diff --git a/man/man1/pynml-archive.1 b/man/man1/pynml-archive.1 index 273738e6..2a84086b 100644 --- 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 index 38fa6195..baa12b5d 100644 --- 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 index dec8d7e6..38a73a26 100644 --- 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 index dbb625e7..ffcfdf09 100644 --- 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 index b97d890f..ab174ed5 100644 --- 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 index 42df0bb8..63b57543 100644 --- 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 index a9b328d6..32990706 100644 --- 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 index f43979be..645698ad 100644 --- 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] [ ...] +usage: pynml\-plottimeseries [\-h] [\-offset] [\-saveToFile ] +.IP +[ ...] .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 +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 index deda27f8..f8b2526a 100644 --- 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 index 7ed1d3f1..b6826f4f 100644 --- 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 index 4d1e78a7..5646dd83 100644 --- 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 index 4a6c6961..57b11121 100644 --- 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 index 4be61fdd..24834a5a 100644 --- 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 index d56b14e2..4f686434 100644 --- 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 index 29765250..3fb4001b 100644 --- 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="", + 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, )