Merge pull request #431 from NeuroML/feat-timeseries-tweaks

Time series plotting tweaks

man/man1/pynml-archive.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-ARCHIVE "1" "September 2024" "pynml-archive v1.3.13" "User Commands"
+.TH PYNML-ARCHIVE "1" "October 2024" "pynml-archive v1.3.13" "User Commands"
 .SH NAME
 pynml-archive \- manual page for pynml-archive v1.3.13
 .SH DESCRIPTION

man/man1/pynml-channelanalysis.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELANALYSIS "1" "September 2024" "pynml-channelanalysis v1.3.13" "User Commands"
+.TH PYNML-CHANNELANALYSIS "1" "October 2024" "pynml-channelanalysis v1.3.13" "User Commands"
 .SH NAME
 pynml-channelanalysis \- manual page for pynml-channelanalysis v1.3.13
 .SH DESCRIPTION

man/man1/pynml-channelml2nml.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-CHANNELML2NML "1" "September 2024" "pynml-channelml2nml v1.3.13" "User Commands"
+.TH PYNML-CHANNELML2NML "1" "October 2024" "pynml-channelml2nml v1.3.13" "User Commands"
 .SH NAME
 pynml-channelml2nml \- manual page for pynml-channelml2nml v1.3.13
 .SH DESCRIPTION

man/man1/pynml-modchananalysis.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-MODCHANANALYSIS "1" "September 2024" "pynml-modchananalysis v1.3.13" "User Commands"
+.TH PYNML-MODCHANANALYSIS "1" "October 2024" "pynml-modchananalysis v1.3.13" "User Commands"
 .SH NAME
 pynml-modchananalysis \- manual page for pynml-modchananalysis v1.3.13
 .SH DESCRIPTION

man/man1/pynml-plotchan.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTCHAN "1" "September 2024" "pynml-plotchan v1.3.13" "User Commands"
+.TH PYNML-PLOTCHAN "1" "October 2024" "pynml-plotchan v1.3.13" "User Commands"
 .SH NAME
 pynml-plotchan \- manual page for pynml-plotchan v1.3.13
 .SH DESCRIPTION

man/man1/pynml-plotmorph.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTMORPH "1" "September 2024" "pynml-plotmorph v1.3.13" "User Commands"
+.TH PYNML-PLOTMORPH "1" "October 2024" "pynml-plotmorph v1.3.13" "User Commands"
 .SH NAME
 pynml-plotmorph \- manual page for pynml-plotmorph v1.3.13
 .SH DESCRIPTION

man/man1/pynml-plotspikes.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTSPIKES "1" "September 2024" "pynml-plotspikes v1.3.13" "User Commands"
+.TH PYNML-PLOTSPIKES "1" "October 2024" "pynml-plotspikes v1.3.13" "User Commands"
 .SH NAME
 pynml-plotspikes \- manual page for pynml-plotspikes v1.3.13
 .SH DESCRIPTION

man/man1/pynml-plottimeseries.1

@@ -1,10 +1,13 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-PLOTTIMESERIES "1" "September 2024" "pynml-plottimeseries v1.3.13" "User Commands"
+.TH PYNML-PLOTTIMESERIES "1" "October 2024" "pynml-plottimeseries v1.3.13" "User Commands"
 .SH NAME
 pynml-plottimeseries \- manual page for pynml-plottimeseries v1.3.13
 .SH DESCRIPTION
-usage: pynml\-plottimeseries [\-h] [\-offset] [\-saveToFile <Image file name>]
-.IP
+usage: pynml\-plottimeseries [\-h] [\-columns [<column indices to plot> ...]]
+.TP
+[\-labels] [\-offset]
+[\-saveToFile <Image file name>]
+<a LEMS file or data files>
 [<a LEMS file or data files> ...]
 .PP
 A script to plot time series data from data files or LEMS files
@@ -18,8 +21,14 @@ series from
 \fB\-h\fR, \fB\-\-help\fR
 show this help message and exit
 .TP
+\fB\-columns\fR [<column indices to plot> ...]
+column indices to plot if data files are provided
+.TP
+\fB\-labels\fR
+Label plots
+.TP
 \fB\-offset\fR
-Toggle whether plots are overlaid or offset
+Offset plots
 .TP
 \fB\-saveToFile\fR <Image file name>
 Name of the image file to save plot to

man/man1/pynml-povray.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-POVRAY "1" "September 2024" "pynml-povray v1.3.13" "User Commands"
+.TH PYNML-POVRAY "1" "October 2024" "pynml-povray v1.3.13" "User Commands"
 .SH NAME
 pynml-povray \- manual page for pynml-povray v1.3.13
 .SH DESCRIPTION

man/man1/pynml-sonata.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SONATA "1" "September 2024" "pynml-sonata v1.3.13" "User Commands"
+.TH PYNML-SONATA "1" "October 2024" "pynml-sonata v1.3.13" "User Commands"
 .SH NAME
 pynml-sonata \- manual page for pynml-sonata v1.3.13
 .SH DESCRIPTION

man/man1/pynml-summary.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SUMMARY "1" "September 2024" "pynml-summary v1.3.13" "User Commands"
+.TH PYNML-SUMMARY "1" "October 2024" "pynml-summary v1.3.13" "User Commands"
 .SH NAME
 pynml-summary \- manual page for pynml-summary v1.3.13
 .SH DESCRIPTION

man/man1/pynml-swc2nml.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-SWC2NML "1" "September 2024" "pynml-swc2nml v1.3.13" "User Commands"
+.TH PYNML-SWC2NML "1" "October 2024" "pynml-swc2nml v1.3.13" "User Commands"
 .SH NAME
 pynml-swc2nml \- manual page for pynml-swc2nml v1.3.13
 .SH DESCRIPTION

man/man1/pynml-tune.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-TUNE "1" "September 2024" "pynml-tune v1.3.13" "User Commands"
+.TH PYNML-TUNE "1" "October 2024" "pynml-tune v1.3.13" "User Commands"
 .SH NAME
 pynml-tune \- manual page for pynml-tune v1.3.13
 .SH DESCRIPTION

man/man1/pynml-xpp.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML-XPP "1" "September 2024" "pynml-xpp v1.3.13" "User Commands"
+.TH PYNML-XPP "1" "October 2024" "pynml-xpp v1.3.13" "User Commands"
 .SH NAME
 pynml-xpp \- manual page for pynml-xpp v1.3.13
 .SH DESCRIPTION

man/man1/pynml.1

@@ -1,5 +1,5 @@
 .\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
-.TH PYNML "1" "September 2024" "pynml v1.3.13" "User Commands"
+.TH PYNML "1" "October 2024" "pynml v1.3.13" "User Commands"
 .SH NAME
 pynml \- manual page for pynml v1.3.13
 .SH DESCRIPTION

pyneuroml/plot/PlotTimeSeries.py

@@ -24,7 +24,10 @@
 logger.setLevel(logging.WARNING)
 
 
-TIME_SERIES_PLOTTER_DEFAULTS = {"offset": False}
+TIME_SERIES_PLOTTER_DEFAULTS = {
+    "offset": False,
+    "labels": False,
+}
 
 
 def plot_time_series(
@@ -143,13 +146,15 @@ def plot_time_series(
     else:
         show_yticklabels = True
 
+    # if a scalebar is to be set, we need to wait for it to be added before
+    # showing the plot
     ax = pynmlplt.generate_plot(
         xvalues=xs,
         yvalues=ys,
         title=title,
         labels=labelvals,
         show_yticklabels=show_yticklabels,
-        show_plot_already=False,
+        show_plot_already=False if scalebar_location is not None else True,
         **kwargs_generate_plot,
     )
 
@@ -170,12 +175,16 @@ def plot_time_series(
         print(f"Note: length of the scalebar is {scalebar_length} units")
         ax.add_artist(scalebar_)
 
-    if show_plot_already is True:
-        plt.show()
+        if show_plot_already is True:
+            plt.show()
 
 
 def plot_time_series_from_lems_file(
-    lems_file_name: str, base_dir: str = ".", title: str = "", **kwargs
+    lems_file_name: str,
+    base_dir: str = ".",
+    title: str = "",
+    labels: bool = True,
+    **kwargs,
 ) -> None:
     """Plot time series from a LEMS file.
 
@@ -193,6 +202,8 @@ def plot_time_series_from_lems_file(
     :type lems_file_name: str
     :param base_dir: directory where LEMS file resides
     :type base_dir: str
+    :param labels: toggle whether plots should be labelled
+    :type labels: bool
     :param kwargs: other arguments passed to `plot_time_series`
     :returns: None
 
@@ -201,11 +212,14 @@ def plot_time_series_from_lems_file(
         lems_file_name, get_events=False, get_traces=True
     )
 
-    plot_time_series(traces, xaxis="Time (s)", **kwargs)
+    plot_time_series(traces, labels=labels, xaxis="Time (s)", **kwargs)
 
 
 def plot_time_series_from_data_files(
-    data_file_names: typing.Union[str, typing.List[str]], **kwargs
+    data_file_names: typing.Union[str, typing.List[str]],
+    labels: bool = True,
+    columns: typing.Optional[typing.List[int]] = None,
+    **kwargs,
 ):
     """Plot time series from a data file.
 
@@ -215,6 +229,10 @@ def plot_time_series_from_data_files(
 
     :param data_file_names: name/path to data file(s)
     :type data_file_names: str or list of strings
+    :param labels: toggle whether plots should be labelled
+    :type labels: bool
+    :param columns: column indices to plot
+    :type columns: list of ints: [1, 2, 3]
     :param kwargs: other key word arguments that are passed to the
         `plot_time_series` function
 
@@ -230,10 +248,14 @@ def plot_time_series_from_data_files(
         traces["t"] = data_array[:, 0]
         num_cols = numpy.shape(data_array)[1]
         for i in range(1, num_cols, 1):
-            traces[str(i)] = data_array[:, i]
+            if columns and len(columns) > 0:
+                if i not in columns:
+                    logger.warning(f"Skipping column {i}")
+                    continue
+            traces[f"{f}_{i}"] = data_array[:, i]
         all_traces.append(traces)
 
-    plot_time_series(all_traces, labels=False, **kwargs)
+    plot_time_series(all_traces, labels=labels, **kwargs)
 
 
 def _process_time_series_plotter_args():
@@ -248,15 +270,28 @@ def _process_time_series_plotter_args():
         "input_files",
         type=str,
         metavar="<a LEMS file or data files>",
-        nargs="*",
+        nargs="+",
         help="a LEMS file (LEMS_..) or data files to plot time series from",
     )
 
+    parser.add_argument(
+        "-columns",
+        type=int,
+        metavar="<column indices to plot>",
+        nargs="*",
+        help="column indices to plot if data files are provided",
+    )
+    parser.add_argument(
+        "-labels",
+        action="store_true",
+        default=TIME_SERIES_PLOTTER_DEFAULTS["labels"],
+        help=("Label plots"),
+    )
     parser.add_argument(
         "-offset",
         action="store_true",
         default=TIME_SERIES_PLOTTER_DEFAULTS["offset"],
-        help=("Toggle whether plots are overlaid or offset"),
+        help=("Offset plots"),
     )
     parser.add_argument(
         "-saveToFile",
@@ -280,13 +315,16 @@ def _time_series_plotter_main(args=None):
         plot_time_series_from_lems_file(
             a.input_files[0],
             offset=a.offset,
+            labels=a.labels,
             bottom_left_spines_only=True,
             save_figure_to=a.save_to_file,
         )
     else:
         plot_time_series_from_data_files(
             a.input_files,
+            columns=a.columns,
             offset=a.offset,
+            labels=a.labels,
             bottom_left_spines_only=True,
             save_figure_to=a.save_to_file,
         )