Let matplotlib choose its default backend

docs/source/jupyter.rst

@@ -0,0 +1,51 @@
+#######################
+ Jupyter notebook usage
+#######################
+
+IDStools command-line tools can also be used directly from Jupyter notebooks.
+Import ``idstools`` once in the notebook kernel to register the IDStools
+commands as IPython line magics:
+
+.. code-block:: python
+
+   import idstools
+
+After that, commands such as ``idsprint`` and ``plotequilibrium`` can be
+called with ``%``:
+
+.. code-block:: python
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p
+
+.. code-block:: python
+
+   %plotequilibrium -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5"
+
+
+******************************
+ Interactive Matplotlib plots
+******************************
+
+For interactive Matplotlib figures in Jupyter, use the ``ipympl`` backend. If
+``ipympl`` is installed in the same Python environment as IDStools, the backend
+can be selected with Matplotlib's notebook magic before plotting:
+
+.. code-block:: python
+
+   %matplotlib widget
+   import idstools
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p
+
+Alternatively, the backend can be selected through the IDStools ``--rc``
+option before Matplotlib has been imported in the current kernel:
+
+.. code-block:: python
+
+   import idstools
+
+   %idsprint -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/134174/117#core_profiles/profiles_1d[0]/electrons/temperature" -p --rc "backend='module://ipympl.backend_nbagg'"
+
+.. code-block:: python
+
+   %plotequilibrium -u "imas:hdf5?path=/work/imas/shared/imasdb/ITER/3/100507/5" --rc "backend='module://ipympl.backend_nbagg'"

docs/source/tools.rst

@@ -12,3 +12,4 @@ Following are the different command line tools available in the
    ids_manipulation_tools
    database_tools
    scenariodb_tools
+   jupyter

idstools/compute/equilibrium.py

@@ -1384,7 +1384,7 @@ def get_profiles_1d_quantities(self, time_slice, attributes=None):
             if ids_field.has_value:
                 quantities[attribute] = eval(f"self.ids.time_slice[{time_slice}].profiles_1d.{attribute}")
             else:
-                logger.error(f"self.ids.time_slice[{time_slice}].profiles_1d.{attribute} not found")
+                logger.warning(f"self.ids.time_slice[{time_slice}].profiles_1d.{attribute} not found")
         return quantities
 
     def get_global_quantities(self, time_slice=None, attributes=None):

idstools/scripts/bin/dblist

@@ -234,7 +234,15 @@ def print_times(dbs, args, print_times=False, pulse_number=None, run_number=None
                             print(TAB * 4 + " Run: " + extended(str(run), RUN_STR_LEN))
                         available_ids_and_times = get_available_ids_and_times(connection)
                         for idsname, times in available_ids_and_times:
-                            if len(times) == 1 and np.isnan(times[0]):
+                            if times is None:
+                                print(
+                                    TAB * 5
+                                    + extended(idsname, IDSNAME_STR_LEN)
+                                    + ": "
+                                    + extended("N/A", SLICENUM_STR_LEN)
+                                    + " slices ( time unavailable )"
+                                )
+                            elif len(times) == 1 and np.isnan(times[0]):
                                 print(
                                     TAB * 5
                                     + extended(idsname, IDSNAME_STR_LEN)
@@ -311,7 +319,15 @@ def print_times_with_folder(dbs, print_times=False, pulse_number=None, run_numbe
                 continue
             available_ids_and_times = get_available_ids_and_times(connection)
             for idsname, times in available_ids_and_times:
-                if times is not None:
+                if times is None:
+                    print(
+                        TAB * 15
+                        + extended(idsname, IDSNAME_STR_LEN)
+                        + ": "
+                        + extended("N/A", SLICENUM_STR_LEN)
+                        + " slices ( time unavailable )"
+                    )
+                else:
                     if len(times) == 1 and np.isnan(times[0]):
                         print(
                             TAB * 15

idstools/scripts/bin/idsdiff

@@ -10,6 +10,7 @@ import sys
 import time
 from io import BytesIO
 
+from idstools.view.common import PlotCanvas
 import matplotlib.pyplot as plt
 import numpy as np
 import rich
@@ -43,8 +44,6 @@ slicing_methods = {
 
 
 def view_plot(ax, field, coordinate, field_name="", coordinate_name="", field_unit="", coordinate_unit="", **kwargs):
-    from idstools.view.common import PlotCanvas
-
     if not isinstance(field, (imas.ids_primitive.IDSNumericArray, np.ndarray)):
         print("Not a numeric array, Please select ids path")
         return
@@ -506,7 +505,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(
@@ -702,8 +704,6 @@ if __name__ == "__main__":
                             ] = compare_data
 
                         if args.plot and not args.html:
-                            from idstools.view.common import PlotCanvas
-
                             canvas = PlotCanvas(1, 1)
                             canvas.update_style(args.rc)
                             ax = canvas.add_axes(title="", xlabel="", row=0, col=0)

idstools/scripts/bin/idslist

@@ -184,8 +184,8 @@ if __name__ == "__main__":
                 type = time_array
             elif time_array is None:
                 value = f"{not_applicable}"
-                type = "unknown"
-            table.add_row(ids_name, value, Pretty(type))
+                type = not_applicable
+            table.add_row(ids_name, value, type if isinstance(type, str) else Pretty(type))
         if args.fullarray is True:
             with np.printoptions(threshold=sys.maxsize, linewidth=1024, precision=4):
                 console.print(table)

idstools/scripts/bin/idsprint

@@ -522,7 +522,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(
@@ -559,7 +562,10 @@ if __name__ == "__main__":
         table.add_column("SLICES", style="green")
         table.add_column("TIME", style="green")
         for ids_name, time_array in available_ids_and_times:
-            if len(time_array) == 1 and np.isnan(time_array[0]):
+            if time_array is None:
+                value = "N/A"
+                type = "unknown"
+            elif len(time_array) == 1 and np.isnan(time_array[0]):
                 value = f"{question_string}"
                 type = "heterogeneous IDS"
             elif len(time_array) == 1 and time_array[0] == -np.inf:

idstools/scripts/bin/plotcoresources

@@ -35,7 +35,10 @@ if __name__ == "__main__":
     parser.add_argument("-t", "--time", help="time", required=False, type=float, default=-99.0)
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotcoretransport

@@ -64,7 +64,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/ploteccomposition

@@ -52,7 +52,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotecray

@@ -68,7 +68,10 @@ if __name__ == "__main__":
 
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotecstrayradiation

@@ -56,7 +56,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotedgeprofiles

@@ -59,7 +59,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotequicomp

@@ -10,6 +10,9 @@ try:
 except ImportError:
     import imas
 import numpy as np
+
+# PlotCanvas configures a --rc backend before Matplotlib is imported.
+from idstools.view.common import PROVENANCE_TITLE_STYLE, PlotCanvas
 from matplotlib.animation import FuncAnimation
 from matplotlib.widgets import Slider
 from rich_argparse import RichHelpFormatter
@@ -20,7 +23,6 @@ from idstools.utils.clihelper import (
     rcparam_parser,
 )
 from idstools.utils.idslogger import setup_logger
-from idstools.view.common import PROVENANCE_TITLE_STYLE, PlotCanvas
 from idstools.view.equilibrium import EquilibriumView
 from idstools.view.wall import WallView
 
@@ -58,7 +60,10 @@ if __name__ == "__main__":
 
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotequilibrium

@@ -12,6 +12,8 @@ try:
     import imaspy as imas
 except ImportError:
     import imas
+# PlotCanvas configures a --rc backend before mpl_toolkits imports Matplotlib.
+from idstools.view.common import PlotCanvas
 from mpl_toolkits.axes_grid1.inset_locator import inset_axes
 from rich_argparse import RichHelpFormatter
 
@@ -27,7 +29,6 @@ from idstools.utils.clihelper import (
     rcparam_parser,
 )
 from idstools.utils.idslogger import setup_logger
-from idstools.view.common import PlotCanvas
 from idstools.view.domain.mdplot import plot_machine_description
 from idstools.view.equilibrium import EquilibriumView
 
@@ -86,7 +87,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plothcd

@@ -272,7 +272,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plothcddistributions

@@ -92,7 +92,10 @@ if __name__ == "__main__":
 
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plothcdwaves

@@ -127,7 +127,10 @@ if __name__ == "__main__":
     parser.add_argument("-l", "--hide_legend", help="remove the legend from graphs", action="store_true")
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotkineticprofiles

@@ -36,7 +36,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotmachinedescription

@@ -52,7 +52,10 @@ if __name__ == "__main__":
     )
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotneutron

@@ -38,7 +38,10 @@ if __name__ == "__main__":
     parser.add_argument("-t", "--time", help="Time", required=False, type=float, default=-99.0)
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotpressure

@@ -40,7 +40,10 @@ if __name__ == "__main__":
     parser.add_argument("-t", "--time", type=float, help="Time", default=-99)
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(

idstools/scripts/bin/plotrotation

@@ -36,7 +36,10 @@ if __name__ == "__main__":
     parser.add_argument("-t", "--time", help="Time", required=False, type=float, default=99.0)
     parser.add_argument(
         "--save",
-        help="Save figure at default location",
+        help=(
+            "Save the plot to a file instead of opening a window. "
+            "If no plot window is available, it is saved automatically."
+        ),
         action="store_true",
     )
     parser.add_argument(