings
+        c0, c1 = chans
+
+        def spectral(column):
+            return ms.getcolslice(column, [c0, 0], [c1 - 1, 3], [], start, count)
+
+        self.uvw = ms.getcol('UVW', start, count)
+        tidx = np.searchsorted(info.times, ms.getcol('TIME', start, count))
+        t0, t1 = s.interval or (0, 0)
+        t1 = t1 if t1 > t0 else len(info.times)
+        in_range = (tidx >= t0) & (tidx < t1)
+        interval = np.minimum((tidx - t0) * s.intervals_out // max(t1 - t0, 1), s.intervals_out - 1)
+        self.image_of_row = {}
+        for p, parity in enumerate(s.parities):
+            keep = in_range.copy()
+            if parity != 'all':
+                keep &= tidx % 2 == (0 if parity == 'even' else 1)
+            self.image_of_row[p] = np.where(keep, interval, -1)
+        flags = spectral('FLAG')
+        flags |= (ms.getcol('FLAG_ROW', start, count) |
+                  (ms.getcol('ANTENNA1', start, count) == ms.getcol('ANTENNA2', start, count)))[:, None, None]
+        dist = np.linalg.norm(self.uvw, axis=1)
+        if s.minuvw_m is not None:
+            flags |= (dist < s.minuvw_m)[:, None, None]
+        if s.maxuvw_m is not None:
+            flags |= (dist > s.maxuvw_m)[:, None, None]
+        self.flags = flags
+        if 'WEIGHT_SPECTRUM' in ms.colnames():
+            self.corr_weights = spectral('WEIGHT_SPECTRUM')
+        else:
+            self.corr_weights = np.broadcast_to(ms.getcol('WEIGHT', start, count)[:, None], flags.shape)
+        self.data = spectral(s.data_column) if data else None
+        self.mode = s.visibility_weighting
+
+    def weights(self, rows, chans, stokes):
+        """Visibility weights of a Stokes product: from the smaller of its two correlation weights,
+        zero if either is flagged."""
+        (a, b), _ = STOKES['I' if stokes == 'psf' else stokes]
+        flags, w = self.flags[rows][:, chans], self.corr_weights[rows][:, chans]
+        w = np.minimum(w[..., a], w[..., b]).astype(np.float64)
+        bad = flags[..., a] | flags[..., b] | ~(w > 0)
+        if self.mode == 'unit':
+            w = np.ones_like(w)
+        elif self.mode == 'squared':
+            w = w ** 2
+        w[bad] = 0
+        return w
+
+    def visibilities(self, rows, chans, stokes):
+        if stokes == 'psf':
+            return None
+        (a, b), (ca, cb) = STOKES[stokes]
+        data = self.data[rows][:, chans]
+        return ca * data[..., a].astype(np.complex128) + cb * data[..., b]
+
+
+class Image:
+    """Weighted sums of the products of one image (interval, parity, output channel)."""
+
+    def __init__(self, nproducts, size):
+        self.sums = np.zeros((nproducts, size[1], size[0]))
+        self.norm = np.zeros(nproducts)
+        # Stokes I statistics: visibilities, visibility weights, imaging weights, sum(w), sum(w^2)
+        self.stats = np.zeros(5)
+
+
+class Imager:
+    """Images the selected data of one or more MSs into WSClean-like dirty and PSF images."""
+
+    def __init__(self, ms_paths, settings):
+        s = self.settings = settings
+        self.infos = [read_ms_info(p, s.data_column) for p in ms_paths]
+        first = self.infos[0]
+        for info in self.infos[1:]:
+            if not (np.allclose(info.freqs, first.freqs) and np.allclose(info.phase_rad, first.phase_rad)):
+                raise ValueError(f'{info.path}: frequencies or phase centre differ from {first.path}')
+        nchan = len(first.freqs)
+        self.chans = s.channel_range or (0, nchan)
+        if not 0 <= self.chans[0] < self.chans[1] <= nchan:
+            raise ValueError(f'Channel range must satisfy 0 <= start < end <= {nchan}')
+        self.blocks = channel_blocks(*self.chans, s.channels_out)
+        self.freqs = first.freqs[self.chans[0]:self.chans[1]]
+        self.keys = [(p, k, c) for p in range(len(s.parities)) for k in range(s.intervals_out)
+                     for c in range(len(self.blocks))]
+        self.index = {key: i for i, key in enumerate(self.keys)}
+        self.images = [Image(len(s.products), s.size) for _ in self.keys]
+        self.grid = WeightingGrid(s, len(self.keys))
+        # Output channels gridded at once, and the threads of each ducc0 call
+        self.workers = min(s.parallel_gridding, len(self.blocks))
+        self.gridder_threads = max(1, s.threads // self.workers)
+
+    def rows_per_chunk(self):
+        s = self.settings
+        mem = (s.abs_mem_gb * 1e9 if s.abs_mem_gb else
+               os.sysconf('SC_PAGE_SIZE') * os.sysconf('SC_PHYS_PAGES') * s.mem_percent / 100)
+        # DATA, WEIGHT_SPECTRUM and FLAG cells (8+4+1 bytes), doubled for the working copies
+        return max(1, int(mem // (2 * 13 * 4 * len(self.freqs))))
+
+    def chunks(self, data):
+        nrows = self.rows_per_chunk()
+        for info in self.infos:
+            with table(str(info.path), ack=False) as ms:
+                for start in range(0, info.nrow, nrows):
+                    count = min(nrows, info.nrow - start)
+                    yield Chunk(ms, start, count, info, self.settings, self.chans, data=data)
+
+    def block_samples(self, chunk, p, c, k):
+        """Rows of image (p, k, c) and its input channels, relative to the selected range."""
+        b0, b1 = self.blocks[c]
+        chans = slice(b0 - self.chans[0], b1 - self.chans[0])
+        return np.where(chunk.image_of_row[p] == k)[0], chans
+
+    def run(self):
+        s = self.settings
+        if s.weight != 'natural':
+            for chunk in self.chunks(data=False):
+                for (p, k, c), i in self.index.items():
+                    rows, chans = self.block_samples(chunk, p, c, k)
+                    cells = self.grid.cells(chunk.uvw[rows], self.freqs[chans])
+                    self.grid.add(i, cells, chunk.weights(rows, chans, 'I'))
+            self.grid.finish()
+        # A first ducc0 call imports its numpy bindings; concurrent first calls can deadlock
+        vis2dirty(uvw=np.zeros((1, 3)), freq=np.array([1e8]), vis=np.ones((1, 1), np.complex128),
+                  npix_x=16, npix_y=16, pixsize_x=1e-3, pixsize_y=1e-3, epsilon=1e-4)
+        with ThreadPoolExecutor(self.workers) as pool:
+            for chunk in self.chunks(data=True):
+                list(pool.map(lambda c, chunk=chunk: self.grid_channel(chunk, c), range(len(self.blocks))))
+        return self.write()
+
+    def grid_channel(self, chunk, c):
+        s = self.settings
+        for p in range(len(s.parities)):
+            for k in range(s.intervals_out):
+                i = self.index[(p, k, c)]
+                rows, chans = self.block_samples(chunk, p, c, k)
+                if not len(rows):
+                    continue
+                uvw, freq = chunk.uvw[rows], self.freqs[chans]
+                taper = self.grid.taper(i, self.grid.cells(uvw, freq), uvw, freq)
+                image = self.images[i]
+                # WSC* statistics from the Stokes I weights, as WSClean, whatever the products
+                vw_i = chunk.weights(rows, chans, 'I')
+                w_i = vw_i * taper
+                used = w_i > 0
+                image.stats += [np.count_nonzero(used), vw_i[used].sum(), taper[used].sum(),
+                                w_i.sum(), (w_i ** 2).sum()]
+                for j, product in enumerate(s.products):
+                    w = w_i if product in ('I', 'Q', 'psf') else chunk.weights(rows, chans, product) * taper
+                    if not w.any():
+                        continue
+                    vis = chunk.visibilities(rows, chans, product)
+                    vis = (w > 0).astype(np.complex128) if vis is None else np.where(w > 0, vis, 0)
+                    image.sums[j] += vis2dirty(
+                        uvw=uvw, freq=freq, vis=vis, wgt=w, mask=(w > 0).astype(np.uint8),
+                        npix_x=s.size[0], npix_y=s.size[1], pixsize_x=self.grid.pixel,
+                        pixsize_y=self.grid.pixel, epsilon=s.epsilon, do_wgridding=True,
+                        nthreads=self.gridder_threads, flip_v=True, divide_by_n=False).T
+                    image.norm[j] += w.sum()
+
+    def write(self):
+        """Write the FITS files; return their paths."""
+        s, paths = self.settings, []
+        for (p, k, c), i in self.index.items():
+            image = self.images[i]
+            data = np.divide(image.sums, image.norm[:, None, None],
+                             out=np.full_like(image.sums, np.nan), where=image.norm[:, None, None] > 0)
+            beam = fit_beam(data[s.products.index('psf')], s.scale_deg) if s.make_psf else None
+            header = self.header(c, image, beam)
+            base = s.name + (f'-{s.parities[p]}' if s.parity == 'both' else '')
+            base += (f'-t{k:04d}' if s.intervals_out > 1 else '')
+            base += (f'-{c:04d}' if len(self.blocks) > 1 else '')
+            for j, product in enumerate(s.products):
+                header['CRVAL4'] = STOKES_CODE[product]
+                if product == 'psf':
+                    names = [f'{base}-psf.fits']
+                else:
+                    pol = f'-{product}' if len(s.pols) > 1 else ''
+                    names = [f'{base}{pol}-image.fits']
+                    names += [f'{base}{pol}-dirty.fits'] if s.write_dirty else []
+                for name in names:
+                    Path(name).parent.mkdir(parents=True, exist_ok=True)
+                    hdu = fits.PrimaryHDU(data[j][None, None].astype(np.float32), header)
+                    hdu.writeto(name, overwrite=True)
+                    paths.append(name)
+        return paths
+
+    def header(self, c, image, beam):
+        s, info = self.settings, self.infos[0]
+        b0, b1 = self.blocks[c]
+        freqs, widths = info.freqs[b0:b1], info.widths[b0:b1]
+        ra, dec = np.degrees(info.phase_rad)
+        nvis, vwsum, imgwsum, wsum, w2sum = image.stats
+        h = fits.Header()
+        h['BUNIT'] = 'JY/BEAM'
+        if beam:
+            h['BMAJ'], h['BMIN'], h['BPA'] = beam
+        h.update({'EQUINOX': 2000., 'BTYPE': 'Intensity', 'TELESCOP': info.telescope,
+                  'OBSERVER': info.observer, 'OBJECT': info.field_name, 'ORIGIN': 'psimager'})
+        axes = [('RA---SIN', s.size[0] / 2 + 1, ra % 360, -s.scale_deg),
+                ('DEC--SIN', s.size[1] / 2 + 1, dec, s.scale_deg),
+                ('FREQ', 1., freqs.mean(), np.abs(widths).sum()), ('STOKES', 1., 1., 1.)]
+        for n, (ctype, crpix, crval, cdelt) in enumerate(axes, 1):
+            h.update({f'CTYPE{n}': ctype, f'CRPIX{n}': crpix, f'CRVAL{n}': crval, f'CDELT{n}': cdelt})
+        h['CUNIT1'], h['CUNIT2'], h['CUNIT3'] = 'deg', 'deg', 'Hz'
+        h['SPECSYS'] = 'TOPOCENT'
+        h['DATE-OBS'] = Time(info.times[0] / 86400, format='mjd').isot
+        h.update({'WSCDATAC': s.data_column, 'WSCWEIGH': self.weight_name(),
+                  'WSCCHANS': self.chans[0], 'WSCCHANE': self.chans[1], 'WSCNVIS': nvis,
+                  'WSCENVIS': wsum ** 2 / w2sum if w2sum > 0 else 0., 'WSCVWSUM': vwsum,
+                  'WSCIMGWG': imgwsum, 'WSCNORMF': wsum, 'PSIVERSI': __version__})
+        return h
+
+    def weight_name(self):
+        s = self.settings
+        return f'briggs({s.robust:g})' if s.weight == 'briggs' else s.weight
+
+
+def fit_beam(psf, scale_deg):
+    """Gaussian fitted to the PSF main lobe (above half maximum): BMAJ, BMIN (deg), BPA (deg)."""
+    cy, cx = psf.shape[0] // 2, psf.shape[1] // 2
+    half = 1
+    while half < min(cx, cy) - 1 and max(psf[cy, cx + half], psf[cy + half, cx]) > .5:
+        half += 1
+    box = psf[cy - 2 * half:cy + 2 * half + 1, cx - 2 * half:cx + 2 * half + 1]
+    y, x = np.mgrid[-2 * half:2 * half + 1, -2 * half:2 * half + 1]
+    keep = (box > .5) & np.isfinite(box)
+    # ln(psf) = -(a x^2 + b x y + c y^2) / 2 for a Gaussian peaking at 1
+    a, b, c = np.linalg.lstsq(np.stack([x[keep] ** 2, x[keep] * y[keep], y[keep] ** 2], 1),
+                              -2 * np.log(box[keep]), rcond=None)[0]
+    vals, vecs = np.linalg.eigh(np.array([[a, b / 2], [b / 2, c]]))
+    if np.any(vals <= 0):
+        return None
+    sigma_maj, sigma_min = 1 / np.sqrt(vals)
+    vx, vy = vecs[:, 0]
+    # Position angle from north (+y) through east (-x, RA increases to the left)
+    bpa = np.degrees(np.arctan2(-vx, vy)) % 180
+    fwhm = 2 * np.sqrt(2 * np.log(2)) * scale_deg
+    return float(sigma_maj * fwhm), float(sigma_min * fwhm), float(bpa)

psimager-0.1.dist-info/METADATA

@@ -0,0 +1,80 @@
+Metadata-Version: 2.4
+Name: psimager
+Version: 0.1
+Summary: Fast dirty imaging of measurement sets for power spectrum analyses, with the ducc0 w-gridder and WSClean's options
+License-Expression: GPL-3.0-or-later
+License-File: LICENSE
+Author: Florent Mertens
+Author-email: florent.mertens@gmail.com
+Requires-Python: >=3.10,<4.0
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Provides-Extra: dev
+Requires-Dist: astropy (>=5.0)
+Requires-Dist: click (>=8.0)
+Requires-Dist: ducc0 (>=0.27)
+Requires-Dist: numpy (>=1.22)
+Requires-Dist: pytest (>=8.0) ; extra == "dev"
+Requires-Dist: pytest-cov (>=5.0) ; extra == "dev"
+Requires-Dist: python-casacore (>=3.0)
+Requires-Dist: ruff (==0.16.1) ; extra == "dev"
+Project-URL: Homepage, https://gitlab.com/flomertens/psimager
+Project-URL: Issues, https://gitlab.com/flomertens/psimager/-/issues
+Project-URL: Repository, https://gitlab.com/flomertens/psimager
+Description-Content-Type: text/markdown
+
+# psimager
+
+Fast dirty imaging of measurement sets for power spectrum analyses: dirty Stokes and PSF images
+with the [ducc0](https://gitlab.mpcdf.mpg.de/mtr/ducc) w-gridder, with the options, file names and
+FITS keywords of [WSClean](https://wsclean.readthedocs.io), so that pspipe and ps_eor read them as
+WSClean images.
+
+The MSs are read once, in large row chunks, and the output channels are gridded in parallel, each
+by one ducc0 call. Imaging many channels is then many times faster than with WSClean, which
+reorders the data on disk and grids one image at a time.
+
+## Installation
+
+```bash
+pip install psimager
+```
+
+## Usage
+
+```bash
+psimager -name img -size 400 400 -scale 6amin -pol IV -channels-out 363 -weight natural \
+    -minuv-l 5 -maxuv-l 100 -data-column CORRECTED_DATA -even-odd -make-psf -no-dirty obs*.MS
+```
+
+writes `img-even-0000-I-image.fits`, `img-even-0000-V-image.fits`, `img-even-0000-psf.fits`, ...,
+for each output channel, for the even and the odd time steps.
+
+## Options
+
+As WSClean's: `-name`, `-data-column`, `-pol`, `-size`, `-scale`, `-channel-range`,
+`-channels-out`, `-interval`, `-intervals-out`, `-even-timesteps`, `-odd-timesteps`, `-minuv-l`,
+`-maxuv-l`, `-minuvw-m`, `-maxuvw-m`, `-weight natural|uniform|briggs ROBUST`,
+`-visibility-weighting-mode`, `-taper-edge`, `-padding` (of the weighting grid),
+`-wgridder-accuracy`, `-j`, `-parallel-gridding`, `-mem`, `-abs-mem`, `-make-psf`, `-no-dirty`.
+See `psimager --help`.
+
+Differences with WSClean:
+
+- `-even-odd` images the even and the odd time steps in one pass, as `NAME-even-*` and
+  `NAME-odd-*`.
+- `-parallel-gridding` defaults to `-j`: one thread per output channel, which is the fastest.
+- No deconvolution and no `-MFS-` images.
+- WSClean's gridding options (`-oversampling`, `-kernel-size`, `-nwlayers`, `-grid-mode`,
+  `-reorder`, `-temp-dir`, ...) are accepted and ignored, with a warning, so that a WSClean command
+  line runs unchanged.
+- Only single-field, single-SPW MSs with linear correlations.
+
+Images are in Jy/PSF (the PSF peaks at 1), one file per output channel and Stokes parameter, with
+WSClean's `WSCNVIS`, `WSCENVIS`, `WSCVWSUM`, `WSCIMGWG` and `WSCNORMF` computed from the Stokes I
+weights, and `BMAJ`, `BMIN`, `BPA` fitted to the PSF.
+

psimager-0.1.dist-info/RECORD

@@ -0,0 +1,8 @@
+psimager/__init__.py,sha256=Af6Tmzn8mqMayx9gH3G63aHXtVYgBcBaKzSLF1R0gmQ,95
+psimager/cli.py,sha256=bM_YCkQFerl4Tm9MVq8eSuOs0itXEDhi3fwhMT3MwQk,7153
+psimager/imager.py,sha256=XZsxBDq56uMoaNU94WXXnjzhIQh1uYjAvuH5XWCMiVo,20601
+psimager-0.1.dist-info/METADATA,sha256=tpKaH_RLxy7Pmx-Jmw8F9CgtHJt2IpWyfYUXPBwts_o,3446
+psimager-0.1.dist-info/WHEEL,sha256=EGEvSphFYqXKs23-kQBeyNoJP1nrT8ZJKQoi5p5DYL8,88
+psimager-0.1.dist-info/entry_points.txt,sha256=2onAbVZfvYrqBDkownpRk3kVKVD8gr1scSHy4S-L8xM,46
+psimager-0.1.dist-info/licenses/LICENSE,sha256=CJnwZdrEih1PbSeQBXLGniQm2z-lZeciapwAdm78ph0,35057
+psimager-0.1.dist-info/RECORD,,

psimager-0.1.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: poetry-core 2.4.0
+Root-Is-Purelib: true
+Tag: py3-none-any

psimager-0.1.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+psimager=psimager.cli:main
+

psimager-0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
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+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
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+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
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+  7. Additional Terms.
+
+  "Additional permissions" are terms that supplement the terms of this
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+Additional permissions that are applicable to the entire Program shall
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+  When you convey a copy of a covered work, you may at your option
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+  You may not propagate or modify a covered work except as expressly
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+  However, if you cease all violation of this License, then your
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+  Termination of your rights under this section does not terminate the
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+
+  9. Acceptance Not Required for Having Copies.
+
+  You are not required to accept this License in order to receive or
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+  10. Automatic Licensing of Downstream Recipients.
+
+  Each time you convey a covered work, the recipient automatically
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+  An "entity transaction" is a transaction transferring control of an
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+any patent claim is infringed by making, using, selling, offering for
+sale, or importing the Program or any portion of it.
+
+  11. Patents.
+
+  A "contributor" is a copyright holder who authorizes use under this
+License of the Program or a work on which the Program is based.  The
+work thus licensed is called the contributor's "contributor version".
+
+  A contributor's "essential patent claims" are all patent claims
+owned or controlled by the contributor, whether already acquired or
+hereafter acquired, that would be infringed by some manner, permitted
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+purposes of this definition, "control" includes the right to grant
+patent sublicenses in a manner consistent with the requirements of
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+
+  Each contributor grants you a non-exclusive, worldwide, royalty-free
+patent license under the contributor's essential patent claims, to
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+
+  In the following three paragraphs, a "patent license" is any express
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+
+  If you convey a covered work, knowingly relying on a patent license,
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+available, or (2) arrange to deprive yourself of the benefit of the
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+consistent with the requirements of this License, to extend the patent
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+actual knowledge that, but for the patent license, your conveying the
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+country that you have reason to believe are valid.
+
+  If, pursuant to or in connection with a single transaction or
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+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
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+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
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+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
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+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
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+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
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+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
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+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    pspipe
+    Copyright (C) 2020  Florent
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    pspipe  Copyright (C) 2020  Florent
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.