From bbd13628c4ba269fdcbdd4c01476dac2e6d28549 Mon Sep 17 00:00:00 2001
From: Aaron Cuevas Lopez <aacuelo@teleco.upv.es>
Date: Wed, 24 Aug 2016 18:36:18 +0200
Subject: [PATCH] Add default datasets
---
Source/Plugins/NWBFormat/NWBFormat.cpp | 25 +++++++++++++++++++----
Source/Plugins/NWBFormat/NWBFormat.h | 5 +++--
Source/Plugins/NWBFormat/NWBRecording.cpp | 10 ++++++++-
Source/Plugins/NWBFormat/NWBRecording.h | 3 +++
4 files changed, 36 insertions(+), 7 deletions(-)
diff --git a/Source/Plugins/NWBFormat/NWBFormat.cpp b/Source/Plugins/NWBFormat/NWBFormat.cpp
index d650c930d..8b1047fa4 100644
--- a/Source/Plugins/NWBFormat/NWBFormat.cpp
+++ b/Source/Plugins/NWBFormat/NWBFormat.cpp
@@ -36,7 +36,7 @@
#define SPIKE_CHUNK_YSIZE 40
#endif
- NWBFile::NWBFile(String fName, String ver) : HDF5FileBase(), filename(fName), GUIVersion(ver), spikeMaxSize(0)
+ NWBFile::NWBFile(String fName, String ver, String idText) : HDF5FileBase(), filename(fName), identifierText(idText), GUIVersion(ver), spikeMaxSize(0)
{
//Init stuff
readyToOpen=true; //In KWIK this is in initFile, but the new recordEngine methods make it safe for it to be here
@@ -76,6 +76,13 @@ int NWBFile::createFileStructure()
CHECK_ERROR(setAttributeStr(*xmlText, "/general/data_collection", "configuration"));
//TODO: Add default datasets
+ //Modify this one once we have JUCE4 to allow UTC time
+ String time = Time::getCurrentTime().formatted("%Y-%m-%dT%H:%M:%S");
+ createTextDataSet("", "file_create_date", time);
+ createTextDataSet("", "identifier", identifierText);
+ createTextDataSet("", "nwb_version", "NWB-1.0.4_beta");
+ createTextDataSet("", "session_description", " ");
+ createTextDataSet("", "session_start_time", time);
return 0;
}
@@ -298,8 +305,8 @@ int NWBFile::createFileStructure()
{
return filename;
}
-
- HDF5RecordingData* NWBFile::createRecordingStructures(String basePath, NWBRecordingInfo& info, String helpText, int chunk_size, String ancestry)
+
+ HDF5RecordingData* NWBFile::createRecordingStructures(String basePath, NWBRecordingInfo& info, String helpText, int chunk_size, String ancestry)
{
StringArray ancestryStrings;
ancestryStrings.add("TimeSeries");
@@ -322,4 +329,14 @@ int NWBFile::createFileStructure()
return tsSet;
}
-
\ No newline at end of file
+
+ void NWBFile::createTextDataSet(String path, String name, String text)
+ {
+ ScopedPointer<HDF5RecordingData> dSet;
+
+ if (text.isEmpty()) text = " "; //to avoid 0-length strings, which cause errors
+
+ dSet = createDataSet(STR, 1, 0, path + "/" + name);
+ if (!dSet) return;
+ dSet->writeDataBlock(1, STR, text.toUTF8());
+ }
\ No newline at end of file
diff --git a/Source/Plugins/NWBFormat/NWBFormat.h b/Source/Plugins/NWBFormat/NWBFormat.h
index e082babcb..fd3f488ec 100644
--- a/Source/Plugins/NWBFormat/NWBFormat.h
+++ b/Source/Plugins/NWBFormat/NWBFormat.h
@@ -44,7 +44,7 @@ namespace NWBRecording
class NWBFile : public HDF5FileBase
{
public:
- NWBFile(String fName, String ver); //with whatever arguments it's necessary
+ NWBFile(String fName, String ver, String idText); //with whatever arguments it's necessary
~NWBFile();
bool startNewRecording(int recordingNumber, const Array<NWBRecordingInfo>& continuousArray, const Array<NWBRecordingInfo>& electrodeArray);
void stopRecording();
@@ -61,6 +61,7 @@ namespace NWBRecording
private:
HDF5RecordingData* createRecordingStructures(String basePath, NWBRecordingInfo& info, String helpText, int chunk_size, String ancestry);
+ void createTextDataSet(String path, String name, String text);
const String filename;
const String GUIVersion;
@@ -90,8 +91,8 @@ namespace NWBRecording
int spikeMaxSize;
const String* xmlText;
+ const String identifierText;
- //whatever is needed
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(NWBFile);
};
diff --git a/Source/Plugins/NWBFormat/NWBRecording.cpp b/Source/Plugins/NWBFormat/NWBRecording.cpp
index 64497e99a..856189570 100644
--- a/Source/Plugins/NWBFormat/NWBRecording.cpp
+++ b/Source/Plugins/NWBFormat/NWBRecording.cpp
@@ -48,7 +48,7 @@
//Called when acquisition starts, to open the files
String basepath = rootFolder.getFullPathName() + rootFolder.separatorString + "experiment_" + String(experimentNumber) + ".nwb";
- recordFile = new NWBFile(basepath, CoreServices::getGUIVersion());
+ recordFile = new NWBFile(basepath, CoreServices::getGUIVersion(), identifierText);
recordFile->setXmlText(getLatestSettingsXml());
int recProcs = getNumRecordedProcessors();
@@ -217,6 +217,14 @@ 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("NWB", "NWB", &(engineFactory<NWBRecordEngine>));
+ EngineParameter* param;
+ param = new EngineParameter(EngineParameter::STR, 0, "Identifier Text", String::empty);
+ man->addParameter(param);
return man;
+}
+
+void NWBRecordEngine::setParameter(EngineParameter& parameter)
+{
+ strParameter(0, identifierText);
}
\ No newline at end of file
diff --git a/Source/Plugins/NWBFormat/NWBRecording.h b/Source/Plugins/NWBFormat/NWBRecording.h
index 2c218d7b0..2364d8683 100644
--- a/Source/Plugins/NWBFormat/NWBRecording.h
+++ b/Source/Plugins/NWBFormat/NWBRecording.h
@@ -43,6 +43,7 @@
void addSpikeElectrode(int index,const SpikeRecordInfo* elec) override;
void writeSpike(int electrodeIndex, const SpikeObject& spike, int64 timestamp) override;
void resetChannels() override;
+ void setParameter(EngineParameter& parameter) override;
static RecordEngineManager* getEngineManager();
@@ -61,6 +62,8 @@
HeapBlock<int16> intBuffer;
HeapBlock<double> tsBuffer;
int bufferSize;
+
+ String identifierText;
JUCE_DECLARE_NON_COPYABLE_WITH_LEAK_DETECTOR(NWBRecordEngine);
--
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