Merge pull request #178 from transientskp/Fix_172

Fix 172

Author: HannoSpreeuw

sourcefinder/extract.py

@@ -18,7 +18,7 @@
 )
 from sourcefinder.utility import coordinates
 from sourcefinder.utility.uncertain import Uncertain
-from . import measuring
+from . import measure
 from . import utils
 from .config import Conf, ImgConf
 from .gaussian import gaussian
@@ -812,18 +812,11 @@ def _error_bars_from_moments(self, noise, correlation_lengths, threshold):
         if errortheta > np.pi / 2.0:
             errortheta = np.pi / 2.0
 
-        # The peak from "moments" is just the value of the maximum pixel
-        # times a correction, fudge_max_pix, for the fact that the
-        # centre of the Gaussian is not at the centre of the pixel.
-        # This correction is performed in measuring.py. The maximum pixel
-        # method introduces a peak dependent error corresponding to the last
-        # term in the expression below for errorpeaksq.
-        # To this, we add, in quadrature, the errors corresponding
-        # to the first and last term of the rhs of equation 37 of the
-        # NVSS paper. The middle term in that equation 37 is heuristically
-        # replaced by noise**2 since the threshold should not affect
-        # the error from the (corrected) maximum pixel method,
-        # while it is part of the expression for rho_sq above.
+        # Basically, this is equation 37 of the NVSS paper, with the middle
+        # term of the rhs of that equation heuristically replaced by
+        # noise**2 since the threshold is not expected to affect the error
+        # on peak brightnesses from tweaked moments, while it is part of the
+        # expression for rho_sq above.
         errorpeaksq = (
             (frac_flux_cal_error * peak) ** 2 + clean_bias_error**2 + noise**2
         )
@@ -1105,7 +1098,7 @@ def source_profile_and_errors(
             # Moments can only be computed if no parameters are fixed.
             try:
                 param.update(
-                    measuring.moments(
+                    measure.moments(
                         data,
                         fudge_max_pix_factor,
                         beam,
@@ -1122,7 +1115,7 @@ def source_profile_and_errors(
             except ValueError:
                 logger.warning("Moments computations failed, use defaults.")
         try:
-            gaussian_soln = measuring.fitgaussian(
+            gaussian_soln = measure.fitgaussian(
                 data, param, fixed=fixed, bounds=param.bounds
             )
             param.update(gaussian_soln)
@@ -1173,7 +1166,7 @@ def source_profile_and_errors(
         gauss_island_filled = gauss_island_masked
         gauss_resid_filled = gauss_resid_masked
 
-    param.chisq, param.reduced_chisq = measuring.goodness_of_fit(
+    param.chisq, param.reduced_chisq = measure.goodness_of_fit(
         gauss_resid_masked, rms, correlation_lengths
     )
 
@@ -2307,7 +2300,7 @@ def source_measurements_vectorised(
     # array. In this way Numba can infer the shape of the output array.
     with np.errstate(invalid="ignore"):
         # Context manager added to fix issue #165.
-        measuring.moments_enhanced(
+        measure.moments_enhanced(
             sources,
             noises,
             chunk_positions,

sourcefinder/measuring.py sourcefinder/measure.pysourcefinder/measuring.py renamed to sourcefinder/measure.py

@@ -757,10 +757,10 @@ def moments_enhanced(
         errortheta = np.pi / 2.0
 
     # This should reflect the equivalent of equation 37 of the NVSS paper for
-    # moments calculations. The middle term in that equation 37 is heuristically
-    # replaced by noise**2 since the threshold should not affect the error from
-    # the (corrected) maximum pixel method, while it is part of the expression
-    # for rho_sq above.
+    # moments calculations. The middle term of the rhs of that equation is
+    # heuristically replaced by noise**2 since the threshold is not expected to
+    # affect the error on peak brightnesses from tweaked moments, while it
+    # is part of the expression for rho_sq above.
     errorpeaksq = (
         (frac_flux_cal_error * peak) ** 2 + clean_bias_error**2 + noise**2
     )

test/test_FDR.py

@@ -40,16 +40,16 @@
 
 from sourcefinder import accessors
 from sourcefinder.config import Conf, ImgConf
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 from sourcefinder.testutil.decorators import requires_data, duration
 
 from sourcefinder import image
 
 NUMBER_INSERTED = float(3969)
 
-uncorr_path = os.path.join(DATAPATH, 'uncorrelated_noise.fits')
-corr_path = os.path.join(DATAPATH, 'correlated_noise.fits')
-deconv_path = os.path.join(DATAPATH, 'deconvolved.fits')
+uncorr_path = os.path.join(DATAPATH, "uncorrelated_noise.fits")
+corr_path = os.path.join(DATAPATH, "correlated_noise.fits")
+deconv_path = os.path.join(DATAPATH, "deconvolved.fits")
 
 
 @requires_data(uncorr_path)
@@ -108,22 +108,29 @@ def test_normal(self):
 
     def test_alpha0_1(self):
         self.number_alpha_10pc = len(
-            self.image_with_sources.fd_extract(alpha=0.1))
-        self.assertTrue((self.number_alpha_10pc - NUMBER_INSERTED) /
-                        NUMBER_INSERTED < 0.1)
+            self.image_with_sources.fd_extract(alpha=0.1)
+        )
+        self.assertTrue(
+            (self.number_alpha_10pc - NUMBER_INSERTED) / NUMBER_INSERTED < 0.1
+        )
 
     def test_alpha0_01(self):
         self.number_alpha_1pc = len(
-            self.image_with_sources.fd_extract(alpha=0.01))
-        self.assertTrue((self.number_alpha_1pc - NUMBER_INSERTED) /
-                        NUMBER_INSERTED < 0.01)
+            self.image_with_sources.fd_extract(alpha=0.01)
+        )
+        self.assertTrue(
+            (self.number_alpha_1pc - NUMBER_INSERTED) / NUMBER_INSERTED < 0.01
+        )
 
     def test_alpha0_001(self):
         self.number_alpha_point1pc = len(
-            self.image_with_sources.fd_extract(alpha=0.001))
-        self.assertTrue((self.number_alpha_point1pc - NUMBER_INSERTED) /
-                        NUMBER_INSERTED < 0.001)
+            self.image_with_sources.fd_extract(alpha=0.001)
+        )
+        self.assertTrue(
+            (self.number_alpha_point1pc - NUMBER_INSERTED) / NUMBER_INSERTED
+            < 0.001
+        )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     unittest.main()

test/test_L15_12h_const.py

@@ -4,7 +4,7 @@
 import os
 import unittest
 
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 from sourcefinder.testutil.decorators import requires_data
 
 import sourcefinder.accessors.fitsimage

test/test_aartfaaccasatable.py

@@ -6,10 +6,10 @@
 from sourcefinder.accessors.aartfaaccasaimage import AartfaacCasaImage
 from sourcefinder.testutil.decorators import requires_data
 from sourcefinder.utility.coordinates import angsep
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
 
-casatable = os.path.join(DATAPATH, 'accessors/aartfaac.table')
+casatable = os.path.join(DATAPATH, "accessors/aartfaac.table")
 
 
 class TestAartfaacCasaImage(unittest.TestCase):
@@ -51,11 +51,14 @@ def test_pix_scale(self):
         p2_pix = (p1_pix[0], p1_pix[1] + pixel_sep)
         p2_sky = self.accessor.wcs.p2s(p2_pix)
 
-        coord_dist_deg = angsep(p1_sky[0], p1_sky[1], p2_sky[0], p2_sky[1]) / 3600.0
+        coord_dist_deg = (
+            angsep(p1_sky[0], p1_sky[1], p2_sky[0], p2_sky[1]) / 3600.0
+        )
         pix_dist_deg = pixel_sep * self.accessor.pixelsize[1]
 
         # 6 decimal places => 1e-6*degree / 10pix => 1e-7*degree / 1pix
         #  => Approx 0.15 arcseconds drift across 512 pixels
         # (Probably OK).
-        self.assertAlmostEqual(abs(coord_dist_deg), abs(pix_dist_deg), places=3)
-
+        self.assertAlmostEqual(
+            abs(coord_dist_deg), abs(pix_dist_deg), places=3
+        )

test/test_accessors.py

@@ -4,12 +4,14 @@
 
 from sourcefinder import accessors
 
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
 lofar_casatable = os.path.join(
     DATAPATH,
-    ("casatable/L55596_000TO009_skymodellsc_wmax6000_noise_mult10_cell40_" +
-     "npix512_wplanes215.img.restored.corr"),
+    (
+        "casatable/L55596_000TO009_skymodellsc_wmax6000_noise_mult10_cell40_"
+        + "npix512_wplanes215.img.restored.corr"
+    ),
 )
 
 

test/test_amicasatable.py

@@ -6,10 +6,10 @@
 from sourcefinder.accessors.amicasaimage import AmiCasaImage
 from sourcefinder.testutil.decorators import requires_data
 from sourcefinder.utility.coordinates import angsep
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
 
-casatable = os.path.join(DATAPATH, 'accessors/ami-la.image')
+casatable = os.path.join(DATAPATH, "accessors/ami-la.image")
 
 
 class TestAmiLaCasaImage(unittest.TestCase):
@@ -22,9 +22,11 @@ def test_casaimage(self):
         results = self.accessor.extract_metadata()
         sfimage = accessors.sourcefinder_image_from_accessor(self.accessor)
 
-        known_bmaj, known_bmin, known_bpa = (4.002118682861328,
-                                            2.4657058715820312,
-                                            0.3598241556754317)
+        known_bmaj, known_bmin, known_bpa = (
+            4.002118682861328,
+            2.4657058715820312,
+            0.3598241556754317,
+        )
 
         bmaj, bmin, bpa = self.accessor.beam
         self.assertAlmostEqual(known_bmaj, bmaj, 2)
@@ -50,15 +52,18 @@ def test_pix_scale(self):
         p1_sky = (self.accessor.centre_ra, self.accessor.centre_decl)
         p1_pix = self.accessor.wcs.s2p(p1_sky)
 
-        pixel_sep = 10 #Along a single axis
+        pixel_sep = 10  # Along a single axis
         p2_pix = (p1_pix[0], p1_pix[1] + pixel_sep)
         p2_sky = self.accessor.wcs.p2s(p2_pix)
 
-        coord_dist_deg = angsep(p1_sky[0], p1_sky[1], p2_sky[0], p2_sky[1]) / 3600.0
+        coord_dist_deg = (
+            angsep(p1_sky[0], p1_sky[1], p2_sky[0], p2_sky[1]) / 3600.0
+        )
         pix_dist_deg = pixel_sep * self.accessor.pixelsize[1]
 
-        #6 decimal places => 1e-6*degree / 10pix => 1e-7*degree / 1pix
+        # 6 decimal places => 1e-6*degree / 10pix => 1e-7*degree / 1pix
         #  => Approx 0.15 arcseconds drift across 512 pixels
         # (Probably OK).
-        self.assertAlmostEqual(abs(coord_dist_deg), abs(pix_dist_deg), places=6)
-
+        self.assertAlmostEqual(
+            abs(coord_dist_deg), abs(pix_dist_deg), places=6
+        )

test/test_casatable.py

@@ -2,12 +2,11 @@
 
 import unittest
 
-import pytest
 import sourcefinder.accessors as accessors
 from sourcefinder.testutil.decorators import requires_data
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
-casatable = os.path.join(DATAPATH, 'accessors/casa.table')
+casatable = os.path.join(DATAPATH, "accessors/casa.table")
 
 
 @requires_data(casatable)

test/test_config.py

@@ -10,11 +10,12 @@
 from sourcefinder.config import validate_nested
 from sourcefinder.config import validate_types
 
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
 _image = {"rms_filter": 0.1, "structuring_element": [[2] * 3] * 3}
 _export = {"file_type": "hdf5", "source_params": ["foo", "bar"]}
 
+
 @pytest.mark.parametrize(
     "conf_t, conf",
     [
@@ -72,7 +73,12 @@ def test_assert_t_err(key, val, types):
         ("listany", ["a", 1, True], list, ()),
         ("liststr", list("abc"), list, (str,)),
         ("dictionary", {"a": 1, "b": 2}, dict, (str, int)),
-        ("dictionarymixed", {"a": 3.14, "b": 2}, dict, (str, float)),  # compatible
+        (
+            "dictionarymixed",
+            {"a": 3.14, "b": 2},
+            dict,
+            (str, float),
+        ),  # compatible
     ],
 )
 def test_nested(key, value, origin_t, args):
@@ -108,7 +114,11 @@ def test_nested_warn(key, value, origin_t, args):
         ("listany", ["a", 1, True], list),
         ("liststr", list("abc"), list[str,]),
         ("dictionary", {"a": 1, "b": 2}, dict[str, int]),
-        ("dictionarymixed", {"a": 3.14, "b": 2}, dict[str, float]),  # compatible
+        (
+            "dictionarymixed",
+            {"a": 3.14, "b": 2},
+            dict[str, float],
+        ),  # compatible
         ("union", 42, (NoneType | int)),  # uniontype
     ],
 )

test/test_detection.py

@@ -2,23 +2,29 @@
 
 import unittest
 
-import pytest
 import sourcefinder.accessors as accessors
-from sourcefinder.accessors.detection import isfits, islofarhdf5, detect, iscasa
+from sourcefinder.accessors.detection import (
+    isfits,
+    islofarhdf5,
+    detect,
+    iscasa,
+)
 from sourcefinder.accessors.lofarcasaimage import LofarCasaImage
-from sourcefinder.accessors.casaimage import CasaImage
 from sourcefinder.accessors.fitsimage import FitsImage
 from sourcefinder.accessors.amicasaimage import AmiCasaImage
 from sourcefinder.testutil.decorators import requires_data
-from .conftest import DATAPATH
+from test.conftest import DATAPATH
 
 
-lofarcasatable = os.path.join(DATAPATH, "casatable/L55596_000TO009_skymodellsc_wmax6000_noise_mult10_cell40_npix512_wplanes215.img.restored.corr")
-casatable = os.path.join(DATAPATH, 'accessors/casa.table')
-fitsfile = os.path.join(DATAPATH, 'accessors/lofar.fits')
-hdf5file = os.path.join(DATAPATH, 'accessors/lofar.h5')
-antennafile = os.path.join(DATAPATH, 'lofar/CS001-AntennaArrays.conf')
-amicasatable = os.path.join(DATAPATH, 'accessors/ami-la.image')
+lofarcasatable = os.path.join(
+    DATAPATH,
+    "casatable/L55596_000TO009_skymodellsc_wmax6000_noise_mult10_cell40_npix512_wplanes215.img.restored.corr",
+)
+casatable = os.path.join(DATAPATH, "accessors/casa.table")
+fitsfile = os.path.join(DATAPATH, "accessors/lofar.fits")
+hdf5file = os.path.join(DATAPATH, "accessors/lofar.h5")
+antennafile = os.path.join(DATAPATH, "lofar/CS001-AntennaArrays.conf")
+amicasatable = os.path.join(DATAPATH, "accessors/ami-la.image")
 
 
 class TestAutodetect(unittest.TestCase):
@@ -55,7 +61,7 @@ def test_open(self):
         accessor = accessors.open(lofarcasatable)
         self.assertEqual(accessor.__class__, LofarCasaImage)
         self.assertRaises(OSError, accessors.open, antennafile)
-        self.assertRaises(OSError, accessors.open, 'doesntexists')
+        self.assertRaises(OSError, accessors.open, "doesntexists")
 
     @requires_data(amicasatable)
     def test_isamicasa(self):