Merge branch 'add-electrode-table'

.github/workflows/linux.yml

@@ -35,6 +35,7 @@ jobs:
 #    - name: test
 #      run: cd build && ctest
     - name: deploy
+      if: github.ref == 'refs/heads/main'
       env:
         artifactoryApiKey: ${{ secrets.artifactoryApiKey }}
         build_dir: "Build"

.github/workflows/mac.yml

@@ -33,6 +33,7 @@ jobs:
 #    - name: test
 #      run: cd build && ctest
     - name: deploy
+      if: github.ref == 'refs/heads/main'
       env:
         artifactoryApiKey: ${{ secrets.artifactoryApiKey }}
         build_dir: "Build/Release"

.github/workflows/windows.yml

@@ -54,6 +54,7 @@ jobs:
 #    - name: test
 #      run: cd build && ctest
     - name: deploy
+      if: github.ref == 'refs/heads/main'
       env:
         artifactoryApiKey: ${{ secrets.artifactoryApiKey }}
         build_dir: "Build/Release"

Source/OpenEphysLib.cpp

@@ -40,7 +40,7 @@ extern "C" EXPORT void getLibInfo(Plugin::LibraryInfo* info)
 {
 	info->apiVersion = PLUGIN_API_VER;
 	info->name = "NWB2 Format";
-	info->libVersion = "0.2.0";
+	info->libVersion = "0.2.1";
 	info->numPlugins = NUM_PLUGINS;
 }
 

Source/RecordEngine/NWBFormat.cpp

@@ -79,6 +79,17 @@ int NWBFile::createFileStructure()
 	if (createGroup("/general")) return -1;
 	if (createGroup("general/devices")) return -1;
 	if (createGroup("general/extracellular_ephys")) return -1;
+	if (createGroup("general/extracellular_ephys/electrodes")) return -1;
+
+	StringArray colnames;
+	colnames.add("group");
+	colnames.add("group_name");
+	setAttributeStrArray(colnames, "general/extracellular_ephys/electrodes", "colnames");
+	setAttributeStr("metadata about extracellular electrodes", "general/extracellular_ephys/electrodes", "description");
+	setAttributeStr("hdmf-common", "general/extracellular_ephys/electrodes", "namespace");
+	setAttributeStr("DynamicTable", "general/extracellular_ephys/electrodes", "neurodata_type");
+	setAttributeStr(generateUuid(), "general/extracellular_ephys/electrodes", "object_id");
+
 	if (createGroup("/processing")) return -1;
 
 	if (createGroup("/stimulus")) return -1;
@@ -144,6 +155,9 @@ bool NWBFile::startNewRecording(
 	eventDataSets.clearQuick(true);
 
     int totalChannelCount = 0;
+	Array<int> all_electrode_inds;
+	StringArray groupNames;
+	StringArray groupReferences;
 
     // 1. Create continuous datasets
 	for (int i = 0; i < continuousArray.size(); i++)
@@ -158,16 +172,38 @@ bool NWBFile::startNewRecording(
             channel_conversion.add(group[ch]->getBitVolts() / 1e6);
         }
 
+		String groupName = group[0]->getSourceNodeName() + "-"
+			+ String(group[0]->getSourceNodeId())
+			+ "." + group[0]->getStreamName();
+
+		String fullPath = "general/extracellular_ephys/" + groupName;
+		createGroup(fullPath);
+		setAttributeStr("description", fullPath, "description");
+		setAttributeStr("unknown", fullPath, "location");
+		setAttributeStr("core", fullPath, "namespace");
+		setAttributeStr("ElectrodeGroup", fullPath, "neurodata_type");
+		setAttributeStr(generateUuid(), fullPath, "object_id");
+
+		createGroup("general/devices/" + groupName);
+
+		setAttributeStr("description", "general/devices/" + groupName, "description");
+		setAttributeStr("unknown", "general/devices/" + groupName, "manufacturer");
+		setAttributeStr("core", "general/devices/" + groupName, "namespace");
+		setAttributeStr("Device", "general/devices/" + groupName, "neurodata_type");
+		setAttributeStr(generateUuid(), "general/devices/" + groupName, "object_id");
+
+		createReference("/" + fullPath + "/device", "/general/devices/" + groupName);
+
         Array<int> electrode_inds;
         for (int ch = 0; ch < group.size(); ch++)
         {
+			int index = group[ch]->getGlobalIndex();
             electrode_inds.add(totalChannelCount++);
+			all_electrode_inds.add(index);
+			groupNames.add(groupName);
+			groupReferences.add("/general/extracellular_ephys/" + groupName);
         }
 
-		String groupName = group[0]->getSourceNodeName() + "-"
-					+ String(group[0]->getSourceNodeId())
-					+  "." + group[0]->getStreamName();
-
         ecephys::ElectricalSeries* electricalSeries =
             new ecephys::ElectricalSeries(rootPath,
                                           groupName,
@@ -235,7 +271,19 @@ bool NWBFile::startNewRecording(
 
         for (int ch = 0; ch < sourceInfo->getNumChannels(); ch++)
         {
-            electrode_inds.add(sourceInfo->getSourceChannels()[0]->getGlobalIndex());
+			int globalIndex = sourceInfo->getSourceChannels()[ch]->getGlobalIndex();
+			int tableIndex = all_electrode_inds.indexOf(globalIndex);
+
+			if (tableIndex > -1)
+			{
+				electrode_inds.add(tableIndex);
+			}
+			else
+			{
+				// If we don't have a matching electrode row, just use zero for now.
+				// In the future this should create a new table row.
+				electrode_inds.add(0);
+			}
         }
 
         ecephys::SpikeEventSeries* spikeEventSeries =
@@ -385,6 +433,36 @@ bool NWBFile::startNewRecording(
 
     syncMsgDataSet.reset(annotationSeries);
 
+	// 5. Create electrode table
+	ScopedPointer<HDF5RecordingData> elSet = createDataSet(BaseDataType::I32, 1, 1, "general/extracellular_ephys/electrodes/id");
+
+	std::vector<int> electrodeNumbers;
+	for (auto i : all_electrode_inds)
+		electrodeNumbers.push_back(i);
+
+	CHECK_ERROR(elSet->writeDataBlock(electrodeNumbers.size(), BaseDataType::I32, &electrodeNumbers[0]));
+
+	setAttributeStr("hdmf-common", "general/extracellular_ephys/electrodes/id", "namespace");
+	setAttributeStr("ElementIdentifiers", "general/extracellular_ephys/electrodes/id", "neurodata_type");
+	setAttributeStr(generateUuid(), "general/extracellular_ephys/electrodes/id", "object_id");
+
+	ScopedPointer<HDF5RecordingData> groupNamesDataset = createDataSet(BaseDataType::STR(250), 0, 1, "general/extracellular_ephys/electrodes/group_name");
+
+	for (int i = 0; i < groupNames.size(); i++)
+		groupNamesDataset->writeDataBlock(1, BaseDataType::STR(groupNames[i].length()), groupNames[i].toUTF8());
+
+	setAttributeStr("the name of the ElectrodeGroup this electrode is a part of", "general/extracellular_ephys/electrodes/group_name", "description");
+	setAttributeStr("hdmf-common", "general/extracellular_ephys/electrodes/group_name", "namespace");
+	setAttributeStr("VectorData", "general/extracellular_ephys/electrodes/group_name", "neurodata_type");
+	setAttributeStr(generateUuid(), "general/extracellular_ephys/electrodes/group_name", "object_id");
+
+	createReferenceDataSet("general/extracellular_ephys/electrodes/group", groupReferences);
+
+	setAttributeStr("a reference to the ElectrodeGroup this electrode is a part of", "general/extracellular_ephys/electrodes/group", "description");
+	setAttributeStr("hdmf-common", "general/extracellular_ephys/electrodes/group", "namespace");
+	setAttributeStr("VectorData", "general/extracellular_ephys/electrodes/group", "neurodata_type");
+	setAttributeStr(generateUuid(), "general/extracellular_ephys/electrodes/group", "object_id");
+
 	return true;
 
  }
@@ -643,6 +721,8 @@ HDF5RecordingData *NWBFile::createElectrodeDataSet(String path, String descripti
 		CHECK_ERROR(setAttributeStr(description, path, "description"));
 		CHECK_ERROR(setAttributeStr("hdmf-common", path, "namespace"));
 		CHECK_ERROR(setAttributeStr("DynamicTableRegion", path, "neurodata_type"));
+		CHECK_ERROR(setAttributeStr(generateUuid(), path, "object_id"));
+		CHECK_ERROR(setAttributeRef("general/extracellular_ephys/electrodes", path, "table"));
 	}
 	return elSet;
 }