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plot-timeseries: expose option in cli to allow saving plot to a file #311

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Merged
Parent: Added segment picking from faces
merged 2 commits into from
Mar 5, 2024
Merged

plot-timeseries: expose option in cli to allow saving plot to a file #311

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c3e3986
feat(time-series): allow saving plots to a file
sanjayankur31 Mar 5, 2024
9bd0cdc
chore: regen man pages
sanjayankur31 Mar 5, 2024
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2 changes: 1 addition & 1 deletion man/man1/pynml-archive.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-channelanalysis.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-channelml2nml.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-modchananalysis.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-plotchan.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-plotmorph.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-plotspikes.1
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Expand Up @@ -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)
9 changes: 7 additions & 2 deletions man/man1/pynml-plottimeseries.1
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Expand Up @@ -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:"
Expand All @@ -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),
Expand All @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-povray.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-sonata.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-summary.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml-tune.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/pynml.1
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Expand Up @@ -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)
2 changes: 1 addition & 1 deletion man/man1/version.h2m
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@@ -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)
17 changes: 15 additions & 2 deletions pyneuroml/plot/PlotTimeSeries.py
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Expand Up @@ -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()

Expand All @@ -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,
)