Merge branch 'main' into docs/user_guide/usage

docs/source/reference/index.md

@@ -5,5 +5,6 @@
 
 catalog
 config
+plots
 analysis
 ```

docs/source/reference/plots.md

@@ -0,0 +1,20 @@
+# Plotting functions
+
+```{eval-rst}
+.. currentmodule:: seismostats
+```
+
+## 
+
+```{eval-rst}
+.. autosummary::
+    :toctree: api/
+
+    :func: 
+    plot_cum_fmd
+    plot_fmd
+    plot_cum_count
+    plot_mags_in_time
+    plot_in_space
+    plot_mc_vs_b
+```

seismostats/plots/basics.py

@@ -35,10 +35,10 @@ def plot_cum_fmd(
     bin_position: str = "center",
     legend: bool | str | list = True,
 ) -> plt.Axes:
-    """Plots cumulative frequency magnitude distribution, optionally with a
-    corresponding theoretical Gutenberg-Richter (GR) distribution (using the
-    provided b-value). Unlike plot_cum_fmd, plots values for all bins and
-    requires binning.
+    """
+    Plots cumulative frequency magnitude distribution, optionally with a
+    corresponding theoretical Gutenberg-Richter (GR) distribution. The GR
+    distribution is plotted provided the b-value is given.
 
     Args:
         mags    : array of magnitudes
@@ -47,10 +47,13 @@ def plot_cum_fmd(
         mc      : completeness magnitude of the theoretical GR distribution
         delta_m : discretization of the magnitudes, important for the correct
                 visualization of the data
-        color   : color of the data. If theoretical GR distribution should be
-            colored differently this should be a list with two entries
-        size    : size of scattered data
-        grid    : bool, include grid lines or not
+        color   : color of the data. If one value is given, it is used for
+            points, and the line of the theoretical GR distribution if it
+            is plotted. If a list of colors is given, the first entry is
+            the color of the points, and the second of the line representing
+            the GR distribution.
+        size    : size of data points
+        grid    : whether to include grid lines or not
         bin_position    : position of the bin, options are  'center' and 'left'
                         accordingly, left edges of bins or center points are
                         returned.
@@ -113,11 +116,11 @@ def plot_cum_fmd(
     ax.set_xlabel("Magnitude")
     ax.set_ylabel("N")
 
-    if grid is True:
+    if grid:
         ax.grid(True)
         ax.grid(which="minor", alpha=0.3)
 
-    if legend is not False:
+    if legend:
         ax.legend()
 
     return ax
@@ -133,18 +136,19 @@ def plot_fmd(
     bin_position: str = "center",
     legend: bool | str | list = True,
 ) -> plt.Axes:
-    """Plots frequency magnitude distribution. Unlike plot_fmd,
-    plots values for all bins and requires binning.
+    """
+    Plots frequency magnitude distribution. If no binning is specified, the
+    assumed value of ``delta_m`` is 0.1.
 
     Args:
         mags    : array of magnitudes
         ax      : axis where figure should be plotted
         delta_m : discretization of the magnitudes, important for the correct
                 visualization of the data
-        color   : color of the data.
-        size    : size of scattered data
-        grid    : bool, include grid lines or not
-        bin_position    : position of the bin, options are  'center' and 'left'
+        color   : color of the data
+        size    : size of data points
+        grid    : whether to include grid lines or not
+        bin_position    : position of the bin, options are  "center" and "left"
                         accordingly, left edges of bins or center points are
                         returned.
 
@@ -174,11 +178,11 @@ def plot_fmd(
     ax.set_xlabel("Magnitude")
     ax.set_ylabel("N")
 
-    if grid is True:
+    if grid:
         ax.grid(True)
         ax.grid(which="minor", alpha=0.3)
 
-    if legend is not False:
+    if legend:
         ax.legend()
 
     return ax
@@ -192,7 +196,8 @@ def plot_cum_count(
 ) -> plt.Axes:
     """
     Plots cumulative count of earthquakes in given catalog above given Mc
-    through time. Plots a line for each given Mc.
+    through time. Plots a line for each given completeness magnitude in
+    the array ``mcs``.
 
     Args:
         ax: axis where figure should be plotted
@@ -226,8 +231,8 @@ def plot_cum_count(
             label=f"Mc={np.round(mc, 2)}",
         )
 
-    ax.set_xlabel("time")
-    ax.set_ylabel("count - cumulative")
+    ax.set_xlabel("Time")
+    ax.set_ylabel("Cumulative number of events")
     ax.legend()
     return ax
 
@@ -240,25 +245,29 @@ def plot_mags_in_time(
     dot_smallest: int = 10,
     dot_largest: int = 200,
     dot_interpolation_power: int = 2,
+    color_dots: str = "blue",
+    color_line: str = "#eb4034",
 ) -> plt.Axes:
     """
-    Creates a scatter plot, each dot is an event. Time shown on x-axis,
-    magnitude shown on y-axis, but also in size of the dot.
+    Creates a scatter plot, each dot is an event. Time shown on the x-axis,
+    magnitude shown on the y-axis, but also reflected in the size of dots.
 
     Optionally, adds lines that represent the change in completeness magnitude.
-    For example, mc_change_times = [2000, 2005] and mcs = [3.5, 3.0] means that
-    between 2000 and 2005, Mc is 3.5 and after 2005, Mc is 3.0.
+    For example, ``mc_change_times = [2000, 2005]`` and ``mcs = [3.5, 3.0]``
+    means that between 2000 and 2005, Mc is 3.5 and after 2005, Mc is 3.0.
 
     Args:
         ax: axis where figure should be plotted
         cat: catalog given as a pandas dataframe, should contain the column
              "magnitude" and  either "time" or "year"
         mc_change_times: list of points in time when Mc changes, sorted in
             increasing order, can be given as a list of datetimes or ints (yrs).
-        mcs: changed values of Mc at times given in 'mc_change_times'
+        mcs: changed values of Mc at times given in ``mc_change_times``
         dot_smallest: smallest dot size for magnitude scaling
-        dot_largest:largest dot size for magnitude scaling
+        dot_largest: largest dot size for magnitude scaling
         dot_interpolation_power: interpolation power for scaling
+        color_dots: color of the dots representing the events
+        color_line: color of the line representing the Mc changes
 
     Returns:
         ax that was plotted on
@@ -287,7 +296,7 @@ def plot_mags_in_time(
             largest=dot_largest,
             interpolation_power=dot_interpolation_power,
         ),
-        c="b",
+        c=color_dots,
         linewidth=0.5,
         alpha=0.8,
         edgecolor="k",
@@ -301,20 +310,22 @@ def plot_mags_in_time(
 
         mc_change_times.append(np.max(times))
         mcs.append(mcs[-1])
-        ax.step(mc_change_times, mcs, where="post", c="#eb4034")
+        ax.step(mc_change_times, mcs, where="post", c=color_line)
 
-    ax.set_xlabel("time")
-    ax.set_ylabel("magnitude")
+    ax.set_xlabel("Time")
+    ax.set_ylabel("Magnitude")
     return ax
 
 
 def dot_size(
     magnitudes: np.array,
-    smallest: int = 10,
-    largest: int = 200,
+    smallest: float = 10,
+    largest: float = 200,
     interpolation_power: int = 1,
 ) -> np.array:
-    """Compute dot sizes proportional to a given array of magnitudes.
+    """
+    Auxiliary function, computes dot sizes proportional to a given array of
+    magnitudes.
 
     The dot sizes are computed using a power interpolation between the smallest
     and largest size, with the given interpolation power.
@@ -336,7 +347,7 @@ def dot_size(
     -------
     sizes : ndarray of float, shape (n_samples,)
         The sizes of the dots, proportional to their magnitudes.
-        The returned sizes are between `smallest` and `largest`.
+        The returned sizes are between ``smallest`` and ``largest``.
     """
     if largest <= smallest:
         print(

seismostats/plots/seismicity.py

@@ -29,37 +29,38 @@ def plot_in_space(
     dot_labels: str = "auto",
 ) -> cartopy.mpl.geoaxes.GeoAxes:
     """
-     Function plots seismicity on the surface. If include_map is chosen True,
-    a nice natural earth map is used, otherwise the seismicity is just
-    plotted on a blank grid. In the latter case, the grid is stretched to
+    This function plots seismicity on a surface. If ``include_map`` is
+    set to ``True``, a nice natural earth map is used, otherwise the seismicity
+    is just plotted on a blank grid. In the latter case, the grid is stretched
     according to the midpoint latitude.
 
     Args:
-        cat:            dataframe- needs to have latitude, longitude and
+        cat:            dataframe - needs to have latitude, longitude and
                         depth as entries
-        resolution:     resolution of map, '10m', '50m' and '110m' available
+        resolution:     resolution of map, "10m", "50m" and "110m" available
         include_map:    if True, seismicity will be plotted on natural earth
                         map, otherwise it will be plotted on a blank grid.
         country:        name of country, if None map will fit to data points
         colors:         color of background. if None is chosen, is will be
                         either white or standard natural earth colors.
-        style:          style of map, 'satellite' or 'street' are available
+        style:          style of map, "satellite" or "street" are available
         dot_smallest:   smallest dot size for magnitude scaling
         dot_largest:    largest dot size for magnitude scaling
         dot_interpolation_power: interpolation power for scaling
         dot_labels:     int, None, "auto" (default), list, or
-                        `~.ticker.Locator`. Determines, how labels for
-                        magnitudes can be created. Input for matplotlib
-                        PathCollection.legend_elements. If None, no label is
-                        shown. If an integer, target to use dot_labels
-                        elements in the normed range. If "auto", an automatic
-                        range is chosen for the labels (default). If a list,
-                        use elements of list which are between minimum and
-                        maximum magnitude of dataset for the legend.
-                        Finally, a `~.ticker.Locator` can be provided to use
-                        a predefined matplotlib.ticker (e.g. FixedLocator,
-                        which results in the same legend as providing a list
-                        of values).
+                        ``~.ticker.Locator``. Determines how labels for
+                        magnitudes can be created. Input for matplotlib's
+                        ``PathCollection.legend_elements``. If ``None``, no
+                        label is shown. If an integer, target to use
+                        ``dot_labels`` elements in the normed range.
+                        If "auto", an automatic range is chosen for the
+                        labels (default). If a list, uses elements of list
+                        which are between minimum and maximum magnitude of
+                        dataset for the legend.
+                        Finally, a ``~.ticker.Locator`` can be provided to use
+                        a predefined ``matplotlib.ticker`` (e.g.
+                        ``FixedLocator``, which results in the same legend as
+                        providing a list of values).
     Returns:
         GeoAxis object
     """