Fixed all the documentation for coordinate_system and changed names f…

…rom 'pixel'/'sky' to 'euclidean'/'celestial'

clmm/dataops/__init__.py

@@ -31,7 +31,7 @@ def compute_tangential_and_cross_components(
     dec_source,
     shear1,
     shear2,
-    coordinate_system="pixel",
+    coordinate_system="euclidean",
     geometry="curve",
     is_deltasigma=False,
     sigma_c=None,
@@ -99,8 +99,8 @@ def compute_tangential_and_cross_components(
     shear2: array
         The measured shear (or reduced shear or ellipticity) of the source galaxies
     coordinate_system: str, optional
-        Coordinate system of the ellipticity components. Options are 'pixel' or 'sky'.
-        Default is 'pixel'.
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
+        Default is 'euclidean'.
     geometry: str, optional
         Sky geometry to compute angular separation.
         Options are curve (uses astropy) or flat.
@@ -341,7 +341,7 @@ def compute_galaxy_weights(
 
 
 def _compute_lensing_angles_flatsky(
-    ra_lens, dec_lens, ra_source_list, dec_source_list, coordinate_system="pixel"
+    ra_lens, dec_lens, ra_source_list, dec_source_list, coordinate_system="euclidean"
 ):
     r"""Compute the angular separation between the lens and the source and the azimuthal
     angle from the lens to the source in radians.
@@ -367,8 +367,8 @@ def _compute_lensing_angles_flatsky(
     dec_source_list: array
         Declinations of each source galaxy in degrees
     coordinate_system: str, optional
-        Coordinate system of the ellipticity components. Options are 'pixel' or 'sky'.
-        Default is 'pixel'.
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
+        Default is 'euclidean'.
 
     Returns
     -------
@@ -392,15 +392,15 @@ def _compute_lensing_angles_flatsky(
         phi[angsep == 0.0] = 0.0
     else:
         phi = 0.0 if angsep == 0.0 else phi
-    if coordinate_system == "sky":
+    if coordinate_system == "celestial":
         phi = np.pi - phi
     if np.any(angsep > np.pi / 180.0):
         warnings.warn("Using the flat-sky approximation with separations >1 deg may be inaccurate")
     return angsep, phi
 
 
 def _compute_lensing_angles_astropy(
-    ra_lens, dec_lens, ra_source_list, dec_source_list, coordinate_system="pixel"
+    ra_lens, dec_lens, ra_source_list, dec_source_list, coordinate_system="euclidean"
 ):
     r"""Compute the angular separation between the lens and the source and the azimuthal
     angle from the lens to the source in radians.
@@ -415,6 +415,9 @@ def _compute_lensing_angles_astropy(
         Right ascensions of each source galaxy in degrees
     dec_source_list: array
         Declinations of each source galaxy in degrees
+    coordinate_system: str, optional
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
+        Default is 'euclidean'.
 
     Returns
     -------
@@ -434,7 +437,7 @@ def _compute_lensing_angles_astropy(
     else:
         phi -= 2 * np.pi if phi > np.pi else 0
         phi = 0 if angsep == 0 else phi
-    if coordinate_system == "sky":
+    if coordinate_system == "celestial":
         phi = np.pi - phi
     return angsep, phi
 

clmm/galaxycluster.py

@@ -37,9 +37,9 @@ class GalaxyCluster:
         Redshift of galaxy cluster center
     galcat : GCData
         Table of background galaxy data containing at least galaxy_id, ra, dec, e1, e2, z
-    coordinate_system : str
-        Coordinate system of the galaxy cluster center (pixel or sky)
-
+    coordinate_system : str, optional
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
+        Default is 'euclidean'.
     validate_input: bool
         Validade each input argument
     """
@@ -63,7 +63,7 @@ def _add_values(
         dec: float,
         z: float,
         galcat: GCData,
-        coordinate_system: str = "pixel",
+        coordinate_system: str = "euclidean",
     ):
         """Add values for all attributes"""
         self.unique_id = unique_id
@@ -257,9 +257,6 @@ def compute_tangential_and_cross_components(
             Name of the column to be added to the `galcat` astropy table that will contain the
             cross component computed from columns `shape_component1` and `shape_component2`.
             Default: `ex`
-        coordinate_system: str, optional
-            Coordinate system of the ellipticity components. Options are 'pixel' or 'sky'.
-            Default: 'pixel'
         geometry: str, optional
             Sky geometry to compute angular separation.
             Options are curve (uses astropy) or flat.

clmm/support/mock_data.py

@@ -1,4 +1,5 @@
 """Functions to generate mock source galaxy distributions to demo lensing code"""
+
 import warnings
 import numpy as np
 from astropy import units as u
@@ -38,7 +39,7 @@ def generate_galaxy_catalog(
     ngal_density=None,
     pz_bins=101,
     pzpdf_type="shared_bins",
-    coordinate_system="pixel",
+    coordinate_system="euclidean",
     validate_input=True,
 ):
     r"""Generates a mock dataset of sheared background galaxies.
@@ -158,7 +159,8 @@ def generate_galaxy_catalog(
         The number of galaxies to be drawn will then depend on the redshift distribution and
         user-defined redshift range.  If specified, the ngals argument will be ignored.
     coordinate_system : str, optional
-        The coordinate system to use for the output catalog. Options are 'pixel' and 'sky'.
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
+        Default is 'euclidean'.
 
     validate_input: bool
         Validade each input argument
@@ -366,7 +368,7 @@ def _generate_galaxy_catalog(
     photoz_sigma_unscaled=None,
     pz_bins=101,
     pzpdf_type="shared_bins",
-    coordinate_system="pixel",
+    coordinate_system="euclidean",
     field_size=None,
 ):
     """A private function that skips the sanity checks on derived properties. This
@@ -428,7 +430,7 @@ def _generate_galaxy_catalog(
     _, posangle = c_cl.separation(c_gal).rad, c_cl.position_angle(c_gal).rad
     posangle += 0.5 * np.pi  # for right convention
 
-    if coordinate_system == "sky":
+    if coordinate_system == "celestial":
         posangle = np.pi - posangle  # ellipticity coordinate system conversion
 
     # corresponding shear1,2 components

clmm/utils/validation.py

@@ -235,13 +235,13 @@ def _validate_coordinate_system(loc, coordinate_system, valid_type):
     loc: dict
         Dictionary with all input arguments. Should be locals().
     coordinate_system: str
-        Coordinate system used for the input data.
+        Coordinate system of the ellipticity components. Must be either 'celestial' or 'euclidean'.
     valid_type: str, type
         Valid types for argument, options are object types, list/tuple of types, or:
 
             * 'int_array' - interger, interger array
             * 'float_array' - float, float array
     """
     validate_argument(loc, coordinate_system, valid_type)
-    if loc[coordinate_system] not in ["sky", "pixel"]:
-        raise ValueError(f"{coordinate_system} must be 'sky' or 'pixel'.")
+    if loc[coordinate_system] not in ["celestial", "euclidean"]:
+        raise ValueError(f"{coordinate_system} must be 'celestial' or 'euclidean'.")

examples/demo_mock_cluster.ipynb

@@ -130,7 +130,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "It is also possible to choose the coordinate system for the generated ellipticities. Possible options are either \"sky\" or \"pixel\". The default choice is \"pixel\"."
+    "It is also possible to choose the coordinate system for the generated ellipticities. Possible options are either \"celestial\" or \"euclidean\". The default choice is \"euclidean\"."
    ]
   },
   {
@@ -139,7 +139,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "coordinate_system = \"pixel\"\n"
+    "coordinate_system = \"euclidean\"\n"
    ]
   },
   {

tests/test_dataops.py

@@ -139,10 +139,10 @@ def test_compute_lensing_angles_flatsky():
     ra_l, dec_l = 161.32, 51.49
     ra_s, dec_s = np.array([161.29, 161.34]), np.array([51.45, 51.55])
     thetas_pixel, phis_pixel = da._compute_lensing_angles_flatsky(
-        ra_l, dec_l, ra_s, dec_s, coordinate_system="pixel"
+        ra_l, dec_l, ra_s, dec_s, coordinate_system="euclidean"
     )
     thetas_sky, phis_sky = da._compute_lensing_angles_flatsky(
-        ra_l, dec_l, ra_s, dec_s, coordinate_system="sky"
+        ra_l, dec_l, ra_s, dec_s, coordinate_system="celestial"
     )
 
     assert_allclose(
@@ -167,10 +167,10 @@ def test_compute_lensing_angles_astropy():
     ra_l, dec_l = 161.32, 51.49
     ra_s, dec_s = np.array([161.29, 161.34]), np.array([51.45, 51.55])
     thetas_pixel, phis_pixel = da._compute_lensing_angles_astropy(
-        ra_l, dec_l, ra_s, dec_s, coordinate_system="pixel"
+        ra_l, dec_l, ra_s, dec_s, coordinate_system="euclidean"
     )
     thetas_sky, phis_sky = da._compute_lensing_angles_astropy(
-        ra_l, dec_l, ra_s, dec_s, coordinate_system="sky"
+        ra_l, dec_l, ra_s, dec_s, coordinate_system="celestial"
     )
 
     assert_allclose(

tests/test_galaxycluster.py

@@ -20,7 +20,7 @@ def test_initialization():
         "dec": 34.0,
         "z": 0.3,
         "galcat": GCData(),
-        "coordinate_system": "pixel",
+        "coordinate_system": "euclidean",
     }
     cl1 = clmm.GalaxyCluster(**testdict1)
 
@@ -49,7 +49,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         ValueError,
@@ -59,7 +59,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         ValueError,
@@ -69,7 +69,7 @@ def test_integrity():  # Converge on name
         dec=95.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         ValueError,
@@ -79,7 +79,7 @@ def test_integrity():  # Converge on name
         dec=-95.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         ValueError,
@@ -89,7 +89,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=-0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         ValueError,
@@ -111,7 +111,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -121,7 +121,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=1,
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -131,7 +131,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=[],
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -141,7 +141,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -151,7 +151,7 @@ def test_integrity():  # Converge on name
         dec=None,
         z=0.3,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -161,7 +161,7 @@ def test_integrity():  # Converge on name
         dec=34.0,
         z=None,
         galcat=GCData(),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     assert_raises(
         TypeError,
@@ -177,13 +177,13 @@ def test_integrity():  # Converge on name
     # Test that id can support numbers and strings
     assert isinstance(
         clmm.GalaxyCluster(
-            unique_id=1, ra=161.3, dec=34.0, z=0.3, galcat=GCData(), coordinate_system="pixel"
+            unique_id=1, ra=161.3, dec=34.0, z=0.3, galcat=GCData(), coordinate_system="euclidean"
         ).unique_id,
         str,
     )
     assert isinstance(
         clmm.GalaxyCluster(
-            unique_id="1", ra=161.3, dec=34.0, z=0.3, galcat=GCData(), coordinate_system="pixel"
+            unique_id="1", ra=161.3, dec=34.0, z=0.3, galcat=GCData(), coordinate_system="euclidean"
         ).unique_id,
         str,
     )
@@ -513,7 +513,7 @@ def test_coordinate_system():
             [ra_source, dec_source, shear1, shear2_pixel, z_src],
             names=("ra", "dec", "e1", "e2", "z"),
         ),
-        coordinate_system="pixel",
+        coordinate_system="euclidean",
     )
     cl_sky = clmm.GalaxyCluster(
         unique_id="test",
@@ -523,7 +523,7 @@ def test_coordinate_system():
         galcat=GCData(
             [ra_source, dec_source, shear1, shear2_sky, z_src], names=("ra", "dec", "e1", "e2", "z")
         ),
-        coordinate_system="sky",
+        coordinate_system="celestial",
     )
 
     cl_pixel.compute_tangential_and_cross_components()

tests/test_mockdata.py

@@ -264,17 +264,13 @@ def test_shapenoise():
 
     # Verify that the shape noise is Gaussian around 0 (for the very small shear here)
     sigma = 0.25
-    data = mock.generate_galaxy_catalog(
-        10**12.0, 0.3, 4, cosmo, 0.8, ngals=50000, shapenoise=sigma
-    )
+    data = mock.generate_galaxy_catalog(10**12.0, 0.3, 4, cosmo, 0.8, ngals=50000, shapenoise=sigma)
     # Check that there are no galaxies with |e|>1
     assert_equal(np.count_nonzero((data["e1"] > 1) | (data["e1"] < -1)), 0)
     assert_equal(np.count_nonzero((data["e2"] > 1) | (data["e2"] < -1)), 0)
     # Check that shape noise is Guassian with correct std dev
     bins = np.arange(-1, 1.1, 0.1)
-    gauss = (
-        5000 * np.exp(-0.5 * (bins[:-1] + 0.05) ** 2 / sigma**2) / (sigma * np.sqrt(2 * np.pi))
-    )
+    gauss = 5000 * np.exp(-0.5 * (bins[:-1] + 0.05) ** 2 / sigma**2) / (sigma * np.sqrt(2 * np.pi))
     assert_allclose(np.histogram(data["e1"], bins=bins)[0], gauss, atol=50, rtol=0.05)
     assert_allclose(np.histogram(data["e2"], bins=bins)[0], gauss, atol=50, rtol=0.05)
 
@@ -289,11 +285,11 @@ def test_coordinate_system():
     # Verify that the coordinate system is correctly set up
     np.random.seed(285713)
     pixel_data = mock.generate_galaxy_catalog(
-        10**15.0, 0.3, 4, cosmo, 0.8, ngals=50000, coordinate_system="pixel"
+        10**15.0, 0.3, 4, cosmo, 0.8, ngals=50000, coordinate_system="euclidean"
     )
     np.random.seed(285713)
     sky_data = mock.generate_galaxy_catalog(
-        10**15.0, 0.3, 4, cosmo, 0.8, ngals=50000, coordinate_system="sky"
+        10**15.0, 0.3, 4, cosmo, 0.8, ngals=50000, coordinate_system="celestial"
     )
 
     assert_equal(pixel_data["ra"], sky_data["ra"])