public Match(
DatabaseFin unknownFin,
DarwinDatabase db,
UpdateDisplayOutlinesDelegate updateOutlines,
List <MatchFactor> matchFactors,
bool createDefaultFactors = false)
: this(unknownFin, db, updateOutlines)
{
if (!createDefaultFactors)
{
MatchFactors = matchFactors;
}
else if (Database.CatalogScheme != null)
{
switch (db.CatalogScheme.FeatureSetType)
{
case FeatureSetType.DorsalFin:
SetMatchOptions(RegistrationMethodType.TrimOptimalTip, true);
break;
case FeatureSetType.Bear:
MatchFactors = MatchFactorPresets.CreateBearMatchFactors(db);
break;
}
}
CheckUnknownForRequiredFeatures();
// Force rediscovery (for debugging/testing, can uncomment
//UnknownFin.FinOutline.RediscoverFeaturePoints(Database.CatalogScheme.FeatureSetType);
}
public static List <MatchFactor> CreateBearMatchFactorsOld(DarwinDatabase database)
{
var matchFactors = new List <MatchFactor>();
var controlPoints = new List <FeaturePointType>()
{
FeaturePointType.Nasion,
FeaturePointType.Tip,
FeaturePointType.PointOfInflection
};
var benchmarkFeatures = new List <FeaturePointType>()
{
FeaturePointType.Nasion,
FeaturePointType.Tip
//FeaturePointType.Tip,
//FeaturePointType.Notch
};
var landmarkFeatures = new List <FeaturePointType>()
{
//FeaturePointType.LeadingEdgeBegin,
FeaturePointType.Tip,
FeaturePointType.Nasion,
FeaturePointType.Notch,
FeaturePointType.UpperLip,
FeaturePointType.PointOfInflection
};
matchFactors.Add(MatchFactor.CreateOutlineFactor(
0.6f,
controlPoints,
//OutlineErrorFunctions.MeanSquaredErrorBetweenOutlinesWithControlPoints,
OutlineErrorFunctions.MeanSquaredErrorBetweenOutlineSegments,
OutlineErrorFunctions.FindErrorBetweenOutlinesWithControlPointJitter,
new OutlineMatchOptions
{
MoveTip = true,
MoveEndsInAndOut = false,
UseFullFinError = true
}));
matchFactors.Add(MatchFactor.CreateFeaturePointFactor(
0.4f,
benchmarkFeatures,
landmarkFeatures,
5, // Number of desired ratios
database.AllFins,
//FeaturePointErrorFunctions.ComputeEigenValueWeightedCosineDistance,
FeaturePointErrorFunctions.ComputeMahalanobisDistance,
new FeatureSetMatchOptions
{
UseRemappedOutline = false
}));
return(matchFactors);
}
public Match(
DatabaseFin unknownFin,
DarwinDatabase db,
UpdateDisplayOutlinesDelegate updateOutlines,
RegistrationMethodType registrationMethod,
bool useFullFinError)
: this(unknownFin, db, updateOutlines)
{
SetMatchOptions(registrationMethod, useFullFinError);
}
public Match(
DatabaseFin unknownFin,
DarwinDatabase db,
UpdateDisplayOutlinesDelegate updateOutlines)
{
if (unknownFin == null)
{
throw new ArgumentNullException(nameof(unknownFin));
}
if (db == null)
{
throw new ArgumentNullException(nameof(db));
}
UnknownFin = new DatabaseFin(unknownFin);
Database = db;
_updateOutlines = updateOutlines;
CurrentFinIndex = 0;
MatchResults = new MatchResults(unknownFin.IDCode, unknownFin?.FinFilename, db?.Filename);
}
public static List <MatchFactor> CreateBearMatchFactors(DarwinDatabase database)
{
var matchFactors = new List <MatchFactor>();
var controlPoints = new List <FeaturePointType>()
{
FeaturePointType.Nasion,
FeaturePointType.Tip,
FeaturePointType.PointOfInflection,
// Our alternate control point to also try a mapping on
FeaturePointType.BottomLipProtrusion
};
matchFactors.Add(MatchFactor.CreateOutlineFactor(
0.55f,
controlPoints,
//OutlineErrorFunctions.MeanSquaredErrorBetweenOutlinesWithControlPoints,
OutlineErrorFunctions.MeanSquaredErrorBetweenOutlineSegments,
OutlineErrorFunctions.FindErrorBetweenOutlinesWithControlPointJitter,
new OutlineMatchOptions
{
MoveTip = true,
MoveEndsInAndOut = false,
UseFullFinError = true,
JumpDistancePercentage = 0.01f,
TrimBeginLeadingEdge = true,
// Also need to make sure there are 4 control points passed in if this is true
TryAlternateControlPoint3 = false
}));
matchFactors.Add(MatchFactor.CreateFeatureFactor(
0.1f,
FeatureErrorFunctions.ComputeCurvatureError,
FeatureType.BrowCurvature));
matchFactors.Add(MatchFactor.CreateFeatureFactor(
0.05f,
FeatureErrorFunctions.ComputeMouthDentError,
FeatureType.HasMouthDent));
var benchmarkFeatures = new List <FeaturePointType>()
{
//FeaturePointType.Nasion,
//FeaturePointType.Tip
FeaturePointType.Tip,
FeaturePointType.Notch
};
var landmarkFeatures = new List <FeaturePointType>()
{
//FeaturePointType.LeadingEdgeBegin,
FeaturePointType.Tip,
FeaturePointType.Nasion,
FeaturePointType.Notch,
FeaturePointType.UpperLip,
FeaturePointType.PointOfInflection
};
matchFactors.Add(MatchFactor.CreateFeaturePointFactor(
0.35f,
benchmarkFeatures,
landmarkFeatures,
// Pass in a specific set of ratios. If not passed, it'll automatically
// compute the ratio permutations of all the landmarks we pass in.
//GetVerticalFeaturePointCombinations(),
5, // Number of desired ratios
database.AllFins,
//FeaturePointErrorFunctions.ComputeEigenValueWeightedCosineDistance,
FeaturePointErrorFunctions.ComputeMahalanobisDistance,
// The option below will compare after using the lowest error mapping
// from the outline error function above, assuming there's an outline error
// function before this.
new FeatureSetMatchOptions
{
UseRemappedOutline = false
}));
return(matchFactors);
}
public static List <MatchFactor> CreateBearMatchFactorsOld2(DarwinDatabase database)
{
var matchFactors = new List <MatchFactor>();
var controlPoints = new List <FeaturePointType>()
{
FeaturePointType.Nasion,
FeaturePointType.Tip,
FeaturePointType.PointOfInflection,
// Our alternate control point to also try a mapping on
FeaturePointType.BottomLipProtrusion
};
matchFactors.Add(MatchFactor.CreateOutlineFactor(
0.55f,
controlPoints,
//OutlineErrorFunctions.MeanSquaredErrorBetweenOutlinesWithControlPoints,
OutlineErrorFunctions.MeanSquaredErrorBetweenOutlineSegments,
OutlineErrorFunctions.FindErrorBetweenOutlinesWithControlPointJitter,
new OutlineMatchOptions
{
MoveTip = true,
MoveEndsInAndOut = false,
UseFullFinError = true,
JumpDistancePercentage = 0.01f,
TrimBeginLeadingEdge = true,
TryAlternateControlPoint3 = true
}));
matchFactors.Add(MatchFactor.CreateFeatureFactor(
0.1f,
FeatureErrorFunctions.ComputeCurvatureError,
FeatureType.BrowCurvature));
matchFactors.Add(MatchFactor.CreateFeatureFactor(
0.05f,
FeatureErrorFunctions.ComputeMouthDentError,
FeatureType.HasMouthDent));
var benchmarkFeatures = new List <FeaturePointType>()
{
FeaturePointType.Nasion,
FeaturePointType.Tip
//FeaturePointType.Tip,
//FeaturePointType.Notch
};
var landmarkFeatures = new List <FeaturePointType>()
{
//FeaturePointType.LeadingEdgeBegin,
FeaturePointType.Tip,
FeaturePointType.Nasion,
FeaturePointType.Notch,
FeaturePointType.UpperLip,
FeaturePointType.PointOfInflection
};
matchFactors.Add(MatchFactor.CreateFeaturePointFactor(
0.35f,
benchmarkFeatures,
landmarkFeatures,
5, // Number of desired ratios
database.AllFins,
//FeaturePointErrorFunctions.ComputeEigenValueWeightedCosineDistance,
FeaturePointErrorFunctions.ComputeMahalanobisDistance,
new FeatureSetMatchOptions
{
UseRemappedOutline = false
}));
return(matchFactors);
}
public static void SaveDatasetImages(string datasetDirectory, DarwinDatabase database)
{
if (datasetDirectory == null)
{
throw new ArgumentNullException(nameof(datasetDirectory));
}
if (database == null)
{
throw new ArgumentNullException(nameof(database));
}
if (!Directory.Exists(datasetDirectory))
{
throw new ArgumentOutOfRangeException(nameof(datasetDirectory));
}
Trace.WriteLine("Starting dataset export...");
string fullImagesDirectory = Path.Combine(datasetDirectory, ImagesDirectoryName);
Directory.CreateDirectory(fullImagesDirectory);
var csvRecords = new List <MLCsvRecord>();
int individualNum = 1;
foreach (var dbFin in database.AllFins)
{
var fin = CatalogSupport.FullyLoadFin(dbFin);
if (!string.IsNullOrEmpty(fin?.IDCode))
{
Trace.WriteLine("Exporting " + fin.IDCode);
}
if (fin.FinOutline.FeatureSet.CoordinateFeaturePoints == null ||
fin.FinOutline.FeatureSet.CoordinateFeaturePoints.Count < 1 ||
!fin.FinOutline.FeatureSet.CoordinateFeaturePoints.ContainsKey(Features.FeaturePointType.Eye))
{
// If we don't have the features we need, skip to the next one
continue;
}
var mlImage = ConvertDatabaseFinToMLImage(fin.FinImage, fin.FinOutline.ChainPoints, fin.Scale);
string imageFilename = individualNum.ToString().PadLeft(6, '0') + ".jpg";
mlImage.Image.Save(Path.Combine(fullImagesDirectory, imageFilename), ImageFormat.Jpeg);
csvRecords.Add(new MLCsvRecord
{
image = imageFilename,
eye_x = mlImage.XRatio * (float)(fin.FinOutline.FeatureSet.CoordinateFeaturePoints[Features.FeaturePointType.Eye].Coordinate.X / fin.Scale - mlImage.XMin),
eye_y = mlImage.YRatio * (float)(fin.FinOutline.FeatureSet.CoordinateFeaturePoints[Features.FeaturePointType.Eye].Coordinate.Y / fin.Scale - mlImage.YMin),
nasalfold_x = mlImage.XRatio * (float)(fin.FinOutline.FeatureSet.CoordinateFeaturePoints[Features.FeaturePointType.NasalLateralCommissure].Coordinate.X / fin.Scale - mlImage.XMin),
nasalfold_y = mlImage.YRatio * (float)(fin.FinOutline.FeatureSet.CoordinateFeaturePoints[Features.FeaturePointType.NasalLateralCommissure].Coordinate.Y / fin.Scale - mlImage.YMin)
});
individualNum += 1;
}
using (var writer = new StreamWriter(Path.Combine(datasetDirectory, CsvFilename), false))
using (var csv = new CsvWriter(writer, CultureInfo.InvariantCulture))
{
csv.WriteRecords(csvRecords);
}
Trace.WriteLine("done.");
}
// 1.1 - the following functions used in MatchQueue context
public static MatchResults Load(string fileName, out DarwinDatabase db, out DatabaseFin databaseFin)
{
MatchResults result = new MatchResults();
db = null;
databaseFin = null;
if (string.IsNullOrEmpty(fileName))
{
throw new ArgumentNullException(nameof(fileName));
}
if (!File.Exists(fileName))
{
throw new ArgumentOutOfRangeException(nameof(fileName));
}
var lines = File.ReadAllLines(fileName);
if (lines.Length < 6 || !lines[0].StartsWith("Results for ID:"))
{
return(result);
}
result._finID = lines[0].Substring(lines[0].LastIndexOf(":") + 1).Trim();
result.TracedFinFile = lines[1].Substring(lines[1].IndexOf(":") + 1).Trim();
result.DatabaseFile = lines[2].Substring(lines[2].IndexOf(":") + 1).Trim();
db = CatalogSupport.OpenDatabase(result.DatabaseFile, Options.CurrentUserOptions.DefaultCatalogScheme, false);
//***2.2 - if we can, determine if database path has just changed drive letter
// or some part of path that is a prefix to the SurveyArea. If the database
// is in the same SurveyArea and has the same database name, then we can
// proceed with the building of the MatchResults
//int p = mDatabaseFile.find("surveyAreas");
//string rqdAreaAndDB = mDatabaseFile.substr(p); // survey area and database name
//string rqdPreamble = mDatabaseFile.substr(0, p); // strip it to get preamble
//string currentDBFile = db->getFilename();
//p = currentDBFile.find("surveyAreas");
//string currentAreaAndDB = currentDBFile.substr(p); // survey area and catalog name
//string currentPreamble = currentDBFile.substr(0, p); // strip it to get preamble
//if (db.Filename.ToLower() != DatabaseFile.ToLower())
//{
// //cout << mDatabaseFile << endl;
// //cout << rqdPreamble << " " << rqdAreaAndDB << endl;
// //cout << currentDBFile << endl;
// //cout << currentPreamble << " " << currentAreaAndDB << endl;
// if (currentAreaAndDB == rqdAreaAndDB)
// {
// string msg = "The Survey Area and Catalog for the match results appear corrrect,\n";
// msg += "but the path to DARWIN's home folder seems to have changed.\n";
// msg += "Is it OK to open the indicated catalog in the current location\n";
// msg += "as shown below?\n\n";
// msg += (currentPreamble + rqdAreaAndDB);
// Trace.WriteLine(msg);
// //ErrorDialog *err = new ErrorDialog(msg);
// //err->show();
// //***2.2 - path possibly has to be fixed to FIN file as well
// if ((currentDBFile != mDatabaseFile) && (currentAreaAndDB == rqdAreaAndDB))
// {
// //add preamble of current DARWINHOME to FINs relative location
// p = mTracedFinFile.find("surveyAreas");
// string currentFinAreaPlus = mTracedFinFile.substr(p);
// mTracedFinFile = currentPreamble + currentFinAreaPlus;
// cout << mTracedFinFile << endl;
// }
// }
// else
// {
// string msg = "The WRONG database is currently loaded for viewing these results ...\n\n";
// msg += "LOADED DB:\n " + db->getFilename() + "\n\n";
// msg += "REQUIRED DB:\n " + mDatabaseFile + "\n\n";
// msg += "Please load the required database from the main window\n";
// msg += "and then reload the desired results file.";
// //ErrorDialog *err = new ErrorDialog(msg);
// //err->show();
// //***2.22 - replacing own ErrorDialog with GtkMessageDialogs
// GtkWidget* errd = gtk_message_dialog_new(NULL,
// GTK_DIALOG_DESTROY_WITH_PARENT,
// GTK_MESSAGE_ERROR,
// GTK_BUTTONS_CLOSE,
// msg.c_str());
// gtk_dialog_run(GTK_DIALOG(errd));
// gtk_widget_destroy(errd);
// return NULL;
// }
//}
DatabaseFin unkFin = CatalogSupport.OpenFinz(result.TracedFinFile);
// get match info on each matched database fin
// After skipping some of the headers
for (int i = 6; i < lines.Length; i++)
{
string line = lines[i];
int pos = line.IndexOf("\t");
//string rank = line.Substring(0, pos);
line = line.Substring(pos + 1);
pos = line.IndexOf("\t");
string error = line.Substring(0, pos);
line = line.Substring(pos + 1);
pos = line.IndexOf("\t");
string dbFinID = line.Substring(0, pos);
line = line.Substring(pos + 1);
//cout << "dbFinID[" << dbFinID << "]"; //*** 2.2 - show for now
string numStr;
int
dbFinPosition,
uBegin, uTip, uEnd,
dbBegin, dbTip, dbEnd;
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
line = line.Substring(pos + 1);
dbFinPosition = int.Parse(numStr);
//cout << "[" << dbFinPosition << "]" << endl; //*** 2.2 - show for now
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
uBegin = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << uBegin << "]";
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
uTip = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << uTip << "]";
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
uEnd = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << uEnd << "]";
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
dbBegin = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << dbBegin << "]";
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
dbTip = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << dbTip << "]";
pos = line.IndexOf("\t");
numStr = line.Substring(0, pos);
dbEnd = int.Parse(numStr);
line = line.Substring(pos + 1);
//cout << "[" << dbEnd << "]";
//string damage = line;
//cout << "[" << damage << "]" << endl;
// The position is written starting at 1, but our index is 0 based
DatabaseFin thisDBFin = db.AllFins[dbFinPosition - 1];
// TODO: Should this throw an exception instead?
if (thisDBFin.IDCode != dbFinID)
{
Trace.WriteLine("Disaster " + thisDBFin.IDCode + " " + dbFinID);
}
FloatContour mappedUnknownContour = unkFin.FinOutline.ChainPoints.MapContour(
unkFin.FinOutline.ChainPoints[uTip],
unkFin.FinOutline.ChainPoints[uBegin],
unkFin.FinOutline.ChainPoints[uEnd],
thisDBFin.FinOutline.ChainPoints[dbTip],
thisDBFin.FinOutline.ChainPoints[dbBegin],
thisDBFin.FinOutline.ChainPoints[dbEnd]);
Result r = new Result(
mappedUnknownContour, //***1.3 - Mem Leak - constructor make copy now
thisDBFin.FinOutline.ChainPoints, //***1.3 - Mem Leak - constructor make copy now
thisDBFin.ID,
// TODO - This image filename stuff is a little ugly.
(string.IsNullOrEmpty(thisDBFin.OriginalImageFilename)) ? thisDBFin.ImageFilename : thisDBFin.OriginalImageFilename,
thisDBFin.ThumbnailFilenameUri,
dbFinPosition - 1, // position of fin in database
double.Parse(error),
thisDBFin.IDCode,
thisDBFin.Name,
thisDBFin.DamageCategory,
thisDBFin.DateOfSighting,
thisDBFin.LocationCode);
r.SetMappingControlPoints(
uBegin, uTip, uEnd, // beginning, tip & end of unknown fin
dbBegin, dbTip, dbEnd); // beginning, tip & end of database fin
result.Results.Add(r);
}
databaseFin = unkFin;
result.SetRankings();
return(result);
}
