private void databaseConnect()
{
Action EmptyDelegate = delegate() { };
control.ShadowBoxText.Text = "Connecting to Database...";
control.ShadowBox.Visibility = Visibility.Visible;
control.UpdateLayout();
control.Dispatcher.Invoke(DispatcherPriority.Render, EmptyDelegate);
bool isConnected = DatabaseHandler.Connect();
if (isConnected)
{
if (!DatabaseHandler.ChangeDatabase(Properties.Settings.Default.DatabaseName))
{
Properties.Settings.Default.DatabaseName = null;
Properties.Settings.Default.Save();
}
}
else
{
MessageTools.Warning("Unable to connect to database, please check your settings");
Properties.Settings.Default.DatabaseAutoLogin = false;
Properties.Settings.Default.Save();
}
updateNavigator();
control.ShadowBox.Visibility = Visibility.Collapsed;
control.ShadowBoxText.Text = "Loading Data...";
}
private void AnnoList_Drop(object sender, DragEventArgs e)
{
if (e.Data.GetDataPresent(DataFormats.FileDrop))
{
string[] filenames = e.Data.GetData(DataFormats.FileDrop, true) as string[];
if (filenames != null && filenames[0].EndsWith(".annotation"))
{
try
{
AnnoList list = AnnoList.LoadfromFile(filenames[0]);
if (list.Scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
foreach (var item in list.Scheme.Labels)
{
Label label = new Label()
{
Name = item.Name, Color = item.Color
};
if (!items.Contains(label) && label.Name != "GARBAGE" && label.Name != "")
{
items.Add(label);
}
}
}
else if (list.Scheme.Type == AnnoScheme.TYPE.FREE)
{
HashSet <string> labelNames = new HashSet <string>();
foreach (AnnoListItem item in list)
{
labelNames.Add(item.Label);
}
foreach (string name in labelNames)
{
Label label = new Label()
{
Name = name, Color = list.Scheme.MaxOrForeColor
};
if (!items.Contains(label) && label.Name != "GARBAGE" && label.Name != "")
{
items.Add(label);
}
}
}
else
{
return;
}
schemeNameTextField.Text = list.Scheme.Name;
backroundColorPicket.SelectedColor = list.Scheme.MinOrBackColor;
}
catch
{
MessageTools.Warning("This is not a valid annotation file");
}
}
}
}
private void ApplyButton_Click(object sender, RoutedEventArgs e)
{
if (DBHost.Text != "" && DBHost.Text != "")
{
if (Properties.Settings.Default.serverhistory == "")
{
Properties.Settings.Default.serverhistory = DBHost.Text + ":" + DBPort.Text;
}
else if (!Properties.Settings.Default.serverhistory.Contains(DBHost.Text + ":" + DBPort.Text))
{
Properties.Settings.Default.serverhistory = Properties.Settings.Default.serverhistory + ";" + DBHost.Text + ":" + DBPort.Text;
}
if (Properties.Settings.Default.DatabaseDirectory != DownloadDirectory.Text)
{
if (Directory.Exists(DownloadDirectory.Text))
{
Directory.CreateDirectory(DownloadDirectory.Text);
Properties.Settings.Default.DatabaseDirectory = DownloadDirectory.Text;
Properties.Settings.Default.Save();
}
else
{
MessageTools.Warning("Directory does not exist '" + DownloadDirectory.Text + "'");
return;
}
}
if (Properties.Settings.Default.CMLDirectory != CMLDirectory.Text)
{
if (Directory.Exists(CMLDirectory.Text))
{
Directory.CreateDirectory(CMLDirectory.Text);
Properties.Settings.Default.CMLDirectory = CMLDirectory.Text;
Properties.Settings.Default.Save();
}
else
{
MessageTools.Warning("Directory does not exist '" + CMLDirectory.Text + "'");
return;
}
}
DialogResult = true;
Close();
}
else
{
MessageBox.Show("Host and IP can't be empty!");
}
}
private void ApplyButton_Click(object sender, RoutedEventArgs e)
{
if (Properties.Settings.Default.DatabaseDirectory != DownloadDirectory.Text)
{
if (Directory.Exists(DownloadDirectory.Text))
{
Directory.CreateDirectory(DownloadDirectory.Text);
Properties.Settings.Default.DatabaseDirectory = DownloadDirectory.Text;
Properties.Settings.Default.Save();
}
else
{
MessageTools.Warning("Directory does not exist '" + DownloadDirectory.Text + "'");
return;
}
}
if (Properties.Settings.Default.CMLDirectory != CMLDirectory.Text)
{
if (Directory.Exists(CMLDirectory.Text))
{
Directory.CreateDirectory(CMLDirectory.Text);
Properties.Settings.Default.CMLDirectory = CMLDirectory.Text;
Properties.Settings.Default.Save();
}
else
{
MessageTools.Warning("Directory does not exist '" + CMLDirectory.Text + "'");
return;
}
}
DialogResult = true;
Close();
}
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);
}
private void addNewAnnotationDatabase()
{
if (Time.TotalDuration > 0)
{
string annoScheme = DatabaseHandler.SelectScheme();
if (annoScheme == null)
{
return;
}
string role = DatabaseHandler.SelectRole();
if (role == null)
{
return;
}
AnnoScheme scheme = DatabaseHandler.GetAnnotationScheme(annoScheme);
if (scheme == null)
{
return;
}
scheme.Labels.Add(new AnnoScheme.Label("GARBAGE", Colors.Black));
ObjectId annotatid = DatabaseHandler.GetObjectID(DatabaseDefinitionCollections.Annotators, "name", Properties.Settings.Default.MongoDBUser);
string annotator = Properties.Settings.Default.MongoDBUser;
// DatabaseHandler.FetchDBRef(DatabaseDefinitionCollections.Annotators, "fullname", annotatid);
AnnoList annoList;
if (DatabaseHandler.AnnotationExists(annotator, DatabaseHandler.SessionName, role, scheme.Name))
{
DatabaseAnnotation annotation = new DatabaseAnnotation()
{
Annotator = annotator,
Session = DatabaseHandler.SessionName,
Role = role,
Scheme = scheme.Name
};
annoList = DatabaseHandler.LoadAnnoList(annotation, false);
annoList.HasChanged = false;
}
else
{
annoList = new AnnoList();
annoList.Meta.Role = role;
annoList.Meta.Annotator = annotator;
string annotatorFullName = DatabaseHandler.GetUserInfo(annotator).Fullname;
annoList.Meta.AnnotatorFullName = annotatorFullName;
annoList.Scheme = scheme;
annoList.Source.StoreToDatabase = true;
annoList.Source.Database.Session = DatabaseHandler.SessionName;
annoList.HasChanged = true;
}
addAnnoTier(annoList);
control.annoListControl.editComboBox.SelectedIndex = 0;
}
else
{
MessageTools.Warning("Nothing to annotate, load some data first.");
}
}
public void ReloadAnnoTierFromDatabase(AnnoTier tier, bool loadBackup)
{
if (tier == null || tier.AnnoList == null)
{
return;
}
if (loadBackup && tier.AnnoList.Source.Database.DataBackupOID == AnnoSource.DatabaseSource.ZERO)
{
MessageTools.Warning("No backup exists");
return;
}
Action EmptyDelegate = delegate() { };
control.ShadowBoxText.Text = "Reloading Annotation";
control.ShadowBox.Visibility = Visibility.Visible;
control.UpdateLayout();
control.Dispatcher.Invoke(DispatcherPriority.Render, EmptyDelegate);
DatabaseAnnotation annotation = new DatabaseAnnotation();
annotation.Role = tier.AnnoList.Meta.Role;
annotation.Scheme = tier.AnnoList.Scheme.Name;
annotation.AnnotatorFullName = tier.AnnoList.Meta.AnnotatorFullName;
annotation.Annotator = tier.AnnoList.Meta.Annotator;
annotation.Session = DatabaseHandler.SessionName;
AnnoList annoList = DatabaseHandler.LoadAnnoList(annotation, loadBackup);
double maxdur = 0;
if (annoList != null && annoList.Count > 0 && annoList.Scheme.Type == AnnoScheme.TYPE.DISCRETE || annoList.Scheme.Type == AnnoScheme.TYPE.FREE)
{
maxdur = annoList[annoList.Count - 1].Stop;
setAnnoList(annoList);
tier.Children.Clear();
tier.AnnoList.Clear();
tier.segments.Clear();
tier.AnnoList = annoList;
foreach (AnnoListItem item in annoList)
{
tier.AddSegment(item);
}
tier.TimeRangeChanged(Time);
updateTimeRange(maxdur);
tier.AnnoList.HasChanged = false;
}
else if (annoList != null && annoList.Count > 0 && annoList.Scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
maxdur = annoList[annoList.Count - 1].Stop;
setAnnoList(annoList);
tier.AnnoList.Clear();
tier.AnnoList = annoList;
tier.TimeRangeChanged(Time);
updateTimeRange(maxdur);
AnnoTier.Selected.TimeRangeChanged(MainHandler.Time);
tier.AnnoList.HasChanged = false;
}
control.ShadowBox.Visibility = Visibility.Collapsed;
}
private void Extract()
{
if (ChainsBox.SelectedItem == null)
{
MessageTools.Warning("select a chain first");
return;
}
string featureName = FeatureNameTextBox.Text;
if (featureName == "" || featureName.IndexOfAny(Path.GetInvalidFileNameChars()) >= 0)
{
MessageTools.Warning("not a valid feature name");
return;
}
Chain chain = (Chain)ChainsBox.SelectedItem;
bool force = ForceCheckBox.IsChecked.Value;
if (!File.Exists(chain.Path))
{
MessageTools.Warning("file does not exist '" + chain.Path + "'");
return;
}
string database = DatabaseHandler.DatabaseName;
var sessions = SessionsBox.SelectedItems;
var roles = RolesBox.SelectedItems;
DatabaseStream stream = (DatabaseStream)StreamsBox.SelectedItem;
string leftContext = LeftContextTextBox.Text;
string frameStep = FrameStepTextBox.Text;
string rightContext = RightContextTextBox.Text;
int nParallel = 1;
int.TryParse(NParallelTextBox.Text, out nParallel);
logTextBox.Text = "";
// prepare lists
int nFiles = 0;
using (StreamWriter fileListIn = new StreamWriter(tempInListPath))
{
using (StreamWriter fileListOut = new StreamWriter(tempOutListPath))
{
foreach (DatabaseSession session in sessions)
{
foreach (DatabaseRole role in roles)
{
string fromPath = Properties.Settings.Default.DatabaseDirectory + "\\"
+ database + "\\"
+ session.Name + "\\"
+ role.Name + "." + stream.Name + "." + stream.FileExt;
string toPath = Path.GetDirectoryName(fromPath) + "\\"
+ role.Name + "." + featureName + ".stream";
if (force || !File.Exists(toPath))
{
nFiles++;
fileListIn.WriteLine(fromPath);
fileListOut.WriteLine(toPath);
}
else
{
logTextBox.Text += "skip " + fromPath + "\n";
}
}
}
}
}
// start feature extraction
Chain selectedChain = (Chain)ChainsBox.SelectedItem;
DatabaseStream selectedStream = (DatabaseStream)StreamsBox.SelectedItem;
if (nFiles > 0)
{
string type = Defaults.CML.StreamTypeNameFeature;
string name = featureName;
string ext = "stream";
double sr = frameStepToSampleRate(frameStep, stream.SampleRate);
DatabaseStream streamType = new DatabaseStream()
{
Name = name, Type = type, FileExt = ext, SampleRate = sr
};
DatabaseHandler.AddStream(streamType);
try
{
logTextBox.Text += handler.CMLExtractFeature(chain.Path, nParallel, tempInListPath, tempOutListPath, frameStep, leftContext, rightContext);
}
catch (Exception e) { MessageBox.Show("There was an error in the feature extaction pipeline: " + e); }
}
File.Delete(tempInListPath);
File.Delete(tempOutListPath);
GetStreams(selectedStream);
foreach (Chain item in ChainsBox.Items)
{
if (item.Name == selectedChain.Name)
{
ChainsBox.SelectedItem = item;
break;
}
}
}
private void Apply_Click(object sender, RoutedEventArgs e)
{
Trainer trainer = (Trainer)TrainerPathComboBox.SelectedItem;
bool force = mode == Mode.COMPLETE || ForceCheckBox.IsChecked.Value;
if (!File.Exists(trainer.Path))
{
MessageTools.Warning("file does not exist '" + trainer.Path + "'");
return;
}
string database = DatabaseHandler.DatabaseName;
DatabaseStream stream = (DatabaseStream)StreamsBox.SelectedItem;
string sessionList = "";
var sessions = SessionsBox.SelectedItems;
foreach (DatabaseSession session in sessions)
{
if (sessionList == "")
{
sessionList += session.Name;
}
else
{
sessionList += ";" + session.Name;
}
}
DatabaseScheme scheme = (DatabaseScheme)SchemesBox.SelectedItem;
string rolesList = "";
var roles = RolesBox.SelectedItems;
foreach (DatabaseRole role in roles)
{
if (rolesList == "")
{
rolesList += role.Name;
}
else
{
rolesList += ";" + role.Name;
}
}
DatabaseAnnotator annotator = (DatabaseAnnotator)AnnotatorsBox.SelectedItem;
string trainerLeftContext = LeftContextTextBox.Text;
string trainerRightContext = RightContextTextBox.Text;
string trainerBalance = ((ComboBoxItem)BalanceComboBox.SelectedItem).Content.ToString();
logTextBox.Text = "";
if (mode == Mode.TRAIN ||
mode == Mode.COMPLETE)
{
string streamName = "";
string[] streamParts = stream.Name.Split('.');
if (streamParts.Length <= 1)
{
streamName = stream.Name;
}
else
{
streamName = streamParts[1];
for (int i = 2; i < streamParts.Length; i++)
{
streamName += "." + streamParts[i];
}
}
string trainerDir = Properties.Settings.Default.CMLDirectory + "\\" +
Defaults.CML.ModelsFolderName + "\\" +
Defaults.CML.ModelsTrainerFolderName + "\\" +
scheme.Type.ToString().ToLower() + "\\" +
scheme.Name + "\\" +
stream.Type + "{" +
streamName + "}\\" +
trainer.Name + "\\";
Directory.CreateDirectory(trainerDir);
string trainerName = TrainerNameTextBox.Text == "" ? trainer.Name : TrainerNameTextBox.Text;
string trainerOutPath = mode == Mode.COMPLETE ? tempTrainerPath : trainerDir + trainerName;
if (force || !File.Exists(trainerOutPath + ".trainer"))
{
try
{
logTextBox.Text += handler.CMLTrainModel(trainer.Path,
trainerOutPath,
Properties.Settings.Default.DatabaseDirectory,
Properties.Settings.Default.DatabaseAddress,
Properties.Settings.Default.MongoDBUser,
MainHandler.Decode(Properties.Settings.Default.MongoDBPass),
database,
sessionList,
scheme.Name,
rolesList,
annotator.Name,
stream.Name,
trainerLeftContext,
trainerRightContext,
trainerBalance,
mode == Mode.COMPLETE);
}
catch (Exception ex)
{
logTextBox.Text += ex;
}
}
else
{
logTextBox.Text += "skip " + trainerOutPath + "\n";
}
}
if (mode == Mode.PREDICT ||
mode == Mode.COMPLETE)
{
if (true || force)
{
double confidence = -1.0;
if (ConfidenceCheckBox.IsChecked == true && ConfidenceTextBox.IsEnabled)
{
double.TryParse(ConfidenceTextBox.Text, out confidence);
Properties.Settings.Default.CMLDefaultConf = confidence;
}
double minGap = 0.0;
if (FillGapCheckBox.IsChecked == true && FillGapTextBox.IsEnabled)
{
double.TryParse(FillGapTextBox.Text, out minGap);
Properties.Settings.Default.CMLDefaultGap = minGap;
}
double minDur = 0.0;
if (RemoveLabelCheckBox.IsChecked == true && RemoveLabelTextBox.IsEnabled)
{
double.TryParse(RemoveLabelTextBox.Text, out minDur);
Properties.Settings.Default.CMLDefaultMinDur = minDur;
}
Properties.Settings.Default.Save();
try
{
logTextBox.Text += handler.CMLPredictAnnos(mode == Mode.COMPLETE ? tempTrainerPath : trainer.Path,
Properties.Settings.Default.DatabaseDirectory,
Properties.Settings.Default.DatabaseAddress,
Properties.Settings.Default.MongoDBUser,
MainHandler.Decode(Properties.Settings.Default.MongoDBPass),
database,
sessionList,
scheme.Name,
rolesList,
annotator.Name,
stream.Name,
trainerLeftContext,
trainerRightContext,
confidence,
minGap,
minDur,
mode == Mode.COMPLETE);
}
catch (Exception ex)
{
logTextBox.Text += ex;
}
}
}
if (mode == Mode.EVALUATE)
{
string evalOutPath = Properties.Settings.Default.CMLDirectory + "\\" + Path.GetFileNameWithoutExtension(Path.GetRandomFileName());
try
{
logTextBox.Text += handler.CMLEvaluateModel(evalOutPath,
trainer.Path,
Properties.Settings.Default.DatabaseDirectory,
Properties.Settings.Default.DatabaseAddress,
Properties.Settings.Default.MongoDBUser,
MainHandler.Decode(Properties.Settings.Default.MongoDBPass),
database,
sessionList,
scheme.Name,
rolesList,
annotator.Name,
stream.Name,
LosoCheckBox.IsChecked.Value);
if (File.Exists(evalOutPath))
{
ConfmatWindow confmat = new ConfmatWindow(evalOutPath);
confmat.ShowDialog();
File.Delete(evalOutPath);
}
}
catch (Exception ex)
{
logTextBox.Text += ex;
}
}
if (mode == Mode.COMPLETE)
{
handler.ReloadAnnoTierFromDatabase(AnnoTierStatic.Selected, false);
var dir = new DirectoryInfo(Path.GetDirectoryName(tempTrainerPath));
foreach (var file in dir.EnumerateFiles(Path.GetFileName(tempTrainerPath) + "*"))
{
file.Delete();
}
Close();
}
}
private void Merge()
{
string featureName = FeatureNameTextBox.Text;
if (featureName == "" || featureName.IndexOfAny(Path.GetInvalidFileNameChars()) >= 0)
{
MessageTools.Warning("not a valid feature name");
return;
}
string database = (string)DatabasesBox.SelectedItem;
var sessions = SessionsBox.SelectedItems;
var roles = RolesBox.SelectedItems;
var streams = StreamsBox.SelectedItems;
bool force = ForceCheckBox.IsChecked.Value;
string sessionList = "";
foreach (DatabaseSession session in sessions)
{
if (sessionList == "")
{
sessionList = session.Name;
}
else
{
sessionList += ";" + session.Name;
}
}
string roleList = "";
foreach (var role in roles)
{
if (roleList == "")
{
roleList = ((DatabaseRole)role).Name;
}
else
{
roleList += ";" + ((DatabaseRole)role).Name;
}
}
string[] streamsNames = new string[streams.Count];
int i = 0;
foreach (DatabaseStream stream in streams)
{
streamsNames[i++] = stream.Name;
}
Array.Sort(streamsNames);
string streamList = "";
double sampleRate = ((DatabaseStream)streams[0]).SampleRate;
foreach (string stream in streamsNames)
{
if (streamList == "")
{
streamList = stream;
}
else
{
streamList += ";" + stream;
}
}
string rootDir = Properties.Settings.Default.DatabaseDirectory + "\\" + database;
logTextBox.Text = handler.CMLMergeFeature(rootDir, sessionList, roleList, streamList, featureName, force);
string type = Defaults.CML.StreamTypeNameFeature;
string ext = "stream";
DatabaseStream streamType = new DatabaseStream()
{
Name = featureName, Type = type, FileExt = ext, SampleRate = sampleRate
};
DatabaseHandler.AddStream(streamType);
GetStreams(streamType);
}
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 void loadProjectFile(string filepath)
{
clearWorkspace();
string workdir = Path.GetDirectoryName(filepath);
XmlDocument doc = new XmlDocument();
try
{
doc.Load(filepath);
foreach (XmlNode node in doc.SelectNodes("//media"))
{
string path = FileTools.GetAbsolutePath(node.InnerText, workdir);
loadFile(path);
}
foreach (XmlNode node in doc.SelectNodes("//signal"))
{
Color background = Defaults.Colors.Background;
Color foreground = Defaults.Colors.Foreground;
if (node.Attributes["bg"] != null)
{
background = (Color)ColorConverter.ConvertFromString(node.Attributes["bg"].LastChild.Value);
}
if (node.Attributes["fg"] != null)
{
foreground = (Color)ColorConverter.ConvertFromString(node.Attributes["fg"].LastChild.Value);
}
string path = FileTools.GetAbsolutePath(node.InnerText, workdir);
loadFile(path, foreground, background);
}
if (DatabaseHandler.IsConnected)
{
XmlNode node = doc.SelectSingleNode("//tiers");
if (node != null && node.Attributes["database"] != null)
{
DatabaseHandler.ChangeDatabase(node.Attributes["database"].LastChild.Value);
}
}
foreach (XmlNode node in (doc.SelectNodes("//tier")))
{
string path = node.InnerText;
if (!Path.HasExtension(path))
{
AnnoList annoList = DatabaseHandler.LoadAnnoList(path);
if (annoList != null)
{
addAnnoTier(annoList);
}
else
{
MessageTools.Warning("Could not load annotation from database with id '" + node.InnerText + "'");
}
}
else
{
if (path == "")
{
path = node.Attributes["filepath"].LastChild.Value;
}
path = FileTools.GetAbsolutePath(path, workdir);
loadFile(path);
}
}
}
catch (Exception e)
{
MessageTools.Error(e.ToString());
}
}
public static AnnoScheme GetAnnotationScheme(string annoName, AnnoScheme.TYPE annoType)
{
MongoClient mongo = new MongoClient(ServerConnectionString);
IMongoDatabase database = mongo.GetDatabase(Properties.Settings.Default.DatabaseName);
AnnoScheme scheme = new AnnoScheme();
scheme.Type = annoType;
var annoSchemes = database.GetCollection <BsonDocument>(DatabaseDefinitionCollections.Schemes);
var builder = Builders <BsonDocument> .Filter;
FilterDefinition <BsonDocument> annoSchemeFilter = builder.Eq("name", annoName) & builder.Eq("type", annoType.ToString());
BsonDocument annoSchemeDocument = null;
try
{
annoSchemeDocument = annoSchemes.Find(annoSchemeFilter).Single();
if (annoSchemeDocument["type"].ToString() == annoType.ToString())
{
scheme.Name = annoSchemeDocument["name"].ToString();
if (scheme.Type == AnnoScheme.TYPE.CONTINUOUS)
{
scheme.MinScore = annoSchemeDocument["min"].ToDouble();
scheme.MaxScore = annoSchemeDocument["max"].ToDouble();
scheme.SampleRate = annoSchemeDocument["sr"].ToDouble();
scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annoSchemeDocument["min_color"].ToString());
scheme.MaxOrForeColor = (Color)ColorConverter.ConvertFromString(annoSchemeDocument["max_color"].ToString());
}
else if (scheme.Type == AnnoScheme.TYPE.DISCRETE)
{
scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annoSchemeDocument["color"].ToString());
BsonArray schemeLabelsArray = annoSchemeDocument["labels"].AsBsonArray;
string SchemeLabel = "";
string SchemeColor = "#000000";
for (int j = 0; j < schemeLabelsArray.Count; j++)
{
try
{
if (schemeLabelsArray[j]["isValid"].AsBoolean == true)
{
SchemeLabel = schemeLabelsArray[j]["name"].ToString();
SchemeColor = schemeLabelsArray[j]["color"].ToString();
AnnoScheme.Label lcp = new AnnoScheme.Label(schemeLabelsArray[j]["name"].ToString(), (Color)ColorConverter.ConvertFromString(schemeLabelsArray[j]["color"].ToString()));
scheme.Labels.Add(lcp);
}
}
catch
{
SchemeLabel = schemeLabelsArray[j]["name"].ToString();
SchemeColor = schemeLabelsArray[j]["color"].ToString();
AnnoScheme.Label lcp = new AnnoScheme.Label(schemeLabelsArray[j]["name"].ToString(), (Color)ColorConverter.ConvertFromString(schemeLabelsArray[j]["color"].ToString()));
scheme.Labels.Add(lcp);
}
}
}
else if (scheme.Type == AnnoScheme.TYPE.FREE)
{
scheme.MinOrBackColor = (Color)ColorConverter.ConvertFromString(annoSchemeDocument["color"].ToString());
}
}
}
catch (Exception ex)
{
MessageTools.Warning(ex.ToString());
}
return(scheme);
}
private void navigatorNewAnno_Click(object sender, RoutedEventArgs e)
{
if (Time.TotalDuration > 0)
{
AnnoTierNewSchemeWindow dialog = new AnnoTierNewSchemeWindow();
dialog.WindowStartupLocation = WindowStartupLocation.CenterScreen;
dialog.ShowDialog();
if (dialog.DialogResult == true)
{
AnnoScheme.TYPE annoType = dialog.Result();
if (DatabaseLoaded)
{
databaseAddNewAnnotation(annoType);
}
else
{
if (annoType == AnnoScheme.TYPE.FREE)
{
AnnoTierNewFreeSchemeWindow dialog2 = new AnnoTierNewFreeSchemeWindow();
dialog2.WindowStartupLocation = WindowStartupLocation.CenterScreen;
dialog2.ShowDialog();
if (dialog2.DialogResult == true)
{
AnnoScheme annoScheme = dialog2.Result;
AnnoList annoList = new AnnoList()
{
Scheme = annoScheme
};
addAnnoTier(annoList);
}
}
else if (annoType == AnnoScheme.TYPE.DISCRETE)
{
AnnoTierNewDiscreteSchemeWindow dialog2 = new AnnoTierNewDiscreteSchemeWindow();
dialog2.WindowStartupLocation = WindowStartupLocation.CenterScreen;
dialog2.ShowDialog();
if (dialog2.DialogResult == true)
{
AnnoList annoList = dialog2.GetAnnoList();
addAnnoTier(annoList);
}
}
else if (annoType == AnnoScheme.TYPE.CONTINUOUS)
{
double defaultSr = 25.0;
foreach (IMedia m in mediaList.Medias)
{
if (m.IsVideo())
{
defaultSr = m.GetSampleRate();
break;
}
}
AnnoTierNewContinuousSchemeWindow.Input input = new AnnoTierNewContinuousSchemeWindow.Input()
{
SampleRate = defaultSr, MinScore = 0.0, MaxScore = 1.0, MinColor = Colors.LightBlue, MaxColor = Colors.Red
};
AnnoTierNewContinuousSchemeWindow dialog2 = new AnnoTierNewContinuousSchemeWindow(input);
dialog2.WindowStartupLocation = WindowStartupLocation.CenterScreen;
dialog2.ShowDialog();
if (dialog2.DialogResult == true)
{
AnnoScheme annoScheme = dialog2.Result;
AnnoList annoList = new AnnoList()
{
Scheme = annoScheme
};
addAnnoTier(annoList);
}
}
}
}
}
else
{
MessageTools.Warning("Nothing to annotate, load some data first.");
}
}
