diff --git a/.clang-format b/.clang-format
new file mode 100644
index 0000000..bd1691e
--- /dev/null
+++ b/.clang-format
@@ -0,0 +1,64 @@
+---
+Language: Cpp
+# BasedOnStyle: JUCE (Custom)
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands: Align
+AlignTrailingComments: false
+AllowAllParametersOfDeclarationOnNextLine: false
+AllowShortBlocksOnASingleLine: Never
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: Yes
+BinPackArguments: false
+BinPackParameters: false
+BreakAfterJavaFieldAnnotations: false
+BreakBeforeBinaryOperators: NonAssignment
+BreakBeforeBraces: Allman
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializers: BeforeColon
+BreakInheritanceList : BeforeColon
+BreakStringLiterals: false
+ColumnLimit: 0
+# ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: false
+DerivePointerAlignment: false
+DisableFormat: false
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: true
+IndentWidth: 4
+IndentWrappedFunctionNames: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MaxEmptyLinesToKeep: 1
+NamespaceIndentation: Inner
+PackConstructorInitializers: CurrentLine
+PointerAlignment: Left
+ReflowComments: false
+SortIncludes: true
+SpaceAfterCStyleCast: true
+SpaceAfterLogicalNot: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: true
+SpaceBeforeParens: NonEmptyParentheses
+SpaceInEmptyParentheses: false
+SpaceBeforeInheritanceColon: true
+SpacesInAngles: false
+SpacesInCStyleCastParentheses: false
+SpacesInContainerLiterals: true
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: "c++17"
+TabWidth: 4
+UseTab: Never
+---
+
diff --git a/Source/FileSource/NWBFileSource.cpp b/Source/FileSource/NWBFileSource.cpp
index 5bd8714..fa0fffb 100644
--- a/Source/FileSource/NWBFileSource.cpp
+++ b/Source/FileSource/NWBFileSource.cpp
@@ -2,7 +2,7 @@
------------------------------------------------------------------
This file is part of the Open Ephys GUI
- Copyright (C) 2013 Open Ephys
+ Copyright (C) 2024 Open Ephys
------------------------------------------------------------------
@@ -20,16 +20,16 @@
along with this program. If not, see .
*/
+
#include
#include "NWBFileSource.h"
#include
-
using namespace H5;
#define PROCESS_ERROR std::cerr << "NWBFilesource exception: " << error.getCDetailMsg() << std::endl
-NWBFileSource::NWBFileSource() : samplePos(0), skipRecordEngineCheck(false)
+NWBFileSource::NWBFileSource() : samplePos (0), skipRecordEngineCheck (false)
{
}
@@ -37,20 +37,19 @@ NWBFileSource::~NWBFileSource()
{
}
-bool NWBFileSource::open(File file)
+bool NWBFileSource::open (File file)
{
ScopedPointer tmpFile;
Attribute ver;
uint16 vernum;
try
{
- tmpFile = new H5File(file.getFullPathName().toUTF8(),H5F_ACC_RDONLY);
+ tmpFile = new H5File (file.getFullPathName().toUTF8(), H5F_ACC_RDONLY);
//TODO: Verify NWBVersion
sourceFile = tmpFile;
return true;
-
}
catch (FileIException error)
{
@@ -69,24 +68,20 @@ bool NWBFileSource::open(File file)
void NWBFileSource::fillRecordInfo()
{
-
Group acquisition;
try
{
+ acquisition = sourceFile->openGroup ("/acquisition/");
- acquisition = sourceFile->openGroup("/acquisition/");
-
int dataSources = (int) acquisition.getNumObjs();
std::map startSampleNumbers;
for (int i = 0; i < dataSources; i++)
{
-
try
{
-
DataSet data;
Attribute attr;
DataSpace dSpace;
@@ -94,41 +89,40 @@ void NWBFileSource::fillRecordInfo()
float bitVolts;
hsize_t dims[3];
- H5std_string dataSourceName = acquisition.getObjnameByIdx(hsize_t(i));
- Group dataSource = acquisition.openGroup(dataSourceName);
+ H5std_string dataSourceName = acquisition.getObjnameByIdx (hsize_t (i));
+ Group dataSource = acquisition.openGroup (dataSourceName);
- if (dataSource.attrExists("neurodata_type"))
+ if (dataSource.attrExists ("neurodata_type"))
{
- attr = dataSource.openAttribute("neurodata_type");
+ attr = dataSource.openAttribute ("neurodata_type");
H5::StrType type = attr.getStrType();
std::string type_str;
- attr.read(type, type_str);
+ attr.read (type, type_str);
- if (!type_str.compare("ElectricalSeries"))
+ if (! type_str.compare ("ElectricalSeries"))
{
-
RecordInfo info;
- data = dataSource.openDataSet("data");
+ data = dataSource.openDataSet ("data");
dSpace = data.getSpace();
- dSpace.getSimpleExtentDims(dims);
+ dSpace.getSimpleExtentDims (dims);
info.name = dataSourceName;
info.numSamples = dims[0];
- attr = data.openAttribute("conversion");
- attr.read(PredType::NATIVE_FLOAT, &bitVolts);
+ attr = data.openAttribute ("conversion");
+ attr.read (PredType::NATIVE_FLOAT, &bitVolts);
- data = dataSource.openDataSet("timestamps");
+ data = dataSource.openDataSet ("timestamps");
info.sampleRate = -1.0f;
- if (data.attrExists("interval"))
+ if (data.attrExists ("interval"))
{
- attr = data.openAttribute("interval");
+ attr = data.openAttribute ("interval");
double interval;
- attr.read(PredType::NATIVE_DOUBLE, &interval);
+ attr.read (PredType::NATIVE_DOUBLE, &interval);
double sampleRate = 1.0f / interval;
info.sampleRate = sampleRate;
@@ -136,84 +130,83 @@ void NWBFileSource::fillRecordInfo()
else
{
dSpace = data.getSpace();
- dSpace.getSimpleExtentDims(dims);
+ dSpace.getSimpleExtentDims (dims);
- HeapBlock tsArray(dims[0]);
- data.read(tsArray.getData(), PredType::NATIVE_DOUBLE);
+ HeapBlock tsArray (dims[0]);
+ data.read (tsArray.getData(), PredType::NATIVE_DOUBLE);
if (tsArray[2] > 0 && tsArray[0] > 0)
info.sampleRate = 2 / (tsArray[2] - tsArray[0]);
}
//Get the first sample number to align events
- data = dataSource.openDataSet("sync");
+ data = dataSource.openDataSet ("sync");
- dSpace = data.getSpace();
- dSpace.getSimpleExtentDims(dims);
+ dSpace = data.getSpace();
+ dSpace.getSimpleExtentDims (dims);
- HeapBlock syncArray(dims[0]);
- data.read(syncArray.getData(), PredType::NATIVE_INT);
+ HeapBlock syncArray (dims[0]);
+ data.read (syncArray.getData(), PredType::NATIVE_INT);
startSampleNumbers[dataSourceName] = syncArray[0];
- HeapBlock ccArray(dims[1]);
- data = dataSource.openDataSet("channel_conversion");
- data.read(ccArray.getData(), PredType::NATIVE_FLOAT);
+ HeapBlock ccArray (dims[1]);
+ data = dataSource.openDataSet ("channel_conversion");
+ data.read (ccArray.getData(), PredType::NATIVE_FLOAT);
try
{
for (int k = 0; k < dims[1]; k++)
{
RecordedChannelInfo c;
- c.name = "CH" + String(k);
+ c.name = "CH" + String (k);
c.bitVolts = ccArray[k] * 1e6;
- info.channels.add(c);
- }
- infoArray.add(info);
- availableDataSets.add(numRecords);
- dataPaths.set(numRecords, dataSourceName);
+ info.channels.add (c);
+ }
+ infoArray.add (info);
+ availableDataSets.add (numRecords);
+ dataPaths.set (numRecords, dataSourceName);
numRecords++;
-
- } catch (GroupIException)
+ }
+ catch (GroupIException)
{
- std::cout << "!!!GroupIException!!!" << std::endl;
- } catch (AttributeIException)
+ std::cout << "!!!GroupIException!!!" << std::endl;
+ }
+ catch (AttributeIException)
{
std::cout << "!!!AttributeIException!!!" << std::endl;
}
-
}
- else if (!type_str.compare("TimeSeries"))
+ else if (! type_str.compare ("TimeSeries"))
{
// Load TTL events
- dataSourceName.erase(dataSourceName.find_last_not_of(".TTL")+1);
+ dataSourceName.erase (dataSourceName.find_last_not_of (".TTL") + 1);
EventInfo info;
- data = dataSource.openDataSet("data");
+ data = dataSource.openDataSet ("data");
dSpace = data.getSpace();
- dSpace.getSimpleExtentDims(dims);
+ dSpace.getSimpleExtentDims (dims);
int numEvents = dims[0];
- HeapBlock stateArray(dims[0]);
- data.read(stateArray.getData(), PredType::NATIVE_INT);
+ HeapBlock stateArray (dims[0]);
+ data.read (stateArray.getData(), PredType::NATIVE_INT);
- data = dataSource.openDataSet("sync");
+ data = dataSource.openDataSet ("sync");
- HeapBlock tsArray(dims[0]);
- data.read(tsArray.getData(), PredType::NATIVE_DOUBLE);
+ HeapBlock tsArray (dims[0]);
+ data.read (tsArray.getData(), PredType::NATIVE_DOUBLE);
for (int k = 0; k < numEvents; k++)
{
- info.channels.push_back(abs(stateArray[k]));
- info.channelStates.push_back(stateArray[k] > 0);
- info.timestamps.push_back(tsArray[k] - startSampleNumbers[dataSourceName]);
+ info.channels.push_back (abs (stateArray[k]));
+ info.channelStates.push_back (stateArray[k] > 0);
+ info.timestamps.push_back (tsArray[k] - startSampleNumbers[dataSourceName]);
}
eventInfoMap[dataSourceName] = info;
-
}
}
}
@@ -233,9 +226,7 @@ void NWBFileSource::fillRecordInfo()
{
std::cout << "!!!DataSpaceIException!!!" << std::endl;
}
-
}
-
}
catch (FileIException error)
{
@@ -247,18 +238,16 @@ void NWBFileSource::fillRecordInfo()
std::cout << "!!!GroupIException!!!" << std::endl;
PROCESS_ERROR;
}
-
}
-void NWBFileSource::updateActiveRecord(int index)
+void NWBFileSource::updateActiveRecord (int index)
{
-
samplePos = 0;
-
+
try
{
String path = "/acquisition/" + dataPaths[index] + "/data";
- dataSet = new DataSet(sourceFile->openDataSet(path.toUTF8()));
+ dataSet = new DataSet (sourceFile->openDataSet (path.toUTF8()));
}
catch (FileIException error)
{
@@ -272,18 +261,17 @@ void NWBFileSource::updateActiveRecord(int index)
currentStream = dataPaths[index];
}
-void NWBFileSource::seekTo(int64 sample)
+void NWBFileSource::seekTo (int64 sample)
{
samplePos = sample % getActiveNumSamples();
}
-int NWBFileSource::readData(int16* buffer, int nSamples)
+int NWBFileSource::readData (int16* buffer, int nSamples)
{
-
- DataSpace fSpace,mSpace;
+ DataSpace fSpace, mSpace;
int samplesToRead;
int nChannels = getActiveNumChannels();
- hsize_t dim[3],offset[3];
+ hsize_t dim[3], offset[3];
if (samplePos + nSamples > getActiveNumSamples())
{
@@ -304,13 +292,12 @@ int NWBFileSource::readData(int16* buffer, int nSamples)
offset[1] = 0;
offset[2] = 0;
- fSpace.selectHyperslab(H5S_SELECT_SET,dim,offset);
- mSpace = DataSpace(2,dim);
+ fSpace.selectHyperslab (H5S_SELECT_SET, dim, offset);
+ mSpace = DataSpace (2, dim);
- dataSet->read(buffer,PredType::NATIVE_INT16,mSpace,fSpace);
+ dataSet->read (buffer, PredType::NATIVE_INT16, mSpace, fSpace);
samplePos += samplesToRead;
return samplesToRead;
-
}
catch (DataSetIException error)
{
@@ -325,40 +312,38 @@ int NWBFileSource::readData(int16* buffer, int nSamples)
return 0;
}
-void NWBFileSource::processChannelData(int16* inBuffer, float* outBuffer, int channel, int64 numSamples)
+void NWBFileSource::processChannelData (int16* inBuffer, float* outBuffer, int channel, int64 numSamples)
{
int n = getActiveNumChannels();
- float bitVolts = getChannelInfo(activeRecord.get(), channel).bitVolts;
+ float bitVolts = getChannelInfo (activeRecord.get(), channel).bitVolts;
- for (int i=0; i < numSamples; i++)
+ for (int i = 0; i < numSamples; i++)
{
- *(outBuffer+i) = *(inBuffer+(n*i)+channel) * bitVolts;
+ *(outBuffer + i) = *(inBuffer + (n * i) + channel) * bitVolts;
}
-
}
-void NWBFileSource::processEventData(EventInfo &eventInfo, int64 start, int64 stop)
+void NWBFileSource::processEventData (EventInfo& eventInfo, int64 start, int64 stop)
{
+ int local_start = start % getActiveNumSamples();
+ ;
+ int local_stop = stop % getActiveNumSamples();
+ int loop_count = start / getActiveNumSamples();
- int local_start = start % getActiveNumSamples();;
- int local_stop = stop % getActiveNumSamples();
- int loop_count = start / getActiveNumSamples();
+ EventInfo info = eventInfoMap[currentStream];
- EventInfo info = eventInfoMap[currentStream];
-
- int i = 0;
-
- while (i < info.timestamps.size())
- {
- if (info.timestamps[i] >= local_start && info.timestamps[i] < local_stop)
- {
- eventInfo.channels.push_back(info.channels[i] - 1);
- eventInfo.channelStates.push_back((info.channelStates[i]));
- eventInfo.timestamps.push_back(info.timestamps[i] + loop_count*getActiveNumSamples());
- }
- i++;
- }
+ int i = 0;
+ while (i < info.timestamps.size())
+ {
+ if (info.timestamps[i] >= local_start && info.timestamps[i] < local_stop)
+ {
+ eventInfo.channels.push_back (info.channels[i] - 1);
+ eventInfo.channelStates.push_back ((info.channelStates[i]));
+ eventInfo.timestamps.push_back (info.timestamps[i] + loop_count * getActiveNumSamples());
+ }
+ i++;
+ }
}
bool NWBFileSource::isReady()
@@ -392,4 +377,3 @@ bool NWBFileSource::isReady()
return true;
}
-
diff --git a/Source/FileSource/NWBFileSource.h b/Source/FileSource/NWBFileSource.h
index 9886c03..8decf53 100644
--- a/Source/FileSource/NWBFileSource.h
+++ b/Source/FileSource/NWBFileSource.h
@@ -2,7 +2,7 @@
------------------------------------------------------------------
This file is part of the Open Ephys GUI
- Copyright (C) 2021 Open Ephys
+ Copyright (C) 2024 Open Ephys
------------------------------------------------------------------
@@ -27,8 +27,8 @@
#include
//TODO: Define these:
-//#define MIN_NWB_VERSION
-//#define MAX_NWB_VERSION
+//#define MIN_NWB_VERSION
+//#define MAX_NWB_VERSION
class HDF5RecordingData;
namespace H5
@@ -36,7 +36,7 @@ namespace H5
class DataSet;
class H5File;
class DataType;
-}
+} // namespace H5
/**
A File Source plugin that can read data from NWB 2.0 files
@@ -44,21 +44,20 @@ class DataType;
class NWBFileSource : public FileSource
{
public:
-
/** Constructor */
NWBFileSource();
-
+
/** Destructor */
~NWBFileSource();
-
+
/** Attempt to open the file, and return true if successful */
bool open (File file) override;
-
+
/** Fill rthe infoArray and eventInfoAray with the relevant information for all recordings*/
void fillRecordInfo() override;
/** Update the recording to be read in */
- void updateActiveRecord(int index) override;
+ void updateActiveRecord (int index) override;
/** Reads nSamples of int16 data into a temporary buffer */
int readData (int16* buffer, int nSamples) override;
@@ -68,16 +67,14 @@ class NWBFileSource : public FileSource
/** Convert nSamples of data from int16 to float */
void processChannelData (int16* inBuffer, float* outBuffer, int channel, int64 numSamples) override;
-
+
/** Add info about events occurring within a sample range */
- void processEventData(EventInfo &info, int64 startTimestamp, int64 stopTimestamp) override;
+ void processEventData (EventInfo& info, int64 startTimestamp, int64 stopTimestamp) override;
/** Return false if file is not able to be opened */
bool isReady() override;
-
private:
-
ScopedPointer sourceFile;
ScopedPointer dataSet;
@@ -92,6 +89,4 @@ class NWBFileSource : public FileSource
bool hasEventData;
};
-
-
-#endif // NWBFILESOURCE_H_INCLUDED
+#endif // NWBFILESOURCE_H_INCLUDED
diff --git a/Source/OpenEphysLib.cpp b/Source/OpenEphysLib.cpp
index 495990c..3758690 100644
--- a/Source/OpenEphysLib.cpp
+++ b/Source/OpenEphysLib.cpp
@@ -1,23 +1,23 @@
/*
-------------------------------------------------------------------
+ ------------------------------------------------------------------
-This file is part of the Open Ephys GUI
-Copyright (C) 2013 Open Ephys
+ This file is part of the Open Ephys GUI
+ Copyright (C) 2024 Open Ephys
-------------------------------------------------------------------
+ ------------------------------------------------------------------
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, either version 3 of the License, or
-(at your option) any later version.
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
-You should have received a copy of the GNU General Public License
-along with this program. If not, see .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
*/
@@ -27,51 +27,50 @@ along with this program. If not, see .
#include
#ifdef WIN32
#include
-#define EXPORT __declspec(dllexport)
+#define EXPORT __declspec (dllexport)
#else
-#define EXPORT __attribute__((visibility("default")))
+#define EXPORT __attribute__ ((visibility ("default")))
#endif
-
using namespace Plugin;
#define NUM_PLUGINS 2
-extern "C" EXPORT void getLibInfo(Plugin::LibraryInfo* info)
+extern "C" EXPORT void getLibInfo (Plugin::LibraryInfo* info)
{
- info->apiVersion = PLUGIN_API_VER;
- info->name = "NWB2 Format";
- info->libVersion = "0.2.2";
- info->numPlugins = NUM_PLUGINS;
+ info->apiVersion = PLUGIN_API_VER;
+ info->name = "NWB2 Format";
+ info->libVersion = "0.2.2";
+ info->numPlugins = NUM_PLUGINS;
}
-extern "C" EXPORT int getPluginInfo(int index, Plugin::PluginInfo* info)
+extern "C" EXPORT int getPluginInfo (int index, Plugin::PluginInfo* info)
{
- switch (index)
- {
- case 0:
- info->type = Plugin::RECORD_ENGINE;
- info->recordEngine.name = "NWB2";
- info->recordEngine.creator = &(Plugin::createRecordEngine);
- break;
- case 1:
- info->type = Plugin::FILE_SOURCE;
- info->fileSource.name = "NWB File";
- info->fileSource.creator = &(Plugin::createFileSource);
- info->fileSource.extensions = "nwb";
- break;
- default:
- return -1;
- }
+ switch (index)
+ {
+ case 0:
+ info->type = Plugin::RECORD_ENGINE;
+ info->recordEngine.name = "NWB2";
+ info->recordEngine.creator = &(Plugin::createRecordEngine);
+ break;
+ case 1:
+ info->type = Plugin::FILE_SOURCE;
+ info->fileSource.name = "NWB File";
+ info->fileSource.creator = &(Plugin::createFileSource);
+ info->fileSource.extensions = "nwb";
+ break;
+ default:
+ return -1;
+ }
- return 0;
+ return 0;
}
#ifdef WIN32
-BOOL WINAPI DllMain(IN HINSTANCE hDllHandle,
- IN DWORD nReason,
- IN LPVOID Reserved)
+BOOL WINAPI DllMain (IN HINSTANCE hDllHandle,
+ IN DWORD nReason,
+ IN LPVOID Reserved)
{
- return TRUE;
+ return TRUE;
}
#endif
diff --git a/Source/RecordEngine/NWBFormat.cpp b/Source/RecordEngine/NWBFormat.cpp
index 32bfcc8..0bad794 100644
--- a/Source/RecordEngine/NWBFormat.cpp
+++ b/Source/RecordEngine/NWBFormat.cpp
@@ -1,29 +1,29 @@
/*
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This file is part of the Open Ephys GUI
- Copyright (C) 2014 Open Ephys
+ This file is part of the Open Ephys GUI
+ Copyright (C) 2024 Open Ephys
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
- */
-
- #include "NWBFormat.h"
-
- using namespace NWBRecording;
+*/
+
+#include "NWBFormat.h"
+
+using namespace NWBRecording;
#ifndef EVENT_CHUNK_SIZE
#define EVENT_CHUNK_SIZE 8
@@ -37,844 +37,857 @@
#define SPIKE_CHUNK_YSIZE 40
#endif
- #define MAX_BUFFER_SIZE 40960
+#define MAX_BUFFER_SIZE 40960
-NWBFile::NWBFile(String fName, String ver, String idText) :
- HDF5FileBase(),
- filename(fName),
- identifierText(idText),
- GUIVersion(ver)
+NWBFile::NWBFile (String fName, String ver, String idText) : HDF5FileBase(),
+ filename (fName),
+ identifierText (idText),
+ GUIVersion (ver)
{
- readyToOpen = true; //In KWIK this is in initFile, but the new recordEngine methods make it safe for it to be here
+ readyToOpen = true; //In KWIK this is in initFile, but the new recordEngine methods make it safe for it to be here
- scaledBuffer.malloc(MAX_BUFFER_SIZE);
- intBuffer.malloc(MAX_BUFFER_SIZE);
- bufferSize = MAX_BUFFER_SIZE;
+ scaledBuffer.malloc (MAX_BUFFER_SIZE);
+ intBuffer.malloc (MAX_BUFFER_SIZE);
+ bufferSize = MAX_BUFFER_SIZE;
}
NWBFile::~NWBFile()
{
- continuousDataSets.clear();
- spikeDataSets.clear();
- eventDataSets.clear();
- syncMsgDataSet.reset();
+ continuousDataSets.clear();
+ spikeDataSets.clear();
+ eventDataSets.clear();
+ syncMsgDataSet.reset();
}
-
+
int NWBFile::createFileStructure()
{
-
- setAttributeStr("core", "/", "namespace");
- setAttributeStr("NWBFile", "/", "neurodata_type");
- setAttributeStr("2.5.0", "/", "nwb_version");
- setAttributeStr(identifierText, "/", "object_id");
-
- if (createGroup("/acquisition")) return -1;
-
- if (createGroup("/analysis")) return -1;
-
- String time = Time::getCurrentTime().formatted("%Y-%m-%dT%H:%M:%S") + Time::getCurrentTime().getUTCOffsetString(true);
-
- createTextDataSet("", "file_create_date", time);
-
- 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");
- colnames.add("location");
- 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;
- if (createGroup("/stimulus/presentation")) return -1;
- if (createGroup("/stimulus/templates")) return -1;
-
- createStringDataSet("/session_description", "Recording with the Open Ephys GUI");
- createStringDataSet("/session_start_time", time);
- createStringDataSet("/timestamps_reference_time", time);
- createStringDataSet("/identifier", "test-identifier");
-
- return 0;
-
+ setAttributeStr ("core", "/", "namespace");
+ setAttributeStr ("NWBFile", "/", "neurodata_type");
+ setAttributeStr ("2.5.0", "/", "nwb_version");
+ setAttributeStr (identifierText, "/", "object_id");
+
+ if (createGroup ("/acquisition"))
+ return -1;
+
+ if (createGroup ("/analysis"))
+ return -1;
+
+ String time = Time::getCurrentTime().formatted ("%Y-%m-%dT%H:%M:%S") + Time::getCurrentTime().getUTCOffsetString (true);
+
+ createTextDataSet ("", "file_create_date", time);
+
+ 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");
+ colnames.add ("location");
+ 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;
+ if (createGroup ("/stimulus/presentation"))
+ return -1;
+ if (createGroup ("/stimulus/templates"))
+ return -1;
+
+ createStringDataSet ("/session_description", "Recording with the Open Ephys GUI");
+ createStringDataSet ("/session_start_time", time);
+ createStringDataSet ("/timestamps_reference_time", time);
+ createStringDataSet ("/identifier", "test-identifier");
+
+ return 0;
}
-TimeSeries::TimeSeries(String rootPath, String name, String description_)
- : basePath(rootPath + name), description(description_)
+TimeSeries::TimeSeries (String rootPath, String name, String description_)
+ : basePath (rootPath + name), description (description_)
{
-
}
-ecephys::ElectricalSeries::ElectricalSeries(String rootPath, String name, String description_,
- int channel_count_, Array channel_conversion_)
- : TimeSeries(rootPath, name, description_),
- channel_conversion(channel_conversion_),
- channel_count(channel_count_)
+ecephys::ElectricalSeries::ElectricalSeries (String rootPath, String name, String description_, int channel_count_, Array channel_conversion_)
+ : TimeSeries (rootPath, name, description_),
+ channel_conversion (channel_conversion_),
+ channel_count (channel_count_)
{
-
}
-ecephys::SpikeEventSeries::SpikeEventSeries(String rootPath, String name, String description_,
- int channel_count, Array channel_conversion_)
- : ecephys::ElectricalSeries(rootPath, name, description_, channel_count, channel_conversion_)
+ecephys::SpikeEventSeries::SpikeEventSeries (String rootPath, String name, String description_, int channel_count, Array channel_conversion_)
+ : ecephys::ElectricalSeries (rootPath, name, description_, channel_count, channel_conversion_)
{
-
}
-TTLEventSeries::TTLEventSeries(String rootPath, String name, String description_)
- : TimeSeries(rootPath, name, description_)
+TTLEventSeries::TTLEventSeries (String rootPath, String name, String description_)
+ : TimeSeries (rootPath, name, description_)
{
-
}
-AnnotationSeries::AnnotationSeries(String rootPath, String name, String description_)
- : TimeSeries(rootPath, name, description_)
+AnnotationSeries::AnnotationSeries (String rootPath, String name, String description_)
+ : TimeSeries (rootPath, name, description_)
{
-
}
-
-bool NWBFile::startNewRecording(
- int recordingNumber,
- const Array& continuousArray,
- const Array& continuousChannels,
- const Array& eventArray,
- const Array& electrodeArray)
+bool NWBFile::startNewRecording (
+ int recordingNumber,
+ const Array& continuousArray,
+ const Array& continuousChannels,
+ const Array& eventArray,
+ const Array& electrodeArray)
{
-
// all recorded data is stored in the "acquisition" group
- String rootPath = "/acquisition/";
+ String rootPath = "/acquisition/";
- continuousDataSets.clearQuick(true);
- spikeDataSets.clearQuick(true);
- eventDataSets.clearQuick(true);
+ continuousDataSets.clearQuick (true);
+ spikeDataSets.clearQuick (true);
+ eventDataSets.clearQuick (true);
- Array all_electrode_inds;
- StringArray groupNames;
- StringArray groupReferences;
+ Array all_electrode_inds;
+ StringArray groupNames;
+ StringArray groupReferences;
- // 0. put global inds into electrode table
- for (auto ch : continuousChannels)
- {
- all_electrode_inds.add(ch->getGlobalIndex());
+ // 0. put global inds into electrode table
+ for (auto ch : continuousChannels)
+ {
+ all_electrode_inds.add (ch->getGlobalIndex());
- String groupName = ch->getSourceNodeName() + "-"
- + String(ch->getSourceNodeId())
- + "." + ch->getStreamName();
+ String groupName = ch->getSourceNodeName() + "-"
+ + String (ch->getSourceNodeId())
+ + "." + ch->getStreamName();
- groupNames.add(groupName);
- groupReferences.add("/general/extracellular_ephys/" + groupName);
- }
+ groupNames.add (groupName);
+ groupReferences.add ("/general/extracellular_ephys/" + groupName);
+ }
// 1. Create continuous datasets
- for (int i = 0; i < continuousArray.size(); i++)
- {
+ for (int i = 0; i < continuousArray.size(); i++)
+ {
+ // Get the scaling info for each channel
+ ContinuousGroup group = continuousArray.getReference (i);
- // Get the scaling info for each channel
- ContinuousGroup group = continuousArray.getReference(i);
-
Array channel_conversion;
for (int ch = 0; ch < group.size(); ch++)
{
- channel_conversion.add(group[ch]->getBitVolts() / 1e6);
+ 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");
+ 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);
+ 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");
+ 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);
+ createReference ("/" + fullPath + "/device", "/general/devices/" + groupName);
Array electrode_inds;
for (int ch = 0; ch < group.size(); ch++)
{
- int index = group[ch]->getGlobalIndex();
- electrode_inds.add(index);
+ int index = group[ch]->getGlobalIndex();
+ electrode_inds.add (index);
}
ecephys::ElectricalSeries* electricalSeries =
- new ecephys::ElectricalSeries(rootPath,
- groupName,
- "Stores continuously sampled voltage data from an extracellular ephys recording",
- group.size(),
- channel_conversion
- );
+ new ecephys::ElectricalSeries (rootPath,
+ groupName,
+ "Stores continuously sampled voltage data from an extracellular ephys recording",
+ group.size(),
+ channel_conversion);
if (recordingNumber == 0)
- if (!createTimeSeriesBase(electricalSeries))
+ if (! createTimeSeriesBase (electricalSeries))
return false;
- electricalSeries->baseDataSet = createDataSet(BaseDataType::I16,
- 0,
- electricalSeries->channel_count,
- CHUNK_XSIZE,
- electricalSeries->basePath + "/data");
-
+ electricalSeries->baseDataSet = createDataSet (BaseDataType::I16,
+ 0,
+ electricalSeries->channel_count,
+ CHUNK_XSIZE,
+ electricalSeries->basePath + "/data");
+
if (electricalSeries->baseDataSet == nullptr)
{
std::cerr << "Error creating dataset for " << groupName << std::endl;
return false;
- } else {
- createDataAttributes(electricalSeries->basePath, channel_conversion[0], -1.0f, "volts");
+ }
+ else
+ {
+ createDataAttributes (electricalSeries->basePath, channel_conversion[0], -1.0f, "volts");
}
electricalSeries->timestampDataSet =
- createTimestampDataSet(electricalSeries->basePath + "/timestamps", CHUNK_XSIZE, 1/group[0]->getSampleRate());
- if (electricalSeries->timestampDataSet == nullptr) return false;
-
+ createTimestampDataSet (electricalSeries->basePath + "/timestamps", CHUNK_XSIZE, 1 / group[0]->getSampleRate());
+ if (electricalSeries->timestampDataSet == nullptr)
+ return false;
+
electricalSeries->sampleNumberDataSet =
- createSampleNumberDataSet(electricalSeries->basePath + "/sync", CHUNK_XSIZE);
- if (electricalSeries->sampleNumberDataSet == nullptr) return false;
-
- electricalSeries->channelConversionDataSet = createChannelConversionDataSet(electricalSeries->basePath + "/channel_conversion", "Bit volts values for all channels", CHUNK_XSIZE);
-
- if (electricalSeries->channelConversionDataSet == nullptr) return false;
- writeChannelConversions(electricalSeries);
-
- electricalSeries->electrodeDataSet = createElectrodeDataSet(electricalSeries->basePath + "/electrodes", "Electrode index for each channel", CHUNK_XSIZE);
-
- if (electricalSeries->electrodeDataSet == nullptr) return false;
- writeElectrodes(electricalSeries, electrode_inds);
-
- continuousDataSets.add(electricalSeries);
- }
+ createSampleNumberDataSet (electricalSeries->basePath + "/sync", CHUNK_XSIZE);
+ if (electricalSeries->sampleNumberDataSet == nullptr)
+ return false;
+
+ electricalSeries->channelConversionDataSet = createChannelConversionDataSet (electricalSeries->basePath + "/channel_conversion", "Bit volts values for all channels", CHUNK_XSIZE);
+
+ if (electricalSeries->channelConversionDataSet == nullptr)
+ return false;
+ writeChannelConversions (electricalSeries);
+
+ electricalSeries->electrodeDataSet = createElectrodeDataSet (electricalSeries->basePath + "/electrodes", "Electrode index for each channel", CHUNK_XSIZE);
+
+ if (electricalSeries->electrodeDataSet == nullptr)
+ return false;
+ writeElectrodes (electricalSeries, electrode_inds);
+
+ continuousDataSets.add (electricalSeries);
+ }
// 2. create spike datasets
- for (int i = 0; i < electrodeArray.size(); i++)
- {
- const SpikeChannel* sourceInfo = electrodeArray[i];
+ for (int i = 0; i < electrodeArray.size(); i++)
+ {
+ const SpikeChannel* sourceInfo = electrodeArray[i];
- String sourceName = sourceInfo->getSourceNodeName() + "-" + String(sourceInfo->getSourceNodeId());
- sourceName += "." + sourceInfo->getStreamName();
+ String sourceName = sourceInfo->getSourceNodeName() + "-" + String (sourceInfo->getSourceNodeId());
+ sourceName += "." + sourceInfo->getStreamName();
sourceName += "." + sourceInfo->getName();
-
+
Array channel_conversion;
-
+
for (int ch = 0; ch < sourceInfo->getNumChannels(); ch++)
{
- channel_conversion.add(sourceInfo->getSourceChannels()[0]->getBitVolts() / 1e6);
+ channel_conversion.add (sourceInfo->getSourceChannels()[0]->getBitVolts() / 1e6);
}
-
+
Array electrode_inds;
-
+
for (int ch = 0; ch < sourceInfo->getNumChannels(); ch++)
{
- int globalIndex = sourceInfo->getSourceChannels()[ch]->getGlobalIndex();
+ int globalIndex = sourceInfo->getSourceChannels()[ch]->getGlobalIndex();
- electrode_inds.add(globalIndex);
+ electrode_inds.add (globalIndex);
}
-
+
ecephys::SpikeEventSeries* spikeEventSeries =
- new ecephys::SpikeEventSeries(rootPath, sourceName,
- "Stores spike waveforms from an extracellular ephys recording",
- sourceInfo->getNumChannels(),
- channel_conversion);
-
+ new ecephys::SpikeEventSeries (rootPath, sourceName, "Stores spike waveforms from an extracellular ephys recording", sourceInfo->getNumChannels(), channel_conversion);
+
if (recordingNumber == 0)
- if (!createTimeSeriesBase(spikeEventSeries))
+ if (! createTimeSeriesBase (spikeEventSeries))
return false;
- spikeEventSeries->baseDataSet = createDataSet(BaseDataType::I16, 0, sourceInfo->getNumChannels(), sourceInfo->getTotalSamples(), SPIKE_CHUNK_XSIZE, spikeEventSeries->basePath + "/data");
-
+ spikeEventSeries->baseDataSet = createDataSet (BaseDataType::I16, 0, sourceInfo->getNumChannels(), sourceInfo->getTotalSamples(), SPIKE_CHUNK_XSIZE, spikeEventSeries->basePath + "/data");
+
if (spikeEventSeries->baseDataSet == nullptr)
{
std::cerr << "Error creating dataset for electrode " << i << std::endl;
return false;
- } else {
- createDataAttributes(spikeEventSeries->basePath, channel_conversion[0], -1.0f, "volts");
}
-
+ else
+ {
+ createDataAttributes (spikeEventSeries->basePath, channel_conversion[0], -1.0f, "volts");
+ }
+
spikeEventSeries->timestampDataSet =
- createTimestampDataSet(spikeEventSeries->basePath + "/timestamps", CHUNK_XSIZE, 1/sourceInfo->getSourceChannels()[0]->getSampleRate());
- if (spikeEventSeries->timestampDataSet == nullptr) return false;
-
+ createTimestampDataSet (spikeEventSeries->basePath + "/timestamps", CHUNK_XSIZE, 1 / sourceInfo->getSourceChannels()[0]->getSampleRate());
+ if (spikeEventSeries->timestampDataSet == nullptr)
+ return false;
+
spikeEventSeries->sampleNumberDataSet =
- createSampleNumberDataSet(spikeEventSeries->basePath + "/sync", CHUNK_XSIZE);
- if (spikeEventSeries->sampleNumberDataSet == nullptr) return false;
-
- spikeEventSeries->channelConversionDataSet = createChannelConversionDataSet(spikeEventSeries->basePath + "/channel_conversion", "Bit volts values for all channels", CHUNK_XSIZE);
-
- if (spikeEventSeries->channelConversionDataSet == nullptr) return false;
- writeChannelConversions(spikeEventSeries);
-
- spikeEventSeries->electrodeDataSet = createElectrodeDataSet(spikeEventSeries->basePath + "/electrodes", "Electrode index for each channel", CHUNK_XSIZE);
-
- if (spikeEventSeries->electrodeDataSet == nullptr) return false;
- writeElectrodes(spikeEventSeries, electrode_inds);
-
- spikeDataSets.add(spikeEventSeries);
-
- }
-
+ createSampleNumberDataSet (spikeEventSeries->basePath + "/sync", CHUNK_XSIZE);
+ if (spikeEventSeries->sampleNumberDataSet == nullptr)
+ return false;
+
+ spikeEventSeries->channelConversionDataSet = createChannelConversionDataSet (spikeEventSeries->basePath + "/channel_conversion", "Bit volts values for all channels", CHUNK_XSIZE);
+
+ if (spikeEventSeries->channelConversionDataSet == nullptr)
+ return false;
+ writeChannelConversions (spikeEventSeries);
+
+ spikeEventSeries->electrodeDataSet = createElectrodeDataSet (spikeEventSeries->basePath + "/electrodes", "Electrode index for each channel", CHUNK_XSIZE);
+
+ if (spikeEventSeries->electrodeDataSet == nullptr)
+ return false;
+ writeElectrodes (spikeEventSeries, electrode_inds);
+
+ spikeDataSets.add (spikeEventSeries);
+ }
+
// 3. Create event channel datasets
- for (int i = 0; i < eventArray.size(); i++)
- {
-
- const EventChannel* info = eventArray[i];
-
- String sourceName = info->getSourceNodeName() + "-" + String(info->getSourceNodeId());
- sourceName += "." + info->getStreamName();
-
- String typeString, description;
-
+ for (int i = 0; i < eventArray.size(); i++)
+ {
+ const EventChannel* info = eventArray[i];
+
+ String sourceName = info->getSourceNodeName() + "-" + String (info->getSourceNodeId());
+ sourceName += "." + info->getStreamName();
+
+ String typeString, description;
+
if (info->getType() == EventChannel::TTL)
{
TTLEventSeries* ttlEventSeries =
- new TTLEventSeries(rootPath, sourceName + ".TTL", "Stores the times and lines of TTL events");
-
+ new TTLEventSeries (rootPath, sourceName + ".TTL", "Stores the times and lines of TTL events");
+
if (recordingNumber == 0)
- if (!createTimeSeriesBase(ttlEventSeries)) return false;
-
- ttlEventSeries->baseDataSet = createDataSet(getEventH5Type(info->getType(), info->getLength()), 0, EVENT_CHUNK_SIZE, ttlEventSeries->basePath + "/data");
-
+ if (! createTimeSeriesBase (ttlEventSeries))
+ return false;
+
+ ttlEventSeries->baseDataSet = createDataSet (getEventH5Type (info->getType(), info->getLength()), 0, EVENT_CHUNK_SIZE, ttlEventSeries->basePath + "/data");
+
if (ttlEventSeries->baseDataSet == nullptr)
{
std::cerr << "Error creating dataset for event " << info->getName() << std::endl;
return false;
}
-
- ttlEventSeries->timestampDataSet =
- createTimestampDataSet(ttlEventSeries->basePath + "/timestamps", EVENT_CHUNK_SIZE, 1/info->getSampleRate());
- if (ttlEventSeries->timestampDataSet == nullptr) return false;
-
- ttlEventSeries->sampleNumberDataSet = createSampleNumberDataSet(ttlEventSeries->basePath + "/sync", EVENT_CHUNK_SIZE);
- if (ttlEventSeries->sampleNumberDataSet == nullptr) return false;
-
- ttlEventSeries->ttlWordDataSet = createDataSet(BaseDataType::U64, 0, info->getDataSize(), EVENT_CHUNK_SIZE, ttlEventSeries->basePath + "/full_word");
- if (ttlEventSeries->ttlWordDataSet == nullptr) return false;
-
- eventDataSets.add(ttlEventSeries);
+ ttlEventSeries->timestampDataSet =
+ createTimestampDataSet (ttlEventSeries->basePath + "/timestamps", EVENT_CHUNK_SIZE, 1 / info->getSampleRate());
+ if (ttlEventSeries->timestampDataSet == nullptr)
+ return false;
+
+ ttlEventSeries->sampleNumberDataSet = createSampleNumberDataSet (ttlEventSeries->basePath + "/sync", EVENT_CHUNK_SIZE);
+ if (ttlEventSeries->sampleNumberDataSet == nullptr)
+ return false;
+
+ ttlEventSeries->ttlWordDataSet = createDataSet (BaseDataType::U64, 0, info->getDataSize(), EVENT_CHUNK_SIZE, ttlEventSeries->basePath + "/full_word");
+ if (ttlEventSeries->ttlWordDataSet == nullptr)
+ return false;
+
+ eventDataSets.add (ttlEventSeries);
}
- else if (info->getType() == EventChannel::TEXT)
+ else if (info->getType() == EventChannel::TEXT)
{
- AnnotationSeries* annotationSeries = new AnnotationSeries(rootPath, "messages", "Stores timestamped messages generated during an experiment");
-
+ AnnotationSeries* annotationSeries = new AnnotationSeries (rootPath, "messages", "Stores timestamped messages generated during an experiment");
+
if (recordingNumber == 0)
- if (!createTimeSeriesBase(annotationSeries)) return false;
-
- annotationSeries->baseDataSet = createDataSet(getEventH5Type(info->getType(), info->getLength()), 0, EVENT_CHUNK_SIZE, annotationSeries->basePath + "/data");
-
+ if (! createTimeSeriesBase (annotationSeries))
+ return false;
+
+ annotationSeries->baseDataSet = createDataSet (getEventH5Type (info->getType(), info->getLength()), 0, EVENT_CHUNK_SIZE, annotationSeries->basePath + "/data");
+
if (annotationSeries->baseDataSet == nullptr)
{
std::cerr << "Error creating dataset for event " << info->getName() << std::endl;
return false;
}
-
- annotationSeries->timestampDataSet = createTimestampDataSet(annotationSeries->basePath + "/timestamps", EVENT_CHUNK_SIZE, 1/info->getSampleRate());
- if (annotationSeries->timestampDataSet == nullptr) return false;
-
- annotationSeries->sampleNumberDataSet = createSampleNumberDataSet(annotationSeries->basePath + "/sync", EVENT_CHUNK_SIZE);
- if (annotationSeries->sampleNumberDataSet == nullptr) return false;
-
- messagesDataSet.reset(annotationSeries);
+
+ annotationSeries->timestampDataSet = createTimestampDataSet (annotationSeries->basePath + "/timestamps", EVENT_CHUNK_SIZE, 1 / info->getSampleRate());
+ if (annotationSeries->timestampDataSet == nullptr)
+ return false;
+
+ annotationSeries->sampleNumberDataSet = createSampleNumberDataSet (annotationSeries->basePath + "/sync", EVENT_CHUNK_SIZE);
+ if (annotationSeries->sampleNumberDataSet == nullptr)
+ return false;
+
+ messagesDataSet.reset (annotationSeries);
}
+ }
- }
+ //4. Create sync messages dataset
+ String desc = "Stores recording start timestamps for each processor in text format";
- //4. Create sync messages dataset
- String desc = "Stores recording start timestamps for each processor in text format";
-
- AnnotationSeries* annotationSeries = new AnnotationSeries(rootPath, "sync_messages", desc);
+ AnnotationSeries* annotationSeries = new AnnotationSeries (rootPath, "sync_messages", desc);
if (recordingNumber == 0)
{
- if (!createTimeSeriesBase(annotationSeries)) return false;
+ if (! createTimeSeriesBase (annotationSeries))
+ return false;
+
+ annotationSeries->baseDataSet = createDataSet (BaseDataType::STR (100), 0, 1, annotationSeries->basePath + "/data");
- annotationSeries->baseDataSet = createDataSet(BaseDataType::STR(100), 0, 1, annotationSeries->basePath + "/data");
-
if (annotationSeries->baseDataSet == nullptr)
{
std::cerr << "Error creating dataset for sync messages" << std::endl;
return false;
}
- }
- else {
- annotationSeries->baseDataSet = getDataSet(annotationSeries->basePath + "/data");
- }
+ }
+ else
+ {
+ annotationSeries->baseDataSet = getDataSet (annotationSeries->basePath + "/data");
+ }
if (recordingNumber == 0)
{
- annotationSeries->sampleNumberDataSet = createSampleNumberDataSet(annotationSeries->basePath + "/sync", 1);
- if (annotationSeries->sampleNumberDataSet == nullptr) return false;
- }
- else {
- annotationSeries->sampleNumberDataSet = getDataSet(annotationSeries->basePath + "/sync");
- }
-
- if (recordingNumber == 0)
- {
- annotationSeries->timestampDataSet = createTimestampDataSet(annotationSeries->basePath + "/timestamps", 1, 1);
- if (annotationSeries->timestampDataSet == nullptr) return false;
- }
- else {
- annotationSeries->timestampDataSet = getDataSet(annotationSeries->basePath + "/timestamps");
- }
-
- syncMsgDataSet.reset(annotationSeries);
-
- // 5. Create electrode table
- ScopedPointer elSet = createDataSet(BaseDataType::I32, 1, 1, "general/extracellular_ephys/electrodes/id");
-
- std::vector 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 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");
-
- ScopedPointer locationsDataset = createDataSet(BaseDataType::STR(250), 0, 1, "general/extracellular_ephys/electrodes/location");
-
- for (int i = 0; i < groupNames.size(); i++)
- locationsDataset->writeDataBlock(1, BaseDataType::STR(7), String("unknown").toUTF8());
-
- setAttributeStr("the location of channel within the subject e.g. brain region", "general/extracellular_ephys/electrodes/location", "description");
- setAttributeStr("hdmf-common", "general/extracellular_ephys/electrodes/location", "namespace");
- setAttributeStr("VectorData", "general/extracellular_ephys/electrodes/location", "neurodata_type");
- setAttributeStr(generateUuid(), "general/extracellular_ephys/electrodes/location", "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;
-
- }
-
- void NWBFile::stopRecording()
- {
-
- const TimeSeries* tsStruct;
-
- for (int i = 0; i < continuousDataSets.size(); i++)
- {
- tsStruct = continuousDataSets[i];
- CHECK_ERROR(setAttribute(BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
- }
-
- for (int i = 0; i < spikeDataSets.size(); i++)
- {
- tsStruct = spikeDataSets[i];
- CHECK_ERROR(setAttribute(BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
- }
-
- for (int i = 0; i < eventDataSets.size(); i++)
- {
- tsStruct = eventDataSets[i];
- CHECK_ERROR(setAttribute(BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
- }
-
- CHECK_ERROR(setAttribute(BaseDataType::U64, &(syncMsgDataSet->numSamples), syncMsgDataSet->basePath, "num_samples"));
- }
-
- void NWBFile::writeData(int datasetID, int channel, int nSamples, const float* data, float bitVolts)
- {
- if (!continuousDataSets[datasetID])
- return;
-
- if (nSamples > bufferSize) //Shouldn't happen, and if it happens it'll be slow, but better this than crashing. Will be reset on file close and reset.
- {
- std::cerr << "Write buffer overrun, resizing to" << nSamples << std::endl;
- bufferSize = nSamples;
- scaledBuffer.malloc(nSamples);
- intBuffer.malloc(nSamples);
- }
-
- double multFactor = 1 / (float(0x7fff) * bitVolts);
- FloatVectorOperations::copyWithMultiply(scaledBuffer.getData(), data, multFactor, nSamples);
- AudioDataConverters::convertFloatToInt16LE(scaledBuffer.getData(), intBuffer.getData(), nSamples);
-
- continuousDataSets[datasetID]->baseDataSet->writeDataRow(channel, nSamples, BaseDataType::I16, intBuffer);
- //CHECK_ERROR();
-
- /* Since channels are filled asynchronouysly by the Record Thread, there is no guarantee
+ annotationSeries->sampleNumberDataSet = createSampleNumberDataSet (annotationSeries->basePath + "/sync", 1);
+ if (annotationSeries->sampleNumberDataSet == nullptr)
+ return false;
+ }
+ else
+ {
+ annotationSeries->sampleNumberDataSet = getDataSet (annotationSeries->basePath + "/sync");
+ }
+
+ if (recordingNumber == 0)
+ {
+ annotationSeries->timestampDataSet = createTimestampDataSet (annotationSeries->basePath + "/timestamps", 1, 1);
+ if (annotationSeries->timestampDataSet == nullptr)
+ return false;
+ }
+ else
+ {
+ annotationSeries->timestampDataSet = getDataSet (annotationSeries->basePath + "/timestamps");
+ }
+
+ syncMsgDataSet.reset (annotationSeries);
+
+ // 5. Create electrode table
+ ScopedPointer elSet = createDataSet (BaseDataType::I32, 1, 1, "general/extracellular_ephys/electrodes/id");
+
+ std::vector 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 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");
+
+ ScopedPointer locationsDataset = createDataSet (BaseDataType::STR (250), 0, 1, "general/extracellular_ephys/electrodes/location");
+
+ for (int i = 0; i < groupNames.size(); i++)
+ locationsDataset->writeDataBlock (1, BaseDataType::STR (7), String ("unknown").toUTF8());
+
+ setAttributeStr ("the location of channel within the subject e.g. brain region", "general/extracellular_ephys/electrodes/location", "description");
+ setAttributeStr ("hdmf-common", "general/extracellular_ephys/electrodes/location", "namespace");
+ setAttributeStr ("VectorData", "general/extracellular_ephys/electrodes/location", "neurodata_type");
+ setAttributeStr (generateUuid(), "general/extracellular_ephys/electrodes/location", "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;
+}
+
+void NWBFile::stopRecording()
+{
+ const TimeSeries* tsStruct;
+
+ for (int i = 0; i < continuousDataSets.size(); i++)
+ {
+ tsStruct = continuousDataSets[i];
+ CHECK_ERROR (setAttribute (BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
+ }
+
+ for (int i = 0; i < spikeDataSets.size(); i++)
+ {
+ tsStruct = spikeDataSets[i];
+ CHECK_ERROR (setAttribute (BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
+ }
+
+ for (int i = 0; i < eventDataSets.size(); i++)
+ {
+ tsStruct = eventDataSets[i];
+ CHECK_ERROR (setAttribute (BaseDataType::U64, &(tsStruct->numSamples), tsStruct->basePath, "num_samples"));
+ }
+
+ CHECK_ERROR (setAttribute (BaseDataType::U64, &(syncMsgDataSet->numSamples), syncMsgDataSet->basePath, "num_samples"));
+}
+
+void NWBFile::writeData (int datasetID, int channel, int nSamples, const float* data, float bitVolts)
+{
+ if (! continuousDataSets[datasetID])
+ return;
+
+ if (nSamples > bufferSize) //Shouldn't happen, and if it happens it'll be slow, but better this than crashing. Will be reset on file close and reset.
+ {
+ std::cerr << "Write buffer overrun, resizing to" << nSamples << std::endl;
+ bufferSize = nSamples;
+ scaledBuffer.malloc (nSamples);
+ intBuffer.malloc (nSamples);
+ }
+
+ double multFactor = 1 / (float (0x7fff) * bitVolts);
+ FloatVectorOperations::copyWithMultiply (scaledBuffer.getData(), data, multFactor, nSamples);
+ AudioDataConverters::convertFloatToInt16LE (scaledBuffer.getData(), intBuffer.getData(), nSamples);
+
+ continuousDataSets[datasetID]->baseDataSet->writeDataRow (channel, nSamples, BaseDataType::I16, intBuffer);
+ //CHECK_ERROR();
+
+ /* Since channels are filled asynchronouysly by the Record Thread, there is no guarantee
that at a any point in time all channels in a dataset have the same number of filled samples.
However, since each dataset is filled from a single source, all channels must have the
same number of samples at acquisition stop. To keep track of the written samples we must chose
an arbitrary channel, and at the end all channels will be the same. */
- if (channel == 0) //there will always be a first channel or there wouldn't be dataset
- continuousDataSets[datasetID]->numSamples += nSamples;
- }
+ if (channel == 0) //there will always be a first channel or there wouldn't be dataset
+ continuousDataSets[datasetID]->numSamples += nSamples;
+}
+
+void NWBFile::writeSampleNumbers (int datasetID, int nSamples, const int64* data)
+{
+ if (! continuousDataSets[datasetID])
+ return;
+
+ CHECK_ERROR (continuousDataSets[datasetID]->sampleNumberDataSet->writeDataBlock (nSamples, BaseDataType::I64, data));
+}
+
+void NWBFile::writeTimestamps (int datasetID, int nSamples, const double* data)
+{
+ if (! continuousDataSets[datasetID])
+ return;
+
+ CHECK_ERROR (continuousDataSets[datasetID]->timestampDataSet->writeDataBlock (nSamples, BaseDataType::F64, data));
+}
+
+void NWBFile::writeChannelConversions (ecephys::ElectricalSeries* electricalSeries)
+{
+ std::vector conversions;
+ for (auto c : electricalSeries->channel_conversion)
+ conversions.push_back (c);
+
+ CHECK_ERROR (electricalSeries->channelConversionDataSet->writeDataBlock (conversions.size(), BaseDataType::F32, &conversions[0]));
+}
+
+void NWBFile::writeElectrodes (ecephys::ElectricalSeries* electricalSeries, Array electrodeInds)
+{
+ std::vector electrodeNumbers;
+ for (auto i : electrodeInds)
+ electrodeNumbers.push_back (i);
+
+ CHECK_ERROR (electricalSeries->electrodeDataSet->writeDataBlock (electricalSeries->channel_count, BaseDataType::I32, &electrodeNumbers[0]));
+}
+
+void NWBFile::writeSpike (int electrodeId, const SpikeChannel* channel, const Spike* event)
+{
+ if (! spikeDataSets[electrodeId])
+ return;
+ int nSamples = channel->getTotalSamples() * channel->getNumChannels();
+
+ if (nSamples > bufferSize) //Shouldn't happen, and if it happens it'll be slow, but better this than crashing. Will be reset on file close and reset.
+ {
+ std::cerr << "Write buffer overrun, resizing to" << nSamples << std::endl;
+ bufferSize = nSamples;
+ scaledBuffer.malloc (nSamples);
+ intBuffer.malloc (nSamples);
+ }
+
+ double multFactor = 1 / (float (0x7fff) * channel->getChannelBitVolts (0));
+ FloatVectorOperations::copyWithMultiply (scaledBuffer.getData(), event->getDataPointer(), multFactor, nSamples);
+ AudioDataConverters::convertFloatToInt16LE (scaledBuffer.getData(), intBuffer.getData(), nSamples);
+
+ double timestampSec = event->getTimestampInSeconds();
+
+ CHECK_ERROR (spikeDataSets[electrodeId]->baseDataSet->writeDataBlock (1, BaseDataType::I16, intBuffer));
+ CHECK_ERROR (spikeDataSets[electrodeId]->timestampDataSet->writeDataBlock (1, BaseDataType::F64, ×tampSec));
+ writeEventMetadata (spikeDataSets[electrodeId], channel, event);
+
+ const int64 sampleNumber = event->getSampleNumber();
+
+ CHECK_ERROR (spikeDataSets[electrodeId]->sampleNumberDataSet->writeDataBlock (1, BaseDataType::I64, &sampleNumber));
+
+ spikeDataSets[electrodeId]->numSamples += 1;
+}
+
+void NWBFile::writeEvent (int eventID, const EventChannel* channel, const Event* event)
+{
+ const void* dataSrc;
+ BaseDataType type;
+ int8 ttlVal;
+ String text;
+
+ switch (event->getEventType())
+ {
+ case EventChannel::TTL:
+ ttlVal = (static_cast (event)->getState() ? 1 : -1) * (static_cast (event)->getLine() + 1);
+ dataSrc = &ttlVal;
+ type = BaseDataType::I8;
+ break;
+ case EventChannel::TEXT:
+ text = static_cast (event)->getText();
+ dataSrc = text.toUTF8().getAddress();
+ type = BaseDataType::STR (text.length());
+ break;
+ default:
+ dataSrc = static_cast (event)->getBinaryDataPointer();
+ type = getEventH5Type (event->getEventType());
+ break;
+ }
+
+ if (eventID == eventDataSets.size()) //MessageCenter event
+ {
+ CHECK_ERROR (messagesDataSet->baseDataSet->writeDataBlock (1, BaseDataType::STR (text.length()), text.toUTF8()));
+
+ const int64 sampleNumber = event->getSampleNumber();
+
+ CHECK_ERROR (messagesDataSet->sampleNumberDataSet->writeDataBlock (1, BaseDataType::I64, &sampleNumber));
+
+ const double timeSec = event->getTimestampInSeconds();
+
+ CHECK_ERROR (messagesDataSet->timestampDataSet->writeDataBlock (1, BaseDataType::F64, &timeSec));
+
+ messagesDataSet->numSamples += 1;
+ }
+ else if (eventDataSets[eventID])
+ {
+ CHECK_ERROR (eventDataSets[eventID]->baseDataSet->writeDataBlock (1, type, dataSrc));
+
+ const double timeSec = event->getTimestampInSeconds();
+
+ CHECK_ERROR (eventDataSets[eventID]->timestampDataSet->writeDataBlock (1, BaseDataType::F64, &timeSec));
+
+ const int64 sampleNumber = event->getSampleNumber();
+
+ CHECK_ERROR (eventDataSets[eventID]->sampleNumberDataSet->writeDataBlock (1, BaseDataType::I64, &sampleNumber));
+
+ if (event->getEventType() == EventChannel::TTL)
+ {
+ const uint64 ttlWord = static_cast (event)->getWord();
+ CHECK_ERROR (eventDataSets[eventID]->ttlWordDataSet->writeDataBlock (1, BaseDataType::U64, &ttlWord));
+ }
+
+ eventDataSets[eventID]->numSamples += 1;
+ }
+ else
+ {
+ //Attempted to write an event to disk from unknown event source
+ }
+}
+
+void NWBFile::writeTimestampSyncText (uint16 sourceID, int64 sampleNumber, float sourceSampleRate, String text)
+{
+ CHECK_ERROR (syncMsgDataSet->baseDataSet->writeDataBlock (1, BaseDataType::STR (text.length()), text.toUTF8()));
+
+ CHECK_ERROR (syncMsgDataSet->sampleNumberDataSet->writeDataBlock (1, BaseDataType::I64, &sampleNumber));
- void NWBFile::writeSampleNumbers(int datasetID, int nSamples, const int64* data)
- {
- if (!continuousDataSets[datasetID])
- return;
+ double timestamp = (double) sampleNumber;
- CHECK_ERROR(continuousDataSets[datasetID]->sampleNumberDataSet->writeDataBlock(nSamples, BaseDataType::I64, data));
- }
+ CHECK_ERROR (syncMsgDataSet->timestampDataSet->writeDataBlock (1, BaseDataType::F64, ×tamp));
- void NWBFile::writeTimestamps(int datasetID, int nSamples, const double* data)
- {
- if (!continuousDataSets[datasetID])
- return;
+ syncMsgDataSet->numSamples += 1;
+}
- CHECK_ERROR(continuousDataSets[datasetID]->timestampDataSet->writeDataBlock(nSamples, BaseDataType::F64, data));
- }
+String NWBFile::getFileName()
+{
+ return filename;
+}
-void NWBFile::writeChannelConversions(ecephys::ElectricalSeries* electricalSeries)
+bool NWBFile::createTimeSeriesBase (TimeSeries* timeSeries)
{
- std::vector conversions;
- for (auto c : electricalSeries->channel_conversion)
- conversions.push_back(c);
+ if (createGroup (timeSeries->basePath))
+ return false;
+ CHECK_ERROR (setAttributeStr (" ", timeSeries->basePath, "comments"));
+ CHECK_ERROR (setAttributeStr (timeSeries->description, timeSeries->basePath, "description"));
+ CHECK_ERROR (setAttributeStr ("core", timeSeries->basePath, "namespace"));
+ CHECK_ERROR (setAttributeStr (generateUuid(), timeSeries->basePath, "object_id"));
+ CHECK_ERROR (setAttributeStr (timeSeries->getNeurodataType(), timeSeries->basePath, "neurodata_type"));
+ return true;
+}
- CHECK_ERROR(electricalSeries->channelConversionDataSet->writeDataBlock(conversions.size(), BaseDataType::F32, &conversions[0]));
+void NWBFile::createDataAttributes (String basePath, float conversion, float resolution, String unit)
+{
+ CHECK_ERROR (setAttribute (BaseDataType::F32, &conversion, basePath + "/data", "conversion"));
+ CHECK_ERROR (setAttribute (BaseDataType::F32, &resolution, basePath + "/data", "resolution"));
+ CHECK_ERROR (setAttributeStr (unit, basePath + "/data", "unit"));
}
- void NWBFile::writeElectrodes(ecephys::ElectricalSeries* electricalSeries, Array electrodeInds)
- {
- std::vector electrodeNumbers;
- for (auto i : electrodeInds)
- electrodeNumbers.push_back(i);
+HDF5RecordingData* NWBFile::createTimestampDataSet (String path, int chunk_size, float interval)
+{
+ HDF5RecordingData* tsSet = createDataSet (BaseDataType::F64, 0, chunk_size, path);
- CHECK_ERROR(electricalSeries->electrodeDataSet->writeDataBlock(electricalSeries->channel_count, BaseDataType::I32, &electrodeNumbers[0]));
- }
+ if (! tsSet)
+ std::cerr << "Error creating timestamp dataset in " << path << std::endl;
+ else
+ {
+ CHECK_ERROR (setAttribute (BaseDataType::F32, &interval, path, "interval"));
+ CHECK_ERROR (setAttributeStr ("seconds", path, "unit"));
+ }
- void NWBFile::writeSpike(int electrodeId, const SpikeChannel* channel, const Spike* event)
- {
- if (!spikeDataSets[electrodeId])
- return;
- int nSamples = channel->getTotalSamples() * channel->getNumChannels();
+ return tsSet;
+}
- if (nSamples > bufferSize) //Shouldn't happen, and if it happens it'll be slow, but better this than crashing. Will be reset on file close and reset.
- {
- std::cerr << "Write buffer overrun, resizing to" << nSamples << std::endl;
- bufferSize = nSamples;
- scaledBuffer.malloc(nSamples);
- intBuffer.malloc(nSamples);
- }
+HDF5RecordingData* NWBFile::createSampleNumberDataSet (String path, int chunk_size)
+{
+ HDF5RecordingData* tsSet = createDataSet (BaseDataType::I64, 0, chunk_size, path);
+ if (! tsSet)
+ std::cerr << "Error creating sample number dataset in " << path << std::endl;
+ else
+ {
+ const int32 one = 1;
+ CHECK_ERROR (setAttribute (BaseDataType::I32, &one, path, "interval"));
+ CHECK_ERROR (setAttributeStr ("samples", path, "unit"));
+ }
+ return tsSet;
+}
- double multFactor = 1 / (float(0x7fff) * channel->getChannelBitVolts(0));
- FloatVectorOperations::copyWithMultiply(scaledBuffer.getData(), event->getDataPointer(), multFactor, nSamples);
- AudioDataConverters::convertFloatToInt16LE(scaledBuffer.getData(), intBuffer.getData(), nSamples);
+HDF5RecordingData* NWBFile::createChannelConversionDataSet (String path, String description, int chunk_size)
+{
+ HDF5RecordingData* elSet = createDataSet (BaseDataType::F32, 1, chunk_size, path);
- double timestampSec = event->getTimestampInSeconds();
+ if (! elSet)
+ std::cerr << "Error creating electrode dataset in " << path << std::endl;
+ else
+ {
+ CHECK_ERROR (setAttributeStr (description, path, "description"));
+ CHECK_ERROR (setAttributeStr ("hdmf-common", path, "namespace"));
+ CHECK_ERROR (setAttributeStr (generateUuid(), path, "object_id"));
+ }
+ return elSet;
+}
- CHECK_ERROR(spikeDataSets[electrodeId]->baseDataSet->writeDataBlock(1, BaseDataType::I16, intBuffer));
- CHECK_ERROR(spikeDataSets[electrodeId]->timestampDataSet->writeDataBlock(1, BaseDataType::F64, ×tampSec));
- writeEventMetadata(spikeDataSets[electrodeId], channel, event);
+HDF5RecordingData* NWBFile::createElectrodeDataSet (String path, String description, int chunk_size)
+{
+ HDF5RecordingData* elSet = createDataSet (BaseDataType::I32, 1, chunk_size, path);
+ if (! elSet)
+ std::cerr << "Error creating electrode dataset in " << path << std::endl;
+ else
+ {
+ 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;
+}
- const int64 sampleNumber = event->getSampleNumber();
+bool NWBFile::createExtraInfo (String basePath, String name, String desc, String id, uint16 index, uint16 typeIndex)
+{
+ if (createGroup (basePath))
+ return false;
+ CHECK_ERROR (setAttributeStr ("openephys:/", basePath, "schema_id"));
+ CHECK_ERROR (setAttributeStr (name, basePath, "name"));
+ CHECK_ERROR (setAttributeStr (desc, basePath, "description"));
+ CHECK_ERROR (setAttributeStr (id, basePath, "identifier"));
+ CHECK_ERROR (setAttribute (BaseDataType::U16, &index, basePath, "source_index"));
+ CHECK_ERROR (setAttribute (BaseDataType::U16, &typeIndex, basePath, "source_type_index"));
+ return true;
+}
- CHECK_ERROR(spikeDataSets[electrodeId]->sampleNumberDataSet->writeDataBlock(1, BaseDataType::I64, &sampleNumber));
+bool NWBFile::createChannelMetadataSets (String basePath, const MetadataObject* info)
+{
+ if (! info)
+ return false;
+ if (createGroup (basePath))
+ return false;
+ CHECK_ERROR (setAttributeStr ("openephys:/", basePath, "schema_id"));
+ int nMetadata = info->getMetadataCount();
+
+ for (int i = 0; i < nMetadata; i++)
+ {
+ const MetadataDescriptor* desc = info->getMetadataDescriptor (i);
+ String fieldName = "Field_" + String (i + 1);
+ String name = desc->getName();
+ String description = desc->getDescription();
+ String identifier = desc->getIdentifier();
+ BaseDataType type = getMetadataH5Type (desc->getType(), desc->getLength()); //only string types use length, for others is always set to 1. If array types are implemented, change this
+ int length = desc->getType() == MetadataDescriptor::CHAR ? 1 : desc->getLength(); //strings are a single element of length set in the type (see above) while other elements are saved a
+ HeapBlock data (desc->getDataSize());
+ info->getMetadataValue (i)->getValue (static_cast (data.getData()));
+ createBinaryDataSet (basePath, fieldName, type, length, data.getData());
+ String fullPath = basePath + "/" + fieldName;
+ CHECK_ERROR (setAttributeStr ("openephys:/", fullPath, "schema_id"));
+ CHECK_ERROR (setAttributeStr (name, fullPath, "name"));
+ CHECK_ERROR (setAttributeStr (description, fullPath, "description"));
+ CHECK_ERROR (setAttributeStr (identifier, fullPath, "identifier"));
+ }
+ return true;
+}
+bool NWBFile::createEventMetadataSets (String basePath, TimeSeries* timeSeries, const MetadataEventObject* info)
+{
+ if (! info)
+ return false;
+ if (createGroup (basePath))
+ return false;
+ CHECK_ERROR (setAttributeStr ("openephys:/", basePath, "schema_id"));
+ int nMetadata = info->getEventMetadataCount();
+
+ timeSeries->metaDataSet.clear(); //just in case
+ for (int i = 0; i < nMetadata; i++)
+ {
+ const MetadataDescriptor* desc = info->getEventMetadataDescriptor (i);
+ String fieldName = "Field_" + String (i + 1);
+ String name = desc->getName();
+ String description = desc->getDescription();
+ String identifier = desc->getIdentifier();
+ BaseDataType type = getMetadataH5Type (desc->getType(), desc->getLength()); //only string types use length, for others is always set to 1. If array types are implemented, change this
+ int length = desc->getType() == MetadataDescriptor::CHAR ? 1 : desc->getLength(); //strings are a single element of length set in the type (see above) while other elements are saved as arrays
+ String fullPath = basePath + "/" + fieldName;
+ HDF5RecordingData* dSet = createDataSet (type, 0, length, EVENT_CHUNK_SIZE, fullPath);
+ if (! dSet)
+ return false;
+ timeSeries->metaDataSet.add (dSet);
+
+ CHECK_ERROR (setAttributeStr ("openephys:/", fullPath, "schema_id"));
+ CHECK_ERROR (setAttributeStr (name, fullPath, "name"));
+ CHECK_ERROR (setAttributeStr (description, fullPath, "description"));
+ CHECK_ERROR (setAttributeStr (identifier, fullPath, "identifier"));
+ }
+ return true;
+}
- spikeDataSets[electrodeId]->numSamples += 1;
+void NWBFile::writeEventMetadata (TimeSeries* timeSeries, const MetadataEventObject* info, const MetadataEvent* event)
+{
+ jassert (timeSeries->metaDataSet.size() == event->getMetadataValueCount());
+ jassert (info->getEventMetadataCount() == event->getMetadataValueCount());
+ int nMetadata = event->getMetadataValueCount();
+ for (int i = 0; i < nMetadata; i++)
+ {
+ BaseDataType type = getMetadataH5Type (info->getEventMetadataDescriptor (i)->getType(), info->getEventMetadataDescriptor (i)->getLength());
+ timeSeries->metaDataSet[i]->writeDataBlock (1, type, event->getMetadataValue (i)->getRawValuePointer());
+ }
+}
- }
+void NWBFile::createTextDataSet (String path, String name, String text)
+{
+ ScopedPointer dSet;
- void NWBFile::writeEvent(int eventID, const EventChannel* channel, const Event* event)
- {
+ if (text.isEmpty())
+ text = " "; //to avoid 0-length strings, which cause errors
+ BaseDataType type = BaseDataType::STR (text.length());
- const void* dataSrc;
- BaseDataType type;
- int8 ttlVal;
- String text;
+ dSet = createDataSet (type, 1, 0, path + "/" + name);
+ if (! dSet)
+ return;
+ dSet->writeDataBlock (1, type, text.toUTF8());
+}
- switch (event->getEventType())
- {
- case EventChannel::TTL:
- ttlVal = (static_cast(event)->getState() ? 1 : -1) * (static_cast(event)->getLine() + 1);
- dataSrc = &ttlVal;
- type = BaseDataType::I8;
- break;
- case EventChannel::TEXT:
- text = static_cast(event)->getText();
- dataSrc = text.toUTF8().getAddress();
- type = BaseDataType::STR(text.length());
- break;
- default:
- dataSrc = static_cast(event)->getBinaryDataPointer();
- type = getEventH5Type(event->getEventType());
- break;
- }
-
- if (eventID == eventDataSets.size()) //MessageCenter event
- {
- CHECK_ERROR(messagesDataSet->baseDataSet->writeDataBlock(1, BaseDataType::STR(text.length()), text.toUTF8()));
-
- const int64 sampleNumber = event->getSampleNumber();
-
- CHECK_ERROR(messagesDataSet->sampleNumberDataSet->writeDataBlock(1, BaseDataType::I64, &sampleNumber));
-
- const double timeSec = event->getTimestampInSeconds();
-
- CHECK_ERROR(messagesDataSet->timestampDataSet->writeDataBlock(1, BaseDataType::F64, &timeSec));
-
- messagesDataSet->numSamples += 1;
-
- }
- else if (eventDataSets[eventID])
- {
- CHECK_ERROR(eventDataSets[eventID]->baseDataSet->writeDataBlock(1, type, dataSrc));
-
- const double timeSec = event->getTimestampInSeconds();
-
- CHECK_ERROR(eventDataSets[eventID]->timestampDataSet->writeDataBlock(1, BaseDataType::F64, &timeSec));
-
- const int64 sampleNumber = event->getSampleNumber();
-
- CHECK_ERROR(eventDataSets[eventID]->sampleNumberDataSet->writeDataBlock(1, BaseDataType::I64, &sampleNumber));
-
- if (event->getEventType() == EventChannel::TTL)
- {
- const uint64 ttlWord = static_cast(event)->getWord();
- CHECK_ERROR(eventDataSets[eventID]->ttlWordDataSet->writeDataBlock(1, BaseDataType::U64, &ttlWord));
- }
-
- eventDataSets[eventID]->numSamples += 1;
- }
- else
- {
- //Attempted to write an event to disk from unknown event source
- }
-
- }
-
- void NWBFile::writeTimestampSyncText(uint16 sourceID, int64 sampleNumber, float sourceSampleRate, String text)
- {
- CHECK_ERROR(syncMsgDataSet->baseDataSet->writeDataBlock(1, BaseDataType::STR(text.length()), text.toUTF8()));
-
- CHECK_ERROR(syncMsgDataSet->sampleNumberDataSet->writeDataBlock(1, BaseDataType::I64, &sampleNumber));
-
- double timestamp = (double)sampleNumber;
-
- CHECK_ERROR(syncMsgDataSet->timestampDataSet->writeDataBlock(1, BaseDataType::F64, ×tamp));
-
- syncMsgDataSet->numSamples += 1;
- }
-
-
- String NWBFile::getFileName()
- {
- return filename;
- }
-
- bool NWBFile::createTimeSeriesBase(TimeSeries* timeSeries)
- {
- if (createGroup(timeSeries->basePath)) return false;
- CHECK_ERROR(setAttributeStr(" ", timeSeries->basePath, "comments"));
- CHECK_ERROR(setAttributeStr(timeSeries->description, timeSeries->basePath, "description"));
- CHECK_ERROR(setAttributeStr("core", timeSeries->basePath, "namespace"));
- CHECK_ERROR(setAttributeStr(generateUuid(), timeSeries->basePath, "object_id"));
- CHECK_ERROR(setAttributeStr(timeSeries->getNeurodataType(), timeSeries->basePath, "neurodata_type"));
- return true;
- }
-
- void NWBFile::createDataAttributes(String basePath, float conversion, float resolution, String unit)
- {
- CHECK_ERROR(setAttribute(BaseDataType::F32, &conversion, basePath + "/data", "conversion"));
- CHECK_ERROR(setAttribute(BaseDataType::F32, &resolution, basePath + "/data", "resolution"));
- CHECK_ERROR(setAttributeStr(unit, basePath + "/data", "unit"));
- }
-
- HDF5RecordingData* NWBFile::createTimestampDataSet(String path, int chunk_size, float interval)
- {
-
- HDF5RecordingData* tsSet = createDataSet(BaseDataType::F64, 0, chunk_size, path);
-
- if (!tsSet)
- std::cerr << "Error creating timestamp dataset in " << path << std::endl;
- else
- {
- CHECK_ERROR(setAttribute(BaseDataType::F32, &interval, path, "interval"));
- CHECK_ERROR(setAttributeStr("seconds", path, "unit"));
- }
-
- return tsSet;
- }
-
- HDF5RecordingData* NWBFile::createSampleNumberDataSet(String path, int chunk_size)
- {
- HDF5RecordingData* tsSet = createDataSet(BaseDataType::I64, 0, chunk_size, path);
- if (!tsSet)
- std::cerr << "Error creating sample number dataset in " << path << std::endl;
- else
- {
- const int32 one = 1;
- CHECK_ERROR(setAttribute(BaseDataType::I32, &one, path, "interval"));
- CHECK_ERROR(setAttributeStr("samples", path, "unit"));
- }
- return tsSet;
- }
-
-HDF5RecordingData *NWBFile::createChannelConversionDataSet(String path, String description, int chunk_size)
-{
- HDF5RecordingData *elSet = createDataSet(BaseDataType::F32, 1, chunk_size, path);
-
- if (!elSet)
- std::cerr << "Error creating electrode dataset in " << path << std::endl;
- else
- {
- CHECK_ERROR(setAttributeStr(description, path, "description"));
- CHECK_ERROR(setAttributeStr("hdmf-common", path, "namespace"));
- CHECK_ERROR(setAttributeStr(generateUuid(), path, "object_id"));
- }
- return elSet;
-}
-
-HDF5RecordingData *NWBFile::createElectrodeDataSet(String path, String description, int chunk_size)
-{
- HDF5RecordingData *elSet = createDataSet(BaseDataType::I32, 1, chunk_size, path);
- if (!elSet)
- std::cerr << "Error creating electrode dataset in " << path << std::endl;
- else
- {
- 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;
-}
-
- bool NWBFile::createExtraInfo(String basePath, String name, String desc, String id, uint16 index, uint16 typeIndex)
- {
- if (createGroup(basePath)) return false;
- CHECK_ERROR(setAttributeStr("openephys:/", basePath, "schema_id"));
- CHECK_ERROR(setAttributeStr(name, basePath, "name"));
- CHECK_ERROR(setAttributeStr(desc, basePath, "description"));
- CHECK_ERROR(setAttributeStr(id, basePath, "identifier"));
- CHECK_ERROR(setAttribute(BaseDataType::U16, &index, basePath, "source_index"));
- CHECK_ERROR(setAttribute(BaseDataType::U16, &typeIndex, basePath, "source_type_index"));
- return true;
- }
-
- bool NWBFile::createChannelMetadataSets(String basePath, const MetadataObject* info)
- {
- if (!info) return false;
- if (createGroup(basePath)) return false;
- CHECK_ERROR(setAttributeStr("openephys:/", basePath, "schema_id"));
- int nMetadata = info->getMetadataCount();
-
- for (int i
- = 0; i < nMetadata; i++)
- {
- const MetadataDescriptor* desc = info->getMetadataDescriptor(i);
- String fieldName = "Field_" + String(i+1);
- String name = desc->getName();
- String description = desc->getDescription();
- String identifier = desc->getIdentifier();
- BaseDataType type = getMetadataH5Type(desc->getType(), desc->getLength()); //only string types use length, for others is always set to 1. If array types are implemented, change this
- int length = desc->getType() == MetadataDescriptor::CHAR ? 1 : desc->getLength(); //strings are a single element of length set in the type (see above) while other elements are saved a
- HeapBlock data(desc->getDataSize());
- info->getMetadataValue(i)->getValue(static_cast(data.getData()));
- createBinaryDataSet(basePath, fieldName, type, length, data.getData());
- String fullPath = basePath + "/" + fieldName;
- CHECK_ERROR(setAttributeStr("openephys:/", fullPath, "schema_id"));
- CHECK_ERROR(setAttributeStr(name, fullPath, "name"));
- CHECK_ERROR(setAttributeStr(description, fullPath, "description"));
- CHECK_ERROR(setAttributeStr(identifier, fullPath, "identifier"));
- }
- return true;
- }
-
-
- bool NWBFile::createEventMetadataSets(String basePath, TimeSeries* timeSeries, const MetadataEventObject* info)
- {
- if (!info) return false;
- if (createGroup(basePath)) return false;
- CHECK_ERROR(setAttributeStr("openephys:/", basePath, "schema_id"));
- int nMetadata = info->getEventMetadataCount();
-
- timeSeries->metaDataSet.clear(); //just in case
- for (int i = 0; i < nMetadata; i++)
- {
- const MetadataDescriptor* desc = info->getEventMetadataDescriptor(i);
- String fieldName = "Field_" + String(i+1);
- String name = desc->getName();
- String description = desc->getDescription();
- String identifier = desc->getIdentifier();
- BaseDataType type = getMetadataH5Type(desc->getType(), desc->getLength()); //only string types use length, for others is always set to 1. If array types are implemented, change this
- int length = desc->getType() == MetadataDescriptor::CHAR ? 1 : desc->getLength(); //strings are a single element of length set in the type (see above) while other elements are saved as arrays
- String fullPath = basePath + "/" + fieldName;
- HDF5RecordingData* dSet = createDataSet(type, 0, length, EVENT_CHUNK_SIZE, fullPath);
- if (!dSet) return false;
- timeSeries->metaDataSet.add(dSet);
-
- CHECK_ERROR(setAttributeStr("openephys:/", fullPath, "schema_id"));
- CHECK_ERROR(setAttributeStr(name, fullPath, "name"));
- CHECK_ERROR(setAttributeStr(description, fullPath, "description"));
- CHECK_ERROR(setAttributeStr(identifier, fullPath, "identifier"));
- }
- return true;
- }
-
- void NWBFile::writeEventMetadata(TimeSeries* timeSeries, const MetadataEventObject* info, const MetadataEvent* event)
- {
- jassert(timeSeries->metaDataSet.size() == event->getMetadataValueCount());
- jassert(info->getEventMetadataCount() == event->getMetadataValueCount());
- int nMetadata = event->getMetadataValueCount();
- for (int i = 0; i < nMetadata; i++)
- {
- BaseDataType type = getMetadataH5Type(info->getEventMetadataDescriptor(i)->getType(), info->getEventMetadataDescriptor(i)->getLength());
- timeSeries->metaDataSet[i]->writeDataBlock(1, type, event->getMetadataValue(i)->getRawValuePointer());
- }
-
- }
-
- void NWBFile::createTextDataSet(String path, String name, String text)
- {
- ScopedPointer dSet;
-
- if (text.isEmpty()) text = " "; //to avoid 0-length strings, which cause errors
- BaseDataType type = BaseDataType::STR(text.length());
-
- dSet = createDataSet(type, 1, 0, path + "/" + name);
- if (!dSet) return;
- dSet->writeDataBlock(1, type, text.toUTF8());
- }
-
- void NWBFile::createBinaryDataSet(String path, String name, BaseDataType type, int length, void* data)
- {
- ScopedPointer dSet;
- if ((length < 1) || !data) return;
-
- dSet = createDataSet(type, 1, length, 1, path + "/" + name);
- if (!dSet) return;
- dSet->writeDataBlock(1, type, data);
- }
+void NWBFile::createBinaryDataSet (String path, String name, BaseDataType type, int length, void* data)
+{
+ ScopedPointer dSet;
+ if ((length < 1) || ! data)
+ return;
+
+ dSet = createDataSet (type, 1, length, 1, path + "/" + name);
+ if (! dSet)
+ return;
+ dSet->writeDataBlock (1, type, data);
+}
String NWBFile::generateUuid()
{
@@ -882,65 +895,65 @@ String NWBFile::generateUuid()
return id.toDashedString();
}
- //These two methods whould be easy to adapt to support array types for all base types, for now
- //length is only used for string types.
- NWBFile::BaseDataType NWBFile::getEventH5Type(EventChannel::Type type, int length)
- {
- switch (type)
- {
- case EventChannel::INT8_ARRAY:
- return BaseDataType::I8;
- case EventChannel::UINT8_ARRAY:
- return BaseDataType::U8;
- case EventChannel::INT16_ARRAY:
- return BaseDataType::I16;
- case EventChannel::UINT16_ARRAY:
- return BaseDataType::U16;
- case EventChannel::INT32_ARRAY:
- return BaseDataType::I32;
- case EventChannel::UINT32_ARRAY:
- return BaseDataType::U32;
- case EventChannel::INT64_ARRAY:
- return BaseDataType::I64;
- case EventChannel::UINT64_ARRAY:
- return BaseDataType::U64;
- case EventChannel::FLOAT_ARRAY:
- return BaseDataType::F32;
- case EventChannel::DOUBLE_ARRAY:
- return BaseDataType::F64;
- case EventChannel::TEXT:
- return BaseDataType::STR(length);
- default:
- return BaseDataType::I8;
- }
- }
- NWBFile::BaseDataType NWBFile::getMetadataH5Type(MetadataDescriptor::MetadataType type, int length)
- {
- switch (type)
- {
- case MetadataDescriptor::INT8:
- return BaseDataType::I8;
- case MetadataDescriptor::UINT8:
- return BaseDataType::U8;
- case MetadataDescriptor::INT16:
- return BaseDataType::I16;
- case MetadataDescriptor::UINT16:
- return BaseDataType::U16;
- case MetadataDescriptor::INT32:
- return BaseDataType::I32;
- case MetadataDescriptor::UINT32:
- return BaseDataType::U32;
- case MetadataDescriptor::INT64:
- return BaseDataType::I64;
- case MetadataDescriptor::UINT64:
- return BaseDataType::U64;
- case MetadataDescriptor::FLOAT:
- return BaseDataType::F32;
- case MetadataDescriptor::DOUBLE:
- return BaseDataType::F64;
- case MetadataDescriptor::CHAR:
- return BaseDataType::STR(length);
- default:
- return BaseDataType::I8;
- }
- }
+//These two methods whould be easy to adapt to support array types for all base types, for now
+//length is only used for string types.
+NWBFile::BaseDataType NWBFile::getEventH5Type (EventChannel::Type type, int length)
+{
+ switch (type)
+ {
+ case EventChannel::INT8_ARRAY:
+ return BaseDataType::I8;
+ case EventChannel::UINT8_ARRAY:
+ return BaseDataType::U8;
+ case EventChannel::INT16_ARRAY:
+ return BaseDataType::I16;
+ case EventChannel::UINT16_ARRAY:
+ return BaseDataType::U16;
+ case EventChannel::INT32_ARRAY:
+ return BaseDataType::I32;
+ case EventChannel::UINT32_ARRAY:
+ return BaseDataType::U32;
+ case EventChannel::INT64_ARRAY:
+ return BaseDataType::I64;
+ case EventChannel::UINT64_ARRAY:
+ return BaseDataType::U64;
+ case EventChannel::FLOAT_ARRAY:
+ return BaseDataType::F32;
+ case EventChannel::DOUBLE_ARRAY:
+ return BaseDataType::F64;
+ case EventChannel::TEXT:
+ return BaseDataType::STR (length);
+ default:
+ return BaseDataType::I8;
+ }
+}
+NWBFile::BaseDataType NWBFile::getMetadataH5Type (MetadataDescriptor::MetadataType type, int length)
+{
+ switch (type)
+ {
+ case MetadataDescriptor::INT8:
+ return BaseDataType::I8;
+ case MetadataDescriptor::UINT8:
+ return BaseDataType::U8;
+ case MetadataDescriptor::INT16:
+ return BaseDataType::I16;
+ case MetadataDescriptor::UINT16:
+ return BaseDataType::U16;
+ case MetadataDescriptor::INT32:
+ return BaseDataType::I32;
+ case MetadataDescriptor::UINT32:
+ return BaseDataType::U32;
+ case MetadataDescriptor::INT64:
+ return BaseDataType::I64;
+ case MetadataDescriptor::UINT64:
+ return BaseDataType::U64;
+ case MetadataDescriptor::FLOAT:
+ return BaseDataType::F32;
+ case MetadataDescriptor::DOUBLE:
+ return BaseDataType::F64;
+ case MetadataDescriptor::CHAR:
+ return BaseDataType::STR (length);
+ default:
+ return BaseDataType::I8;
+ }
+}
diff --git a/Source/RecordEngine/NWBFormat.h b/Source/RecordEngine/NWBFormat.h
index e85f6d8..4d7f53c 100644
--- a/Source/RecordEngine/NWBFormat.h
+++ b/Source/RecordEngine/NWBFormat.h
@@ -1,25 +1,25 @@
/*
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This file is part of the Open Ephys GUI
- Copyright (C) 2014 Open Ephys
+ This file is part of the Open Ephys GUI
+ Copyright (C) 2024 Open Ephys
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
- */
+*/
#ifndef NWBFORMAT_H
#define NWBFORMAT_H
@@ -33,45 +33,44 @@ using namespace OpenEphysHDF5;
namespace NWBRecording
{
- typedef Array ContinuousGroup;
+typedef Array ContinuousGroup;
- /**
+/**
Represents a generic NWB TimeSeries dataset
*/
- class TimeSeries
- {
- public:
-
- /** Constructor */
- TimeSeries(String rootPath, String name, String description);
-
- /** Holds the sample data */
- ScopedPointer baseDataSet;
-
- /** Holds the timestamps (in seconds) for each sample */
- ScopedPointer timestampDataSet;
-
- /** Holds the sample number for each sample (relative to the start of acquisition) */
- ScopedPointer sampleNumberDataSet;
-
- /** Holds metadata for this time series */
- OwnedArray metaDataSet;
-
- /** The path to this dataset within the NWB file */
- String basePath;
-
- /** The description of this dataset*/
- String description;
-
- /** Total number of samples written */
- uint64 numSamples = 0;
-
- /** Get neurodata_type */
- virtual String getNeurodataType() { return "TimeSeries";}
-
- };
+class TimeSeries
+{
+public:
+ /** Constructor */
+ TimeSeries (String rootPath, String name, String description);
+
+ /** Holds the sample data */
+ ScopedPointer baseDataSet;
- namespace ecephys {
+ /** Holds the timestamps (in seconds) for each sample */
+ ScopedPointer timestampDataSet;
+
+ /** Holds the sample number for each sample (relative to the start of acquisition) */
+ ScopedPointer sampleNumberDataSet;
+
+ /** Holds metadata for this time series */
+ OwnedArray metaDataSet;
+
+ /** The path to this dataset within the NWB file */
+ String basePath;
+
+ /** The description of this dataset*/
+ String description;
+
+ /** Total number of samples written */
+ uint64 numSamples = 0;
+
+ /** Get neurodata_type */
+ virtual String getNeurodataType() { return "TimeSeries"; }
+};
+
+namespace ecephys
+{
/**
Represents an NWB ElectricalSeries dataset
*/
@@ -79,23 +78,22 @@ namespace NWBRecording
{
public:
/** Constructor */
- ElectricalSeries(String rootPath, String name, String description,
- int channel_count, Array channel_conversion);
-
+ ElectricalSeries (String rootPath, String name, String description, int channel_count, Array channel_conversion);
+
/** Holds the sample number for each sample (relative to the start of acquisition) */
ScopedPointer channelConversionDataSet;
-
+
/** Holds the DynamicTableRegion index of each electrode */
ScopedPointer electrodeDataSet;
-
+
/** Channel conversion values */
Array channel_conversion;
-
+
/** Number of channels to write */
int channel_count;
-
+
/** Get neurodata_type */
- virtual String getNeurodataType() override { return "ElectricalSeries";}
+ virtual String getNeurodataType() override { return "ElectricalSeries"; }
};
/**
@@ -103,172 +101,174 @@ namespace NWBRecording
*/
class SpikeEventSeries : public ElectricalSeries
{
-
public:
/** Constructor */
- SpikeEventSeries(String rootPath, String name, String description,
- int channel_count, Array channel_conversion);
-
+ SpikeEventSeries (String rootPath, String name, String description, int channel_count, Array channel_conversion);
+
/** Get neurodata_type */
- virtual String getNeurodataType() override { return "SpikeEventSeries";}
+ virtual String getNeurodataType() override { return "SpikeEventSeries"; }
};
- }
+} // namespace ecephys
- /**
+/**
Represents a TTL event series (not a core NWB data type)
*/
- class TTLEventSeries : public TimeSeries
- {
- public:
- /** Constructor */
- TTLEventSeries(String rootPath, String name, String description);
-
- /** Holds the TTL word for each sample */
- ScopedPointer ttlWordDataSet;
-
- /** Get neurodata_type */
- virtual String getNeurodataType() override { return "TimeSeries";}
- };
+class TTLEventSeries : public TimeSeries
+{
+public:
+ /** Constructor */
+ TTLEventSeries (String rootPath, String name, String description);
- /**
+ /** Holds the TTL word for each sample */
+ ScopedPointer ttlWordDataSet;
+
+ /** Get neurodata_type */
+ virtual String getNeurodataType() override { return "TimeSeries"; }
+};
+
+/**
Represents a sequence of string annotations
*/
- class AnnotationSeries : public TimeSeries
- {
- public:
- /** Constructor */
- AnnotationSeries(String rootPath, String name, String description);
-
- /** Get neurodata_type */
- virtual String getNeurodataType() override { return "AnnotationSeries";}
- };
+class AnnotationSeries : public TimeSeries
+{
+public:
+ /** Constructor */
+ AnnotationSeries (String rootPath, String name, String description);
- /**
+ /** Get neurodata_type */
+ virtual String getNeurodataType() override { return "AnnotationSeries"; }
+};
+
+/**
Represents an NWB 2.0 File (a specific type of HDF5 file)
*/
- class NWBFile : public HDF5FileBase
- {
- public:
-
- /** Constructor */
- NWBFile(String fName, String ver, String identifier);
-
- /** Destructor */
- ~NWBFile();
-
- /** Creates the groups required for a new recording, given an array of continuous channels, event channels, and spike channels*/
- bool startNewRecording(int recordingNumber,
- const Array& continuousArray,
- const Array& continuousChannels,
- const Array& eventArray,
- const Array& electrodeArray);
-
- /** Writes the num_samples value and closes the relevent datasets */
- void stopRecording();
-
- /** Writes continuous data for a particular channel */
- void writeData(int datasetID, int channel, int nSamples, const float* data, float bitVolts);
-
- /** Writes synchronized timestamps for a particular continuous dataset */
- void writeTimestamps(int datasetID, int nSamples, const double* data);
-
- /** Writes sample numbers for a particular continuous dataset */
- void writeSampleNumbers(int datasetID, int nSamples, const int64* data);
-
- /** Writes electrode numbers for a continuous dataset */
- void writeElectrodes(ecephys::ElectricalSeries* electricalSeries, Array electrodeInds);
-
- /** Writes channel conversion values */
- void writeChannelConversions(ecephys::ElectricalSeries* series);
-
- /** Writes a spike event*/
- void writeSpike(int electrodeId, const SpikeChannel* channel, const Spike* event);
-
- /** Writes an event (TEXT or TTL) */
- void writeEvent(int eventID, const EventChannel* channel, const Event* event);
-
- /** Writes a timestamp sync text event */
- void writeTimestampSyncText(uint16 sourceID,
- int64 timestamp,
- float sourceSampleRate,
- String text);
-
- /** Returns the name of this NWB file */
- String getFileName() override;
-
- /** Generate a new uuid string*/
- String generateUuid();
+class NWBFile : public HDF5FileBase
+{
+public:
+ /** Constructor */
+ NWBFile (String fName, String ver, String identifier);
+ /** Destructor */
+ ~NWBFile();
+
+ /** Creates the groups required for a new recording, given an array of continuous channels, event channels, and spike channels*/
+ bool startNewRecording (int recordingNumber,
+ const Array& continuousArray,
+ const Array& continuousChannels,
+ const Array& eventArray,
+ const Array& electrodeArray);
+
+ /** Writes the num_samples value and closes the relevent datasets */
+ void stopRecording();
+
+ /** Writes continuous data for a particular channel */
+ void writeData (int datasetID, int channel, int nSamples, const float* data, float bitVolts);
+
+ /** Writes synchronized timestamps for a particular continuous dataset */
+ void writeTimestamps (int datasetID, int nSamples, const double* data);
+
+ /** Writes sample numbers for a particular continuous dataset */
+ void writeSampleNumbers (int datasetID, int nSamples, const int64* data);
+
+ /** Writes electrode numbers for a continuous dataset */
+ void writeElectrodes (ecephys::ElectricalSeries* electricalSeries, Array electrodeInds);
+
+ /** Writes channel conversion values */
+ void writeChannelConversions (ecephys::ElectricalSeries* series);
+
+ /** Writes a spike event*/
+ void writeSpike (int electrodeId, const SpikeChannel* channel, const Spike* event);
+
+ /** Writes an event (TEXT or TTL) */
+ void writeEvent (int eventID, const EventChannel* channel, const Event* event);
+
+ /** Writes a timestamp sync text event */
+ void writeTimestampSyncText (uint16 sourceID,
+ int64 timestamp,
+ float sourceSampleRate,
+ String text);
+
+ /** Returns the name of this NWB file */
+ String getFileName() override;
+
+ /** Generate a new uuid string*/
+ String generateUuid();
+
+ protected:
protected:
- /** Initializes the default groups */
- int createFileStructure() override;
+protected:
+
+ /** Initializes the default groups */
+ int createFileStructure() override;
private:
+ private:
- /** Creates a new dataset to hold text data (messages) */
- void createTextDataSet(String path, String name, String text);
-
- /** Creates a new dataset to hold binary events */
- void createBinaryDataSet(String path, String name, HDF5FileBase::BaseDataType type, int length, void* data);
-
- /** Returns the HDF5 data type for a given event channel type */
- static HDF5FileBase::BaseDataType getEventH5Type(EventChannel::Type type, int length = 1);
-
- /** Returns the HDF5 data type for a given metadata type*/
- static HDF5FileBase::BaseDataType getMetadataH5Type(MetadataDescriptor::MetadataType type, int length = 1);
-
- /** Creates a time series dataset*/
- bool createTimeSeriesBase(TimeSeries* timeSeries);
-
- /** Creates dataset attributes */
- bool createExtraInfo(String basePath, String name, String desc, String id, uint16 index, uint16 typeIndex);
-
- /** Creates a dataset of synchronized timestamps (interval = 1/sample_rate) */
- HDF5RecordingData* createTimestampDataSet(String basePath, int chunk_size, float interval);
-
- /** Creates a dataset of sample numbers */
- HDF5RecordingData* createSampleNumberDataSet(String basePath, int chunk_size);
-
- /** Creates a dataset for electrode indices */
- HDF5RecordingData* createElectrodeDataSet(String basePath, String description, int chunk_size);
-
- /** Creates a dataset for electrode indices */
- HDF5RecordingData* createChannelConversionDataSet(String basePath, String description, int chunk_size);
-
- /** Adds attributes (e.g. conversion, resolution) to a continuous dataset */
- void createDataAttributes(String basePath, float conversion, float resolution, String unit);
-
- /** Creates a dataset for channel metdata */
- bool createChannelMetadataSets(String basePath, const MetadataObject* info);
-
- /** Creates a dataset for event metdata */
- bool createEventMetadataSets(String basePath, TimeSeries* timeSeries, const MetadataEventObject* info);
-
- /** Writes metadata associated with an event*/
- void writeEventMetadata(TimeSeries* timeSeries, const MetadataEventObject* info, const MetadataEvent* event);
-
- const String filename;
- const String GUIVersion;
-
- OwnedArray continuousDataSets;
- OwnedArray spikeDataSets;
- OwnedArray eventDataSets;
- std::unique_ptr messagesDataSet;
- std::unique_ptr syncMsgDataSet;
-
- const String identifierText;
-
- HeapBlock scaledBuffer;
- HeapBlock intBuffer;
- size_t bufferSize;
-
- JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(NWBFile);
-
- };
-
-}
+private:
+
+ /** Creates a new dataset to hold text data (messages) */
+ void createTextDataSet (String path, String name, String text);
+
+ /** Creates a new dataset to hold binary events */
+ void createBinaryDataSet (String path, String name, HDF5FileBase::BaseDataType type, int length, void* data);
+
+ /** Returns the HDF5 data type for a given event channel type */
+ static HDF5FileBase::BaseDataType getEventH5Type (EventChannel::Type type, int length = 1);
+
+ /** Returns the HDF5 data type for a given metadata type*/
+ static HDF5FileBase::BaseDataType getMetadataH5Type (MetadataDescriptor::MetadataType type, int length = 1);
+
+ /** Creates a time series dataset*/
+ bool createTimeSeriesBase (TimeSeries* timeSeries);
+
+ /** Creates dataset attributes */
+ bool createExtraInfo (String basePath, String name, String desc, String id, uint16 index, uint16 typeIndex);
+
+ /** Creates a dataset of synchronized timestamps (interval = 1/sample_rate) */
+ HDF5RecordingData* createTimestampDataSet (String basePath, int chunk_size, float interval);
+
+ /** Creates a dataset of sample numbers */
+ HDF5RecordingData* createSampleNumberDataSet (String basePath, int chunk_size);
+
+ /** Creates a dataset for electrode indices */
+ HDF5RecordingData* createElectrodeDataSet (String basePath, String description, int chunk_size);
+
+ /** Creates a dataset for electrode indices */
+ HDF5RecordingData* createChannelConversionDataSet (String basePath, String description, int chunk_size);
+
+ /** Adds attributes (e.g. conversion, resolution) to a continuous dataset */
+ void createDataAttributes (String basePath, float conversion, float resolution, String unit);
+
+ /** Creates a dataset for channel metdata */
+ bool createChannelMetadataSets (String basePath, const MetadataObject* info);
+
+ /** Creates a dataset for event metdata */
+ bool createEventMetadataSets (String basePath, TimeSeries* timeSeries, const MetadataEventObject* info);
+
+ /** Writes metadata associated with an event*/
+ void writeEventMetadata (TimeSeries* timeSeries, const MetadataEventObject* info, const MetadataEvent* event);
+
+ const String filename;
+ const String GUIVersion;
+
+ OwnedArray continuousDataSets;
+ OwnedArray spikeDataSets;
+ OwnedArray eventDataSets;
+ std::unique_ptr messagesDataSet;
+ std::unique_ptr syncMsgDataSet;
+
+ const String identifierText;
+
+ HeapBlock scaledBuffer;
+ HeapBlock intBuffer;
+ size_t bufferSize;
+
+ JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR (NWBFile);
+};
+
+} // namespace NWBRecording
#endif
diff --git a/Source/RecordEngine/NWBRecording.cpp b/Source/RecordEngine/NWBRecording.cpp
index fa603bf..d026cfc 100644
--- a/Source/RecordEngine/NWBRecording.cpp
+++ b/Source/RecordEngine/NWBRecording.cpp
@@ -1,176 +1,163 @@
/*
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This file is part of the Open Ephys GUI
- Copyright (C) 2014 Open Ephys
+ This file is part of the Open Ephys GUI
+ Copyright (C) 2024 Open Ephys
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
- */
-
- #include "NWBRecording.h"
+*/
-#include "../../plugin-GUI/Source/Processors/RecordNode/RecordNode.h"
+#include "NWBRecording.h"
+#include "../../plugin-GUI/Source/Processors/RecordNode/RecordNode.h"
#define MAX_BUFFER_SIZE 40960
-
- using namespace NWBRecording;
-
- NWBRecordEngine::NWBRecordEngine()
- {
- smpBuffer.malloc(MAX_BUFFER_SIZE);
- }
-
-
- NWBRecordEngine::~NWBRecordEngine()
- {
- if (nwb != nullptr)
- {
- spikeChannels.clear();
- eventChannels.clear();
- continuousChannelGroups.clear();
- datasetIndexes.clear();
- writeChannelIndexes.clear();
-
- nwb->close();
- nwb.reset();
- }
- }
+
+using namespace NWBRecording;
+
+NWBRecordEngine::NWBRecordEngine()
+{
+ smpBuffer.malloc (MAX_BUFFER_SIZE);
+}
+
+NWBRecordEngine::~NWBRecordEngine()
+{
+ if (nwb != nullptr)
+ {
+ spikeChannels.clear();
+ eventChannels.clear();
+ continuousChannelGroups.clear();
+ datasetIndexes.clear();
+ writeChannelIndexes.clear();
+
+ nwb->close();
+ nwb.reset();
+ }
+}
RecordEngineManager* NWBRecordEngine::getEngineManager()
{
//static factory that instantiates the engine manager, which allows to configure recording options among other things. See OriginalRecording to see how to create options for a record engine
- RecordEngineManager* man = new RecordEngineManager("NWB2", "NWB2", &(engineFactory));
+ RecordEngineManager* man = new RecordEngineManager ("NWB2", "NWB2", &(engineFactory) );
EngineParameter* param;
- param = new EngineParameter(EngineParameter::STR, 0, "Identifier Text", String());
- man->addParameter(param);
+ param = new EngineParameter (EngineParameter::STR, 0, "Identifier Text", String());
+ man->addParameter (param);
return man;
-
}
-
- void NWBRecordEngine::openFiles(File rootFolder, int experimentNumber, int recordingNumber)
- {
-
- if (recordingNumber == 0) // new file needed
- {
- spikeChannels.clear();
- eventChannels.clear();
- continuousChannels.clear();
- continuousChannelGroups.clear();
- datasetIndexes.clear();
- writeChannelIndexes.clear();
-
- // New file for each experiment, e.g. experiment1.nwb, epxperiment2.nwb, etc.
- String basepath = rootFolder.getFullPathName() +
- rootFolder.getSeparatorString() +
- "experiment" + String(experimentNumber) +
- ".nwb";
-
- if (nwb != nullptr)
- {
- nwb->close();
- nwb.reset();
- }
-
- // create a unique identifier for the file if it doesn't exist
- Uuid identifier;
- identifierText = identifier.toString();
+void NWBRecordEngine::openFiles (File rootFolder, int experimentNumber, int recordingNumber)
+{
+ if (recordingNumber == 0) // new file needed
+ {
+ spikeChannels.clear();
+ eventChannels.clear();
+ continuousChannels.clear();
+ continuousChannelGroups.clear();
+ datasetIndexes.clear();
+ writeChannelIndexes.clear();
- nwb = std::make_unique(basepath, CoreServices::getGUIVersion(), identifierText);
+ // New file for each experiment, e.g. experiment1.nwb, epxperiment2.nwb, etc.
+ String basepath = rootFolder.getFullPathName() + rootFolder.getSeparatorString() + "experiment" + String (experimentNumber) + ".nwb";
- // get pointers to all continuous channels for electrode table
- for (int i = 0; i < recordNode->getNumOutputs(); i++)
- {
- const ContinuousChannel* channelInfo = getContinuousChannel(i); // channel info object
+ if (nwb != nullptr)
+ {
+ nwb->close();
+ nwb.reset();
+ }
- continuousChannels.add(channelInfo);
- }
+ // create a unique identifier for the file if it doesn't exist
+ Uuid identifier;
+ identifierText = identifier.toString();
- datasetIndexes.insertMultiple(0, 0, getNumRecordedContinuousChannels());
- writeChannelIndexes.insertMultiple(0, 0, getNumRecordedContinuousChannels());
- continuousChannelGroups.clear();
+ nwb = std::make_unique (basepath, CoreServices::getGUIVersion(), identifierText);
- int streamIndex = -1;
- uint16 lastStreamId = 0;
- int indexWithinStream = 0;
+ // get pointers to all continuous channels for electrode table
+ for (int i = 0; i < recordNode->getNumOutputs(); i++)
+ {
+ const ContinuousChannel* channelInfo = getContinuousChannel (i); // channel info object
- for (int ch = 0; ch < getNumRecordedContinuousChannels(); ch++)
- {
+ continuousChannels.add (channelInfo);
+ }
- int globalIndex = getGlobalIndex(ch); // the global channel index (across all channels entering the Record Node)
- int localIndex = getLocalIndex(ch); // the local channel index (within a stream)
+ datasetIndexes.insertMultiple (0, 0, getNumRecordedContinuousChannels());
+ writeChannelIndexes.insertMultiple (0, 0, getNumRecordedContinuousChannels());
+ continuousChannelGroups.clear();
- const ContinuousChannel* channelInfo = getContinuousChannel(globalIndex); // channel info object
+ int streamIndex = -1;
+ uint16 lastStreamId = 0;
+ int indexWithinStream = 0;
- int sourceId = channelInfo->getSourceNodeId();
- int streamId = channelInfo->getStreamId();
+ for (int ch = 0; ch < getNumRecordedContinuousChannels(); ch++)
+ {
+ int globalIndex = getGlobalIndex (ch); // the global channel index (across all channels entering the Record Node)
+ int localIndex = getLocalIndex (ch); // the local channel index (within a stream)
- if (streamId != lastStreamId)
- {
- streamIndex++;
- indexWithinStream = 0;
+ const ContinuousChannel* channelInfo = getContinuousChannel (globalIndex); // channel info object
- ContinuousGroup newGroup;
- continuousChannelGroups.add(newGroup);
+ int sourceId = channelInfo->getSourceNodeId();
+ int streamId = channelInfo->getStreamId();
- }
+ if (streamId != lastStreamId)
+ {
+ streamIndex++;
+ indexWithinStream = 0;
- continuousChannelGroups.getReference(streamIndex).add(channelInfo);
+ ContinuousGroup newGroup;
+ continuousChannelGroups.add (newGroup);
+ }
- datasetIndexes.set(ch, streamIndex);
- writeChannelIndexes.set(ch, indexWithinStream++);
+ continuousChannelGroups.getReference (streamIndex).add (channelInfo);
- lastStreamId = streamId;
- }
+ datasetIndexes.set (ch, streamIndex);
+ writeChannelIndexes.set (ch, indexWithinStream++);
- for (int i = 0; i < getNumRecordedEventChannels(); i++)
- eventChannels.add(getEventChannel(i));
+ lastStreamId = streamId;
+ }
- for (int i = 0; i < getNumRecordedSpikeChannels(); i++)
- spikeChannels.add(getSpikeChannel(i));
+ for (int i = 0; i < getNumRecordedEventChannels(); i++)
+ eventChannels.add (getEventChannel (i));
- //open the file
- nwb->open(getNumRecordedContinuousChannels() + continuousChannelGroups.size() + eventChannels.size() + spikeChannels.size()); //total channels + timestamp arrays, to create a big enough buffer
+ for (int i = 0; i < getNumRecordedSpikeChannels(); i++)
+ spikeChannels.add (getSpikeChannel (i));
- //create the recording
- nwb->startNewRecording(recordingNumber, continuousChannelGroups, continuousChannels, eventChannels, spikeChannels);
- }
- }
+ //open the file
+ nwb->open (getNumRecordedContinuousChannels() + continuousChannelGroups.size() + eventChannels.size() + spikeChannels.size()); //total channels + timestamp arrays, to create a big enough buffer
-
- void NWBRecordEngine::closeFiles()
- {
- nwb->stopRecording();
- }
+ //create the recording
+ nwb->startNewRecording (recordingNumber, continuousChannelGroups, continuousChannels, eventChannels, spikeChannels);
+ }
+}
-
+void NWBRecordEngine::closeFiles()
+{
+ nwb->stopRecording();
+}
-void NWBRecordEngine::writeContinuousData(int writeChannel,
- int realChannel,
- const float* dataBuffer,
- const double* timestampBuffer,
- int size)
+void NWBRecordEngine::writeContinuousData (int writeChannel,
+ int realChannel,
+ const float* dataBuffer,
+ const double* timestampBuffer,
+ int size)
{
- nwb->writeData(datasetIndexes[writeChannel],
- writeChannelIndexes[writeChannel],
- size,
- dataBuffer,
- getContinuousChannel(realChannel)->getBitVolts());
+ nwb->writeData (datasetIndexes[writeChannel],
+ writeChannelIndexes[writeChannel],
+ size,
+ dataBuffer,
+ getContinuousChannel (realChannel)->getBitVolts());
/* All channels in a dataset have the same number of samples and share timestamps.
But since this method is called asynchronously, the timestamps might not be
@@ -178,42 +165,39 @@ void NWBRecordEngine::writeContinuousData(int writeChannel,
when writing that channel's data */
if (writeChannelIndexes[writeChannel] == 0)
{
- int64 baseTS = getLatestSampleNumber(writeChannel);
-
+ int64 baseTS = getLatestSampleNumber (writeChannel);
+
for (int i = 0; i < size; i++)
{
smpBuffer[i] = baseTS + i;
}
-
- nwb->writeTimestamps(datasetIndexes[writeChannel], size, timestampBuffer);
- nwb->writeSampleNumbers(datasetIndexes[writeChannel], size, smpBuffer);
+
+ nwb->writeTimestamps (datasetIndexes[writeChannel], size, timestampBuffer);
+ nwb->writeSampleNumbers (datasetIndexes[writeChannel], size, smpBuffer);
}
}
-
-void NWBRecordEngine::writeEvent(int eventIndex, const MidiMessage& event)
+
+void NWBRecordEngine::writeEvent (int eventIndex, const MidiMessage& event)
{
- const EventChannel* channel = getEventChannel(eventIndex);
- EventPtr eventStruct = Event::deserialize(event, channel);
+ const EventChannel* channel = getEventChannel (eventIndex);
+ EventPtr eventStruct = Event::deserialize (event, channel);
- nwb->writeEvent(eventIndex, channel, eventStruct);
+ nwb->writeEvent (eventIndex, channel, eventStruct);
}
-void NWBRecordEngine::writeTimestampSyncText(uint64 streamId, int64 timestamp, float sourceSampleRate, String text)
+void NWBRecordEngine::writeTimestampSyncText (uint64 streamId, int64 timestamp, float sourceSampleRate, String text)
{
- nwb->writeTimestampSyncText(streamId, timestamp, sourceSampleRate, text);
+ nwb->writeTimestampSyncText (streamId, timestamp, sourceSampleRate, text);
}
-
-void NWBRecordEngine::writeSpike(int electrodeIndex, const Spike* spike)
+void NWBRecordEngine::writeSpike (int electrodeIndex, const Spike* spike)
{
- const SpikeChannel* channel = getSpikeChannel(electrodeIndex);
+ const SpikeChannel* channel = getSpikeChannel (electrodeIndex);
- nwb->writeSpike(electrodeIndex, channel, spike);
+ nwb->writeSpike (electrodeIndex, channel, spike);
}
-
-
-void NWBRecordEngine::setParameter(EngineParameter& parameter)
+void NWBRecordEngine::setParameter (EngineParameter& parameter)
{
- strParameter(0, identifierText);
+ strParameter (0, identifierText);
}
diff --git a/Source/RecordEngine/NWBRecording.h b/Source/RecordEngine/NWBRecording.h
index a2aba61..8a7a14a 100644
--- a/Source/RecordEngine/NWBRecording.h
+++ b/Source/RecordEngine/NWBRecording.h
@@ -1,25 +1,25 @@
/*
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This file is part of the Open Ephys GUI
- Copyright (C) 2014 Open Ephys
+ This file is part of the Open Ephys GUI
+ Copyright (C) 2024 Open Ephys
- ------------------------------------------------------------------
+ ------------------------------------------------------------------
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
- You should have received a copy of the GNU General Public License
- along with this program. If not, see .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
- */
+*/
#ifndef NWBRECORDING_H
#define NWBRECORDING_H
@@ -31,81 +31,81 @@
namespace NWBRecording
{
- /**
+/**
Record Engine that writes data into NWB 2.0 format
*/
- class NWBRecordEngine : public RecordEngine
- {
- public:
- /** Constructor */
- NWBRecordEngine();
+class NWBRecordEngine : public RecordEngine
+{
+public:
+ /** Constructor */
+ NWBRecordEngine();
- /** Destructor */
- ~NWBRecordEngine();
+ /** Destructor */
+ ~NWBRecordEngine();
- /** Launches the manager for this engine */
- static RecordEngineManager* getEngineManager();
+ /** Launches the manager for this engine */
+ static RecordEngineManager* getEngineManager();
- /** Returns a (hopefully unique) string identifier for this engine */
- String getEngineId() const override { return "NWB2"; }
+ /** Returns a (hopefully unique) string identifier for this engine */
+ String getEngineId() const override { return "NWB2"; }
- /** Called when recording starts to open all needed files */
- void openFiles(File rootFolder, int experimentNumber, int recordingNumber) override;
+ /** Called when recording starts to open all needed files */
+ void openFiles (File rootFolder, int experimentNumber, int recordingNumber) override;
- /** Called when recording stops to close all files and do all the necessary cleanup */
- void closeFiles() override;
+ /** Called when recording stops to close all files and do all the necessary cleanup */
+ void closeFiles() override;
- /** Write continuous data for a channel, including synchronized float timestamps for each sample */
- void writeContinuousData(int writeChannel,
- int realChannel,
- const float *dataBuffer,
- const double *timestampBuffer,
- int size) override;
+ /** Write continuous data for a channel, including synchronized float timestamps for each sample */
+ void writeContinuousData (int writeChannel,
+ int realChannel,
+ const float* dataBuffer,
+ const double* timestampBuffer,
+ int size) override;
- /** Write a single event to disk (TTL or TEXT) */
- void writeEvent(int eventIndex, const MidiMessage &event) override;
+ /** Write a single event to disk (TTL or TEXT) */
+ void writeEvent (int eventIndex, const MidiMessage& event) override;
- /** Write a spike to disk */
- void writeSpike(int electrodeIndex, const Spike *spike) override;
+ /** Write a spike to disk */
+ void writeSpike (int electrodeIndex, const Spike* spike) override;
- /** Write the timestamp sync text messages to disk*/
- void writeTimestampSyncText(uint64 streamId, int64 timestamp, float sourceSampleRate, String text) override;
+ /** Write the timestamp sync text messages to disk*/
+ void writeTimestampSyncText (uint64 streamId, int64 timestamp, float sourceSampleRate, String text) override;
- /** Allows the file identifier to be set externally*/
- void setParameter(EngineParameter ¶meter) override;
+ /** Allows the file identifier to be set externally*/
+ void setParameter (EngineParameter& parameter) override;
- private:
- /** Pointer to the current NWB file */
- std::unique_ptr nwb;
+private:
+ /** Pointer to the current NWB file */
+ std::unique_ptr nwb;
- /** For each incoming recorded channel, which dataset (stream) is it associated with? */
- Array datasetIndexes;
+ /** For each incoming recorded channel, which dataset (stream) is it associated with? */
+ Array datasetIndexes;
- /** For each incoming recorded channel, what is the local index within a stream? */
- Array writeChannelIndexes;
+ /** For each incoming recorded channel, what is the local index within a stream? */
+ Array writeChannelIndexes;
- /** Holds pointers to all recorded channels within a stream */
- Array continuousChannelGroups;
+ /** Holds pointers to all recorded channels within a stream */
+ Array continuousChannelGroups;
- /** Holds pointers to all recorded event channels*/
- Array eventChannels;
+ /** Holds pointers to all recorded event channels*/
+ Array eventChannels;
- /** Holds pointers to all recorded spike channels*/
- Array spikeChannels;
+ /** Holds pointers to all recorded spike channels*/
+ Array spikeChannels;
- /** Holds pointers to all incoming continuous channels (used for electrode table)*/
- Array continuousChannels;
+ /** Holds pointers to all incoming continuous channels (used for electrode table)*/
+ Array continuousChannels;
- /** Holds integer sample numbers for writing */
- HeapBlock smpBuffer;
+ /** Holds integer sample numbers for writing */
+ HeapBlock smpBuffer;
- /** The identifier for the current file (can be set externally) */
- String identifierText;
+ /** The identifier for the current file (can be set externally) */
+ String identifierText;
- JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(NWBRecordEngine);
- };
-}
+ JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR (NWBRecordEngine);
+};
+} // namespace NWBRecording
#endif