Merge pull request #266 from abostroem/replace_gala

Replace gala dependency with standalone files

Author: ShebMichel

episodes/02-coords.md

@@ -395,7 +395,7 @@ perpendicular to the direction of the stream (the y-axis in Figure 1).
 These are called the $\phi_1$ and $\phi_2$ coordinates, respectively.
 
 ```python
-from gala.coordinates import GD1Koposov10
+from gd1 import GD1Koposov10
 
 gd1_frame = GD1Koposov10()
 gd1_frame
@@ -405,6 +405,21 @@ gd1_frame
 <GD1Koposov10 Frame>
 ```
 
+:::::::::::::::::::::::::::::::::::::::::  callout
+
+## GD1Koposov10 import
+
+The `GD1Koposov10` reference frame is part of the `gala` package. For convience we provide 
+the stand alone file as part of the `student_download` zip file you downloaded. If your notebook 
+is not in your `student_download` directory, you will need to add the following before the import
+statement
+```python
+import sys
+sys.path.append(<path to student_download>)
+```
+Where `<path to student_download>` is the path to your `student_download` directory ending with `student_download`.
+::::::::::::::::::::::::::::::::::::::::::::::::::
+
 We can use it to find the coordinates of Betelgeuse in the GD-1 frame,
 like this:
 

episodes/03-transform.md

@@ -63,17 +63,21 @@ Whether you are working from a new notebook or coming back from a checkpoint,
 reloading the data will save you from having to run the query again.
 
 If you are starting this episode here or starting this episode in a new notebook,
-you will need to run the following lines of code.
+you will need to run the following lines of code. The last two lines of the import
+statements assume your notebook is being run in the `student_download` directory. 
+If you are running it from a different directory you will need to add the path using 
+`sys.path.append(<path to student download>)` where `<path to student_download>` is 
+the path to your `student_download` directory ending with `student_download`.
 
 This imports previously imported functions:
 
 ```python
 import astropy.units as u
 from astropy.coordinates import SkyCoord
-from gala.coordinates import GD1Koposov10
 from astropy.table import Table
 
 from episode_functions import *
+from gd1 import GD1Koposov10
 ```
 
 The following code loads in the data (instructions for downloading data can be
@@ -430,10 +434,11 @@ That might seem like a strange thing to do, but here is the motivation:
 With this preparation, we can use `reflex_correct` from Gala
 ([documentation
 here](https://gala-astro.readthedocs.io/en/latest/api/gala.coordinates.reflex_correct.html))
-to correct for the motion of the solar system.
+to correct for the motion of the solar system which we have included as a stand alone file
+in the `student_download`.
 
 ```python
-from gala.coordinates import reflex_correct
+from reflex import reflex_correct
 
 skycoord_gd1 = reflex_correct(transformed)
 ```

episodes/05-select.md

@@ -64,7 +64,12 @@ Whether you are working from a new notebook or coming back from a checkpoint,
 reloading the data will save you from having to run the query again.
 
 If you are starting this episode here or starting this episode in a new notebook,
-you will need to run the following lines of code.
+you will need to run the following lines of code. The last two lines of the import
+statements assume your notebook is being run in the `student_download` directory. 
+If you are running it from a different directory you will need to add the path using 
+`sys.path.append(<path to student download>)` where `<path to student_download>` is 
+the path to your `student_download` directory ending with `student_download`.
+
 
 This imports previously imported functions:
 
@@ -77,6 +82,8 @@ import matplotlib.pyplot as plt
 import pandas as pd
 
 from episode_functions import *
+from gd1 import GD1Koposov10
+from reflex import reflex_correct
 ```
 
 The following code loads in the data (instructions for downloading data can be

student_download/episode_functions.py

@@ -7,7 +7,8 @@
 
 import astropy.units as u
 from astropy.coordinates import SkyCoord
-from gala.coordinates import GD1Koposov10, reflex_correct
+from gd1 import GD1Koposov10
+from reflex import reflex_correct
 
 ##########################
 # Episode 2

student_download/gd1.py

@@ -0,0 +1,96 @@
+"""Astropy coordinate class for the GD-1 coordinate system"""
+
+import astropy.coordinates as coord
+import astropy.units as u
+import numpy as np
+from astropy.coordinates import frame_transform_graph
+
+__all__ = ["GD1Koposov10"]
+
+
+class GD1Koposov10(coord.BaseCoordinateFrame):
+    """
+    A Heliocentric spherical coordinate system defined by the orbit of the GD1 stream,
+    as described in Koposov et al. 2010 (see: `<http://arxiv.org/abs/0907.1085>`_).
+
+    For more information about this class, see the Astropy documentation on coordinate
+    frames in :mod:`~astropy.coordinates`.
+
+    Parameters
+    ----------
+    representation : :class:`~astropy.coordinates.BaseRepresentation` or None
+        A representation object or None to have no data (or use the other keywords)
+    phi1 : angle_like, optional, must be keyword
+        The longitude-like angle corresponding to GD-1's orbit.
+    phi2 : angle_like, optional, must be keyword
+        The latitude-like angle corresponding to GD-1's orbit.
+    distance : :class:`~astropy.units.Quantity`, optional, must be keyword
+        The Distance for this object along the line-of-sight.
+    pm_phi1_cosphi2 : :class:`~astropy.units.Quantity`, optional, must be keyword
+        The proper motion in the longitude-like direction corresponding to
+        the GD-1 stream's orbit.
+    pm_phi2 : :class:`~astropy.units.Quantity`, optional, must be keyword
+        The proper motion in the latitude-like direction perpendicular to the
+        GD-1 stream's orbit.
+    radial_velocity : :class:`~astropy.units.Quantity`, optional, must be keyword
+        The radial velocity for this object along the line-of-sight.
+
+    """
+
+    default_representation = coord.SphericalRepresentation
+    default_differential = coord.SphericalCosLatDifferential
+
+    frame_specific_representation_info = {
+        coord.SphericalRepresentation: [
+            coord.RepresentationMapping("lon", "phi1"),
+            coord.RepresentationMapping("lat", "phi2"),
+            coord.RepresentationMapping("distance", "distance"),
+        ],
+    }
+
+    _default_wrap_angle = 180 * u.deg
+
+    def __init__(self, *args, **kwargs):
+        wrap = kwargs.pop("wrap_longitude", True)
+        super().__init__(*args, **kwargs)
+        if wrap and isinstance(
+            self._data,
+            coord.UnitSphericalRepresentation | coord.SphericalRepresentation,
+        ):
+            self._data.lon.wrap_angle = self._default_wrap_angle
+
+    # TODO: remove this. This is a hack required as of astropy v3.1 in order
+    # to have the longitude components wrap at the desired angle
+    def represent_as(self, base, s="base", in_frame_units=False):
+        r = super().represent_as(base, s=s, in_frame_units=in_frame_units)
+        if hasattr(r, "lon"):
+            r.lon.wrap_angle = self._default_wrap_angle
+        return r
+
+    represent_as.__doc__ = coord.BaseCoordinateFrame.represent_as.__doc__
+
+
+# Rotation matrix as defined in the Appendix of Koposov et al. (2010)
+R = np.array(
+    [
+        [-0.4776303088, -0.1738432154, 0.8611897727],
+        [0.510844589, -0.8524449229, 0.111245042],
+        [0.7147776536, 0.4930681392, 0.4959603976],
+    ]
+)
+
+
+@frame_transform_graph.transform(coord.StaticMatrixTransform, coord.ICRS, GD1Koposov10)
+def icrs_to_gd1():
+    """
+    Compute the transformation from ICRS spherical to heliocentric GD-1 coordinates.
+    """
+    return R
+
+
+@frame_transform_graph.transform(coord.StaticMatrixTransform, GD1Koposov10, coord.ICRS)
+def gd1_to_icrs():
+    """
+    Compute the transformation from heliocentric GD-1 coordinates to ICRS spherical.
+    """
+    return icrs_to_gd1().T

student_download/reflex.py

@@ -0,0 +1,43 @@
+import astropy.coordinates as coord
+
+__all__ = ["reflex_correct"]
+
+
+def reflex_correct(coords, galactocentric_frame=None):
+    """Correct the input Astropy coordinate object for solar reflex motion.
+
+    The input coordinate instance must have distance and radial velocity information.
+    So, if the radial velocity is not known, fill the radial velocity values with zeros
+    to reflex-correct the proper motions.
+
+    Parameters
+    ----------
+    coords : `~astropy.coordinates.SkyCoord`
+        The Astropy coordinate object with position and velocity information.
+    galactocentric_frame : `~astropy.coordinates.Galactocentric` (optional)
+        To change properties of the Galactocentric frame, like the height of the
+        sun above the midplane, or the velocity of the sun in a Galactocentric
+        intertial frame, set arguments of the
+        `~astropy.coordinates.Galactocentric` object and pass in to this
+        function with your coordinates.
+
+    Returns
+    -------
+    coords : `~astropy.coordinates.SkyCoord`
+        The coordinates in the same frame as input, but with solar motion
+        removed.
+
+    """
+    c = coord.SkyCoord(coords)
+
+    # If not specified, use the Astropy default Galactocentric frame
+    if galactocentric_frame is None:
+        galactocentric_frame = coord.Galactocentric()
+
+    v_sun = galactocentric_frame.galcen_v_sun
+
+    observed = c.transform_to(galactocentric_frame)
+    rep = observed.cartesian.without_differentials()
+    rep = rep.with_differentials(observed.cartesian.differentials["s"] + v_sun)
+    fr = galactocentric_frame.realize_frame(rep).transform_to(c.frame)
+    return coord.SkyCoord(fr)

student_download/test_setup.ipynb

@@ -195,31 +195,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import gala.coordinates as gc"
+    "from gd1 import GD1Koposov10\n",
+    "from reflex import reflex_correct"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 7,
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Created TAP+ (v20200428.1) - Connection:\n",
-      "\tHost: gea.esac.esa.int\n",
-      "\tUse HTTPS: True\n",
-      "\tPort: 443\n",
-      "\tSSL Port: 443\n",
-      "Created TAP+ (v20200428.1) - Connection:\n",
-      "\tHost: gea.esac.esa.int\n",
-      "\tUse HTTPS: True\n",
-      "\tPort: 443\n",
-      "\tSSL Port: 443\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "# Note: running this import statement opens a connection\n",
     "# to a Gaia server, so it will fail if you are not connected\n",
@@ -258,9 +242,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python (AstronomicalData)",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "astronomicaldata"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -272,7 +256,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.6"
+   "version": "3.9.17"
   }
  },
  "nbformat": 4,