Merge pull request #62 from osyris-project/repair_loaders

Better select behaviour in loaders

README.md

@@ -31,7 +31,7 @@ data = osyris.Dataset(8, scale="au", path="data").load()
 osyris.histogram2d(data["hydro"]["density"], data["hydro"]["B_field"],
                    norm="log", loglog=True)
 ```
-![hist2d](https://osyris.readthedocs.io/en/stable/_images/plotting_3_1.png)
+![hist2d](https://osyris.readthedocs.io/en/stable/_images/plotting_histograms_13_1.png)
 
 Create a 2D gas density slice 2000 au wide through the plane normal to ``z``,
 with velocity vectors overlayed as arrows, once again using ``layers``:
@@ -45,7 +45,7 @@ osyris.plane({"data": data["hydro"]["density"], "norm": "log"}, # layer 1
              origin=center,
              direction="z")
 ```
-![map2d](https://osyris.readthedocs.io/en/stable/_images/plotting_7_1.png)
+![map2d](https://osyris.readthedocs.io/en/stable/_images/plotting_maps_23_1.png)
 
 ## Have a problem or need a new feature?
 

docs/basics.ipynb

@@ -148,7 +148,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "## Simple cut plane\n",
+    "## Simple 2D map\n",
     "\n",
     "The goal here is to create a 2D gas density slice, 2000 au wide, through the plane normal to `z`,\n",
     "that passes through the center of the young star forming system.\n",
@@ -172,7 +172,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Once we have this center coordinate, we can use it as the origin for our cut plane:"
+    "Once we have this center coordinate, we can use it as the origin for our cut plane and create a map:"
    ]
   },
   {
@@ -181,24 +181,24 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=2000 * osyris.units('au'),\n",
-    "             origin=center,\n",
-    "             direction=\"z\")"
+    "osyris.map({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
+    "           dx=2000 * osyris.units('au'),\n",
+    "           origin=center,\n",
+    "           direction=\"z\")"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "where the first argument is the variable to display, `dx` is the extent of the vieweing region,\n",
-    "and `direction` is the normal to the slice plane."
+    "where the first argument is the variable to display, `dx` is the extent of the viewing region,\n",
+    "and `direction` is the normal to the slicing plane."
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -212,9 +212,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.10"
+   "version": "3.9.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

docs/installation.ipynb

@@ -22,6 +22,40 @@
     "$ pip install osyris"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "If you have already installed `osyris` in the past, but would like to upgrade, use"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "$ pip install osyris --upgrade"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "<div class=\"alert alert-warning\">\n",
+    "\n",
+    "**Warning**\n",
+    "\n",
+    "If you are upgrading from an old version to a version >= 2.6.0,\n",
+    "and you are getting some strange errors,\n",
+    "you may need to update your `config_osyris.py` configuration file in `/home/user/.osyris`.\n",
+    "\n",
+    "- If you had never touched the configuration file, it is safe to simply delete it (a new one will be created when importing `osyris`).\n",
+    "- If you had made changes to the configuration, the easiest is probably to move it to a new location/filename. Then import `osyris` and update the newly created file to incorporate the changes you had made previously.\n",
+    "\n",
+    "</div>"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -73,7 +107,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -87,7 +121,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.9.5"
   },
   "nbsphinx": {
    "execute": "never"

docs/loading_data.ipynb

@@ -117,19 +117,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=1000 * osyris.units('au'),\n",
-    "             origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
-    "             direction='z')"
+    "osyris.map({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
+    "           dx=1000 * osyris.units('au'),\n",
+    "           origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
+    "           direction='z')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Only loading certain variables\n",
+    "### Only loading certain groups or variables\n",
     "\n",
-    "It is also possible to skip a variable entirely by setting the key to `False` in the `select` dict:"
+    "It is also possible to select which groups to load.\n",
+    "The different groups are `'amr'`, `'hydro'`, `'grav'`, `'rt'`, and `'part'`.\n",
+    "For example, to load only the `amr` and `hydro` groups, use"
    ]
   },
   {
@@ -138,18 +140,21 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
-    "    select={\"hydro\": {\"density\": False}})\n",
-    "\"density\" in data[\"hydro\"]"
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(['amr', 'hydro'])\n",
+    "data.keys()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Entire groups of variables can also be skipped.\n",
-    "The different groups are `'amr'`, `'hydro'`, `'grav'` (or `'gravity'`), `'rt'`, and `'part'`.\n",
-    "Loading all but the hydro variables can be achieved via"
+    "It is also possible to load or skip only a single variable in a group,\n",
+    "by setting the key to `True` or `False` in the `select` dict.\n",
+    "\n",
+    "The convention is:\n",
+    "\n",
+    "- If at least one key in a group is set to `True`, all unspecified variables in the group are skipped\n",
+    "- If a key is set to `False` in a group, all other variables are loaded"
    ]
   },
   {
@@ -159,8 +164,19 @@
    "outputs": [],
    "source": [
     "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
-    "    select={\"hydro\": False})\n",
-    "data"
+    "    select={\"hydro\": {\"density\": False}})\n",
+    "\"density\" in data[\"hydro\"]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(\n",
+    "    select={\"hydro\": {\"temperature\": True, \"thermal_pressure\": True}})\n",
+    "data[\"hydro\"].keys()"
    ]
   },
   {
@@ -234,10 +250,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.plane({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
-    "             dx=2000 * osyris.units(\"au\"),\n",
-    "             origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
-    "             direction='z')"
+    "osyris.map({\"data\": data[\"hydro\"][\"density\"], \"norm\": \"log\"},\n",
+    "           dx=2000 * osyris.units(\"au\"),\n",
+    "           origin=data[\"amr\"][\"xyz\"][np.argmax(data[\"hydro\"][\"density\"]).values],\n",
+    "           direction='z')"
    ]
   },
   {
@@ -254,11 +270,95 @@
     "\n",
     "</div>"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Example: loading a region around a sink particle\n",
+    "\n",
+    "Combining some of the methods illustrated above,\n",
+    "we show here how to load only a small region 400 AU wide around a sink particle.\n",
+    "\n",
+    "We begin by loading only the sink particle data, by using `select='sink'` in the `load` method:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data = osyris.Dataset(8, scale=\"au\", path=path).load(select='sink')\n",
+    "data"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "The `sink` data group contains the positions of the sink particles.\n",
+    "We wish to load the region around the first sink particle, which will be the center of our domain."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "center = data['sink']['xyz'][0:1]\n",
+    "dx = 200 * osyris.units('au')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We are now in a position to load the rest of the data (`amr`, `hydro`, etc.)\n",
+    "and perform a spatial selection based on the sink's position\n",
+    "(note how the loading below is only looking through 6 files, as opposed to 12 at the top of the notebook,\n",
+    "because it uses the knowledge from the Hilbert space-filling curve to skip CPUs that are not connected\n",
+    "to the domain of interest)."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data.load(\n",
+    "    select={\"amr\": {\"x\": lambda x : np.logical_and(x > center.x - dx, x < center.x + dx),\n",
+    "                    \"y\": lambda y : np.logical_and(y > center.y - dx, y < center.y + dx),\n",
+    "                    \"z\": lambda z : np.logical_and(z > center.z - dx, z < center.z + dx)}\n",
+    "           })"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Finally, we can make a map of the gas density around our sink particle\n",
+    "(note that no spatial limits are specified in the `map` call,\n",
+    "it is making a map using all the cells that have been loaded)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "osyris.map(data[\"hydro\"][\"density\"],\n",
+    "           {\"data\": data[\"sink\"][\"xyz\"], \"mode\": \"scatter\", \"c\": \"white\"},\n",
+    "           norm='log', direction=\"z\", origin=center[0])"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -272,9 +372,9 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.1"
+   "version": "3.9.5"
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = osyris
-version = 2.5.1
+version = 2.6.0
 author = Neil Vaytet
 author_email = [email protected]
 description = A package to visualize AMR data from the RAMSES code

src/osyris/config/defaults.py

@@ -17,7 +17,7 @@
 }
 
 
-def get_unit(string, ud, ul, ut):
+def get_unit(string, ud, ul, ut, scale):
 
     density = ud * (ureg.g / (ureg.cm**3))
     velocity = (ul / ut) * (ureg.cm / ureg.s)
@@ -29,6 +29,11 @@ def get_unit(string, ud, ul, ut):
     length = ul * ureg.cm
     mass = density * (length**3)
 
+    scaling = length
+    if scale is not None:
+        scale = ureg(scale)
+        scaling = (length.to(scale) / scale).magnitude * scale
+
     ramses_units = {
         'density': density,
         'velocity': velocity,
@@ -67,10 +72,16 @@ def get_unit(string, ud, ul, ut):
         'radiative_energy_1': energy,
         'temperature': 1.0 * ureg.K,
         'time': time,
-        'x': length,
-        'y': length,
-        'z': length,
-        'dx': length,
+        'x': scaling,
+        'y': scaling,
+        'z': scaling,
+        'xyz_x': scaling,
+        'xyz_y': scaling,
+        'xyz_z': scaling,
+        'position_x': scaling,
+        'position_y': scaling,
+        'position_z': scaling,
+        'dx': scaling,
         'mass': mass
     }