protected void MarkStim(object sender, EventArgs e)
{
if (!MainClass.devices[0].isrunning())
{
return;
}
double time = nirsdata[0].time[nirsdata[0].time.Count - 1];
string condname = comboboxentry_stimtype.ActiveText;
#if ADDLSL
if (checkbutton_LSLStimOutlet.Active)
{
string[] stim = new string[2];
stim[0] = string.Format("{0}:{1}", condname, "Event");
stim[1] = string.Format("{0}", time);
stimulusLSL.push_sample(stim);
}
#endif
int index = 0;
bool found = false;
nirs.Stimulus ev = new nirs.Stimulus();;
for (int i = 0; i < nirsdata[0].stimulus.Count; i++)
{
if (nirsdata[0].stimulus[i].name.Equals(condname))
{
ev = nirsdata[0].stimulus[i];
ev.onsets.Add(time);
ev.amplitude.Add(1);
ev.duration.Add(1);
found = true;
nirsdata[0].stimulus[i] = ev;
index = i;
}
}
if (!found)
{
ev = new nirs.Stimulus
{
onsets = new List <double>(),
duration = new List <double>(),
amplitude = new List <double>(),
name = condname
};
ev.onsets.Add(time);
ev.amplitude.Add(1);
ev.duration.Add(1);
nirsdata[0].stimulus.Add(ev);
index = ev.duration.Count;
}
_handles.stimListStore.AppendValues(condname, ev.onsets[ev.onsets.Count - 1],
ev.duration[ev.duration.Count - 1], ev.amplitude[ev.amplitude.Count - 1]);
label_numstim.Text = string.Format("Marks: {0}", ev.amplitude.Count);
_handles.StimTree.QueueDraw();
}
private void EditStimTable(object sender, Gtk.EditedArgs args, string type)
{
Gtk.TreeIter iter;
_handles.stimListStore.GetIter(out iter, new TreePath(args.Path));
string Oldname = (string)_handles.stimListStore.GetValue(iter, 0);
double Oldonset = (double)_handles.stimListStore.GetValue(iter, 1);
double Olddur = (double)_handles.stimListStore.GetValue(iter, 2);
double Oldamp = (double)_handles.stimListStore.GetValue(iter, 3);
string name = (string)_handles.stimListStore.GetValue(iter, 0);
double onset = (double)_handles.stimListStore.GetValue(iter, 1);
double dur = (double)_handles.stimListStore.GetValue(iter, 2);
double amp = (double)_handles.stimListStore.GetValue(iter, 3);
_handles.stimListStore.Remove(ref iter);
if (type.Equals("name"))
{
name = args.NewText;
}
else if (type.Equals("onset"))
{
onset = Convert.ToDouble(args.NewText);
}
else if (type.Equals("dur"))
{
dur = Convert.ToDouble(args.NewText);
}
else if (type.Equals("amp"))
{
amp = Convert.ToDouble(args.NewText);
}
_handles.stimListStore.AppendValues(name, onset, dur, amp);
_handles.stimListStore.SetSortColumnId(1, SortType.Ascending);
nirs.Stimulus ev;
nirs.Stimulus ev2 = new nirs.Stimulus();;
for (int i = 0; i < nirsdata[0].stimulus.Count; i++)
{
ev = nirsdata[0].stimulus[i];
if (ev.name == Oldname)
{
for (int j = 0; j < ev.onsets.Count; j++)
{
if (ev.onsets[j] == Oldonset)
{
if (type.Equals("name"))
{
ev.onsets.RemoveAt(j);
ev.duration.RemoveAt(j);
ev.amplitude.RemoveAt(j);
nirsdata[0].stimulus[i] = ev;
bool found = false;
for (int k = 0; k < nirsdata[0].stimulus.Count; k++)
{
ev2 = nirsdata[0].stimulus[k];
if (ev2.name == name)
{
ev2.amplitude.Add(amp);
ev2.duration.Add(dur);
ev2.onsets.Add(onset);
nirsdata[0].stimulus[k] = ev2;
found = true;
}
}
if (!found)
{
ev2.name = name;
ev2.amplitude = new List <double>();
ev2.duration = new List <double>();
ev2.onsets = new List <double>();
ev2.amplitude.Add(amp);
ev2.duration.Add(dur);
ev2.onsets.Add(onset);
nirsdata[0].stimulus.Add(ev2);
}
}
else
{
ev.onsets[j] = onset;
ev.duration[j] = dur;
ev.amplitude[j] = amp;
nirsdata[0].stimulus[i] = ev;
}
}
}
}
}
drawingarea_Data.QueueDraw();
drawingarea_Data2.QueueDraw();
return;
}
{ // methods devoted to file I/O
public static core.Data[] readSNIRF(string filename)
{
List <nirs.HDF5info> info = nirs.io.SNIRFinfo(filename);
hid_t fileId = H5F.open(filename, H5F.ACC_RDONLY);
string formatVersion = nirs.io.ReadDataString(fileId, "/formatVersion");
List <string> dataLst = new List <string>();
List <string> nirsLst = new List <string>();
for (int i = 0; i < info.Count; i++)
{
if (info[i].field.Contains("/nirs") & info[i].field.Contains("/data"))
{
int cnt = info[i].field.IndexOf("/");
cnt = info[i].field.IndexOf("/", cnt + 1);
int cnt2 = cnt;
cnt = info[i].field.IndexOf("/", cnt + 1); // find the third instance
string str = info[i].field.Substring(0, cnt);
string str2 = info[i].field.Substring(0, cnt2);
if (str.Contains("/nirs") & str.Contains("/data"))
{
if (!dataLst.Contains(str))
{
dataLst.Add(str);
}
}
if (str2.Contains("/nirs"))
{
if (!nirsLst.Contains(str2))
{
nirsLst.Add(str2);
}
}
}
}
core.Probe[] probes = new core.Probe[nirsLst.Count];
Dictionary[] demographics = new Dictionary[nirsLst.Count];
core.Data[] data = new core.Data[dataLst.Count];
List <Stimulus>[] stimuli = new List <Stimulus> [nirsLst.Count];
auxillary[][] aux = new auxillary[nirsLst.Count][];
for (int i = 0; i < nirsLst.Count; i++)
{
demographics[i] = new Dictionary();
for (int j = 0; j < info.Count; j++)
{
if (info[j].field.Contains(string.Format("{0}/metaDataTags", nirsLst[i])))
{
string fld = info[j].field.Substring(string.Format("{0}/metaDataTags", nirsLst[i]).Length + 1);
if (nirs.io.IsHDF5String(fileId, info[j].field))
{
string val = nirs.io.ReadDataString(fileId, info[j].field);
demographics[i].set(fld, val);
}
else
{
double val = nirs.io.ReadDataValue(fileId, info[j].field);
demographics[i].set(fld, val);
}
}
}
//aux events
List <string> auxList = new List <string>();
for (int j = 0; j < info.Count; j++)
{
if (info[j].field.Contains(string.Format("{0}/aux", nirsLst[i])) &
info[j].field.Contains("/name"))
{
string str = info[j].field.Substring(0, info[j].field.LastIndexOf("/"));
auxList.Add(str);
}
}
aux[i] = new auxillary[auxList.Count];
for (int j = 0; j < auxList.Count; j++)
{
double[] daux = nirs.io.ReadDataVector(fileId, string.Format("{0}/dataTimeSeries", auxList[j]));
double[] taux = nirs.io.ReadDataVector(fileId, string.Format("{0}/time", auxList[j]));
aux[i][j] = new auxillary();
aux[i][j].name = nirs.io.ReadDataString(fileId, string.Format("{0}/name", auxList[j]));
aux[i][j].timeOffset = nirs.io.ReadDataValue(fileId, string.Format("{0}/timeOffset", auxList[j]));
aux[i][j].data = new List <double>();
aux[i][j].time = new List <double>();
for (int k = 0; k < daux.Length; k++)
{
aux[i][j].data.Add(daux[k]);
aux[i][j].time.Add(taux[k]);
}
}
// stim events
stimuli[i] = new List <Stimulus>();
for (int j = 0; j < info.Count; j++)
{
if (info[j].field.Contains(string.Format("{0}/stim", nirsLst[i])) &
info[j].field.Contains("/name"))
{
string str = info[j].field.Substring(0, info[j].field.LastIndexOf("/"));
string stimname = nirs.io.ReadDataString(fileId, string.Format("{0}/name", str));
double[,] times = nirs.io.ReadDataArray(fileId, string.Format("{0}/data", str));
if (times.GetLength(0) == 3 & times.GetLength(1) != 3)
{
times = nirs.io.ReadDataArray(fileId, string.Format("{0}/data", str), true);
}
Stimulus stim = new Stimulus();
stim.name = stimname;
stim.onsets = new List <double>();
stim.duration = new List <double>();
stim.amplitude = new List <double>();
for (int ii = 0; ii < times.GetLength(0); ii++)
{
stim.onsets.Add(times[ii, 0]);
stim.duration.Add(times[ii, 1]);
stim.amplitude.Add(times[ii, 2]);
}
stimuli[i].Add(stim);
}
}
// read the probe
probes[i] = new core.Probe();
double[] wav;
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/wavelengths", nirsLst[i])))
{
wav = nirs.io.ReadDataVector(fileId, String.Format("{0}/probe/wavelengths", nirsLst[i]));
}
else
{
wav = new double[0];
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/sourcePos2D", nirsLst[i])))
{
probes[i].SrcPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos2D", nirsLst[i]));
if (probes[i].SrcPos.GetLength(0) == 3 & probes[i].SrcPos.GetLength(1) != 3)
{
probes[i].SrcPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos2D", nirsLst[i]), true);
}
}
else
{
probes[i].SrcPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos", nirsLst[i]));
if (probes[i].SrcPos.GetLength(0) == 3 & probes[i].SrcPos.GetLength(1) != 3)
{
probes[i].SrcPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos", nirsLst[i]), true);
}
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/detectorPos2D", nirsLst[i])))
{
probes[i].DetPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos2D", nirsLst[i]));
if (probes[i].DetPos.GetLength(0) == 3 & probes[i].SrcPos.GetLength(1) != 3)
{
probes[i].DetPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos2D", nirsLst[i]), true);
}
}
else
{
probes[i].DetPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos", nirsLst[i]));
if (probes[i].DetPos.GetLength(0) == 3 & probes[i].DetPos.GetLength(1) != 3)
{
probes[i].DetPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos", nirsLst[i]), true);
}
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/landmarkPos2D", nirsLst[i])))
{
probes[i].LandmarkPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos2D", nirsLst[i]));
if (probes[i].LandmarkPos.GetLength(0) == 3 & probes[i].LandmarkPos.GetLength(1) != 3)
{
probes[i].LandmarkPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos2D", nirsLst[i]), true);
}
}
else if (nirs.io.groupexists(fileId, String.Format("{0}/probe/landmarkPos", nirsLst[i])))
{
probes[i].LandmarkPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos", nirsLst[i]));
if (probes[i].LandmarkPos.GetLength(0) == 3 & probes[i].LandmarkPos.GetLength(1) != 3)
{
probes[i].LandmarkPos = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos", nirsLst[i]), true);
}
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/sourcePos3D", nirsLst[i])))
{
probes[i].SrcPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos3D", nirsLst[i]));
if (probes[i].SrcPos3D.GetLength(0) == 3 & probes[i].SrcPos3D.GetLength(1) != 3)
{
probes[i].SrcPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/sourcePos3D", nirsLst[i]), true);
}
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/detectorPos3D", nirsLst[i])))
{
probes[i].DetPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos3D", nirsLst[i]));
if (probes[i].DetPos3D.GetLength(0) == 3 & probes[i].DetPos3D.GetLength(1) != 3)
{
probes[i].DetPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/detectorPos3D", nirsLst[i]), true);
}
}
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/landmarkPos3D", nirsLst[i])))
{
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/landmarkPos3D", nirsLst[i])))
{
probes[i].LandmarkPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos3D", nirsLst[i]));
if (probes[i].LandmarkPos3D.GetLength(0) == 3 & probes[i].LandmarkPos3D.GetLength(1) != 3)
{
probes[i].LandmarkPos3D = nirs.io.ReadDataArray(fileId, String.Format("{0}/probe/landmarkPos3D", nirsLst[i]), true);
}
}
}
probes[i].numDet = probes[i].DetPos.GetLength(0);
probes[i].numSrc = probes[i].SrcPos.GetLength(0);
probes[i].numWavelengths = wav.Length;
probes[i].SourceLabels = new string[probes[i].SrcPos.GetLength(0)];
for (int j = 0; j < probes[i].SrcPos.GetLength(0); j++)
{
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/sourceLabels{1}", nirsLst[i], j + 1)))
{
probes[i].SourceLabels[j] = nirs.io.ReadDataString(fileId, String.Format("{0}/probe/sourceLabels{1}", nirsLst[i], j + 1));
}
else
{
probes[i].SourceLabels[j] = string.Format("Source-{0}", j + 1);
}
}
probes[i].DetectorLabels = new string[probes[i].DetPos.GetLength(0)];
for (int j = 0; j < probes[i].DetPos.GetLength(0); j++)
{
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/detectorLabels{1}", nirsLst[i], j + 1)))
{
probes[i].DetectorLabels[j] = nirs.io.ReadDataString(fileId, String.Format("{0}/probe/detectorLabels{1}", nirsLst[i], j + 1));
}
else
{
probes[i].DetectorLabels[j] = string.Format("Detector-{0}", j + 1);
}
}
if (probes[i].LandmarkPos != null)
{
probes[i].LandmarkLabels = new string[probes[i].LandmarkPos.GetLength(0)];
for (int j = 0; j < probes[i].LandmarkPos.GetLength(0); j++)
{
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/landmarkLabels{1}", nirsLst[i], j + 1)))
{
probes[i].LandmarkLabels[j] = nirs.io.ReadDataString(fileId, String.Format("{0}/probe/landmarkLabels{1}", nirsLst[i], j + 1));
}
else
{
probes[i].LandmarkLabels[j] = string.Format("Landmark-{0}", j + 1);
}
}
}
}
// Now, load the data
for (int i = 0; i < dataLst.Count; i++)
{
double[] wav = new double[0];
data[i] = new core.Data();
data[i].description = dataLst[i];
for (int j = 0; j < nirsLst.Count; j++)
{
if (dataLst[i].Contains(string.Format("{0}/data", nirsLst[j])))
{
data[i].probe = probes[j];
data[i].demographics = demographics[j];
if (nirs.io.groupexists(fileId, String.Format("{0}/probe/wavelengths", nirsLst[j])))
{
wav = nirs.io.ReadDataVector(fileId, String.Format("{0}/probe/wavelengths", nirsLst[j]));
}
else
{
wav = new double[0];
}
data[i].stimulus = stimuli[j];
data[i].auxillaries = aux[i];
}
}
double[] t = nirs.io.ReadDataVector(fileId, String.Format("{0}/time", dataLst[i]));
data[i].time = new List <double>();
for (int ii = 0; ii < t.Length; ii++)
{
data[i].time.Add(t[ii]);
}
double[,] d = nirs.io.ReadDataArray(fileId, String.Format("{0}/dataTimeSeries", dataLst[i]));
if (d.GetLength(0) == t.Length)
{
d = nirs.io.ReadDataArray(fileId, String.Format("{0}/dataTimeSeries", dataLst[i]), true);
}
data[i].data = new List <double> [d.GetLength(0)];
for (int ii = 0; ii < d.GetLength(0); ii++)
{
data[i].data[ii] = new List <double>();
for (int jj = 0; jj < d.GetLength(1); jj++)
{
data[i].data[ii].Add(d[ii, jj]);
}
}
data[i].numsamples = data[i].time.Count;
data[i].probe.numChannels = data[i].data.Length;
data[i].probe.ChannelMap = new ChannelMap[data[i].probe.numChannels];
for (int j = 0; j < data[i].probe.numChannels; j++)
{
data[i].probe.ChannelMap[j] = new ChannelMap();
data[i].probe.ChannelMap[j].sourceindex = (int)nirs.io.ReadDataValue(fileId,
String.Format("{0}/measurementList{1}/sourceIndex", dataLst[i], j + 1)) - 1;
data[i].probe.ChannelMap[j].detectorindex = (int)nirs.io.ReadDataValue(fileId,
String.Format("{0}/measurementList{1}/detectorIndex", dataLst[i], j + 1)) - 1;
if (wav.Length > 0)
{
data[i].probe.ChannelMap[j].wavelength = wav[(int)nirs.io.ReadDataValue(fileId,
String.Format("{0}/measurementList{1}/wavelengthIndex", dataLst[i], j + 1)) - 1];
}
int datatypeIdx = (int)nirs.io.ReadDataValue(fileId, String.Format("{0}/measurementList{1}/dataType", dataLst[i], j + 1));
data[i].probe.ChannelMap[j].datatype = (datatype)Enum.ToObject(typeof(datatype), datatypeIdx);
if (wav.Length > 0)
{
data[i].probe.ChannelMap[j].datasubtype = String.Format("{0}nm", data[i].probe.ChannelMap[j].wavelength);
}
else
{
data[i].probe.ChannelMap[j].datasubtype = nirs.io.ReadDataString(fileId,
String.Format("{0}/measurementList{1}/dataTypeLabel", dataLst[i], j + 1));
}
data[i].probe.ChannelMap[j].channelname = String.Format("Src{0}-Det{1}", data[i].probe.ChannelMap[j].sourceindex + 1,
data[i].probe.ChannelMap[j].detectorindex + 1);
//{optional}
if (nirs.io.groupexists(fileId, String.Format("{0}/measurementList{1}/moduleIndex", dataLst[i], j + 1)))
{
data[i].probe.ChannelMap[j].moduleIndex = (int)nirs.io.ReadDataValue(fileId, String.Format("{0}/measurementList{1}/moduleIndex", dataLst[i], j + 1));
}
if (nirs.io.groupexists(fileId, String.Format("{0}/measurementList{1}/detectorGain", dataLst[i], j + 1)))
{
data[i].probe.ChannelMap[j].DetectorGain = nirs.io.ReadDataValue(fileId, String.Format("{0}/measurementList{1}/detectorGain", dataLst[i], j + 1));
}
if (nirs.io.groupexists(fileId, String.Format("{0}/measurementList{1}/sourcePower", dataLst[i], j + 1)))
{
data[i].probe.ChannelMap[j].SourcePower = nirs.io.ReadDataValue(fileId, String.Format("{0}/measurementList{1}/sourcePower", dataLst[i], j + 1));
}
}
}
return(data);
// data#/probe/useLocalIndex [int] = 0
}
{ // methods devoted to file I/O
/// <subjid>.wl1 - wavelength #1 data
/// <subjid>.wl2 - wavelength #2 data
/// <subjid>_config.txt - config file
/// <subjid>.evt - stimulus events(data taken from config file)
/// <subjid>_probeInfo.mat - probe file
/// <subjid>.tpl -topology file(data taken from config file)
///
public static core.Data readNIRx(string filename)
{
core.Data data = new core.Data();
filename = filename.Substring(0, filename.IndexOf(".wl1", StringComparison.Ordinal));
// Read the header file
List <string> hdrFields = new List <string>();
List <string> hdrValues = new List <string>();
string line;
System.IO.StreamReader file = new System.IO.StreamReader(filename + ".hdr");
while ((line = file.ReadLine()) != null)
{
if (line.Contains("="))
{
int found = line.IndexOf("=", StringComparison.Ordinal);
hdrFields.Add(line.Substring(0, found));
string value = line.Substring(found + 1);
if (value.Contains("#"))
{
value = "";
while ((line = file.ReadLine()) != null)
{
if (line.Contains("#"))
{
break;
}
value = value + "\r" + line;
}
}
if (value.Contains("\""))
{
value = value.Substring(1, value.Length - 2);
}
hdrValues.Add(value);
}
}
file.Close();
string targetDirectory = Path.GetDirectoryName(filename + ".hdr");
string[] fileEntries = Directory.GetFiles(targetDirectory);
string probeFile = Path.Combine(targetDirectory, "Standard_probeInfo.mat");
foreach (string i in fileEntries)
{
if (i.Contains("probeInfo.mat"))
{
probeFile = Path.Combine(targetDirectory, i);
break;
}
}
// Now, read the Probe_info.mat file
MatFileReader mfr = new MatFileReader(probeFile);
MLStructure probeInfo = (mfr.Content["probeInfo"] as MLStructure);
MLStructure probes = (probeInfo["probes"] as MLStructure);
MLDouble coords_s2 = (probes["coords_s2"] as MLDouble);
MLDouble coords_d2 = (probes["coords_d2"] as MLDouble);
MLDouble coords_c2 = (probes["coords_c2"] as MLDouble);
double[][] srcpos = coords_s2.GetArray();
double[][] detpos = coords_d2.GetArray();
double[][] landpos = coords_c2.GetArray();
// TODO read all the 3D stuff too
MLDouble coords_s3 = (probes["coords_s3"] as MLDouble);
MLDouble coords_d3 = (probes["coords_d3"] as MLDouble);
MLDouble coords_c3 = (probes["coords_c3"] as MLDouble);
double[][] srcpos3D = coords_s3.GetArray();
double[][] detpos3D = coords_d3.GetArray();
double[][] landpos3D = coords_c3.GetArray();
data.probe.numSrc = srcpos.Length;
data.probe.numDet = detpos.Length;
data.probe.DetPos = new double[detpos.Length, 3];
data.probe.DetectorLabels = new string[detpos.Length];
for (int i = 0; i < detpos.Length; i++)
{
data.probe.DetPos[i, 0] = (float)detpos[i][0];
data.probe.DetPos[i, 1] = (float)detpos[i][1];
data.probe.DetPos[i, 2] = 0;
data.probe.DetectorLabels[i] = string.Format("Detector-{0}", i + 1);
}
data.probe.SrcPos = new double[srcpos.Length, 3];
data.probe.SourceLabels = new string[srcpos.Length];
for (int i = 0; i < srcpos.Length; i++)
{
data.probe.SrcPos[i, 0] = (float)srcpos[i][0];
data.probe.SrcPos[i, 1] = (float)srcpos[i][1];
data.probe.SrcPos[i, 2] = 0;
data.probe.SourceLabels[i] = string.Format("Source-{0}", i + 1);
}
data.probe.LandmarkPos = new double[landpos.Length, 3];
data.probe.LandmarkLabels = new string[landpos.Length];
for (int i = 0; i < landpos.Length; i++)
{
data.probe.LandmarkPos[i, 0] = (float)landpos[i][0];
data.probe.LandmarkPos[i, 1] = (float)landpos[i][1];
data.probe.LandmarkPos[i, 2] = 0;
data.probe.LandmarkLabels[i] = string.Format("Landmark(temp)-{0}", i + 1);
}
data.probe.DetPos3D = new double[detpos3D.Length, 3];
for (int i = 0; i < detpos3D.Length; i++)
{
data.probe.DetPos3D[i, 0] = (double)detpos3D[i][0];
data.probe.DetPos3D[i, 1] = (double)detpos3D[i][1];
data.probe.DetPos3D[i, 2] = (double)detpos3D[i][1];
}
data.probe.SrcPos3D = new double[srcpos3D.Length, 3];
for (int i = 0; i < srcpos3D.Length; i++)
{
data.probe.SrcPos3D[i, 0] = (double)srcpos3D[i][0];
data.probe.SrcPos3D[i, 1] = (double)srcpos3D[i][1];
data.probe.SrcPos3D[i, 2] = (double)srcpos3D[i][2];
}
data.probe.LandmarkPos3D = new double[landpos.Length, 3];
for (int i = 0; i < landpos.Length; i++)
{
data.probe.LandmarkPos3D[i, 0] = (float)landpos3D[i][0];
data.probe.LandmarkPos3D[i, 1] = (float)landpos3D[i][1];
data.probe.LandmarkPos3D[i, 2] = (float)landpos3D[i][2];
}
data.probe.isregistered = true;
int LambdaIdx = hdrFields.IndexOf("Wavelengths");
string[] lam = hdrValues[LambdaIdx].Split('\t');
double[] lambda = new double[lam.Length];
for (int i = 0; i < lam.Length; i++)
{
lambda[i] = Convert.ToDouble(lam[i]);
}
int SDmaskIdx = hdrFields.IndexOf("S-D-Mask");
string[] mask = hdrValues[SDmaskIdx].Split('\r');
bool[,] SDMask = new bool[data.probe.numSrc, data.probe.numDet];
for (int i = 1; i < data.probe.numSrc + 1; i++)
{
string[] mask2 = mask[i].Split('\t');
for (int j = 0; j < data.probe.numDet; j++)
{
SDMask[i - 1, j] = false;
if (mask2[j].Contains("1"))
{
SDMask[i - 1, j] = true;
}
}
}
int cnt = 0;
for (int i = 0; i < SDMask.GetLength(0); i++)
{
for (int j = 0; j < SDMask.GetLength(1); j++)
{
if (SDMask[i, j])
{
cnt++;
}
}
}
data.probe.ChannelMap = new ChannelMap[cnt * lambda.Length];
cnt = 0;
List <int> ChanIdx = new List <int>();
int cnt2 = 0;
for (int w = 0; w < lambda.Length; w++)
{
for (int i = 0; i < SDMask.GetLength(0); i++)
{
for (int j = 0; j < SDMask.GetLength(1); j++)
{
if (SDMask[i, j])
{
data.probe.ChannelMap[cnt] = new ChannelMap();
data.probe.ChannelMap[cnt].sourceindex = i;
data.probe.ChannelMap[cnt].detectorindex = j;
data.probe.ChannelMap[cnt].channelname = String.Format("Src{0}-Det{1}",
data.probe.ChannelMap[cnt].sourceindex + 1,
data.probe.ChannelMap[cnt].detectorindex + 1);
data.probe.ChannelMap[cnt].wavelength = lambda[w];
data.probe.ChannelMap[cnt].datasubtype = String.Format("{0}nm", data.probe.ChannelMap[cnt].wavelength);
cnt++;
if (w == 0)
{
ChanIdx.Add(cnt2);
}
}
cnt2++;
}
}
}
data.probe.numChannels = data.probe.ChannelMap.Length;
data.probe.measlistAct = new bool[data.probe.numChannels];
for (int i = 0; i < data.probe.numChannels; i++)
{
data.probe.measlistAct[i] = false;
}
data.probe.measlistAct[0] = true;
// read the actual data
System.IO.StreamReader file2 = new System.IO.StreamReader(filename + ".wl1");
string lines = file2.ReadToEnd();
string[] tpts = lines.Split('\r');
data.data = new List <double> [data.probe.numChannels];
for (int i = 0; i < data.data.Length; i++)
{
data.data[i] = new List <double>();
}
for (int i = 0; i < tpts.Length - 1; i++)
{
if (tpts[i].Contains("\n"))
{
tpts[i] = tpts[i].Substring(1, tpts[i].Length - 1);
}
string[] pts = tpts[i].Split(' ');
for (int j = 0; j < ChanIdx.Count; j++)
{
data.data[j].Add(Convert.ToDouble(pts[ChanIdx[j]]));
}
}
file2 = new System.IO.StreamReader(filename + ".wl2");
lines = file2.ReadToEnd();
tpts = lines.Split('\r');
for (int i = 0; i < tpts.Length - 1; i++)
{
if (tpts[i].Contains("\n"))
{
tpts[i] = tpts[i].Substring(1, tpts[i].Length - 1);
}
string[] pts = tpts[i].Split(' ');
for (int j = 0; j < ChanIdx.Count; j++)
{
data.data[j + data.probe.numChannels / 2].Add(Convert.ToDouble(pts[ChanIdx[j]]));
}
}
// finally, the time vector
int fsIdx = hdrFields.IndexOf("SamplingRate");
double fs = Convert.ToDouble(hdrValues[fsIdx]);
data.numsamples = data.data.GetLength(1);
data.time = new List <double>();
for (int i = 0; i < data.numsamples; i++)
{
data.time.Add(i / fs);
}
// TODO add stimulus information
int EventIdx = hdrFields.IndexOf("Events");
string[] eventline = hdrValues[EventIdx].Split('\r');
double[,] events = new double[eventline.Length - 1, 3];
for (int i = 1; i < eventline.Length; i++)
{
string[] eventline2 = eventline[i].Split('\t');
for (int j = 0; j < 2; j++)
{
events[i - 1, j] = Convert.ToDouble(eventline2[j]);
}
}
List <double> uniqEvents = new List <double>();
int[] uniqEventCount = new int[events.GetLength(0)];
for (int i = 0; i < events.GetLength(0); i++)
{
uniqEventCount[i] = 0;
if (!uniqEvents.Contains(events[i, 1]))
{
uniqEvents.Add(events[i, 1]);
}
int ii = uniqEvents.IndexOf(events[i, 1]);
uniqEventCount[ii]++;
}
data.stimulus = new List <Stimulus>();
for (int i = 0; i < uniqEvents.Count; i++)
{
Stimulus stimulus = new Stimulus();
stimulus.name = String.Format("Event-{0}", uniqEvents[i]);
stimulus.onsets = new List <double>();
stimulus.duration = new List <double>();
stimulus.amplitude = new List <double>();
int n = 0;
for (int j = 0; j < events.GetLength(0); j++)
{
if (Math.Abs(events[j, 1] - uniqEvents[i]) < 0.0001)
{
stimulus.onsets.Add(events[j, 0]);
stimulus.duration.Add(1);
stimulus.amplitude.Add(1);
n++;
}
}
data.stimulus.Add(stimulus);
}
//add demographics info
List <string> Fields = new List <string>()
{
"Subject", "notes", "FileName", "Date", "Device", "Source",
"Mod", "APD", "NIRStar", "Mod Amp"
};
for (int i = 0; i < Fields.Count; i++)
{
int idx = hdrFields.IndexOf(Fields[i]);
if (idx > -1)
{
data.demographics.set(Fields[i], hdrValues[idx]);
}
}
data.description = targetDirectory;
return(data);
}
