Merge pull request #311 from NeuroML/feat/time-series-save-to-file

sanjayankur31 · web-flow · commit 24b17b291cf4 · 2024-03-05T16:59:23.000Z
plot-timeseries: expose option in cli to allow saving plot to a file
diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1
@@ -45,4 +45,4 @@ Explicit list of files to create archive of.
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-channelanalysis.1 b/man/man1/pynml-channelanalysis.1
@@ -110,4 +110,4 @@ plot current vs voltage for ion channel
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-channelml2nml.1 b/man/man1/pynml-channelml2nml.1
@@ -41,4 +41,4 @@ Name of the outputfile file
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-modchananalysis.1 b/man/man1/pynml-modchananalysis.1
@@ -72,4 +72,4 @@ Name of the mod file containing the channel
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-plotchan.1 b/man/man1/pynml-plotchan.1
@@ -41,4 +41,4 @@ Do not show plots as they are generated
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-plotmorph.1 b/man/man1/pynml-plotmorph.1
@@ -71,4 +71,4 @@ Scale axes so that image is approximately square, for
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-plotspikes.1 b/man/man1/pynml-plotspikes.1
@@ -60,4 +60,4 @@ Number of bins for rate histogram
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-plottimeseries.1 b/man/man1/pynml-plottimeseries.1
@@ -3,7 +3,9 @@
 .SH NAME
 pynml-plottimeseries \- manual page for pynml-plottimeseries v1.2.5
 .SH DESCRIPTION
-usage: pynml\-plottimeseries [\-h] [\-offset] [<a LEMS file or data files> ...]
+usage: pynml\-plottimeseries [\-h] [\-offset] [\-saveToFile <Image file name>]
+.IP
+[<a LEMS file or data files> ...]
 .PP
 A script to plot time series data from data files or LEMS files
 .SS "positional arguments:"
@@ -18,6 +20,9 @@ show this help message and exit
 .TP
 \fB\-offset\fR
 Toggle whether plots are overlaid or offset
+.TP
+\fB\-saveToFile\fR <Image file name>
+Name of the image file to save plot to
 .SH "SEE-ALSO"
 .BR pynml (1),
 .BR pynml-archive (1),
@@ -36,4 +41,4 @@ Toggle whether plots are overlaid or offset
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-povray.1 b/man/man1/pynml-povray.1
@@ -112,4 +112,4 @@ Show segment ids
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-sonata.1 b/man/man1/pynml-sonata.1
@@ -50,4 +50,4 @@ jNeuroML_NEURON
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-summary.1 b/man/man1/pynml-summary.1
@@ -35,4 +35,4 @@ print this help text and exit
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml-tune.1 b/man/man1/pynml-tune.1
@@ -148,4 +148,4 @@ as optimisation progresses?
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/pynml.1 b/man/man1/pynml.1
@@ -221,4 +221,4 @@ Validate SEDML file(s)
 Please see https://docs.neuroml.org for complete documentation on the NeuroML standard and the software ecosystem.
 .SH ENVIRONMENT
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/man/man1/version.h2m b/man/man1/version.h2m
@@ -1,3 +1,3 @@
 [environment]
 .PP
-pyNeuroML v1.2.5 (libNeuroML v0.5.8, jNeuroML v0.13.0)
+pyNeuroML v1.2.5 (libNeuroML v0.5.9, jNeuroML v0.13.0)
diff --git a/pyneuroml/plot/PlotTimeSeries.py b/pyneuroml/plot/PlotTimeSeries.py
@@ -256,6 +256,13 @@ def _process_time_series_plotter_args():
         default=TIME_SERIES_PLOTTER_DEFAULTS["offset"],
         help=("Toggle whether plots are overlaid or offset"),
     )
+    parser.add_argument(
+        "-saveToFile",
+        type=str,
+        metavar="<Image file name>",
+        default=None,
+        help="Name of the image file to save plot to",
+    )
 
     return parser.parse_args()
 
@@ -269,9 +276,15 @@ def _time_series_plotter_main(args=None):
     logger.debug(a)
     if len(a.input_files) == 1 and a.input_files[0].startswith("LEMS_"):
         plot_time_series_from_lems_file(
-            a.input_files[0], offset=a.offset, bottom_left_spines_only=True
+            a.input_files[0],
+            offset=a.offset,
+            bottom_left_spines_only=True,
+            save_figure_to=a.save_to_file,
         )
     else:
         plot_time_series_from_data_files(
-            a.input_files, offset=a.offset, bottom_left_spines_only=True
+            a.input_files,
+            offset=a.offset,
+            bottom_left_spines_only=True,
+            save_figure_to=a.save_to_file,
         )
