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Only export ProbeInterface contact annotations if they exist #368

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merged 1 commit into from
Nov 8, 2024
Merged

Only export ProbeInterface contact annotations if they exist #368

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7 changes: 6 additions & 1 deletion OpenEphys.Onix1.Design/DesignHelper.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -50,7 +50,12 @@ static class DesignHelper

public static void SerializeObject(object _object, string filepath)
{
var stringJson = JsonConvert.SerializeObject(_object, Formatting.Indented);
var serializerSettings = new JsonSerializerSettings()
{
NullValueHandling = NullValueHandling.Ignore,
};

var stringJson = JsonConvert.SerializeObject(_object, Formatting.Indented, serializerSettings);

File.WriteAllText(filepath, stringJson);
}
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2 changes: 1 addition & 1 deletion OpenEphys.Onix1.Design/OpenEphys.Onix1.Design.csproj
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Expand Up @@ -15,7 +15,7 @@
<PackageReference Include="Bonsai.Design" Version="2.8.5" />
<PackageReference Include="Bonsai.Design.Visualizers" Version="2.8.0" />
<PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
<PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.1.1" />
<PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.2.0" />
<PackageReference Include="ZedGraph" Version="5.1.7" />
</ItemGroup>

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37 changes: 21 additions & 16 deletions OpenEphys.Onix1/NeuropixelsV1eProbeGroup.cs
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Expand Up @@ -15,25 +15,30 @@ public class NeuropixelsV1eProbeGroup : ProbeGroup
/// Initializes a new instance of the <see cref="NeuropixelsV1eProbeGroup"/> class.
/// </summary>
public NeuropixelsV1eProbeGroup()
: base("probeinterface", "0.2.21",
new List<Probe>()
{
new(ProbeNdim.Two,
ProbeSiUnits.um,
new ProbeAnnotations("Neuropixels 1.0", "IMEC"),
new ContactAnnotations(new string[0]),
DefaultContactPositions(NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactPlaneAxes(NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactShapes(NeuropixelsV1.ElectrodeCount, ContactShape.Square),
Probe.DefaultSquareParams(NeuropixelsV1.ElectrodeCount, 12.0f),
DefaultProbePlanarContour(),
DefaultDeviceChannelIndices(NeuropixelsV1.ChannelCount, NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactIds(NeuropixelsV1.ElectrodeCount),
DefaultShankIds(NeuropixelsV1.ElectrodeCount))
}.ToArray())
: base("probeinterface", "0.2.21", DefaultProbes())
{
}

private static Probe[] DefaultProbes()
{
var probe = new Probe[1];

probe[0] = new(ProbeNdim.Two,
ProbeSiUnits.um,
new ProbeAnnotations("Neuropixels 1.0", "IMEC"),
null,
DefaultContactPositions(NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactPlaneAxes(NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactShapes(NeuropixelsV1.ElectrodeCount, ContactShape.Square),
Probe.DefaultSquareParams(NeuropixelsV1.ElectrodeCount, 12.0f),
DefaultProbePlanarContour(),
DefaultDeviceChannelIndices(NeuropixelsV1.ChannelCount, NeuropixelsV1.ElectrodeCount),
Probe.DefaultContactIds(NeuropixelsV1.ElectrodeCount),
DefaultShankIds(NeuropixelsV1.ElectrodeCount));

return probe;
}

/// <summary>
/// Initializes a new instance of the <see cref="NeuropixelsV1eProbeGroup"/> class.
/// </summary>
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37 changes: 21 additions & 16 deletions OpenEphys.Onix1/NeuropixelsV2eProbeGroup.cs
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Expand Up @@ -24,25 +24,30 @@ public class NeuropixelsV2eProbeGroup : ProbeGroup
/// the default settings for all contacts, including their positions, shapes, and IDs.
/// </remarks>
public NeuropixelsV2eProbeGroup()
: base("probeinterface", "0.2.21",
new List<Probe>()
{
new(ProbeNdim.Two,
ProbeSiUnits.um,
new ProbeAnnotations("Neuropixels 2.0 - Multishank", "IMEC"),
new ContactAnnotations(new string[0]),
DefaultContactPositions(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactPlaneAxes(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactShapes(NeuropixelsV2.ElectrodePerShank * numberOfShanks, ContactShape.Square),
Probe.DefaultSquareParams(NeuropixelsV2.ElectrodePerShank * numberOfShanks, 12.0f),
DefaultProbePlanarContourQuadShank(),
DefaultDeviceChannelIndices(NeuropixelsV2.ChannelCount, NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactIds(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
DefaultShankIds(NeuropixelsV2.ElectrodePerShank * numberOfShanks))
})
: base("probeinterface", "0.2.21", DefaultProbes())
{
}

private static Probe[] DefaultProbes()
{
var probe = new Probe[1];

probe[0] = new(ProbeNdim.Two,
ProbeSiUnits.um,
new ProbeAnnotations("Neuropixels 2.0 - Multishank", "IMEC"),
null,
DefaultContactPositions(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactPlaneAxes(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactShapes(NeuropixelsV2.ElectrodePerShank * numberOfShanks, ContactShape.Square),
Probe.DefaultSquareParams(NeuropixelsV2.ElectrodePerShank * numberOfShanks, 12.0f),
DefaultProbePlanarContourQuadShank(),
DefaultDeviceChannelIndices(NeuropixelsV2.ChannelCount, NeuropixelsV2.ElectrodePerShank * numberOfShanks),
Probe.DefaultContactIds(NeuropixelsV2.ElectrodePerShank * numberOfShanks),
DefaultShankIds(NeuropixelsV2.ElectrodePerShank * numberOfShanks));

return probe;
}

/// <summary>
/// Initializes a new instance of the <see cref="NeuropixelsV2eProbeGroup"/> class.
/// </summary>
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2 changes: 1 addition & 1 deletion OpenEphys.Onix1/OpenEphys.Onix1.csproj
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Expand Up @@ -13,6 +13,6 @@
<PackageReference Include="Bonsai.Core" Version="2.8.5" />
<PackageReference Include="clroni" Version="6.1.2" />
<PackageReference Include="OpenCV.Net" Version="3.4.2" />
<PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.1.1" />
<PackageReference Include="OpenEphys.ProbeInterface.NET" Version="0.2.0" />
</ItemGroup>
</Project>
64 changes: 34 additions & 30 deletions OpenEphys.Onix1/Rhs2116ProbeGroup.cs
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Expand Up @@ -20,37 +20,41 @@ public class Rhs2116ProbeGroup : ProbeGroup
/// the default settings for two probes, including the contact positions, shapes, and IDs.
/// </remarks>
public Rhs2116ProbeGroup()
: base("probeinterface", "0.2.21",
new List<Probe>()
{
new(
ProbeNdim.Two,
ProbeSiUnits.mm,
new ProbeAnnotations("Rhs2116A", ""),
new ContactAnnotations(new string[0]),
DefaultContactPositions(DefaultNumberOfChannelsPerProbe, 0),
Probe.DefaultContactPlaneAxes(DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactShapes(DefaultNumberOfChannelsPerProbe, ContactShape.Circle),
Probe.DefaultCircleParams(DefaultNumberOfChannelsPerProbe, 0.3f),
DefaultProbePlanarContour(0),
Probe.DefaultDeviceChannelIndices(DefaultNumberOfChannelsPerProbe, 0),
Probe.DefaultContactIds(DefaultNumberOfChannelsPerProbe),
Probe.DefaultShankIds(DefaultNumberOfChannelsPerProbe)),
new(
ProbeNdim.Two,
ProbeSiUnits.mm,
new ProbeAnnotations("Rhs2116B", ""),
new ContactAnnotations(new string[0]),
DefaultContactPositions(DefaultNumberOfChannelsPerProbe, 1),
Probe.DefaultContactPlaneAxes(DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactShapes(DefaultNumberOfChannelsPerProbe, ContactShape.Circle),
Probe.DefaultCircleParams(DefaultNumberOfChannelsPerProbe, 0.3f),
DefaultProbePlanarContour(1),
Probe.DefaultDeviceChannelIndices(DefaultNumberOfChannelsPerProbe, DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactIds(DefaultNumberOfChannelsPerProbe),
Probe.DefaultShankIds(DefaultNumberOfChannelsPerProbe))
}.ToArray())
: base("probeinterface", "0.2.21", DefaultProbes())
{
}

private static Probe[] DefaultProbes()
{
var probe = new Probe[2];

probe[0] = new(ProbeNdim.Two,
ProbeSiUnits.mm,
new ProbeAnnotations("Rhs2116A", ""),
null,
DefaultContactPositions(DefaultNumberOfChannelsPerProbe, 0),
Probe.DefaultContactPlaneAxes(DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactShapes(DefaultNumberOfChannelsPerProbe, ContactShape.Circle),
Probe.DefaultCircleParams(DefaultNumberOfChannelsPerProbe, 0.3f),
DefaultProbePlanarContour(0),
Probe.DefaultDeviceChannelIndices(DefaultNumberOfChannelsPerProbe, 0),
Probe.DefaultContactIds(DefaultNumberOfChannelsPerProbe),
Probe.DefaultShankIds(DefaultNumberOfChannelsPerProbe));

probe[1] = new(ProbeNdim.Two,
ProbeSiUnits.mm,
new ProbeAnnotations("Rhs2116B", ""),
null,
DefaultContactPositions(DefaultNumberOfChannelsPerProbe, 1),
Probe.DefaultContactPlaneAxes(DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactShapes(DefaultNumberOfChannelsPerProbe, ContactShape.Circle),
Probe.DefaultCircleParams(DefaultNumberOfChannelsPerProbe, 0.3f),
DefaultProbePlanarContour(1),
Probe.DefaultDeviceChannelIndices(DefaultNumberOfChannelsPerProbe, DefaultNumberOfChannelsPerProbe),
Probe.DefaultContactIds(DefaultNumberOfChannelsPerProbe),
Probe.DefaultShankIds(DefaultNumberOfChannelsPerProbe));

return probe;
}

/// <summary>
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