Merge pull request #147 from transientskp/Fix_143

Settles part of the discussion from #143 that we want to settle.

Author: HannoSpreeuw

pyproject.toml

@@ -91,6 +91,7 @@ extend-exclude ='''
 '''
 
 [tool.mypy]
+python_version = "3.12"
 ignore_missing_imports = true
 check_untyped_defs = true
 files = "sourcefinder"

sourcefinder/accessors/casaimage.py

@@ -4,6 +4,7 @@
 
 from casacore.tables import table as casacore_table
 
+from sourcefinder.utils import is_valid_beam_tuple
 from sourcefinder.accessors.dataaccessor import DataAccessor
 from sourcefinder.utility.coordinates import WCS
 from sourcefinder.utility.coordinates import mjd2datetime
@@ -48,12 +49,15 @@ def __init__(self, url, plane=0, beam=None):
         self.freq_eff, self.freq_bw = self.parse_frequency(table)
         self.pixelsize = self.parse_pixelsize()
 
-        if beam:
-            (bmaj, bmin, bpa) = beam
-        else:
-            bmaj, bmin, bpa = self.parse_beam(table)
-        self.beam = self.degrees2pixels(bmaj, bmin, bpa, self.pixelsize[0],
-                                        self.pixelsize[1])
+        if is_valid_beam_tuple(beam) or not is_valid_beam_tuple(self.beam):
+            # An argument-supplied beam overrides a beam derived from
+            # (bmaj, bmin, bpa) in a config.toml. Only if those two options
+            # are not specified, we parse the beam from the header.
+            bmaj, bmin, bpa = beam if is_valid_beam_tuple(beam) else (
+                self.parse_beam(table))
+            self.beam = self.degrees2pixels(
+                bmaj, bmin, bpa, self.pixelsize[0], self.pixelsize[1]
+            )
 
     def parse_data(self, table, plane=0):
         """

sourcefinder/accessors/dataaccessor.py

@@ -1,9 +1,12 @@
 import logging
 
-import numpy
+import numpy as np
 from math import degrees, sqrt, sin, pi, cos
-from dataclasses import dataclass
+from dataclasses import dataclass, field
+from sourcefinder.utils import is_valid_beam_tuple
 from sourcefinder.utility.coordinates import WCS
+from sourcefinder.config import ImgConf
+from typing import Optional, cast
 
 logger = logging.getLogger(__name__)
 
@@ -16,7 +19,7 @@ class DataAccessor:
     Data accessors provide a uniform way for the ImageData class (i.e.,
     generic image representation) to access the various ways in which
     images may be stored (FITS files, arrays in memory, potentially HDF5,
-    etc).
+    etc.).
     
     This class cannot be instantiated directly, but should be subclassed
     and the abstract properties provided. Note that all abstract
@@ -66,17 +69,26 @@ class DataAccessor:
     provides key info in a simple dict format.
     """
 
-    beam: tuple
     centre_ra: float
     centre_decl: float
-    data: numpy.ndarray
+    data: np.ndarray
     freq_bw: float
     freq_eff: float
     pixelsize: tuple
     tau_time: float
     taustart_ts: float
     url: str
     wcs: WCS
+    beam: Optional[tuple[float, float, float]] = field(default=None)
+    conf: Optional[ImgConf] = field(default=None, repr=False)
+
+    def __post_init__(self):
+        if self.conf is not None:
+            beam_tuple = (self.conf.bmaj, self.conf.bmin, self.conf.bpa)
+            if is_valid_beam_tuple(beam_tuple):
+                deltax, deltay = self.pixelsize
+                self.beam = DataAccessor.degrees2pixels(*beam_tuple,
+                                                        deltax, deltay)
 
     def extract_metadata(self) -> dict:
         """
@@ -94,22 +106,30 @@ def extract_metadata(self) -> dict:
             A dictionary containing key-value pairs of class attributes
             formatted for database storage.
         """
-        return {
+        metadata = {
             'tau_time': self.tau_time,
             'freq_eff': self.freq_eff,
             'freq_bw': self.freq_bw,
             'taustart_ts': self.taustart_ts,
             'url': self.url,
-            'beam_smaj_pix': self.beam[0],
-            'beam_smin_pix': self.beam[1],
-            'beam_pa_rad': self.beam[2],
             'centre_ra': self.centre_ra,
             'centre_decl': self.centre_decl,
             'deltax': self.pixelsize[0],
             'deltay': self.pixelsize[1],
         }
 
-    def parse_pixelsize(self):
+
+        if is_valid_beam_tuple(self.beam):
+            beam = cast(tuple[float, float, float], self.beam)
+            metadata.update({
+                'beam_smaj_pix': beam[0],
+                'beam_smin_pix': beam[1],
+                'beam_pa_rad': beam[2],
+            })
+
+        return metadata
+
+    def parse_pixelsize(self) -> tuple[float, float]:
         """
         Returns
         -------
@@ -141,7 +161,8 @@ def parse_pixelsize(self):
         return deltax, deltay
 
     @staticmethod
-    def degrees2pixels(bmaj, bmin, bpa, deltax, deltay):
+    def degrees2pixels(bmaj, bmin, bpa, deltax, deltay) -> (
+            tuple)[float, float, float]:
         """
         Convert beam in degrees to beam in pixels and radians.
         For example, FITS beam parameters are in degrees.
@@ -161,12 +182,14 @@ def degrees2pixels(bmaj, bmin, bpa, deltax, deltay):
 
         Returns
         -------
-        semimaj : float
-            Beam semi-major axis in pixels.
-        semimin : float
-            Beam semi-minor axis in pixels.
-        theta : float
-            Beam position angle in radians.
+        tuple
+            A tuple containing:
+            - semimaj : float
+                Beam semi-major axis in pixels.
+            - semimin : float
+                Beam semi-minor axis in pixels.
+            - theta : float
+                Beam position angle in radians.
         """
         theta = pi * bpa / 180
         semimaj = (bmaj / 2.) * (sqrt(

sourcefinder/accessors/fitsimage.py

@@ -7,6 +7,7 @@
 
 import astropy.io.fits as pyfits
 
+from sourcefinder.utils import is_valid_beam_tuple
 from sourcefinder.accessors.dataaccessor import DataAccessor
 from sourcefinder.utility.coordinates import WCS
 
@@ -41,13 +42,17 @@ def __init__(self, url, plane=None, beam=None, hdu_index=0):
         self.taustart_ts, self.tau_time = self.parse_times()
         self.freq_eff, self.freq_bw = self.parse_frequency()
         self.pixelsize = self.parse_pixelsize()
-        if beam:
-            (bmaj, bmin, bpa) = beam
-        else:
-            (bmaj, bmin, bpa) = self.parse_beam()
-        self.beam = self.degrees2pixels(
-            bmaj, bmin, bpa, self.pixelsize[0], self.pixelsize[1]
-        )
+
+        if is_valid_beam_tuple(beam) or not is_valid_beam_tuple(self.beam):
+            # An argument-supplied beam overrides a beam derived from
+            # (bmaj, bmin, bpa) in a config.toml. Only if those two options
+            # are not specified, we parse the beam from the header.
+            bmaj, bmin, bpa = beam if is_valid_beam_tuple(beam) else (
+                self.parse_beam())
+            self.beam = self.degrees2pixels(
+                bmaj, bmin, bpa, self.pixelsize[0], self.pixelsize[1]
+            )
+
         self.centre_ra, self.centre_decl = self.calculate_phase_centre()
 
         # Bonus attribute

sourcefinder/accessors/fitsimageblob.py

@@ -2,6 +2,7 @@
 
 import numpy
 
+from sourcefinder.utils import is_valid_beam_tuple
 from sourcefinder.accessors.fitsimage import FitsImage
 
 logger = logging.getLogger(__name__)
@@ -40,13 +41,16 @@ def __init__(self, hdulist, plane=None, beam=None, hdu_index=0):
                    self.freq_eff, self.freq_bw
         self.url = "_".join([str(x) for x in elements])
 
-        if beam:
-            (bmaj, bmin, bpa) = beam
-        else:
-            (bmaj, bmin, bpa) = self.parse_beam()
-        self.beam = self.degrees2pixels(
-            bmaj, bmin, bpa, self.pixelsize[0], self.pixelsize[1]
-        )
+        if is_valid_beam_tuple(beam) or not is_valid_beam_tuple(self.beam):
+            # An argument-supplied beam overrides a beam derived from
+            # (bmaj, bmin, bpa) in a config.toml. Only if those two options
+            # are not specified, we parse the beam from the header.
+            bmaj, bmin, bpa = beam if is_valid_beam_tuple(beam) else (
+                self.parse_beam())
+            self.beam = self.degrees2pixels(
+                bmaj, bmin, bpa, self.pixelsize[0], self.pixelsize[1]
+            )
+
         self.centre_ra, self.centre_decl = self.calculate_phase_centre()
 
         # Bonus attribute

sourcefinder/image.py

@@ -88,9 +88,17 @@ def __init__(self, data, beam, wcs, conf: Conf = Conf(image=ImgConf(),
         # single precision is good enough in all cases.
         self.rawdata = np.ascontiguousarray(data, dtype=np.float32)
         self.wcs = wcs  # a utility.coordinates.wcs instance
-        self.beam = beam  # tuple of (semimaj, semimin, theta) with semimaj and
-        # semimin in pixel coordinates and theta, the position angle, in
-        # radians.
+
+        if utils.is_valid_beam_tuple(beam):
+            self.beam = beam # tuple of (semimaj, semimin, theta) with
+            # semimaj and semimin in pixel coordinates and theta, the position
+            # angle, in radians.
+        else:
+            raise ValueError(("Partial beam specification: one or more of "
+                              "(bmaj, bmin, bpa) are not specified, "
+                              "adequately, image processing is not possible.",
+                              RuntimeWarning))
+
         # These three quantities are only dependent on the beam, so should be
         # calculated once the beam is known and not for each source separately.
         self.fudge_max_pix_factor = utils.fudge_max_pix(beam[0], beam[1],

sourcefinder/utils.py

@@ -4,6 +4,7 @@
 
 import math
 import numpy as np
+from numbers import Real
 import scipy.integrate
 from scipy.ndimage import distance_transform_edt
 
@@ -204,6 +205,12 @@ def generate_result_maps(data, sourcelist):
 
     return gaussian_map, residual_map
 
+def is_valid_beam_tuple(b) -> bool:
+    return (
+            isinstance(b, tuple)
+            and len(b) == 3
+            and all(isinstance(x, Real) and x is not None for x in b)
+    )
 
 def calculate_correlation_lengths(semimajor, semiminor):
     """Calculate the Condon correlation lengths.