fix various things based upon changes in astropy (#37)

* fix naxis access

* removed _naxis and fixed np.where with units problem

* small approx in assert unit test

* shouldn't call fixtures

e.g. pytest-dev/pytest#3950 (comment)

* maybe fix to array_sequence_equal

* fix fixture names test_psf

* removed duplicated test functions

* use more recent packages travis

* Revert "use more recent packages travis"

This reverts commit 6c55f18.

gunagala/imager.py

@@ -250,7 +250,7 @@ def __init__(self, optic, camera, filters, psf, sky, num_imagers=1, num_per_comp
 
         # Construct a simple template WCS to store the focal plane configuration parameters
         self.wcs = WCS(naxis=2)
-        self.wcs._naxis2, self.wcs._naxis1 = self.camera.resolution.value.astype(int)
+        self.wcs.pixel_shape = self.camera.resolution.value.astype(int)
         self.wcs.wcs.crpix = [(self.camera.resolution[1].value - 1) / 2,
                               (self.camera.resolution[0].value - 1) / 2]
         self.wcs.wcs.cdelt = [self.pixel_scale.to(u.degree / u.pixel).value,
@@ -422,9 +422,8 @@ def extended_source_signal_noise(self, surface_brightness, filter_name, total_ex
                 # Sky counts already included in _is_saturated, need to avoid counting them twice
                 saturated = self._is_saturated(
                     0 * u.electron / (u.pixel * u.second), sub_exp_time, filter_name)
-            # np.where strips units, need to manually put them back.
-            signal = np.where(saturated, 0, signal) * u.electron / u.pixel
-            noise = np.where(saturated, 0, noise) * u.electron / u.pixel
+            signal = np.where(saturated, 0 * u.electron / u.pixel, signal)
+            noise = np.where(saturated, 0 * u.electron / u.pixel, noise)
 
         # Totals per (binned) pixel for all imagers.
         signal = signal * self.num_imagers * binning
@@ -483,8 +482,7 @@ def extended_source_snr(self, surface_brightness, filter_name, total_exp_time, s
         signal, noise = self.extended_source_signal_noise(surface_brightness, filter_name, total_exp_time,
                                                           sub_exp_time, calc_type, saturation_check, binning)
 
-        # np.where() strips units, need to manually put them back
-        snr = np.where(noise != 0.0, signal / noise, 0.0) * u.dimensionless_unscaled
+        snr = np.where(noise != 0.0, signal / noise, 0.0 * u.dimensionless_unscaled)
 
         return snr
 
@@ -1003,9 +1001,8 @@ def point_source_signal_noise(self, brightness, filter_name, total_exp_time, sub
         # in a single sub exposure, and check against saturation_level.
         if saturation_check:
             saturated = self._is_saturated(rate * self.psf.peak, sub_exp_time, filter_name)
-            # np.where strips units, need to manually put them back.
-            signal = np.where(saturated, 0.0, signal) * u.electron
-            noise = np.where(saturated, 0.0, noise) * u.electron
+            signal = np.where(saturated, 0.0 * u.electron, signal)
+            noise = np.where(saturated, 0.0 * u.electron , noise)
 
         return signal, noise
 
@@ -1046,8 +1043,7 @@ def point_source_snr(self, brightness, filter_name, total_exp_time, sub_exp_time
         signal, noise = self.point_source_signal_noise(brightness, filter_name,
                                                        total_exp_time, sub_exp_time, saturation_check)
 
-        # np.where() strips units, need to manually put them back.
-        snr = np.where(noise != 0.0, signal / noise, 0.0) * u.dimensionless_unscaled
+        snr = np.where(noise != 0.0, signal / noise, 0.0 * u.dimensionless_unscaled)
 
         return snr
 
@@ -1096,8 +1092,7 @@ def point_source_etc(self, brightness, filter_name, snr_target, sub_exp_time, sa
         # in a single sub exposure, and check against saturation_level.
         if saturation_check:
             saturated = self._is_saturated(rate * self.psf.peak, sub_exp_time, filter_name)
-            # np.where() strips units, need to manually put them back
-            total_exp_time = np.where(saturated, 0.0, total_exp_time) * u.second
+            total_exp_time = np.where(saturated, 0.0 * u.second, total_exp_time)
 
         return total_exp_time
 
@@ -1507,6 +1502,7 @@ def snr_vs_ABmag(self, exp_times, filter_name, magnitude_interval=0.02 * u.ABmag
                                                                  filter_name=filter_name,
                                                                  total_exp_time=exp_time,
                                                                  sub_exp_time=exp_time)
+                # print(total_signals, signals, "LALA")
                 total_signals += signals
                 total_noises_squared += noises**2
 
@@ -1557,7 +1553,8 @@ def get_pixel_coords(self):
         of the centre of all the pixels in the image.
         """
         # Arrays of pixel coordinates
-        XY = np.meshgrid(np.arange(self.wcs._naxis1), np.arange(self.wcs._naxis2))
+        naxis1, naxis2 = self.wcs.pixel_shape
+        XY = np.meshgrid(np.arange(naxis1), np.arange(naxis2))
 
         # Convert to arrays of RA, dec (ICRS, decimal degrees)
         try:
@@ -1607,8 +1604,8 @@ def make_noiseless_image(self,
         if isinstance(self.psf, FittablePSF):
             raise NotImplementedError("Analytical PSFs currently don't work.\n They will take all system memory. See: https://github.com/AstroHuntsman/gunagala/pull/16#issuecomment-426844974 ")
 
-        electrons = np.zeros((self.wcs._naxis2,
-                              self.wcs._naxis1)) * u.electron / (u.second * u.pixel)
+        naxis1, naxis2 = self.wcs.pixel_shape
+        electrons = np.zeros((naxis2, naxis1)) * u.electron / (u.second * u.pixel)
         self.set_WCS_centre(centre, **centre_kwargs)
 
         # Calculate observed sky background

gunagala/tests/test_imager.py

@@ -1,5 +1,6 @@
 # Tests for the signal-to-noise module
 import pytest
+from pytest import approx
 import numpy as np
 import astropy.units as u
 import astropy.constants as c
@@ -336,11 +337,11 @@ def test_extended_rates(imager, filter_name):
                                                saturation_check=True)
 
     # Calculating surface brightness given exposure time and SNR should match original surface brightness
-    assert imager.rate_to_SB(rate, filter_name) == imager.extended_source_limit(total_exp_time=t_exp,
+    assert approx(imager.rate_to_SB(rate, filter_name).value) == imager.extended_source_limit(total_exp_time=t_exp,
                                                                                 filter_name=filter_name,
                                                                                 snr_target=snr,
                                                                                 sub_exp_time=t_sub,
-                                                                                calc_type='per arcsecond squared')
+                                                                                calc_type='per arcsecond squared').value
 
     # Can't use pixel binning with per arcsecond squared signal, noise values
     with pytest.raises(ValueError):
@@ -754,8 +755,8 @@ def test_get_pixel_coords_with_WCS_call_first(imager_function_scope):
     # now set WCS centre first, then try and get_pixel_coords
     imager_function_scope.set_WCS_centre(test_coord_string, unit='deg')
     centre_field_pixels = imager_function_scope.get_pixel_coords()
-    assert imager_function_scope.wcs._naxis1 == centre_field_pixels.shape[1]
-    assert imager_function_scope.wcs._naxis2 == centre_field_pixels.shape[0]
+    assert imager_function_scope.wcs.pixel_shape[0] == centre_field_pixels.shape[1]
+    assert imager_function_scope.wcs.pixel_shape[1] == centre_field_pixels.shape[0]
 
 
 def test_create_imagers():

gunagala/tests/test_psf.py

@@ -7,12 +7,20 @@
 
 @pytest.fixture(scope='module')
 def psf_moffat():
+    return make_moffat()
+
+
+def make_moffat():
     psf = MoffatPSF(FWHM=1 / 30 * u.arcminute, shape=4.7)
     return psf
 
 
 @pytest.fixture(scope='module')
 def psf_pixellated():
+    return make_pixellated()
+
+
+def make_pixellated():
     psf_data = np.array([[0.0, 0.0, 0.1, 0.0, 0.0],
                          [0.0, 0.3, 0.7, 0.4, 0.0],
                          [0.1, 0.8, 1.0, 0.6, 0.1],
@@ -29,72 +37,59 @@ def psf_pixellated():
 def test_base():
     with pytest.raises(TypeError):
         # Try to instantiate abstract base class, should fail
-        psf_base = PSF(FWHM=1 / 30 * u.arcminute)
+        _ = PSF(FWHM=1 / 30 * u.arcminute)
 
 
 @pytest.mark.parametrize("psf, type", [
-    (psf_moffat(), MoffatPSF),
-    (psf_pixellated(), PixellatedPSF)],
+    (make_moffat(), MoffatPSF),
+    (make_pixellated(), PixellatedPSF)],
     ids=["moffat", "pixellated"]
 )
 def test_instance(psf, type):
     assert isinstance(psf, type)
     assert isinstance(psf, PSF)
 
 
-def test_pix(pix_psf):
-    assert isinstance(pix_psf, PixellatedPSF)
-    assert isinstance(pix_psf, PSF)
+def test_pix(psf_pixellated):
+    assert isinstance(psf_pixellated, PixellatedPSF)
+    assert isinstance(psf_pixellated, PSF)
 
 
-def test_FWHM(psf):
-    assert psf.FWHM == 2 * u.arcsecond
-    psf.FWHM = 4 * u.arcsecond
-    assert psf.FWHM == 1 / 15 * u.arcminute
+def test_FWHM(psf_moffat):
+    assert psf_moffat.FWHM == 2 * u.arcsecond
+    psf_moffat.FWHM = 4 * u.arcsecond
+    assert psf_moffat.FWHM == 1 / 15 * u.arcminute
     with pytest.raises(ValueError):
-        psf.FWHM = -1 * u.degree
-    psf.FWHM = 2 * u.arcsecond
-
-
-def test_pixel_scale(psf):
-    psf.pixel_scale = 2.85 * u.arcsecond / u.pixel
-    assert psf.pixel_scale == 2.85 * u.arcsecond / u.pixel
-
-
-def test_pixel_scale_pix(pix_psf):
-    pix_psf.pixel_scale = (1 / 3) * u.arcsecond / u.pixel
-    assert pix_psf.pixel_scale == (1 / 3) * u.arcsecond / u.pixel
-    pix_psf.pixel_scale = (2 / 3) * u.arcsecond / u.pixel
-
-
-def test_n_pix(psf):
-    assert psf.n_pix == 4.25754067000986 * u.pixel
+        psf_moffat.FWHM = -1 * u.degree
+    psf_moffat.FWHM = 2 * u.arcsecond
 
 
-def test_n_pix_pix(pix_psf):
-    assert pix_psf.n_pix.to(u.pixel).value == pytest.approx(21.01351017)
+def test_pixel_scale_pix(psf_pixellated):
+    psf_pixellated.pixel_scale = (1 / 3) * u.arcsecond / u.pixel
+    assert psf_pixellated.pixel_scale == (1 / 3) * u.arcsecond / u.pixel
+    psf_pixellated.pixel_scale = (2 / 3) * u.arcsecond / u.pixel
 
 
-def test_peak(psf):
-    assert psf.peak == 0.7134084656751443 / u.pixel
+def test_n_pix_pix(psf_pixellated):
+    assert psf_pixellated.n_pix.to(u.pixel).value == pytest.approx(21.0699454)
 
 
-def test_peak_pix(pix_psf):
-    assert pix_psf.peak.to(1 / u.pixel).value == pytest.approx(0.08073066)
+def test_peak_pix(psf_pixellated):
+    assert psf_pixellated.peak.to(1 / u.pixel).value == pytest.approx(0.08073066)
 
 
-def test_shape(psf):
-    assert psf.shape == 4.7
-    psf.shape = 2.5
-    assert psf.shape == 2.5
+def test_shape(psf_moffat):
+    assert psf_moffat.shape == 4.7
+    psf_moffat.shape = 2.5
+    assert psf_moffat.shape == 2.5
     with pytest.raises(ValueError):
         psf_moffat.FWHM = -1 * u.degree
     psf_moffat.FWHM = 2 * u.arcsecond
 
 
 @pytest.mark.parametrize("psf, t_pixel_scale, pixel_scale", [
-    (psf_moffat(), 2.85, 2.85),
-    (psf_pixellated(), (1 / 3), (2 / 3))],
+    (make_moffat(), 2.85, 2.85),
+    (make_pixellated(), (1 / 3), (2 / 3))],
     ids=["moffat", "pixellated"]
 )
 def test_pixel_scale(psf, t_pixel_scale, pixel_scale):
@@ -104,8 +99,8 @@ def test_pixel_scale(psf, t_pixel_scale, pixel_scale):
 
 
 @pytest.mark.parametrize("psf, expected_n_pix, pixel_scale", [
-    (psf_moffat(), 4.25754067000986, 2.85),
-    (psf_pixellated(), 21.06994544, (2 / 3))],
+    (make_moffat(), 4.25754067000986, 2.85),
+    (make_pixellated(), 21.06994544, (2 / 3))],
     ids=["moffat", "pixellated"]
 )
 def test_n_pix(psf, expected_n_pix, pixel_scale):
@@ -114,29 +109,20 @@ def test_n_pix(psf, expected_n_pix, pixel_scale):
 
 
 @pytest.mark.parametrize("psf, expected_peak, pixel_scale", [
-    (psf_moffat(), 0.7134084656751443, 2.85),
-    (psf_pixellated(), 0.08073066, (2 / 3))],
+    (make_moffat(), 0.7134084656751443, 2.85),
+    (make_pixellated(), 0.08073066, (2 / 3))],
     ids=["moffat", "pixellated"]
 )
 def test_peak(psf, expected_peak, pixel_scale):
     psf.pixel_scale = pixel_scale * u.arcsecond / u.pixel
     assert psf.peak.to(1 / (u.pixel)).value == pytest.approx(expected_peak)
 
 
-def test_shape(psf_moffat):
-    assert psf_moffat.shape == 4.7
-    psf_moffat.shape = 2.5
-    assert psf_moffat.shape == 2.5
-    with pytest.raises(ValueError):
-        psf_moffat.shape = 0.5
-    psf_moffat.shape = 4.7
-
-
 @pytest.mark.parametrize("psf, image_size", [
-    (psf_moffat(), (21, 21)),
-    (psf_pixellated(), (21, 21)),
-    (psf_moffat(), (7, 9)),
-    (psf_pixellated(), (7, 9))],
+    (make_moffat(), (21, 21)),
+    (make_pixellated(), (21, 21)),
+    (make_moffat(), (7, 9)),
+    (make_pixellated(), (7, 9))],
     ids=["moffat_square",
          "pixellated_square",
          "moffat_rectangle",
@@ -155,10 +141,10 @@ def test_pixellated_dimension(psf, image_size):
 
 
 @pytest.mark.parametrize("psf, offset", [
-    (psf_moffat(), (0.0, 0.0)),
-    (psf_pixellated(), (0.0, 0.0)),
-    (psf_moffat(), (0.3, -0.7)),
-    (psf_pixellated(), (0.3, -0.7))],
+    (make_moffat(), (0.0, 0.0)),
+    (make_pixellated(), (0.0, 0.0)),
+    (make_moffat(), (0.3, -0.7)),
+    (make_pixellated(), (0.3, -0.7))],
     ids=["moffat_centre_offsets",
          "pixellated_centre_offsets",
          "moffat_noncentre_offsets",
@@ -172,8 +158,8 @@ def test_offsets(psf, offset):
 
 
 @pytest.mark.parametrize("psf, test_size", [
-    (psf_moffat(), (1.3, -1.3)),
-    (psf_pixellated(), (-1.3, 1.3))],
+    (make_moffat(), (1.3, -1.3)),
+    (make_pixellated(), (-1.3, 1.3))],
     ids=["moffat", "pixellated"]
 )
 def test_pixellated_invalid_size(psf, test_size):

gunagala/utils/__init__.py

@@ -123,9 +123,9 @@ def array_sequence_equal(array_sequence, reference=None):
         for array in array_sequence:
             try:
                 assert (array == reference).all()
-            except (AttributeError, AssertionError):
+            except (AttributeError, ValueError, AssertionError):
                 # Attribute error if array & reference different lengths, Assertion Error if same
-                # length but one or more elements differ in value.
+                # length but one or more elements differ in value. ValueError if different lengths.
                 return False
         return True