disko 1.3.0__tar.gz → 1.3.3__tar.gz

{disko-1.3.0 → disko-1.3.3}/CHANGES.md

@@ -1,6 +1,6 @@
 # Changes
 
-## 1.3.0 (2026-06-19)
+## 1.3.3 (2026-06-19)
 
 - Vectorize `get_harmonics`, `make_gamma`, and matrix-free operators (`DiSkOOperator`, `DirectImagingOperator`) using broadcasting and blocked BLAS-level operations (10-50x speedup)
 - Fix FISTA solver: remove unconditional `eps = 1e-9` override, switch from broken analysis formulation (`SOp=Apre`) to synthesis formulation, use proper initial guess (`abs(Apre @ d)`) instead of zeros
@@ -12,6 +12,9 @@
 - CI: target `disko/` directory in flake8 to avoid scanning dependencies
 - Configure flake8 exclusions for `.venv`, `.git`, `__pycache__` in `setup.cfg`
 - Fix various flake8 lint issues (unused imports, variables, long lines)
+- Fix `disko_bayes` MS reading: replace broken `DiSkO.from_ms()` with `disko_from_ms()`, add visibility conjugation, geo-location, and file-exists check
+- Fix `disko_bayes` output: remove invalid `fov` argument from `to_fits()` and `to_svg()` calls
+- Fix publish workflow: use concrete Python version (`3.12` instead of `3.x`), pin `actions/checkout@v4`, fix `--outdir` → `--out-dir`
 
 ## 1.2.0 (2026-06-18)
 

{disko-1.3.0 → disko-1.3.3}/Makefile

@@ -31,7 +31,7 @@ svd:
 
 bayes:
 	#rm -f *.npz
-	uv run disko_bayes --fov 155 --ms test_data/test.ms  --mu --PNG --SVG --arcmin=90  --dir test_out --title 'bayes_tart' --sigma-v=0.15
+	uv run disko_bayes --healpix --fov 155 --res 30arcmin --ms test_data/test.ms  --mu --var --PNG --SVG --arcmin=90  --dir test_out --title 'bayes_tart' --sigma-v=0.15
 #	${TIME} uv run disko --fov 155 --ms ../tart2ms/test.ms --SVG --arcmin=120  --title 'tart' --tikhonov --alpha=0.01
 
 ngc1194:

{disko-1.3.0 → disko-1.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: disko
-Version: 1.3.0
+Version: 1.3.3
 Summary: Discrete Sky Operator (DiSkO) Aperture Synthesis Radio Imaging
 Author-email: Tim Molteno <tim@elec.ac.nz>
 License: GPLv3

disko-1.3.3/disko/bayes_cli.py

@@ -0,0 +1,434 @@
+#!/usr/bin/env python
+import argparse
+import datetime
+import json
+import logging
+import os
+import time
+from copy import deepcopy
+
+import matplotlib
+import matplotlib.pyplot as plt
+import numpy as np
+import scipy.special
+from tart.imaging import calibration, elaz, visibility
+from tart.operation import settings
+from tart_tools import api_imaging
+
+from .cli import disko_from_ms
+from .disko import DiSkO, vis_to_real
+from .ms_helper import get_array_location
+from .multivariate_gaussian import MultivariateGaussian
+from .parser_support import sphere_args_parser, sphere_from_args
+from .telescope_operator import TelescopeOperator
+
+logger = logging.getLogger(__name__)
+logger.addHandler(
+    logging.NullHandler()
+)  # Add other handlers if you're using this as a library
+logger.setLevel(logging.INFO)
+
+
+def create_prior(vis_arr, sphere, hdf_prior):
+    """Based on the size of the visibilities, try and calculate
+    what range the image should have.
+    """
+    if hdf_prior is not None:
+        return MultivariateGaussian.from_hdf5(hdf_prior)
+
+    vabs = np.abs(vis_arr)
+
+    p05, p50, p95, p100 = np.percentile(vabs, [5, 50, 95, 100])
+
+    var = p95 * p95
+    logger.info("Extimated Sky Prior variance={}".format(var))
+    prior = MultivariateGaussian(
+        np.zeros(sphere.npix) + p50, sigma=p95 * np.identity(sphere.npix)
+    )
+
+    return prior
+
+
+def do_inference(disko, sphere, prior, sigma_v=None):
+    real_vis = vis_to_real(disko.vis_arr)
+
+    to = TelescopeOperator(disko, sphere)
+
+    # Transform to the natural basis.
+    n_prior = prior.linear_transform(to.Vh)
+    n_v = real_vis.shape[0]
+
+    # TODO create a proper covariance that ensures the real and imaginary components are linked.
+    if sigma_v is None:
+        diag = np.diag(disko.rms**2)
+    else:
+        diag = np.diag(np.ones(n_v // 2) * (sigma_v) ** 2)
+
+    logger.info(f"do_inference(sigma_v={diag[0, 0]})")
+
+    sigma_vis = np.block([[diag, 0.5 * diag], [0.5 * diag, diag]])  # .rechunk('auto')
+
+    # now invert sigma_vis
+    sigma_precision = MultivariateGaussian.sp_inv(sigma_vis)
+    del sigma_vis
+
+    if True:
+        prior_r = n_prior.block(0, to.rank)
+        prior_n = n_prior.block(to.rank, to.n_s)
+
+        A_r = to.A_r
+        V = to.V
+
+        del to
+        posterior_r = prior_r.bayes_update(sigma_precision, real_vis, A_r)
+        posterior_n = prior_n
+
+        del A_r
+        del sigma_precision
+        del prior_r
+        del prior_n
+        del n_prior
+
+        posterior = MultivariateGaussian.outer(posterior_r, posterior_n)
+
+        del posterior_r
+        del posterior_n
+
+        logger.info("Transforming posterior")
+
+        posterior = posterior.linear_transform(V)
+
+        del V
+    else:
+        posterior = to.sequential_inference(n_prior, real_vis, sigma_precision)
+        del to
+        del sigma_precision
+        del n_prior
+
+    return posterior
+
+
+def handle_bayes(ARGS):
+
+    sphere = sphere_from_args(ARGS)
+
+    # Create a prior.
+    if ARGS.file:
+        logger.info("Getting Data from file: {}".format(ARGS.file))
+        # Load data from a JSON file
+        with open(ARGS.file, "r") as json_file:
+            calib_info = json.load(json_file)
+
+        info = calib_info["info"]
+        ant_pos = calib_info["ant_pos"]
+        config = settings.from_api_json(info["info"], ant_pos)
+
+        flag_list = []  # [4, 5, 14, 22]
+
+        original_positions = deepcopy(config.get_antenna_positions())
+
+        gains_json = calib_info["gains"]
+        gains = np.asarray(gains_json["gain"])
+        phase_offsets = np.asarray(gains_json["phase_offset"])
+        config = settings.from_api_json(info["info"], ant_pos)
+
+        measurements = []
+        for d in calib_info["data"]:
+            vis_json, source_json = d
+            cv, timestamp = api_imaging.vis_calibrated(
+                vis_json, config, gains, phase_offsets, flag_list
+            )
+            src_list = elaz.from_json(source_json, 0.0)
+
+        if ARGS.sigma_v is None:
+            raise RuntimeError(
+                "The --sigma-v option must be supplied when --file JSON input is used"
+            )
+
+        prior = create_prior(cv.v, sphere, ARGS.prior)
+        timestamp = cv.get_timestamp()
+        disko = DiSkO.from_cal_vis(cv)
+
+        posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
+        handle_output(ARGS, timestamp, posterior, sphere, disko)
+
+    elif ARGS.hdf:
+        logger.info(f"Getting data from file {ARGS.hdf}")
+        if ARGS.sigma_v is None:
+            raise RuntimeError(
+                "The --sigma-v option must be supplied when HDF5 input is used"
+            )
+
+        data = visibility.from_hdf5(ARGS.hdf)
+
+        prior = create_prior(data["vis_list"][0].v, sphere, ARGS.prior)
+        posterior = None
+
+        for v in data["vis_list"]:
+            if posterior is not None:
+                prior = posterior
+            cv = calibration.CalibratedVisibility(v)
+            cv.set_config(v.config)
+            cv.set_phase_offset(
+                list(range(cv.get_config().get_num_antenna())),
+                np.array(data["phase_offset"]),
+            )
+            cv.set_gain(
+                list(range(cv.get_config().get_num_antenna())), np.array(data["gain"])
+            )
+            timestamp = cv.get_timestamp()
+            disko = DiSkO.from_cal_vis(cv)
+
+            # TODO Calibrate the vis with gains and phases?
+            posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
+            handle_output(ARGS, timestamp, posterior, sphere, disko)
+    else:
+        logger.info("Getting Data from MS file: {}".format(ARGS.ms))
+
+        if not os.path.exists(ARGS.ms):
+            raise RuntimeError("Measurement set {} not found".format(ARGS.ms))
+
+        min_res = sphere.min_res()
+        logger.info(f"Min Res {min_res}")
+        disko = disko_from_ms(
+            ARGS.ms,
+            "DATA",
+            ARGS.nvis,
+            res=min_res,
+            channel=ARGS.channel,
+            field_id=ARGS.field,
+        )
+        # CASAcore UVW is conjugated; conjugate visibilities for consistency.
+        disko.vis_arr = disko.vis_arr.conjugate()
+
+        # Convert from reduced Julian Date to timestamp.
+        timestamp = disko.timestamp
+
+        json_info = get_array_location(ARGS.ms)
+        lat = json_info["lat"]
+        lon = json_info["lon"]
+        height = json_info["height"]
+        sphere.set_info(timestamp=timestamp, lon=lon, lat=lat, height=height)
+
+        src_list = None
+
+        prior = create_prior(disko.vis_arr, sphere, ARGS.prior)
+
+        posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
+        handle_output(ARGS, timestamp, posterior, sphere, disko)
+
+
+def handle_output(ARGS, timestamp, posterior, sphere, disko=None):
+
+    if not ARGS.show_sources:
+        src_list = None
+
+    time_repr = "{:%Y_%m_%d_%H_%M_%S_%Z}".format(timestamp)
+
+    # Now save the files.
+    if ARGS.posterior is not None:
+        posterior.to_hdf5(ARGS.posterior)
+
+    def path(ending, image_title):
+        os.makedirs(ARGS.dir, exist_ok=True)
+        fname = "{}.{}".format(image_title, ending)
+        return os.path.join(ARGS.dir, fname)
+
+    def save_images(image_title, source_list):
+        # Save as a FITS file
+
+        if ARGS.FITS:
+            sphere.to_fits(fname=path("fits", image_title), info=disko.info)
+
+        if ARGS.SVG:
+            fname = path("svg", image_title)
+            sphere.to_svg(
+                fname=fname,
+                show_grid=True,
+                src_list=source_list,
+                title=image_title,
+                show_cbar=True,
+            )
+            logger.info("Generating {}".format(fname))
+        if ARGS.PNG:
+            fname = path("png", image_title)
+            sphere.plot(plt, source_list)
+            plt.title(image_title)
+            plt.tight_layout()
+            plt.savefig(fname, dpi=300)
+            plt.close()
+            logger.info("Generating {}".format(fname))
+        if ARGS.PDF:
+            fname = path("pdf", image_title)
+            sphere.plot(plt, source_list)
+            plt.title(image_title)
+            plt.savefig(fname, dpi=600)
+            plt.close()
+            logger.info("Generating {}".format(fname))
+
+    if ARGS.PDF or ARGS.PNG or ARGS.SVG or ARGS.FITS:
+        if ARGS.mu:
+            logger.info("Computing pixels")
+            tic = time.perf_counter()
+            # mu_positive = np.array(da.clip(posterior.mu, 0, None))
+            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
+            stat = sphere.set_visible_pixels(np.array(posterior.mu), scale=False)
+            stat["sigma-v"] = ARGS.sigma_v
+            logger.info(json.dumps(stat, sort_keys=True))
+            save_images("{}_{}_mu".format(ARGS.title, time_repr), source_list=src_list)
+
+        if ARGS.var:
+            tic = time.perf_counter()
+            logger.info("Computing variance...")
+            variance = np.array(posterior.variance())
+            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
+            sphere.set_visible_pixels(variance, scale=False)
+            save_images("{}_{}_var".format(ARGS.title, time_repr), source_list=None)
+
+        if ARGS.pcf:
+            tic = time.perf_counter()
+            logger.info("Computing point covariance...")
+
+            brightest_pixel = np.argmax(posterior.mu)
+            pix_cov = np.array(posterior.sigma()[brightest_pixel, :])
+            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
+
+            sphere.set_visible_pixels(pix_cov, scale=False)
+            save_images("{}_{}_pcf".format(ARGS.title, time_repr), source_list=None)
+
+        for i in range(ARGS.nsamples):
+            sphere.set_visible_pixels(posterior.sample(), scale=False)
+            save_images(
+                image_title="{}_{}_s{:0>5}".format(ARGS.title, time_repr, i),
+                source_list=None,
+            )
+
+
+def main():
+    np.random.seed(42)
+    sphere_parsers = sphere_args_parser()
+
+    parser = argparse.ArgumentParser(
+        description="DiSkO: Bayesian inference of a posterior sky",
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+        parents=sphere_parsers,
+    )
+
+    parser.add_argument(
+        "--hdf", required=False, default=None, help="Exported Multi-visibility file"
+    )
+    parser.add_argument("--ms", required=False, default=None, help="visibility file")
+    parser.add_argument(
+        "--file",
+        required=False,
+        default=None,
+        help="Snapshot observation saved JSON file (visiblities, positions and more).",
+    )
+
+    parser.add_argument(
+        "--channel", type=int, default=0, help="Use this frequency channel."
+    )
+    parser.add_argument(
+        "--field",
+        type=int,
+        default=0,
+        help="Use this FIELD_ID from the measurement set.",
+    )
+
+    parser.add_argument("--dir", required=False, default=".", help="Output directory.")
+    parser.add_argument(
+        "--nvis", type=int, default=1000, help="Number of visibilities to use."
+    )
+    parser.add_argument(
+        "--arcmin",
+        type=float,
+        default=None,
+        help="Highest allowed res of the sky in arc minutes.",
+    )
+
+    parser.add_argument(
+        "--sigma-v",
+        type=float,
+        default=None,
+        help="Diagonal components of the visibility covariance. If not supplied use measurement set values",
+    )
+
+    parser.add_argument(
+        "--PNG", action="store_true", help="Generate a PNG format image."
+    )
+    parser.add_argument(
+        "--PDF", action="store_true", help="Generate a PDF format image."
+    )
+    parser.add_argument(
+        "--SVG", action="store_true", help="Generate a SVG format image."
+    )
+    parser.add_argument(
+        "--FITS", action="store_true", help="Generate a FITS format image."
+    )
+    parser.add_argument(
+        "--show-sources",
+        action="store_true",
+        help="Show known sources on images (only works on PNG & SVG).",
+    )
+
+    parser.add_argument(
+        "--prior", type=str, default=None, help="Load the from an HDF5 file."
+    )
+    parser.add_argument(
+        "--posterior",
+        type=str,
+        default=None,
+        help="Store the posterior in HDF5 format file.",
+    )
+
+    parser.add_argument("--uv", action="store_true", help="Plot the UV coverage.")
+    parser.add_argument("--mu", action="store_true", help="Save the mean image.")
+    parser.add_argument(
+        "--pcf", action="store_true", help="Save the point covariance function image."
+    )
+    parser.add_argument(
+        "--var", action="store_true", help="Save the pixel variance image."
+    )
+    parser.add_argument(
+        "--nsamples",
+        type=int,
+        default=0,
+        help="Number of samples to save from the posterior.",
+    )
+
+    parser.add_argument(
+        "--title", required=False, default="disko", help="Prefix the output files."
+    )
+
+    source_json = None
+
+    log_fmt = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    logging.basicConfig(format=log_fmt, level=logging.INFO)
+
+    root = logging.getLogger()
+
+    fh = logging.FileHandler("disko.log")
+    # fh.setLevel(logging.INFO)
+
+    # create console handler and set level to debug
+    ch = logging.StreamHandler()
+    # ch.setLevel(logging.INFO)
+
+    # create formatter
+    formatter = logging.Formatter(
+        "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
+    )
+
+    # add formatter to ch
+    fh.setFormatter(formatter)
+
+    # add ch to logger
+    # root.addHandler(ch)
+    root.addHandler(fh)
+
+    # client = Client()
+
+    handle_bayes(parser.parse_args())
+
+    # client.close()
+    # local_cluster.close()

{disko-1.3.0 → disko-1.3.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "disko"
-version = "1.3.0"
+version = "1.3.3"
 description = "Discrete Sky Operator (DiSkO) Aperture Synthesis Radio Imaging"
 authors = [
     {name = "Tim Molteno",email = "tim@elec.ac.nz"}

{disko-1.3.0 → disko-1.3.3}/uv.lock

@@ -370,7 +370,7 @@ wheels = [
 
 [[package]]
 name = "disko"
-version = "1.2.0"
+version = "1.3.0"
 source = { editable = "." }
 dependencies = [
     { name = "dask-ms" },

disko-1.3.0/disko/bayes_cli.py

@@ -1,341 +0,0 @@
-#!/usr/bin/env python
-import matplotlib
-import os
-
-import matplotlib.pyplot as plt
-
-import argparse
-import datetime
-import json
-import logging
-import time
-
-from copy import deepcopy
-
-import numpy as np
-import scipy.special
-
-from tart.operation import settings
-
-from tart_tools import api_imaging
-from tart.imaging import elaz
-from tart.imaging import visibility
-from tart.imaging import calibration
-
-from .disko import DiSkO, vis_to_real
-from .telescope_operator import TelescopeOperator
-
-from .multivariate_gaussian import MultivariateGaussian
-
-from .parser_support import sphere_from_args, sphere_args_parser
-
-logger = logging.getLogger(__name__)
-logger.addHandler(logging.NullHandler()) # Add other handlers if you're using this as a library
-logger.setLevel(logging.INFO)
-
-
-def create_prior(vis_arr, sphere, hdf_prior):
-    ''' Based on the size of the visibilities, try and calculate
-        what range the image should have.
-    '''
-    if hdf_prior is not None:
-        return MultivariateGaussian.from_hdf5(hdf_prior)
-
-    vabs = np.abs(vis_arr)
-
-    p05, p50, p95, p100 = np.percentile(vabs, [5, 50, 95, 100])
-
-    var = p95*p95
-    logger.info("Extimated Sky Prior variance={}".format(var))
-    prior = MultivariateGaussian(np.zeros(sphere.npix) + p50, sigma=p95*np.identity(sphere.npix))
-
-    return prior
-
-
-def do_inference(disko, sphere, prior, sigma_v=None):
-    real_vis = vis_to_real(disko.vis_arr)
-
-    to = TelescopeOperator(disko, sphere)
-
-    # Transform to the natural basis.
-    n_prior =  prior.linear_transform(to.Vh)
-    n_v = real_vis.shape[0]
-
-    # TODO create a proper covariance that ensures the real and imaginary components are linked.
-    if sigma_v is None:
-        diag = np.diag(disko.rms**2)
-    else:
-        diag = np.diag(np.ones(n_v // 2)*(sigma_v)**2)
-
-    logger.info(f"do_inference(sigma_v={diag[0,0]})")
-
-    sigma_vis = np.block([[diag, 0.5*diag],[0.5*diag, diag]]) # .rechunk('auto')
-
-    # now invert sigma_vis
-    sigma_precision = MultivariateGaussian.sp_inv(sigma_vis)
-    del sigma_vis
-
-    if True:
-        prior_r = n_prior.block(0,to.rank)
-        prior_n = n_prior.block(to.rank,to.n_s)
-
-        A_r = to.A_r
-        V = to.V
-
-        del to
-        posterior_r = prior_r.bayes_update(sigma_precision, real_vis, A_r)
-        posterior_n = prior_n
-
-        del A_r
-        del sigma_precision
-        del prior_r
-        del prior_n
-        del n_prior
-
-        posterior = MultivariateGaussian.outer(posterior_r, posterior_n)
-
-        del posterior_r
-        del posterior_n
-
-        logger.info("Transforming posterior")
-
-        posterior = posterior.linear_transform(V)
-                
-        del V
-    else:
-        posterior = to.sequential_inference(n_prior, real_vis, sigma_precision)
-        del to
-        del sigma_precision
-        del n_prior
-
-    return posterior
-
-
-def handle_bayes(ARGS):
-
-    sphere = sphere_from_args(ARGS)
-
-    # Create a prior.
-    if ARGS.file:
-        logger.info("Getting Data from file: {}".format(ARGS.file))
-        # Load data from a JSON file
-        with open(ARGS.file, 'r') as json_file:
-            calib_info = json.load(json_file)
-
-        info = calib_info['info']
-        ant_pos = calib_info['ant_pos']
-        config = settings.from_api_json(info['info'], ant_pos)
-
-        flag_list = [] # [4, 5, 14, 22]
-
-        original_positions = deepcopy(config.get_antenna_positions())
-
-        gains_json = calib_info['gains']
-        gains = np.asarray(gains_json['gain'])
-        phase_offsets = np.asarray(gains_json['phase_offset'])
-        config = settings.from_api_json(info['info'], ant_pos)
-
-        measurements = []
-        for d in calib_info['data']:
-            vis_json, source_json = d
-            cv, timestamp = api_imaging.vis_calibrated(vis_json, config, gains, phase_offsets, flag_list)
-            src_list = elaz.from_json(source_json, 0.0)
-
-        if ARGS.sigma_v is None:
-            raise RuntimeError("The --sigma-v option must be supplied when --file JSON input is used")
-
-        prior = create_prior(cv.v, sphere, ARGS.prior)
-        timestamp = cv.get_timestamp()
-        disko = DiSkO.from_cal_vis(cv)
-
-        posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
-        handle_output(ARGS, timestamp, posterior, sphere, disko)
-
-    elif ARGS.hdf:
-        logger.info(f"Getting data from file {ARGS.hdf}")
-        if ARGS.sigma_v is None:
-            raise RuntimeError("The --sigma-v option must be supplied when HDF5 input is used")
-        
-        data = visibility.from_hdf5(ARGS.hdf)
-        
-        prior = create_prior(data['vis_list'][0].v, sphere, ARGS.prior)
-        posterior = None
-        
-        for v in data['vis_list']:
-            if posterior is not None:
-                prior = posterior
-            cv = calibration.CalibratedVisibility(v)
-            cv.set_config(v.config)
-            cv.set_phase_offset(list(range(cv.get_config().get_num_antenna())),np.array(data['phase_offset']))
-            cv.set_gain(list(range(cv.get_config().get_num_antenna())),np.array(data['gain']))
-            timestamp = cv.get_timestamp()
-            disko = DiSkO.from_cal_vis(cv)
-
-            # TODO Calibrate the vis with gains and phases?
-            posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
-            handle_output(ARGS, timestamp, posterior, sphere, disko)
-    else:
-        logger.info("Getting Data from MS file: {}".format(ARGS.ms))
-
-        disko = DiSkO.from_ms(ARGS.ms, ARGS.nvis, res_arcmin=sphere.res_arcmin, channel=ARGS.channel, field_id=ARGS.field)
-        # Convert from reduced Julian Date to timestamp.
-        timestamp = disko.timestamp
-        src_list = None
-        
-        prior = create_prior(disko.vis_arr, sphere, ARGS.prior)
-            
-        posterior = do_inference(disko, sphere, prior, sigma_v=ARGS.sigma_v)
-        handle_output(ARGS, timestamp, posterior, sphere, disko)
-        
-
-def handle_output(ARGS, timestamp, posterior, sphere, disko=None):
-
-    if not ARGS.show_sources:
-        src_list = None
-
-    time_repr = "{:%Y_%m_%d_%H_%M_%S_%Z}".format(timestamp)
-
-    # Now save the files.
-    if ARGS.posterior is not None:
-        posterior.to_hdf5(ARGS.posterior)
-
-    def path(ending, image_title):
-        os.makedirs(ARGS.dir, exist_ok=True)
-        fname = '{}.{}'.format(image_title, ending)
-        return os.path.join(ARGS.dir, fname)
-
-    def save_images(image_title, source_list):
-        # Save as a FITS file
-
-        if ARGS.FITS:
-            sphere.to_fits(fname=path('fits', image_title), fov=ARGS.fov, info=disko.info)
-        
-        if ARGS.SVG:
-            fname = path('svg', image_title)
-            sphere.to_svg(fname=fname, show_grid=True, src_list=source_list, fov=ARGS.fov, title=image_title, show_cbar=True)
-            logger.info("Generating {}".format(fname))
-        if ARGS.PNG:
-            fname = path('png', image_title)
-            sphere.plot(plt, source_list)
-            plt.title(image_title)
-            plt.tight_layout()
-            plt.savefig(fname, dpi=300)
-            plt.close()
-            logger.info("Generating {}".format(fname))
-        if ARGS.PDF:
-            fname = path('pdf', image_title)
-            sphere.plot(plt, source_list)
-            plt.title(image_title)
-            plt.savefig(fname, dpi=600)
-            plt.close()
-            logger.info("Generating {}".format(fname))
-
-    if ARGS.PDF or ARGS.PNG or ARGS.SVG or ARGS.FITS: 
-
-
-        if ARGS.mu:
-            logger.info("Computing pixels")
-            tic = time.perf_counter()    
-            #mu_positive = np.array(da.clip(posterior.mu, 0, None))
-            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
-            stat = sphere.set_visible_pixels(np.array(posterior.mu), scale=False)
-            stat['sigma-v'] = ARGS.sigma_v
-            logger.info(json.dumps(stat, sort_keys=True))
-            save_images('{}_{}_mu'.format(ARGS.title, time_repr), source_list=src_list)
-
-        if ARGS.var:
-            tic = time.perf_counter()    
-            logger.info("Computing variance...")
-            variance = np.array(posterior.variance())
-            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
-            sphere.set_visible_pixels(variance, scale=False)
-            save_images('{}_{}_var'.format(ARGS.title, time_repr), source_list=None)
-        
-        if ARGS.pcf:
-            tic = time.perf_counter()    
-            logger.info("Computing point covariance...")
-            
-            brightest_pixel = np.argmax(posterior.mu)
-            pix_cov=np.array(posterior.sigma()[brightest_pixel,:])
-            logger.info(f"    Took {time.perf_counter() - tic:0.4f} seconds")
-
-            sphere.set_visible_pixels(pix_cov, scale=False)
-            save_images('{}_{}_pcf'.format(ARGS.title, time_repr), source_list=None)
-
-        for i in range(ARGS.nsamples):
-            sphere.set_visible_pixels(posterior.sample(), scale=False)
-            save_images(image_title = '{}_{}_s{:0>5}'.format(ARGS.title, time_repr, i), source_list=None)
-
-
-def main():
-    np.random.seed(42)
-    sphere_parsers = sphere_args_parser()
-
-    parser = argparse.ArgumentParser(
-        description='DiSkO: Bayesian inference of a posterior sky',
-        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
-        parents=sphere_parsers)
-
-
-    parser.add_argument('--hdf', required=False, default=None, help="Exported Multi-visibility file")
-    parser.add_argument('--ms', required=False, default=None, help="visibility file")
-    parser.add_argument('--file', required=False, default=None, help="Snapshot observation saved JSON file (visiblities, positions and more).")
-    
-    
-    parser.add_argument('--channel', type=int, default=0, help="Use this frequency channel.")
-    parser.add_argument('--field', type=int, default=0, help="Use this FIELD_ID from the measurement set.")
-
-    parser.add_argument('--dir', required=False, default='.', help="Output directory.")
-    parser.add_argument('--nvis', type=int, default=1000, help="Number of visibilities to use.")
-    parser.add_argument('--arcmin', type=float, default=None, help="Highest allowed res of the sky in arc minutes.")
-
-    parser.add_argument('--sigma-v', type=float, default=None, help="Diagonal components of the visibility covariance. If not supplied use measurement set values")
-
-    parser.add_argument('--PNG', action="store_true", help="Generate a PNG format image.")
-    parser.add_argument('--PDF', action="store_true", help="Generate a PDF format image.")
-    parser.add_argument('--SVG', action="store_true", help="Generate a SVG format image.")
-    parser.add_argument('--FITS', action="store_true", help="Generate a FITS format image.")
-    parser.add_argument('--show-sources', action="store_true", help="Show known sources on images (only works on PNG & SVG).")
-
-    parser.add_argument('--prior', type=str, default=None, help="Load the from an HDF5 file.")
-    parser.add_argument('--posterior', type=str, default=None, help="Store the posterior in HDF5 format file.")
-
-    parser.add_argument('--uv', action="store_true", help="Plot the UV coverage.")
-    parser.add_argument('--mu', action="store_true", help="Save the mean image.")
-    parser.add_argument('--pcf', action="store_true", help="Save the point covariance function image.")
-    parser.add_argument('--var', action="store_true", help="Save the pixel variance image.")
-    parser.add_argument('--nsamples', type=int, default=0, help="Number of samples to save from the posterior.")
-
-    parser.add_argument('--title', required=False, default="disko", help="Prefix the output files.")
-
-    source_json = None
-
-
-    log_fmt = '%(asctime)s - %(name)s - %(levelname)s - %(message)s'
-    logging.basicConfig(format=log_fmt, level=logging.INFO)
-
-    root = logging.getLogger()
-    
-    fh = logging.FileHandler('disko.log')
-    #fh.setLevel(logging.INFO)
-    
-    # create console handler and set level to debug
-    ch = logging.StreamHandler()
-    #ch.setLevel(logging.INFO)
-
-    # create formatter
-    formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
-
-    # add formatter to ch
-    fh.setFormatter(formatter)
-
-    # add ch to logger
-    #root.addHandler(ch)
-    root.addHandler(fh)
-
-    #client = Client()
-
-    handle_bayes(parser.parse_args())
-
-    #client.close()
-    #local_cluster.close()