private AnnoList ConvertDiscreteAnnoListToContinuousList(AnnoList annolist, double chunksize, double end, string restclass = "Rest")
{
AnnoList result = new AnnoList();
result.Scheme = annolist.Scheme;
result.Meta = annolist.Meta;
double currentpos = 0;
bool foundlabel = false;
while (currentpos < end)
{
foundlabel = false;
foreach (AnnoListItem orgitem in annolist)
{
if (orgitem.Start * 1000 < currentpos && orgitem.Stop * 1000 > currentpos)
{
AnnoListItem ali = new AnnoListItem(currentpos, chunksize, orgitem.Label);
result.Add(ali);
foundlabel = true;
break;
}
}
if (foundlabel == false)
{
AnnoListItem ali = new AnnoListItem(currentpos, chunksize, restclass);
result.Add(ali);
}
currentpos = currentpos + chunksize;
}
return(result);
}
private AnnoList ResampleContinuousList(AnnoList annolist, double targetsr)
{
double sr = annolist.Scheme.SampleRate;
if (sr == targetsr)
{
return(annolist);
}
AnnoList result = new AnnoList();
result.Scheme = annolist.Scheme;
result.Meta = annolist.Meta;
//upsample
if (sr < targetsr)
{
double factor = targetsr / sr;
double round = Math.Round(factor);
if (factor - round == 0)
{
for (int i = 0; i < annolist.Count; i++)
{
for (int j = 0; j < round; j++)
{
AnnoListItem ali = new AnnoListItem(annolist[i].Start + j * (1.0 / round), (1.0 / round), annolist[i].Score);
result.Add(ali);
}
}
}
else
{
return(null);
}
}
//downsample
else if (sr > targetsr)
{
double factor = sr / targetsr;
double round = Math.Round(factor);
for (int i = 0; i < annolist.Count; i = i + (int)round)
{
result.Add(annolist[i]);
}
}
return(result);
}
public static AnnoList ConvertFreetoDiscreteAnnotation(AnnoList list)
{
if (list.Scheme.Type != AnnoScheme.TYPE.FREE)
{
return(list);
}
AnnoList al = new AnnoList();
AnnoScheme scheme = new AnnoScheme();
scheme.Type = AnnoScheme.TYPE.DISCRETE;
foreach (AnnoListItem ali in list)
{
al.Add(ali);
if (scheme.Labels.Find(x => x.Name == ali.Label) == null)
{
AnnoScheme.Label l = new AnnoScheme.Label(ali.Label, Colors.Black);
scheme.Labels.Add(l);
}
}
scheme.Name = list.Scheme.Name;
al.Scheme = scheme;
al.Meta = list.Meta;
return(al);
}
public AnnoList ExportToAnno()
{
AnnoList annoList = new AnnoList();
annoList.Scheme = new AnnoScheme();
annoList.Scheme.Type = AnnoScheme.TYPE.CONTINUOUS;
annoList.Scheme.MinScore = min[ShowDim];
annoList.Scheme.MaxScore = max[ShowDim];
annoList.Scheme.SampleRate = rate;
AnnoListItem annoListItem;
double dur = 1 / rate;
for (int i = 0; i < number; i++)
{
annoListItem = new AnnoListItem(i * dur, dur, data[i * dim + ShowDim].ToString(), "", annoList.Scheme.MaxOrForeColor);
annoList.Add(annoListItem);
annoList.Scheme.Name = Name;
}
return(annoList);
}
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 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);
}
private void ExportAnnoContinuousToDiscrete()
{
if (AnnoTierStatic.Selected != null && !AnnoTierStatic.Selected.IsDiscreteOrFree)
{
Dictionary <string, UserInputWindow.Input> input = new Dictionary <string, UserInputWindow.Input>();
input["labels"] = new UserInputWindow.Input()
{
Label = "Class labels (separated by ;)", DefaultValue = Properties.Settings.Default.ConvertToDiscreteClasses
};
input["thresholds"] = new UserInputWindow.Input()
{
Label = "Upper thresholds (separated by ;)", DefaultValue = Properties.Settings.Default.ConvertToDiscreteThreshs
};
input["offset"] = new UserInputWindow.Input()
{
Label = "Optional offset (s)", DefaultValue = Properties.Settings.Default.ConvertToDiscreteDelays
};
UserInputWindow dialog = new UserInputWindow("Convert to discrete annotation", input);
dialog.ShowDialog();
List <string> classes = new List <string>();
List <double> upperThresholds = new List <double>();
double offset = 0.0;
if (dialog.DialogResult == true)
{
Properties.Settings.Default.ConvertToDiscreteClasses = dialog.Result("labels");
Properties.Settings.Default.ConvertToDiscreteThreshs = dialog.Result("thresholds");
Properties.Settings.Default.ConvertToDiscreteDelays = dialog.Result("offset");
Properties.Settings.Default.Save();
string[] labels = dialog.Result("labels").Split(';');
for (int i = 0; i < labels.Length; i++)
{
classes.Add(labels[i]);
}
string[] thresholds = dialog.Result("thresholds").Split(';');
for (int i = 0; i < thresholds.Length; i++)
{
double thresh = -1;
double.TryParse(thresholds[i], out thresh);
if (thresh > -1)
{
upperThresholds.Add(thresh);
}
else
{
MessageTools.Warning("Could not parse input");
}
}
if (thresholds.Length == labels.Length - 1)
{
upperThresholds.Add(1.0);
}
else if (thresholds.Length == labels.Length + 1)
{
classes.Add("REST");
}
else if (thresholds.Length != labels.Length)
{
MessageBox.Show("Number of labels does not match number of threshholds");
}
double.TryParse(dialog.Result("offset"), out offset);
}
Mouse.SetCursor(Cursors.No);
AnnoList discretevalues = new AnnoList();
discretevalues.Scheme = new AnnoScheme();
discretevalues.Scheme.Type = AnnoScheme.TYPE.DISCRETE;
discretevalues.Meta.Role = AnnoTier.Selected.AnnoList.Meta.Role;
discretevalues.Meta.Annotator = AnnoTier.Selected.AnnoList.Meta.Annotator;
discretevalues.Scheme.Name = AnnoTier.Selected.AnnoList.Scheme.Name;
foreach (string label in classes)
{
AnnoScheme.Label item = new AnnoScheme.Label(label, System.Windows.Media.Colors.Black);
discretevalues.Scheme.Labels.Add(item);
}
AnnoScheme.Label garbage = new AnnoScheme.Label("GARBAGE", Colors.Black);
discretevalues.Scheme.Labels.Add(garbage);
double lowThres = -Double.MaxValue;
double highThres = 1.0;
foreach (AnnoListItem ali in AnnoTierStatic.Selected.AnnoList)
{
double val = ali.Score;
for (int i = 0; i < classes.Count; i++)
{
highThres = upperThresholds[i];
if (i > 0)
{
lowThres = upperThresholds[i - 1];
}
else
{
lowThres = -Double.MaxValue;
}
if (val > lowThres && val <= highThres)
{
if (!(discretevalues.Count > 0 && discretevalues[discretevalues.Count - 1].Label == classes[i]))
{
AnnoListItem newItem = new AnnoListItem(ali.Start + offset, ali.Duration, classes[i], "", discretevalues.Scheme.GetColorForLabel(classes[i]));
if (newItem.Start < 0.0)
{
newItem.Duration = ali.Duration + offset + newItem.Start;
newItem.Start = 0.0;
newItem.Stop = newItem.Duration;
}
if (newItem.Duration > 0.0)
{
discretevalues.Add(newItem);
}
}
else
{
discretevalues[discretevalues.Count - 1].Stop = discretevalues[discretevalues.Count - 1].Stop + ali.Duration;
}
break;
}
}
}
AnnoTier.Unselect();
addAnnoTierFromList(discretevalues);
Mouse.SetCursor(System.Windows.Input.Cursors.Arrow);
}
else
{
MessageBox.Show("Tier is already discrete");
}
}
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);
}