Merge branch 'master' into runid-sort

Author: dschwoerer

xbout/boutdataarray.py

@@ -352,7 +352,7 @@ def interpolate_parallel(
         da[ycoord].attrs = {}
 
         da = da.interp(
-            {ycoord: y_fine.data},
+            {ycoord: y_fine},
             assume_sorted=True,
             method=method,
             kwargs={"fill_value": "extrapolate"},

xbout/boutdataset.py

@@ -1239,10 +1239,15 @@ def is_list(variable):
                             aspect=this_aspect,
                             vmin=this_vmin,
                             vmax=this_vmax,
+                            logscale=this_logscale,
                             **this_kwargs,
                         )
                     )
                 else:
+                    if this_vmin is None:
+                        this_vmin = min(np.min(w).values for w in v)
+                    if this_vmax is None:
+                        this_vmax = max(np.max(w).values for w in v)
                     for w in v:
                         blocks.append(
                             animate_line(
@@ -1254,6 +1259,7 @@ def is_list(variable):
                                 aspect=this_aspect,
                                 vmin=this_vmin,
                                 vmax=this_vmax,
+                                logscale=this_logscale,
                                 label=w.name,
                                 **this_kwargs,
                             )

xbout/load.py

@@ -11,7 +11,13 @@
 from natsort import natsorted
 
 from . import geometries
-from .utils import _set_attrs_on_all_vars, _separate_metadata, _check_filetype, _is_path
+from .utils import (
+    _set_attrs_on_all_vars,
+    _separate_metadata,
+    _check_filetype,
+    _is_path,
+    _is_dir,
+)
 
 
 _BOUT_PER_PROC_VARIABLES = [
@@ -60,6 +66,7 @@ def open_boutdataset(
     inputfilepath=None,
     geometry=None,
     gridfilepath=None,
+    grid_mismatch="raise",  #: Union[Literal["raise"], Literal["warn"], Literal["ignore"]]
     chunks=None,
     keep_xboundaries=True,
     keep_yboundaries=False,
@@ -121,6 +128,12 @@ def open_boutdataset(
     gridfilepath : str, optional
         The path to a grid file, containing any variables needed to apply the geometry
         specified by the 'geometry' option, which are not contained in the dump files.
+        This may either be the path of the grid file itself, or the directory
+        relative to which the grid from the settings file can be found.
+    grid_mismatch : str, optional
+        How to handle if the grid is not the grid that has been used for the
+        simulation. Can be "raise" to raise a RuntimeError, "warn" to raise a
+        warning, or ignore to ignore the mismatch silently.
     keep_xboundaries : bool, optional
         If true, keep x-direction boundary cells (the cells past the physical
         edges of the grid, where boundary conditions are set); increases the
@@ -302,6 +315,13 @@ def attrs_remove_section(obj, section):
         if info:
             print("Applying {} geometry conventions".format(geometry))
 
+        if _is_dir(gridfilepath):
+            if "grid" in ds.options:
+                gridfilepath += "/" + ds.options["grid"]
+            else:
+                warn(
+                    "gridfilepath set to a directory, but no grid used in simulation. Continuing without grid."
+                )
         if gridfilepath is not None:
             grid = _open_grid(
                 gridfilepath,
@@ -317,6 +337,19 @@ def attrs_remove_section(obj, section):
         if info:
             warn("No geometry type found, no physical coordinates will be added")
 
+    if grid:
+        grididoptions = ds.metadata.get("grid_id", None)
+        grididfile = grid.get("grid_id", None)
+        if grididoptions and grididfile and grididfile != grididoptions:
+            msg = f"""The grid used for the simulation is not the one used.
+For the simulation {grididoptions} was used,
+but we did load {grididfile}."""
+            if grid_mismatch == "warn":
+                warn(msg)
+            elif grid_mismatch == "ignore":
+                pass
+            else:
+                raise ValueError(msg)
     # Update coordinates to match particular geometry of grid
     ds = geometries.apply_geometry(ds, geometry, grid=grid)
 

xbout/plotting/animate.py

@@ -520,6 +520,7 @@ def animate_line(
     axis_coords=None,
     vmin=None,
     vmax=None,
+    logscale=False,
     fps=10,
     save_as=None,
     sep_pos=None,
@@ -555,6 +556,12 @@ def animate_line(
     vmax : float, optional
         Maximum value to use for colorbar. Default is to use maximum value of
         data across whole timeseries.
+    logscale : bool or float, optional
+        If True, default to a logarithmic color scale instead of a linear one.
+        If a non-bool type is passed it is treated as a float used to set the linear
+        threshold of a symmetric logarithmic scale as
+        linthresh=min(abs(vmin),abs(vmax))*logscale, defaults to 1e-5 if True is
+        passed.
     fps : int, optional
         Frames per second of resulting gif
     save_as : True or str, optional
@@ -640,6 +647,17 @@ def animate_line(
         y_label = y_label + f" [{data.units}]"
     ax.set_ylabel(y_label)
 
+    if logscale:
+        if vmin * vmax > 0.0:
+            ax.set_yscale("log")
+        else:
+            if not isinstance(logscale, bool):
+                linear_scale = logscale
+            else:
+                linear_scale = 1.0e-5
+            linear_threshold = min(abs(vmin), abs(vmax)) * linear_scale
+            ax.set_yscale("symlog", linthresh=linear_threshold)
+
     # Plot separatrix
     if sep_pos:
         ax.plot_vline(sep_pos, "--")

xbout/utils.py

@@ -1,6 +1,7 @@
 from copy import deepcopy
 from itertools import chain
 from pathlib import Path
+import os
 
 import numpy as np
 import xarray as xr
@@ -46,6 +47,10 @@ def _is_path(p):
         return False
 
 
+def _is_dir(p):
+    return _is_path(p) and os.path.isdir(p)
+
+
 def _separate_metadata(ds):
     """
     Extract the metadata (nxpe, myg etc.) from the Dataset.