} /* RunLogAddMsg */
private void RunLogMsgQueueFlush()
{
String msg = runLogMsgQueue.GetNextMsg();
while (msg != null)
{
RunLog.AppendText(msg + "\n");
backGroundLog.Writeln(msg);
msg = runLogMsgQueue.GetNextMsg();
}
} /* RunLogMsgQueueFlush */
} /* ToCmdLine */
private void ImportImagesIntoDeploymentProcess()
{
importingRunning = true;
importingCompleted = false;
PicesDataBase.ThreadInit();
PicesRunLog runLog = new PicesRunLog();
PicesDataBase threadConn = PicesDataBase.GetGlobalDatabaseManagerNewInstance(runLog);
extractionLogEntryId = threadConn.LogEntriesProcessStart("II",
"ImportImagesIntoDeployment",
ExecutableDateTimeStamp(),
ToCmdLine(),
""
);
totalImagesUpdated = 0;
ImportImagesFromDirectoryStructure(threadConn, sourceDirectory);
if (cancelImporting)
{
runLog.Writeln("\n" + "Importing Images has been Canceled." + "\n\n");
}
else
{
runLog.Writeln("\n\n" + "Total Images[" + totalImagesUpdated.ToString("###,##0") + "\n\n");
}
threadConn.Close();
threadConn = null;
GC.Collect();
PicesDataBase.ThreadEnd();
importingRunning = false;
importingCompleted = true;
} /* ImportImagesIntoDeploymentProcess */
} /* RunLogAddMsg */
private void RunLogMsgQueueFlush()
{
runLogGoalie.StartBlock();
if (runLogMsgQueue != null)
{
while (runLogMsgQueue.Count > 0)
{
String msg = runLogMsgQueue.Dequeue();
RunLog.AppendText(msg + "\n");
backGroundLog.Writeln(msg);
}
}
runLogGoalie.EndBlock();
} /* RunLogMsgQueueFlush */
} /* SuperScriptExponent */
private void UpdateChartAreas()
{
if (integratedDensityDistribution == null)
{
return;
}
goalie.StartBlock();
String t1 = "Abundance by Size";
switch (statistic)
{
case '0': t1 = "Abundance by Size"; break;
case '1': t1 = "Abundance by Estimated Diameter"; break;
case '2': t1 = "Abundance by Estimated Spheroid Volume"; break;
case '3': t1 = "Abundance by Estimated Ellipsoid Volume"; break;
}
String t2 = "Cruise: " + cruise + " Station: " + station;
if (String.IsNullOrEmpty(deployment))
{
t2 += " Deployment: " + deployment;
}
t2 += " Class: " + classToPlot.Name;
ProfileChart.Titles.Clear();
ProfileChart.Titles.Add(new Title(t1, Docking.Top, titleFont, Color.Black));
ProfileChart.Titles.Add(new Title(t2, Docking.Top, titleFont, Color.Black));
if (!String.IsNullOrEmpty(criteriaStr))
{
ProfileChart.Titles.Add(new Title(criteriaStr, Docking.Top, titleFont, Color.Black));
}
ProfileChart.Series.Clear();
ChartArea ca = ProfileChart.ChartAreas[0];
Series s = new Series("Size Distribution");
s.ChartArea = "ChartArea1";
s.ChartType = SeriesChartType.Column;
float[] startValues = bucketsDisplayed.SizeStartValues();
float[] endValues = bucketsDisplayed.SizeEndValues();
float minX = float.MaxValue;
float minY = float.MaxValue;
float maxX = float.MinValue;
float maxY = float.MinValue;
List <CustomLabel> customLabels = new List <CustomLabel> ();
for (int x = 0; x < integratedDensityDistribution.Length; ++x)
{
float sv = startValues[x];
float ev = sv * growthRate;
if (sv <= 0.0f)
{
sv = initialSizeValue / growthRate;
ev = initialSizeValue;
}
float midPoint = (sv + ev) / 2.0f;
{
double svLog10 = Math.Log10(sv);
double evLog10 = Math.Log10(ev);
CustomLabel cl = null;
if (midPoint < 1.0f)
{
cl = new CustomLabel(svLog10, evLog10, midPoint.ToString("#0.000"), 0, LabelMarkStyle.SideMark);
}
else if (midPoint < 10.0f)
{
cl = new CustomLabel(svLog10, evLog10, midPoint.ToString("#0.00"), 0, LabelMarkStyle.SideMark);
}
else if (midPoint < 100.0f)
{
cl = new CustomLabel(svLog10, evLog10, midPoint.ToString("##0.0"), 0, LabelMarkStyle.SideMark);
}
else
{
cl = new CustomLabel(svLog10, evLog10, midPoint.ToString("##,##0"), 0, LabelMarkStyle.SideMark);
}
customLabels.Add(cl);
}
double d = (double)integratedDensityDistribution[x];
float log10D = (float)Math.Log10(d + 1.0);
minY = Math.Min(minY, log10D);
maxY = Math.Max(maxY, log10D);
minX = Math.Min(minX, midPoint);
maxX = Math.Max(maxX, midPoint);
DataPoint dp = new DataPoint(midPoint, log10D);
s.Points.Add(dp);
}
s.XAxisType = AxisType.Primary;
s.YAxisType = AxisType.Primary;
ProfileChart.ChartAreas[0].AxisY.LogarithmBase = 10.0;
ProfileChart.ChartAreas[0].AxisY.LabelStyle.Format = "##,###,##0";
{
ca.AxisX.CustomLabels.Clear();
ca.AxisX.CustomLabels.Add(customLabels[1]);
int n = 8;
float interSpace = (float)customLabels.Count / (float)(n + 1);
for (int x = 1; x <= n; ++x)
{
int idx = 1 + (int)((float)x * interSpace + 0.5f);
ca.AxisX.CustomLabels.Add(customLabels[idx]);
}
ca.AxisX.CustomLabels.Add(customLabels[customLabels.Count - 1]);
}
ca.AxisY.Title = SubInSuperScriptExponent("Log 10 Abundance");
switch (statistic)
{
case '0':
ca.AxisX.Title = SubInSuperScriptExponent("area(m-2)");
//ca.AxisX.LabelStyle.Format = "##,##0.000";
break;
case '1':
ca.AxisX.Title = SubInSuperScriptExponent("Length(mili-meters)");
//ca.AxisX.LabelStyle.Format = "##00.00";
break;
case '2':
ca.AxisX.Title = SubInSuperScriptExponent("Volume(mm-3)");
//ca.AxisX.LabelStyle.Format = "##0.0000";
break;
case '3':
ca.AxisX.Title = SubInSuperScriptExponent("Volume(mm-3)");
//ca.AxisX.LabelStyle.Format = "##0.0000";
break;
}
ca.AxisX.IsLogarithmic = true;
//ca.AxisX.Minimum = 0.0;
ca.AxisX.Maximum = maxX;
ca.AxisX.LabelStyle.Angle = 45;
ca.AxisX.LabelStyle.Font = axisLabelFont;
ca.AxisX.TitleFont = axisLabelFont;
ca.AxisY.Minimum = 0.0;
ca.AxisY.IsLogarithmic = false;
ca.AxisY.LabelStyle.Font = axisLabelFont;
ca.AxisY.TitleFont = axisLabelFont;
//ca.AxisX.IsLogarithmic = true;
s.BorderWidth = 2;
ProfileChart.Series.Add(s);
try
{
ProfileChart.ChartAreas[0].RecalculateAxesScale();
}
catch (Exception e)
{
runLog.Writeln(e.ToString());
}
goalie.EndBlock();
} /* UpdateChartAreas */
} /* StartReconciliationThread */
private void ReconciliationThread()
{
reconcilingRunLog.SetLoggingLevel(10);
reconcilingRunLog.Writeln("Source Directory [" + SourceDirectory.Text + "]" + "\n");
reconcilingRunLog.Writeln("Start Date/Time [" + DateTime.Now.ToString("yyyy-MMM-dd HH:mm:ss") + "]" + "\n");
reconcilingRunLog.Writeln("Active DataBase [" + dbConn.Server.Description + "]" + "\n");
reconcilingRunning = true;
String rootDir = SourceDirectory.Text;
DirectoryInfo di = null;
try { di = new DirectoryInfo(rootDir); } catch (Exception) { di = null; }
if (di == null)
{
return;
}
CountDirectory(di);
if (!cancelReconciling)
{
reconcilingRunLog.Writeln("Total Images To Process[" + runStatsTotalImages.ToString("###,###,##0") + "]" + "\n");
ProcessDirectory(di);
}
reconcilingRunLog.Writeln("Total Images" + "\t" + runStatsTotalImages.ToString("###,###,##0"));
reconcilingRunLog.Writeln("In Database" + "\t" + runStatsImagesInDataBase.ToString("###,###,##0"));
reconcilingRunLog.Writeln("Not Found" + "\t" + runStatsImagesNotInDataBase.ToString("###,###,##0"));
reconcilingRunLog.Writeln("Fixed" + "\t" + runStatsImagesFixed.ToString("###,###,##0"));
reconcilingRunning = false;
} /* ProcessAllDirectories */
} /* SuperScriptExponent */
private void UpdateChartAreas()
{
goalie.StartBlock();
bool plotLogDensity = PlotLogDensity.Checked;
String t1 = "Abundance by Size";
switch (statistic)
{
case '0': t1 = "Abundance by Size"; break;
case '1': t1 = "Abundance by Diameter (ESD)"; break;
case '2': t1 = "Abundance by Volume (EBv"; break;
case '3': t1 = "Abundance by Estimated Ellipsoid Volume"; break;
}
String t2 = cruise + "-" + station;
if (!String.IsNullOrEmpty(deployment))
{
t2 += ("-" + deployment);
}
t2 += (" " + classToPlot.Name);
t2 += " ";
t2 += (cast + "-Cast" + " Size-Range(" + sizeStart.ToString() + " - " + sizeEnd.ToString() + ")");
ProfileChart.Titles.Clear();
ProfileChart.Titles.Add(new Title(t1, Docking.Top, titleFont, Color.Black));
ProfileChart.Titles.Add(new Title(t2, Docking.Top, titleFont, Color.Black));
//ProfileChart.Titles.Add (new Title (t3, Docking.Top, titleFont, Color.Black));
ProfileChart.Series.Clear();
ChartArea ca1 = ProfileChart.ChartAreas[0];
ChartArea ca2 = ProfileChart.ChartAreas[1];
Series s = new Series("Size Distribution");
s.ChartArea = "ChartArea1";
s.ChartType = SeriesChartType.Line;
Series s2 = new Series("Volume Sampled");
s2.ChartArea = "ChartArea2";
s2.ChartType = SeriesChartType.Line;
float minX = float.MaxValue;
float minY = float.MaxValue;
float maxX = float.MinValue;
float maxY = float.MinValue;
int numDepthBins = sizeDistribution.NumDepthBins;
for (uint depthBin = 0; depthBin < numDepthBins; ++depthBin)
{
PicesImageSizeDistributionRow row = sizeDistribution.GetDepthBin(depthBin);
if (row == null)
{
continue;
}
float depth = row.Depth;
double density = 0.0;
if (depthBin < depthProfile.Length)
{
density = (double)depthProfile[depthBin];
}
if (plotLogDensity)
{
density = (float)Math.Log10(density + 1.0);
}
minX = Math.Min(minX, (float)density);
maxX = Math.Max(maxX, (float)density);
minY = Math.Min(minY, depth);
maxY = Math.Max(maxY, depth);
DataPoint dp = new DataPoint(density, depth);
s.Points.Add(dp);
double vs = 0.0;
if (depthBin < volumeSampled.Length)
{
vs = volumeSampled[depthBin];
}
DataPoint dp2 = new DataPoint(vs, depth);
s2.Points.Add(dp2);
}
s.XAxisType = AxisType.Primary;
s.YAxisType = AxisType.Primary;
s2.XAxisType = AxisType.Primary;
s2.YAxisType = AxisType.Primary;
s2.Color = Color.Black;
if (plotLogDensity)
{
ca1.AxisX.Title = SubInSuperScriptExponent("Log 10 Abundance");
}
else
{
ca1.AxisX.Title = SubInSuperScriptExponent("Abundance");
}
ca1.AxisY.Title = SubInSuperScriptExponent("Depth (Meters)");
ca1.AxisY.LabelStyle.Format = "##,##0";
ca1.AxisX.IsLogarithmic = false;
ca1.AxisX.Minimum = 0.0;
//ca1.AxisX.Maximum = maxX;
ca1.AxisX.LabelStyle.Angle = 90;
ca1.AxisX.LabelStyle.Font = axisLabelFont;
ca1.AxisX.TitleFont = axisLabelFont;
ca1.AxisY.Minimum = 0.0;
ca1.AxisY.IsLogarithmic = false;
ca1.AxisY.LabelStyle.Font = axisLabelFont;
ca1.AxisY.TitleFont = axisLabelFont;
if (plotLogDensity)
{
ca1.AxisX.LabelStyle.Format = "##,##0.0";
}
else
{
ca1.AxisX.LabelStyle.Format = "##,##0";
}
ca2.AxisX.Title = SubInSuperScriptExponent("Volume Sampled (mm-3)");
ca2.AxisX.Minimum = 0.0;
ca2.AxisX.IsLogarithmic = false;
ca2.AxisX.LabelStyle.Font = axisLabelFont;
ca2.AxisX.TitleFont = axisLabelFont;
ca2.AxisX.LabelStyle.Format = "##0.00";
ca2.AxisX.LabelStyle.Angle = 90;
s.BorderWidth = 2;
ProfileChart.Series.Add(s);
ProfileChart.Series.Add(s2);
try
{
ProfileChart.ChartAreas[0].RecalculateAxesScale();
}
catch (Exception e)
{
runLog.Writeln(e.ToString());
}
goalie.EndBlock();
} /* UpdateChartAreas */
private void ImportImage(PicesDataBase threadConn,
String sipperFileRootName,
String fileName,
ref bool successful
)
{
successful = false;
String rootName = OSservices.GetRootName(fileName);
String picesRootName = sipperFileRootName + "_" + rootName;
PicesDataBaseImage dbi = threadConn.ImageLoad(picesRootName);
if (dbi != null)
{
return;
}
PicesRaster r = new PicesRaster(fileName);
r = r.RemoveZooscanBrackets();
PicesFeatureVector fv = new PicesFeatureVector(r, picesRootName, null, runLog);
fv.ExampleFileName = picesRootName;
int imageId = 0;
uint centroidRow = (uint)(0.5f + fv.CentroidRow);
uint centroidCol = (uint)(0.5f + fv.CentroidCol);
if ((centroidRow < 0) || (centroidRow > r.Height))
{
centroidRow = (uint)(r.Height / 2);
}
if ((centroidCol < 0) || (centroidCol > r.Width))
{
centroidCol = (uint)(r.Width / 2);
}
threadConn.ImageInsert(r,
picesRootName,
sipperFileRootName,
0, 0, 0,
(uint)r.Height, (uint)r.Width,
(uint)fv.OrigSize,
3,
extractionLogEntryId.LogEntryId, extractionLogEntryId.LogEntryId,
centroidRow, centroidCol,
unknownClass, 1.0f, null, 0.0f, null,
0.0f, // depth,
0.0f, // Image Size
null,
ref imageId,
ref successful
);
if (successful)
{
threadConn.FeatureDataInsertRow(sipperFileRootName, fv);
}
else
{
runLog.Writeln("RootName[" + rootName + "] Failed: " + threadConn.LastErrorDesc() + "\n");
}
} /* ImportImage */
} /* ProcessOneFeatureVector */
private PicesClass UpdateClassId(PicesClass mlClass)
{
// We lock 'predictionUpdateQueue' because all other classification processes refer to it.
//
lock (predictionUpdateQueue)
{
// Maybe another Classification process already updated the database and hence updated the classId field.
if (mlClass.ClassId >= 0)
{
//int zed = 888;
}
else
{
String className = mlClass.Name;
String parentName = mlClass.ParentName;
if (String.IsNullOrEmpty(parentName))
{
parentName = "AllClasses";
mlClass.Parent = PicesClassList.GetUniqueClass(parentName, "");
}
if (runLog == null)
{
runLog = new PicesRunLog();
}
PicesDataBase dbConn = null;
if (dbServer == null)
{
dbConn = PicesDataBase.GetGlobalDatabaseManagerNewInstance(runLog);
}
else
{
dbConn = new PicesDataBase(dbServer, runLog);
}
mlClass.Description = "Added by 'Classification'";
dbConn.MLClassInsert(mlClass);
if (mlClass.ClassId < 0)
{
PicesClass pc = dbConn.MLClassLoad(className);
if (mlClass.ClassId < 0)
{
runLog.Writeln("ClassifierProcess.UpdateClassId ***ERROR*** mlClass.ClassId < 0 ClassName[" + className + "]");
}
}
// I do not know what the impact of opening and closing a lot of connections
// to the MySQL data base will be, and since this method should only get called
// when a new MLClass is introduced I want to sleep a little to make
// sure that we do not over stress resources that I am not aware of.
Thread.Sleep(100);
//dbConn.Close ();
dbConn = null;
GC.Collect();
}
}
return(mlClass);
}