public static AnnoList LoadFromCSVFile(String filepath, double samplerate = 1, string type = "legacy", string filter = null)
{
AnnoList list = new AnnoList();
list.Source.File.Path = filepath;
list.Scheme = new AnnoScheme();
try
{
StreamReader sr = new StreamReader(filepath, System.Text.Encoding.Default);
string line = null;
while ((line = sr.ReadLine()) != null)
{
if (type == "semicolon")
{
list.Scheme.Type = AnnoScheme.TYPE.FREE;
string[] data = line.Split(';');
double start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double duration = Convert.ToDouble(data[1]) - Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
string label = "";
string tier = "";
string meta = "";
double confidence = 1.0;
if (data.Length > 2)
{
label = data[2];
}
if (data.Length > 3)
{
if (data[3].Contains("#"))
{
tier = data[3];
tier = tier.Remove(0, 1);
}
else
{
bool isconfidence = double.TryParse(data[3], out confidence);
}
}
if (data.Length > 4)
{
for (int i = 4; i < data.Length; i++)
{
meta += data[i] + ";";
}
}
AnnoListItem e = new AnnoListItem(start, duration, label, meta, Colors.Black, confidence);
if (filter == null || tier == filter)
{
list.AddSorted(e);
}
}
else if (type == "continuous")
{
list.Scheme.Type = AnnoScheme.TYPE.CONTINUOUS;
list.Scheme.SampleRate = samplerate;
string[] data = line.Split(';');
double start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double score = double.NaN;
string tier = "";
double confidence = 1.0;
if (data.Length > 1)
{
double.TryParse(data[1], out score);
}
if (data.Length > 2)
{
bool isconfidence = double.TryParse(data[2], out confidence);
}
if (data.Length > 3)
{
list.Scheme.MinScore = double.Parse(data[3]);
if (data.Length > 4)
{
list.Scheme.MaxScore = double.Parse(data[4]);
}
AnnoListItem e = new AnnoListItem(start, samplerate == 0 ? 0 : 1 / samplerate, score, "Range: " + list.Scheme.MinScore + "-" + list.Scheme.MaxScore, Colors.Black);
list.AddSorted(e);
}
else
{
AnnoListItem e = new AnnoListItem(start, samplerate == 0 ? 0 : 1 / samplerate, score, "", Colors.Black, 1);
if (filter == null || tier == filter)
{
list.AddSorted(e);
}
}
}
else if (type == "legacy")
{
list.Scheme.Type = AnnoScheme.TYPE.FREE;
string[] data;
data = line.Split(' ');
if (data.Length < 2)
{
data = line.Split('\t');
}
if (data.Length < 2)
{
data = line.Split(';');
}
double start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double duration = Convert.ToDouble(data[1], CultureInfo.InvariantCulture) - Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
string label = "";
string tier = "";
if (data.Length > 2)
{
label = data[2];
}
if (data.Length > 3)
{
tier = data[3];
}
for (int i = 4; i < data.Length; i++)
{
label += " " + data[i];
}
AnnoListItem e = new AnnoListItem(start, duration, label, "", Colors.Black, 1);
if (filter == null || tier == filter)
{
list.AddSorted(e);
}
}
}
sr.Close();;
list.HasChanged = false;
}
catch
{
MessageBox.Show("An exception occured while reading annotation from '" + filepath + "'");
}
return(list);
}
public static List <AnnoList> LoadfromElanFile(String filepath)
{
List <AnnoList> list = new List <AnnoList>();
try
{
XmlDocument doc = new XmlDocument();
doc.Load(filepath);
//Get time order references
XmlNode time_order = doc.SelectSingleNode("//TIME_ORDER");
List <KeyValuePair <string, string> > time_order_list = new List <KeyValuePair <string, string> >();
foreach (XmlNode node in time_order.ChildNodes)
{
time_order_list.Add(new KeyValuePair <string, string>(node.Attributes[0].Value.ToString(), node.Attributes[1].Value.ToString()));
}
//Get number of tiers
int i = 0;
foreach (XmlNode tier in doc.SelectNodes("//TIER"))
{
AnnoList al = new AnnoList();
AnnoScheme scheme = new AnnoScheme();
scheme.Type = AnnoScheme.TYPE.FREE;
string tierid = tier.Attributes.GetNamedItem("TIER_ID").Value.ToString();
string role = "";
try
{
role = tier.Attributes.GetNamedItem("PARTICIPANT").Value.ToString();
}
catch { }
al = new AnnoList();
al.Source.File.Path = filepath;
foreach (XmlNode annotation in tier.ChildNodes)
{
string label = null;
string starttmp = "";
string endtmp = "";
double start = -1;
double end = -1;
double duration = -1;
XmlNode alignable_annotation = annotation.FirstChild;
starttmp = (from kvp in time_order_list where kvp.Key == alignable_annotation.Attributes.GetNamedItem("TIME_SLOT_REF1").Value.ToString() select kvp.Value).ToList()[0];
start = double.Parse(starttmp, CultureInfo.InvariantCulture) / 1000;
endtmp = (from kvp in time_order_list where kvp.Key == alignable_annotation.Attributes.GetNamedItem("TIME_SLOT_REF2").Value.ToString() select kvp.Value).ToList()[0];
end = double.Parse(endtmp, CultureInfo.InvariantCulture) / 1000;
label = alignable_annotation.FirstChild.InnerText;
AnnoScheme.Label l = new AnnoScheme.Label(label, Colors.Black);
if (scheme.Type == AnnoScheme.TYPE.DISCRETE && scheme.Labels.Find(x => x.Name == label) == null)
{
scheme.Labels.Add(l);
}
duration = end - start;
al.AddSorted(new AnnoListItem(start, duration, label, "", Colors.Black));
//The tier is used as metainformation as well. Might be changed if thats relevant in the future
}
i++;
al.Scheme = scheme;
al.Meta.Role = role;
al.Scheme.Name = tierid;
list.Add(al);
}
}
catch (Exception ex)
{
MessageTools.Error(ex.ToString());
}
return(list);
}
public static AnnoList LoadFromEventFile(String filepath)
{
AnnoList list = new AnnoList();
try
{
XDocument doc = XDocument.Load(filepath);
var events = doc.Descendants("event");
//list.Scheme.Type = AnnoScheme.TYPE.DISCRETE;
//list.Scheme.Labels = new List<AnnoScheme.Label>();
foreach (var e in events)
{
string label = null;
string meta = "";
double start = -1;
double duration = -1;
Type type = Type.EMPTY;
var sender_attr = e.Attribute("sender");
var event_attr = e.Attribute("event");
label = (event_attr == null ? "" : event_attr.Value);
//+ "@"
//+ (sender_attr == null ? "" : sender_attr.Value);
var from_attr = e.Attribute("from");
if (from_attr != null)
{
start = double.Parse(from_attr.Value) / 1000.0;
}
var dur_attr = e.Attribute("dur");
if (dur_attr != null)
{
duration = double.Parse(dur_attr.Value) / 1000.0;
}
var type_attr = e.Attribute("type");
if (type_attr != null)
{
switch (type_attr.Value)
{
case "MAP":
type = Type.MAP;
break;
case "TUPLE":
type = Type.TUPLE;
break;
case "STRING":
type = Type.STRING;
break;
//depricated, matched to tuple
case "FLOATS":
type = Type.TUPLE;
break;
//depricated, matched to map
case "NTUPLE":
type = Type.MAP;
break;
}
}
switch (type)
{
case Type.MAP:
var tuples = e.Descendants("tuple");
foreach (var tuple in tuples)
{
var string_attr = tuple.Attribute("string");
var value_attr = tuple.Attribute("value");
meta = meta + ((string_attr == null ? "" : string_attr.Value)
+ "="
+ (value_attr == null ? "" : value_attr.Value)) + ";";
}
break;
case Type.STRING:
if (e.Value != "")
{
label = e.Value;
}
break;
case Type.TUPLE:
meta = e.Value == null ? "" : e.Value;
break;
}
AnnoScheme.Label asl = new AnnoScheme.Label(label, Colors.Black);
if (!list.Scheme.Labels.Any(item => item.Name == asl.Name))
{
list.Scheme.Labels.Add(asl);
}
var state_attr = e.Attribute("state");
if (state_attr.Value.ToString().ToUpper() == "COMPLETED")
{
Color color = Colors.Black;
//if (list.Scheme.Labels.Find(x => x.Name == label) != null)
//{
// color = list.Scheme.Labels.Find(x => x.Name == label).Color;
//}
list.AddSorted(new AnnoListItem(start, duration, label, meta, color));
}
}
}
catch (Exception ex)
{
MessageTools.Error(ex.ToString());
}
//AnnoScheme.Label garbage = new AnnoScheme.Label("GARBAGE", Colors.Black);
//list.Scheme.Labels.Add(garbage);
return(list);
}
public static AnnoList LoadfromFile(string filepath)
{
AnnoList list = new AnnoList();
list.Source.File.Path = filepath;
list.Scheme = new AnnoScheme();
list.Scheme.Labels = new List <AnnoScheme.Label>();
//try
{
XmlDocument doc = new XmlDocument();
doc.Load(filepath);
XmlNode annotation = doc.SelectSingleNode("annotation");
XmlNode info = annotation.SelectSingleNode("info");
list.Source.File.Type = info.Attributes["ftype"].Value == AnnoSource.FileSource.TYPE.ASCII.ToString() ? AnnoSource.FileSource.TYPE.ASCII : AnnoSource.FileSource.TYPE.BINARY;
int size = int.Parse(info.Attributes["size"].Value);
XmlNode meta = annotation.SelectSingleNode("meta");
if (meta != null)
{
if (meta.Attributes["role"] != null)
{
list.Meta.Role = meta.Attributes["role"].Value;
}
if (meta.Attributes["annotator"] != null)
{
list.Meta.Annotator = meta.Attributes["annotator"].Value;
}
}
XmlNode scheme = annotation.SelectSingleNode("scheme");
if (scheme.Attributes["name"] != null)
{
list.Scheme.Name = scheme.Attributes["name"].Value;
}
string type = "FREE";
if (scheme.Attributes["type"] != null)
{
type = scheme.Attributes["type"].Value;
}
if (type == AnnoScheme.TYPE.DISCRETE.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.DISCRETE;
}
else if (type == AnnoScheme.TYPE.CONTINUOUS.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.CONTINUOUS;
}
else if (type == AnnoScheme.TYPE.FREE.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.FREE;
}
else if (type == AnnoScheme.TYPE.POINT.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.POINT;
}
else if (type == AnnoScheme.TYPE.POLYGON.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.POLYGON;
}
else if (type == AnnoScheme.TYPE.GRAPH.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.GRAPH;
}
else if (type == AnnoScheme.TYPE.SEGMENTATION.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.SEGMENTATION;
}
if (scheme.Attributes["color"] != null)
{
list.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["color"].Value);
}
else if (scheme.Attributes["mincolor"] != null)
{
list.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["mincolor"].Value);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.MinOrBackColor = Defaults.Colors.GradientMin;
}
if (scheme.Attributes["maxcolor"] != null)
{
list.Scheme.MaxOrForeColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["maxcolor"].Value);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.MaxOrForeColor = Defaults.Colors.GradientMax;
}
Dictionary <string, string> LabelIds = new Dictionary <string, string>();
if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
foreach (XmlNode item in scheme)
{
LabelIds.Add(item.Attributes["id"].Value, item.Attributes["name"].Value);
Color color = Defaults.Colors.Foreground;
if (item.Attributes["color"] != null)
{
color = (Color)ColorConverter.ConvertFromString(item.Attributes["color"].Value);
}
AnnoScheme.Label lcp = new AnnoScheme.Label(item.Attributes["name"].Value, color);
list.Scheme.Labels.Add(lcp);
}
AnnoScheme.Label garbage = new AnnoScheme.Label("GARBAGE", Defaults.Colors.Foreground);
list.Scheme.Labels.Add(garbage);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.MinScore = double.Parse(scheme.Attributes["min"].Value);
list.Scheme.MaxScore = double.Parse(scheme.Attributes["max"].Value);
list.Scheme.SampleRate = double.Parse(scheme.Attributes["sr"].Value);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.POINT ||
list.Scheme.Type == AnnoScheme.TYPE.POLYGON || list.Scheme.Type == AnnoScheme.TYPE.GRAPH ||
list.Scheme.Type == AnnoScheme.TYPE.SEGMENTATION)
{
list.Scheme.SampleRate = double.Parse(scheme.Attributes["sr"].Value);
list.Scheme.NumberOfPoints = int.Parse(scheme.Attributes["num"].Value);
}
if (File.Exists(filepath + "~"))
{
if (list.Source.File.Type == AnnoSource.FileSource.TYPE.ASCII)
{
StreamReader sr = new StreamReader(filepath + "~", System.Text.Encoding.UTF8);
string line = null;
double start = 0.0;
while ((line = sr.ReadLine()) != null)
{
string[] data = line.Split(';');
if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
double value = double.NaN;
double.TryParse(data[0], out value);
double confidence = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
AnnoListItem e = new AnnoListItem(start, 1 / list.Scheme.SampleRate, value, "", Defaults.Colors.Foreground, confidence);
list.Add(e);
start = start + 1 / list.Scheme.SampleRate;
}
else if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double stop = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
double dur = stop - start;
string label = "";
if (int.Parse(data[2]) < 0)
{
label = "GARBAGE";
}
else
{
LabelIds.TryGetValue(data[2], out label);
}
Color color = Colors.Black;
if (list.Scheme.Labels.Find(x => x.Name == label) != null)
{
color = list.Scheme.Labels.Find(x => x.Name == label).Color;
}
double confidence = Convert.ToDouble(data[3], CultureInfo.InvariantCulture);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double stop = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
double dur = stop - start;
string label = data[2];
double confidence = Convert.ToDouble(data[3], CultureInfo.InvariantCulture);
Color color = Colors.Black;
if (data.Length > 4)
{
string[] metapairs = data[4].Split('=');
for (int i = 0; i < metapairs.Length; i++)
{
if (metapairs[i].Contains("color"))
{
color = (Color)ColorConverter.ConvertFromString(metapairs[i + 1]);
break;
}
}
}
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.POINT)
{
string frameLabel = data[0];
double frameConfidence = Convert.ToDouble(data[data.Count() - 1], CultureInfo.InvariantCulture);
PointList points = new PointList();
for (int i = 1; i < data.Count() - 1; ++i)
{
string pd = data[i].Replace("(", "");
pd = pd.Replace(")", "");
string[] pointData = pd.Split(':');
points.Add(new PointListItem(double.Parse(pointData[1]), double.Parse(pointData[2]), pointData[0], double.Parse(pointData[3])));
}
AnnoListItem ali = new AnnoListItem(start, 1 / list.Scheme.SampleRate, frameLabel, "", list.Scheme.MinOrBackColor, frameConfidence, true, points);
list.Add(ali);
start = start + 1 / list.Scheme.SampleRate;
}
}
sr.Close();
}
else if (list.Source.File.Type == AnnoSource.FileSource.TYPE.BINARY)
{
BinaryReader binaryReader = new BinaryReader(File.Open(filepath + "~", FileMode.Open));
long length = (binaryReader.BaseStream.Length);
double start = 0.0;
while (binaryReader.BaseStream.Position < binaryReader.BaseStream.Length)
{
if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
double value = (double)binaryReader.ReadSingle();
double confidence = (double)binaryReader.ReadSingle();
AnnoListItem e = new AnnoListItem(start, 1 / list.Scheme.SampleRate, value, "", Defaults.Colors.Foreground, confidence);
list.Add(e);
start = start + 1 / list.Scheme.SampleRate;
}
else if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
start = binaryReader.ReadDouble();
double stop = binaryReader.ReadDouble();
double dur = stop - start;
string label = "";
int index = binaryReader.ReadInt32();
if (index < 0)
{
label = "GARBAGE";
}
else
{
LabelIds.TryGetValue(index.ToString(), out label);
}
Color color = Colors.Black;
if (list.Scheme.Labels.Find(x => x.Name == label) != null)
{
color = list.Scheme.Labels.Find(x => x.Name == label).Color;
}
double confidence = Math.Round(binaryReader.ReadSingle(), 3, MidpointRounding.AwayFromZero);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
start = binaryReader.ReadDouble();
double stop = binaryReader.ReadDouble();
double dur = stop - start;
int stringlength = (int)binaryReader.ReadUInt32();
byte[] labelasbytes = (binaryReader.ReadBytes(stringlength));
string label = System.Text.Encoding.Default.GetString(labelasbytes);
Color color = Colors.Black;
double confidence = Math.Round(binaryReader.ReadSingle(), 3, MidpointRounding.AwayFromZero);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
}
binaryReader.Close();
}
}
//Plugin logic should be called after parsing
if (meta != null && meta.Attributes["trigger"] != null)
{
string[] triggers = meta.Attributes["trigger"].Value.Split(';');
foreach (string trigger in triggers)
{
try
{
Match match = Regex.Match(trigger, @"([^{]+)\{([^}]*)\}");
if (match.Success && match.Groups.Count == 3)
{
string dllName = match.Groups[1].Value;
string arguments = match.Groups[2].Value;
Dictionary <string, object> args = arguments.Split(new[] { ',' }, StringSplitOptions.RemoveEmptyEntries)
.Select(part => part.Split('='))
.ToDictionary(split => split[0], split => (object)split[1]);
PluginCaller pluginCaller = new PluginCaller(dllName + ".dll", dllName);
AnnoTrigger annoTrigger = new AnnoTrigger(list, pluginCaller, args);
list.Meta.Trigger.Add(annoTrigger);
}
else
{
MessageTools.Warning("could not parse trigger '" + trigger + "'");
}
}
catch (Exception)
{
MessageTools.Warning("could not parse trigger '" + trigger + "'");
}
}
}
if (meta != null && meta.Attributes["pipeline"] != null)
{
string[] pipelines = meta.Attributes["pipeline"].Value.Split(';');
foreach (string pipeline in pipelines)
{
try
{
Pipeline pipe = new Pipeline(list, pipeline);
list.Meta.Pipeline.Add(pipe);
}
catch (Exception)
{
MessageTools.Warning("could not parse pipeline '" + pipeline + "'");
}
}
}
}
//catch(Exception e)
//{
// MessageBox.Show("An exception occured while reading annotation from '" + filepath + "'");
//}
return(list);
}
public static AnnoList LoadFromEventFile(String filepath)
{
AnnoList list = new AnnoList();
try
{
XDocument doc = XDocument.Load(filepath);
var events = doc.Descendants("event");
foreach (var e in events)
{
string label = null;
string meta = "";
double start = -1;
double duration = -1;
Type type = Type.EMPTY;
var sender_attr = e.Attribute("sender");
var event_attr = e.Attribute("event");
label = (event_attr == null ? "" : event_attr.Value);
//+ "@"
//+ (sender_attr == null ? "" : sender_attr.Value);
var from_attr = e.Attribute("from");
if (from_attr != null)
{
start = double.Parse(from_attr.Value) / 1000.0;
}
var dur_attr = e.Attribute("dur");
if (dur_attr != null)
{
duration = double.Parse(dur_attr.Value) / 1000.0;
}
var type_attr = e.Attribute("type");
if (type_attr != null)
{
switch (type_attr.Value)
{
case "MAP":
type = Type.MAP;
break;
case "TUPLE":
type = Type.TUPLE;
break;
case "STRING":
type = Type.STRING;
break;
//depricated, matched to tuple
case "FLOATS":
type = Type.TUPLE;
break;
//depricated, matched to map
case "NTUPLE":
type = Type.MAP;
break;
}
}
switch (type)
{
case Type.MAP:
var tuples = e.Descendants("tuple");
foreach (var tuple in tuples)
{
var string_attr = tuple.Attribute("string");
var value_attr = tuple.Attribute("value");
meta = meta + ((string_attr == null ? "" : string_attr.Value)
+ "="
+ (value_attr == null ? "" : value_attr.Value)) + ";";
}
break;
case Type.STRING:
if (e.Value != "")
{
label = e.Value;
}
break;
case Type.TUPLE:
meta = e.Value == null ? "" : e.Value;
break;
}
var state_attr = e.Attribute("state");
if (state_attr.Value.ToString().ToUpper() == "COMPLETED")
{
list.AddSorted(new AnnoListItem(start, duration, label, meta));
}
}
}
catch (Exception ex)
{
MessageTools.Error(ex.ToString());
}
return(list);
}
public static AnnoList LoadfromFile(string filepath)
{
AnnoList list = new AnnoList();
list.Source.File.Path = filepath;
list.Scheme = new AnnoScheme();
list.Scheme.Labels = new List <AnnoScheme.Label>();
try
{
XmlDocument doc = new XmlDocument();
doc.Load(filepath);
XmlNode annotation = doc.SelectSingleNode("annotation");
XmlNode info = annotation.SelectSingleNode("info");
list.Source.File.Type = info.Attributes["ftype"].Value == AnnoSource.FileSource.TYPE.ASCII.ToString() ? AnnoSource.FileSource.TYPE.ASCII : AnnoSource.FileSource.TYPE.BINARY;
int size = int.Parse(info.Attributes["size"].Value);
XmlNode meta = annotation.SelectSingleNode("meta");
if (meta != null)
{
if (meta.Attributes["role"] != null)
{
list.Meta.Role = meta.Attributes["role"].Value;
}
if (meta.Attributes["annotator"] != null)
{
list.Meta.Annotator = meta.Attributes["annotator"].Value;
}
}
XmlNode scheme = annotation.SelectSingleNode("scheme");
if (scheme.Attributes["name"] != null)
{
list.Scheme.Name = scheme.Attributes["name"].Value;
}
string type = "FREE";
if (scheme.Attributes["type"] != null)
{
type = scheme.Attributes["type"].Value;
}
if (type == AnnoScheme.TYPE.DISCRETE.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.DISCRETE;
}
else if (type == AnnoScheme.TYPE.CONTINUOUS.ToString())
{
list.Scheme.Type = AnnoScheme.TYPE.CONTINUOUS;
}
else
{
list.Scheme.Type = AnnoScheme.TYPE.FREE;
}
if (scheme.Attributes["color"] != null)
{
list.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["color"].Value);
}
else if (scheme.Attributes["mincolor"] != null)
{
list.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["mincolor"].Value);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.MinOrBackColor = Colors.Orange;
}
if (scheme.Attributes["maxcolor"] != null)
{
list.Scheme.MaxOrForeColor = (Color)ColorConverter.ConvertFromString(scheme.Attributes["maxcolor"].Value);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.MaxOrForeColor = Colors.LightBlue;
}
Dictionary <string, string> LabelIds = new Dictionary <string, string>();
if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
foreach (XmlNode item in scheme)
{
LabelIds.Add(item.Attributes["id"].Value, item.Attributes["name"].Value);
Color color = Colors.Black;
if (item.Attributes["color"] != null)
{
color = (Color)ColorConverter.ConvertFromString(item.Attributes["color"].Value);
}
AnnoScheme.Label lcp = new AnnoScheme.Label(item.Attributes["name"].Value, color);
list.Scheme.Labels.Add(lcp);
}
AnnoScheme.Label garbage = new AnnoScheme.Label("GARBAGE", Colors.Black);
list.Scheme.Labels.Add(garbage);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
}
else if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
list.Scheme.SampleRate = double.Parse(scheme.Attributes["sr"].Value);
list.Scheme.MinScore = double.Parse(scheme.Attributes["min"].Value);
list.Scheme.MaxScore = double.Parse(scheme.Attributes["max"].Value);
}
if (File.Exists(filepath + "~"))
{
if (list.Source.File.Type == AnnoSource.FileSource.TYPE.ASCII)
{
StreamReader sr = new StreamReader(filepath + "~", System.Text.Encoding.Default);
string line = null;
double start = 0.0;
while ((line = sr.ReadLine()) != null)
{
string[] data = line.Split(';');
if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
string value = data[0];
double confidence = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
AnnoListItem e = new AnnoListItem(start, (1000.0 / list.Scheme.SampleRate) / 1000.0, value, "", Colors.Black, confidence);
list.Add(e);
start = start + (1000.0 / list.Scheme.SampleRate) / 1000.0;
}
else if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double stop = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
double dur = stop - start;
string label = "";
if (int.Parse(data[2]) < 0)
{
label = "GARBAGE";
}
else
{
LabelIds.TryGetValue(data[2], out label);
}
Color color = Colors.Black;
if (list.Scheme.Labels.Find(x => x.Name == label) != null)
{
color = list.Scheme.Labels.Find(x => x.Name == label).Color;
}
double confidence = Convert.ToDouble(data[3], CultureInfo.InvariantCulture);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
start = Convert.ToDouble(data[0], CultureInfo.InvariantCulture);
double stop = Convert.ToDouble(data[1], CultureInfo.InvariantCulture);
double dur = stop - start;
string label = data[2];
double confidence = Convert.ToDouble(data[3], CultureInfo.InvariantCulture);
Color color = Colors.Black;
if (data.Length > 4)
{
string[] metapairs = data[4].Split('=');
for (int i = 0; i < metapairs.Length; i++)
{
if (metapairs[i].Contains("color"))
{
color = (Color)ColorConverter.ConvertFromString(metapairs[i + 1]);
break;
}
}
}
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
}
sr.Close();
}
else if (list.Source.File.Type == AnnoSource.FileSource.TYPE.BINARY)
{
BinaryReader binaryReader = new BinaryReader(File.Open(filepath + "~", FileMode.Open));
long length = (binaryReader.BaseStream.Length);
double start = 0.0;
while (binaryReader.BaseStream.Position < binaryReader.BaseStream.Length)
{
if (list.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
string value = binaryReader.ReadSingle().ToString();
double confidence = (double)binaryReader.ReadSingle();
AnnoListItem e = new AnnoListItem(start, (1000.0 / list.Scheme.SampleRate) / 1000.0, value, "", Colors.Black, confidence);
list.Add(e);
start = start + (1000.0 / list.Scheme.SampleRate) / 1000.0;
}
else if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
start = binaryReader.ReadDouble();
double stop = binaryReader.ReadDouble();
double dur = stop - start;
string label = "";
int index = binaryReader.ReadInt32();
if (index < 0)
{
label = "GARBAGE";
}
else
{
LabelIds.TryGetValue(index.ToString(), out label);
}
Color color = Colors.Black;
if (list.Scheme.Labels.Find(x => x.Name == label) != null)
{
color = list.Scheme.Labels.Find(x => x.Name == label).Color;
}
double confidence = Math.Round(binaryReader.ReadSingle(), 3, MidpointRounding.AwayFromZero);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
start = binaryReader.ReadDouble();
double stop = binaryReader.ReadDouble();
double dur = stop - start;
int stringlength = (int)binaryReader.ReadUInt32();
byte[] labelasbytes = (binaryReader.ReadBytes(stringlength));
string label = System.Text.Encoding.Default.GetString(labelasbytes);
Color color = Colors.Black;
double confidence = Math.Round(binaryReader.ReadSingle(), 3, MidpointRounding.AwayFromZero);
AnnoListItem e = new AnnoListItem(start, dur, label, "", color, confidence);
list.AddSorted(e);
}
}
binaryReader.Close();
}
}
else
{
MessageBox.Show("Annotation data was not found, load scheme only from '" + filepath + "'");
}
list.HasChanged = false;
}
catch (Exception e)
{
MessageBox.Show("An exception occured while reading annotation from '" + filepath + "'");
}
return(list);
}
public static List <AnnoList> LoadFromDatabase(System.Collections.IList collections, string databaseName, string sessionName, string userName)
{
MongoClient mongo = new MongoClient(ServerConnectionString);
IMongoDatabase database = mongo.GetDatabase(databaseName);
var collection = database.GetCollection <BsonDocument>(DatabaseDefinitionCollections.Annotations);
var roles = database.GetCollection <BsonDocument>(DatabaseDefinitionCollections.Roles);
var annoSchemes = database.GetCollection <BsonDocument>(DatabaseDefinitionCollections.Schemes);
List <AnnoList> annoLists = new List <AnnoList>();
foreach (DatabaseAnno anno in collections)
{
BsonElement value;
AnnoList annoList = new AnnoList();
ObjectId roleid = GetObjectID(database, DatabaseDefinitionCollections.Roles, "name", anno.Role);
string roledb = FetchDBRef(database, DatabaseDefinitionCollections.Roles, "name", roleid);
ObjectId annoSchemeId = GetObjectID(database, DatabaseDefinitionCollections.Schemes, "name", anno.AnnoScheme);
string annotdb = FetchDBRef(database, DatabaseDefinitionCollections.Schemes, "name", annoSchemeId);
ObjectId annotatorId = GetObjectID(database, DatabaseDefinitionCollections.Annotators, "fullname", anno.AnnotatorFullname);
string annotatdb = FetchDBRef(database, DatabaseDefinitionCollections.Annotators, "name", annotatorId);
string annotatdbfn = FetchDBRef(database, DatabaseDefinitionCollections.Annotators, "fullname", annotatorId);
annoList.Meta.Annotator = annotatdb;
annoList.Meta.AnnotatorFullName = annotatdbfn;
ObjectId sessionid = GetObjectID(database, DatabaseDefinitionCollections.Sessions, "name", sessionName);
string sessiondb = FetchDBRef(database, DatabaseDefinitionCollections.Sessions, "name", sessionid);
var builder = Builders <BsonDocument> .Filter;
var filterscheme = builder.Eq("_id", annoSchemeId);
var result = collection.Find(filterscheme);
var annosch = annoSchemes.Find(filterscheme).Single();
var filter = builder.Eq("role_id", roleid) & builder.Eq("scheme_id", annoSchemeId) & builder.Eq("annotator_id", annotatorId) & builder.Eq("session_id", sessionid);
var documents = collection.Find(filter).ToList();
annoList.Scheme = new AnnoScheme();
if (annosch.TryGetElement("type", out value) && annosch["type"].ToString() == AnnoScheme.TYPE.DISCRETE.ToString())
{
annoList.Scheme.Type = AnnoScheme.TYPE.DISCRETE;
}
else if (annosch.TryGetElement("type", out value) && annosch["type"].ToString() == AnnoScheme.TYPE.FREE.ToString())
{
annoList.Scheme.Type = AnnoScheme.TYPE.FREE;
}
else if (annosch.TryGetElement("type", out value) && annosch["type"].ToString() == AnnoScheme.TYPE.CONTINUOUS.ToString())
{
annoList.Scheme.Type = AnnoScheme.TYPE.CONTINUOUS;
}
annoList.Meta.Role = roledb;
annoList.Scheme.Name = annosch["name"].ToString();
var labels = documents[0]["labels"].AsBsonArray;
if (annoList.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
if (annosch.TryGetElement("min", out value))
{
annoList.Scheme.MinScore = double.Parse(annosch["min"].ToString());
}
if (annosch.TryGetElement("max", out value))
{
annoList.Scheme.MaxScore = double.Parse(annosch["max"].ToString());
}
if (annosch.TryGetElement("sr", out value))
{
annoList.Scheme.SampleRate = double.Parse(annosch["sr"].ToString());
}
if (annosch.TryGetElement("min_color", out value))
{
annoList.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annosch["min_color"].ToString());
}
if (annosch.TryGetElement("max_color", out value))
{
annoList.Scheme.MaxOrForeColor = (Color)ColorConverter.ConvertFromString(annosch["max_color"].ToString());
}
annoList.Scheme.MinScore = annoList.Scheme.MinScore;
annoList.Scheme.MaxScore = annoList.Scheme.MaxScore;
annoList.Scheme.SampleRate = annoList.Scheme.SampleRate;
for (int i = 0; i < labels.Count; i++)
{
string label = labels[i]["score"].ToString();
string confidence = labels[i]["conf"].ToString();
double start = i * ((1000.0 / annoList.Scheme.SampleRate) / 1000.0);
double dur = (1000.0 / annoList.Scheme.SampleRate) / 1000.0;
AnnoListItem ali = new AnnoListItem(start, dur, label, "", Colors.Black, double.Parse(confidence));
annoList.Add(ali);
}
}
else if (annoList.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
annoList.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annosch["color"].ToString());
annoList.Scheme.Labels = new List <AnnoScheme.Label>();
BsonArray schemelabels = annosch["labels"].AsBsonArray;
for (int j = 0; j < schemelabels.Count; j++)
{
//in case flag is set, if not ignore isValid
try
{
if (schemelabels[j]["isValid"].AsBoolean == true)
{
annoList.Scheme.Labels.Add(new AnnoScheme.Label(schemelabels[j]["name"].ToString(), (Color)ColorConverter.ConvertFromString(schemelabels[j]["color"].ToString())));
}
}
catch
{
annoList.Scheme.Labels.Add(new AnnoScheme.Label(schemelabels[j]["name"].ToString(), (Color)ColorConverter.ConvertFromString(schemelabels[j]["color"].ToString())));
}
}
annoList.Scheme.Labels.Add(new AnnoScheme.Label(GARBAGELABEL, GARBAGECOLOR));
for (int i = 0; i < labels.Count; i++)
{
string SchemeLabel = "";
Color SchemeColor = Colors.Black;
bool idfound = false;
for (int j = 0; j < schemelabels.Count; j++)
{
if (labels[i]["id"].AsInt32 == schemelabels[j]["id"].AsInt32)
{
SchemeLabel = schemelabels[j]["name"].ToString();
SchemeColor = (Color)ColorConverter.ConvertFromString(schemelabels[j]["color"].ToString());
idfound = true;
break;
}
}
if (labels[i]["id"].AsInt32 == -1 || idfound == false)
{
SchemeLabel = GARBAGELABEL;
SchemeColor = GARBAGECOLOR;
}
double start = double.Parse(labels[i]["from"].ToString());
double stop = double.Parse(labels[i]["to"].ToString());
double duration = stop - start;
string label = SchemeLabel;
string confidence = labels[i]["conf"].ToString();
AnnoListItem ali = new AnnoListItem(start, duration, label, "", SchemeColor, double.Parse(confidence));
annoList.AddSorted(ali);
}
}
else if (annoList.Scheme.Type == AnnoScheme.TYPE.FREE)
{
annoList.Scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annosch["color"].ToString());
for (int i = 0; i < labels.Count; i++)
{
double start = double.Parse(labels[i]["from"].ToString());
double stop = double.Parse(labels[i]["to"].ToString());
double duration = stop - start;
string label = labels[i]["name"].ToString();
string confidence = labels[i]["conf"].ToString();
AnnoListItem ali = new AnnoListItem(start, duration, label, "", Colors.Black, double.Parse(confidence));
annoList.AddSorted(ali);
}
}
annoList.Source.Database.OID = anno.Id;
annoLists.Add(annoList);
annoList = null;
}
return(annoLists);
}
