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Regenerated files & minor gui fix #65

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Dec 14, 2023
Merged

Regenerated files & minor gui fix #65

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c686cd3
Regenerated nml
pgleeson Dec 14, 2023
8342b57
Fix 3d plot
pgleeson Dec 14, 2023
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1 change: 1 addition & 0 deletions examples/Example4.py
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Original file line number Diff line number Diff line change
Expand Up @@ -109,6 +109,7 @@
print(net.to_json())
net_json_file = net.to_json_file("%s.json" % net.id)
net_yaml_file = net.to_yaml_file("%s.yaml" % net.id)
net_xml_file = net.to_xml_file("%s.nmllite.xml" % net.id)


################################################################################
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49 changes: 24 additions & 25 deletions examples/LEMS_SimExample3.xml
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@@ -1,34 +1,33 @@
<Lems>

<!--

This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)

-->

<!-- Specify which component to run -->
<Target component="SimExample3" reportFile="report.SimExample3.txt"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="PyNN.xml"/>
<Include file="Example3_Network.net.nml"/>
<Include file="test_files/inputs.nml"/>
<Include file="test_files/hhcell.cell.nml"/>

<Simulation id="SimExample3" length="1000.0ms" step="0.025ms" target="Example3_Network" seed="5678"> <!-- Note seed: ensures same random numbers used every run -->

<Display id="pop0_v" title="Plots of pop0_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
<Line id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v" scale="1mV" color="#98e752" timeScale="1ms"/>
<Line id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v" scale="1mV" color="#bca074" timeScale="1ms"/>
<Line id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v" scale="1mV" color="#632794" timeScale="1ms"/>
</Display>

<Display id="pop1_v" title="Plots of pop1_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v" scale="1mV" color="#8a5d88" timeScale="1ms"/>
<Line id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v" scale="1mV" color="#df5954" timeScale="1ms"/>
Expand All @@ -41,28 +40,28 @@
<Line id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v" scale="1mV" color="#5fa56f" timeScale="1ms"/>
<Line id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v" scale="1mV" color="#b5b5a2" timeScale="1ms"/>
</Display>

<OutputFile id="SimExample3_pop0_v_dat" fileName="SimExample3.pop0.v.dat">
<OutputColumn id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v"/>
<OutputColumn id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v"/>
<OutputColumn id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v"/>
<OutputColumn id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v"/>
<OutputColumn id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v"/>
<OutputColumn id="pop0_0_hhcell_v" quantity="pop0/0/hhcell/v"/>
<OutputColumn id="pop0_1_hhcell_v" quantity="pop0/1/hhcell/v"/>
<OutputColumn id="pop0_2_hhcell_v" quantity="pop0/2/hhcell/v"/>
<OutputColumn id="pop0_3_hhcell_v" quantity="pop0/3/hhcell/v"/>
<OutputColumn id="pop0_4_hhcell_v" quantity="pop0/4/hhcell/v"/>
</OutputFile>

<OutputFile id="SimExample3_pop1_v_dat" fileName="SimExample3.pop1.v.dat">
<OutputColumn id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v"/>
<OutputColumn id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v"/>
<OutputColumn id="pop1_2_hhcell_v" quantity="pop1/2/hhcell/v"/>
<OutputColumn id="pop1_3_hhcell_v" quantity="pop1/3/hhcell/v"/>
<OutputColumn id="pop1_4_hhcell_v" quantity="pop1/4/hhcell/v"/>
<OutputColumn id="pop1_5_hhcell_v" quantity="pop1/5/hhcell/v"/>
<OutputColumn id="pop1_6_hhcell_v" quantity="pop1/6/hhcell/v"/>
<OutputColumn id="pop1_7_hhcell_v" quantity="pop1/7/hhcell/v"/>
<OutputColumn id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v"/>
<OutputColumn id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v"/>
<OutputColumn id="pop1_0_hhcell_v" quantity="pop1/0/hhcell/v"/>
<OutputColumn id="pop1_1_hhcell_v" quantity="pop1/1/hhcell/v"/>
<OutputColumn id="pop1_2_hhcell_v" quantity="pop1/2/hhcell/v"/>
<OutputColumn id="pop1_3_hhcell_v" quantity="pop1/3/hhcell/v"/>
<OutputColumn id="pop1_4_hhcell_v" quantity="pop1/4/hhcell/v"/>
<OutputColumn id="pop1_5_hhcell_v" quantity="pop1/5/hhcell/v"/>
<OutputColumn id="pop1_6_hhcell_v" quantity="pop1/6/hhcell/v"/>
<OutputColumn id="pop1_7_hhcell_v" quantity="pop1/7/hhcell/v"/>
<OutputColumn id="pop1_8_hhcell_v" quantity="pop1/8/hhcell/v"/>
<OutputColumn id="pop1_9_hhcell_v" quantity="pop1/9/hhcell/v"/>
</OutputFile>

</Simulation>

</Lems>
39 changes: 19 additions & 20 deletions examples/LEMS_SimExample4.xml
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Original file line number Diff line number Diff line change
@@ -1,57 +1,56 @@
<Lems>

<!--

This LEMS file has been automatically generated using PyNeuroML v1.1.1 (libNeuroML v0.5.5)
This LEMS file has been automatically generated using PyNeuroML v1.1.10 (libNeuroML v0.5.8)

-->

<!-- Specify which component to run -->
<Target component="SimExample4" reportFile="report.SimExample4.txt"/>

<!-- Include core NeuroML2 ComponentType definitions -->
<Include file="Cells.xml"/>
<Include file="Networks.xml"/>
<Include file="Simulation.xml"/>

<Include file="PyNN.xml"/>
<Include file="Example4_PyNN.net.nml"/>

<Simulation id="SimExample4" length="1000.0ms" step="0.01ms" target="Example4_PyNN" seed="5678"> <!-- Note seed: ensures same random numbers used every run -->

<Display id="pop0_v" title="Plots of pop0_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop0_0_testcell_v" quantity="pop0/0/testcell/v" scale="1mV" color="#d54f33" timeScale="1ms"/>
<Line id="pop0_1_testcell_v" quantity="pop0/1/testcell/v" scale="1mV" color="#0534e4" timeScale="1ms"/>
</Display>

<Display id="pop1_v" title="Plots of pop1_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v" scale="1mV" color="#98e752" timeScale="1ms"/>
<Line id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v" scale="1mV" color="#bca074" timeScale="1ms"/>
</Display>

<Display id="pop2_v" title="Plots of pop2_v" timeScale="1ms" xmin="-100.0" xmax="1100.0" ymin="-80" ymax="40">
<Line id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v" scale="1mV" color="#632794" timeScale="1ms"/>
</Display>

<OutputFile id="SimExample4_pop0_v_dat" fileName="SimExample4.pop0.v.dat">
<OutputColumn id="pop0_0_testcell_v" quantity="pop0/0/testcell/v"/>
<OutputColumn id="pop0_1_testcell_v" quantity="pop0/1/testcell/v"/>
<OutputColumn id="pop0_0_testcell_v" quantity="pop0/0/testcell/v"/>
<OutputColumn id="pop0_1_testcell_v" quantity="pop0/1/testcell/v"/>
</OutputFile>

<OutputFile id="SimExample4_pop1_v_dat" fileName="SimExample4.pop1.v.dat">
<OutputColumn id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v"/>
<OutputColumn id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v"/>
<OutputColumn id="pop1_0_testcell2_v" quantity="pop1/0/testcell2/v"/>
<OutputColumn id="pop1_1_testcell2_v" quantity="pop1/1/testcell2/v"/>
</OutputFile>

<OutputFile id="SimExample4_pop2_v_dat" fileName="SimExample4.pop2.v.dat">
<OutputColumn id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v"/>
<OutputColumn id="pop2_0_testcell2_v" quantity="pop2/0/testcell2/v"/>
</OutputFile>

<EventOutputFile id="SimExample4_pop0_spikes" fileName="SimExample4.pop0.spikes" format="ID_TIME">
<EventSelection id="0" select="pop0/0/testcell" eventPort="spike"/>
<EventSelection id="1" select="pop0/1/testcell" eventPort="spike"/>
<EventSelection id="0" select="pop0/0/testcell" eventPort="spike"/>
<EventSelection id="1" select="pop0/1/testcell" eventPort="spike"/>
</EventOutputFile>

</Simulation>

</Lems>
2 changes: 1 addition & 1 deletion neuromllite/gui/NMLliteUI.py
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Expand Up @@ -1128,7 +1128,7 @@ def replotSimResults(self):
# ax_3d = fig.add_subplot(111)
from mpl_toolkits.mplot3d import Axes3D

ax_3d = fig.gca(projection="3d")
ax_3d = fig.add_subplot(projection="3d")

ax_3d.clear()
xs = self.current_traces[info["x_axis"]]
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