Merge pull request #137 from osyris-project/new-hist2d

New hist2d
osyris-project · Jul 4, 2024 · 615e33e · 615e33e
2 parents c90f15a + 4405d69
commit 615e33e
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Showing 14 changed files with 262 additions and 332 deletions.
diff --git a/README.md b/README.md
@@ -30,8 +30,8 @@ import numpy as np
 import osyris
 
 data = osyris.RamsesDataset(8, path="data").load()
-osyris.histogram2d(data["mesh"]["density"], data["mesh"]["B_field"],
-                   norm="log", loglog=True)
+osyris.hist2d(data["mesh"]["density"], data["mesh"]["B_field"],
+              norm="log", loglog=True)
 ```
 ![hist2d](https://osyris.readthedocs.io/en/stable/_images/plotting_histograms_13_1.png)
 

diff --git a/docs/api.rst b/docs/api.rst
@@ -22,8 +22,8 @@ Plotting
 .. autosummary::
    :toctree: generated
 
-   histogram1d
-   histogram2d
+   hist1d
+   hist2d
    map
    plot
    scatter
diff --git a/docs/basics.ipynb b/docs/basics.ipynb
@@ -137,9 +137,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
-    "    data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True\n",
-    ")"
+    "osyris.hist2d(data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True)"
    ]
   },
   {

diff --git a/docs/custom_datasets.ipynb b/docs/custom_datasets.ipynb
@@ -121,7 +121,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram1d(dg[\"density\"])"
+    "osyris.hist1d(dg[\"density\"])"
    ]
   },
   {

diff --git a/docs/loading_data.ipynb b/docs/loading_data.ipynb
@@ -49,9 +49,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
-    "    data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True\n",
-    ")"
+    "osyris.hist2d(data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True)"
    ]
   },
   {
@@ -91,9 +89,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
-    "    data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True\n",
-    ")"
+    "osyris.hist2d(data[\"mesh\"][\"density\"], data[\"mesh\"][\"B_field\"], norm=\"log\", loglog=True)"
    ]
   },
   {

diff --git a/docs/plotting_histograms.ipynb b/docs/plotting_histograms.ipynb
@@ -33,8 +33,8 @@
    "source": [
     "## 1D histograms\n",
     "\n",
-    "The `histogram1d` function provides a simple way to make 1D histogram plots.\n",
-    "When a vector quantity is supplied, by default `histogram1d` will use the norm of the vectors.\n",
+    "The `hist1d` function provides a simple way to make 1D histogram plots.\n",
+    "When a vector quantity is supplied, by default `hist1d` will use the norm of the vectors.\n",
     "\n",
     "### A 1D histogram of gas density\n",
     "\n",
@@ -47,7 +47,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram1d(mesh[\"density\"], logx=True)"
+    "osyris.hist1d(mesh[\"density\"], logx=True)"
    ]
   },
   {
@@ -66,7 +66,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram1d(mesh[\"density\"], logx=True, bins=np.logspace(-18.0, -13.0, 10))"
+    "osyris.hist1d(mesh[\"density\"], logx=True, bins=np.logspace(-18.0, -13.0, 10))"
    ]
   },
   {
@@ -75,7 +75,7 @@
    "source": [
     "### Weighted histogram\n",
     "\n",
-    "By default, `histogram1d` will show a binned count of cells, but it does also support weights.\n",
+    "By default, `hist1d` will show a binned count of cells, but it does also support weights.\n",
     "For example, creating a mass-weighted histogram of the gas density can be achieved via"
    ]
   },
@@ -86,7 +86,7 @@
    "outputs": [],
    "source": [
     "mesh[\"mass\"] = (mesh[\"density\"] * (mesh[\"dx\"] ** 3)).to(\"M_sun\")\n",
-    "osyris.histogram1d(mesh[\"density\"], weights=mesh[\"mass\"], logx=True)"
+    "osyris.hist1d(mesh[\"density\"], weights=mesh[\"mass\"], logx=True)"
    ]
   },
   {
@@ -107,7 +107,7 @@
    "outputs": [],
    "source": [
     "bins = np.linspace(-0.15, 0.15, 40)\n",
-    "osyris.histogram1d(\n",
+    "osyris.hist1d(\n",
     "    mesh.layer(\"B_field\", alpha=0.5).x,\n",
     "    mesh.layer(\"B_field\", alpha=0.5).y,\n",
     "    mesh.layer(\"B_field\", alpha=0.5).z,\n",
@@ -129,7 +129,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram1d(\n",
+    "osyris.hist1d(\n",
     "    mesh.layer(\"B_field\", alpha=0.5, bins=40).x,\n",
     "    mesh.layer(\"B_field\", alpha=0.5, bins=10).y,\n",
     "    logy=True,\n",
@@ -142,8 +142,8 @@
    "source": [
     "## 2D histograms\n",
     "\n",
-    "The `histogram2d` function can be used to make 2D histograms with two different quantities as input.\n",
-    "When a vector quantity is supplied, by default `histogram2d` will use the norm of the vectors\n",
+    "The `hist2d` function can be used to make 2D histograms with two different quantities as input.\n",
+    "When a vector quantity is supplied, by default `hist2d` will use the norm of the vectors\n",
     "\n",
     "### A 2D histogram of gas density vs magnetic field magnitude\n",
     "\n",
@@ -156,7 +156,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(mesh[\"density\"], mesh[\"B_field\"], norm=\"log\", loglog=True)"
+    "osyris.hist2d(mesh[\"density\"], mesh[\"B_field\"], norm=\"log\", loglog=True)"
    ]
   },
   {
@@ -174,7 +174,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    norm=\"log\",\n",
@@ -192,7 +192,7 @@
     "### Controlling the horizontal and vertical range\n",
     "\n",
     "To control the range covered by the horizontal and vertical binning,\n",
-    "the `xmin`, `xmax`, `ymin`, `ymax` arguments are provided."
+    "specify the bins manually."
    ]
   },
   {
@@ -201,13 +201,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    norm=\"log\",\n",
     "    loglog=True,\n",
-    "    xmax=1.0e-16,\n",
-    "    ymax=1.0e-3,\n",
+    "    bins=(np.logspace(-19, -16, 301), np.logspace(-5, -3, 301)),\n",
     ")"
    ]
   },
@@ -217,7 +216,7 @@
    "source": [
     "### Using a layer for the colormap instead of counting cells\n",
     "\n",
-    "By default, `histogram2d` will show a binned count of cells.\n",
+    "By default, `hist2d` will show a binned count of cells.\n",
     "However, the colors can represent the histogram of a supplied `Array` instead."
    ]
   },
@@ -227,7 +226,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    mesh.layer(\"mass\", norm=\"log\"),\n",
@@ -255,7 +254,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    mesh.layer(\"level\", operation=\"mean\"),\n",
@@ -269,7 +268,7 @@
    "source": [
     "### Multiple layers\n",
     "\n",
-    "One can use any number of layers to overlay, although anything being two layers is probably not very useful."
+    "One can use any number of layers to overlay, although anything beyond two layers is probably not very useful."
    ]
   },
   {
@@ -278,7 +277,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    mesh.layer(\"mass\", norm=\"log\"),  # layer 1\n",
@@ -301,9 +300,7 @@
     "### Controlling the resolution\n",
     "\n",
     "By default, the histograms have a resolution of 256x256 pixels.\n",
-    "This can be changed via the keyword argument `resolution`,\n",
-    "which can either be an integer (in which case the same resolution is applied to both the x and y dimension)\n",
-    "or a dict with the syntax `resolution={'x': nx, 'y': ny}`."
+    "To change the resolution, we use the `bins` argument:"
    ]
   },
   {
@@ -312,12 +309,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    norm=\"log\",\n",
     "    loglog=True,\n",
-    "    resolution=64,\n",
+    "    bins=64,\n",
     ")"
    ]
   },
@@ -345,15 +342,15 @@
     "\n",
     "fig, ax = plt.subplots(2, 2, figsize=(12, 9))\n",
     "\n",
-    "osyris.histogram1d(mesh[\"density\"], logx=True, ax=ax[0, 0])\n",
-    "osyris.histogram2d(\n",
+    "osyris.hist1d(mesh[\"density\"], logx=True, ax=ax[0, 0])\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"B_field\"],\n",
     "    norm=\"log\",\n",
     "    loglog=True,\n",
     "    ax=ax[0, 1],\n",
     ")\n",
-    "osyris.histogram1d(\n",
+    "osyris.hist1d(\n",
     "    mesh[\"B_field\"].x,\n",
     "    mesh[\"B_field\"].y,\n",
     "    mesh[\"B_field\"].z,\n",
@@ -362,7 +359,7 @@
     "    bins=np.linspace(-0.15, 0.15, 40),\n",
     "    ax=ax[1, 0],\n",
     ")\n",
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    mesh[\"density\"],\n",
     "    mesh[\"velocity\"],\n",
     "    mesh[\"mass\"],\n",
@@ -389,8 +386,7 @@
    "mimetype": "text/x-python",
    "name": "python",
    "nbconvert_exporter": "python",
-   "pygments_lexer": "ipython3",
-   "version": "3.10.12"
+   "pygments_lexer": "ipython3"
   }
  },
  "nbformat": 4,

diff --git a/docs/plotting_particles.ipynb b/docs/plotting_particles.ipynb
@@ -59,11 +59,11 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "osyris.histogram2d(\n",
+    "osyris.hist2d(\n",
     "    part[\"position\"].x,\n",
     "    part[\"position\"].y,\n",
     "    part[\"mass\"],\n",
-    "    resolution=512,\n",
+    "    bins=512,\n",
     "    norm=\"log\",\n",
     ")"
    ]

diff --git a/docs/recipes.ipynb b/docs/recipes.ipynb
@@ -33,10 +33,10 @@
     "\n",
     "Here, we want to make a map of the difference in 2D histograms between two snapshots (outputs `5` and `8`).\n",
     "Because we do not necessarily have the same number of cells at the same place,\n",
-    "we first have to make uniform 2D maps using the `histogram2d` function,\n",
+    "we first have to make uniform 2D maps using the `hist2d` function,\n",
     "which we can then directly compare.\n",
     "\n",
-    "The `histogram2d` function actually returns an object that contains the raw data that was used to create the figure.\n",
+    "The `hist2d` function actually returns an object that contains the raw data that was used to create the figure.\n",
     "By using the `plot=False` argument, we can silence the figure generation, and use the data in a custom figure.\n",
     "\n",
     "**Note:** For the comparison to make sense, both histograms have to use the same horizontal and vertical range."
@@ -48,15 +48,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "hist5 = osyris.histogram2d(\n",
+    "hist5 = osyris.hist2d(\n",
     "    data5[\"mesh\"][\"density\"],\n",
     "    data5[\"mesh\"][\"B_field\"],\n",
     "    norm=\"log\",\n",
     "    loglog=True,\n",
     "    plot=False,\n",
     ")\n",
     "\n",
-    "hist8 = osyris.histogram2d(\n",
+    "hist8 = osyris.hist2d(\n",
     "    data8[\"mesh\"][\"density\"],\n",
     "    data8[\"mesh\"][\"B_field\"],\n",
     "    norm=\"log\",\n",

diff --git a/src/osyris/__init__.py b/src/osyris/__init__.py
@@ -1,9 +1,9 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Osyris contributors (https://github.com/osyris-project/osyris)
 
-""" Osyris: A Python package for the analysis of astrophysical simulations
+"""Osyris: A Python package for the analysis of astrophysical simulations
 
-   isort:skip_file
+isort:skip_file
 """
 
 import importlib.metadata
@@ -12,7 +12,7 @@
 from .units import units
 from .core import Array, Datagroup, Dataset, Plot, Vector, VectorBasis
 from .io import RamsesDataset
-from .plot import histogram1d, histogram2d, map, plot, scatter
+from .plot import hist1d, hist2d, map, plot, scatter
 from .spatial import extract_box, extract_sphere
 
 try:
@@ -32,8 +32,8 @@
     "RamsesDataset",
     "config",
     "units",
-    "histogram1d",
-    "histogram2d",
+    "hist1d",
+    "hist2d",
     "scatter",
     "map",
     "plot",

diff --git a/src/osyris/plot/__init__.py b/src/osyris/plot/__init__.py
@@ -1,11 +1,11 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # Copyright (c) 2024 Osyris contributors (https://github.com/osyris-project/osyris)
 
-from .histogram1d import histogram1d
-from .histogram2d import histogram2d
+from .hist1d import hist1d
+from .hist2d import hist2d
 from .map import map
 from .plot import plot
 from .render import render
 from .scatter import scatter
 
-__all__ = ["histogram1d", "histogram2d", "map", "plot", "render", "scatter"]
+__all__ = ["hist1d", "hist2d", "map", "plot", "render", "scatter"]