pyvlasiator 0.1.1__tar.gz → 0.1.3__tar.gz

{pyvlasiator-0.1.1 → pyvlasiator-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyvlasiator
-Version: 0.1.1
+Version: 0.1.3
 Summary: Python utilities for processing Vlasiator data
 Author: Hongyang Zhou
 Author-email: hyzhou@umich.edu

{pyvlasiator-0.1.1 → pyvlasiator-0.1.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "pyvlasiator"
-version = "0.1.1"
+version = "0.1.3"
 description = "Python utilities for processing Vlasiator data"
 authors = ["Hongyang Zhou <hyzhou@umich.edu>"]
 readme = "README.md"

{pyvlasiator-0.1.1 → pyvlasiator-0.1.3}/src/pyvlasiator/plot/__init__.py

@@ -6,6 +6,7 @@ This provides supports for plotting VLSV data via Matplotlib.
 
 from pyvlasiator.plot.plot import (
     plot,
+    scatter,
     pcolormesh,
     contour,
     contourf,

{pyvlasiator-0.1.1 → pyvlasiator-0.1.3}/src/pyvlasiator/plot/plot.py

@@ -96,24 +96,91 @@ def plot(
     >>> axes = vlsv_file.plot("helium/vg_v", ax=my_axes)  # Plot velocity on an existing axes
     """
 
-    import matplotlib.pyplot as plt
+    fig, ax = set_figure(ax, figsize, **kwargs)
 
-    fig = kwargs.pop(
-        "figure", plt.gcf() if plt.get_fignums() else plt.figure(figsize=figsize)
+    return _plot1d(
+        self,
+        ax.plot,
+        var=var,
+        **kwargs,
     )
-    if ax is None:
-        ax = fig.gca()
 
-    if not self.has_variable(var):
-        raise ValueError(f"Variable {var} not found in the file")
 
-    x = np.linspace(self.coordmin[0], self.coordmax[0], self.ncells[0])
+def scatter(
+    self: Vlsv,
+    var: str = "",
+    ax=None,
+    figsize: tuple[float, float] | None = None,
+    **kwargs,
+) -> matplotlib.collections.PathCollection:
+    """
+    Plots 1D VLSV data as scattered points.
 
-    data = self.read_variable(var)
-    axes = ax.plot(x, data, **kwargs)
+    Parameters
+    ----------
+    var : str
+        Name of the variable to plot from the VLSV file.
+    ax : matplotlib.axes._axes.Axes, optional
+        Axes object to plot on. If not provided, a new figure and axes will be created.
+    figsize : tuple[float, float], optional
+        Size of the figure in inches (width, height). Only used if a new
+        figure is created.
+    **kwargs
+        Additional keyword arguments passed to Matplotlib's `plot` function.
 
-    return axes
+    Returns
+    -------
+    matplotlib.collections.PathCollection
 
+    Raises
+    ------
+    ValueError
+        If the specified variable is not found in the VLSV file.
+
+    Examples
+    --------
+    >>> vlsv_file = Vlsv("my_vlsv_file.vlsv")
+    >>> axes = vlsv_file.scatter("proton/vg_rho")  # Plot density on a new figure
+    """
+
+    fig, ax = set_figure(ax, figsize, **kwargs)
+
+    return _plot1d(
+        self,
+        ax.scatter,
+        var=var,
+        **kwargs,
+    )
+
+
+def _plot1d(
+    meta: Vlsv,
+    plot_func: Callable,
+    var: str = "",
+    **kwargs,
+):
+    """
+    Plot 1d data with `plot_func`.
+
+    Parameters
+    ----------
+    var : str
+        Variable name from the VLSV file.
+
+    Returns
+    -------
+
+    """
+
+    if not meta.has_variable(var):
+        raise ValueError(f"Variable {var} not found in the file")
+
+    x = np.linspace(meta.coordmin[0], meta.coordmax[0], meta.ncells[0])
+    y = meta.read_variable(var)
+
+    c = plot_func(x, y, **kwargs)
+
+    return c
 
 def pcolormesh(
     self: Vlsv,
@@ -839,13 +906,13 @@ def configure_plot(
             cb.ax.set_ylabel(colorbar_title)
         cb.ax.tick_params(direction="in")
 
-    # Set plot title and labels
+    # Set title and labels
     ax.set_title(title, fontweight="bold")
     ax.set_xlabel(x_label)
     ax.set_ylabel(y_label)
     ax.set_aspect("equal")
 
-    # Style plot borders and ticks
+    # Style borders and ticks
     for spine in ax.spines.values():
         spine.set_linewidth(2.0)
     ax.tick_params(axis="both", which="major", width=2.0, length=3)
@@ -867,6 +934,7 @@ def vdfslice(
     center: str = None,
     weight: str = "particle",
     flimit: float = -1.0,
+    addcolorbar: bool = True,
     **kwargs,
 ):
     v1, v2, r1, r2, weights, strx, stry, str_title = prep_vdf(
@@ -908,9 +976,10 @@ def vdfslice(
     ax.grid(color="grey", linestyle="-")
     ax.tick_params(direction="in")
 
-    cb = plt.colorbar(h[3], ax=ax, fraction=0.04, pad=0.02)
-    cb.ax.tick_params(which="both", direction="in")
-    cb_title = cb.ax.set_ylabel("f(v)")
+    if addcolorbar:
+        cb = plt.colorbar(h[3], ax=ax, fraction=0.04, pad=0.02)
+        cb.ax.tick_params(which="both", direction="in")
+        cb_title = cb.ax.set_ylabel("f(v)")
 
     # TODO: Draw vector of magnetic field direction
     # if slicetype in ("xy", "xz", "yz"):
@@ -1108,6 +1177,7 @@ def prep_vdf(
 
 # Append plotting functions
 Vlsv.plot = plot
+Vlsv.scatter = scatter
 Vlsv.pcolormesh = pcolormesh
 Vlsv.contourf = contourf
 Vlsv.contour = contour

{pyvlasiator-0.1.1 → pyvlasiator-0.1.3}/src/pyvlasiator/vlsv/reader.py

@@ -405,14 +405,16 @@ class Vlsv:
         )
         if hasattr(cellids, "__len__"):  # part of cells requested
             return np.float32(raw)
-
-        if sorted:
-            if raw.ndim == 1:
-                v = raw[self.cellindex]
+        elif cellids == -1:
+            if sorted:
+                if raw.ndim == 1:
+                    v = raw[self.cellindex]
+                else:
+                    v = raw[self.cellindex, :]
+                if v.dtype == np.float64:  # 32-bit is enough for analysis
+                    v = np.float32(v)
             else:
-                v = raw[self.cellindex, :]
-            if v.dtype == np.float64:  # 32-bit is enough for analysis
-                v = np.float32(v)
+                v = raw
         else:
             v = raw