Checks to cube convolution and linmos (#176)

* added execuutor type for convolve_cube

* added comment to astropy version/broke convolve test up

* added specific git commit to pyproject

---------

Co-authored-by: tgalvin <[email protected]>

flint/convol.py

@@ -7,7 +7,7 @@
 import warnings
 from argparse import ArgumentParser
 from pathlib import Path
-from typing import Collection, List, NamedTuple, Optional
+from typing import Collection, List, Literal, NamedTuple, Optional
 
 import astropy.units as u
 import numpy as np
@@ -131,6 +131,7 @@ def convolve_cubes(
     beam_shapes: List[BeamShape],
     cutoff: Optional[float] = None,
     convol_suffix: str = "conv",
+    executor_type: Literal["thread", "process", "mpi"] = "thread",
 ) -> Collection[Path]:
     logger.info(f"Will attempt to convol {len(cube_paths)} cubes")
     if cutoff:
@@ -155,6 +156,7 @@ def convolve_cubes(
         bmin=beam_minor_list,
         bpa=beam_pa_list,
         suffix=convol_suffix,
+        executor_type=executor_type,
     )
 
     # Construct the name of the new file created. For the moment this is done

pyproject.toml

@@ -17,7 +17,7 @@ include = [
 
 [tool.poetry.dependencies]
 python = "^3.11"
-astropy = "6.1.0"
+astropy = "6.1.3" # fixing until units change in 6.1.4 addressed in radio-beam
 numpy = "^1.26.0"
 python-casacore = "3.5.2" # newer version caused MS errors (maybe related to pre-built wheel)
 pydantic = "2.8.2" # version 2.9.0 caused prefect model validation error
@@ -28,7 +28,7 @@ matplotlib = "*"
 prefect = "^2.10.0"
 prefect-dask = "^0.2.4"
 dask-jobqueue = "*"
-RACS-tools = "*"
+RACS-tools = { git = "https://github.com/AlecThomson/RACS-tools.git@8e5d919e9938eda19fc7b8a915f855e8b8e0e514" } # allows array of beam shapes in beamcon_3D
 aegeantools = "2.3.0"
 radio-beam = "^0.3.4"
 reproject = "*"

tests/test_convol.py

@@ -67,9 +67,139 @@ def test_get_cube_common_beam_and_convol_cubes(cube_fits) -> None:
     assert len(beam_list) == data_shape[0]
     assert all([isinstance(b, BeamShape) for b in beam_list])
 
+
+def test_beam_list_convol(cube_fits):
+    # These come from the beam_list above
+    bmaj_arcsec = [
+        14.7,
+        14.5,
+        14.3,
+        14.2,
+        14.0,
+        13.8,
+        13.8,
+        13.5,
+        13.4,
+        32.9,
+        float("nan"),
+        147.5,
+        13.0,
+        12.9,
+        12.9,
+        12.8,
+        12.7,
+        13.0,
+        40.7,
+        12.7,
+        12.3,
+        12.3,
+        12.2,
+        12.1,
+        12.0,
+        11.9,
+        11.9,
+        11.6,
+        11.4,
+        11.6,
+        11.6,
+        11.5,
+        11.4,
+        11.4,
+        11.4,
+        11.3,
+    ]
+    bmin_arcsec = [
+        12.4,
+        12.2,
+        12.1,
+        12.0,
+        11.8,
+        11.7,
+        11.7,
+        11.6,
+        11.4,
+        16.2,
+        float("nan"),
+        63.7,
+        11.0,
+        10.9,
+        10.8,
+        10.7,
+        10.6,
+        10.8,
+        16.6,
+        10.6,
+        10.3,
+        10.2,
+        10.1,
+        10.0,
+        9.9,
+        9.9,
+        9.8,
+        9.7,
+        9.3,
+        9.6,
+        9.5,
+        9.4,
+        9.4,
+        9.3,
+        9.2,
+        9.2,
+    ]
+    bpa_deg = [
+        75.25,
+        75.02,
+        74.82,
+        74.82,
+        75.0,
+        75.01,
+        75.33,
+        76.03,
+        75.43,
+        -21.79,
+        float("nan"),
+        160.53,
+        73.28,
+        73.22,
+        76.36,
+        76.14,
+        76.07,
+        74.09,
+        55.61,
+        76.84,
+        75.9,
+        75.76,
+        75.96,
+        75.1,
+        75.76,
+        75.65,
+        75.66,
+        73.47,
+        71.63,
+        75.29,
+        75.35,
+        75.69,
+        75.11,
+        75.78,
+        75.84,
+        75.89,
+    ]
+
+    beam_list = [
+        BeamShape(bmaj_arcsec=bmaj, bmin_arcsec=bmin, bpa_deg=bpa)
+        for bmaj, bmin, bpa in zip(bmaj_arcsec, bmin_arcsec, bpa_deg)
+    ]
+
+    fits_files = list(cube_fits.glob("*sub.fits"))
+    assert len(fits_files) == 10
     # This appears to make pytest lock up
-    # cube_paths = convolve_cubes(
-    #     cube_paths=fits_files, beam_shapes=beam_list, cutoff=150.0
-    # )
-    # assert all([isinstance(p, Path) for p in cube_paths])
-    # assert all([p.exists() for p in cube_paths])
+    from flint.convol import convolve_cubes
+
+    cube_paths = convolve_cubes(
+        cube_paths=fits_files,
+        beam_shapes=beam_list,
+        cutoff=150.0,
+        executor_type="process",
+    )
+    assert all([isinstance(p, Path) for p in cube_paths])
+    assert all([p.exists() for p in cube_paths])