Update for new deps (#80)

* Version bumps

* Bump verions

* Fix beamcon API

* Flag the rms!!

* Fix prefect verions

* Bump versions

* Bump racs-tools

* API fixes

* Bump racs-tools

Author: AlecThomson

arrakis/imager.py

@@ -580,14 +580,31 @@ def make_cube(
     logger = get_run_logger()
 
     logger.info(f"Creating cube for {pol=} {image_set.ms=}")
-    image_list = image_set.image_lists[pol]
+    image_list = [Path(i) for i in image_set.image_lists[pol]]
 
     image_type = "restored" if aux_mode is None else aux_mode
 
+    # Create a cube name
+    old_name = image_list[0]
+    out_dir = os.path.dirname(old_name)
+    old_base = os.path.basename(old_name)
+    new_base = old_base
+    b_idx = new_base.find("beam") + len("beam") + 2
+    sub = new_base[b_idx:]
+    new_base = new_base.replace(sub, ".conv.fits")
+    new_base = new_base.replace("image", f"image.{image_type}.{pol.lower()}")
+    new_name = Path(out_dir) / new_base
+
     # First combine images into cubes
-    hdu_list, freqs = combine_fits(file_list=image_list, create_blanks=True)
-    new_header = hdu_list[0].header
-    data_cube = hdu_list[0].data
+    _ = combine_fits(
+        file_list=image_list,
+        out_cube=new_name,
+        create_blanks=True,
+        overwrite=True,
+    )
+    with fits.open(new_name, mode="denywrite", memmap=True) as hdu_list:
+        new_header = hdu_list[0].header
+        data_cube = hdu_list[0].data
 
     # Add pol angle to header
     new_header["INSTRUMENT_RECEPTOR_ANGLE"] = (
@@ -610,16 +627,6 @@ def make_cube(
     # Calculate rms noise
     rmss_arr = mad_std(data_cube, axis=(1, 2, 3), ignore_nan=True)
 
-    # Create a cube name
-    old_name = image_list[0]
-    out_dir = os.path.dirname(old_name)
-    old_base = os.path.basename(old_name)
-    new_base = old_base
-    b_idx = new_base.find("beam") + len("beam") + 2
-    sub = new_base[b_idx:]
-    new_base = new_base.replace(sub, ".conv.fits")
-    new_base = new_base.replace("image", f"image.{image_type}.{pol.lower()}")
-    new_name = os.path.join(out_dir, new_base)
     # Deserialise beam
     with open(common_beam_pkl, "rb") as f:
         common_beam = pickle.load(f)
@@ -633,9 +640,9 @@ def make_cube(
     # 0 1234.5
     # 1 6789.0
     # etc.
-    new_w_name = new_name.replace(
-        f"image.{image_type}", f"weights.{image_type}"
-    ).replace(".fits", ".txt")
+    new_w_name = Path(
+        new_name.as_posix().replace(f"image.{image_type}", f"weights.{image_type}")
+    ).with_suffix(".txt")
     data = dict(
         Channel=np.arange(len(rmss_arr)),
         Weight=1 / rmss_arr**2,  # Want inverse variance
@@ -673,8 +680,26 @@ def get_beam(image_set: ImageSet, cutoff: Optional[float]) -> Path:
 
     # Create a unique hash for the beam log filename
     image_hash = hashlib.md5("".join(image_list).encode()).hexdigest()
+    try:
+        common_beam, _ = beamcon_2D.get_common_beam(files=image_list, cutoff=cutoff)
+    except Exception as e:
+        import traceback
+        import sys
+
+        tbe = traceback.TracebackException.from_exception(e)
+        logger.error(f"Local {''.join(tbe.format())}")
+        f = sys.exc_info()[2].tb_frame
+        f = f.f_back
+        while f is not None:
+            tbe.stack.append(
+                traceback.FrameSummary(
+                    f.f_code.co_filename, f.f_lineno, f.f_code.co_name
+                )
+            )
+            f = f.f_back
 
-    common_beam, _ = beamcon_2D.getmaxbeam(files=image_list, cutoff=cutoff)
+        logger.error(f"Full {''.join(tbe.format())}")
+        raise e
 
     logger.info(f"The common beam is: {common_beam=}")
 
@@ -740,8 +765,8 @@ def smooth_imageset(
             for img in pol_images:
                 logger.info(f"Smoothing {img}")
                 last_result = executor.submit(
-                    beamcon_2D.worker,
-                    file=img,
+                    beamcon_2D.beamcon_2d_on_fits,
+                    file=Path(img),
                     outdir=None,
                     new_beam=common_beam,
                     conv_mode="robust",

arrakis/linmos.py

@@ -123,21 +123,18 @@ def smooth_images(
     """
     smooth_dict: Dict[str, ImagePaths] = {}
     for stoke, image_list in image_dict.items():
-        infiles: List[str] = []
+        infiles: List[Path] = []
         for im in image_list.images:
             if im.suffix == ".fits":
-                infiles.append(im.resolve().as_posix())
-        datadict = beamcon_3D.main(
-            infile=[im.resolve().as_posix() for im in image_list.images],
+                infiles.append(im.resolve())
+        _, _, output_files = beamcon_3D.smooth_fits_cube(
+            infiles_list=infiles,
             uselogs=False,
             mode="total",
             conv_mode="robust",
             suffix="cres",
         )
-        smooth_files: List[Path] = []
-        for key, val in datadict.items():
-            smooth_files.append(Path(val["outfile"]))
-        smooth_dict[stoke] = ImagePaths(smooth_files, image_list.weights)
+        smooth_dict[stoke] = ImagePaths(output_files, image_list.weights)
 
     return smooth_dict
 

arrakis/rmsynth_oncuts.py

@@ -359,10 +359,15 @@ def sigma_clip_spectra(
     for spectrum in stokes_spectra:
         filtered_data = spectrum.data.copy()
         filtered_data[filter_idx] = np.nan
+        filtered_rms = spectrum.rms.copy()
+        # Set the RMS to NaN where the data is NaN!
+        filtered_rms[filter_idx] = np.nan
+        filtered_bkg = spectrum.bkg.copy()
+        filtered_bkg[filter_idx] = np.nan
         filtered_spectrum = Spectrum(
             data=filtered_data,
-            rms=spectrum.rms,
-            bkg=spectrum.bkg,
+            rms=filtered_rms,
+            bkg=filtered_bkg,
             filename=spectrum.filename,
             header=spectrum.header,
         )

pyproject.toml

@@ -34,7 +34,7 @@ dask = "*"
 distributed = {git="https://github.com/AlecThomson/distributed", branch="drainclose"}
 dask_jobqueue = {version=">=0.8.3", optional=true}
 dask_mpi = "*"
-FRion = ">=1.1.3"
+FRion = ">=1.1.4"
 h5py = "*"
 ipython = "*"
 matplotlib = ">=3.8"
@@ -46,9 +46,9 @@ pymongo = "*"
 pymultinest = "*"
 pytest = "*"
 python_casacore = "*"
-RACS-tools = ">=3.0.5"
+RACS-tools = ">=4.1.2"
 radio_beam = "*"
-RMextract = {git = "https://github.com/lofar-astron/RMextract", optional=true}
+RMextract = ">=0.5.1"
 schwimmbad = "*"
 scipy = "*"
 spectral_cube = ">=0.6.3"
@@ -57,14 +57,13 @@ tqdm = "*"
 vorbin = "*"
 graphviz = "*"
 bokeh = "<3"
-prefect = ">=2"
-prefect-dask = "*"
+prefect = {version=">=2,<3", extras=["dask"]}
 RMTable = ">=1.2.1"
 RM-Tools = ">=1.4.2"
 PolSpectra = ">=1.1.0"
 setuptools = "*"
-fixms = ">=0.2.6"
-fitscube = ">=0.3"
+fixms = ">=0.3.3"
+fitscube = ">=0.5.4"
 psycopg2-binary = "*"
 sqlalchemy = "*"
 scikit-image = ">=0.23"