Truncated visualisation checks

docs/source/index.rst

@@ -19,6 +19,7 @@ Documentation contents
    halo_catalogues/index
    masking/index
    iterating/index
+   visualisation/index
    modules/index
 
 Citing SWIFTGalaxy

docs/source/visualisation/index.rst

@@ -0,0 +1,30 @@
+Visualisation
+=============
+
+:class:`~swiftgalaxy.reader.SWIFTGalaxy` objects behave just like :class:`~swiftsimio.reader.SWIFTDataset` objects for the purposes of using the :mod:`~swiftsimio.visualisation` tools. Keep in mind that a :class:`~swiftgalaxy.reader.SWIFTGalaxy` has usually applied a mask to particles and has recentered and/or transformed the coordinate frame. The mask is one reason that it is usually best to set ``periodic=False`` when calling visualisation routines.
+
+.. warning::
+   The :mod:`swiftsimio` visualisation tools do correctly handle periodic boundaries when coordinates have been rotated. The visualisation tools cannot currently detect whether a :class:`~swiftgalaxy.reader.SWIFTGalaxy` object has been rotated, and can give incorrect results if periodic boundaries are used. It is therefore recommended to always set ``periodic=False`` in all calls to :mod:`swiftsimio` visualisation routines.
+
+When a :class:`~swiftgalaxy.reader.SWIFTGalaxy` has been recentered (the default behaviour) the visualisation ``region`` should be given relative to the centre, not the box coordinates. For example:
+
+.. code-block:: python
+
+   from swiftsimio.visualisation.projection import project_gas
+   sg = SWIFTGalaxy(..., auto_recenter=True)  # the default
+   image = project_gas(
+       sg,
+       project="masses",
+       parallel=True,
+       periodic=False,
+       resolution=256,
+       region=cosmo_array(
+           [-0.5, 0.5, -0.5, 0.5],
+	   u.Mpc,
+	   comoving=True,
+	   scale_factor=sg.metadata.a,
+	   scale_exponent=1,
+       )
+   )
+
+For general information on the visualisation routines consult the swiftsimio documentation pages.

swiftgalaxy/reader.py

@@ -141,7 +141,7 @@ def _apply_rotmat(coords: cosmo_array, rotation_matrix: np.ndarray) -> cosmo_arr
 
 
 def _apply_4transform(
-    coords: cosmo_array, transform: np.ndarray, transform_units: unyt.unyt_quantity
+    coords: cosmo_array, transform: np.ndarray, transform_units: unyt.unit_object.Unit
 ) -> cosmo_array:
     """
     Apply an arbitary coordinate transformation (translation mixed with rotation) to a
@@ -158,7 +158,7 @@ def _apply_4transform(
         The coordinate array to be transformed.
     transform : :class:`~numpy.ndarray`
         The 4x4 transformation matrix.
-    transform_units : :class:`unyt.unyt_quantity`
+    transform_units : :class:`unyt.unit_object.Unit`
         The units assumed in the translation portion of the transformation matrix.
 
     Returns

tests/test_visualisation.py

@@ -0,0 +1,127 @@
+import pytest
+import numpy as np
+import unyt as u
+from swiftsimio import cosmo_array, cosmo_quantity
+from swiftsimio.visualisation.projection import project_gas
+from swiftsimio.visualisation.slice import slice_gas
+from swiftsimio.visualisation.volume_render import render_gas
+
+
+@pytest.mark.parametrize("periodic", [False, True])
+class TestRecenteredVisualisation:
+
+    @pytest.mark.parametrize("z_cut", [False, True])
+    def test_recentered_projection(self, sg, sg_autorecentre_off, z_cut, periodic):
+        """
+        We should be able to make the same projections whether we recentered or not.
+        """
+        z_limits = [1.9, 2.1] if z_cut else []
+        recentered_z_limits = [-0.1, 0.1] if z_cut else []
+        kwargs = {
+            "resolution": 4,
+            "project": "masses",
+            "parallel": True,
+            "periodic": periodic,
+        }
+        ref_img = project_gas(
+            sg_autorecentre_off,
+            region=cosmo_array(
+                [1.5, 2.5, 1.5, 2.5] + z_limits,
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        recentered_img = project_gas(
+            sg,
+            region=cosmo_array(
+                [-0.5, 0.5, -0.5, 0.5] + recentered_z_limits,
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        assert (ref_img > 0).any()
+        assert np.allclose(ref_img, recentered_img)
+
+    def test_recentered_slice(self, sg, sg_autorecentre_off, periodic):
+        """
+        We should be able to make the same slice whether we recentered or not.
+        """
+        z_slice = cosmo_quantity(
+            1.95, u.Mpc, comoving=True, scale_factor=1, scale_exponent=1
+        )
+        recentered_z_slice = cosmo_quantity(
+            -0.05, u.Mpc, comoving=True, scale_factor=1, scale_exponent=1
+        )
+        kwargs = {
+            "resolution": 4,
+            "project": "masses",
+            "parallel": True,
+            "periodic": periodic,
+        }
+        ref_img = slice_gas(
+            sg_autorecentre_off,
+            z_slice=z_slice,
+            region=cosmo_array(
+                [1.5, 2.5, 1.5, 2.5],
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        recentered_img = slice_gas(
+            sg,
+            z_slice=recentered_z_slice,
+            region=cosmo_array(
+                [-0.5, 0.5, -0.5, 0.5],
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        assert (ref_img > 0).any()
+        assert np.allclose(ref_img, recentered_img)
+
+    def test_recentered_volume_render(self, sg, sg_autorecentre_off, periodic):
+        """
+        We should be able to make the same rendering whether we recentered or not.
+        """
+        kwargs = {
+            "resolution": 4,
+            "project": "masses",
+            "parallel": True,
+            "periodic": periodic,
+        }
+        ref_img = render_gas(
+            sg_autorecentre_off,
+            region=cosmo_array(
+                [1.5, 2.5, 1.5, 2.5, 1.5, 2.5],
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        recentered_img = render_gas(
+            sg,
+            region=cosmo_array(
+                [-0.5, 0.5, -0.5, 0.5, -0.5, 0.5],
+                u.Mpc,
+                comoving=True,
+                scale_factor=1,
+                scale_exponent=1,
+            ),
+            **kwargs,
+        )
+        assert (ref_img > 0).any()
+        assert np.allclose(ref_img, recentered_img)

tests/toysnap.py

@@ -186,6 +186,8 @@ def create_toysnap(
     """
     Creates a sample dataset of a toy galaxy.
     """
+    if os.path.isfile(snapfile):
+        return
 
     sd = Writer(cosmo_units, np.ones(3, dtype=float) * boxsize)
 
@@ -663,7 +665,8 @@ def create_toysnap(
 
 
 def remove_toysnap(snapfile=toysnap_filename):
-    os.remove(snapfile)
+    if os.path.isfile(snapfile):
+        os.remove(snapfile)
     return