// This restores the last Study/probe used
public void RegisterQuickStart(object sender, EventArgs e)
{
string path = System.IO.Path.GetDirectoryName(Assembly.GetEntryAssembly().Location);
path = System.IO.Path.Combine(path, "LastSettings.xml");
// Read the Config.xml file
XmlDocument doc = new XmlDocument();
doc.Load(path);
XmlNodeList elemList;
elemList = doc.GetElementsByTagName("Investigator");
string investigator = elemList[0].InnerXml.Trim();
elemList = doc.GetElementsByTagName("Study");
string study = elemList[0].InnerXml.Trim();
elemList = doc.GetElementsByTagName("probefile");
string probefile = elemList[0].InnerXml.Trim();
int[] lambda = MainClass.win.settings.system_Info.wavelengths;
nirs.core.Probe probe = nirs.io.LoadProbe(probefile, lambda);
// Add channels for Optical Density, HbO2, and HbR
int cnt = probe.ChannelMap.Length;
nirs.ChannelMap[] ChannelMap = new nirs.ChannelMap[cnt * 2 + 2 * cnt / probe.numWavelengths];
for (int ii = 0; ii < cnt; ii++)
{
ChannelMap[ii] = probe.ChannelMap[ii];
}
for (int ii = 0; ii < cnt; ii++)
{
ChannelMap[ii + cnt] = probe.ChannelMap[ii];
ChannelMap[ii + cnt].datasubtype = string.Format("ΔOD {0}nm", ChannelMap[ii].wavelength);
}
for (int ii = 0; ii < cnt / probe.numWavelengths; ii++)
{
ChannelMap[ii + 2 * cnt] = probe.ChannelMap[ii];
ChannelMap[ii + 2 * cnt].datasubtype = "HbO2";
}
for (int ii = cnt / probe.numWavelengths; ii < cnt; ii++)
{
ChannelMap[ii + 2 * cnt] = probe.ChannelMap[ii];
ChannelMap[ii + 2 * cnt].datasubtype = "Hb";
}
probe.ChannelMap = ChannelMap;
probe.measlistAct = new bool[probe.ChannelMap.Length];
for (int ii = 0; ii < probe.ChannelMap.Length; ii++)
{
probe.measlistAct[ii] = true;
}
Gdk.Color[] cmap = new Gdk.Color[probe.ChannelMap.Length];
for (int ii = 0; ii < probe.numChannels; ii++)
{
cmap[ii] = probe.colormap[ii];
cmap[probe.numChannels + ii] = probe.colormap[ii];
cmap[probe.numChannels * 2 + ii] = probe.colormap[ii];
}
probe.colormap = cmap;
nirsdata = new List <nirs.core.Data>();
for (int i = 0; i < MainClass.devices.Length; i++)
{
nirs.core.Data data = new nirs.core.Data
{
demographics = new nirs.Dictionary()
};
data.demographics.set("SubjID", "");
data.demographics.set("Investigator", investigator);
data.demographics.set("Study", study);
data.demographics.set("Gender", "");
data.demographics.set("Group", "");
data.demographics.set("Age", "");
data.demographics.set("Instrument", MainClass.win.settings.SYSTEM);
data.demographics.set("head_circumference", "");
data.demographics.set("Technician", "");
data.demographics.set("comments", "");
DateTime now = DateTime.Now;
data.demographics.set("scan_date", now.ToString("F"));
data.probe = probe.Clone();
nirsdata.Add(data);
}
ListStore ClearList = new ListStore(typeof(string));
MainClass.win._handles.whichdata.Model = ClearList;
List <string> datatypes = new List <string>();
for (int ii = 0; ii < probe.ChannelMap.Length; ii++)
{
datatypes.Add(probe.ChannelMap[ii].datasubtype);
}
datatypes = datatypes.Distinct().ToList();
foreach (string s in datatypes)
{
MainClass.win._handles.whichdata.AppendText(s);
}
for (int dI = probe.numDet; dI < MainClass.win._handles.detectors.Count; dI++)
{
MainClass.win._handles.detectors[dI].frame.Sensitive = false;
MainClass.win._handles.detectors[dI].vScale.Sensitive = false;
MainClass.win._handles.detectors[dI].vScale.Value = 0;
MainClass.win._handles.detectors[dI].led.Color = new Gdk.Color(93, 93, 93);
}
for (int sI = probe.numSrc; sI < MainClass.win._handles.lasers.Count; sI++)
{
MainClass.win._handles.lasers[sI].frame.Sensitive = false;
for (int wI = 0; wI < MainClass.win._handles.lasers[sI].buttons.Length; wI++)
{
MainClass.win._handles.lasers[sI].spinButtons[wI].Sensitive = false;
MainClass.win._handles.lasers[sI].buttons[wI].Sensitive = false;
}
}
#if ADDLSL
MainClass.win.dataLSL = new LSL.liblsl.StreamOutlet[MainClass.devices.Length];
for (int ii = 0; ii < MainClass.devices.Length; ii++)
{
int fs = MainClass.devices[ii].GetSampleRate();
string name = string.Format("NIRSRecordIRData_{0}", ii + 1);
LSL.liblsl.StreamInfo info = new LSL.liblsl.StreamInfo(name, "NIRS", MainClass.win.nirsdata[ii].probe.numChannels,
(double)fs, LSL.liblsl.channel_format_t.cf_int32);
MainClass.win.dataLSL[ii] = new LSL.liblsl.StreamOutlet(info);
}
#endif
comboboxdeviceDemo.Active = 0;
MainClass.win._handles.whichdata.Active = 0;
MainClass.win.EnableControls(true);
MainClass.win._handles.SDGplot.QueueDraw();
}
private static nirs.core.Probe loadSDprobe(string file, int[] lambda)
{
nirs.core.Probe probe = new core.Probe();
MatFileReader mfr = new MatFileReader(file);
MLStructure SD = (mfr.Content["SD"] as MLStructure);
MLDouble MLsrcpos = null;
if (SD.Keys.Contains("SrcPos"))
{
MLsrcpos = (SD["SrcPos"] as MLDouble);
}
else if (SD.Keys.Contains("srcpos"))
{
MLsrcpos = (SD["srcpos"] as MLDouble);
}
MLDouble MLdetpos = null;
if (SD.Keys.Contains("DetPos"))
{
MLdetpos = (SD["DetPos"] as MLDouble);
}
else if (SD.Keys.Contains("detpos"))
{
MLdetpos = (SD["detpos"] as MLDouble);
}
if (MLdetpos != null)
{
double[][] detpos = MLdetpos.GetArray();
probe.DetPos = new double[detpos.Length, 3];
probe.DetectorLabels = new string[detpos.Length];
for (int i = 0; i < detpos.Length; i++)
{
probe.DetPos[i, 0] = (float)detpos[i][0];
probe.DetPos[i, 1] = (float)detpos[i][1];
probe.DetPos[i, 2] = (float)detpos[i][2];
probe.DetectorLabels[i] = String.Format("Detector-{0}", +1);
}
probe.numDet = detpos.Length;
}
if (MLsrcpos != null)
{
double[][] srcpos = MLsrcpos.GetArray();
probe.SrcPos = new double[srcpos.Length, 3];
probe.SourceLabels = new string[srcpos.Length];
for (int i = 0; i < srcpos.Length; i++)
{
probe.SrcPos[i, 0] = (float)srcpos[i][0];
probe.SrcPos[i, 1] = (float)srcpos[i][1];
probe.SrcPos[i, 2] = (float)srcpos[i][2];
probe.SourceLabels[i] = String.Format("Source-{0}", i + 1);
}
probe.numSrc = srcpos.Length;
}
MLDouble mlMeasList = null;
if (mfr.Content.ContainsKey("ml"))
{
mlMeasList = (mfr.Content["ml"] as MLDouble);
}
else
{
mlMeasList = (SD["MeasList"] as MLDouble);
}
if (mlMeasList != null)
{
double[][] ml = mlMeasList.GetArray();
probe.ChannelMap = new ChannelMap[ml.Length];
for (int i = 0; i < ml.Length; i++)
{
probe.ChannelMap[i] = new ChannelMap();
probe.ChannelMap[i].sourceindex = (int)ml[i][0] - 1;
probe.ChannelMap[i].detectorindex = (int)ml[i][1] - 1;
probe.ChannelMap[i].channelname = String.Format("Src{0}-Det{1}",
probe.ChannelMap[i].sourceindex + 1,
probe.ChannelMap[i].detectorindex + 1);
probe.ChannelMap[i].wavelength = lambda[(int)ml[i][3] - 1];
probe.ChannelMap[i].datasubtype = String.Format("{0}nm", probe.ChannelMap[i].wavelength);
}
}
probe.numChannels = probe.ChannelMap.Length;
probe.measlistAct = new bool[probe.numChannels];
for (int i = 0; i < probe.numChannels; i++)
{
probe.measlistAct[i] = false;
}
probe.measlistAct[0] = true;
probe.numWavelengths = lambda.Length;
return(probe);
}
{ // 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
}
private static nirs.core.Probe loadxmlprobe(string file, int[] lambda)
{ // This function loads a probe from an xml file
nirs.core.Probe probe = new core.Probe();
XmlDocument doc = new XmlDocument();
XmlDocument doc2;
XmlDocument doc3;
doc.Load(file);
XmlNodeList elemList;
XmlNodeList elemListsub;
XmlNodeList elemListsub2;
probe.numWavelengths = lambda.Length;
// Source-positions
elemList = doc.GetElementsByTagName("srcpos");
probe.numSrc = elemList.Count;
probe.SrcPos = new double[probe.numSrc, 2];
for (int i = 0; i < elemList.Count; i++)
{
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("index");
int index = Convert.ToInt32(elemListsub[0].InnerXml) - 1;
elemListsub = doc2.GetElementsByTagName("x");
probe.SrcPos[index, 0] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("y");
probe.SrcPos[index, 1] = Convert.ToDouble(elemListsub[0].InnerXml);
}
// Detector-positions
elemList = doc.GetElementsByTagName("detpos");
probe.numDet = elemList.Count;
probe.DetPos = new double[probe.numDet, 2];
for (int i = 0; i < elemList.Count; i++)
{
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("index");
int index = Convert.ToInt32(elemListsub[0].InnerXml) - 1;
elemListsub = doc2.GetElementsByTagName("x");
probe.DetPos[index, 0] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("y");
probe.DetPos[index, 1] = Convert.ToDouble(elemListsub[0].InnerXml);
}
// 3D corrdinates
// Source-positions
elemList = doc.GetElementsByTagName("srcpos3D");
if (elemList.Count > 0)
{
probe.SrcPos3D = new double[probe.numSrc, 3];
for (int i = 0; i < elemList.Count; i++)
{
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("index");
int index = Convert.ToInt32(elemListsub[0].InnerXml) - 1;
elemListsub = doc2.GetElementsByTagName("x");
probe.SrcPos3D[index, 0] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("y");
probe.SrcPos3D[index, 1] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("z");
probe.SrcPos3D[index, 2] = Convert.ToDouble(elemListsub[0].InnerXml);
probe.isregistered = true;
}
// Detector-positions
elemList = doc.GetElementsByTagName("detpos3D");
probe.DetPos3D = new double[probe.numDet, 3];
for (int i = 0; i < elemList.Count; i++)
{
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("index");
int index = Convert.ToInt32(elemListsub[0].InnerXml) - 1;
elemListsub = doc2.GetElementsByTagName("x");
probe.DetPos3D[index, 0] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("y");
probe.DetPos3D[index, 1] = Convert.ToDouble(elemListsub[0].InnerXml);
elemListsub = doc2.GetElementsByTagName("z");
probe.DetPos3D[index, 2] = Convert.ToDouble(elemListsub[0].InnerXml);
}
}
else
{
probe.isregistered = false;
}
// Measurement list
elemList = doc.GetElementsByTagName("ml");
probe.ChannelMap = new ChannelMap[elemList.Count * lambda.Length];
probe.numChannels = elemList.Count * lambda.Length;
for (int j = 0; j < lambda.Length; j++)
{
for (int i = 0; i < elemList.Count; i++)
{
int ii = i + j * elemList.Count;
probe.ChannelMap[ii] = new ChannelMap();
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("src");
probe.ChannelMap[ii].sourceindex = Convert.ToInt16(elemListsub[0].InnerXml) - 1;
elemListsub = doc2.GetElementsByTagName("det");
probe.ChannelMap[ii].detectorindex = Convert.ToInt16(elemListsub[0].InnerXml) - 1;
probe.ChannelMap[ii].wavelength = lambda[j];
probe.ChannelMap[ii].moduleIndex = 0;
probe.ChannelMap[ii].SourcePower = 0;
probe.ChannelMap[ii].DetectorGain = 0;
probe.ChannelMap[ii].datatype = datatype.CW_absoption;
probe.ChannelMap[ii].datasubtype = String.Format("raw {0}nm", probe.ChannelMap[ii].wavelength);
probe.ChannelMap[ii].channelname = String.Format("Src{0}-Det{1} [{2}nm]", probe.ChannelMap[i].sourceindex + 1,
probe.ChannelMap[ii].detectorindex + 1, probe.ChannelMap[ii].wavelength);
probe.ChannelMap[ii].dataindex = 0;
}
}
probe.measlistAct = new bool[probe.ChannelMap.Length];
for (int i = 0; i < probe.ChannelMap.Length; i++)
{
probe.measlistAct[i] = true;
}
//ROI information
probe.ROIs = new List <ROI>();
elemList = doc.GetElementsByTagName("ROI");
for (int i = 0; i < elemList.Count; i++)
{
ROI rOI = new ROI();
doc2 = new XmlDocument();
doc2.LoadXml("<root>" + elemList[i].InnerXml + "</root>");
elemListsub = doc2.GetElementsByTagName("name");
rOI.name = elemListsub[0].InnerXml;
rOI.sourceindex = new List <int>();
rOI.detectorindex = new List <int>();
rOI.weight = new List <double>();
elemListsub = doc2.GetElementsByTagName("meas");
for (int j = 0; j < elemListsub.Count; j++)
{
doc3 = new XmlDocument();
doc3.LoadXml("<root>" + elemListsub[j].InnerXml + "</root>");
elemListsub2 = doc3.GetElementsByTagName("src");
rOI.sourceindex.Add(Convert.ToInt16(elemListsub2[0].InnerXml) - 1);
elemListsub2 = doc3.GetElementsByTagName("det");
rOI.detectorindex.Add(Convert.ToInt16(elemListsub2[0].InnerXml) - 1);
elemListsub2 = doc3.GetElementsByTagName("weight");
if (elemListsub2.Count > 0)
{
rOI.weight.Add(Convert.ToDouble(elemListsub2[0].InnerXml));
}
else
{
rOI.weight.Add(1);
}
}
probe.ROIs.Add(rOI);
}
return(probe);
}